Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
PLoS One. 2012;7(1):e30287. doi: 10.1371/journal.pone.0030287. Epub 2012 Jan 27.
The mucosal microbiota is recognised as an important factor for our health, with many disease states linked to imbalances in the normal community structure. Hence, there is considerable interest in identifying the molecular basis of human-microbe interactions. In this work we investigated the capacity of microbes to thrive on mucosal surfaces, either as mutualists, commensals or pathogens, using comparative genomics to identify co-occurring molecular traits. We identified a novel domain we named M60-like/PF13402 (new Pfam entry PF13402), which was detected mainly among proteins from animal host mucosa-associated prokaryotic and eukaryotic microbes ranging from mutualists to pathogens. Lateral gene transfers between distantly related microbes explained their shared M60-like/PF13402 domain. The novel domain is characterised by a zinc-metallopeptidase-like motif and is distantly related to known viral enhancin zinc-metallopeptidases. Signal peptides and/or cell surface anchoring features were detected in most microbial M60-like/PF13402 domain-containing proteins, indicating that these proteins target an extracellular substrate. A significant subset of these putative peptidases was further characterised by the presence of associated domains belonging to carbohydrate-binding module family 5/12, 32 and 51 and other glycan-binding domains, suggesting that these novel proteases are targeted to complex glycoproteins such as mucins. An in vitro mucinase assay demonstrated degradation of mammalian mucins by a recombinant form of an M60-like/PF13402-containing protein from the gut mutualist Bacteroides thetaiotaomicron. This study reveals that M60-like domains are peptidases targeting host glycoproteins. These peptidases likely play an important role in successful colonisation of both vertebrate mucosal surfaces and the invertebrate digestive tract by both mutualistic and pathogenic microbes. Moreover, 141 entries across various peptidase families described in the MEROPS database were also identified with carbohydrate-binding modules defining a new functional context for these glycan-binding domains and providing opportunities to engineer proteases targeting specific glycoproteins for both biomedical and industrial applications.
黏膜微生物群被认为是健康的重要因素，许多疾病状态都与正常群落结构的失衡有关。因此，人们对识别人类-微生物相互作用的分子基础产生了浓厚的兴趣。在这项工作中，我们使用比较基因组学来识别共同发生的分子特征，研究了微生物在黏膜表面上作为共生体、共生体或病原体茁壮成长的能力。我们发现了一个新的结构域，我们将其命名为 M60 样/PF13402（新 Pfam 条目 PF13402），该结构域主要存在于动物宿主黏膜相关原核和真核微生物的蛋白质中，这些微生物从共生体到病原体都有。远缘微生物之间的横向基因转移解释了它们共享的 M60 样/PF13402 结构域。该新结构域的特征是锌金属肽酶样基序，与已知的病毒增强锌金属肽酶远相关。信号肽和/或细胞表面锚定特征在大多数微生物 M60 样/PF13402 结构域含有的蛋白质中被检测到，这表明这些蛋白质靶向细胞外底物。这些假定肽酶的一个显著子集进一步通过存在属于碳水化合物结合模块家族 5/12、32 和 51 以及其他糖结合结构域的相关结构域来表征，这表明这些新型蛋白酶被靶向复杂糖蛋白，如粘蛋白。体外粘蛋白酶测定表明，一种来自肠道共生菌 Bacteroides thetaiotaomicron 的含有 M60 样/PF13402 结构域的蛋白质可降解哺乳动物粘蛋白。这项研究揭示了 M60 样结构域是靶向宿主糖蛋白的肽酶。这些肽酶可能在共生体和病原体微生物在脊椎动物黏膜表面和无脊椎动物消化道的成功定植中发挥重要作用。此外，还在 MEROPS 数据库中描述的各种肽酶家族中鉴定出 141 个条目，这些条目还带有碳水化合物结合模块，为这些糖结合结构域定义了一个新的功能背景，并为工程针对特定糖蛋白的蛋白酶提供了机会，以用于生物医学和工业应用。
