Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.
Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.
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DOI：
10.1371/journal.pgen.1004231
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发表时间：
2014-03
期刊：
影响因子：
4.5
通讯作者：
Li J
中科院分区：
文献类型：
--
作者：
Xie JB;Du Z;Bai L;Tian C;Zhang Y;Xie JY;Wang T;Liu X;Chen X;Cheng Q;Chen S;Li J
我们在这里提供了类芽孢杆菌属内的31个菌株的比较基因组分析，包括11个新的N2固定菌株的基因组序列。31个基因组（15个固氮类芽孢杆菌和16个非固氮类芽孢杆菌）的异质性反映在壳基因组的大尺寸上，其占泛基因组中基因的约65.2%。大量的转座因子可能与异质性有关。结果表明，这15株固氮菌的固氮酶基因组成了一个最小的nif簇，由nifB、nifH、nifD、nifK、nifE、nifN、nifX、hesA和nifV 9个基因组成。nif簇受σ70依赖性启动子控制，并在启动子中具有GlnR/TnrA结合位点。编码[Fe-S]簇的Suf系统在固氮菌和非固氮菌中高度保守。此外，我们证明了nif簇使大肠杆菌JM 109能够固氮。串联的NifHDK序列的系统发育表明类芽孢杆菌属和弗兰克氏菌属是姐妹群。串联的275个单拷贝核心基因的系统发育表明，祖先类芽孢杆菌没有固定氮。通过从与Frankia相关的来源经由水平基因转移（HGT）获得nif簇来产生N2固定类芽孢杆菌属菌株。在进化过程中，nif基因簇丢失，产生了一些不固氮的菌株，并获得了编码V-固氮酶的vnf或编码Fe-固氮酶的anf，使一些菌株进一步多样化。此外，一些N2固定菌株还具有额外的nif和nif样基因，这可能是基因重复造成的。类芽孢杆菌固氮的进化涉及到nif/anf/vnf基因的获得、丢失、HGT和复制的混合。该研究不仅揭示了类芽孢杆菌固氮基因的组织和分布，而且为了解固氮的复杂进化历史提供了新的视角。我们对11株固氮类芽孢杆菌属菌株的基因组进行了测序，并通过将这些菌株相互比较以及与先前测序的20株其他菌株（4株固氮菌株和16株非固氮菌株）进行比较来证明类芽孢杆菌属的基因组多样性。对串联的275个单拷贝核心基因的系统发育分析表明，祖先类芽孢杆菌不固氮，固氮菌株分为两个亚组，它们可能起源于固氮的共同祖先。一个最小的和紧凑的nif簇，包括9个nif基因编码钼固氮酶是高度保守的15固氮菌株。两个亚群之间的nif簇和nif簇周围的染色体区域中的变化意味着在类芽孢杆菌的早期进化历史中在不同基因组位点中插入不同的nif簇变体的至少两个独立的收购。串联的NifHDK序列的系统发育表明类芽孢杆菌属和弗兰克氏菌属是姐妹群。固氮功能单元nif簇丢失，产生一些非固氮菌株。最近有vnf和anf基因的获得事件，导致一些菌株的进一步多样化。类芽孢杆菌固氮的进化涉及到nif/anf/vnf基因的获得、丢失、HGT和复制的混合。
We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation. We sequenced the genomes of 11 N2-fixing Paenibacillus strains and demonstrated the genomic diversity of the genus Paenibacillus by comparing these strains to each other and to 20 other strains (4 N2-fixing and 16 non-N2-fixing strains) that were sequenced previously. Phylogenetic analysis of the concatenated 275 single-copy core genes suggests that ancestral Paenibacillus did not fix nitrogen and the N2-fixing strains fall into two sub-groups, which were likely originated from a N2-fixing common ancestor. A minimal and compact nif cluster comprising nine nif genes encoding Mo-nitrogenase is highly conserved in the 15 N2-fixing strains. Variations in the nif cluster and in the chromosomal regions surrounding the nif cluster between two sub-groups imply at least two independent acquisitions with insertion of distinct nif cluster variants in different genomic sites of Paenibacillus in early evolutionary history. Phylogeny of the concatenated NifHDK sequences suggests that Paenibacillus and Frankia are sister groups. The nif cluster, a functional unit for nitrogen fixation, was lost, producing some non-N2-fixing strains. There were recent events of acquisition of vnf and anf genes, causing further diversification of some strains. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes.
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影响因子：
3.2
作者：
Davis, R;Lehman, L;Ludden, PW
通讯作者：
Ludden, PW
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
3.2
作者：
CHISNELL, JR;PREMAKUMAR, R;BISHOP, PE
通讯作者：
BISHOP, PE
影响因子：
1.2
作者：
Doroshchuk, N. A.;Gelfand, M. S.;Rodionov, D. A.
通讯作者：
Rodionov, D. A.
DOI：
10.1073/pnas.1932838100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Baar, C;Eppinger, M;Schuster, SC
通讯作者：
Schuster, SC