"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system

Microbiome
A E NaasPhillip B Pope

Abstract

In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrange...Continue Reading

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Citations

Jul 1, 2020·International Journal of Systematic and Evolutionary Microbiology·Aharon OrenMartha E Trujillo
Apr 11, 2020·Frontiers in Microbiology·Rosalind A GilbertEleanor Jameson
Aug 8, 2020·Methods : a Companion to Methods in Enzymology·Thea Os AndersenPhillip B Pope
Feb 8, 2021·International Journal of Biological Macromolecules·Shohreh AriaeenejadGhasem Hosseini Salekdeh
May 27, 2021·Environmental Microbiology Reports·Lauren S McKeeJohan Larsbrink
Jan 18, 2022·Applied Microbiology and Biotechnology·Feng JiangTongzuo Zhang

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Methods Mentioned

BETA
gene knock-out
protein assay
acetylation
gel filtration
X-ray

Software Mentioned

iMOSFLM
PHASER
SignalP
HMMER
PHENIX
SCALA
RAxML
Coot
HMMERv3
dbCAN

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