Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo, Postal 565-A, Cuernavaca, Morelos, México.
BMC Microbiol. 2011 Apr 5;11:66. doi: 10.1186/1471-2180-11-66.
A traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. Exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. The genome sequence of R. etli CFN42 predicts the presence of panC and panB genes clustered together on the 642 kb plasmid p42f and a second copy of panB on plasmid p42e. They encode putative pantothenate biosynthesis enzymes (pantoate-β-alanine ligase and 3-methyl-2-oxobutanoate hydroxymethyltransferase, respectively). Due to their ubiquitous distribution and relevance in the central metabolism of the cell, these genes are considered part of the core genome; thus, their occurrence in a plasmid is noteworthy. In this study we investigate the contribution of these genes to pantothenate biosynthesis, examine whether their presence in plasmids is a prevalent characteristic of the Rhizobiales with multipartite genomes, and assess the possibility that the panCB genes may have reached plasmids by horizontal gene transfer.
Analysis of mutants confirmed that the panC and panB genes located on plasmid p42f are indispensable for the synthesis of pantothenate. A screening of the location of panCB genes among members of the Rhizobiales showed that only R. etli and R. leguminosarum strains carry panCB genes in plasmids. The panCB phylogeny attested a common origin for chromosomal and plasmid-borne panCB sequences, suggesting that the R. etli and R. leguminosarum panCB genes are orthologs rather than xenologs. The panCB genes could not totally restore the ability of a strain cured of plasmid p42f to grow in minimal medium.
This study shows experimental evidence that core panCB genes located in plasmids of R. etli and R. leguminosarum are indispensable for the synthesis of pantothenate. The unusual presence of panCB genes in plasmids of Rhizobiales may be due to an intragenomic transfer from chromosome to plasmid. Plasmid p42f encodes other functions required for growth in minimal medium. Our results support the hypothesis of cooperation among different replicons for basic cellular functions in multipartite rhizobia genomes.
细菌遗传学中的一个传统概念认为，参与维持细胞基本代谢功能的管家基因编码在染色体上，而应对挑战性环境条件的基因则位于质粒上。具有多分区基因组的细菌的基因组序列数据已经出现了对此规则的例外。R. etli CFN42 的基因组序列预测存在 panC 和 panB 基因簇在 642 kb 质粒 p42f 上，而质粒 p42e 上则存在第二个 panB 副本。它们分别编码泛酸生物合成酶（泛酸-β-丙氨酸连接酶和 3-甲基-2-氧代丁酸羟甲基转移酶）。由于这些基因在细胞的中心代谢中具有普遍分布和重要性，因此被认为是核心基因组的一部分；因此，它们在质粒中的存在是值得注意的。在这项研究中，我们研究了这些基因对泛酸生物合成的贡献，检查了它们在质粒中的存在是否是多分区 Rhizobiales 的普遍特征，并评估了 panCB 基因可能通过水平基因转移到达质粒的可能性。
突变体分析证实，位于质粒 p42f 上的 panC 和 panB 基因对于泛酸的合成是必不可少的。对 Rhizobiales 成员中 panCB 基因的位置进行筛选发现，只有 R. etli 和 R. leguminosarum 菌株在质粒中携带 panCB 基因。panCB 系统发育证明了染色体和质粒携带的 panCB 序列具有共同的起源，表明 R. etli 和 R. leguminosarum 的 panCB 基因是同源基因而不是异源基因。panCB 基因不能完全恢复被去除质粒 p42f 的菌株在最小培养基中生长的能力。
本研究提供了实验证据，表明位于 R. etli 和 R. leguminosarum 质粒中的核心 panCB 基因对于泛酸的合成是必不可少的。Rhizobiales 质粒中异常存在 panCB 基因可能是由于染色体到质粒的基因组内转移所致。质粒 p42f 编码其他在最小培养基中生长所需的功能。我们的结果支持了不同复制子在多分区根瘤菌基因组中基本细胞功能合作的假设。
