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首页> 外文期刊>Biology Direct >Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons
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Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

机译：多样的细菌基因组编码两个基因的操纵子，其中一个是异常的I类释放因子，它可能识别除正常终止密码子以外的非典型mRNA信号

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Background While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria, there are two RFs with overlapping specificity, RF1 recognizes UA(A/G) and RF2 recognizes U(A/G)A. The hypothesis First, we hypothesize that orthologues of the E. coli K12 pseudogene prfH encode a third class-I RF that we designate RFH. Second, it is likely that RFH responds to signals other than conventional stop codons. Supporting evidence comes from the following facts: (i) A number of bacterial genomes contain prfH orthologues with no discernable interruptions in their ORFs. (ii) RFH shares strong sequence similarity with other class-I bacterial RFs. (iii) RFH contains a highly conserved GGQ motif associated with peptidyl hydrolysis activity (iv) residues located in the areas supposedly interacting with mRNA and the ribosomal decoding center are highly conserved in RFH, but different from other RFs. RFH lacks the functional, but non-essential domain 1. Yet, RFH-encoding genes are invariably accompanied by a highly conserved gene of unknown function, which is absent in genomes that lack a gene for RFH. The accompanying gene is always located upstream of the RFH gene and with the same orientation. The proximity of the 3' end of the former with the 5' end of the RFH gene makes it likely that their expression is co-regulated via translational coupling. In summary, RFH has the characteristics expected for a class-I RF, but likely with different specificity than RF1 and RF2. Testing the hypothesis The most puzzling question is which signals RFH recognizes to trigger its release function. Genetic swapping of RFH mRNA recognition components with its RF1 or RF2 counterparts may reveal the nature of RFH signals. Implications of the hypothesis The hypothesis implies a greater versatility of release-factor like activity in the ribosomal A-site than previously appreciated. A closer study of RFH may provide insight into the evolution of the genetic code and of the translational machinery responsible for termination of translation. Reviewers This article was reviewed by Daniel Wilson (nominated by Eugene Koonin), Warren Tate (nominated by Eugene Koonin), Yoshikazu Nakamura (nominated by Eugene Koonin) and Eugene Koonin.
机译：背景技术虽然所有指定氨基酸的密码子都可以被tRNA分子普遍识别，但信号翻译终止的密码子被称为I类释放因子（RF）的蛋白质识别。在大多数真核生物和古细菌中，单个RF完成了所有三个终止密码子的终止。在大多数细菌中，有两个RF具有重叠的特异性，RF1识别UA（A / G），RF2识别U（A / G）A。假设首先，我们假设大肠杆菌K12假基因prfH的直向同源物编码第三类I RF，我们将其指定为RFH。其次，RFH可能会响应常规终止密码子以外的信号。有力的证据来自以下事实：（i）许多细菌基因组包含prfH直向同源物，其ORF没有明显的中断。 （ii）RFH与其他I类细菌RF具有很强的序列相似性。 （iii）RFH含有与肽水解活性相关的高度保守的GGQ基序（iv）位于RFH和核糖体解码中心据推测与RNA相互作用的区域中的残基在RFH中高度保守，但不同于其他RF。 RFH缺乏功能性但非必需的结构域1。然而，RFH编码基因总是伴随着高度保守的未知功能基因，而该基因在缺少RFH基因的基因组中不存在。伴随基因始终位于RFH基因的上游，且方向相同。前者的3'末端与RFH基因的5'末端接近使得它们的表达可能通过翻译偶联而共同调控。总之，RFH具有I类RF所期望的特性，但可能具有与RF1和RF2不同的特异性。测试假设最令人困惑的问题是RFH识别出哪些信号触发其释放功能。 RFH mRNA识别组件与其RF1或RF2对应物的遗传交换可能揭示RFH信号的性质。假设的含义假设意味着在核糖体A位点，释放因子样活性的多功能性高于以前的认识。对RFH的深入研究可能会提供有关遗传密码和负责翻译终止的翻译机制进化的见解。审阅者本文由Daniel Wilson（由Eugene Koonin提名），Warren Tate（由Eugene Koonin提名），Yoshikazu Nakamura（由Eugene Koonin提名）和Eugene Koonin进行了评论。

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