Pandoraea sp. B-6和Cupriavidus basilensis B-8降解碱木质素及其模型苯化合物的机制研究
|
摘要
摘要：木质素是地球上最丰富的苯化合物。自然界中由木质素构成的生物量仅次于纤维素和半纤维素位于地球生物总量的第二位。木质素结构复杂,相对分子量高,难溶于水,这些特点使其很难被降解。木质素的微生物降解已经成为国内外研究的热点,而且微生物主要集中于真菌。近年来越来越多的研究表明,由于具有极强的环境适应性和丰富的生化多样性,细菌将在木质素生物降解中起到越来越重要的作用。
论文以碱木质素及木质素模型苯化合物为对象,利用从被微生物腐蚀的三国吴简的浸泡液中分离的Pandoraea sp.B-6和Cupriavidus basilensis B-8对木质素及其模式苯化合物降解的特性和机制进行了比较系统的研究,获得如下研究成果：
系统研究了Pandoraea sp.B-6和Cupriavidus basilensis B-8的木质素降解特性,首次发现Pandoraea属和Cupriavidus属的菌株具有木质素降解能力。两株细菌降解碱木质素的最适pH和温度分别为10,30℃和7,30℃；两株细菌在初始浓度为1-6g/L的碱木质素培养基中COD和色度分别降低38.2%,41.6%和31.3%,37.5%以上。两株细菌分泌胞外过氧化物酶降解木质素,其中Pandoraea sp.B-6中锰过氧化物酶和漆酶的最大活性分别为2249.2U/L和1120.6U/L, Cupriavidus basilegnsis B-8中锰过氧化物酶和漆酶的最大活性分别为1685.3U/L和815.6U/L。通过GC-MS分析两株细菌降解碱木质素过程中产生的中间代谢物,发现有多种化合物(如阿魏酸、肉桂酸等),由此推测两株细菌首先将木质素解聚成低聚物,然后进一步降解成木质素单体苯化合物及其他小分子化合物直至进入三羧酸循环被矿化。
Pandoraea sp.B-6和Cupriavidus basilensis B-8在以阿魏酸和对香豆酸为唯一碳源的培养基中正常生长的同时还能够高效的降解这两种化合物。除了Pandoraea sp.B-6降解对香豆酸的最适pH为8以外,两株细菌降解这两种化合物的最适pH和温度均分别为7和30℃,完全降解这两种苯化合物的最大浓度分别为1000mg/L,800mg/L和1000mg/L,1000mg/L.通过两株细菌降解苯化合物的液相色谱分析,在Pandoraea sp.B-6和Cupriavidus basilemsis B-8降解对香豆酸的过程中只发现对羟基苯甲酸这一种中间产物(最大浓度分别为169mg/L和253mg/L)；在Pandoraea sp.B-6降解阿魏酸的过程中发现了香草酸和香草醛,最大浓度分别为426mg/L和193mg/L；在Cupriavidus basilensis B-8降解阿魏酸的过程中发现了4-乙烯基愈创木酚,香草酸和香草醛,最大浓度为别为548mg/L,238mg/L和低于30mg/L。通过基因RT-PCR(逆转录PCR)分析发现两株细菌都是通过β-酮中心代谢途径对两种苯化合物进行降解,而Cupriavidus basilensis B-8中还存在另外一条降解阿魏酸的途径—还原转化途径。
准确测定了Pandoraea sp.B-6和Cupriavidus basilensis B-8的全基因组序列。结果发现,这两株细菌的基因组均具有单染色体,大小分别为5037162bp(136contigs)和8705938bp(1458contigs).平均GC含量分别为63.56%和65.40%。两株细菌基因组编码区的GC含量(分别为64.02%和65.62%)均比非编码区的GC含量(分别为60.08%和64.29%)高。Pandoraea sp.B-6基因组中共有4803个编码序列,总长度为4312731bp,其中包括4692或4695个蛋白编码基因,55个代表20种氨基酸的tRNA编码基因,5个核糖体RNA编码基因,3个或5个rRNA编码基因,31个sRNA编码基因以及15个miRNA编码基因。Cupriavidus basilensis B-8基因组中共有8448个编码序列,总长度为6740730bp,其中包括8371个蛋白编码基因,65个代表20种氨基酸的tRNA编码基因,5个核糖体RNA编码基因,12个rRNA编码基因。
对两株细菌的基因组及特定的表达蛋白进行系统的生物信息学分析和RT-PCR分析。结果发现：Pandoraea sp.B-6和Cupriavidus basilenisis B-8均含有多种降解木质素及苯化合物的基因和降解途径。Pandoraea sp.B-6共发现119个木质素及苯化合物降解相关基因；四种木质素降解相关途径：β-酮中心代谢途径降,龙胆酸代谢途径,2,3-二羟基苯基丙酸间位裂解途径和Box途径；以及5种其他苯化合物降解途径：3,4-二羟基苯乙酸甲酯间位裂解途径,苯基乙酰辅酶A开环途径,2,5-二羟基苯乙酸途径,2-氨基苯甲酰基-辅酶A途径和3-羟基邻氨基苯甲酸途径。Cuprjavidus basilensis B-8共发现165个木质素基本化合物降解相关基因；5种木质素降解相关途径：β-酮中心代谢途径,苯酚代谢途径,龙胆酸代谢途径,2,3-二羟基苯基丙酸间位裂解途径和Box途径；以及5种其他苯化合物降解途径：3,4-二羟基苯乙酸甲酯间位裂解途径,苯基乙酰辅酶A开环途径,2,5-二羟基苯乙酸途径,2-氨基苯甲酰基-辅酶A途径和3-羟基邻氨基苯甲酸途径。
研究结果证实了Pandoraea sp.B-6和Cupriavidus basilensis B-8具有降解木质素及其模型苯化合物的能力。全基因组的测序和分析确定了这两株细菌降解木质素和苯化合物的步骤和降解产物。研究对木质素及苯化合物降解机制及木质素降解应用研究具有重要意义。
Abstract:Lignin is the most abundant aromatic compound on earth and is second only to cellulose in its contribution to living terrestrial biomass. The structural complexity of lignin, its high molecular weight and its insolubility make its degradation very difficult. Microbio-degradation of lignin has become a research hotspot, mainly focused on the fungi. In recent years, a variety of literature has shown that given the immense environmental adaptability and biochemical versatility, bacterial could play a potential role in lignin degradation.
In present study, two bacterial strains Pandoraea sp. B-6and Cupriavidus basilensis B-8were isolated from the steeping fluid of the eroding bamboo slips. Characterization and biochemical and molecular mechanisms of lignin and aromatic compounds degradation were studied. Through a series of studies, the research finding and conclusions of this paper are as follows:
Kraft Lignin (KL) degradation capability of Pandoraea sp. B-6and Cupriavidus basilensis B-8were firstly investigated. The optimum pH and temperature for KL degradation were10and30℃, respectively, for Pandoraea sp. B-6, and7and30℃, respectively, for Cupriavidus basilensis B-8. At least38.2%of COD and41.6%of color for Pandoraea sp. B-6, and31.3%COD and37.5%color for Cupriavidus basilensis B-8could be removed in7days under the initial concentrations from1g/L to6g/L. The extracellular peroxidase enzymes were detected during KL degradation by these two strains. The greatest activities of2249.2U/L for manganese peroxidase and1120.6U/L for laccase from Pandoraea sp. B-6, and1120.6U/L for manganese peroxidase and815.6U/L for laccase from Cupriavidus basilensis B-8were observed. Many intermediates such as ferulic acid, cinnamic acid and so on, were formed during the period of KL degradation base on GC-MS analysis. Thus we predicated that these two strains were able to depolymerize lignin polymer into oligomers and fuither degrade into lignin aromatic monomer compounds and other small molecule compounds and finally enter into tricarboxylic acid cycle.
Pandoraea sp. B-6and Cupriavidus basilensis B-8grew well and displayed great degradation capability in the medium using ferulic acid and ρ-coumaric acid as the sole carbon source, respectively. The optimum pH and temperature for these two compounds degradation were all10and30℃, respectively, except that the optimum pH for ρ-coumaric acid by Pandoraea sp. B-6was8. The maximum concentration of complete degradation for these two compounds degradation were all1000mg/L, except that for ρ-coumaric acid by Pandoraea sp. B-6was800mg/L. The HPLC analysis of aromatic compounds degradation by these two strains showed that ρ-hydroxybenzoic acid was the only compounds detected during the process of ρ-coumaric acid degradation by Pandoraea sp. B-6and Cupriavidus basilensis B-8, and the maximum cumulative concentration were169mg/L and253mg/L, respectively. The vanillic acid and vanillin were detected duri4ng the process of ferulic acid degradation, the maximum cumulative concentration were426mg/L and193mg/L, respectively, by Pandoraea sp. B-6, and238mg/L and less than30mg/L, respectively, by Cupriavidus basilensis B-8. In addition,4-vinylguaiacol was detected during the process of ferulic acid degradation, the maximum cumulative concentration were548mg/L. RT-PCR analysis showed that these two compounds were all degraded through β-ketoadipate central pathway, furthermore, another ferulic acid degradation pathway, reductive transformation pathways, were found.
The whole genomes of Pandoraea sp. B-6and Cupriavidus basilensis B-8were accurately sequenced. The Pandoraea sp. B-6genome consists of a single circular chromosome of5,037,162bp (136contigs) with an average G+C content of63.56%. The G+C content of the coding region (64.02%) is higher than the G+C content of the noncoding region (60.82%).4803putative coding sequences (CDSs) with the length of4,312,731bp were identified. It contained4692or4695protein-coding genes,55tRNA genes representing all20amino acids,5scattered ribosomal RNA genes,3or5rRNA genes,31sRNA genes and15miRMA genes. Cupriavidus basilensis B-8genome consists of a single circular chromosome of8,705,938bp (1458contigs) with an average G+C content of65.40%(Fig.1). The G+C content of the coding region (65.62%) is higher than the G+C content of the noncoding region (64.29%).8,448putative coding sequences (CDSs) with the length of6,740,730bp were identified. It contained8371protein-coding genes,65tRNA genes representing all20amino acids,12rRNA genes.
Many lignin and aromatic compounds degradation related genes and metabolic pathways were founds through bioinformatics analysis combined with RT-PCR. In Pandoraea sp. B-6,119related genes were identified. Four metabolic pathways for lignin degradation included β-ketoadipate central pathway, gentisate pathway, the2,3-dihydroxyphenylpropionate meta ring-cleavage pathway and box pathway, five metabolic pathways for other aromatic compounds degradation included3,4-dihydroxyphenylacetate meta-cleavage pathway, the phenylacetyl-CoA ring-cleavage pathway, homogentisate pathway,2-aminobenzoyl-CoA pathway and3-hydroxyanthranilate pathway were confirmed. In Pandoraea sp. B-6,165related genes were identified. Five metabolic pathways for lignin degradation included β-ketoadipate central pathway, phenol degradation pathway, gentisate pathway, the2,3-dihydroxyphenylpropionate meta ring-cleavage pathway and box pathway, five metabolic pathways for other aromatic compounds degradation included3,4-dihydroxyphenylacetate meta-cleavage pathway, the phenylacetyl-CoA ring-cleavage pathway, homogentisate pathway,2-aminobenzoyl-CoA pathway and3-hydroxyanthranilate pathway were confirmed.
These results confirmed the capability of Pandoraea sp. B-6and Cupriavidus basilensis B-8to promote lingnin and aromatic compounds degradation. Whole genomic sequencing and systematic analysis of the Pandoraea sp. B-6and Cupriavidus basilensis B-8genome identified degradation steps and intermediates. Our findings provide a theoretical basis for research into the mechanisms of lignin and aromatic compounds degradation as well as a practical basis for biofuel production using lignin materials.
论文以碱木质素及木质素模型苯化合物为对象,利用从被微生物腐蚀的三国吴简的浸泡液中分离的Pandoraea sp.B-6和Cupriavidus basilensis B-8对木质素及其模式苯化合物降解的特性和机制进行了比较系统的研究,获得如下研究成果：
系统研究了Pandoraea sp.B-6和Cupriavidus basilensis B-8的木质素降解特性,首次发现Pandoraea属和Cupriavidus属的菌株具有木质素降解能力。两株细菌降解碱木质素的最适pH和温度分别为10,30℃和7,30℃；两株细菌在初始浓度为1-6g/L的碱木质素培养基中COD和色度分别降低38.2%,41.6%和31.3%,37.5%以上。两株细菌分泌胞外过氧化物酶降解木质素,其中Pandoraea sp.B-6中锰过氧化物酶和漆酶的最大活性分别为2249.2U/L和1120.6U/L, Cupriavidus basilegnsis B-8中锰过氧化物酶和漆酶的最大活性分别为1685.3U/L和815.6U/L。通过GC-MS分析两株细菌降解碱木质素过程中产生的中间代谢物,发现有多种化合物(如阿魏酸、肉桂酸等),由此推测两株细菌首先将木质素解聚成低聚物,然后进一步降解成木质素单体苯化合物及其他小分子化合物直至进入三羧酸循环被矿化。
Pandoraea sp.B-6和Cupriavidus basilensis B-8在以阿魏酸和对香豆酸为唯一碳源的培养基中正常生长的同时还能够高效的降解这两种化合物。除了Pandoraea sp.B-6降解对香豆酸的最适pH为8以外,两株细菌降解这两种化合物的最适pH和温度均分别为7和30℃,完全降解这两种苯化合物的最大浓度分别为1000mg/L,800mg/L和1000mg/L,1000mg/L.通过两株细菌降解苯化合物的液相色谱分析,在Pandoraea sp.B-6和Cupriavidus basilemsis B-8降解对香豆酸的过程中只发现对羟基苯甲酸这一种中间产物(最大浓度分别为169mg/L和253mg/L)；在Pandoraea sp.B-6降解阿魏酸的过程中发现了香草酸和香草醛,最大浓度分别为426mg/L和193mg/L；在Cupriavidus basilensis B-8降解阿魏酸的过程中发现了4-乙烯基愈创木酚,香草酸和香草醛,最大浓度为别为548mg/L,238mg/L和低于30mg/L。通过基因RT-PCR(逆转录PCR)分析发现两株细菌都是通过β-酮中心代谢途径对两种苯化合物进行降解,而Cupriavidus basilensis B-8中还存在另外一条降解阿魏酸的途径—还原转化途径。
准确测定了Pandoraea sp.B-6和Cupriavidus basilensis B-8的全基因组序列。结果发现,这两株细菌的基因组均具有单染色体,大小分别为5037162bp(136contigs)和8705938bp(1458contigs).平均GC含量分别为63.56%和65.40%。两株细菌基因组编码区的GC含量(分别为64.02%和65.62%)均比非编码区的GC含量(分别为60.08%和64.29%)高。Pandoraea sp.B-6基因组中共有4803个编码序列,总长度为4312731bp,其中包括4692或4695个蛋白编码基因,55个代表20种氨基酸的tRNA编码基因,5个核糖体RNA编码基因,3个或5个rRNA编码基因,31个sRNA编码基因以及15个miRNA编码基因。Cupriavidus basilensis B-8基因组中共有8448个编码序列,总长度为6740730bp,其中包括8371个蛋白编码基因,65个代表20种氨基酸的tRNA编码基因,5个核糖体RNA编码基因,12个rRNA编码基因。
对两株细菌的基因组及特定的表达蛋白进行系统的生物信息学分析和RT-PCR分析。结果发现：Pandoraea sp.B-6和Cupriavidus basilenisis B-8均含有多种降解木质素及苯化合物的基因和降解途径。Pandoraea sp.B-6共发现119个木质素及苯化合物降解相关基因；四种木质素降解相关途径：β-酮中心代谢途径降,龙胆酸代谢途径,2,3-二羟基苯基丙酸间位裂解途径和Box途径；以及5种其他苯化合物降解途径：3,4-二羟基苯乙酸甲酯间位裂解途径,苯基乙酰辅酶A开环途径,2,5-二羟基苯乙酸途径,2-氨基苯甲酰基-辅酶A途径和3-羟基邻氨基苯甲酸途径。Cuprjavidus basilensis B-8共发现165个木质素基本化合物降解相关基因；5种木质素降解相关途径：β-酮中心代谢途径,苯酚代谢途径,龙胆酸代谢途径,2,3-二羟基苯基丙酸间位裂解途径和Box途径；以及5种其他苯化合物降解途径：3,4-二羟基苯乙酸甲酯间位裂解途径,苯基乙酰辅酶A开环途径,2,5-二羟基苯乙酸途径,2-氨基苯甲酰基-辅酶A途径和3-羟基邻氨基苯甲酸途径。
研究结果证实了Pandoraea sp.B-6和Cupriavidus basilensis B-8具有降解木质素及其模型苯化合物的能力。全基因组的测序和分析确定了这两株细菌降解木质素和苯化合物的步骤和降解产物。研究对木质素及苯化合物降解机制及木质素降解应用研究具有重要意义。
Abstract:Lignin is the most abundant aromatic compound on earth and is second only to cellulose in its contribution to living terrestrial biomass. The structural complexity of lignin, its high molecular weight and its insolubility make its degradation very difficult. Microbio-degradation of lignin has become a research hotspot, mainly focused on the fungi. In recent years, a variety of literature has shown that given the immense environmental adaptability and biochemical versatility, bacterial could play a potential role in lignin degradation.
In present study, two bacterial strains Pandoraea sp. B-6and Cupriavidus basilensis B-8were isolated from the steeping fluid of the eroding bamboo slips. Characterization and biochemical and molecular mechanisms of lignin and aromatic compounds degradation were studied. Through a series of studies, the research finding and conclusions of this paper are as follows:
Kraft Lignin (KL) degradation capability of Pandoraea sp. B-6and Cupriavidus basilensis B-8were firstly investigated. The optimum pH and temperature for KL degradation were10and30℃, respectively, for Pandoraea sp. B-6, and7and30℃, respectively, for Cupriavidus basilensis B-8. At least38.2%of COD and41.6%of color for Pandoraea sp. B-6, and31.3%COD and37.5%color for Cupriavidus basilensis B-8could be removed in7days under the initial concentrations from1g/L to6g/L. The extracellular peroxidase enzymes were detected during KL degradation by these two strains. The greatest activities of2249.2U/L for manganese peroxidase and1120.6U/L for laccase from Pandoraea sp. B-6, and1120.6U/L for manganese peroxidase and815.6U/L for laccase from Cupriavidus basilensis B-8were observed. Many intermediates such as ferulic acid, cinnamic acid and so on, were formed during the period of KL degradation base on GC-MS analysis. Thus we predicated that these two strains were able to depolymerize lignin polymer into oligomers and fuither degrade into lignin aromatic monomer compounds and other small molecule compounds and finally enter into tricarboxylic acid cycle.
Pandoraea sp. B-6and Cupriavidus basilensis B-8grew well and displayed great degradation capability in the medium using ferulic acid and ρ-coumaric acid as the sole carbon source, respectively. The optimum pH and temperature for these two compounds degradation were all10and30℃, respectively, except that the optimum pH for ρ-coumaric acid by Pandoraea sp. B-6was8. The maximum concentration of complete degradation for these two compounds degradation were all1000mg/L, except that for ρ-coumaric acid by Pandoraea sp. B-6was800mg/L. The HPLC analysis of aromatic compounds degradation by these two strains showed that ρ-hydroxybenzoic acid was the only compounds detected during the process of ρ-coumaric acid degradation by Pandoraea sp. B-6and Cupriavidus basilensis B-8, and the maximum cumulative concentration were169mg/L and253mg/L, respectively. The vanillic acid and vanillin were detected duri4ng the process of ferulic acid degradation, the maximum cumulative concentration were426mg/L and193mg/L, respectively, by Pandoraea sp. B-6, and238mg/L and less than30mg/L, respectively, by Cupriavidus basilensis B-8. In addition,4-vinylguaiacol was detected during the process of ferulic acid degradation, the maximum cumulative concentration were548mg/L. RT-PCR analysis showed that these two compounds were all degraded through β-ketoadipate central pathway, furthermore, another ferulic acid degradation pathway, reductive transformation pathways, were found.
The whole genomes of Pandoraea sp. B-6and Cupriavidus basilensis B-8were accurately sequenced. The Pandoraea sp. B-6genome consists of a single circular chromosome of5,037,162bp (136contigs) with an average G+C content of63.56%. The G+C content of the coding region (64.02%) is higher than the G+C content of the noncoding region (60.82%).4803putative coding sequences (CDSs) with the length of4,312,731bp were identified. It contained4692or4695protein-coding genes,55tRNA genes representing all20amino acids,5scattered ribosomal RNA genes,3or5rRNA genes,31sRNA genes and15miRMA genes. Cupriavidus basilensis B-8genome consists of a single circular chromosome of8,705,938bp (1458contigs) with an average G+C content of65.40%(Fig.1). The G+C content of the coding region (65.62%) is higher than the G+C content of the noncoding region (64.29%).8,448putative coding sequences (CDSs) with the length of6,740,730bp were identified. It contained8371protein-coding genes,65tRNA genes representing all20amino acids,12rRNA genes.
Many lignin and aromatic compounds degradation related genes and metabolic pathways were founds through bioinformatics analysis combined with RT-PCR. In Pandoraea sp. B-6,119related genes were identified. Four metabolic pathways for lignin degradation included β-ketoadipate central pathway, gentisate pathway, the2,3-dihydroxyphenylpropionate meta ring-cleavage pathway and box pathway, five metabolic pathways for other aromatic compounds degradation included3,4-dihydroxyphenylacetate meta-cleavage pathway, the phenylacetyl-CoA ring-cleavage pathway, homogentisate pathway,2-aminobenzoyl-CoA pathway and3-hydroxyanthranilate pathway were confirmed. In Pandoraea sp. B-6,165related genes were identified. Five metabolic pathways for lignin degradation included β-ketoadipate central pathway, phenol degradation pathway, gentisate pathway, the2,3-dihydroxyphenylpropionate meta ring-cleavage pathway and box pathway, five metabolic pathways for other aromatic compounds degradation included3,4-dihydroxyphenylacetate meta-cleavage pathway, the phenylacetyl-CoA ring-cleavage pathway, homogentisate pathway,2-aminobenzoyl-CoA pathway and3-hydroxyanthranilate pathway were confirmed.
These results confirmed the capability of Pandoraea sp. B-6and Cupriavidus basilensis B-8to promote lingnin and aromatic compounds degradation. Whole genomic sequencing and systematic analysis of the Pandoraea sp. B-6and Cupriavidus basilensis B-8genome identified degradation steps and intermediates. Our findings provide a theoretical basis for research into the mechanisms of lignin and aromatic compounds degradation as well as a practical basis for biofuel production using lignin materials.
引文
[1]孙永明,袁振宏,孙振钧.中国生物质能源与生物质利用现状与展望[J].可再生能源2006,2(126),78-82.
[2]朱清时,阎立峰,郭庆祥.生物质洁净能源[M].化学工业出版社：2002.
[3]高培基,许平.资源环境微生物技术[M].化学工业出版社：2004.
[4]殷福珊.挑战纤维素的利用[J].日用化学品科学2009,32(1),24-26.
[5]Buranov, A. U., Mazza, G. Lignin in straw of herbaceous crops [J]. Industrial crops and products 2008,28 (3),237-259.
[6]霍弗里希特,Hofrichter, M.,施泰因比歇尔,等生物高分子：木质素,腐殖质和煤[M].化学工业出版社：2004.
[7]胡鸿达,江卓丽.木质素性质与综合利用[J].华东纸业2010,6,018.
[8]冯攀,谌凡更.木质素在环氧树脂合成中的应用进展[J].纤维素科学与技术2010,18(002),54-60.
[9]黎先发,罗学刚.木质素在塑料中的应用研究进展[J].塑料2004,33(4),58-61.
[10]查刘生.木质素基碳纤维的研制情况[J].炭素1992,(4),44-47.
[11]Faix O. Classification of lignins from different botanical origins by FT-IR spectroscopy [J]. Holzforschung-International Journal of the Biology, Chemistry, Physics and Technology of Wood 1991,45 (s1),21-28.
[12]Freudenberg K. Lignin:Its Constitution and Formation from p-Hydroxy-cinnamyl Alcohols:Lignin is duplicated by dehydrogenation of these alcohols; intermediates explain formation and structure [J]. Science (New York, NY) 1965,148 (3670),595.
[13]Higuchi T. Formation and biological degradation of lignins [J]. Advances in Enzymology and Related Areas of Molecular Biology, Volume 34 1971, 207-283.
[14]Eggeman T, Elander RT. Process and economic analysis of pretreatment technologies [J]. Bioresource technology 2005,96 (18),2019-2025.
[15]Zakzeski J, Bruijnincx PC, Jongerius AL, et al. The catalytic valorization of lignin for the production of renewable chemicals [J]. Chemical reviews 2010, 110 (6),3552.
[16]Pickett J, Anderson D, Bowles D, et al. Sustainable biofuels:prospects and challenges [J]. The Royal Society, London, UK 2008.
[17]Kastner M, Hofrichter M, Steinbuchel A. Biodegradation of humic substances [J]. Biopolymers:Lignin, Humic Substances and Coal 2001,349-378.
[18]Kirk TK, Farrell RL. Enzymatic "combustion":the microbial degradation of lignin [J]. Annual Reviews in Microbiology 1987,41 (1),465-501.
[19]Guillen F, Martinez MJ, Gutierrez A. Biodegradation of lignocellu-losics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin [J]. International Microbiology 2005,8,195-204.
[20]Bumpus JA, Aust SD. Biodegradation of environmental pollutants by the white rot fungus Phanerochaete chrysosporium:involvement of the lignin degrading system [J]. Bioessays 1987,6(4),166-170.
[21]Levasseur A, Piumi F, Coutinho PM., et al. FOLy:an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds [J]. Fungal genetics and biology 2008,45 (5),638-645.
[22]Macarena S, Fernando LL, Monica V, et al. Incomplete processing of peroxidase transcripts in the lignin degrading fungus Phanerochaete chrysosporium [J]. FEMS microbiology letters 2005,242 (1),37-44.
[23]Edwards SL, Raag R, Wariishi H, et al. Crystal structure of lignin peroxidase [J]. Proceedings of the National Academy of Sciences 1993,90 (2),750-754.
[24]Sundaramoorthy M, Kishi K, Gold MH, et al. The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06-A resolution [J]. Journal of Biological Chemistry 1994,269 (52),32759-32767.
[25]Banci L, Ciofi-Baffoni S, Tien M. Lignin and Mn peroxidase-catalyzed oxidation of phenolic lignin oligomers [J]. Biochemistry 1999,38 (10), 3205-3210.
[26]Martinez AT. Molecular biology and structure-function of lignin-degrading heme peroxidases [J]. Enzyme and Microbial Technology 2002,30 (4), 425-444.
[27]Hofrichter M. Review:lignin conversion by manganese peroxidase (MnP) [J]. Enzyme and Microbial Technology 2002,30 (4),454-466.
[28]Wariishi H, Dunford HB, MacDonald I, et al. Manganese peroxidase from the lignin-degrading basidiomycete Phanerochaete chrysosporium. Transient state kinetics and reaction mechanism [J]. Journal of Biological Chemistry 1989,264 (6),3335-3.340.
[29]Tuor U, Wariishi H, Schoemaker HE, et al. Oxidation of phenolic arylglycerol. beta.-aryl ether lignin model compounds by manganese peroxidase from Phanerochaete chrysosporium:oxidative cleavage of an. alpha.-carbonyl model compound [J]. Biochemistry 1992,31 (21),4986-4995.
[30]Cai D, Tien M. Lignin-degrading peroxidases of Phanerochaete chrysosporium [J]. Journal of biotechnology 1993,30(1),79-90.
[31]Tien M, Kirk TK, Bull C, et al. Steady-state and transient-state kinetic studies on the oxidation of 3,4-dimethoxybenzyl alcohol catalyzed by the ligninase of Phanerocheate chrysosporium Burds [J]. Journal of Biological Chemistry 1986, 261 (4),1687-1693.
[32]Doyle WA, Blodig W, Veitch NC, et al. Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis [J]. Biochemistry 1998,37 (43),15097-15105.
[33]Khindaria A, Yamazaki I, Aust SD. Stabilization of the veratryl alcohol cation radical by lignin peroxidase [J]. Biochemistry 1996,35 (20),6418-6424.
[34]Candeias LP, Harvey PJ. Lifetime and reactivity of the veratryl alcohol radical cation. Implications for lignin peroxidase catalysis [J]. Journal of Biological Chemistry 1995,270 (28),16745-16748.
[35]Hammel KE, Tien M, Kalyanaraman B, et al. Mechanism of oxidative C alpha-C beta cleavage of a lignin model dimer by Phanerochaete chrysosporium ligninase. Stoichiometry and involvement of free radicals [J]. Journal of Biological Chemistry 1985,260 (14),8348-8353.
[36]Hammel KE, Cullen D. Role of fungal peroxidases in biological ligninolysis [J]. Current opinion in plant biology 2008,11 (3),349-355.
[37]Hammel KE, Jensen K, Mozuch MD, et al. Ligninolysis by a purified lignin peroxidase [J]. Journal of Biological Chemistry 1993,268 (17),12274-12281.
[38]Wariishi H, Valli K, Gold MH. In vitro depolymerization of lignin by manganese peroxidase of Phanerochaete chrysosporium [J]. Biochemical and biophysical research communications 1991,176 (1),269-275.
[39]Shleev S, Persson P, Shumakovich G, et al. Interaction of fungal laccases and laccase-mediator systems with lignin [J]. Enzyme and Microbial Technology 2006,39 (4),841-847.
[40]Camarero S, Garcia O, Vidal T, et al. Efficient bleaching of non-wood high-quality paper pulp using laccase-mediator system [J]. Enzyme and Microbial Technology 2004,35 (2),113-120.
[41]Arora DS, Sharma RK. Ligninolytic fungal laccases and their biotechnological applications [J]. Applied biochemistry and biotechnology 2010,160 (6), 1760-1788.
[42]Giardina P, Faraco V, Pezzella C, et al. Laccases:a never-ending story [J]. Cellular and Molecular Life Sciences 2010,67 (3),369-385.
[43]Bento I, Silva CS, Chen Z, et al. Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer [J]. BMC structural biology 2010,10 (1),28.
[44]Bertrand T, Jolivalt C, Briozzo P, et al. Crystal structure of a four-copper laccase complexed with an arylamine:insights into substrate recognition and correlation with kinetics [J]. Biochemistry 2002,41 (23),7325-7333.
[45]Piontek K, Antorini M, Choinowski T. Crystal Structure of a Laccase from the FungusTrametes versicolor at 1.90-A resolution containing a full complement of coppers [J]. Journal of Biological Chemistry 2002,277 (40),37663-37669.
[46]Jonsson L, Sjostrom K, Haggstrom I, et al. Characterization of a laccase gene from the white-rot fungus Trametes versicolor and structural features of basidiomycete laccases [J]. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology 1995,1251 (2),210-215.
[47]Niku-Paavola ML, Karhunen E, Kantelinen A, et al. The effect of culture conditions on the production of lignin modifying enzymes by the white-rot fungus Phlebia radiata [J]. Journal of biotechnology 1990,13 (2),211-221.
[48]Bermek H, Li K, Eriksson KEL. Laccase-less mutants of the white-rot fungus Pycnoporus cinnabarinus cannot delignify kraft pulp [J]. Journal of biotechnology 1998,66(2),117-124.
[49]Ander, P., Eriksson, K.-E. The importance of phenol oxidase activity in lignin degradation by the white-rot fungus Sporotrichum pulverulentum [J]. Archives of Microbiology 1976,109 (1-2),1-8.
[50]Kawai S, Umezawa T, Higuchi T. Degradation mechanisms of phenolic β-1 lignin substructure model compounds by laccase of Coriolus versicolor [J]. Archives of biochemistry and biophysics 1988,262 (1),99-110.
[51]Bourbonnais R, Paice MG. Oxidation of non-phenolic substrates:an expanded role for laccase in lignin biodegradation [J]. FEBS letters 1990,267 (1), 99-102.
[52]Thurston CF. The structure and function of fungal laccases [J]. Microbiology 1994,140(1),19-26.
[53]Martinez D, Larrondo LF, Putnam N, et al. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78 [J]. Nature biotechnology 2004,22 (6),695-700.
[54]Kersten P, Cullen D. Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium [J]. Fungal genetics and biology 2007,44 (2),77-87.
[55]Vicuna R. Bacterial degradation of lignin [J]. Enzyme and Microbial Technology 1988,10 (11),646-655.
[56]Zimmermann W. Degradation of lignin by bacteria [J]. Journal of biotechnology 1990,13 (2),119-130.
[57]Ramachandra M, Crawford DL, Hertel, G. Characterization of an extracellular lignin peroxidase of the lignocellulolytic actinomycete Streptomyces viridosporus [J]. Applied and Environmental Microbiology 1988,54 (12), 3057-3063.
[58]Masai E, Katayama Y, Fukuda M. Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds [J]. Bioscience, biotechnology, and biochemistry 2007,71 (1),1-15.
[59]Ahmad M, Taylor CR, Pink D, et al. Development of novel assays for lignin degradation:comparative analysis of bacterial and fungal lignin degraders [J]. Molecular bioSystems 2010,6(5),815-821.
[60]Bugg TD, Ahmad M, Hardiman EM, et al. The emerging role for bacteria in lignin degradation and bio-product formation [J]. Current opinion in biotechnology 2011,22 (3),394-400.
[61]Ahmad M, Roberts JN, Hardiman EM., et al. Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase [J]. Biochemistry 2011,50 (23),5096-5107.
[62]Roberts JN, Singh R, Grigg JC, et al. Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1 [J]. Biochemistry 2011,50 (23), 5108-5119.
[63]Adav SS, Ng CS, Arulmani M, et al. Quantitative iTRAQ secretome analysis of cellulolytic Thermobifida fusca [J]. Journal of proteome research 2010,9 (6), 3016-3024.
[64]Brown ME, Walker MC, Nakashige TG, et al. Discovery and characterization of heme enzymes from unsequenced bacteria:application to microbial lignin degradation [J]. Journal of the American Chemical Society 2011,133 (45), 18006-18009.
[65]Chen CL, Chang HM, Kirk TK. Aromatic acids produced during degradation of lignin in spruce wood by Phanerochaete chrysosporium [J]. Holzforschung-International Journal of the Biology, Chemistry, Physics and Technology of Wood 1982,36(1),3-9.
[66]Chen CL, Chang HM, Kirk TK. Carboxylic acids produced through oxidative cleavage of aromatic rings during degradation of lignin in spruce wood by Phanerochaete chrysosporium [J]. Journal of Wood Chemistry and Technology 1983,3(1),35-57.
[67]Reid ID. Fate of residual lignin during delignification of kraft pulp by Trametes versicolor [J]. Applied and Environmental Microbiology 1998,64 (6), 2117-2125.
[68]Raj A, Krishna Reddy M., Chandra R. Identification of low molecular weight aromatic compounds by gas chromatography-mass spectrometry (GC-MS) from kraft lignin degradation by three Bacillus sp [J]. International biodeterioration & biodegradation 2007,59 (4),292-296.
[69]Gupta VK, Minocha AK, Jain N. Batch and continuous studies on treatment of pulp mill wastewater by Aeromonas formicans [J]. Journal of Chemical Technology and Biotechnology 2001,76 (6),547-552.
[70]Grandy AS, Neff JC, Weintraub MN. Carbon structure and enzyme activities in alpine and forest ecosystems [J]. Soil Biology and Biochemistry 2007,39 (11), 2701-2711.
[71]Crawford DL, Pometto AL, Crawford RL. Lignin degradation by Streptomyces viridosporus:isolation and characterization of a new polymeric lignin degradation intermediate [J]. Applied and Environmental Microbiology 1983, 45 (3),898-904.
[72]Trigo C, Ball A. Production of extracellular enzymes during the solubilisation of straw by Thermomonospora fusca BD25 [J]. Applied microbiology and biotechnology 1994,41 (3),366-372.
[73]Masai E, Katayama Y, Nishikawa S, et al. Detection and localization of a new enzyme catalyzing the β-aryl ether cleavage in the soil bacterium Pseudomonas paucimobilis SYK-6) [J]. FEBS letters 1989,249 (2),348-352.
[74]Masai E, Katayama Y, Kubota S, et al. A bacterial enzyme degrading the model lignin compound β-etherase is a member of the glutathione-S-transferase superfamily [J]. FEBS letters 1993,323 (1),135-140.
[75]Masai E, Ichimura A, Sato Y, et al. Roles of the enantioselective glutathione-S-transferases in cleavage of (3-aryl ether [J]. Journal of bacteriology 2003,185 (6),1768-1775.
[76]Vicuna R, Gonzalez B, Mozuch M, et al. Metabolism of lignin model compounds of the arylglycerol-β-aryl ether type by Pseudomonas acidovorans D3 [J]. Applied and Environmental Microbiology 1987,53(11),2605-2609.
[77]Camarero S, Ibarra D, Martinez MJ, et al. Lignin-derived compounds as efficient laccase mediators for decolorization of different types of recalcitrant dyes [J]. Applied and Environmental Microbiology 2005,71 (4),1775-1784.
[78]Otsuka Y, Sonoki T, Ikeda S, et al. Detection and characterization of a novel extracellular fungal enzyme that catalyzes the specific and hydrolytic cleavage of lignin guaiacylglycerol β-aryl ether linkages [J]. European Journal of Biochemistry 2003,270 (11),2353-2362.
[79]Abe T, Masai E, Miyauchi K, et al. tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6 [J]. Journal of bacteriology 2005,187 (6),2030-2037.
[80]Brunel F, Davison J. Cloning and sequencing of Pseudomonas genes encoding vanillate demethylase [J]. Journal of bacteriology 1988,170(10),4924-4930.
[81]Segura A, Bunz PV, D'Argenio DA, et al. Genetic Analysis of a Chromosomal Region ContainingvanA and vanB, Genes Required for Conversion of Either Ferulate or Vanillate to Protocatechuate in Acinetobacter [J]. Journal of bacteriology 1999,181 (11),3494-3504.
[82]Enoki A, Goldsby GP, Gold MH. Metabolism of the lignin model compounds veratrylglycerol-β-guaiacyl ether and 4-ethoxy-3-methoxyphenylglycerol-β-guaiacyl ether by Phanerochaete chrysosporium [J]. Archives of Microbiology 1980,125 (3), 227-231.
[83]Masai E, Yamamoto Y, Inoue T, et al. Characterization of ligV essential for catabolism of vanillin by Sphingomonas paucimobilis SYK-6 [J]. Bioscience, biotechnology, and biochemistry 2007,71 (10),2487-2492.
[84]Priefert H, Rabenhorst J, Steinbuchel A. Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate [J]. Journal of bacteriology 1997,179 (8),2595-2607.
[85]Pieper DH. Aerobic degradation of poly chlorinated biphenyls [J]. Applied microbiology and biotechnology 2005,67 (2),170-191.
[86]Sonoki T, Obi T, Kubota S, et al. Coexistence of two different O demethylation systems in lignin metabolism by Sphingomonas paucimobilis SYK-6:cloning and sequencing of the lignin biphenyl-specific O-demethylase (LigX) gene [J]. Applied and Environmental Microbiology 2000,66 (5),2125-2132.
[87]Peng X, Egashira T, Hanashiro K, et al. Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme [J]. Applied and Environmental Microbiology 1998,64 (7),2520-2527.
[88]Peng X, Masai E, Katayama Y, et al. Characterization of the meta-Cleavage Compound Hydrolase Gene involved in degradation of the lignin-related biphenyl structure by Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 1999,65 (6),2789-2793.
[89]Masai E, Harada K, Peng X, et al. Cloning and characterization of the ferulic acid catabolic genes of Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 2002,68 (9),4416-4424.
[90]Peng X, Masai E, Kasai D, et al. A second 5-carboxyvanillate decarboxylase gene, ligW2, is important for lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 2005,71 (9),5014-5021.
[91]Pollard JR, Bugg TD. Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli [J]. European Journal of Biochemistry 1998,251(1-2),98-106.
[92]Hara H, Masai E, Miyauchi K, et al. Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6 [J]. Journal of bacteriology 2003,185 (1),41-50.
[93]Maruyama, K., Miwa, M., Tsujii, N., Nagai, T., Tomita, N., Harada, T., Sobajima, H., Sugisaki, H. Cloning, sequencing, and expression of the gene encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1 [J]. Bioscience, biotechnology, and biochemistry 2001,65 (12),2701-2709.
[94]Enoki A, Gold MH. Degradation of the diarylpropane lignin model compound 1-(3',4'-diethoxyphenyl)-1,3-dihydroxy-2-(4''-methoxyphenyl)-propane and derivatives by the basidiomycete Phanerochaete chrysosporium [J]. Archives of Microbiology 1982,132 (2),123-130.
[95]Gold MH, Kuwahara M, Chiu AA., et al. Purification and characterization of an extracellular H2O2-requiring diarylpropane oxygenase from the white rot basidiomycete, Phanerochaete chrysosporium [J]. Archives of biochemistry and biophysics 1984,234 (2),353-362.
[96]Kamoda S, Saburi Y. Cloning, expression and sequence analysis of a lignostilbene-a, b-dioxygenase gene from Pseudomonas paucimobilis TMY1009 [J]. Biosci. Biotechnol. Biochem 1993,57,926-930.
[97]Giuliano G, Al-Babili S, von Lintig J. Carotenoid oxygenases:cleave it or leave it [J]. Trends in plant science 2003,8 (4),145-149.
[98]Marasco EK, Schmidt-Dannert C. Identification of bacterial carotenoid cleavage dioxygenase homologues that cleave the interphenyl α,β double bond of stilbene derivatives via a monooxygenase reaction [J]. ChemBioChem 2008,9 (9),1450-1461.
[99]Nakatsubo F, Kirk TK, Shimada M, et al. Metabolism of a phenylcoumaran substructure lignin model compound in ligninolytic cultures of Phanerochaete chrysosporium [J]. Archives of Microbiology 1981,128 (4),416-420.
[100]Ohta M, Higuchi T, Iwahara S. Microbial degradation of dehydrodiconiferyl alcohol, a lignin substructure model [J]. Archives of Microbiology 1979,121 (1),23-28.
[101]Kamaya Y, Nakatsubo F, Higuchi T, et al. Degradation of d,1-syringaresinol, a β-β'linked lignin model compound, by Fusarium solani M-13-1 [J]. Archives of Microbiology 1981,129 (4),305-309.
[102]Cui F, Dolphin D. Iron porphyrin catalyzed oxidation of lignin model compounds:oxidation of phenylpropane and phenylpropene model compounds [J]. Canadian journal of chemistry 1995,73 (12),2153-2157.
[103]Williamson G, Kroon PA, Faulds CB. Hairy plant polysaccharides:a close shave with microbial esterases [J]. Microbiology 1998,144 (8),2011-2023.
[104]Faulds CB, Williamson G. Purification and characterization of a ferulic acid esterase (FAE-III) from Aspergillus niger:specificity for the phenolic moiety and binding to microcrystalline cellulose [J]. Microbiology 1994,140 (4), 779-787.
[105]Faulds CB, Ralet MC, Williamson G, et al. Specificity of an esterase (XYLD) from Pseudomonas fluorescens subsp. cellulosa [J]. Biochimica et Biophysica Acta (BBA)-General Subjects 1995,1243 (2),265-269.
[106]Ferreira P, Diez N, Gutieirrez C, et al. Streptomyces avermitilis CECT 3339 produces a ferulic acid esterase able to release ferulic acid from sugar beet pulp soluble feruloylated oligosaccharides [J]. Journal of the Science of Food and Agriculture 1999,79 (3),440-442.
[107]Peng X, Masai E, Kitayama H, et al. Characterization of the 5-carboxyvanillate decarboxylase gene and its role in lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 2002,68 (9),4407-4415.
[108]Gerlt JA, Babbitt PC. Mechanistically diverse enzyme superfamilies:the importance of chemistry in the evolution of catalysis [J]. Current opinion in chemical biology 1998,2 (5),607-612.
[109]Venturi V, Zennaro F, Degrassi G, et al. Genetics of ferulic acid bioconversion to protocatechuic acid in plant-growth-promoting Pseudomonas putida WCS358 [J]. Microbiology 1998,144 (4),965-973.
[110]Achterholt S, Priefert H, Steinbuchel A. Identification of Amycolatopsis sp. strain HR167 genes, involved in the bioconversion of ferulic acid to vanillin [J]. Applied microbiology and biotechnology 2000,54 (6),799-807.
[111]Prim N, Pastor F, Diaz P. Biochemical studies on cloned Bacillus sp. BP-7 phenolic acid decarboxylase PadA [J]. Applied microbiology and biotechnology 2003,63(1),51-56.
[112]Landete JM, Rodriguez H, Curiel JA, et al. Gene cloning, expression, and characterization of phenolic acid decarboxylase from Lactobacillus brevis RM84 [J]. Journal of industrial microbiology & biotechnology 2010,37 (6), 617-624.
[113]Godoy L, Martinez C, Carrasco N, et al. A. Purification and characterization of a p-coumarate decarboxylase and a vinylphenol reductase fro Brettanomyces bruxellensis [J]. International journal of food microbiology 2008,727(1),6-11.
[114]Kridelbaugh D, Hughes S, Allen T, et al. Production of 4-ethylphenol from 4-hydroxycinnamic acid by Lactobacillus sp. isolated from a swine waste lagoon [J]. Journal of applied microbiology 2010,109 (1),190-198.
[115]Bugg TH, Winfield C. Enzymatic cleavage of aromatic rings:mechanistic aspects of the catechol dioxygenases and later enzymes of bacterial oxidative cleavage pathways [J]. Natural Product Reports 1998,15 (5),513-530.
[116]Bugg TD. Dioxygenase enzymes:catalytic mechanisms and chemical models [J]. Tetrahedron 2003,59 (36),7075-7101.
[117]Noda Y, Nishikawa S, Shiozuka K, et al. Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis [J]. Journal of bacteriology 1990,172 (5),2704-2709.
[118]Sugimoto K, Senda T, Aoshima H, Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions [J]. Structure 1999,7 (8),953-965.
[119]Kasai D, Masai E, Miyauchi K, et al. Characterization of the gallate dioxygenase gene:three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6 [J]. Journal of bacteriology 2005,187 (15),5067-5074.
[120]Harwood CS, Parales RE. The β-ketoadipate pathway and the biology of self-identity [J]. Annual Reviews in Microbiology 1996,50 (1),553-590.
[121]Malliga P, Uma L, Subramanian G. Lignolytic activity of the cyanobacterium Anabaena azollae ML2 and the value of coir waste as a carrier for BGA biofertilizer [J]. Microbios 1996,86 (348),175-183.
[122]Hsueh HT, Chu H, Chang CC. Identification and characteristics of a cyanobacterium isolated from a hot spring with dissolved inorganic carbon [J]. Environmental science & technology 2007,41 (6),1909-1914.
[123]Saha SK, Swaminathan P, Raghavan C, et al. Ligninolytic and antioxidative enzymes of a marine cyanobacterium Oscillatoria willei BDU 130511 during Poly R-478 decolourization [J]. Bioresource technology 2010,101 (9), 3076-3084.
[124]Martone PT, Estevez JM, Lu F, et al. Discovery of lignin in seaweed reveals convergent evolution of cell-wall architecture [J]. Current Biology 2009,19 (2), 169-175.
[125]Tuor U, Winterhalter K, Fiechter A. Enzymes of white-rot fungi involved in lignin degradation and ecological determinants for wood decay [J]. Journal of biotechnology 1995,41 (1),1-17.
[126]Jokela J, Pellinen J, Salkinoja-Salonen M, et al. Biodegradation of two tetrameric lignin model compounds by a mixed bacterial culture [J]. Applied microbiology and biotechnology 1985,23 (1),38-46.
[127]Chandra R, Raj A, Purohit H, et al. Characterisation and optimisation of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste [J]. Chemosphere 2007,67 (4),839-846.
[128]Chandra R, Singh S, Krishna Reddy M, et al. Isolation and characterization of bacterial strains Paenibacillus sp. and Bacillus sp. for kraft lignin decolorization from pulp paper mill waste [J]. The Journal of General and Applied Microbiology 2008,54 (6),399-407.
[129]Raj A, Chandra R, Reddy MMK, et al. Biodegradation of kraft lignin by a newly isolated bacterial strain, Aneurinibacillus aneurinilyticus from the sludge of a pulp paper mill [J]. World Journal of Microbiology and Biotechnology 2007,23 (6),793-799.
[130]Raj A, Reddy MK, Chandra R, et al. Biodegradation of kraft-lignin by Bacillus sp. isolated from sludge of pulp and paper mill [J]. Biodegradation 2007,18 (6), 783-792.
[131]Leisola M, Brown C, Laurila M, et al. Polysaccharide synthesis by Phanerochaete chrysosporium during degradation of kraft lignin [J]. European journal of applied microbiology and biotechnology 1982,15 (3),180-184.
[132]Ball A, Betts W, McCarthy A. Degradation of lignin-related compounds by actinomycetes [J]. Applied and Environmental Microbiology 1989,55 (6), 1642-1644.
[133]Bourbonnais R, Paice M, Reid I, et al. Lignin oxidation by laccase isozymes from Trametes versicolor and role of the mediator 2,2'-azinobis (3-ethylbenzthiazoline-6-sulfonate) in kraft lignin depolymerization [J]. Applied and Environmental Microbiology 1995,61 (5),1876-1880.
[134]Lund M, Ragauskas A. Enzymatic modification of kraft lignin through oxidative coupling with water-soluble phenols [J]. Applied microbiology and biotechnology 2001,55 (6),699-703.
[135]Shintani N, Sugano Y, Shoda M. Decolorization of kraft pulp bleaching effluent by a newly isolated fungus, Geotrichum candidum Dec 1 [J]. Journal of wood science 2002,48 (5),402-408.
[136]Nakagawa Y, Sakamoto Y, Kikuchi S, et al. A chimeric laccase with hybrid properties of the parental Lentinula edodes laccases [J]. Microbiological Research 2010,165 (5),392-401.
[137]Orth AB, Royse D, Tien M. Ubiquity of lignin-degrading peroxidases among various wood-degrading fungi [J]. Applied and Environmental Microbiology 1993,59 (12),4017-4023.
[138]Kapich A, Prior B, Botha A, et al. Effect of lignocellulose-containing substrates on production of ligninolytic peroxidases in submerged cultures of Phanerochaete chrysosporium ME-446 [J]. Enzyme and Microbial Technology 2004,34(2),187-195.
[139]Chen Y, Chai L, Zhu Y, et al. Biodegradation of kraft lignin by a bacterial strain Comamonas sp. B-9 isolated from eroded bamboo slips [J]. Journal of applied microbiology 2012,112 (5),900-906.
[140]Raj A, Reddy M, Chandra R. Decolourisation and treatment of pulp and paper mill effluent by lignin-degrading Bacillus sp [J]. Journal of Chemical Technology and Biotechnology 2007,82 (4),399-406.
[141]Giroux H, Vidal P, Bouchard J, et al. Degradation of Kraft indulin lignin by Streptomyces viridosporus and Streptomyces badius [J]. Applied and Environmental Microbiology 1988,54 (12),3064-3070.
[142]Chandra R, Abhishek A. Bacterial decolorization of black liquor in axenic and mixed condition and characterization of metabolites [J]. Biodegradation 2011, 22 (3),603-611.
[143]Perez J, Munoz-Dorado J, de la Rubia T, et al. Biodegradation and biological treatments of cellulose, hemicellulose and lignin:an overview [J]. International Microbiology 2002,5(2),53-63.
[144]Leonowicz A, Cho N, Luterek J, et al. Fungal laccase:properties and activity on lignin [J]. Journal of Basic Microbiology 2001,41 (3-4),185-227.
[145]Bugg TD, Ahmad M, Hardiman EM, et al. Pathways for degradation of lignin in bacteria and fungi [J]. Natural Product Reports 2011,28 (12),1883-1896.
[146]Hernes PJ, Benner R. Photochemical and microbial degradation of dissolved lignin phenols:Implications for the fate of terrigenous dissolved organic matter in marine environments [J]. Journal of Geophysical Research 2003,108 (C9), 3291.
[147]Hernandez M, Rodriguez J, Perez M, et al.13C NMR cross polarization and magic angle spinning (CPMAS) and gas chromatography/mass spectrometry analysis of the products from a soda pulp mill effluent decolourised by two Streptomyces strains [J]. Applied microbiology and biotechnology 1997,47 (3), 272-278.
[148]Shin KS, Lee YJ. Depolymerisation of lignosulfonate by peroxidase of the white-rot basidiomycete, Pleurotus ostreatus [J]. Biotechnology letters 1999, 21 (7),585-588.
[149]Ksibi M, Ben Amor S, Cherif S, et al. Photodegradation of lignin from black liquor using a UV/TiO2 system [J]. Journal of Photochemistry and Photobiology A:Chemistry 2003,154 (2),211-218.
[150]Hernandez M, Hernandez-Coronado MJ, Montiel MD, et al. Analysis of alkali-lignin in a paper mill effluent decolourised with two Streptomyces strains by gas chromatography-mass spectrometry after cupric oxide degradation [J]. Journal of Chromatography A 2001,919 (2),389-394.
[151]Hedges JI, Ertel JR. Characterization of lignin by gas capillary chromatography of cupric oxide oxidation products [J]. Analytical Chemistry 1982,54 (2), 174-178.
[152]Mathew S, Abraham TE, Sudheesh S. Rapid conversion of ferulic acid to 4-vinyl guaiacol and vanillin metabolites by Debaryomyces hansenii [J]. Journal of Molecular Catalysis B:Enzymatic 2007,44 (2),48-52.
[153]Li X, Yang J, Li X, et al. The metabolism of ferulic acid via 4-vinylguaiacol to vanillin by Enterobacter sp. Px6-4 isolated from Vanilla root [J]. Process Biochemistry 2008,43 (10),1132-1137.
[154]Baqueiro-Pena I, Rodriguez-Serrano G, Gonzalez-Zamora E, et al. Biotransformation of ferulic acid to 4-vinylguaiacol by a wild and a diploid strain of Aspergillus niger [J]. Bioresource technology 2010,101 (12),4721-4724.
[155]Karmakar B, Vohra R, Nandanwar H, et al. Rapid degradation of ferulic acid via 4-vinylguaiacol and vanillin by a newly isolated strain of Bacillus coagulans [J]. Journal of biotechnology 2000,80 (3),195-202.
[156]Barthelmebs L, Divies C, Cavin JF. Knockout of the ρ-coumarate decarboxylase gene from Lactobacillus plantarum reveals the existence of two other inducible enzymatic activities involved in phenolic acid metabolism [J]. Applied and Environmental Microbiology 2000,66 (8),3368-3375.
[157]Grbic-Galic D. Fermentative and oxidative transformation of ferulate by a facultatively anaerobic bacterium isolated from sewage sludge [J]. Applied and Environmental Microbiology 1985,50 (4),1052-1057.
[158]Huang Z, Dostal L, Rosazza J. Mechanisms of ferulic acid conversions to vanillic acid and guaiacol by Rhodotorula rubra [J]. Journal of Biological Chemistry 1993,268 (32),23954-23958.
[159]Overhage J, Priefert H, Steinbuchel A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. strain HR199 [J]. Applied and Environmental Microbiology 1999,65 (11),4837-4847.
[160]Narbad A, Gasson MJ. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens [J]. Microbiology 1998,144 (5),1397-1405.
[161]Nelson K, Weinel C, Paulsen I, et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 [J]. Environmental microbiology 2002,4 (12),799-808.
[162]Weinel C, Ussery DW, Ohlsson H, et al. Comparative genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440:orthologs, codon usage, repetitive extragenic palindromic elements, and oligonucleotide motif signatures [J]. Genome Letters 2002,1(4),175-187.
[163]Nierman WC, Feldblyum TV, Laub MT, et al. Complete genome sequence of Caulobacter crescentus [J].Proceedings of the National Academy of Sciences 2001,98 (7),4136-4141.
[164]Tettelin H, Nelson KE, Paulsen IT, et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae [J]. Science 2001,293 (5529), 498-506.
[165]Nelson CG, Stauffer RA, Stomberg CR, et al. Dynamic bandwidth monitor and adjuster for remote communications with a medical device. Google Patents: 2003.
[166]Li R, Zhu H, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing [J]. Genome research 2010,20 (2), 265-272.
[167]Cadisch G, Giller KE. Driven by nature:plant litter quality and decomposition [M]. CAB INTERNATIONAL:1997.
[168]Diaz E, Ferrandez A, Prieto MA., et al. Biodegradation of aromatic compounds by Escherichia coli [J]. Microbiology and Molecular Biology Reviews 2001, 65 (4),523-569.
[169]MacLean AM, MacPherson G., Aneja P, et al. Characterization of the β-ketoadipate pathway in Sinorhizobium meliloti [J]. Applied and Environmental Microbiology 2006,72 (8),5403-5413.
[170]Barnes MR, Duetz WA., Williams PA. A 3-(3-hydroxyphenyl) propionic acid catabolic pathway in Rhodococcus globerulus PWD1:cloning and characterization of the hpp operon [J]. Journal of bacteriology 1997,179 (19), 6145-6153.
[171]Perez-Pantoja D, Donoso R, Agullo L, et al. Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales [J]. Environmental microbiology 2012,14 (5),1091-1117.
[172]Shen XH, Huang Y, Liu SJ. Genomic analysis and identification of catabolic pathways for aromatic compounds in Corynebacterium glutamicum [J]. Microbes and environments 2005,20 (3),160-167.
[173]Coenye T, Liu L, Vandamme P, et al. Identification of Pandoraea species by 16S ribosomal DNA-based PCR assays [J]. Journal of clinical microbiology 2001,39 (12),4452-4455.
[174]Coenye T, Falsen E, Hoste B, et al. Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb, nov [J]. International journal of systematic and evolutionary microbiology 2000,50 (2),887-899.
[175]Dhindwal S, Patil DN, Mohammadi M, et al. Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme [J]. Journal of Biological Chemistry 2011,286 (42),37011-37022.
[176]Jiang XW, Liu H, Xu Y, et al. Genetic and biochemical analyses of chlorobenzene degradation gene clusters in Pandoraea sp. strain MCB032 [J]. Archives of Microbiology 2009,191 (6),485-492.
[177]Amer R. Newly Isolated Pandoraea sp. Capable of Phenol Biodegradation [J]. Research Journal of Microbiology 2008,3 (10),622-629.
[178]Evans WC. Biochemistry of the bacterial catabolism of aromatic compounds in anaerobic environments [J]. Nature 1977,270 (5632),17-22.
[179]Jimenez JI, Minambres B, Garcia JL, et al. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440 [J]. Environmental microbiology 2002,4(12),824-841.
[180]Hartnett GB, Ornsto LN. Acquisition of apparent DNA slippage structures during extensive evolutionary divergence of pcaD and catD genes encoding identical catalytic activities in Acinetobacter calcoaceticus [J]. Gene 1994,142 (1),23-29.
[181]Eulberg D, Lakner S, Golovleva LA., et al. Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity [J]. Journal of bacteriology 1998,180 (5),1072-1081.
[182]Collier LS, Gaines GL, Neidle EL. Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator [J]. Journal of bacteriology 1998,180 (9),2493-2501.
[183]Perez-Pantoja D, De la Iglesia R, Pieper DH., et al. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134 [J]. FEMS microbiology reviews 2008,32 (5),736-794.
[184]Gupta JK, Hamp SG, Buswell JA, et al. Metabolism of trans-ferulic acid by the white-rot fungus Sporotrichum pulverulentum [J]. Archives of Microbiology 1981,128 (4),349-354.
[185]Falconnier B, Lapierre C, Lesage-Meessen L, et al. Vanillin as a product of ferulic acid biotransformation by the white-rot fungus Pycnoporus cinnabarinus 1-937:Identification of metabolic pathways [J]. Journal of biotechnology 1994,37(2),123-132.
[186]Bertani I, Kojic M, Venturi V. Regulation of the p-hydroxybenzoic acid hydroxylase gene (pobA) in plant-growth-promoting Pseudomonas putida WCS358 [J]. Microbiology 2001,147 (6),1611-1620.
[187]You IS, Ghosal D, Gunsalus IC. Nucleotide sequence analysis of the Pseudomonas putida PpG7 salicylate hydroxylase gene (nahG) and its 3'-flanking region [J]. Biochemistry 1991,30 (6),1635-1641.
[188]Lee J, Oh J, Min KR, et al. Nucleotide Sequence of Salicylate Hydroxylase Gene and Its 5'-Flanking Region of Pseudomonas putida KF715 [J]. Biochemical and biophysical research communications 1996,218 (2),544-548.
[189]Bosch R, Moore ER, Garcia-Valdes E, et al.NahW, a novel, inducible salicylate hydroxylase involved in mineralization of naphthalene by Pseudomonas stutzeri AN10 [J]. Journal of bacteriology 1999,181 (8),2315-2322.
[190]Jones RM, Pagmantidis V, Williams PA. sal genes determining the catabolism of salicylate esters are part of a supraoperonic cluster of catabolic genes in Acinetobacter sp. strain ADP1 [J]. Journal of bacteriology 2000,182 (7), 2018-2025.
[191]Demaneche S, Meyer C, Micoud J, et al. Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons [J]. Applied and Environmental Microbiology 2004,70 (11),6714-6725.
[192]Cho O, Choi KY, Zylstra GJ, et al. Catabolic role of a three-component salicylate oxygenase from Sphingomonas yanoikuyae B1 in polycyclic aromatic hydrocarbon degradation [J]. Biochemical and biophysical research communications 2005,327 (3),656-662.
[193]Harpel M, Lipscomb J. Gentisate 1,2-dioxygenase from pseudomonas. Purification, characterization, and comparison of the enzymes from Pseudomonas testosteroni and Pseudomonas acidovorans [J]. Journal of Biological Chemistry 1990,265 (11),6301-6311.
[194]Goetz FE, Harmuth LJ. Gentisate pathway in Salmonella typhimurium: metabolism of hydroxybenzoate and gentisate [J]. FEMS microbiology letters 1992,97 (1),45-49.
[195]Suarez M, Ferrer E, Garrido-Pertierra A, et al. Purification and characterization of the 3-hydroxybenzoate-6-hydroxylase from Klebsiella pneumoniae [J]. FEMS microbiology letters 1995,126 (3),283-290.
[196]Wang LH, Hamzah RY, Yu Y, et al. Pseudomonas cepacia 3-hydroxybenzoate 6-hydroxylase:induction, purification, and characterization [J]. Biochemistry 1987,26(4),1099-1104.
[197]Diaz E, Ferrandez A, Garcia JL. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12 [J]. Journal of bacteriology 1998,180 (11),2915-2923.
[198]Ferrandez A, Garcia JL, Diaz E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl) propionate catabolic pathway of Escherichia coli K-12 [J]. Journal of bacteriology 1997,179 (8),2573-2581.
[199]Torres B, Porras G, Garcia JL, et al. Regulation of the mhp cluster responsible for 3-(3-hydroxyphenyl) propionic acid degradation in Escherichia coli [J]. Journal of Biological Chemistry 2003,278 (30),27575-27585.
[200]Diaz E. Microbial biodegradation:genomics and molecular biology [M]. Horizon Scientific Press:2008.
[201]Teufel R, Mascaraque V, Ismail W, et al. Bacterial phenylalanine and phenylacetate catabolic pathway revealed [J]. Proceedings of the National Academy of Sciences 2010,107 (32),14390-14395.
[202]Milcamps A, Bruijn FJ. Identification of a novel nutrient-deprivation-induced Sinorhizobium meliloti gene (hmgA) involved in the degradation of tyrosine [J]. Microbiology 1999,145 (4),935-947.
[203]Ferrandez A, Minambres B, Garcia B, et al. Catabolism of phenylacetic acid in Escherichia coli characterization of a new aerobic hybrid pathway [J]. Journal of Biological Chemistry 1998,273 (40),25974-25986.
[204]Berkel WJ, Tweel, WJ. Purification and characteriation of 3-hydroxypheny-lacetate 6-hydroxylase:a novel FAD-dependent monooxygenase from a Flavobacterium species [J]. European Journal of Biochemistry 1991,201 (3), 585-592.
[205]Arias-Barrau E, Olivera ER, Luengo JM, et al. The homogentisate pathway:a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida [J]. Journal of bacteriology 2004,186(15),5062-5077.
[206]Hle KS, Jahn M, Ghisla S, et al. Two Similar Gene Clusters Coding for Enzymes of a New Type of Aerobic 2-Aminobenzoate (Anthranilate) Metabolism in the Bacterium Azoarcus evansii [J].2001.
[207]Kurnasov O, Jablonski L, Polanuyer B, et al. Aerobic tryptophan degradation pathway in bacteria:novel kynurenine formamidase [J]. FEMS microbiology letters 2003,227(2),219-227.
[208]Hasegawa Y, Muraki T, Tokuyama T, et al. A novel degradative pathway of 2-nitrobenzoate via 3-hydroxyanthranilate in Pseudomonas fluorescens strain KU-7 [J]. FEMS microbiology letters 2000,190 (2),185-190.
[209]Muraki T, Taki M, Hasegawa Y, et al. Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7 [J]. Applied and Environmental Microbiology 2003,69 (3),1564-1572.
[210]Martinez-Aguilar L, Caballero-Mellado J, Estrada-de los Santos P. Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov [J]. International journal of systematic and evolutionary microbiology 2013,63 (Pt 1),208-211.
[211]Wierckx N, Koopman F, Bandounas L, et al. Isolation and characterization of Cupriavidus basilensis HMF14 for biological removal of inhibitors from lignocellulosic hydrolysate [J]. Microbial biotechnology 2010,3(3),336-343.
[212]Koopman F, Wierckx N, Winde JH, et al. Identification and characterization of the furfural and 5-(hydroxymethyl) furfural degradation pathways of Cupriavidus basilensis HMF14 [J]. Proceedings of the National Academy of Sciences 2010, 107 (11),4919-4924.
[213]Friman H, Schechter A, Ioffe Y, et al. Current production in a microbial fuel cell using a pure culture of Cupriavidus basilensis growing in acetate or phenol as a carbon source [J]. Microbial biotechnology 2013.
[214]Cserhati M, Kriszt B, Szoboszlay S, et al. De novo genome project of Cupriavidus basilensis OR16 [J], Journal of bacteriology 2012,194 (8), 2109-2110.
[2]朱清时,阎立峰,郭庆祥.生物质洁净能源[M].化学工业出版社：2002.
[3]高培基,许平.资源环境微生物技术[M].化学工业出版社：2004.
[4]殷福珊.挑战纤维素的利用[J].日用化学品科学2009,32(1),24-26.
[5]Buranov, A. U., Mazza, G. Lignin in straw of herbaceous crops [J]. Industrial crops and products 2008,28 (3),237-259.
[6]霍弗里希特,Hofrichter, M.,施泰因比歇尔,等生物高分子：木质素,腐殖质和煤[M].化学工业出版社：2004.
[7]胡鸿达,江卓丽.木质素性质与综合利用[J].华东纸业2010,6,018.
[8]冯攀,谌凡更.木质素在环氧树脂合成中的应用进展[J].纤维素科学与技术2010,18(002),54-60.
[9]黎先发,罗学刚.木质素在塑料中的应用研究进展[J].塑料2004,33(4),58-61.
[10]查刘生.木质素基碳纤维的研制情况[J].炭素1992,(4),44-47.
[11]Faix O. Classification of lignins from different botanical origins by FT-IR spectroscopy [J]. Holzforschung-International Journal of the Biology, Chemistry, Physics and Technology of Wood 1991,45 (s1),21-28.
[12]Freudenberg K. Lignin:Its Constitution and Formation from p-Hydroxy-cinnamyl Alcohols:Lignin is duplicated by dehydrogenation of these alcohols; intermediates explain formation and structure [J]. Science (New York, NY) 1965,148 (3670),595.
[13]Higuchi T. Formation and biological degradation of lignins [J]. Advances in Enzymology and Related Areas of Molecular Biology, Volume 34 1971, 207-283.
[14]Eggeman T, Elander RT. Process and economic analysis of pretreatment technologies [J]. Bioresource technology 2005,96 (18),2019-2025.
[15]Zakzeski J, Bruijnincx PC, Jongerius AL, et al. The catalytic valorization of lignin for the production of renewable chemicals [J]. Chemical reviews 2010, 110 (6),3552.
[16]Pickett J, Anderson D, Bowles D, et al. Sustainable biofuels:prospects and challenges [J]. The Royal Society, London, UK 2008.
[17]Kastner M, Hofrichter M, Steinbuchel A. Biodegradation of humic substances [J]. Biopolymers:Lignin, Humic Substances and Coal 2001,349-378.
[18]Kirk TK, Farrell RL. Enzymatic "combustion":the microbial degradation of lignin [J]. Annual Reviews in Microbiology 1987,41 (1),465-501.
[19]Guillen F, Martinez MJ, Gutierrez A. Biodegradation of lignocellu-losics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin [J]. International Microbiology 2005,8,195-204.
[20]Bumpus JA, Aust SD. Biodegradation of environmental pollutants by the white rot fungus Phanerochaete chrysosporium:involvement of the lignin degrading system [J]. Bioessays 1987,6(4),166-170.
[21]Levasseur A, Piumi F, Coutinho PM., et al. FOLy:an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds [J]. Fungal genetics and biology 2008,45 (5),638-645.
[22]Macarena S, Fernando LL, Monica V, et al. Incomplete processing of peroxidase transcripts in the lignin degrading fungus Phanerochaete chrysosporium [J]. FEMS microbiology letters 2005,242 (1),37-44.
[23]Edwards SL, Raag R, Wariishi H, et al. Crystal structure of lignin peroxidase [J]. Proceedings of the National Academy of Sciences 1993,90 (2),750-754.
[24]Sundaramoorthy M, Kishi K, Gold MH, et al. The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06-A resolution [J]. Journal of Biological Chemistry 1994,269 (52),32759-32767.
[25]Banci L, Ciofi-Baffoni S, Tien M. Lignin and Mn peroxidase-catalyzed oxidation of phenolic lignin oligomers [J]. Biochemistry 1999,38 (10), 3205-3210.
[26]Martinez AT. Molecular biology and structure-function of lignin-degrading heme peroxidases [J]. Enzyme and Microbial Technology 2002,30 (4), 425-444.
[27]Hofrichter M. Review:lignin conversion by manganese peroxidase (MnP) [J]. Enzyme and Microbial Technology 2002,30 (4),454-466.
[28]Wariishi H, Dunford HB, MacDonald I, et al. Manganese peroxidase from the lignin-degrading basidiomycete Phanerochaete chrysosporium. Transient state kinetics and reaction mechanism [J]. Journal of Biological Chemistry 1989,264 (6),3335-3.340.
[29]Tuor U, Wariishi H, Schoemaker HE, et al. Oxidation of phenolic arylglycerol. beta.-aryl ether lignin model compounds by manganese peroxidase from Phanerochaete chrysosporium:oxidative cleavage of an. alpha.-carbonyl model compound [J]. Biochemistry 1992,31 (21),4986-4995.
[30]Cai D, Tien M. Lignin-degrading peroxidases of Phanerochaete chrysosporium [J]. Journal of biotechnology 1993,30(1),79-90.
[31]Tien M, Kirk TK, Bull C, et al. Steady-state and transient-state kinetic studies on the oxidation of 3,4-dimethoxybenzyl alcohol catalyzed by the ligninase of Phanerocheate chrysosporium Burds [J]. Journal of Biological Chemistry 1986, 261 (4),1687-1693.
[32]Doyle WA, Blodig W, Veitch NC, et al. Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis [J]. Biochemistry 1998,37 (43),15097-15105.
[33]Khindaria A, Yamazaki I, Aust SD. Stabilization of the veratryl alcohol cation radical by lignin peroxidase [J]. Biochemistry 1996,35 (20),6418-6424.
[34]Candeias LP, Harvey PJ. Lifetime and reactivity of the veratryl alcohol radical cation. Implications for lignin peroxidase catalysis [J]. Journal of Biological Chemistry 1995,270 (28),16745-16748.
[35]Hammel KE, Tien M, Kalyanaraman B, et al. Mechanism of oxidative C alpha-C beta cleavage of a lignin model dimer by Phanerochaete chrysosporium ligninase. Stoichiometry and involvement of free radicals [J]. Journal of Biological Chemistry 1985,260 (14),8348-8353.
[36]Hammel KE, Cullen D. Role of fungal peroxidases in biological ligninolysis [J]. Current opinion in plant biology 2008,11 (3),349-355.
[37]Hammel KE, Jensen K, Mozuch MD, et al. Ligninolysis by a purified lignin peroxidase [J]. Journal of Biological Chemistry 1993,268 (17),12274-12281.
[38]Wariishi H, Valli K, Gold MH. In vitro depolymerization of lignin by manganese peroxidase of Phanerochaete chrysosporium [J]. Biochemical and biophysical research communications 1991,176 (1),269-275.
[39]Shleev S, Persson P, Shumakovich G, et al. Interaction of fungal laccases and laccase-mediator systems with lignin [J]. Enzyme and Microbial Technology 2006,39 (4),841-847.
[40]Camarero S, Garcia O, Vidal T, et al. Efficient bleaching of non-wood high-quality paper pulp using laccase-mediator system [J]. Enzyme and Microbial Technology 2004,35 (2),113-120.
[41]Arora DS, Sharma RK. Ligninolytic fungal laccases and their biotechnological applications [J]. Applied biochemistry and biotechnology 2010,160 (6), 1760-1788.
[42]Giardina P, Faraco V, Pezzella C, et al. Laccases:a never-ending story [J]. Cellular and Molecular Life Sciences 2010,67 (3),369-385.
[43]Bento I, Silva CS, Chen Z, et al. Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer [J]. BMC structural biology 2010,10 (1),28.
[44]Bertrand T, Jolivalt C, Briozzo P, et al. Crystal structure of a four-copper laccase complexed with an arylamine:insights into substrate recognition and correlation with kinetics [J]. Biochemistry 2002,41 (23),7325-7333.
[45]Piontek K, Antorini M, Choinowski T. Crystal Structure of a Laccase from the FungusTrametes versicolor at 1.90-A resolution containing a full complement of coppers [J]. Journal of Biological Chemistry 2002,277 (40),37663-37669.
[46]Jonsson L, Sjostrom K, Haggstrom I, et al. Characterization of a laccase gene from the white-rot fungus Trametes versicolor and structural features of basidiomycete laccases [J]. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology 1995,1251 (2),210-215.
[47]Niku-Paavola ML, Karhunen E, Kantelinen A, et al. The effect of culture conditions on the production of lignin modifying enzymes by the white-rot fungus Phlebia radiata [J]. Journal of biotechnology 1990,13 (2),211-221.
[48]Bermek H, Li K, Eriksson KEL. Laccase-less mutants of the white-rot fungus Pycnoporus cinnabarinus cannot delignify kraft pulp [J]. Journal of biotechnology 1998,66(2),117-124.
[49]Ander, P., Eriksson, K.-E. The importance of phenol oxidase activity in lignin degradation by the white-rot fungus Sporotrichum pulverulentum [J]. Archives of Microbiology 1976,109 (1-2),1-8.
[50]Kawai S, Umezawa T, Higuchi T. Degradation mechanisms of phenolic β-1 lignin substructure model compounds by laccase of Coriolus versicolor [J]. Archives of biochemistry and biophysics 1988,262 (1),99-110.
[51]Bourbonnais R, Paice MG. Oxidation of non-phenolic substrates:an expanded role for laccase in lignin biodegradation [J]. FEBS letters 1990,267 (1), 99-102.
[52]Thurston CF. The structure and function of fungal laccases [J]. Microbiology 1994,140(1),19-26.
[53]Martinez D, Larrondo LF, Putnam N, et al. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78 [J]. Nature biotechnology 2004,22 (6),695-700.
[54]Kersten P, Cullen D. Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium [J]. Fungal genetics and biology 2007,44 (2),77-87.
[55]Vicuna R. Bacterial degradation of lignin [J]. Enzyme and Microbial Technology 1988,10 (11),646-655.
[56]Zimmermann W. Degradation of lignin by bacteria [J]. Journal of biotechnology 1990,13 (2),119-130.
[57]Ramachandra M, Crawford DL, Hertel, G. Characterization of an extracellular lignin peroxidase of the lignocellulolytic actinomycete Streptomyces viridosporus [J]. Applied and Environmental Microbiology 1988,54 (12), 3057-3063.
[58]Masai E, Katayama Y, Fukuda M. Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds [J]. Bioscience, biotechnology, and biochemistry 2007,71 (1),1-15.
[59]Ahmad M, Taylor CR, Pink D, et al. Development of novel assays for lignin degradation:comparative analysis of bacterial and fungal lignin degraders [J]. Molecular bioSystems 2010,6(5),815-821.
[60]Bugg TD, Ahmad M, Hardiman EM, et al. The emerging role for bacteria in lignin degradation and bio-product formation [J]. Current opinion in biotechnology 2011,22 (3),394-400.
[61]Ahmad M, Roberts JN, Hardiman EM., et al. Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase [J]. Biochemistry 2011,50 (23),5096-5107.
[62]Roberts JN, Singh R, Grigg JC, et al. Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1 [J]. Biochemistry 2011,50 (23), 5108-5119.
[63]Adav SS, Ng CS, Arulmani M, et al. Quantitative iTRAQ secretome analysis of cellulolytic Thermobifida fusca [J]. Journal of proteome research 2010,9 (6), 3016-3024.
[64]Brown ME, Walker MC, Nakashige TG, et al. Discovery and characterization of heme enzymes from unsequenced bacteria:application to microbial lignin degradation [J]. Journal of the American Chemical Society 2011,133 (45), 18006-18009.
[65]Chen CL, Chang HM, Kirk TK. Aromatic acids produced during degradation of lignin in spruce wood by Phanerochaete chrysosporium [J]. Holzforschung-International Journal of the Biology, Chemistry, Physics and Technology of Wood 1982,36(1),3-9.
[66]Chen CL, Chang HM, Kirk TK. Carboxylic acids produced through oxidative cleavage of aromatic rings during degradation of lignin in spruce wood by Phanerochaete chrysosporium [J]. Journal of Wood Chemistry and Technology 1983,3(1),35-57.
[67]Reid ID. Fate of residual lignin during delignification of kraft pulp by Trametes versicolor [J]. Applied and Environmental Microbiology 1998,64 (6), 2117-2125.
[68]Raj A, Krishna Reddy M., Chandra R. Identification of low molecular weight aromatic compounds by gas chromatography-mass spectrometry (GC-MS) from kraft lignin degradation by three Bacillus sp [J]. International biodeterioration & biodegradation 2007,59 (4),292-296.
[69]Gupta VK, Minocha AK, Jain N. Batch and continuous studies on treatment of pulp mill wastewater by Aeromonas formicans [J]. Journal of Chemical Technology and Biotechnology 2001,76 (6),547-552.
[70]Grandy AS, Neff JC, Weintraub MN. Carbon structure and enzyme activities in alpine and forest ecosystems [J]. Soil Biology and Biochemistry 2007,39 (11), 2701-2711.
[71]Crawford DL, Pometto AL, Crawford RL. Lignin degradation by Streptomyces viridosporus:isolation and characterization of a new polymeric lignin degradation intermediate [J]. Applied and Environmental Microbiology 1983, 45 (3),898-904.
[72]Trigo C, Ball A. Production of extracellular enzymes during the solubilisation of straw by Thermomonospora fusca BD25 [J]. Applied microbiology and biotechnology 1994,41 (3),366-372.
[73]Masai E, Katayama Y, Nishikawa S, et al. Detection and localization of a new enzyme catalyzing the β-aryl ether cleavage in the soil bacterium Pseudomonas paucimobilis SYK-6) [J]. FEBS letters 1989,249 (2),348-352.
[74]Masai E, Katayama Y, Kubota S, et al. A bacterial enzyme degrading the model lignin compound β-etherase is a member of the glutathione-S-transferase superfamily [J]. FEBS letters 1993,323 (1),135-140.
[75]Masai E, Ichimura A, Sato Y, et al. Roles of the enantioselective glutathione-S-transferases in cleavage of (3-aryl ether [J]. Journal of bacteriology 2003,185 (6),1768-1775.
[76]Vicuna R, Gonzalez B, Mozuch M, et al. Metabolism of lignin model compounds of the arylglycerol-β-aryl ether type by Pseudomonas acidovorans D3 [J]. Applied and Environmental Microbiology 1987,53(11),2605-2609.
[77]Camarero S, Ibarra D, Martinez MJ, et al. Lignin-derived compounds as efficient laccase mediators for decolorization of different types of recalcitrant dyes [J]. Applied and Environmental Microbiology 2005,71 (4),1775-1784.
[78]Otsuka Y, Sonoki T, Ikeda S, et al. Detection and characterization of a novel extracellular fungal enzyme that catalyzes the specific and hydrolytic cleavage of lignin guaiacylglycerol β-aryl ether linkages [J]. European Journal of Biochemistry 2003,270 (11),2353-2362.
[79]Abe T, Masai E, Miyauchi K, et al. tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6 [J]. Journal of bacteriology 2005,187 (6),2030-2037.
[80]Brunel F, Davison J. Cloning and sequencing of Pseudomonas genes encoding vanillate demethylase [J]. Journal of bacteriology 1988,170(10),4924-4930.
[81]Segura A, Bunz PV, D'Argenio DA, et al. Genetic Analysis of a Chromosomal Region ContainingvanA and vanB, Genes Required for Conversion of Either Ferulate or Vanillate to Protocatechuate in Acinetobacter [J]. Journal of bacteriology 1999,181 (11),3494-3504.
[82]Enoki A, Goldsby GP, Gold MH. Metabolism of the lignin model compounds veratrylglycerol-β-guaiacyl ether and 4-ethoxy-3-methoxyphenylglycerol-β-guaiacyl ether by Phanerochaete chrysosporium [J]. Archives of Microbiology 1980,125 (3), 227-231.
[83]Masai E, Yamamoto Y, Inoue T, et al. Characterization of ligV essential for catabolism of vanillin by Sphingomonas paucimobilis SYK-6 [J]. Bioscience, biotechnology, and biochemistry 2007,71 (10),2487-2492.
[84]Priefert H, Rabenhorst J, Steinbuchel A. Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate [J]. Journal of bacteriology 1997,179 (8),2595-2607.
[85]Pieper DH. Aerobic degradation of poly chlorinated biphenyls [J]. Applied microbiology and biotechnology 2005,67 (2),170-191.
[86]Sonoki T, Obi T, Kubota S, et al. Coexistence of two different O demethylation systems in lignin metabolism by Sphingomonas paucimobilis SYK-6:cloning and sequencing of the lignin biphenyl-specific O-demethylase (LigX) gene [J]. Applied and Environmental Microbiology 2000,66 (5),2125-2132.
[87]Peng X, Egashira T, Hanashiro K, et al. Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme [J]. Applied and Environmental Microbiology 1998,64 (7),2520-2527.
[88]Peng X, Masai E, Katayama Y, et al. Characterization of the meta-Cleavage Compound Hydrolase Gene involved in degradation of the lignin-related biphenyl structure by Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 1999,65 (6),2789-2793.
[89]Masai E, Harada K, Peng X, et al. Cloning and characterization of the ferulic acid catabolic genes of Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 2002,68 (9),4416-4424.
[90]Peng X, Masai E, Kasai D, et al. A second 5-carboxyvanillate decarboxylase gene, ligW2, is important for lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 2005,71 (9),5014-5021.
[91]Pollard JR, Bugg TD. Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli [J]. European Journal of Biochemistry 1998,251(1-2),98-106.
[92]Hara H, Masai E, Miyauchi K, et al. Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6 [J]. Journal of bacteriology 2003,185 (1),41-50.
[93]Maruyama, K., Miwa, M., Tsujii, N., Nagai, T., Tomita, N., Harada, T., Sobajima, H., Sugisaki, H. Cloning, sequencing, and expression of the gene encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1 [J]. Bioscience, biotechnology, and biochemistry 2001,65 (12),2701-2709.
[94]Enoki A, Gold MH. Degradation of the diarylpropane lignin model compound 1-(3',4'-diethoxyphenyl)-1,3-dihydroxy-2-(4''-methoxyphenyl)-propane and derivatives by the basidiomycete Phanerochaete chrysosporium [J]. Archives of Microbiology 1982,132 (2),123-130.
[95]Gold MH, Kuwahara M, Chiu AA., et al. Purification and characterization of an extracellular H2O2-requiring diarylpropane oxygenase from the white rot basidiomycete, Phanerochaete chrysosporium [J]. Archives of biochemistry and biophysics 1984,234 (2),353-362.
[96]Kamoda S, Saburi Y. Cloning, expression and sequence analysis of a lignostilbene-a, b-dioxygenase gene from Pseudomonas paucimobilis TMY1009 [J]. Biosci. Biotechnol. Biochem 1993,57,926-930.
[97]Giuliano G, Al-Babili S, von Lintig J. Carotenoid oxygenases:cleave it or leave it [J]. Trends in plant science 2003,8 (4),145-149.
[98]Marasco EK, Schmidt-Dannert C. Identification of bacterial carotenoid cleavage dioxygenase homologues that cleave the interphenyl α,β double bond of stilbene derivatives via a monooxygenase reaction [J]. ChemBioChem 2008,9 (9),1450-1461.
[99]Nakatsubo F, Kirk TK, Shimada M, et al. Metabolism of a phenylcoumaran substructure lignin model compound in ligninolytic cultures of Phanerochaete chrysosporium [J]. Archives of Microbiology 1981,128 (4),416-420.
[100]Ohta M, Higuchi T, Iwahara S. Microbial degradation of dehydrodiconiferyl alcohol, a lignin substructure model [J]. Archives of Microbiology 1979,121 (1),23-28.
[101]Kamaya Y, Nakatsubo F, Higuchi T, et al. Degradation of d,1-syringaresinol, a β-β'linked lignin model compound, by Fusarium solani M-13-1 [J]. Archives of Microbiology 1981,129 (4),305-309.
[102]Cui F, Dolphin D. Iron porphyrin catalyzed oxidation of lignin model compounds:oxidation of phenylpropane and phenylpropene model compounds [J]. Canadian journal of chemistry 1995,73 (12),2153-2157.
[103]Williamson G, Kroon PA, Faulds CB. Hairy plant polysaccharides:a close shave with microbial esterases [J]. Microbiology 1998,144 (8),2011-2023.
[104]Faulds CB, Williamson G. Purification and characterization of a ferulic acid esterase (FAE-III) from Aspergillus niger:specificity for the phenolic moiety and binding to microcrystalline cellulose [J]. Microbiology 1994,140 (4), 779-787.
[105]Faulds CB, Ralet MC, Williamson G, et al. Specificity of an esterase (XYLD) from Pseudomonas fluorescens subsp. cellulosa [J]. Biochimica et Biophysica Acta (BBA)-General Subjects 1995,1243 (2),265-269.
[106]Ferreira P, Diez N, Gutieirrez C, et al. Streptomyces avermitilis CECT 3339 produces a ferulic acid esterase able to release ferulic acid from sugar beet pulp soluble feruloylated oligosaccharides [J]. Journal of the Science of Food and Agriculture 1999,79 (3),440-442.
[107]Peng X, Masai E, Kitayama H, et al. Characterization of the 5-carboxyvanillate decarboxylase gene and its role in lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6 [J]. Applied and Environmental Microbiology 2002,68 (9),4407-4415.
[108]Gerlt JA, Babbitt PC. Mechanistically diverse enzyme superfamilies:the importance of chemistry in the evolution of catalysis [J]. Current opinion in chemical biology 1998,2 (5),607-612.
[109]Venturi V, Zennaro F, Degrassi G, et al. Genetics of ferulic acid bioconversion to protocatechuic acid in plant-growth-promoting Pseudomonas putida WCS358 [J]. Microbiology 1998,144 (4),965-973.
[110]Achterholt S, Priefert H, Steinbuchel A. Identification of Amycolatopsis sp. strain HR167 genes, involved in the bioconversion of ferulic acid to vanillin [J]. Applied microbiology and biotechnology 2000,54 (6),799-807.
[111]Prim N, Pastor F, Diaz P. Biochemical studies on cloned Bacillus sp. BP-7 phenolic acid decarboxylase PadA [J]. Applied microbiology and biotechnology 2003,63(1),51-56.
[112]Landete JM, Rodriguez H, Curiel JA, et al. Gene cloning, expression, and characterization of phenolic acid decarboxylase from Lactobacillus brevis RM84 [J]. Journal of industrial microbiology & biotechnology 2010,37 (6), 617-624.
[113]Godoy L, Martinez C, Carrasco N, et al. A. Purification and characterization of a p-coumarate decarboxylase and a vinylphenol reductase fro Brettanomyces bruxellensis [J]. International journal of food microbiology 2008,727(1),6-11.
[114]Kridelbaugh D, Hughes S, Allen T, et al. Production of 4-ethylphenol from 4-hydroxycinnamic acid by Lactobacillus sp. isolated from a swine waste lagoon [J]. Journal of applied microbiology 2010,109 (1),190-198.
[115]Bugg TH, Winfield C. Enzymatic cleavage of aromatic rings:mechanistic aspects of the catechol dioxygenases and later enzymes of bacterial oxidative cleavage pathways [J]. Natural Product Reports 1998,15 (5),513-530.
[116]Bugg TD. Dioxygenase enzymes:catalytic mechanisms and chemical models [J]. Tetrahedron 2003,59 (36),7075-7101.
[117]Noda Y, Nishikawa S, Shiozuka K, et al. Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis [J]. Journal of bacteriology 1990,172 (5),2704-2709.
[118]Sugimoto K, Senda T, Aoshima H, Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions [J]. Structure 1999,7 (8),953-965.
[119]Kasai D, Masai E, Miyauchi K, et al. Characterization of the gallate dioxygenase gene:three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6 [J]. Journal of bacteriology 2005,187 (15),5067-5074.
[120]Harwood CS, Parales RE. The β-ketoadipate pathway and the biology of self-identity [J]. Annual Reviews in Microbiology 1996,50 (1),553-590.
[121]Malliga P, Uma L, Subramanian G. Lignolytic activity of the cyanobacterium Anabaena azollae ML2 and the value of coir waste as a carrier for BGA biofertilizer [J]. Microbios 1996,86 (348),175-183.
[122]Hsueh HT, Chu H, Chang CC. Identification and characteristics of a cyanobacterium isolated from a hot spring with dissolved inorganic carbon [J]. Environmental science & technology 2007,41 (6),1909-1914.
[123]Saha SK, Swaminathan P, Raghavan C, et al. Ligninolytic and antioxidative enzymes of a marine cyanobacterium Oscillatoria willei BDU 130511 during Poly R-478 decolourization [J]. Bioresource technology 2010,101 (9), 3076-3084.
[124]Martone PT, Estevez JM, Lu F, et al. Discovery of lignin in seaweed reveals convergent evolution of cell-wall architecture [J]. Current Biology 2009,19 (2), 169-175.
[125]Tuor U, Winterhalter K, Fiechter A. Enzymes of white-rot fungi involved in lignin degradation and ecological determinants for wood decay [J]. Journal of biotechnology 1995,41 (1),1-17.
[126]Jokela J, Pellinen J, Salkinoja-Salonen M, et al. Biodegradation of two tetrameric lignin model compounds by a mixed bacterial culture [J]. Applied microbiology and biotechnology 1985,23 (1),38-46.
[127]Chandra R, Raj A, Purohit H, et al. Characterisation and optimisation of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste [J]. Chemosphere 2007,67 (4),839-846.
[128]Chandra R, Singh S, Krishna Reddy M, et al. Isolation and characterization of bacterial strains Paenibacillus sp. and Bacillus sp. for kraft lignin decolorization from pulp paper mill waste [J]. The Journal of General and Applied Microbiology 2008,54 (6),399-407.
[129]Raj A, Chandra R, Reddy MMK, et al. Biodegradation of kraft lignin by a newly isolated bacterial strain, Aneurinibacillus aneurinilyticus from the sludge of a pulp paper mill [J]. World Journal of Microbiology and Biotechnology 2007,23 (6),793-799.
[130]Raj A, Reddy MK, Chandra R, et al. Biodegradation of kraft-lignin by Bacillus sp. isolated from sludge of pulp and paper mill [J]. Biodegradation 2007,18 (6), 783-792.
[131]Leisola M, Brown C, Laurila M, et al. Polysaccharide synthesis by Phanerochaete chrysosporium during degradation of kraft lignin [J]. European journal of applied microbiology and biotechnology 1982,15 (3),180-184.
[132]Ball A, Betts W, McCarthy A. Degradation of lignin-related compounds by actinomycetes [J]. Applied and Environmental Microbiology 1989,55 (6), 1642-1644.
[133]Bourbonnais R, Paice M, Reid I, et al. Lignin oxidation by laccase isozymes from Trametes versicolor and role of the mediator 2,2'-azinobis (3-ethylbenzthiazoline-6-sulfonate) in kraft lignin depolymerization [J]. Applied and Environmental Microbiology 1995,61 (5),1876-1880.
[134]Lund M, Ragauskas A. Enzymatic modification of kraft lignin through oxidative coupling with water-soluble phenols [J]. Applied microbiology and biotechnology 2001,55 (6),699-703.
[135]Shintani N, Sugano Y, Shoda M. Decolorization of kraft pulp bleaching effluent by a newly isolated fungus, Geotrichum candidum Dec 1 [J]. Journal of wood science 2002,48 (5),402-408.
[136]Nakagawa Y, Sakamoto Y, Kikuchi S, et al. A chimeric laccase with hybrid properties of the parental Lentinula edodes laccases [J]. Microbiological Research 2010,165 (5),392-401.
[137]Orth AB, Royse D, Tien M. Ubiquity of lignin-degrading peroxidases among various wood-degrading fungi [J]. Applied and Environmental Microbiology 1993,59 (12),4017-4023.
[138]Kapich A, Prior B, Botha A, et al. Effect of lignocellulose-containing substrates on production of ligninolytic peroxidases in submerged cultures of Phanerochaete chrysosporium ME-446 [J]. Enzyme and Microbial Technology 2004,34(2),187-195.
[139]Chen Y, Chai L, Zhu Y, et al. Biodegradation of kraft lignin by a bacterial strain Comamonas sp. B-9 isolated from eroded bamboo slips [J]. Journal of applied microbiology 2012,112 (5),900-906.
[140]Raj A, Reddy M, Chandra R. Decolourisation and treatment of pulp and paper mill effluent by lignin-degrading Bacillus sp [J]. Journal of Chemical Technology and Biotechnology 2007,82 (4),399-406.
[141]Giroux H, Vidal P, Bouchard J, et al. Degradation of Kraft indulin lignin by Streptomyces viridosporus and Streptomyces badius [J]. Applied and Environmental Microbiology 1988,54 (12),3064-3070.
[142]Chandra R, Abhishek A. Bacterial decolorization of black liquor in axenic and mixed condition and characterization of metabolites [J]. Biodegradation 2011, 22 (3),603-611.
[143]Perez J, Munoz-Dorado J, de la Rubia T, et al. Biodegradation and biological treatments of cellulose, hemicellulose and lignin:an overview [J]. International Microbiology 2002,5(2),53-63.
[144]Leonowicz A, Cho N, Luterek J, et al. Fungal laccase:properties and activity on lignin [J]. Journal of Basic Microbiology 2001,41 (3-4),185-227.
[145]Bugg TD, Ahmad M, Hardiman EM, et al. Pathways for degradation of lignin in bacteria and fungi [J]. Natural Product Reports 2011,28 (12),1883-1896.
[146]Hernes PJ, Benner R. Photochemical and microbial degradation of dissolved lignin phenols:Implications for the fate of terrigenous dissolved organic matter in marine environments [J]. Journal of Geophysical Research 2003,108 (C9), 3291.
[147]Hernandez M, Rodriguez J, Perez M, et al.13C NMR cross polarization and magic angle spinning (CPMAS) and gas chromatography/mass spectrometry analysis of the products from a soda pulp mill effluent decolourised by two Streptomyces strains [J]. Applied microbiology and biotechnology 1997,47 (3), 272-278.
[148]Shin KS, Lee YJ. Depolymerisation of lignosulfonate by peroxidase of the white-rot basidiomycete, Pleurotus ostreatus [J]. Biotechnology letters 1999, 21 (7),585-588.
[149]Ksibi M, Ben Amor S, Cherif S, et al. Photodegradation of lignin from black liquor using a UV/TiO2 system [J]. Journal of Photochemistry and Photobiology A:Chemistry 2003,154 (2),211-218.
[150]Hernandez M, Hernandez-Coronado MJ, Montiel MD, et al. Analysis of alkali-lignin in a paper mill effluent decolourised with two Streptomyces strains by gas chromatography-mass spectrometry after cupric oxide degradation [J]. Journal of Chromatography A 2001,919 (2),389-394.
[151]Hedges JI, Ertel JR. Characterization of lignin by gas capillary chromatography of cupric oxide oxidation products [J]. Analytical Chemistry 1982,54 (2), 174-178.
[152]Mathew S, Abraham TE, Sudheesh S. Rapid conversion of ferulic acid to 4-vinyl guaiacol and vanillin metabolites by Debaryomyces hansenii [J]. Journal of Molecular Catalysis B:Enzymatic 2007,44 (2),48-52.
[153]Li X, Yang J, Li X, et al. The metabolism of ferulic acid via 4-vinylguaiacol to vanillin by Enterobacter sp. Px6-4 isolated from Vanilla root [J]. Process Biochemistry 2008,43 (10),1132-1137.
[154]Baqueiro-Pena I, Rodriguez-Serrano G, Gonzalez-Zamora E, et al. Biotransformation of ferulic acid to 4-vinylguaiacol by a wild and a diploid strain of Aspergillus niger [J]. Bioresource technology 2010,101 (12),4721-4724.
[155]Karmakar B, Vohra R, Nandanwar H, et al. Rapid degradation of ferulic acid via 4-vinylguaiacol and vanillin by a newly isolated strain of Bacillus coagulans [J]. Journal of biotechnology 2000,80 (3),195-202.
[156]Barthelmebs L, Divies C, Cavin JF. Knockout of the ρ-coumarate decarboxylase gene from Lactobacillus plantarum reveals the existence of two other inducible enzymatic activities involved in phenolic acid metabolism [J]. Applied and Environmental Microbiology 2000,66 (8),3368-3375.
[157]Grbic-Galic D. Fermentative and oxidative transformation of ferulate by a facultatively anaerobic bacterium isolated from sewage sludge [J]. Applied and Environmental Microbiology 1985,50 (4),1052-1057.
[158]Huang Z, Dostal L, Rosazza J. Mechanisms of ferulic acid conversions to vanillic acid and guaiacol by Rhodotorula rubra [J]. Journal of Biological Chemistry 1993,268 (32),23954-23958.
[159]Overhage J, Priefert H, Steinbuchel A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. strain HR199 [J]. Applied and Environmental Microbiology 1999,65 (11),4837-4847.
[160]Narbad A, Gasson MJ. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens [J]. Microbiology 1998,144 (5),1397-1405.
[161]Nelson K, Weinel C, Paulsen I, et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 [J]. Environmental microbiology 2002,4 (12),799-808.
[162]Weinel C, Ussery DW, Ohlsson H, et al. Comparative genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440:orthologs, codon usage, repetitive extragenic palindromic elements, and oligonucleotide motif signatures [J]. Genome Letters 2002,1(4),175-187.
[163]Nierman WC, Feldblyum TV, Laub MT, et al. Complete genome sequence of Caulobacter crescentus [J].Proceedings of the National Academy of Sciences 2001,98 (7),4136-4141.
[164]Tettelin H, Nelson KE, Paulsen IT, et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae [J]. Science 2001,293 (5529), 498-506.
[165]Nelson CG, Stauffer RA, Stomberg CR, et al. Dynamic bandwidth monitor and adjuster for remote communications with a medical device. Google Patents: 2003.
[166]Li R, Zhu H, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing [J]. Genome research 2010,20 (2), 265-272.
[167]Cadisch G, Giller KE. Driven by nature:plant litter quality and decomposition [M]. CAB INTERNATIONAL:1997.
[168]Diaz E, Ferrandez A, Prieto MA., et al. Biodegradation of aromatic compounds by Escherichia coli [J]. Microbiology and Molecular Biology Reviews 2001, 65 (4),523-569.
[169]MacLean AM, MacPherson G., Aneja P, et al. Characterization of the β-ketoadipate pathway in Sinorhizobium meliloti [J]. Applied and Environmental Microbiology 2006,72 (8),5403-5413.
[170]Barnes MR, Duetz WA., Williams PA. A 3-(3-hydroxyphenyl) propionic acid catabolic pathway in Rhodococcus globerulus PWD1:cloning and characterization of the hpp operon [J]. Journal of bacteriology 1997,179 (19), 6145-6153.
[171]Perez-Pantoja D, Donoso R, Agullo L, et al. Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales [J]. Environmental microbiology 2012,14 (5),1091-1117.
[172]Shen XH, Huang Y, Liu SJ. Genomic analysis and identification of catabolic pathways for aromatic compounds in Corynebacterium glutamicum [J]. Microbes and environments 2005,20 (3),160-167.
[173]Coenye T, Liu L, Vandamme P, et al. Identification of Pandoraea species by 16S ribosomal DNA-based PCR assays [J]. Journal of clinical microbiology 2001,39 (12),4452-4455.
[174]Coenye T, Falsen E, Hoste B, et al. Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb, nov [J]. International journal of systematic and evolutionary microbiology 2000,50 (2),887-899.
[175]Dhindwal S, Patil DN, Mohammadi M, et al. Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme [J]. Journal of Biological Chemistry 2011,286 (42),37011-37022.
[176]Jiang XW, Liu H, Xu Y, et al. Genetic and biochemical analyses of chlorobenzene degradation gene clusters in Pandoraea sp. strain MCB032 [J]. Archives of Microbiology 2009,191 (6),485-492.
[177]Amer R. Newly Isolated Pandoraea sp. Capable of Phenol Biodegradation [J]. Research Journal of Microbiology 2008,3 (10),622-629.
[178]Evans WC. Biochemistry of the bacterial catabolism of aromatic compounds in anaerobic environments [J]. Nature 1977,270 (5632),17-22.
[179]Jimenez JI, Minambres B, Garcia JL, et al. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440 [J]. Environmental microbiology 2002,4(12),824-841.
[180]Hartnett GB, Ornsto LN. Acquisition of apparent DNA slippage structures during extensive evolutionary divergence of pcaD and catD genes encoding identical catalytic activities in Acinetobacter calcoaceticus [J]. Gene 1994,142 (1),23-29.
[181]Eulberg D, Lakner S, Golovleva LA., et al. Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity [J]. Journal of bacteriology 1998,180 (5),1072-1081.
[182]Collier LS, Gaines GL, Neidle EL. Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator [J]. Journal of bacteriology 1998,180 (9),2493-2501.
[183]Perez-Pantoja D, De la Iglesia R, Pieper DH., et al. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134 [J]. FEMS microbiology reviews 2008,32 (5),736-794.
[184]Gupta JK, Hamp SG, Buswell JA, et al. Metabolism of trans-ferulic acid by the white-rot fungus Sporotrichum pulverulentum [J]. Archives of Microbiology 1981,128 (4),349-354.
[185]Falconnier B, Lapierre C, Lesage-Meessen L, et al. Vanillin as a product of ferulic acid biotransformation by the white-rot fungus Pycnoporus cinnabarinus 1-937:Identification of metabolic pathways [J]. Journal of biotechnology 1994,37(2),123-132.
[186]Bertani I, Kojic M, Venturi V. Regulation of the p-hydroxybenzoic acid hydroxylase gene (pobA) in plant-growth-promoting Pseudomonas putida WCS358 [J]. Microbiology 2001,147 (6),1611-1620.
[187]You IS, Ghosal D, Gunsalus IC. Nucleotide sequence analysis of the Pseudomonas putida PpG7 salicylate hydroxylase gene (nahG) and its 3'-flanking region [J]. Biochemistry 1991,30 (6),1635-1641.
[188]Lee J, Oh J, Min KR, et al. Nucleotide Sequence of Salicylate Hydroxylase Gene and Its 5'-Flanking Region of Pseudomonas putida KF715 [J]. Biochemical and biophysical research communications 1996,218 (2),544-548.
[189]Bosch R, Moore ER, Garcia-Valdes E, et al.NahW, a novel, inducible salicylate hydroxylase involved in mineralization of naphthalene by Pseudomonas stutzeri AN10 [J]. Journal of bacteriology 1999,181 (8),2315-2322.
[190]Jones RM, Pagmantidis V, Williams PA. sal genes determining the catabolism of salicylate esters are part of a supraoperonic cluster of catabolic genes in Acinetobacter sp. strain ADP1 [J]. Journal of bacteriology 2000,182 (7), 2018-2025.
[191]Demaneche S, Meyer C, Micoud J, et al. Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons [J]. Applied and Environmental Microbiology 2004,70 (11),6714-6725.
[192]Cho O, Choi KY, Zylstra GJ, et al. Catabolic role of a three-component salicylate oxygenase from Sphingomonas yanoikuyae B1 in polycyclic aromatic hydrocarbon degradation [J]. Biochemical and biophysical research communications 2005,327 (3),656-662.
[193]Harpel M, Lipscomb J. Gentisate 1,2-dioxygenase from pseudomonas. Purification, characterization, and comparison of the enzymes from Pseudomonas testosteroni and Pseudomonas acidovorans [J]. Journal of Biological Chemistry 1990,265 (11),6301-6311.
[194]Goetz FE, Harmuth LJ. Gentisate pathway in Salmonella typhimurium: metabolism of hydroxybenzoate and gentisate [J]. FEMS microbiology letters 1992,97 (1),45-49.
[195]Suarez M, Ferrer E, Garrido-Pertierra A, et al. Purification and characterization of the 3-hydroxybenzoate-6-hydroxylase from Klebsiella pneumoniae [J]. FEMS microbiology letters 1995,126 (3),283-290.
[196]Wang LH, Hamzah RY, Yu Y, et al. Pseudomonas cepacia 3-hydroxybenzoate 6-hydroxylase:induction, purification, and characterization [J]. Biochemistry 1987,26(4),1099-1104.
[197]Diaz E, Ferrandez A, Garcia JL. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12 [J]. Journal of bacteriology 1998,180 (11),2915-2923.
[198]Ferrandez A, Garcia JL, Diaz E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl) propionate catabolic pathway of Escherichia coli K-12 [J]. Journal of bacteriology 1997,179 (8),2573-2581.
[199]Torres B, Porras G, Garcia JL, et al. Regulation of the mhp cluster responsible for 3-(3-hydroxyphenyl) propionic acid degradation in Escherichia coli [J]. Journal of Biological Chemistry 2003,278 (30),27575-27585.
[200]Diaz E. Microbial biodegradation:genomics and molecular biology [M]. Horizon Scientific Press:2008.
[201]Teufel R, Mascaraque V, Ismail W, et al. Bacterial phenylalanine and phenylacetate catabolic pathway revealed [J]. Proceedings of the National Academy of Sciences 2010,107 (32),14390-14395.
[202]Milcamps A, Bruijn FJ. Identification of a novel nutrient-deprivation-induced Sinorhizobium meliloti gene (hmgA) involved in the degradation of tyrosine [J]. Microbiology 1999,145 (4),935-947.
[203]Ferrandez A, Minambres B, Garcia B, et al. Catabolism of phenylacetic acid in Escherichia coli characterization of a new aerobic hybrid pathway [J]. Journal of Biological Chemistry 1998,273 (40),25974-25986.
[204]Berkel WJ, Tweel, WJ. Purification and characteriation of 3-hydroxypheny-lacetate 6-hydroxylase:a novel FAD-dependent monooxygenase from a Flavobacterium species [J]. European Journal of Biochemistry 1991,201 (3), 585-592.
[205]Arias-Barrau E, Olivera ER, Luengo JM, et al. The homogentisate pathway:a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida [J]. Journal of bacteriology 2004,186(15),5062-5077.
[206]Hle KS, Jahn M, Ghisla S, et al. Two Similar Gene Clusters Coding for Enzymes of a New Type of Aerobic 2-Aminobenzoate (Anthranilate) Metabolism in the Bacterium Azoarcus evansii [J].2001.
[207]Kurnasov O, Jablonski L, Polanuyer B, et al. Aerobic tryptophan degradation pathway in bacteria:novel kynurenine formamidase [J]. FEMS microbiology letters 2003,227(2),219-227.
[208]Hasegawa Y, Muraki T, Tokuyama T, et al. A novel degradative pathway of 2-nitrobenzoate via 3-hydroxyanthranilate in Pseudomonas fluorescens strain KU-7 [J]. FEMS microbiology letters 2000,190 (2),185-190.
[209]Muraki T, Taki M, Hasegawa Y, et al. Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7 [J]. Applied and Environmental Microbiology 2003,69 (3),1564-1572.
[210]Martinez-Aguilar L, Caballero-Mellado J, Estrada-de los Santos P. Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov [J]. International journal of systematic and evolutionary microbiology 2013,63 (Pt 1),208-211.
[211]Wierckx N, Koopman F, Bandounas L, et al. Isolation and characterization of Cupriavidus basilensis HMF14 for biological removal of inhibitors from lignocellulosic hydrolysate [J]. Microbial biotechnology 2010,3(3),336-343.
[212]Koopman F, Wierckx N, Winde JH, et al. Identification and characterization of the furfural and 5-(hydroxymethyl) furfural degradation pathways of Cupriavidus basilensis HMF14 [J]. Proceedings of the National Academy of Sciences 2010, 107 (11),4919-4924.
[213]Friman H, Schechter A, Ioffe Y, et al. Current production in a microbial fuel cell using a pure culture of Cupriavidus basilensis growing in acetate or phenol as a carbon source [J]. Microbial biotechnology 2013.
[214]Cserhati M, Kriszt B, Szoboszlay S, et al. De novo genome project of Cupriavidus basilensis OR16 [J], Journal of bacteriology 2012,194 (8), 2109-2110.