Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
Microb Genom. 2020 Nov;6(11). doi: 10.1099/mgen.0.000452.
Several monosaccharides constitute naturally occurring glycans, but it is uncertain whether they constitute a universal set like the alphabets of proteins and DNA. Based on the available experimental observations, it is hypothesized herein that the glycan alphabet is not universal. Data on the presence/absence of pathways for the biosynthesis of 55 monosaccharides in 12 939 completely sequenced archaeal and bacterial genomes are presented in support of this hypothesis. Pathways were identified by searching for homologues of biosynthesis pathway enzymes. Substantial variations were observed in the set of monosaccharides used by organisms belonging to the same phylum, genera and even species. Monosaccharides were grouped as common, less common and rare based on their prevalence in Archaea and Bacteria. It was observed that fewer enzymes are sufficient to biosynthesize monosaccharides in the common group. It appears that the common group originated before the formation of the three domains of life. In contrast, the rare group is confined to a few species in a few phyla, suggesting that these monosaccharides evolved much later. Fold conservation, as observed in aminotransferases and SDR (short-chain dehydrogenase reductase) superfamily members involved in monosaccharide biosynthesis, suggests neo- and sub-functionalization of genes led to the formation of the rare group monosaccharides. The non-universality of the glycan alphabet begets questions about the role of different monosaccharides in determining an organism's fitness.
几种单糖构成了天然存在的聚糖，但它们是否构成了像蛋白质和 DNA 的字母一样通用的集合还不确定。基于现有的实验观察结果，本文假设聚糖字母不是通用的。在此提出了支持这一假设的数据，这些数据涉及在 12939 个完全测序的古菌和细菌基因组中，55 种单糖生物合成途径的存在/缺失情况。通过搜索生物合成途径酶的同源物来识别途径。在同一门、属甚至种的生物体中，观察到用于生物体的单糖集合存在很大差异。根据它们在古菌和细菌中的普遍性，将单糖分为常见、较少见和罕见。观察到，生物合成常见单糖所需的酶较少。似乎常见的单糖组起源于生命的三个领域形成之前。相比之下，罕见的单糖组仅局限于少数几个门的少数几个物种，表明这些单糖进化得更晚。在参与单糖生物合成的氨基转移酶和 SDR（短链脱氢酶还原酶）超家族成员中观察到的折叠保守性表明，基因的新功能和亚功能化导致了罕见单糖组的形成。聚糖字母的非通用性引发了关于不同单糖在决定生物体适应性方面的作用的问题。
