Dataset Information

Hemicellulose utilisation in Flavobacterium

ABSTRACT: The plant hemicellulose xyloglucan (XyG) is secreted from the roots of numerous plant species, including cereals, and contributes towards soil aggregate formation in terrestrial systems. Whether XyG represents a key nutrient for plant-associated bacteria is unclear. The phylum Bacteroidota are abundant in the plant microbiome and provide several beneficial functions for their host. However, the metabolic and genomic traits underpinning their success remain poorly understood. Here, we employed whole-cell proteomics to determine the molecular mechanisms responsible for xyloglucan utilisation in two model Flavobacterium species, Flavobacterium johnsoniae DSM2064 and Flavobacterium sp. OSR005. We identified the occurrence of a distinct and conserved gene cluster, referred to as the Xyloglucan Utilisation Loci (XyGUL). Flavobacterium XyGUL is a hybrid of the molecular machinery found in gut Bacteroides spp., Cellvibrio japonicus, and the plant pathogen Xanthomonas. Combining protein biochemistry, computational modelling and phylogenetics, we identified a mutation in the enzyme required for initiating hydrolysis of the XyG polysaccharide, an outer membrane endoxyloglucanase glycoside hydrolase family 5 subfamily 4 (GH5_4), which enhances activity towards XyG.

INSTRUMENT(S):

ORGANISM(S): Flavobacterium Sp. F52

SUBMITTER: Andrew Bottrill

LAB HEAD: Dr Ian Lidbury

PROVIDER: PXD053370 | Pride | 2025-05-07

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	TT_220216_16_MS22-025_2064_GLU1_Slot1-16_1_2286.d.zip	Other
	TT_220216_16_MS22-025_2064_GLU1_Slot1-16_1_2286.mzid.gz	Mzid
	TT_220216_16_MS22-025_2064_GLU1_Slot1-16_1_2286.mzid_TT_220216_16_MS22-025_2064_GLU1_Slot1-16_1_2286.MGF	Mzid
	TT_220216_16_MS22-025_2064_GLU2_Slot1-17_1_2287.d.zip	Other
	TT_220216_16_MS22-025_2064_GLU2_Slot1-17_1_2287.mzid.gz	Mzid

Items per page:

1 - 5 of 54

Publications

Metabolism of hemicelluloses by root-associated Bacteroidota species.

Martin Hannah H Rogers Lucy A LA Moushtaq Laila L Brindley Amanda A AA Forbes Polly P Quinton Amy R AR Murphy Andrew R J ARJ Hipperson Helen H Daniell Tim J TJ Ndeh Didier D Amsbury Sam S Hitchcock Andrew A Lidbury Ian D E A IDEA

The ISME journal 20250101 1

Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species lack high affinity ATP-binding cassette transporters common in other plant-associated bacteria fo ...[more]

PMID: 39913342

Similar Datasets

Project description:Salcedo-Sora2016 - Microbial folate biosynthesis and utilisation This model is described in the article: A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. Enrique Salcedo-Sora J, Mc Auley MT. Mol Biosyst. 2016 Jan 21. Abstract: The metabolic biochemistry of folate biosynthesis and utilisation has evolved into a complex network of reactions. Although this complexity represents challenges to the field of folate research it has also provided a renewed source for antimetabolite targets. A range of improved folate chemotherapy continues to be developed and applied particularly to cancer and chronic inflammatory diseases. However, new or better antifolates against infectious diseases remain much more elusive. In this paper we describe the assembly of a generic deterministic mathematical model of microbial folate metabolism. Our aim is to explore how a mathematical model could be used to explore the dynamics of this inherently complex set of biochemical reactions. Using the model it was found that: (1) a particular small set of folate intermediates are overrepresented, (2) inhibitory profiles can be quantified by the level of key folate products, (3) using the model to scan for the most effective combinatorial inhibitions of folate enzymes we identified specific targets which could complement current antifolates, and (4) the model substantiates the case for a substrate cycle in the folinic acid biosynthesis reaction. Our model is coded in the systems biology markup language and has been deposited in the BioModels Database (MODEL1511020000), this makes it accessible to the community as a whole. This model is hosted on BioModels Database and identified by: MODEL1511020000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.