基于全局转录组分析研究华癸中慢生根瘤菌7653R类菌体分化和固氮机理
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摘要
华癸中慢生根瘤菌7653R (Mesorhizobium huakuii7653R)可以与宿主豆科植物紫云英(Astragalus sinicus)形成生物固氮共生体,也可以在土壤中自由生长。在华癸中慢生根瘤菌7653R的全基因组测序完成之后,为了更好地了解7653R在类菌体分化过程中所发生的生理生化变化,我们采用RNA-Seq和Microarrays技术相结合的方法对7653R在两种代谢条件下(共生和自生)的转录组进行了研究。
1.对类菌体的分离方法进行了比较分析,结果表明：如果需要获得完整的类菌体用于后续形态观察,可以使用物理分离的方法；如果需要获得高质量类菌体RNA用于RNA-Seq或Microarrays实验,可以采用Ambion MICROB Enrich试剂盒直接提取和纯化类菌体RNA的方法。应用上述所建立的技术方法,本文成功制备了华癸中慢生根瘤菌7653R在共生和自生条件下的RNA,进行了RNA-Seq和Microarrays实验。
2.通过同源比对的生物信息学方法,构建了华癸中慢生根瘤菌7653R全局蛋白质互作网络(protein-protein interaction network, PPI)。
3.对华癸中慢生根瘤菌7653R的转录组进行了分析。结果表明：(1)RNA-Seq和Microarrays均鉴定出7653R在两种生长状态下近三千条差异表达的基因。对这些基因进行了共线性分析,发现两种方法检测到的基因及表达特征相似度高,共线性好。(2)采用整合数据的方式(两种方法检测到的差异表达基因的合集),对这些差异表达的基因进行了COG功能分类,代谢途径分析,KEGG富集分析以及GSEA基因集富集分析。结果显示7653R在自生条件下主要是维持基础代谢,而类菌体的功能主要是进行生物固氮。显著上调的基因位于共生质粒上。在类菌体条件下,能量代谢相关基因的表达水平上调明显,而脂肪酸代谢相关基因表达水平变化很小,大多数与细胞周期相关的基因均呈下调表达。(3)利用Cytoscape将基因的差异表达与7653R的全局蛋白质互作网络进行整合分析,解析获得一个与共生固氮密切相关的亚网络。该亚网络包含多个hub基因以及若干未曾报导与固氮过程相关的基因亚网络。(4)鉴于CtrA在细胞分裂和类菌体分化中具有重要调控作用,以CtrA为中心,本文解析获得一个与其直接互作的基因亚网络。这些研究结果对深刻揭示类菌体分化、固氮机理提供了新材料及新视野。
4.选择共生固氮子网中的hub基因MCHK-0866及其相邻的MCHK-0867’进行突变体的构建。构建了单基因突变和双基因突变的置换载体,采用三亲本结合转移的方法筛选获得双基因突变的稳定突变株,基于植物盆栽的共生表型检测为结瘤不固氮。
5.改造了用于构建细菌单杂交随机文库的转录因子表达载体,建立并优化了构建随机文库的方法。结果显示此方法转化效率高,可获得大量转化子。为构建细菌单杂交随机文库,研究转录组中的重要转录因子及调控打下了工作基础。
Mesorhizobium huakuii7653R occurs either in nitrogen-fixing symbiosis with its host plant, Astragalus sinicus, or free-living in the soil. The M. huakuii7653R genome has recently been sequenced. To better understand the complex biochemical and developmental changes that occur in7653R during bacteroid differentiation, RNA-Seq and Microarrays were used to investigate the differential transcriptomes of7653R bacteroids and free-living cells.
1. Comparative analysis of the methods of isolating bacteroids. The results showed that use physical method to get complete form of bacteroids for morphological observation or use Ambion MICROBEnrich kit to get high-quality bacteroids RNA. Using above methods, total RNA of bacteroids and free-living cells was extracted for RNA-Seq and Microarrays analysis.
2. We constructed a protein-protein interaction (PPI) network for7653R using the method of orthologous.
3. RNA-Seq and Microarrays were used to investigate the differential transcriptomes of7653R bacteroids and free-living cells. The results are as follows.(1) Both the two approaches identified about three thousand differentially expressed genes. Correlation between the two methods was high.(2) We have analyzed COG functional categories, biological metabolic pathways, enriched KEGG pathways and Gene set enrichment analysis using the both sources of data following an integrative strategy. These results all showed that free-living cells have a primary role in maintaining basal metabolism, whereas bacteroids have a primary role in nitrogen fixation. The most prominent up-regulation occurred in the symbiosis plasmids. The results suggested that the main energy metabolism is active while fatty acid metabolism is inactive in bacteroid and that most of genes relevant to cell cycle are down-regulated accordingly.(3) Integrated gene expression data into the7653R protein-protein interaction (PPI) network using Cytoscape. A highly inter-connected subnetwork, with function enrichment for nitrogen fixation, was found, and a set of hubs and previously uncharacterized genes participating in nitrogen fixation were identified.(4) In order to identify the subnetwork mediated by CtrA connected with the cell cycle and bacteroid differentiation, we dissected the7653R PPI network by using CtrA as a specific target. Then we got the CtrA subnetwork. The results described here provide a broader biological landscape and novel insights that elucidate rhizobial bacteroid differentiation, nitrogen fixation and related novel gene functions.
4. Construction of mutants of MCHK-0866, one of the hub gene in nitrogen fixation subnetwork, and its adjacent gene MCHK-0867. Construction of single-gene mutation (MCHK-0866-or MCHK-0866-) and double-gene mutation vectors, using three parental hybridization to screen. Finally, obtain stable double-gene mutant and plant symbiotic phenotype detection was Fix-.
5. Modification of transcription factor expression vector used to build the Bacterial one-hybrid random library. Pre-construction of random library of Bacterial one-hybrid with high transformation efficiency. Lay the foundation for constructing the Bacterial one-hybrid random library and analyzing the expression and regulation of important transcription factors in transcriptome results.
1.对类菌体的分离方法进行了比较分析,结果表明：如果需要获得完整的类菌体用于后续形态观察,可以使用物理分离的方法；如果需要获得高质量类菌体RNA用于RNA-Seq或Microarrays实验,可以采用Ambion MICROB Enrich试剂盒直接提取和纯化类菌体RNA的方法。应用上述所建立的技术方法,本文成功制备了华癸中慢生根瘤菌7653R在共生和自生条件下的RNA,进行了RNA-Seq和Microarrays实验。
2.通过同源比对的生物信息学方法,构建了华癸中慢生根瘤菌7653R全局蛋白质互作网络(protein-protein interaction network, PPI)。
3.对华癸中慢生根瘤菌7653R的转录组进行了分析。结果表明：(1)RNA-Seq和Microarrays均鉴定出7653R在两种生长状态下近三千条差异表达的基因。对这些基因进行了共线性分析,发现两种方法检测到的基因及表达特征相似度高,共线性好。(2)采用整合数据的方式(两种方法检测到的差异表达基因的合集),对这些差异表达的基因进行了COG功能分类,代谢途径分析,KEGG富集分析以及GSEA基因集富集分析。结果显示7653R在自生条件下主要是维持基础代谢,而类菌体的功能主要是进行生物固氮。显著上调的基因位于共生质粒上。在类菌体条件下,能量代谢相关基因的表达水平上调明显,而脂肪酸代谢相关基因表达水平变化很小,大多数与细胞周期相关的基因均呈下调表达。(3)利用Cytoscape将基因的差异表达与7653R的全局蛋白质互作网络进行整合分析,解析获得一个与共生固氮密切相关的亚网络。该亚网络包含多个hub基因以及若干未曾报导与固氮过程相关的基因亚网络。(4)鉴于CtrA在细胞分裂和类菌体分化中具有重要调控作用,以CtrA为中心,本文解析获得一个与其直接互作的基因亚网络。这些研究结果对深刻揭示类菌体分化、固氮机理提供了新材料及新视野。
4.选择共生固氮子网中的hub基因MCHK-0866及其相邻的MCHK-0867’进行突变体的构建。构建了单基因突变和双基因突变的置换载体,采用三亲本结合转移的方法筛选获得双基因突变的稳定突变株,基于植物盆栽的共生表型检测为结瘤不固氮。
5.改造了用于构建细菌单杂交随机文库的转录因子表达载体,建立并优化了构建随机文库的方法。结果显示此方法转化效率高,可获得大量转化子。为构建细菌单杂交随机文库,研究转录组中的重要转录因子及调控打下了工作基础。
Mesorhizobium huakuii7653R occurs either in nitrogen-fixing symbiosis with its host plant, Astragalus sinicus, or free-living in the soil. The M. huakuii7653R genome has recently been sequenced. To better understand the complex biochemical and developmental changes that occur in7653R during bacteroid differentiation, RNA-Seq and Microarrays were used to investigate the differential transcriptomes of7653R bacteroids and free-living cells.
1. Comparative analysis of the methods of isolating bacteroids. The results showed that use physical method to get complete form of bacteroids for morphological observation or use Ambion MICROBEnrich kit to get high-quality bacteroids RNA. Using above methods, total RNA of bacteroids and free-living cells was extracted for RNA-Seq and Microarrays analysis.
2. We constructed a protein-protein interaction (PPI) network for7653R using the method of orthologous.
3. RNA-Seq and Microarrays were used to investigate the differential transcriptomes of7653R bacteroids and free-living cells. The results are as follows.(1) Both the two approaches identified about three thousand differentially expressed genes. Correlation between the two methods was high.(2) We have analyzed COG functional categories, biological metabolic pathways, enriched KEGG pathways and Gene set enrichment analysis using the both sources of data following an integrative strategy. These results all showed that free-living cells have a primary role in maintaining basal metabolism, whereas bacteroids have a primary role in nitrogen fixation. The most prominent up-regulation occurred in the symbiosis plasmids. The results suggested that the main energy metabolism is active while fatty acid metabolism is inactive in bacteroid and that most of genes relevant to cell cycle are down-regulated accordingly.(3) Integrated gene expression data into the7653R protein-protein interaction (PPI) network using Cytoscape. A highly inter-connected subnetwork, with function enrichment for nitrogen fixation, was found, and a set of hubs and previously uncharacterized genes participating in nitrogen fixation were identified.(4) In order to identify the subnetwork mediated by CtrA connected with the cell cycle and bacteroid differentiation, we dissected the7653R PPI network by using CtrA as a specific target. Then we got the CtrA subnetwork. The results described here provide a broader biological landscape and novel insights that elucidate rhizobial bacteroid differentiation, nitrogen fixation and related novel gene functions.
4. Construction of mutants of MCHK-0866, one of the hub gene in nitrogen fixation subnetwork, and its adjacent gene MCHK-0867. Construction of single-gene mutation (MCHK-0866-or MCHK-0866-) and double-gene mutation vectors, using three parental hybridization to screen. Finally, obtain stable double-gene mutant and plant symbiotic phenotype detection was Fix-.
5. Modification of transcription factor expression vector used to build the Bacterial one-hybrid random library. Pre-construction of random library of Bacterial one-hybrid with high transformation efficiency. Lay the foundation for constructing the Bacterial one-hybrid random library and analyzing the expression and regulation of important transcription factors in transcriptome results.
引文
1. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Jr., Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature,2000,403:503-511
2. Alunni B, Kevei Z, Redondo-Nieto M, Kondorosi A, Mergaert P, Kondorosi E. Genomic organization and evolutionary insights on GRP and NCR genes, two large nodule-specific gene families in Medicago truncatula. Mol Plant Microbe Interact,2007,20:1138-1148
3. Ampe F, Kiss E, Sabourdy F, Batut J. Transcriptome analysis of Sinorhizobium meliloti during symbiosis. Genome Biol,2003,4:R15
4. Anderson AJ, Dawes EA. Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev,1990,54:450-472
5. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP. Gene expression during the life cycle of Drosophila melanogaster. Science,2002, 297:2270-2275
6. Arcondeguy T, Jack R, Merrick M. P(ii) signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol Mol Biol Rev,2001,65:80-105
7. Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res,2006,16:686-691
8. Babu MM. Early career research award lecture. Structure, evolution and dynamics of transcriptional regulatory networks. Biochem Soc Trans,2010,38:1155-1178
9. Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res, 2005,33:5914-5923
10. Barnett MJ, Hung DY, Reisenauer A, Shapiro L, Long SR. A homolog of the ctra cell cycle regulator is present and essential in Sinorhizobium meliloti. JBacteriol,2001,183:3204-3210
11. Barnett MJ, Toman CJ, Fisher RF, Long SR. A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction. Proc Natl Acad Sci USA,2004, 101:16636-16641
12. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBI GEO:Mining millions of expression profiles--database and tools. Nucleic Acids Res,2005,33:D562-566
13. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO:Archive for functional genomics data sets--update. Nucleic Acids Res, 2013,41:D991-995
14. Becker-Andre M, Hahlbrock K. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a pcr aided transcript titration assay (PATTY). Nucleic Acids Res,1989, 17:9437-9446
15. Becker A, Berges H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, De Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Kuster H, Liebe C, Puhler A, Weidner S, Batut J. Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol Plant Microbe Interact,2004,17:292-303
16. Bertolazzi P, Bock ME, Guerra C. On the functional and structural characterization of hubs in protein-protein interaction networks. Biotechnol Adv,2013,31:274-286
17. Biondi EG, Skerker JM, Arif M, Prasol MS, Perchuk BS, Laub MT. A phosphorelay system controls stalk biogenesis during cell cycle progression in Caulobacter crescentus. Mol Microbiol,2006,59: 386-401
18. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res,2003,31:68-71
19. Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Mol Plant Microbe Interact,2008,21:631-645
20. Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science,2002,296:752-755
21. Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature,2005,433:531-537
22. Capela D, Filipe C, Bobik C, Batut J, Bruand C. Sinorhizobium meliloti differentiation during symbiosis with alfalfa:A transcriptomic dissection. Mol Plant Microbe Interact,2006,19:363-372
23. Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression in vertebrate tissues. J Biol,2009,8:33
24. Chang WS, Franck WL, Cytryn E, Jeong S, Joshi T, Emerich DW, Sadowsky MJ, Xu D, Stacey G. An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum. Mol Plant Microbe Interact,2007,20:1298-1307
25. Ching TM, Hedtke S. Isolation of bacteria, transforming bacteria, and bacteroids from soybean nodules. Plant Physiol,1977,60:771-774
26. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc,2007,2:2366-2382
27. Collier J, Mcadams HH, Shapiro L. A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc Natl Acad Sci USA,2007,104:17111-17116
28. Cytryn EJ, Sangurdekar DP, Streeter JG, Franck WL, Chang W-S, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. JBacteriol,2007,189:6751-6762
29. D'haeze W, Leoff C, Freshour G, Noel KD, Carlson RW. Rhizobium etli CE3 bacteroid lipopolysaccharides are structurally similar but not identical to those produced by cultured CE3 bacteria. JBiol Chem,2007,282:17101-17113
30. De Las Rivas J, Fontanillo C. Protein-protein interactions essentials:Key concepts to building and analyzing interactome networks. PLoS Comput Biol,2010,6:e1000807
31. De Lucena DK, Puhler A, Weidner S. The role of sigma factor RpoHl in the pH stress response of Sinorhizobium meliloti. BMC Microbiol,2010,10:265
32. Dixon R, Kahn D. Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol,2004,2: 621-631
33. Eisen JA. Badomics words and the power and peril of the ome-meme. GigaScience,2012,1:6
34. Fang Z, Cui X. Design and validation issues in RNA-seq experiments. Brief Bioinform,2011,12: 280-287
35. Farkas A, Maroti G, Durgo H, Gyorgypal Z, Lima RM, Medzihradszky KF, Kereszt A, Mergaert P, Kondorosi Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms. Proc Natl Acad Sci USA,2014,111:5183-5188
36. Fauvart M, Sanchez-Rodriguez A, Beullens S, Marchal K, Michiels J. Genome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil. J Bacteriol,2011,193:3158-3159
37. Ferguson BJ, Indrasumunar A, Hayashi S, Lin MH, Lin YH, Reid DE, Gresshoff PM. Molecular analysis of legume nodule development and autoregulation. J Integr Plant Biol,2010,52:61-76
38. Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science,2001,293:668-672
39. Gehlenborg N, O'donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods,2010,7:S56-68
40. Gilles-Gonzalez MA, Ditta GS, Helinski DR. A haemoprotein with kinase activity encoded by the oxygen sensor of Rhizobium meliloti. Nature,1991,350:170-172
41. Glazebrook J, Ichige A, Walker GC. A Rhizobium meliloti homolog of the Escherichia coli peptide-antibiotic transport protein SbmA is essential for bacteroid development. Genes Dev,1993,7:1485-1497
42. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer:Class discovery and class prediction by gene expression monitoring. Science,1999,286:531-537
43. Gonzalez V, Santamaria RI, Bustos P, Hernandez-Gonzalez 1, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramirez MA, Jimenez-Jacinto V, Collado-Vides J, Davila G. The partitioned Rhizobium etli genome:Genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA,2006,103:3834-3839
44. Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, Mullin L, Houmiel K, Gordon J, Vaudin M, Iartchouk O, Epp A, Liu F, Wollam C, Allinger M, Doughty D, et al. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science,2001,294:2323-2328
45. Green LS, Li Y, Emerich DW, Bergersen FJ, Day DA. Catabolism of alpha-ketoglutarate by a sucA mutant of Bradyrhizobium japonicum:Evidence for an alternative tricarboxylic acid cycle. J Bacteriol,2000,182:2838-2844
46. Gresshoff PM, Delves AC. Plant genetic approaches to symbiotic nodulation and nitrogen fixation in legumes, eds., Springer,1986.159-206
47. Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, Mckillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, Vijayraghavan K, et al. A protein complex network of Drosophila melanogaster. Cell,2011,147: 690-703
48. Haag AF, Baloban M, Sani M, Kerscher B, Pierre O, Farkas A, Longhi R, Boncompagni E, Herouart D, Dall'angelo S, Kondorosi E, Zanda M, Mergaert P, Ferguson GP. Protection of Sinorhizobium against host cysteine-rich antimicrobial peptides is critical for symbiosis. PLoS Biol,2011,9: e1001169
49. Haag AF, Arnold MF, Myka KK, Kerscher B, Dall'angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development during Rhizobium-legume symbiosis. FEMS Microbiol Rev,2012a,
50. Haag AF, Kerscher B, Dall'angelo S, Sani M, Longhi R, Baloban M, Wilson HM, Mergaert P, Zanda M, Ferguson GP. Role of cysteine residues and disulfide bonds in the activity of a legume root nodule-specific, cysteine-rich peptide. J Biol Chem,2012b,287:10791-10798
51. Hakoyama T, Niimi K, Watanabe H, Tabata R, Matsubara J, Sato S, Nakamura Y, Tabata S, Jichun L, Matsumoto T. Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation. Nature,2009,462:514-517
52. Hansen KD, Irizarry RA, Zhijin W. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics,2012,13:204-216
53. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, et al. A census of human soluble protein complexes. Cell,2012,150:1068-1081
54. Hengge R. Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol,2009,7:263-273
55. Hinton JC, Hautefort I, Eriksson S, Thompson A, Rhen M. Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr Opin Microbiol,2004,7:277-282
56. Hosie AH, Allaway D, Galloway CS, Dunsby HA, Poole PS. Rhizobium leguminosarum has a second general amino acid permease with unusually broad substrate specificity and high similarity to branched-chain amino acid transporters (Bra/LIV) of the ABC family. J Bacteriol,2002,184: 4071-4080
57. Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics,2002,18 Suppl 1:S233-240
58. Ikeo K, Ishi-I J, Tamura T, Gojobori T, Tateno Y. CIBEX:Center for information biology gene expression database. C R Biol,2003,326:1079-1082
59. Imaoka T, Nishimura M, Tani S, Ishikawa KI, Yamashita S, Ushijima T, Imai T, Shimada Y. Molecular characterization of cancer reveals interactions between ionizing radiation and chemicals on rat mammary carcinogenesis. Int J Cancer,2014,134:1529-1538
60. Jenal U, Fuchs T. An essential protease involved in bacterial cell-cycle control. EMBO J,1998,17: 5658-5669
61. Jensen ES, Peoples MB, Boddey RM, Gresshoff PM, Hauggaard-Nielsen H, Alves BJ, Morrison MJ. Legumes for mitigation of climate change and the provision of feedstock for biofuels and biorefineries. A review. Agron Sustain Dev,2012,32:329-364
62. Jones SE, Ferguson NL, Alley MR. New members of the ctrA regulon:The major chemotaxis operon in Caulobacter is Ctra dependent. Microbiology,2001,147:949-958
63. Kai T, Williams D, Spradling AC. The expression profile of purified Drosophila germline stem cells. Dev Biol,2005,283:486-502
64. Kaiser BN, Moreau S, Castelli J, Thomson R, Lambert A, Bogliolo S, Puppo A, Day DA. The soybean NRAMP homologue, GmDMT1, is a symbiotic divalent metal transporter capable of ferrous iron transport. Plant J,2003,35:295-304
65. Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Mochizuki Y, Nakayama S, Nakazaki N, Shimpo S, et al. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti (supplement). DNA Res,2000,7:381-406
66. Karr DB, Oehrle NW, Emerich DW. Recovery of nitrogenase from aerobically isolated soybean nodule bacteroids. Plant and Soil,2003,257:27-33
67. Karunakaran R, Ramachandran V, Seaman J, East A, Mouhsine B, Mauchline T, Prell J, Skeffington A, Poole P. Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J Bacteriol,2009,191:4002-4014
68. Karunakaran R, Haag AF, East AK, Ramachandran VK, Prell J, James EK, Scocchi M, Ferguson GP, Poole PS. BacA is essential for bacteroid development in nodules of galegoid, but not phaseoloid, legumes. J Bacteriol,2010,192:2920-2928
69. Kereszt A, Mergaert P, Maroti G, Kondorosi E. Innate immunity effectors and virulence factors in symbiosis. Curr Opin Microbiol,2011,14:76-81
70. Khatri P, Draghici S. Ontological analysis of gene expression data:Current tools, limitations, and open problems. Bioinformatics,2005,21:3587-3595
71. Kogenaru S, Qing Y, Guo Y, Wang N. RNA-seq and microarray complement each other in transcriptome profiling. BMC Genomics,2012,13:629
72. Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Analyzing protein-protein interaction networks. JProteome Res,2012,11:2014-2031
73. Kouchi H, Fukai K. Rapid isolation of bacteroids from soybean root nodules by Percoll discontinuous gradient centrifugation. Soil Sci Plant Nutr,1989,35:301-305
74. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature,2006,440:637-643
75. Krummenacher P, Narberhaus F. Two genes encoding a putative multidrug efflux pump of the RND/MFP family are cotranscribed with an rpoH gene in Bradyrhizobium japonicum. Gene,2000, 241:247-254
76. Krusell L, Krause K, Ott T, Desbrosses G, Kramer U, Sato S, Nakamura Y, Tabata S, James EK, Sandal N. The sulfate transporter SST1 is crucial for symbiotic nitrogen fixation in Lotus japonicus root nodules. Plant Cell,2005,17:1625-1636
77. Laub MT, Mcadams HH, Feldblyum T, Fraser CM, Shapiro L. Global analysis of the genetic network controlling a bacterial cell cycle. Science,2000,290:2144-2148
78. Laub MT, Chen SL, Shapiro L, Mcadams HH. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci USA,2002,99:4632-4637
79. Li J, Dai X, Liu T, Zhao PX. LegumeIP:An integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Res,2012,40:D1221-1229
80. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2:An improved ultrafast tool for short read alignment. Bioinformatics,2009,25:1966-1967
81. Li Y, Parsons R, Day DA, Bergersen FJ. Reassessment of major products of N2 fixation by bacteroids from soybean root nodules. Microbiology,2002,148:1959-1966
82. Li Y, Tian CF, Chen WF, Wang L, Sui XH, Chen WX. High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala. PLoS One,2013,8:e70531
83. Lindberg J, Lundeberg J. The plasticity of the mammalian transcriptome. Genomics,2010,95:1-6
84. Lindemann A, Koch M, Pessi G, Muller AJ, Balsiger S, Hennecke H, Fischer HM. Host-specific symbiotic requirement of BdeAB, a RegR-controlled RND-type efflux system in Bradyrhizobium japonicum. FEMS Microbiol Lett,2010,312:184-191
85. Lodwig E, Poole P. Metabolism of Rhizobium bacteroids. Crit Rev Plant Sci,2003,22:37-78
86. Lodwig EM, Hosie AH, Bourdes A, Findlay K, Allaway D, Karunakaran R, Downie JA, Poole PS. Amino-acid cycling drives nitrogen fixation in the Legume-Rhizobium symbiosis. Nature,2003,422: 722-726
87. Lodwig EM, Leonard M, Marroqui S, Wheeler TR, Findlay K, Downie JA, Poole PS. Role of polyhydroxybutyrate and glycogen as carbon storage compounds in pea and bean bacteroids. Mol Plant Microbe Interact,2005,18:67-74
88. Lois AF, Weinstein M, Ditta GS, Helinski DR. Autophosphorylation and phosphatase activities of the oxygen-sensing protein FixL of Rhizobium meliloti are coordinately regulated by oxygen. JBiol Chem,1993,268:4370-4375
89. Madan Babu M, Teichmann SA, Aravind L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol,2006,358:614-633
90. Maere S, Heymans K, Kuiper M. BiNGO:A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics,2005,21:3448-3449
91. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet,2008,9: 387-402
92. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq:An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res,2008,18:1509-1517
93. Martinez-Abarca F, Martinez-Rodriguez L, Lopez-Contreras JA, Jimenez-Zurdo JI, Toro N. Complete genome sequence of the alfalfa symbiont SinorhizobiumlEnsifer meliloti strain GR4. Genome Announc,2013,1:e00174-00112
94. Martinez-Argudo I, Little R, Shearer N, Johnson P, Dixon R. The NifL-NifA system:A multidomain transcriptional regulatory complex that integrates environmental signals. J Bacteriol,2004,186: 601-610
95. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res,2001,11:2120-2126
96. Mcgrath PT, Iniesta AA, Ryan KR, Shapiro L, Mcadams HH. A dynamically localized protease complex and a polar specificity factor control a cell cycle master regulator. Cell,2006,124:535-547
97. Mercer RG, Callister SJ, Lipton MS, Pasa-Tolic L, Strnad H, Paces V, Beatty JT, Lang AS. Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus. J Bacteriol,2010,192:2701-2710
98. Mergaert P, Nikovics K, Kelemen Z, Maunoury N, Vaubert D, Kondorosi A, Kondorosi E. A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. Plant Physiol,2003,132:161-173
99. Mergaert P, Uchiumi T, Alunni B, Evanno G, Cheron A, Catrice O, Mausset AE, Barloy-Hubler F, Galibert F, Kondorosi A, Kondorosi E. Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium-legume symbiosis. Proc Natl Acad Sci USA,2006,103:5230-5235
100. Miller A, Cramer M. Root nitrogen acquisition and assimilation, eds., Springer,2005.1-36
101. Miller TR, Belas R. Motility is involved in Silicibacter sp. Tm 1040 interaction with dinoflagellates. Environ Microbiol,2006,8:1648-1659
102. Mitsui H, Sato T, Sato Y, Ito N, Minamisawa K. Sinorhizobium meliloti RpoHl is required for effective nitrogen-fixing symbiosis with alfalfa. Mol Genet Genomics,2004,271:416-425
103. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods,2008,5:621-628
104. Mulley G, White J, Karunakaran R, Prell J, Bourdes A, Bunnewell S, Hill L, Poole P. Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources. Mol Microbiol,2011,80:149-167
105. Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA,1996,93:10268-10273
106. Newcomb W, Sippell D, Peterson R. The early morphogenesis of Glycine max and Pisum sativum root nodules. Can J Bot,1979,57:2603-2616
107. Ninfa AJ, Atkinson MR. PII signal transduction proteins. Trends Microbiol,2000,8:172-179
108. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature,2002,420:563-573
109. Oldroyd GE, Downie JA. Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol,2008,59:519-546
110. Oldroyd GE, Murray JD, Poole PS, Downie JA. The rules of engagement in the legume-rhizobial symbiosis. Annu Rev Genet,2011,45:119-144
111. Oono R, Denison RF. Comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids. Plant Physiol,2010,154:1541-1548
112. Oono R, Schmitt I, Sprent JI, Denison RF. Multiple evolutionary origins of legume traits leading to extreme rhizobial differentiation. New Phytol,2010,187:508-520
113. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, De Crecy-Lagard V, Diaz N, Disz T, Edwards R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res,2005,33:5691-5702
114. Patriarca EJ, Tate R, Iaccarino M. Key role of bacterial NH4+ metabolism in Rhizobium-plant symbiosis. Microbiol Mol Biol Rev,2002,66:203-222
115. Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, De Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol,2006,24:1140-1150
116. Pessi G, Ahrens CH, Rehrauer H, Lindemann A, Hauser F, Fischer HM, Hennecke H. Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules. Mol Plant Microbe Interact,2007,20:1353-1363
117. Piddock LJ. Multidrug-resistance efflux pumps-not just for resistance. Nat Rev Microbiol,2006, 4:629-636
118. Pietu G, Eveno E, Soury-Segurens B, Fayein NA, Mariage-Samson R, Matingou C, Leroy E, Dechesne C, Krieger S, Ansorge W, Reguigne-Arnould I, Cox D, Dehejia A, Polymeropoulos MH, Devignes MD, Auffray C. The genexpress IMAGE knowledge base of the human muscle transcriptome:A resource of structural, functional, and positional candidate genes for muscle physiology and pathologies. Genome Res,1999,9:1313-1320
119. Pini F, Frage B, Ferri L, De Nisco NJ, Mohapatra SS, Taddei L, Fioravanti A, Dewitte F, Galardini M, Brilli M, Villeret V, Bazzicalupo M, Mengoni A, Walker GC, Becker A, Biondi EG. The DivJ, CbrA and PleC system controls Divk phosphorylation and symbiosis in Sinorhizobium meliloti. Mol Microbiol,2013,90:54-71
120. Prell J, Poole P. Metabolic changes of rhizobia in legume nodules. Trends Microbiol,2006,14:161-168
121. Prell J, White JP, Bourdes A, Bunnewell S, Bongaerts RJ, Poole PS. Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids. Proc Natl Acad Sci USA,2009,106:12477-12482
122. Ptashne M. Regulation of transcription:From lambda to eukaryotes. Trends Biochem Sci,2005,30: 275-279
123. Pumirat P, Vanaporn M, Pinweha P, Tandhavanant S, Korbsrisate S, Chantratita N. The role of short-chain dehydrogenase/oxidoreductase, induced by salt stress, on host interaction of B. pseudomallei. BMC Microbiol,2014,14:1
124. Quon KC, Marczynski GT, Shapiro L. Cell cycle control by an essential bacterial two-component signal transduction protein. Cell,1996,84:83-93
125. Romling U, Galperin MY, Gomelsky M. Cyclic di-GMP:The first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev,2013,77:1-52
126. Reibach PH, Mask PL, Streeter JG. A rapid one-step method for the isolation of bacteroids from root nodules of soybean plants, utilizing self-generating Percoll gradients. Can J Microbiol,1981, 27:491-495
127. Resendis-Antonio O, Hernandez M, Salazar E, Contreras S, Batallar GM, Mora Y, Encarnacion S. Systems biology of bacterial nitrogen fixation:high-throughput technology and its integrative description with constraint-based modeling. BMC Syst Biol,2011,5:120
128. Rodriguez-Llorente I, Caviedes MA, Dary M, Palomares AJ, Canovas FM, Peregrin-Alvarez JM. The Symbiosis Interactome:a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. BMC Syst Biol,2009,3:63
129. Rolfe BG, Gresshoff P. Genetic analysis of legume nodule initiation. Annu Rev Plant Physiol Mol Biol,1988,39:297-319
130. Romanov VI, Hernandez-Lucas I, Martinez-Romero E. Carbon Metabolism Enzymes of Rhizobium tropici Cultures and Bacteroids. Appl Environ Microbiol,1994,60:2339-2342
131. Ronson CW, Astwood PM, Downie JA. Molecular cloning and genetic organization of C4-dicarboxylate transport genes from Rhizobium Leguminosarum. J Bacteriol,1984,160:903-909
132. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature,2005,437:1173-1178
133. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Fame A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, et al. ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res,2013,41:D987-990
134. Ryan RP, Mccarthy Y, Andrade M, Farah CS, Armitage JP, Dow JM. Cell-cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris. Proc Natl Acad Sci USA,2010,107:5989-5994
135. Saalbach G, Erik P, Wienkoop S. Characterisation by proteomics of peribacteroid space and peribacteroid membrane preparations from pea(Pisum sativum) symbiosomes. Proteomics,2002,2: 325-337
136. Santoni D, Swiercz A, Zmienko A, Kasprzak M, Blazewicz M, Bertolazzi P, Felici G. An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics:application on Arabidopsis thaliana. OMICS,2014,18:155-165
137. Sarma AD, Emerich DW. A comparative proteomic evaluation of culture grown vs nodule isolated Bradyrhizobium japonicum. Proteomics,2006,6:3008-3028
138. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science,1995,270:467-470
139. Schmidt AJ, Ryjenkov DA, Gomelsky M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase:enzymatically active and inactive EAL domains. JBacteriol, 2005,187:4774-4781
140. Schwartz S, Oren R, Ast G. Detection and removal of biases in the analysis of next-generation sequencing reads. P LoS One,2011,6:e16685
141. Sen D, Weaver R. A comparison of nitrogen-fixing ability of peanut, cowpea and siratro plants nodulated by different strains of Rhizobium. Plant Soil,1981,60:317-319
142. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape:a software environment for integrated models of biomolecular interaction networks. Genome Res,2003,13:2498-2504
143. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol,2008,26:1135-1145
144. Shimoda Y, Shinpo S, Kohara M, Nakamura Y, Tabata S, Sato S. A large scale analysis of protein-protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti. DNA Res,2008,15:13-23
145. Shin HH, Hwang BH, Seo JH, Cha HJ. Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray. Appl Environ Microbiol,2014,80:366-373
146. Skerker JM, Shapiro L. Identification and cell cycle control of a novel pilus system in Caulobacter crescentus. The EMBO journal,2000,19:3223-3234
147. Skerker JM, Laub MT. Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus. Nat Rev Microbiol,2004,2:325-337
148. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell,1998,9:3273-3297
149. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis:a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A,2005,102: 15545-15550
150. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science,2008,321:956-960
151. Tal R, Wong HC, Calhoon R, Gelfand D, Fear AL, Volman G, Mayer R, Ross P, Amikam D, Weinhouse H, Cohen A, Sapir S, Ohana P, Benziman M. Three cdg operons control cellular turnover of cyclic di-GMP in Acetobacterxylinum:genetic organization and occurrence of conserved domains in isoenzymes. J Bacteriol,1998,180:4416-4425
152. Tan XJ, Cheng Y, Li YX, Li YG, Zhou JC. BacA is indispensable for successful Mesorhizobium-Astragalus symbiosis. Appl Microbiol Biotechnol,2009,84:519-526
153. Tate R, Riccio A, Merrick M, Patriarca EJ. The Rhizobium etli amtB gene coding for an NH4+ transporter is down-regulated early during bacteroid differentiation. Mol Plant Microbe Interact, 1998,11:188-198
154. Terpolilli JJ, Hood GA, Poole PS. What determines the efficiency of N(2)-fixing Rhizobium-legume symbioses? Adv Microb Physiol,2012,60:325-389
155. Tiricz H, Szucs A, Farkas A, Pap B, Lima RM, Maroti G, Kondorosi E, Kereszt A. Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti. Appl Environ Microbiol,2013,79:6737-6746
156. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA,2001,98:5116-5121
157. Uchiumi T, Ohwada T, Itakura M, Mitsui H, Nukui N, Dawadi P, Kaneko T, Tabata S, Yokoyama T, Tejima K, Saeki K, Omori H, Hayashi M, Maekawa T, Sriprang R, Murooka Y, Tajima S, Simomura K, Nomura M, Suzuki A, et al. Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J Bacteriol,2004,186:2439-2448
158. Udvardi MK, Salom CL, Day DA. Transport of L-glutamate across the bacteroid membrane but not the peribacteroid membrane from soybean root nodules. Mol. Plant-Microbe Interact,1988,1: 250-254
159. Van De Velde W, Zehirov G, Szatmari A, Debreczeny M, Ishihara H, Kevei Z, Farkas A, Mikulass K, Nagy A, Tiricz H, Satiat-Jeunemaitre B, Alunni B, Bourge M, Kucho K, Abe M, Kereszt A, Maroti G, Uchiumi T, Kondorosi E, Mergaert P. Plant peptides govern terminal differentiation of bacteria in symbiosis. Science,2010,327:1122-1126
160. Van Der Henst C, Beaufay F, Mignolet J, Didembourg C, Colinet J, Hallet B, Letesson JJ, De Bolle X. The histidine kinase PdhS controls cell cycle progression of the pathogenic alphaproteobacterium Brucella abortus. JBacteriol,2012,194:5305-5314
161. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE, Jr., Hieter P, Vogelstein B, Kinzler KW. Characterization of the yeast transcriptome. Cell,1997,88:243-251
162. Vercruysse M, Fauvart M, Beullens S, Braeken K, Cloots L, Engelen K, Marchal K, Michiels J. A comparative transcriptome analysis of Rhizobium etli bacteroids:specific gene expression during symbiotic nongrowth. Mol Plant Microbe Interact,2011,24:1553-1561
163. Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science, 2000,287:116-122
164. Walshaw DL, Poole PS. The general L-amino acid permease of Rhizobium leguminosarum is an ABC uptake system that also influences efflux of solutes. Mol Microbiol,1996,21:1239-1252
165. Wang C, Sheng X, Equi RC, Trainer MA, Charles TC, Sobral BW. Influence of the poly-3-hydroxybutyrate (PHB) granule-associated proteins (PhaP1 and PhaP2) on PHB accumulation and symbiotic nitrogen fixation in Sinorhizobium meliloti Rm1021. J Bacteriol,2007,189:9050-9056
166. Wang SC, West L, Shapiro L. The bifunctional FtsK protein mediates chromosome partitioning and cell division in Caulobacter. J Bacteriol,2006,188:1497-1508
167. Wang Y, Xu J, Chen A, Wang Y, Zhu J, Yu G, Xu L, Luo L. GGDEF and EAL proteins play different roles in the control of Sinorhizobium meliloti growth, motility, exopolysaccharide production, and competitive nodulation on host alfalfa. Acta Biochim Biophys Sin (Shanghai),2010,42:410-417
168. Wang Z, Gerstein M, Snyder M. RNA-Seq:a revolutionary tool for transcriptomics. Nat Rev Genet, 2009,10:57-63
169. Westermann A J, Gorski S A, Vogel J. Dual RN A-seq of pathogen and host. Nat Rev Microbiol,2012, 10:618-630
170. Wojciechowski MF, Lavin M, Sanderson MJ. A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. Am J Bot,2004,91:1846-1862
171. Wortinger M, Sackett MJ, Brun YV. CtrA mediates a DNA replication checkpoint that prevents cell division in Caulobacter crescentus. EMBO J,2000,19:4503-4512
172. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP:the database of interacting proteins. Nucleic Acids Res,2000,28:289-291
1.73. Yamasaki S, Nagasawa S, Fukushima A, Hayashi-Nishino M, Nishino K. Cooperation of the multidrug efflux pump and lipopolysaccharides in the intrinsic antibiotic resistance of Salmonella enterica serovar Typhimurium. J Antimicrob Chemother,2013,68:1066-1070
174. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci US A,2009,106:3976-3981
175. Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS, Mauchline TH, East AK, Quail MA, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, et al. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol,2006,7:R34
176. Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature,2011,480:520-524
177. Yurgel SN, Kahn ML. Dicarboxylate transport by rhizobia. FEMS Microbiol Rev,2004,28:489-501
178. Yurgel SN, Kahn ML. Sinorhizobium meliloti dctA mutants with partial ability to transport dicarboxylic acids. J Bacteriol,2005,187:1161-1172
179. Yurgel SN, Rice J, Kahn ML. Transcriptome analysis of the role of GlnD/GlnBK in nitrogen stress adaptation by Sinorhizobium meliloti Rm1021. PLoS One,2013,8:e58028
180. Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B. Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature,2007,450:233-237
2. Alunni B, Kevei Z, Redondo-Nieto M, Kondorosi A, Mergaert P, Kondorosi E. Genomic organization and evolutionary insights on GRP and NCR genes, two large nodule-specific gene families in Medicago truncatula. Mol Plant Microbe Interact,2007,20:1138-1148
3. Ampe F, Kiss E, Sabourdy F, Batut J. Transcriptome analysis of Sinorhizobium meliloti during symbiosis. Genome Biol,2003,4:R15
4. Anderson AJ, Dawes EA. Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev,1990,54:450-472
5. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP. Gene expression during the life cycle of Drosophila melanogaster. Science,2002, 297:2270-2275
6. Arcondeguy T, Jack R, Merrick M. P(ii) signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol Mol Biol Rev,2001,65:80-105
7. Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res,2006,16:686-691
8. Babu MM. Early career research award lecture. Structure, evolution and dynamics of transcriptional regulatory networks. Biochem Soc Trans,2010,38:1155-1178
9. Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res, 2005,33:5914-5923
10. Barnett MJ, Hung DY, Reisenauer A, Shapiro L, Long SR. A homolog of the ctra cell cycle regulator is present and essential in Sinorhizobium meliloti. JBacteriol,2001,183:3204-3210
11. Barnett MJ, Toman CJ, Fisher RF, Long SR. A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction. Proc Natl Acad Sci USA,2004, 101:16636-16641
12. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBI GEO:Mining millions of expression profiles--database and tools. Nucleic Acids Res,2005,33:D562-566
13. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO:Archive for functional genomics data sets--update. Nucleic Acids Res, 2013,41:D991-995
14. Becker-Andre M, Hahlbrock K. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a pcr aided transcript titration assay (PATTY). Nucleic Acids Res,1989, 17:9437-9446
15. Becker A, Berges H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, De Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Kuster H, Liebe C, Puhler A, Weidner S, Batut J. Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol Plant Microbe Interact,2004,17:292-303
16. Bertolazzi P, Bock ME, Guerra C. On the functional and structural characterization of hubs in protein-protein interaction networks. Biotechnol Adv,2013,31:274-286
17. Biondi EG, Skerker JM, Arif M, Prasol MS, Perchuk BS, Laub MT. A phosphorelay system controls stalk biogenesis during cell cycle progression in Caulobacter crescentus. Mol Microbiol,2006,59: 386-401
18. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res,2003,31:68-71
19. Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Mol Plant Microbe Interact,2008,21:631-645
20. Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science,2002,296:752-755
21. Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature,2005,433:531-537
22. Capela D, Filipe C, Bobik C, Batut J, Bruand C. Sinorhizobium meliloti differentiation during symbiosis with alfalfa:A transcriptomic dissection. Mol Plant Microbe Interact,2006,19:363-372
23. Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression in vertebrate tissues. J Biol,2009,8:33
24. Chang WS, Franck WL, Cytryn E, Jeong S, Joshi T, Emerich DW, Sadowsky MJ, Xu D, Stacey G. An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum. Mol Plant Microbe Interact,2007,20:1298-1307
25. Ching TM, Hedtke S. Isolation of bacteria, transforming bacteria, and bacteroids from soybean nodules. Plant Physiol,1977,60:771-774
26. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc,2007,2:2366-2382
27. Collier J, Mcadams HH, Shapiro L. A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc Natl Acad Sci USA,2007,104:17111-17116
28. Cytryn EJ, Sangurdekar DP, Streeter JG, Franck WL, Chang W-S, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. JBacteriol,2007,189:6751-6762
29. D'haeze W, Leoff C, Freshour G, Noel KD, Carlson RW. Rhizobium etli CE3 bacteroid lipopolysaccharides are structurally similar but not identical to those produced by cultured CE3 bacteria. JBiol Chem,2007,282:17101-17113
30. De Las Rivas J, Fontanillo C. Protein-protein interactions essentials:Key concepts to building and analyzing interactome networks. PLoS Comput Biol,2010,6:e1000807
31. De Lucena DK, Puhler A, Weidner S. The role of sigma factor RpoHl in the pH stress response of Sinorhizobium meliloti. BMC Microbiol,2010,10:265
32. Dixon R, Kahn D. Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol,2004,2: 621-631
33. Eisen JA. Badomics words and the power and peril of the ome-meme. GigaScience,2012,1:6
34. Fang Z, Cui X. Design and validation issues in RNA-seq experiments. Brief Bioinform,2011,12: 280-287
35. Farkas A, Maroti G, Durgo H, Gyorgypal Z, Lima RM, Medzihradszky KF, Kereszt A, Mergaert P, Kondorosi Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms. Proc Natl Acad Sci USA,2014,111:5183-5188
36. Fauvart M, Sanchez-Rodriguez A, Beullens S, Marchal K, Michiels J. Genome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil. J Bacteriol,2011,193:3158-3159
37. Ferguson BJ, Indrasumunar A, Hayashi S, Lin MH, Lin YH, Reid DE, Gresshoff PM. Molecular analysis of legume nodule development and autoregulation. J Integr Plant Biol,2010,52:61-76
38. Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science,2001,293:668-672
39. Gehlenborg N, O'donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods,2010,7:S56-68
40. Gilles-Gonzalez MA, Ditta GS, Helinski DR. A haemoprotein with kinase activity encoded by the oxygen sensor of Rhizobium meliloti. Nature,1991,350:170-172
41. Glazebrook J, Ichige A, Walker GC. A Rhizobium meliloti homolog of the Escherichia coli peptide-antibiotic transport protein SbmA is essential for bacteroid development. Genes Dev,1993,7:1485-1497
42. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer:Class discovery and class prediction by gene expression monitoring. Science,1999,286:531-537
43. Gonzalez V, Santamaria RI, Bustos P, Hernandez-Gonzalez 1, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramirez MA, Jimenez-Jacinto V, Collado-Vides J, Davila G. The partitioned Rhizobium etli genome:Genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA,2006,103:3834-3839
44. Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, Mullin L, Houmiel K, Gordon J, Vaudin M, Iartchouk O, Epp A, Liu F, Wollam C, Allinger M, Doughty D, et al. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science,2001,294:2323-2328
45. Green LS, Li Y, Emerich DW, Bergersen FJ, Day DA. Catabolism of alpha-ketoglutarate by a sucA mutant of Bradyrhizobium japonicum:Evidence for an alternative tricarboxylic acid cycle. J Bacteriol,2000,182:2838-2844
46. Gresshoff PM, Delves AC. Plant genetic approaches to symbiotic nodulation and nitrogen fixation in legumes, eds., Springer,1986.159-206
47. Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, Mckillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, Vijayraghavan K, et al. A protein complex network of Drosophila melanogaster. Cell,2011,147: 690-703
48. Haag AF, Baloban M, Sani M, Kerscher B, Pierre O, Farkas A, Longhi R, Boncompagni E, Herouart D, Dall'angelo S, Kondorosi E, Zanda M, Mergaert P, Ferguson GP. Protection of Sinorhizobium against host cysteine-rich antimicrobial peptides is critical for symbiosis. PLoS Biol,2011,9: e1001169
49. Haag AF, Arnold MF, Myka KK, Kerscher B, Dall'angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development during Rhizobium-legume symbiosis. FEMS Microbiol Rev,2012a,
50. Haag AF, Kerscher B, Dall'angelo S, Sani M, Longhi R, Baloban M, Wilson HM, Mergaert P, Zanda M, Ferguson GP. Role of cysteine residues and disulfide bonds in the activity of a legume root nodule-specific, cysteine-rich peptide. J Biol Chem,2012b,287:10791-10798
51. Hakoyama T, Niimi K, Watanabe H, Tabata R, Matsubara J, Sato S, Nakamura Y, Tabata S, Jichun L, Matsumoto T. Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation. Nature,2009,462:514-517
52. Hansen KD, Irizarry RA, Zhijin W. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics,2012,13:204-216
53. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, et al. A census of human soluble protein complexes. Cell,2012,150:1068-1081
54. Hengge R. Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol,2009,7:263-273
55. Hinton JC, Hautefort I, Eriksson S, Thompson A, Rhen M. Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr Opin Microbiol,2004,7:277-282
56. Hosie AH, Allaway D, Galloway CS, Dunsby HA, Poole PS. Rhizobium leguminosarum has a second general amino acid permease with unusually broad substrate specificity and high similarity to branched-chain amino acid transporters (Bra/LIV) of the ABC family. J Bacteriol,2002,184: 4071-4080
57. Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics,2002,18 Suppl 1:S233-240
58. Ikeo K, Ishi-I J, Tamura T, Gojobori T, Tateno Y. CIBEX:Center for information biology gene expression database. C R Biol,2003,326:1079-1082
59. Imaoka T, Nishimura M, Tani S, Ishikawa KI, Yamashita S, Ushijima T, Imai T, Shimada Y. Molecular characterization of cancer reveals interactions between ionizing radiation and chemicals on rat mammary carcinogenesis. Int J Cancer,2014,134:1529-1538
60. Jenal U, Fuchs T. An essential protease involved in bacterial cell-cycle control. EMBO J,1998,17: 5658-5669
61. Jensen ES, Peoples MB, Boddey RM, Gresshoff PM, Hauggaard-Nielsen H, Alves BJ, Morrison MJ. Legumes for mitigation of climate change and the provision of feedstock for biofuels and biorefineries. A review. Agron Sustain Dev,2012,32:329-364
62. Jones SE, Ferguson NL, Alley MR. New members of the ctrA regulon:The major chemotaxis operon in Caulobacter is Ctra dependent. Microbiology,2001,147:949-958
63. Kai T, Williams D, Spradling AC. The expression profile of purified Drosophila germline stem cells. Dev Biol,2005,283:486-502
64. Kaiser BN, Moreau S, Castelli J, Thomson R, Lambert A, Bogliolo S, Puppo A, Day DA. The soybean NRAMP homologue, GmDMT1, is a symbiotic divalent metal transporter capable of ferrous iron transport. Plant J,2003,35:295-304
65. Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Mochizuki Y, Nakayama S, Nakazaki N, Shimpo S, et al. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti (supplement). DNA Res,2000,7:381-406
66. Karr DB, Oehrle NW, Emerich DW. Recovery of nitrogenase from aerobically isolated soybean nodule bacteroids. Plant and Soil,2003,257:27-33
67. Karunakaran R, Ramachandran V, Seaman J, East A, Mouhsine B, Mauchline T, Prell J, Skeffington A, Poole P. Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J Bacteriol,2009,191:4002-4014
68. Karunakaran R, Haag AF, East AK, Ramachandran VK, Prell J, James EK, Scocchi M, Ferguson GP, Poole PS. BacA is essential for bacteroid development in nodules of galegoid, but not phaseoloid, legumes. J Bacteriol,2010,192:2920-2928
69. Kereszt A, Mergaert P, Maroti G, Kondorosi E. Innate immunity effectors and virulence factors in symbiosis. Curr Opin Microbiol,2011,14:76-81
70. Khatri P, Draghici S. Ontological analysis of gene expression data:Current tools, limitations, and open problems. Bioinformatics,2005,21:3587-3595
71. Kogenaru S, Qing Y, Guo Y, Wang N. RNA-seq and microarray complement each other in transcriptome profiling. BMC Genomics,2012,13:629
72. Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Analyzing protein-protein interaction networks. JProteome Res,2012,11:2014-2031
73. Kouchi H, Fukai K. Rapid isolation of bacteroids from soybean root nodules by Percoll discontinuous gradient centrifugation. Soil Sci Plant Nutr,1989,35:301-305
74. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature,2006,440:637-643
75. Krummenacher P, Narberhaus F. Two genes encoding a putative multidrug efflux pump of the RND/MFP family are cotranscribed with an rpoH gene in Bradyrhizobium japonicum. Gene,2000, 241:247-254
76. Krusell L, Krause K, Ott T, Desbrosses G, Kramer U, Sato S, Nakamura Y, Tabata S, James EK, Sandal N. The sulfate transporter SST1 is crucial for symbiotic nitrogen fixation in Lotus japonicus root nodules. Plant Cell,2005,17:1625-1636
77. Laub MT, Mcadams HH, Feldblyum T, Fraser CM, Shapiro L. Global analysis of the genetic network controlling a bacterial cell cycle. Science,2000,290:2144-2148
78. Laub MT, Chen SL, Shapiro L, Mcadams HH. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci USA,2002,99:4632-4637
79. Li J, Dai X, Liu T, Zhao PX. LegumeIP:An integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Res,2012,40:D1221-1229
80. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2:An improved ultrafast tool for short read alignment. Bioinformatics,2009,25:1966-1967
81. Li Y, Parsons R, Day DA, Bergersen FJ. Reassessment of major products of N2 fixation by bacteroids from soybean root nodules. Microbiology,2002,148:1959-1966
82. Li Y, Tian CF, Chen WF, Wang L, Sui XH, Chen WX. High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala. PLoS One,2013,8:e70531
83. Lindberg J, Lundeberg J. The plasticity of the mammalian transcriptome. Genomics,2010,95:1-6
84. Lindemann A, Koch M, Pessi G, Muller AJ, Balsiger S, Hennecke H, Fischer HM. Host-specific symbiotic requirement of BdeAB, a RegR-controlled RND-type efflux system in Bradyrhizobium japonicum. FEMS Microbiol Lett,2010,312:184-191
85. Lodwig E, Poole P. Metabolism of Rhizobium bacteroids. Crit Rev Plant Sci,2003,22:37-78
86. Lodwig EM, Hosie AH, Bourdes A, Findlay K, Allaway D, Karunakaran R, Downie JA, Poole PS. Amino-acid cycling drives nitrogen fixation in the Legume-Rhizobium symbiosis. Nature,2003,422: 722-726
87. Lodwig EM, Leonard M, Marroqui S, Wheeler TR, Findlay K, Downie JA, Poole PS. Role of polyhydroxybutyrate and glycogen as carbon storage compounds in pea and bean bacteroids. Mol Plant Microbe Interact,2005,18:67-74
88. Lois AF, Weinstein M, Ditta GS, Helinski DR. Autophosphorylation and phosphatase activities of the oxygen-sensing protein FixL of Rhizobium meliloti are coordinately regulated by oxygen. JBiol Chem,1993,268:4370-4375
89. Madan Babu M, Teichmann SA, Aravind L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol,2006,358:614-633
90. Maere S, Heymans K, Kuiper M. BiNGO:A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics,2005,21:3448-3449
91. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet,2008,9: 387-402
92. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq:An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res,2008,18:1509-1517
93. Martinez-Abarca F, Martinez-Rodriguez L, Lopez-Contreras JA, Jimenez-Zurdo JI, Toro N. Complete genome sequence of the alfalfa symbiont SinorhizobiumlEnsifer meliloti strain GR4. Genome Announc,2013,1:e00174-00112
94. Martinez-Argudo I, Little R, Shearer N, Johnson P, Dixon R. The NifL-NifA system:A multidomain transcriptional regulatory complex that integrates environmental signals. J Bacteriol,2004,186: 601-610
95. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res,2001,11:2120-2126
96. Mcgrath PT, Iniesta AA, Ryan KR, Shapiro L, Mcadams HH. A dynamically localized protease complex and a polar specificity factor control a cell cycle master regulator. Cell,2006,124:535-547
97. Mercer RG, Callister SJ, Lipton MS, Pasa-Tolic L, Strnad H, Paces V, Beatty JT, Lang AS. Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus. J Bacteriol,2010,192:2701-2710
98. Mergaert P, Nikovics K, Kelemen Z, Maunoury N, Vaubert D, Kondorosi A, Kondorosi E. A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. Plant Physiol,2003,132:161-173
99. Mergaert P, Uchiumi T, Alunni B, Evanno G, Cheron A, Catrice O, Mausset AE, Barloy-Hubler F, Galibert F, Kondorosi A, Kondorosi E. Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium-legume symbiosis. Proc Natl Acad Sci USA,2006,103:5230-5235
100. Miller A, Cramer M. Root nitrogen acquisition and assimilation, eds., Springer,2005.1-36
101. Miller TR, Belas R. Motility is involved in Silicibacter sp. Tm 1040 interaction with dinoflagellates. Environ Microbiol,2006,8:1648-1659
102. Mitsui H, Sato T, Sato Y, Ito N, Minamisawa K. Sinorhizobium meliloti RpoHl is required for effective nitrogen-fixing symbiosis with alfalfa. Mol Genet Genomics,2004,271:416-425
103. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods,2008,5:621-628
104. Mulley G, White J, Karunakaran R, Prell J, Bourdes A, Bunnewell S, Hill L, Poole P. Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources. Mol Microbiol,2011,80:149-167
105. Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA,1996,93:10268-10273
106. Newcomb W, Sippell D, Peterson R. The early morphogenesis of Glycine max and Pisum sativum root nodules. Can J Bot,1979,57:2603-2616
107. Ninfa AJ, Atkinson MR. PII signal transduction proteins. Trends Microbiol,2000,8:172-179
108. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature,2002,420:563-573
109. Oldroyd GE, Downie JA. Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol,2008,59:519-546
110. Oldroyd GE, Murray JD, Poole PS, Downie JA. The rules of engagement in the legume-rhizobial symbiosis. Annu Rev Genet,2011,45:119-144
111. Oono R, Denison RF. Comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids. Plant Physiol,2010,154:1541-1548
112. Oono R, Schmitt I, Sprent JI, Denison RF. Multiple evolutionary origins of legume traits leading to extreme rhizobial differentiation. New Phytol,2010,187:508-520
113. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, De Crecy-Lagard V, Diaz N, Disz T, Edwards R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res,2005,33:5691-5702
114. Patriarca EJ, Tate R, Iaccarino M. Key role of bacterial NH4+ metabolism in Rhizobium-plant symbiosis. Microbiol Mol Biol Rev,2002,66:203-222
115. Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, De Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol,2006,24:1140-1150
116. Pessi G, Ahrens CH, Rehrauer H, Lindemann A, Hauser F, Fischer HM, Hennecke H. Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules. Mol Plant Microbe Interact,2007,20:1353-1363
117. Piddock LJ. Multidrug-resistance efflux pumps-not just for resistance. Nat Rev Microbiol,2006, 4:629-636
118. Pietu G, Eveno E, Soury-Segurens B, Fayein NA, Mariage-Samson R, Matingou C, Leroy E, Dechesne C, Krieger S, Ansorge W, Reguigne-Arnould I, Cox D, Dehejia A, Polymeropoulos MH, Devignes MD, Auffray C. The genexpress IMAGE knowledge base of the human muscle transcriptome:A resource of structural, functional, and positional candidate genes for muscle physiology and pathologies. Genome Res,1999,9:1313-1320
119. Pini F, Frage B, Ferri L, De Nisco NJ, Mohapatra SS, Taddei L, Fioravanti A, Dewitte F, Galardini M, Brilli M, Villeret V, Bazzicalupo M, Mengoni A, Walker GC, Becker A, Biondi EG. The DivJ, CbrA and PleC system controls Divk phosphorylation and symbiosis in Sinorhizobium meliloti. Mol Microbiol,2013,90:54-71
120. Prell J, Poole P. Metabolic changes of rhizobia in legume nodules. Trends Microbiol,2006,14:161-168
121. Prell J, White JP, Bourdes A, Bunnewell S, Bongaerts RJ, Poole PS. Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids. Proc Natl Acad Sci USA,2009,106:12477-12482
122. Ptashne M. Regulation of transcription:From lambda to eukaryotes. Trends Biochem Sci,2005,30: 275-279
123. Pumirat P, Vanaporn M, Pinweha P, Tandhavanant S, Korbsrisate S, Chantratita N. The role of short-chain dehydrogenase/oxidoreductase, induced by salt stress, on host interaction of B. pseudomallei. BMC Microbiol,2014,14:1
124. Quon KC, Marczynski GT, Shapiro L. Cell cycle control by an essential bacterial two-component signal transduction protein. Cell,1996,84:83-93
125. Romling U, Galperin MY, Gomelsky M. Cyclic di-GMP:The first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev,2013,77:1-52
126. Reibach PH, Mask PL, Streeter JG. A rapid one-step method for the isolation of bacteroids from root nodules of soybean plants, utilizing self-generating Percoll gradients. Can J Microbiol,1981, 27:491-495
127. Resendis-Antonio O, Hernandez M, Salazar E, Contreras S, Batallar GM, Mora Y, Encarnacion S. Systems biology of bacterial nitrogen fixation:high-throughput technology and its integrative description with constraint-based modeling. BMC Syst Biol,2011,5:120
128. Rodriguez-Llorente I, Caviedes MA, Dary M, Palomares AJ, Canovas FM, Peregrin-Alvarez JM. The Symbiosis Interactome:a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. BMC Syst Biol,2009,3:63
129. Rolfe BG, Gresshoff P. Genetic analysis of legume nodule initiation. Annu Rev Plant Physiol Mol Biol,1988,39:297-319
130. Romanov VI, Hernandez-Lucas I, Martinez-Romero E. Carbon Metabolism Enzymes of Rhizobium tropici Cultures and Bacteroids. Appl Environ Microbiol,1994,60:2339-2342
131. Ronson CW, Astwood PM, Downie JA. Molecular cloning and genetic organization of C4-dicarboxylate transport genes from Rhizobium Leguminosarum. J Bacteriol,1984,160:903-909
132. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature,2005,437:1173-1178
133. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Fame A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, et al. ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res,2013,41:D987-990
134. Ryan RP, Mccarthy Y, Andrade M, Farah CS, Armitage JP, Dow JM. Cell-cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris. Proc Natl Acad Sci USA,2010,107:5989-5994
135. Saalbach G, Erik P, Wienkoop S. Characterisation by proteomics of peribacteroid space and peribacteroid membrane preparations from pea(Pisum sativum) symbiosomes. Proteomics,2002,2: 325-337
136. Santoni D, Swiercz A, Zmienko A, Kasprzak M, Blazewicz M, Bertolazzi P, Felici G. An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics:application on Arabidopsis thaliana. OMICS,2014,18:155-165
137. Sarma AD, Emerich DW. A comparative proteomic evaluation of culture grown vs nodule isolated Bradyrhizobium japonicum. Proteomics,2006,6:3008-3028
138. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science,1995,270:467-470
139. Schmidt AJ, Ryjenkov DA, Gomelsky M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase:enzymatically active and inactive EAL domains. JBacteriol, 2005,187:4774-4781
140. Schwartz S, Oren R, Ast G. Detection and removal of biases in the analysis of next-generation sequencing reads. P LoS One,2011,6:e16685
141. Sen D, Weaver R. A comparison of nitrogen-fixing ability of peanut, cowpea and siratro plants nodulated by different strains of Rhizobium. Plant Soil,1981,60:317-319
142. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape:a software environment for integrated models of biomolecular interaction networks. Genome Res,2003,13:2498-2504
143. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol,2008,26:1135-1145
144. Shimoda Y, Shinpo S, Kohara M, Nakamura Y, Tabata S, Sato S. A large scale analysis of protein-protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti. DNA Res,2008,15:13-23
145. Shin HH, Hwang BH, Seo JH, Cha HJ. Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray. Appl Environ Microbiol,2014,80:366-373
146. Skerker JM, Shapiro L. Identification and cell cycle control of a novel pilus system in Caulobacter crescentus. The EMBO journal,2000,19:3223-3234
147. Skerker JM, Laub MT. Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus. Nat Rev Microbiol,2004,2:325-337
148. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell,1998,9:3273-3297
149. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis:a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A,2005,102: 15545-15550
150. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science,2008,321:956-960
151. Tal R, Wong HC, Calhoon R, Gelfand D, Fear AL, Volman G, Mayer R, Ross P, Amikam D, Weinhouse H, Cohen A, Sapir S, Ohana P, Benziman M. Three cdg operons control cellular turnover of cyclic di-GMP in Acetobacterxylinum:genetic organization and occurrence of conserved domains in isoenzymes. J Bacteriol,1998,180:4416-4425
152. Tan XJ, Cheng Y, Li YX, Li YG, Zhou JC. BacA is indispensable for successful Mesorhizobium-Astragalus symbiosis. Appl Microbiol Biotechnol,2009,84:519-526
153. Tate R, Riccio A, Merrick M, Patriarca EJ. The Rhizobium etli amtB gene coding for an NH4+ transporter is down-regulated early during bacteroid differentiation. Mol Plant Microbe Interact, 1998,11:188-198
154. Terpolilli JJ, Hood GA, Poole PS. What determines the efficiency of N(2)-fixing Rhizobium-legume symbioses? Adv Microb Physiol,2012,60:325-389
155. Tiricz H, Szucs A, Farkas A, Pap B, Lima RM, Maroti G, Kondorosi E, Kereszt A. Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti. Appl Environ Microbiol,2013,79:6737-6746
156. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA,2001,98:5116-5121
157. Uchiumi T, Ohwada T, Itakura M, Mitsui H, Nukui N, Dawadi P, Kaneko T, Tabata S, Yokoyama T, Tejima K, Saeki K, Omori H, Hayashi M, Maekawa T, Sriprang R, Murooka Y, Tajima S, Simomura K, Nomura M, Suzuki A, et al. Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J Bacteriol,2004,186:2439-2448
158. Udvardi MK, Salom CL, Day DA. Transport of L-glutamate across the bacteroid membrane but not the peribacteroid membrane from soybean root nodules. Mol. Plant-Microbe Interact,1988,1: 250-254
159. Van De Velde W, Zehirov G, Szatmari A, Debreczeny M, Ishihara H, Kevei Z, Farkas A, Mikulass K, Nagy A, Tiricz H, Satiat-Jeunemaitre B, Alunni B, Bourge M, Kucho K, Abe M, Kereszt A, Maroti G, Uchiumi T, Kondorosi E, Mergaert P. Plant peptides govern terminal differentiation of bacteria in symbiosis. Science,2010,327:1122-1126
160. Van Der Henst C, Beaufay F, Mignolet J, Didembourg C, Colinet J, Hallet B, Letesson JJ, De Bolle X. The histidine kinase PdhS controls cell cycle progression of the pathogenic alphaproteobacterium Brucella abortus. JBacteriol,2012,194:5305-5314
161. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE, Jr., Hieter P, Vogelstein B, Kinzler KW. Characterization of the yeast transcriptome. Cell,1997,88:243-251
162. Vercruysse M, Fauvart M, Beullens S, Braeken K, Cloots L, Engelen K, Marchal K, Michiels J. A comparative transcriptome analysis of Rhizobium etli bacteroids:specific gene expression during symbiotic nongrowth. Mol Plant Microbe Interact,2011,24:1553-1561
163. Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science, 2000,287:116-122
164. Walshaw DL, Poole PS. The general L-amino acid permease of Rhizobium leguminosarum is an ABC uptake system that also influences efflux of solutes. Mol Microbiol,1996,21:1239-1252
165. Wang C, Sheng X, Equi RC, Trainer MA, Charles TC, Sobral BW. Influence of the poly-3-hydroxybutyrate (PHB) granule-associated proteins (PhaP1 and PhaP2) on PHB accumulation and symbiotic nitrogen fixation in Sinorhizobium meliloti Rm1021. J Bacteriol,2007,189:9050-9056
166. Wang SC, West L, Shapiro L. The bifunctional FtsK protein mediates chromosome partitioning and cell division in Caulobacter. J Bacteriol,2006,188:1497-1508
167. Wang Y, Xu J, Chen A, Wang Y, Zhu J, Yu G, Xu L, Luo L. GGDEF and EAL proteins play different roles in the control of Sinorhizobium meliloti growth, motility, exopolysaccharide production, and competitive nodulation on host alfalfa. Acta Biochim Biophys Sin (Shanghai),2010,42:410-417
168. Wang Z, Gerstein M, Snyder M. RNA-Seq:a revolutionary tool for transcriptomics. Nat Rev Genet, 2009,10:57-63
169. Westermann A J, Gorski S A, Vogel J. Dual RN A-seq of pathogen and host. Nat Rev Microbiol,2012, 10:618-630
170. Wojciechowski MF, Lavin M, Sanderson MJ. A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. Am J Bot,2004,91:1846-1862
171. Wortinger M, Sackett MJ, Brun YV. CtrA mediates a DNA replication checkpoint that prevents cell division in Caulobacter crescentus. EMBO J,2000,19:4503-4512
172. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP:the database of interacting proteins. Nucleic Acids Res,2000,28:289-291
1.73. Yamasaki S, Nagasawa S, Fukushima A, Hayashi-Nishino M, Nishino K. Cooperation of the multidrug efflux pump and lipopolysaccharides in the intrinsic antibiotic resistance of Salmonella enterica serovar Typhimurium. J Antimicrob Chemother,2013,68:1066-1070
174. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci US A,2009,106:3976-3981
175. Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS, Mauchline TH, East AK, Quail MA, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, et al. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol,2006,7:R34
176. Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature,2011,480:520-524
177. Yurgel SN, Kahn ML. Dicarboxylate transport by rhizobia. FEMS Microbiol Rev,2004,28:489-501
178. Yurgel SN, Kahn ML. Sinorhizobium meliloti dctA mutants with partial ability to transport dicarboxylic acids. J Bacteriol,2005,187:1161-1172
179. Yurgel SN, Rice J, Kahn ML. Transcriptome analysis of the role of GlnD/GlnBK in nitrogen stress adaptation by Sinorhizobium meliloti Rm1021. PLoS One,2013,8:e58028
180. Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B. Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature,2007,450:233-237