Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility
Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility
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DOI：
10.1073/pnas.0606924103
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发表时间：
2006-10-17
影响因子：
11.1
通讯作者：
Tiedje, James M.
中科院分区：
文献类型：
--
作者：
Chain, Patrick S. G.;Denef, Vincent J.;Tiedje, James M.
Burkholderia xenovorans LB 400（LB 400）是一种经过充分研究的有效多氯联苯降解剂，具有已知的两种最大的细菌基因组之一，是第一个测序的非致病性Burkholderia分离株。从进化的角度来看，我们发现LB 400的三个复制子之间的功能特化存在显着差异，以及位于两个较小与最大复制子上的基因的选择压力更宽松。LB 400和洋葱伯克霍尔德氏菌复合菌株383之间仅44%的基因保守性证明了伯克霍尔德氏菌属内的高基因组可塑性、多样性和特化性。即使是在四个B中。xenovorans菌株，基因组大小从7.4到9.73 Mbp不等。后者在很大程度上是通过我们的发现来解释的，即> 20%的LB 400序列是最近通过横向基因转移获得的。虽然存在一系列与体内存活和细胞间相互作用相关的遗传因素，但这些遗传因素可能与生态位宽度有关，而不是致病性的决定因素。LB 400中存在至少11个“中心芳香族”和20个“外围芳香族”途径，在任何测序的细菌基因组中是最高的，支持这一假设。最后，除了实验观察到苯甲酸降解和甲醛氧化途径的冗余外，17.6%的蛋白质具有比不同基因组中的直系同源物更好的LB 400同源性的事实突出了基因复制和重复获得的重要性，再加上它们的分歧，提出了关于旁系同源物的作用和大基因组微生物中潜在功能冗余的问题。
Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that > 20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.