Pansegrau W, Lanka E, Barth P T, Figurski D H, Guiney D G, Haas D, Helinski D R, Schwab H, Stanisich V A, Thomas C M
Max-Planck-Institut für Molekulare Genetik Abteilung Schuster, Berlin, F.R.G.
J Mol Biol. 1994 Jun 24;239(5):623-63. doi: 10.1006/jmbi.1994.1404.
The IncP alpha promiscuous plasmid (R18, R68, RK2, RP1 and RP4) comprises 60,099 bp of nucleotide sequence, encoding at least 74 genes. About 40 kb of the genome, designated the IncP core and including all essential replication and transfer functions, can be aligned with equivalent sequences in the IncP beta plasmid R751. The compiled IncP alpha sequence revealed several previously unidentified reading frames that are potential genes. IncP alpha plasmids carry genetic information very efficiently: the coding sequences of the genes are closely packed but rarely overlap, and occupy almost 86% of the genome's nucleotide sequence. All of the 74 genes should be expressed, although there is as yet experimental evidence for expression of only 60 of them. Six examples of tandem-in-frame initiation sites specifying two gene products each are known. Two overlapping gene arrangements occupy different reading frames of the same region. Intergenic regions include most of the 25 promoters; transcripts are usually polycistronic. Translation of most of the open reading frames seems to be initiated independently, each from its own ribosomal binding and initiation site, although, a few cases of coupled translation have been reported. The most frequently used initiation codon is AUG but translation for a few open reading frames begins at GUG or UUG. The most common stop-codon is UGA followed by UAA and then UAG. Regulatory circuits are complex and largely dependent on two components of the central control operon. KorA and KorB are transcriptional repressors controlling at least seven operons. KorA and KorB act synergistically in several cases by recognizing and binding to conserved nucleotide sequences. Twelve KorB binding sites were found around the IncP alpha sequence and these are conserved in R751 (IncP beta) with respect to both sequence and location. Replication of IncP alpha plasmids requires oriV and the plasmid-encoded initiator protein TrfA in combination with the host-encoded replication machinery. Conjugative plasmid transfer depends on two separate regions occupying about half of the genome. The primary segregational stability system designated Par/Mrs consists of a putative site-specific recombinase, a possible partitioning apparatus and a post-segregational lethality mechanism, all encoded in two divergent operons. Proteins related to the products of F sop and P1 par partitioning genes are separately encoded in the central control operon.
IncPα 泛宿主质粒（R18、R68、RK2、RP1 和 RP4）包含 60,099 个碱基对的核苷酸序列，编码至少 74 个基因。基因组中约 40 kb 的区域，称为 IncP 核心区域，包含所有必需的复制和转移功能，可与 IncPβ 质粒 R751 中的等效序列比对。汇编的 IncPα 序列揭示了几个以前未鉴定的潜在基因读码框。IncPα 质粒非常有效地携带遗传信息：基因的编码序列紧密排列但很少重叠，几乎占据了基因组核苷酸序列的 86%。所有 74 个基因都应该表达，尽管目前只有 60 个基因有表达的实验证据。已知有六个串联框内起始位点的例子，每个位点指定两个基因产物。两个重叠的基因排列占据同一区域的不同读码框。基因间区域包括 25 个启动子中的大多数；转录本通常是多顺反子的。大多数开放阅读框的翻译似乎是独立起始的，每个都有自己的核糖体结合和起始位点，不过，也有一些偶联翻译的报道。最常用的起始密码子是 AUG，但少数开放阅读框的翻译从 GUG 或 UUG 开始。最常见的终止密码子是 UGA，其次是 UAA，然后是 UAG。调控回路很复杂，很大程度上依赖于中央控制操纵子的两个组件。KorA 和 KorB 是转录抑制因子，控制至少七个操纵子。KorA 和 KorB 在几种情况下通过识别并结合保守核苷酸序列协同作用。在 IncPα 序列周围发现了 12 个 KorB 结合位点，这些位点在 R751（IncPβ）中在序列和位置上都是保守的。IncPα 质粒的复制需要 oriV 和质粒编码的起始蛋白 TrfA 与宿主编码的复制机制相结合。接合性质粒转移取决于占据基因组约一半的两个独立区域。主要的分离稳定性系统 Par/Mrs 由一个假定的位点特异性重组酶、一个可能的分配装置和一个后分离致死机制组成，所有这些都编码在两个不同的操纵子中。与 F sop 和 P1 par 分配基因产物相关的蛋白质分别编码在中央控制操纵子中。
