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Related Concept Videos

Biosynthesis of Polysaccharides01:26

Biosynthesis of Polysaccharides

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Polysaccharides such as glycogen and starch are synthesized from nucleoside diphosphate sugars, primarily uridine diphosphate glucose (UDPG) and adenosine diphosphate glucose (ADPG). These activated glucose donors act as key intermediates in carbohydrate metabolism and biosynthesis. UDPG primarily involves glycogen synthesis in animals and many bacteria, while ADPG plays a fundamental role in starch synthesis in plants and certain bacteria.UDPG is formed when glucose-1-phosphate reacts with...
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Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
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 Every plant cell has a cell wall that protects the cell, provides structural support, and gives the cell shape. Cellulose, the main structural component of the plant cell wall, makes up over 30% of plant matter. It is the most abundant organic compound on earth.  Cellulose is an unbranched polysaccharide composed of linear chains of glucose molecules linked by β (1→4) glycosidic bonds.
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PULDB: the expanded database of Polysaccharide Utilization Loci.

Nicolas Terrapon1,2, Vincent Lombard1,2, Élodie Drula1,2

  • 1Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.

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The updated Polysaccharide Utilization Loci (PUL) database (PULDB) now includes more genomes and enhanced gene annotations for better visualization and analysis of PULs. A new alignment tool aids in identifying similar PULs across diverse species.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • The Polysaccharide Utilization Loci (PUL) database (PULDB) was established in 2015 to catalog PULs in Bacteroidetes species from the human gut.
  • PULDB has expanded significantly, now encompassing 820 genomes from diverse environments and taxonomic groups.

Purpose of the Study:

  • To update and enhance the PULDB with expanded genomic data and improved functional annotations.
  • To provide advanced tools for visualizing, browsing, and analyzing PULs and associated genes.

Main Methods:

  • Integration of 820 genomes from various environments and taxonomic ranges.
  • Expansion of gene annotations to include functionally relevant protein families near PULs.
  • Development of a PUL alignment tool for sequence-independent comparison.
  • Implementation of 'CAZyme cluster' predictions for incomplete genome assemblies.

Main Results:

  • PULDB now provides access to a broader range of genomic data and taxonomic diversity.
  • Enhanced annotations include sulfatases, proteases, transporters, and more, improving PUL context.
  • New features facilitate literature mining for RNAseq data and biochemical analyses of PULs.
  • The PUL alignment tool enables efficient retrieval of similar PULs based on functional families.

Conclusions:

  • The updated PULDB offers a more comprehensive resource for studying polysaccharide utilization systems.
  • Enhanced visualization and analysis tools improve the discovery and characterization of PULs.
  • PULDB supports research across diverse microbial communities and environments.