Division of Medical Sciences, University of Crete Medical School, Heraklion 71110, Crete, Greece.
BMC Genomics. 2009 Dec 11;10:597. doi: 10.1186/1471-2164-10-597.
Genes of conserved order in bacterial genomes tend to evolve slower than genes whose order is not conserved. In addition, genes with a GC content lower than the GC content of the resident genome are known to be selectively silenced by the histone-like nucleoid structuring protein (H-NS) in Salmonella.
In this study, we use a comparative genomics approach to demonstrate that in Salmonella, genes whose order is not conserved (or genes without homologs) in closely related bacteria possess a significantly lower average GC content in comparison to genes that preserve their relative position in the genome. Moreover, these genes are more frequently targeted by H-NS than genes that have conserved their genomic neighborhood. We also observed that duplicated genes that do not preserve their genomic neighborhood are, on average, under less selective pressure.
We establish a strong association between gene order, GC content and gene silencing in a model bacterial species. This analysis suggests that genes that are not under strong selective pressure (evolve faster than others) in Salmonella tend to accumulate more AT-rich mutations and are eventually silenced by H-NS. Our findings may establish new approaches for a better understanding of bacterial genome evolution and function, using information from functional and comparative genomics.
细菌基因组中保守顺序的基因往往比其顺序不保守的基因进化得更慢。此外，已知 GC 含量低于驻留基因组 GC 含量的基因，会被沙门氏菌中的组蛋白样核结构蛋白（H-NS）选择性沉默。
在这项研究中，我们使用比较基因组学方法证明，在沙门氏菌中，与密切相关的细菌相比，其顺序不保守的基因（或没有同源物的基因）的平均 GC 含量明显较低，与在基因组中保留其相对位置的基因相比。此外，与保守其基因组邻居的基因相比，这些基因更容易被 H-NS 靶向。我们还观察到，不保留其基因组邻居的重复基因平均受到的选择压力较小。
我们在一个模型细菌物种中建立了基因顺序、GC 含量和基因沉默之间的强关联。这种分析表明，在沙门氏菌中，不受强选择压力（比其他基因进化得更快）的基因往往会积累更多的富含 AT 的突变，最终被 H-NS 沉默。我们的发现可能会利用功能和比较基因组学的信息，为更好地理解细菌基因组的进化和功能建立新的方法。
