Kardos Gábor, Laczkó Levente, Kaszab Eszter, Timmer Bálint, Szarka Krisztina, Prépost Eszter, Bányai Krisztián
Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary.
One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary.
Antibiotics (Basel). 2024 Jun 21;13(7):573. doi: 10.3390/antibiotics13070573.
The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage were aligned, and phylogenetic trees were reconstructed. The ligase gene phylogenies were highly similar for both queries, revealing two major clusters. One contained [[vanA:vanM][vanB:vanD]vanF] and related proteins, with proteins from different Bacillaceae, mostly from spp., in basal positions to all, except vanB. Ligases from streptomycetes formed the other cluster. The relative positions of vanH and vanX differed from those of the associated ligases, but the basal position of the spp. and the separation of proteins of origin were similar. The accessory genes vanW, vanY and vanZ were associated with vanB, vanA/vanM and vanA, respectively; the basal branches were always proteins from different Bacillaceae but never from streptomycetes. Multiple homologs of the regulatory genes vanR and vanS were found in the genomes; those associated with the different ligases were unique to the ligases. Similarly to the accessory genes, vanRS from Bacillales and Clostridia, but never from streptomycetes, was found in the basal positions. In conclusion, the core genes vanA/B/D/F/M, vanH and vanX originate most probably from glycopeptide-producing streptomycetes, with spp. (or other Bacillaceae) mediating the transfer, while the accessory genes and the regulatory apparatus probably originate from these Bacillaceae.
研究了糖肽抗性蛋白的系统发育关系。以vanA、vanB、vanR和vanS的氨基酸序列作为查询序列，在NCBI RefSeq数据库中搜索细菌基因组。对氨基酸同一性>60%且查询覆盖率>90%的命中结果进行比对，并重建系统发育树。两个查询序列的连接酶基因系统发育高度相似，揭示了两个主要聚类。一个聚类包含[[vanA:vanM][vanB:vanD]vanF]及相关蛋白，来自不同芽孢杆菌科的蛋白，大多来自 spp.，除vanB外，在所有其他蛋白的基部位置。链霉菌的连接酶形成另一个聚类。vanH和vanX的相对位置与相关连接酶的不同，但 spp.的基部位置以及 来源蛋白的分离情况相似。辅助基因vanW、vanY和vanZ分别与vanB、vanA/vanM和vanA相关；基部分支总是来自不同芽孢杆菌科的蛋白，但从未来自链霉菌。在基因组中发现了调控基因vanR和vanS的多个同源物；与不同连接酶相关的同源物是连接酶所特有的。与辅助基因类似，在基部位置发现了来自芽孢杆菌目和梭菌属但从未来自链霉菌的vanRS。总之，核心基因vanA/B/D/F/M、vanH和vanX很可能起源于产生糖肽的链霉菌，由 spp.（或其他芽孢杆菌科）介导转移，而辅助基因和调控装置可能起源于这些芽孢杆菌科。
