Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas.
Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas.
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假单胞菌属四种代表性植物根际促生细菌的比较基因组分析
DOI：
10.1186/1471-2164-14-271
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发表时间：
2013-04-22
期刊：
影响因子：
4.4
通讯作者：
Zhang X
中科院分区：
文献类型：
--
作者：
Shen X;Hu H;Peng H;Wang W;Zhang X
一些假单胞菌是促进植物生长的主要根瘤菌（PGPR）。在该组中，嗜绿假单胞菌和荧光假单胞菌是非致病性生物防治剂，一些铜绿假单胞菌和假单胞菌菌株是PGPR.P。chlororaphisGP72是一种具有全基因组测序的植物生长促进根杆菌。我们对GP72与其他三种假单胞菌PGPR进行了基因组分析：固氮菌株p.s utzeria1501。我们的目的是利用比较基因组学的方法来确定这些菌株之间的异同点，以阐明植物生长促进活性的机制。结果GP72、Pf-5、M18和A1501的基因组大小在4.6 ~ 7.1 M之间，蛋白质编码基因数量在4个物种之间存在差异。同源基团簇（COGs）分析为预测的蛋白质分配功能。4种植物的COGs分布相似。而编码转座酶及其失活衍生物（COG L）的基因在A1501、GP72、Pf-5和M18中分别占COGs分类基因总数的1.33%、0.21%、0.02%和0.11%。系统发育分析表明，GP72和Pf-5是亲缘关系最密切的菌株，与基因组比对结果一致。GP72和Pf-5的预测编码序列（CDSs）比较发现3544个保守基因。与A1501和M18相比，GP72 CDSs的保守基因较少。通过对4种假单胞菌的比较，发现了GP72中603个保守基因，说明了这些假单胞菌具有共同的植物生长促进性状。保守基因与分解代谢、植物源性化合物的运输、抗逆性和根际定植有关。一些菌株特异性cds与不同种类的生物防治活性或促进植物生长有关。GP72基因组中含有与重金属抗性有关的菌毛柄和一个与IV型菌毛生物合成有关的基因簇，后者赋予菌毛粘附能力。结论对4种具有代表性的假单胞菌PGPR进行比较基因组分析，发现了一些保守区域，显示了这些假单胞菌PGPR的共同特征（植物源性化合物代谢、重金属抗性和根际定植）。每个菌株特有的基因组区域为其生活方式、生态适应和在根际中的生理作用提供了线索。
BackgroundSomePseudomonasstrains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group,Pseudomonas chlororaphisandPseudomonas fluorescensare non-pathogenic biocontrol agents, and somePseudomonas aeruginosaandPseudomonas stutzeristrains are PGPR.P.chlororaphisGP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR:P.fluorescensPf-5,P.aeruginosaM18, and the nitrogen-fixing strainP.stutzeriA1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity.ResultsThe genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the fourPseudomonasspecies revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome contained thecusoperon (related to heavy metal resistance) and a gene cluster involved in type IV pilus biosynthesis, which confers adhesion ability.ConclusionsComparative genomic analysis of four representative PGPR revealed some conserved regions, indicating common characteristics (metabolism of plant-derived compounds, heavy metal resistance, and rhizosphere colonization) among these pseudomonad PGPR. Genomic regions specific to each strain provide clues to its lifestyle, ecological adaptation, and physiological role in the rhizosphere.
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影响因子：
2.9
作者：
Ayub, Nicolas D.;Tribelli, Paula M.;Lopez, Nancy I.
通讯作者：
Lopez, Nancy I.
DOI：
10.1073/pnas.1731982100
发表时间：
2003-09-02
影响因子：
11.1
作者：
Buell, CR;Joardar, V;Collmer, A
通讯作者：
Collmer, A
影响因子：
5.1
作者：
Arias, Sagrario;Olivera, Elias R.;Luengo, Jose M.
通讯作者：
Luengo, Jose M.
影响因子：
3.2
作者：
BARBOUR, MG;BAYLY, RC
通讯作者：
BAYLY, RC
影响因子：
3.5
作者：
Bianciotto, V;Andreotti, S;Perotto, S
通讯作者：
Perotto, S