Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains.
Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains.
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DOI：
10.1016/j.jbc.2023.105494
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发表时间：
2024-01
影响因子：
4.8
通讯作者：
Mesnage, Stephane
中科院分区：
文献类型：
--
作者：
Alaman-Zarate, Marcel G;Rady, Brooks J;Evans, Caroline A;Pian, Brooke;Greetham, Darren;Marecos-Ortiz, Sabrina;Dickman, Mark J;Lidbury, Ian D E A;Lovering, Andrew L;Barstow, Buz M;Mesnage, Stephane
肽聚糖是细菌细胞包膜的重要组成部分，它含有被短肽茎取代的糖链。多肽茎由D，D-转肽酶聚合，在供体茎的第四位氨基酸和受体茎的第三个残基(4-3个交联键)之间建立键。一些细菌肽聚糖还含有3-3个交联键，这是由另一类称为L的酶形成的，D-转肽酶含有YkuD催化结构域。在这项工作中，我们研究了不寻常的细菌1-3肽聚糖交联物的形成。我们描述了一个版本的PGFinder软件，它可以识别1-3个交联链，并报告氧化葡糖杆菌(醋酸杆菌家族中的一种模式生物)的高分辨率肽聚糖结构。我们发现甘草多肽含有由单一丙氨酸组成的多肽茎，以及C-末端含有不寻常氨基酸的几个二肽茎。利用生物信息学的方法，我们从转座子文库中鉴定出一株交链急剧减少的加氧酶突变体。通过在异源宿主中的互补实验和重组蛋白的生产，我们鉴定了一个L，D-转肽酶，其结构域与YkuD结构域远相关，负责这些非典型反应。这项工作回顾了L，D-转肽酶，一个多功能的酶家族，在细菌肽聚糖重塑中发挥关键作用的酶的能力。
Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases which contain a YkuD catalytic domain. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software that can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a bioinformatics approach, we identified a G. oxydans mutant from a transposon library with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling.