Geminiviruses encode a replication initiator protein, Rep, which binds in a sequence-specific fashion to iterated DNA motifs (iterons) functioning as essential elements for virus-specific replication. By using the iterons of more than one hundred geminiviruses as heuristic devices, we have identified a Rep subdomain 8 to 10 residues in length, whose primary structure varies among viruses harboring different iterons, but which is similar among viruses with identical iterons, regardless of their differences in host range, insect vector, geographical origin or genome structure. Close analysis of this iteron-related domain (IRD) revealed consistent correlations between specific Rep residues and defined nucleotides of its cognate iteron, thus providing important insights about the molecular code which dictates the Rep preference for specific DNA sequences. A model of potential Rep-iteron contacts is proposed. The identified IRD is adjacent to a conserved motif characteristic of a superfamily of rolling-circle (RC) replication proteins, and secondary structure predictions suggest that those Rep subdomains form together the core of a novel DNA-binding domain possessing a beta-sheet as recognition subdomain, which is apparently conserved in the replication proteins of nanoviruses, circoviruses, microviruses, and a variety of ssDNA plasmids of eubacteria, archaebacteria and red algae. The evolutionary implications of these findings are discussed.

译文

双子座病毒es编码一种复制起始蛋白Rep,该蛋白以序列特异性方式与作为病毒特异性复制必需元素的迭代DNA基序 (iterons) 结合。通过使用超过100个双生病毒的迭代作为启发式设备,我们已经确定了一个长度为8到10个残基的Rep子域,其一级结构在具有不同迭代的病毒中有所不同,但在具有相同迭代的病毒中是相似的,无论它们在宿主范围,昆虫载体,地理起源或基因组结构。对该iteron相关结构域 (IRD) 的仔细分析显示,特定Rep残基与其同源iteron的定义核苷酸之间存在一致的相关性,从而提供了有关决定Rep对特定DNA序列偏好的分子代码的重要见解。提出了一种潜在代表联系人模型。鉴定出的IRD与滚动圈 (RC) 复制蛋白超家族的保守基序特征相邻,二级结构预测表明,这些Rep子域共同形成了具有 β-折叠的新型DNA结合域的核心作为识别子域,在纳米病毒,圆环病毒,微病毒以及真细菌,古细菌和红藻的各种ssDNA质粒的复制蛋白中显然是保守的。讨论了这些发现的进化意义。

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