Department of Food Science, Cornell University, Ithaca, NY, United States.
Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden.
Front Cell Infect Microbiol. 2023 Jun 8;13:1060519. doi: 10.3389/fcimb.2023.1060519. eCollection 2023.
Mobilized colistin resistance genes () may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel -like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of , putative novel -like, and genes indicated that sequence similarity was insufficient to discriminate from genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the and families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, and were localized within different genomic contexts. Canonical genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, were represented by single-gene operons or adjacent to and , which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing to evolve to function in colistin resistance.
已动员的多黏菌素耐药基因 () 可能对最后一线抗菌药物多黏菌素产生耐药性，并且经常可以水平传播。 编码磷酸乙醇胺转移酶 (PET)，其与染色体编码的固有脂质修饰 PET (i-PET; 例如，EptA、EptB、CptA) 密切相关。为了深入了解 在 i-PET 背景下的进化，我们在 256 个细菌属中鉴定了 69814 种 MCR 样蛋白（通过蛋白质 BLAST 对已知 MCR 家族代表在国家生物技术信息中心 [NCBI] 非冗余蛋白质数据库中的查询获得）。随后，我们鉴定了 125 个推定的新型 - 样基因，这些基因位于与 (i) ≥1 个质粒复制子和 (ii) ≥1 个额外的抗生素耐药基因相同的连续体上（分别通过查询 PlasmidFinder 数据库和 NCBI 的国家抗生素耐药生物体数据库，通过核苷酸 BLAST 获得）。在 80%的氨基酸同一性下，这些推定的新型 MCR 样蛋白形成了 13 个簇，其中 5 个簇代表推定的新型 MCR 家族。 、推定的新型 - 样和 基因的序列相似性和最大似然系统发育表明，序列相似性不足以区分 与 基因。进化的混合效应模型 (MEME) 表明，位点和分支特异性正选择在 和 家族等位基因的进化中发挥了作用。MEME 表明，正选择在几个结构重要区域中的残基多样化中发挥了作用，包括 (i) 连接膜结合和催化周质域的桥接区域，和 (ii) 紧邻底物进入隧道的周质环。此外， 和 定位于不同的基因组环境中。典型的 基因通常在一个与双组分调节系统或紧邻 TetR 型调节剂的操纵子中染色体编码。相反， 由单基因操纵子或紧邻 和 表示，其分别编码 PAP2 家族脂酰基磷酸酶和二酰基甘油激酶。我们的数据表明， 通过各种机制，包括动员、选择和基因组环境和调节途径的多样化，可能产生“多黏菌素耐药基因”。这些机制可能改变了基因表达水平和酶活性，使 进化以发挥多黏菌素耐药性的作用。
