Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz-PR, Algacyr Munhoz Mader street, 3775, Curitiba, Paraná, Brazil.
Graduation Program on Bioinformatics - Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, Brazil.
Microb Genom. 2021 Apr;7(4). doi: 10.1099/mgen.0.000563.
Nonulosonic acids (NulOs) are a group of nine-carbon monosaccharides with different functions in nature. -acetylneuraminic acid (Neu5Ac) is the most common NulO. It covers the membrane surface of all human cells and is a central molecule in the process of self-recognition via SIGLECS receptors. Some pathogenic bacteria escape the immune system by copying the sialylation of the host cell membrane. Neu5Ac production in these bacteria is catalysed by the enzyme NeuB. Some bacteria can also produce other NulOs named pseudaminic and legionaminic acids, through the NeuB homologues PseI and LegI, respectively. In Opisthokonta eukaryotes, the biosynthesis of Neu5Ac is catalysed by the enzyme NanS. In this study, we used publicly available data of sequences of NulOs synthases to investigate its distribution within the three domains of life and its relationship with pathogenic bacteria. We mined the KEGG database and found 425 NeuB sequences. Most NeuB sequences (58.74 %) from the KEGG orthology database were classified as from environmental bacteria; however, sequences from pathogenic bacteria showed higher conservation and prevalence of a specific domain named SAF. Using the HMM profile we identified 13 941 NulO synthase sequences in UniProt. Phylogenetic analysis of these sequences showed that the synthases were divided into three main groups that can be related to the lifestyle of these bacteria: (I) predominantly environmental, (II) intermediate and (III) predominantly pathogenic. NeuB was widely distributed in the groups. However, LegI and PseI were more concentrated in groups II and III, respectively. We also found that PseI appeared later in the evolutionary process, derived from NeuB. We use this same methodology to retrieve sialic acid synthase sequences from Archaea and Eukarya. A large-scale phylogenetic analysis showed that while the Archaea sequences are spread across the tree, the eukaryotic NanS sequences were grouped in a specific branch in group II. None of the bacterial NanS sequences grouped with the eukaryotic branch. The analysis of conserved residues showed that the synthases of Archaea and Eukarya present a mutation in one of the three catalytic residues, an E134D change, related to a reference sequence. We also found that the conservation profile is higher between NeuB of pathogenic bacteria and NanS of eukaryotes than between NeuB of environmental bacteria and NanS of eukaryotes. Our large-scale analysis brings new perspectives on the evolution of NulOs synthases, suggesting their presence in the last common universal ancestor.
非还原性九碳单糖（NulOs）是一组具有不同功能的九碳单糖。N-乙酰神经氨酸（Neu5Ac）是最常见的 NulO。它覆盖了所有人类细胞的膜表面，是通过 SIGLECS 受体进行自我识别的中心分子。一些致病菌通过复制宿主细胞膜的唾液酸化来逃避免疫系统。这些细菌中 Neu5Ac 的产生是由酶 NeuB 催化的。一些细菌还可以通过 NeuB 同源物 PseI 和 LegI 分别产生其他 NulOs，命名为 pseudaminic 和 legionaminic 酸。在 Opisthokonta 真核生物中，Neu5Ac 的生物合成由酶 NanS 催化。在这项研究中，我们使用了公开可用的 NulOs 合成酶序列数据来研究其在生命的三个领域中的分布及其与致病菌的关系。我们从 KEGG 数据库中挖掘到 425 个 NeuB 序列。KEGG 直系同源数据库中大多数 NeuB 序列（58.74%）被归类为环境细菌，但来自致病菌的序列显示出更高的保守性和特定结构域 SAF 的普遍性。使用 HMM 图谱，我们在 UniProt 中鉴定出了 13941 个 NulO 合成酶序列。对这些序列的系统发育分析表明，合成酶分为三个主要组，可以与这些细菌的生活方式相关：（I）主要是环境，（II）中间和（III）主要是致病。NeuB 在这些组中广泛分布。然而，LegI 和 PseI 分别更集中在组 II 和组 III。我们还发现 PseI 出现在进化过程的后期，源自 NeuB。我们使用相同的方法从古菌和真核生物中检索唾液酸合酶序列。大规模的系统发育分析表明，虽然古菌序列分布在整个树中，但真核生物 NanS 序列在组 II 的一个特定分支中分组。没有一个细菌 NanS 序列与真核生物分支分组。保守残基分析表明，古菌和真核生物的合成酶在三个催化残基之一发生突变，即 E134D 变化，与参考序列有关。我们还发现，致病性细菌的 NeuB 与真核生物的 NanS 之间的保守程度高于环境细菌的 NeuB 与真核生物的 NanS 之间的保守程度。我们的大规模分析为 NulOs 合成酶的进化带来了新的视角，表明它们存在于最后的共同祖先中。
