Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany.
Genes (Basel). 2023 Jun 21;14(7):1307. doi: 10.3390/genes14071307.
Sixteen novel circular rep-encoding DNA sequences with high sequence homologies to previously described SPHINX and BMMF sequences were isolated for the first time from non-bovine foods (pork, wild boar, chicken meat, Alaska pollock, pangasius, black tiger shrimp, apple, carrot, and sprouts from alfalfa, radish, and broccoli). The phylogenetic analysis of the full-length circular genomes grouped these together with previously described representatives of SPHINX/BMMF group 1 and 2 sequences (eight in each group). The characterization of genome lengths, genes present, and conserved structures confirmed their relationship to the known SPHINX/BMMF sequences. Further analysis of iteron-like tandem repeats of SPHINX/BMMF group 1-related genomes revealed a correlation with both full-length sequence tree branches as well as Rep protein sequence tree branches and was able to differentiate subtypes of SPHINX/BMMF group 1 members. For the SPHINX/BMMF group 2 members, a distinct grouping of sequences into two clades (A and B) with subgroups could be detected. A deeper investigation of potential functional regions upstream of the gene of the new SPHINX/BMMF group 2 sequences revealed homologies to the and regions of known plasmid groups that replicate via the rolling circle mechanism. Phylogenetic analyses were accomplished by a Rep protein sequence analysis of different ssDNA viruses, pCRESS, and plasmids with the known replication mechanism, as this yielded deeper insights into the relationship of SPHINX/BMMF group 1 and 2 Rep proteins. A clear relation of these proteins to the Rep proteins of plasmids could be confirmed. Interestingly, for SPHINX/BMMF group 2 members, the relationship to rolling circle replication plasmids could also be verified. Furthermore, a relationship of SPHINX/BMMF group 1 Rep proteins to theta-replicating plasmid Reps is discussed.
首次从非牛源食品（猪肉、野猪、鸡肉、阿拉斯加鳕鱼、巴沙鱼、黑虎虾、苹果、胡萝卜、苜蓿、萝卜和西兰花芽）中分离到 16 个新型环状 rep-encoding DNA 序列，这些序列与先前描述的 SPHINX 和 BMMF 序列具有高度序列同源性。全长环状基因组的系统发育分析将这些序列与先前描述的 SPHINX/BMMF 组 1 和 2 序列的代表序列（每组 8 个）聚为一组。基因组长度、存在的基因和保守结构的特征分析证实了它们与已知的 SPHINX/BMMF 序列的关系。进一步分析 SPHINX/BMMF 组 1 相关基因组中的类似倒位重复的串联重复，发现与全长序列树分支以及 Rep 蛋白序列树分支都存在相关性，并且能够区分 SPHINX/BMMF 组 1 成员的亚型。对于 SPHINX/BMMF 组 2 成员，可以检测到序列分为两个分支（A 和 B）和亚群。对新的 SPHINX/BMMF 组 2 序列上游基因的潜在功能区域进行深入研究，发现与已知通过滚环机制复制的质粒组的 和 区域具有同源性。通过对不同 ssDNA 病毒、pCRESS 和具有已知复制机制的质粒的 Rep 蛋白序列分析进行系统发育分析，这为 SPHINX/BMMF 组 1 和 2 Rep 蛋白的关系提供了更深入的了解。可以明确确认这些蛋白与质粒的 Rep 蛋白之间的关系。有趣的是，对于 SPHINX/BMMF 组 2 成员，也可以验证与滚环复制质粒的关系。此外，还讨论了 SPHINX/BMMF 组 1 Rep 蛋白与θ复制质粒 Reps 的关系。
