Balaji, P. V. | Search bioRxiv

bioRxiv2020

Is there a universal glycan alphabet?

Several monosaccharides constitute naturally occurring glycans but it is uncertain if 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 12939 completely sequenced archaeal and bacterial genomes are presented in support of this hypothesis. Pathways were identified by searching for homologs of biosynthesis pathway enzymes. Substantial variations are observed in the set of monosaccharides used by organisms belonging to the same phylum, genera and even species. Monosaccharides are grouped as Common, Less Common and Rare based on their prevalence in Archaea and Bacteria. It is observed that fewer enzymes suffice to biosynthesize the Common group. It appears that the Common group originated before the formation of three domains of life. In contrast, the Rare group are confined to a few species in a few phyla, suggesting that they evolved much later. Fold conservation, as observed in aminotransferases and SDR superfamily members involved in monosaccharide biosynthesis, suggests neo- and sub-functionalization of genes leading to the formation of Rare group monosaccharides. Non-universality of the glycan alphabet begets questions about the role of different monosaccharides in determining an organisms fitness. Impact statementCarbohydrates, nucleic acids and proteins are important classes of biological macromolecules. The universality of DNA, RNA and protein alphabets has been established beyond doubt. However, the universality of glycan alphabet is unknown primarily because of the challenges associated with the elucidation of glycan structures. This has precluded a comprehensive investigation of glycan alphabet. To address this challenge, we have identified the prevalence of 55 monosaccharide biosynthesis pathways in 12939 completely sequenced archaeal and bacterial genomes by searching for homologs of biosynthesis pathway enzymes using HMM profiles, and in a few cases, BLASTp. This revealed that the glycan alphabet is highly variable; in fact, significant differences are found even among different strains of a species. Possible implications of this variability may be significant in understanding the evolution of Archaea and Bacteria in diverse and competitive environments. Factors that drive the choice of monosaccharides used by an organism need to be investigated, and will be of interest in understanding host-pathogen interactions. Additionally, the knowledge of glycan alphabet can be employed for structural characterization / validation of glycans inferred using mass spectrometry. Knowledge of unique monosaccharides and biosynthetic enzymes can also be used as novel drug targets against human pathogens. Data summaryThe curated set of proteins used in this study, with domain assignment, is listed in supplementary_data.xlsx. Corresponding 396 references with evidence of experimental characterization are included in supplementary material. Results of genome scan which include predictions of monosaccharides as well as the biosynthesis pathway enzymes is available at http://www.bio.iitb.ac.in/glycopathdb/ including the aforementioned information. Python script used to scan genomes to search for monosaccharide biosynthesis pathways are available on request.

genomics↗

bioRxiv2019

Highly clade-specific biosynthesis of rhamnose: present in all plants and in only 42% of prokaryotes.Only Pseudomonas uses both D- and L-rhamnose

Rhamnose is a constituent of lipo- and capsular polysaccharides, and cell surface glycoproteins. L-rhamnose is biosynthesized by the rml or udp pathway and D-rhamnose by the gdp pathway. Disruption of its biosynthesis affects survival, colonisation, etc. Rhamnosides are commercially important in pharmaceutical and cosmetics industries. HMM profiles were used to investigate the prevalence of the three pathways in completely sequenced genomes and metagenomes. The three pathways are mutually exclusive except in Pseudomonas which has both rml and gdp pathways. The rml pathway is restricted to bacteria (42% genomes), archaea (21%) and bacteriophages, and absent in eukaryotes and other viruses. The gdp pathway is restricted to Pseudomonas and Aneurinibacillus. The udp pathway is primarily found in plants, fungi and algae, and in human faecal metagenomic samples. The rml pathway is found in >40% genomes of Actinobacteria, Bacteroidetes, Crenarchaeota, Cyanobacteria, Fusobacteria and Proteobacteria but in <20% genomes of Chlamydiae, Euryarchaeota and Tenericutes. The udp pathway is found in all genomes of Streptophyta, <=25% genomes of Ascomycota and Chordata, and none of the genomes of Arthropoda and Basidiomycota. Some genera which lack any of these pathways are Chlamydia, Helicobacter, Listeria, Mycoplasma, Pasteurella, Rickettsia and Staphylococcus. Organisms such as E. coli and Salmonella enterica showed significant strain-specific differences in the presence/absence of rhamnose pathways. Identification of rhamnose biosynthesis genes facilitates profiling their expression pattern, and in turn, better understanding the physiological role of rhamnose. Knowledge of phylogenetic distribution of biosynthesis pathways helps in fine graining the taxonomic profiling of metagenomes. AUTHOR SUMMARYIn the present study, we have investigated the prevalence of rhamnose biosynthesis pathways in completely sequenced genomes and metagenomes. It is observed that the prevalence of rhamnose is highly clade specific: present in all plants but in less than half of all prokaryotes. Among chordates, only the Chinese rufous horseshoe bat has rhamnose biosynthesis pathway and this exclusive presence is quite baffling. The effect of disrupting rhamnose biosynthesis has been reported in a few prokaryotes and all these cases pointed to the essentiality of rhamnose for critical physiological processes such as survival, colonisation, etc. In this background, it is surprising that many of the prokaryotes such as Escherichia coli and Salmonella enterica show significant strain-specific differences in the presence/absence of rhamnose pathway. This study will facilitate the experimental characterization of rhamnose biosynthesis genes in organisms where this pathway has not been characterised yet, eventually leading to the elucidation of the biological role of rhamnose. Phylum-, genus-, species- and strain-level differences found with respect to presence of rhamnose biosynthesis pathway genes can be used as a tool for taxonomic profiling of metagenome samples. This study could also annotate a significant number of orphan proteins in the TrEMBL database.

genomics↗