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Comparative proteomics of Eubacterium maltosivorans: reveal of propionogenic metabolism and bacterial microcompartments in a human intestinal bacterium.

ABSTRACT: This study was conducted in order to explore proteins involved in 1,2-propanediol utilization and microcompartments formation of E. maltosivorans. We also identified the maltose specific ABC transporter in E. maltosivorans when it was grown with this substrate.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Eubacterium Maltosivorans

SUBMITTER: Sjef Boeren

LAB HEAD: Sjef Boeren

PROVIDER: PXD028575 | Pride | 2022-08-12

REPOSITORIES: Pride

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			Action	DRS
	MQresult_NB40-48.zip	Other
	NB40_Beta1.raw	Raw
	NB41_Beta2.raw	Raw
	NB42_Beta3.raw	Raw
	NB43_PD1.raw	Raw

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Publications

Comparative genomics and proteomics of Eubacterium maltosivorans: functional identification of trimethylamine methyltransferases and bacterial microcompartments in a human intestinal bacterium with a versatile lifestyle.

Feng Yuan Y Bui Thi Phuong Nam TPN Stams Alfons J M AJM Boeren Sjef S Sánchez-Andrea Irene I de Vos Willem M WM

Environmental microbiology 20220102 1

Eubacterium maltosivorans YIT is a human intestinal isolate capable of acetogenic, propionogenic and butyrogenic growth. Its 4.3-Mb genome sequence contains coding sequences for 4227 proteins, including 41 different methyltransferases. Comparative proteomics of strain YIT showed the Wood-Ljungdahl pathway proteins to be actively produced during homoacetogenic growth on H2 and CO2 while butyrogenic growth on a mixture of lactate and acetate significantl ...[more]

PMID: 34978130

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Comparative proteomics of Eubacterium maltosivorans: Functional identification of trimethylamine methyltransferases and bacterial microcompartments in a human intestinal bacterium

Project description:This study was conducted in order to explore proteins involved in quaternary amines degradation and microcompartments formation of E. maltosivorans.

2022-08-12 | PXD028574 | Pride

Decoding the stoichiometric composition and organization of bacterial metabolosomes C4PR_LIV

Project description:Self-assembly of proteins into complexes with defined stoichiometry and organization is fundamental to the structure and functionality of many molecular machines in biology. Some enteric bacteria including Salmonella have evolved the propanediol-utilizing microcompartment (Pdu MCP), a specialized proteinaceous organelle that is essential for 1,2-propanediol degradation and enteric pathogenesis. Pdu MCPs are a family of bacterial microcompartments that are self-assembled from thousands of protein molecules within the bacterial cytosol. Inside the Pdu MCP, several catalytical enzymes and cofactors involved in reactions for metabolizing 1,2-propanediol are encapsulated in a semi-permeable protein shell that comprises multi-subunit proteins in hexameric, pentameric, and trimeric states. Here, we seek a comprehensive understanding of the stoichiometric composition and organization of Pdu MCPs. We obtain accurate stoichiometry of shell proteins and internal enzymes of the natural Pdu MCP by QconCAT-driven quantitative mass spectrometry. Genetic deletion of the major shell protein and absolute stoichiometry analysis reveal the stoichiometric and structural remodeling of Pdu MCPs. Our new knowledge about the protein stoichiometry leads us to propose a model of the Pdu metabolosome structure. Moreover, atomic force microscopy of Pdu MCPs at the near-physiological condition illustrates the inherent flexibility of the Pdu MCP structure and the key role of cargo enzymes in maintaining mechanical stiffness of the biological architecture. These structural insights into the Pdu MCP will be critical for both delineating the general principles underlying bacterial organelle formation, structural robustness and function, and repurposing natural microcompartments using synthetic biology for biotechnological applications.

2020-05-11 | PXD015111 | Pride

Maltose utilization by Lactobacillus reuteri 100-23

Project description:Commensal (symbiont) bacteria form communities in various regions of the bodies of vertebrates. Phylogenetic analysis of gut communities is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100-23 and Lactobacillus johnsonii strain 100-33 cohabit in the forestomach of mice. According to the niche exclusion principle, this should not be possible because both strains utilise the two main fermentable carbohydrates present in the stomach digesta: glucose and maltose. We show, based on gene transcription analysis, in vitro physiological assays, and in vivo experiments that the two strains can co-exist in the forestomach habitat because L. reuteri 100-23 transports maltose into its cells more efficiently than does L. johnsonii 100-33. Conversely, strain 100-33 transports glucose more efficiently than 100-23. As a result, 100-23 shows a preference for growth using maltose, whereas 100-33 prefers glucose. Mutation of the maltose phosphorylase gene (malA) of strain 100-23 prevented its growth on maltose-containing culture medium, and resulted in the numerical dominance of 100-33 in the forestomach. The fundamental niche of L. reuteri 100-23 in the mouse forestomach can be defined in terms of glucose and maltose fermentation. Its realised niche when L. johnsonii 100-33 is present is maltose fermentation. Hence nutritional adaptations provided niche differentiation that enabled cohabitation by the two strains through resource partitioning in the mouse forestomach. This real life, trophic phenomenon conforms to a mathematical model. Analysis of the microarray data was obtained from two independent biological replicates. A dye swap was included in the analysis

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Comparative microarrays of Actinoplanes sp. SE50/110 ΔacrA with the Actinoplanes sp. SE50/110 wildtype

Project description:In order to characterize the transcriptional regulator AcrA, comparative genome wide transcriptome analyses were conducted. Therefore, the wild type Actinoplanes sp. SE50/110 and the mutant ΔacrA were each cultivated in triplicates in minimal medium supplemented with maltose or glucose as single carbon source. RNA samples from the biological replicates were taken from the middle of the growth phase of both strains in each maltose and glucose minimal medium, respectively. RNA was isolated and the three replicates were combined for each strain and condition. For each cultivation condition, the data from two arrays (dye swap) were combined to make statistically reliable conclusions.

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Comparative microarrays of Actinoplanes sp. SE50/110 ΔmalT with the Actinoplanes sp. SE50/110 wildtype

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1,2-Propanediol utilization mediated by bacterial microcompartments in Propionibacterium freudenreichii DSM 20271

Project description:This study was conducted to investigate whether 1,2-propanediol could be metabolized by Propionibacterium freudenreichii DSM 20271 through bacterial microcompartment mediated metabolism.

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Transcription start site analysis for Thermotoga maritima [RNA-seq]

Project description:Investigation of 5' transcripts using strand specific sequencing for T. maritima under logphase, maltose minimal media growth conditions Two replicate samples were sequenced after isolating total RNA of cultures grown in maltose minimal media. Cells were harvested in logphase growth.

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