不同碳源条件下广叶绣球菌转录组分析
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摘要
【背景】广叶绣球菌(Sparassis latifolia)是一种名贵的食用菌,其木质纤维素降解的分子机制尚不明确。【目的】了解广叶绣球菌在不同碳源条件下木质纤维素降解相关基因表达动态。【方法】通过转录组测序技术对分别以葡萄糖、纤维素+木质素、纤维素及松木屑为碳源的广叶绣球菌基因表达谱进行分析。以葡萄糖为碳源的样本为对照,分别对不同碳源下广叶绣球菌显著差异表达的基因进行功能分析。【结果】Geneontology(Go)富集分析表明,以葡萄糖为碳源的样本为对照,差异表达基因主要富集在碳水化合物利用的过程,如多糖催化过程、碳水化合物催化过程、碳水化合物代谢过程及多糖代谢过程等。碳水化合物活性酶(Carbohydrate-activeenzymes,CAZymes)功能注释表明,碳源种类主要影响了半纤维素和纤维素降解相关糖苷水解酶家族基因的表达,其中涉及半纤维素降解的相关酶基因上调幅度最大。同时,在纤维素+木质素、松木屑为碳源的处理组中一些转录因子基因上调表达显著。【结论】不同碳源显著影响了广叶绣球菌基因表达谱,这种对碳源的适应也可能反映了广叶绣球菌攻击植物细胞壁的机制,研究结果为深入了解广叶绣球菌木质纤维素降解的分子机理和相关功能基因提供了一些参考。
[Background] Sparassis latifolia is a valuable edible fungi. However, lignocellulose degradation mechanism is poorly understood. [Objective] To understand expression profiles of lignocellulose degradation associated genes cultivated with different carbon sources. [Methods] Based on RNA sequencing, we obtained the whole-genome expression profiles when the mycelia of S. latifolia were cultured with glucose, cellulose, cellulose/lignin and pine sawdust as the carbon source respectively. Using glucose sample as control, functional analysis of differentially expressed genes was carried out. [Results]Gene ontology enrichment analysis showed that, differently expressed genes which compared to glucose as the sole carbon source were mainly involved in polysaccharide catabolic process, carbohydrate catabolic process, polysaccharide metabolic process and carbohydrate metabolic process. Carbohydrate-active enzymes annotation showed that, transcript levels of genes encoding glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose were mainly influenced by the species of carbon source, and in which genes involved in hemicellulose degradation were mostly up-regulated.Several transcription factor genes up-regulated significantly when the carbon source was cellulose/lignin or pine sawdust respectively. [Conclusion] S. latifolia gene expression pattern is influenced substantially by the species of carbon source. Such adaptations to the carbon source may also reflect fundamental mechanisms by which S. latifolia attack plant cell walls. Our findings provide important information in exploring the potential genes responsible for lignocellulose degradation.
[Background] Sparassis latifolia is a valuable edible fungi. However, lignocellulose degradation mechanism is poorly understood. [Objective] To understand expression profiles of lignocellulose degradation associated genes cultivated with different carbon sources. [Methods] Based on RNA sequencing, we obtained the whole-genome expression profiles when the mycelia of S. latifolia were cultured with glucose, cellulose, cellulose/lignin and pine sawdust as the carbon source respectively. Using glucose sample as control, functional analysis of differentially expressed genes was carried out. [Results]Gene ontology enrichment analysis showed that, differently expressed genes which compared to glucose as the sole carbon source were mainly involved in polysaccharide catabolic process, carbohydrate catabolic process, polysaccharide metabolic process and carbohydrate metabolic process. Carbohydrate-active enzymes annotation showed that, transcript levels of genes encoding glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose were mainly influenced by the species of carbon source, and in which genes involved in hemicellulose degradation were mostly up-regulated.Several transcription factor genes up-regulated significantly when the carbon source was cellulose/lignin or pine sawdust respectively. [Conclusion] S. latifolia gene expression pattern is influenced substantially by the species of carbon source. Such adaptations to the carbon source may also reflect fundamental mechanisms by which S. latifolia attack plant cell walls. Our findings provide important information in exploring the potential genes responsible for lignocellulose degradation.
引文
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[15]Li PP,Lei YC,Chen C,et al.Effect of hot water prehydrolysis on the major components of the pine and the hydrolysate[J].China Pulp&Paper,2012,31(11):1-6(in Chinese)李萍萍,雷以超,陈灿,等.热水预水解对松木及其水解液主要化学成分的影响[J].中国造纸,2012,31(11):1-6
[16]Vanden Wymelenberg A,Gaskell J,Mozuch M,et al.Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species[J].Applied and Environmental Microbiology,2011,77(13):4499-4507
[17]Pelkmans JF,Patil MB,Gehrmann T,et al.Transcription factors of Schizophyllum commune involved in mushroom formation and modulation of vegetative growth[J].Scientific Reports,2017,7:310
[18]Vonk PJ,Ohm RA.The role of homeodomain transcription factors in fungal development[J].Fungal Biology Reviews,2018,32(4):219-230
[19]Kameshwar AKS,Qin WS.Analyzing Phanerochaete chrysosporium gene expression patterns controlling the molecular fate of lignocellulose degrading enzymes[J].Process Biochemistry,2018,64:51-62
[20]Benocci T,Aguilar-Pontes MV,Zhou MM,et al.Regulators of plant biomass degradation in ascomycetous fungi[J].Biotechnology for Biofuels,2017,10:152
[2]Black GW,Rixon JE,Clarke JH,et al.Evidence that linker sequences and cellulose-binding domains enhance the activity of hemicellulases against complex substrates[J].Biochemical Journal,1996,319(2):515-520
[3]Floudas D,Binder M,Riley R,et al.The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31fungal genomes[J].Science,2012,336(6089):1715-1719
[4]Rytioja J,Hildén K,Hatakka A,et al.Transcriptional analysis of selected cellulose-acting enzymes encoding genes of the white-rot fungus Dichomitus squalens on spruce wood and microcrystalline cellulose[J].Fungal Genetics and Biology,2014,72:91-98
[5]Kameshwar AKS,Qin WS.Molecular networks of Postia placenta involved in degradation of lignocellulosic biomass revealed from metadata analysis of open access gene expression data[J].International Journal of Biological Sciences,2018,14(3):237-252
[6]Trapnell C,Pachter L,Salzberg SL.TopHat:discovering splice junctions with RNA-Seq[J].Bioinformatics,2009,25(9):1105-1111
[7]Trapnell C,Williams BA,Pertea G,et al.Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J].Nature Biotechnology,2010,28(5):511-515
[8]Wang LK,Feng ZX,Wang X,et al.DEGseq:an R package for identifying differentially expressed genes from RNA-seq data[J].Bioinformatics,2010,26(1):136-138
[9]Ye J,Fang L,Zheng HK,et al.WEGO:a web tool for plotting GO annotations[J].Nucleic Acids Research,2006,34(S2):W293-W297
[10]Yin YB,Mao XZ,Yang JC,et al.dbCAN:a web resource for automated carbohydrate-active enzyme annotation[J].Nucleic Acids Research,2012,40(W1):W445-W451
[11]Todd RB,Zhou MM,Ohm RA,et al.Prevalence of transcription factors in ascomycete and basidiomycete fungi[J].BMC Genomics,2014,15:214
[12]Gaskell J,Blanchette RA,Stewart PE,et al.Transcriptome and secretome analyses of the wood decay fungus Wolfiporia cocos support alternative mechanisms of lignocellulose conversion[J].Applied and Environmental Microbiology,2016,82(13):3979-3987
[13]Hori C,Gaskell J,Igarashi K,et al.Genomewide analysis of polysaccharides degrading enzymes in 11 white-and brown-rot Polyporales provides insight into mechanisms of wood decay[J].Mycologia,2013,105(6):1412-1427
[14]Zhang JW,Presley GN,Hammel KE,et al.Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta[J].Proceedings of the National Academy of Sciences of the United States of America,2016,113(39):10968-10973
[15]Li PP,Lei YC,Chen C,et al.Effect of hot water prehydrolysis on the major components of the pine and the hydrolysate[J].China Pulp&Paper,2012,31(11):1-6(in Chinese)李萍萍,雷以超,陈灿,等.热水预水解对松木及其水解液主要化学成分的影响[J].中国造纸,2012,31(11):1-6
[16]Vanden Wymelenberg A,Gaskell J,Mozuch M,et al.Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species[J].Applied and Environmental Microbiology,2011,77(13):4499-4507
[17]Pelkmans JF,Patil MB,Gehrmann T,et al.Transcription factors of Schizophyllum commune involved in mushroom formation and modulation of vegetative growth[J].Scientific Reports,2017,7:310
[18]Vonk PJ,Ohm RA.The role of homeodomain transcription factors in fungal development[J].Fungal Biology Reviews,2018,32(4):219-230
[19]Kameshwar AKS,Qin WS.Analyzing Phanerochaete chrysosporium gene expression patterns controlling the molecular fate of lignocellulose degrading enzymes[J].Process Biochemistry,2018,64:51-62
[20]Benocci T,Aguilar-Pontes MV,Zhou MM,et al.Regulators of plant biomass degradation in ascomycetous fungi[J].Biotechnology for Biofuels,2017,10:152