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QUORUM SENSING IN A METHANE-OXIDIZING BACTERIUM

ABSTRACT: Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.

ORGANISM(S): Methylobacter tundripaludum 21/22

PROVIDER: GSE85617 | GEO | 2016/08/16

SECONDARY ACCESSION(S): PRJNA338986

REPOSITORIES: GEO

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QUORUM SENSING IN A METHANE-OXIDIZING BACTERIUM

Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-CÂ10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium. Samples are 2 sets of biological replicates of a Methylobacter tundripaludum strain 21/22 mutant where the acyl-homoserine lactone (AHL) synthase gene mbaI (T451DRAFT_0796) has been deleted. The mutant strain was grown to log (48 hours) or stationary (68 hours) phase in the absence or presence of the AHL 3-OH-C10-HSL.

2016-08-16 | E-GEOD-85617 | biostudies-arrayexpress

Interspecies chemical signalling in a methane-oxidizing bacterial community

Project description:Multiple species of bacteria oxidize methane in the environment after it is produced by anaerobic ecosystems. These organisms provide a carbon and energy source for species that cannot oxidize methane themselves, thereby serving a key role in these niches while also sequestering this potent greenhouse gas before it enters the atmosphere. Deciphering the molecular details of how methane-oxidizing bacteria interact in the environment enables us to understand an important aspect that shapes the structure and function these communities. Here we show that many members of the Methylomonas genus possess a LuxR-type acyl-homoserine lactone (acyl-HSL) receptor/transcription factor highly homologous to MbaR from the quorum sensing (QS) system of Methylobacter tundripaludum, another methane-oxidizer that has been isolated from the same environment. We reconstitute this detection system in Escherichia coli and also use mutant and transcriptomic analysis to show that the receptor from Methylomonas species strain LW13 (LW13) is active and alters LW13 gene expression in response to the acyl-HSL produced by M. tundripaludum. These findings provide a molecular mechanism for how two species of bacteria that may compete for resources in the environment can interact in a specific manner through a chemical signal.

2019-01-29 | GSE122293 | GEO

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Project description:Our goal is to convert methane efficiently into liquid fuels that may be more readily transported. Since aerobic oxidation of methane is less efficient, we focused on anaerobic processes to capture methane, which are accomplished by anaerobic methanotrophic archaea (ANME) in consortia. However, no pure culture capable of oxidizing and growing on methane anaerobically has been isolated. In this study, Methanosarcina acetivorans, an archaeal methanogen, was metabolically engineered to take up methane, rather than to generate it. To capture methane, we cloned the DNA coding for the enzyme methyl-coenzyme M reductase (Mcr) from an unculturable archaeal organism from a Black Sea mat into M. acetivorans to effectively run methanogenesis in reverse. The engineered strain produces primarily acetate, and our results demonstrate that pure cultures can grow anaerobically on methane.

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2013-09-28 | E-GEOD-51235 | biostudies-arrayexpress

Transcriptional analysis of ypeIR mutation in Yersinia pestis at 37°C

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Project description:Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental cues in laboratory settings. However, laboratory-based model ecosystems offer a means to better account for natural conditions compared to standard planktonic cultures, aiding in the linking of genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs). This system, referred to as the gradient syringe, is made by inoculating bacteria into semi-solid agarose held within a disposable syringe. Empty space at one end of the syringe is flushed with methane gas, while the other end is open to the atmosphere through a sterile filter. We show this system replicates the methane-oxygen counter gradient typically found in the natural soil environment of methanotrophs. Culturing the methanotroph Methylomonas sp. strain LW13 in this system produced a distinct horizontal band at the intersection of the counter gradient, which we discovered was due not to increased cell growth at this location but instead to an increased amount of extracellular polymeric substances (EPS). We also discovered that different methanotrophic taxa formed EPS bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this EPS band, we identified genes implicated in cell growth and EPS formation within the gradient syringe, and validated the involvement of these genes with knockout strains. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover methanotroph phenotypes missing from standard planktonic cultures, and link these phenotypes their genetic determinants.

2023-10-05 | GSE243827 | GEO

Methylobacter tundripaludum 21/22

Project description:QUORUM SENSING IN A METHANE-OXIDIZING BACTERIUM

| PRJNA338986 | ENA

Transcriptional analysis of ypeIR mutation in Yersinia pestis at 37Â°C

Project description:The etiologic agent of bubonic plague, Yersinia pestis, senses cell density-dependent chemical signals to synchronize transcription between cells of the population in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of YpeIR quorum sensing in Y. pestis has been unclear. YpeIR is one of the AHL quorum sensing system in Y. pestis. In this study we performed transcriptional profiling experiments to identify Y. pestis YpeIR quorum sensing regulated functions at 37Â°C. Six independent RNA samples from Y. pestis CO92 Îpgm ÎypeIR cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.

2016-07-03 | E-GEOD-30341 | biostudies-arrayexpress

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