Literature DB >> 34351427

GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases.

Rahil Taujale1,2, Saber Soleymani3, Amitabh Priyadarshi3, Aarya Venkat4, Wayland Yeung1, Krzysztof J Kochut3, Natarajan Kannan1,4.   

Abstract

Glycosyltransferases (GTs) play a central role in sustaining all forms of life through the biosynthesis of complex carbohydrates. Despite significant strides made in recent years to establish computational resources, databases and tools to understand the nature and role of carbohydrates and related glycoenzymes, a data analytics framework that connects the sequence-structure-function relationships to the evolution of GTs is currently lacking. This hinders the characterization of understudied GTs and the synthetic design of GTs for medical and biotechnology applications. Here, we present GTXplorer as an integrated platform that presents evolutionary information of GTs adopting a GT-A fold in an intuitive format enabling in silico investigation through comparative sequence analysis to derive informed hypotheses about their function. The tree view mode provides an overview of the evolutionary relationships of GT-A families and allows users to select phylogenetically relevant families for comparisons. The selected families can then be compared in the alignment view at the residue level using annotated weblogo stacks of the GT-A core specific to the selected clade, family, or subfamily. All data are easily accessible and can be downloaded for further analysis. GTXplorer can be accessed at https://vulcan.cs.uga.edu/gtxplorer/ or from GitHub at https://github.com/esbgkannan/GTxplorer to deploy locally. By packaging multiple data streams into an accessible, user-friendly format, GTXplorer presents the first evolutionary data analytics platform for comparative glycomics.
© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Entities:  

Keywords:  evolution; glycosyltransferases; phylogeny; visualization; web tool

Mesh:

Substances:

Year:  2021        PMID: 34351427      PMCID: PMC8684471          DOI: 10.1093/glycob/cwab082

Source DB:  PubMed          Journal:  Glycobiology        ISSN: 0959-6658            Impact factor:   5.954


  27 in total

Review 1.  Glycosyltransferase engineering for carbohydrate synthesis.

Authors:  John B McArthur; Xi Chen
Journal:  Biochem Soc Trans       Date:  2016-02       Impact factor: 5.407

2.  Glycosyltransferase genes that cause monogenic congenital disorders of glycosylation are distinct from glycosyltransferase genes associated with complex diseases.

Authors:  Hiren J Joshi; Lars Hansen; Yoshiki Narimatsu; Hudson H Freeze; Bernard Henrissat; Eric Bennett; Hans H Wandall; Henrik Clausen; Katrine T Schjoldager
Journal:  Glycobiology       Date:  2018-05-01       Impact factor: 4.313

3.  Multiple cellulose synthase catalytic subunits are required for cellulose synthesis in Arabidopsis.

Authors:  N G Taylor; S Laurie; S R Turner
Journal:  Plant Cell       Date:  2000-12       Impact factor: 11.277

4.  Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.

Authors:  Serge Pérez; Thibault Tubiana; Anne Imberty; Marc Baaden
Journal:  Glycobiology       Date:  2014-12-04       Impact factor: 4.313

Review 5.  Emerging structural insights into glycosyltransferase-mediated synthesis of glycans.

Authors:  Kelley W Moremen; Robert S Haltiwanger
Journal:  Nat Chem Biol       Date:  2019-08-19       Impact factor: 15.040

6.  NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

Authors:  Kim D Pruitt; Tatiana Tatusova; Donna R Maglott
Journal:  Nucleic Acids Res       Date:  2006-11-27       Impact factor: 16.971

7.  CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.

Authors:  Aron Marchler-Bauer; Yu Bo; Lianyi Han; Jane He; Christopher J Lanczycki; Shennan Lu; Farideh Chitsaz; Myra K Derbyshire; Renata C Geer; Noreen R Gonzales; Marc Gwadz; David I Hurwitz; Fu Lu; Gabriele H Marchler; James S Song; Narmada Thanki; Zhouxi Wang; Roxanne A Yamashita; Dachuan Zhang; Chanjuan Zheng; Lewis Y Geer; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

8.  PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

Authors:  Anita Sarkar; Serge Pérez
Journal:  BMC Bioinformatics       Date:  2012-11-14       Impact factor: 3.169

9.  Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases.

Authors:  Rahil Taujale; Aarya Venkat; Liang-Chin Huang; Zhongliang Zhou; Wayland Yeung; Khaled M Rasheed; Sheng Li; Arthur S Edison; Kelley W Moremen; Natarajan Kannan
Journal:  Elife       Date:  2020-04-01       Impact factor: 8.140

10.  Global analysis of human glycosyltransferases reveals novel targets for pancreatic cancer pathogenesis.

Authors:  Rohitesh Gupta; Frank Leon; Christopher M Thompson; Ramakrishna Nimmakayala; Saswati Karmakar; Palanisamy Nallasamy; Seema Chugh; Dipakkumar R Prajapati; Satyanarayana Rachagani; Sushil Kumar; Moorthy P Ponnusamy
Journal:  Br J Cancer       Date:  2020-03-19       Impact factor: 7.640

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