Evidence map›Paper›PMID 36048714›Full record

ArticleGlycobiology2022

Simple and practical sialoglycan encoding system reveals vast diversity in nature and identifies a universal sialoglycan-recognizing probe derived from AB5 toxin B subunits.

Aniruddha Sasmal, Naazneen Khan, Zahra Khedri, Benjamin P Kellman, Saurabh Srivastava, Andrea Verhagen, Hai Yu, Anders Bech Bruntse, Sandra Diaz, Nissi Varki and 6 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Glycobiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.4field-weighted citation impact, top 43% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 5 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. The diverse landscape of AB5-type toxins.Engineering microbiology · 2023
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors at 4 institutions in 2 countries.

Aniruddha SasmalGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Naazneen KhanGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Zahra KhedriGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Benjamin P KellmanDepartment of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.
Saurabh SrivastavaGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Andrea VerhagenGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Hai YuDepartment of Chemistry, University of California Davis, CA 95616, USA.
Anders Bech BruntseDepartment of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.
Sandra DiazGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Nissi VarkiGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Travis BeddoeDepartment of Animal, Plant and Soil Science and Centre for AgriBioscience, La Trobe University, Bundoora, Victoria 3086, Australia.ORCID 0000-0003-4550-2277
Adrienne W PatonResearch Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.
James C PatonResearch Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.
Xi ChenDepartment of Chemistry, University of California Davis, CA 95616, USA.
Nathan E LewisGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
Ajit VarkiGlycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA.
University of California San Diego · USThe University of Adelaide · AUUniversity of California, Davis · USLa Trobe University · AU

Funding

BIOSYNTHESIS AND REGULATION OF SUBSTITUTED SIALIC ACIDSR01GM032373 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI VARKI, AJIT P · 1985 to 2022
$6.9M
Unraveling the mammalian secretory pathway through systems biology and algorithm developmentR35GM119850 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LEWIS, NATHAN ENOCH · 2016 to 2025
$4.3M
NIGMS NIH HHS R01 GM032373NIGMS NIH HHS R35 GM119850
6 · The paper itself

Abstract

Vertebrate sialic acids (Sias) display much diversity in modifications, linkages, and underlying glycans. Slide microarrays allow high-throughput explorations of sialoglycan-protein interactions. A microarray presenting ~150 structurally defined sialyltrisaccharides with various Sias linkages and modifications still poses challenges in planning, data sorting, visualization, and analysis. To address these issues, we devised a simple 9-digit code for sialyltrisaccharides with terminal Sias and underlying two monosaccharides assigned from the nonreducing end, with 3 digits assigning a monosaccharide, its modifications, and linkage. Calculations based on the encoding system reveal >113,000 likely linear sialyltrisaccharides in nature. Notably, a biantennary N-glycan with 2 terminal sialyltrisaccharides could thus have >1010 potential combinations and a triantennary N-glycan with 3 terminal sequences, >1015 potential combinations. While all possibilities likely do not exist in nature, sialoglycans encode enormous diversity. While glycomic approaches are used to probe such diverse sialomes, naturally occurring bacterial AB5 toxin B subunits are simpler tools to track the dynamic sialome in biological systems. Sialoglycan microarray was utilized to compare sialoglycan-recognizing bacterial toxin B subunits. Unlike the poor correlation between B subunits and species phylogeny, there is stronger correlation with Sia-epitope preferences. Further supporting this pattern, we report a B subunit (YenB) from Yersinia enterocolitica (broad host range) recognizing almost all sialoglycans in the microarray, including 4-O-acetylated-Sias not recognized by a Yersinia pestis orthologue (YpeB). Differential Sia-binding patterns were also observed with phylogenetically related B subunits from Escherichia coli (SubB), Salmonella Typhi (PltB), Salmonella Typhimurium (ArtB), extra-intestinal E.coli (EcPltB), Vibrio cholera (CtxB), and cholera family homologue of E. coli (EcxB).

Indexed as

Bacterial ToxinsEscherichia coliCholera ToxinPolysaccharidesSalmonella typhiSialic AcidsBacterial ToxinsCholera ToxinPolysaccharidesSialic Acidsbacterial toxinglycan codingglycan microarraytoxin B subunitYersinia enterocolitica

Identifiers

PMID36048714
PMCPMC9680115
OpenAlexW3213197098

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.