MacGregor Barbara J
Department of Marine Sciences, University of North Carolina-Chapel Hill Chapel Hill, NC, USA.
Front Microbiol. 2015 Dec 16;6:1397. doi: 10.3389/fmicb.2015.01397. eCollection 2015.
The genome sequences of several giant marine sulfur-oxidizing bacteria present evidence of a possible post-transcriptional regulatory network that may have been transmitted to or from two distantly related bacteria lineages. The draft genome of a Cand. "Maribeggiatoa" filament from the Guaymas Basin (Gulf of California, Mexico) seafloor contains 169 sets of TAACTGA direct repeats and one indirect repeat, with two to six copies per set. Related heptamers are rarely or never found as direct repeats. TAACTGA direct repeats are also found in some other Beggiatoaceae, Thiocystis violascens, a range of Cyanobacteria, and five Bacteroidetes. This phylogenetic distribution suggests they may have been transmitted horizontally, but no mechanism is evident. There is no correlation between total TAACTGA occurrences and repeats per genome. In most species the repeat units are relatively short, but longer arrays of up to 43 copies are found in several Bacteroidetes and Cyanobacteria. The majority of TAACTGA repeats in the Cand. "Maribeggiatoa" Orange Guaymas (BOGUAY) genome are within several nucleotides upstream of a putative start codon, suggesting they may be binding sites for a post-transcriptional regulator. Candidates include members of the ribosomal protein S1, Csp (cold shock protein), and Csr (carbon storage regulator) families. No pattern was evident in the predicted functions of the open reading frames (ORFs) downstream of repeats, but some encode presumably essential products such as ribosomal proteins. Among these is an ORF encoding a possible alternate or modified RNA polymerase beta prime subunit, predicted to have the expected subunit interaction domains but lacking most catalytic residues. A similar ORF was found in the Thioploca ingrica draft genome, but in no others. In both species they are immediately upstream of putative sensor kinase genes with nearly identical domain structures. In the marine Beggiatoaceae, a role for the TAACTGA repeats in translational regulation is suggested. More speculatively, the putative alternate RNA polymerase subunit could be a negative transcriptional regulator.
几种巨型海洋硫氧化细菌的基因组序列表明，可能存在一个转录后调控网络，该网络可能在两个远缘细菌谱系之间传递。来自墨西哥加利福尼亚湾瓜伊马斯海盆海底的丝状念珠菌“Maribeggiatoa”的基因组草图包含169组TAACTGA直接重复序列和一组间接重复序列，每组有2至6个拷贝。相关的七聚体很少或从未作为直接重复序列被发现。TAACTGA直接重复序列也存在于其他一些贝氏硫菌科、紫色硫囊菌以及一系列蓝细菌和五种拟杆菌中。这种系统发育分布表明它们可能是通过水平基因转移传递的，但目前尚未发现明显的机制。TAACTGA的总出现次数与每个基因组中的重复序列之间没有相关性。在大多数物种中，重复单元相对较短，但在几种拟杆菌和蓝细菌中发现了长达43个拷贝的更长阵列。念珠菌“Maribeggiatoa”橙色瓜伊马斯（BOGUAY）基因组中的大多数TAACTGA重复序列位于假定起始密码子上游的几个核苷酸内，这表明它们可能是转录后调节因子的结合位点。候选因子包括核糖体蛋白S1、Csp（冷休克蛋白）和Csr（碳储存调节因子）家族的成员。重复序列下游的开放阅读框（ORF）的预测功能中没有明显的模式，但有些编码可能是必需产物，如核糖体蛋白。其中一个ORF编码一种可能的替代或修饰的RNA聚合酶β'亚基，预计具有预期的亚基相互作用结构域，但缺乏大多数催化残基。在英氏硫丝菌的基因组草图中也发现了类似的ORF，但在其他物种中未发现。在这两个物种中，它们都紧邻具有几乎相同结构域结构的假定传感器激酶基因的上游。在海洋贝氏硫菌科中，TAACTGA重复序列在翻译调控中可能发挥作用。更具推测性的是，假定的替代RNA聚合酶亚基可能是一种负转录调节因子。
