Studying Gene Regulation in Methanogenic Archaea

Rother, Michael; Sattler, Christian; Stock, Tilmann

doi:10.1016/b978-0-12-385112-3.00005-6

Cited by 12 publications

(6 citation statements)

References 73 publications

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“…In the method described, UV mutagenesis was selected as an inexpensive, universally applicable mutagenesis method. Other forward genetics methods employ chemical mutagens or transposable elements, which have their own strengths and weaknesses (13,(41)(42)(43)(44)(45). A particular organism may or may not be sensitive to a particular chemical mutagen, or the cells may have extracellular structures (capsule, hydrophobic pellicle, cell wall structures, etc.)…”

Section: Methods Evaluationmentioning

confidence: 99%

High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea

Walter

Ortiz

Sondgeroth

et al. 2016

Journal of Microbiological Methods

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Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Methanosarcina acetivorans, we have developed high-throughput anaerobic techniques to UV mutagenize, screen, and select for mutant strains in 96-well plates. Using these approaches we have isolated 10 mutant strains that exhibit a variety of physiological changes including increased or decreased growth rate relative to the parent strain when cells use methanol and/or acetate as carbon and energy sources. This method provides an avenue for the first step in identifying new gene functions: associating a genetic mutation with a reproducible phenotype. Mutations in bona fide methanogenesis genes such as corrinoid methyltransferases and proton-translocating FH:methanophenazine oxidoreductase (Fpo) were also generated, opening the door to in vivo functional complementation experiments. Irradiation-based mutagenesis such as from ultraviolet (UV) light, combined with modern genome sequencing, is a useful procedure to discern systems-level gene function in prokaryote taxa that can be axenically cultured but which may be resistant to chemical mutagens.

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Section: Methods Evaluationmentioning

confidence: 99%

High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea

Walter

Ortiz

Sondgeroth

et al. 2016

Journal of Microbiological Methods

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“…Quantification of M. maripaludis RNA was conducted as described (Rother et al ., 2011). Briefly, cultures of M. maripaludis grown on H 2 + CO 2 to late exponential phase were harvested by centrifugation.…”

Section: Methodsmentioning

confidence: 99%

Disruption and complementation of the selenocysteine biosynthesis pathway reveals a hierarchy of selenoprotein gene expression in the archaeon Methanococcus maripaludis

Stock

Selzer

Connery

et al. 2011

Molecular Microbiology

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:selenocysteine synthase with the corresponding genes from M. maripaludis S2 restored the mutant's ability to synthesize selenoproteins. However, only partial restoration of the wild-type selenoproteome was observed as only selenocysteine-containing formate dehydrogenase was synthesized. Quantification of transcripts showed that disrupting the pathway of selenocysteine synthesis leads to downregulation of selenoprotein gene expression, concomitant with upregulation of a selenium-independent backup system, which is not re-adjusted upon complementation. This transcriptional arrest was independent of selenophosphate but depended on the 'history' of the mutants and was inheritable, which suggests that a stable genetic switch may cause the resulting hierarchy of selenoproteins synthesized.

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“…The methanogenic archaea are a taxonomically varied group of obligate anaerobic microorganisms that are distinguished by their capacity and reliance on converting simple C1 and C2 chemicals into methane as a means of sustaining their development [43]. The majority of methanogens, which are alternatively referred to as hydrogenotrophic microorganisms, possess the ability to use hydrogen (or formate) in order to enzymatically convert carbon dioxide into methane via a metabolic process often referred to as methanogenesis [1,44].…”

Section: Archaeal Community Compositionmentioning

confidence: 99%

Lipopeptide Biosurfactants Enhanced Biohydrogen Evolution from Lignocellulose Biomass and Shaped the Microbial Community and Diversity

Phulpoto,

Bobo,

Qazi

et al. 2024

International Journal of Energy Research

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Biohydrogen is a renewable and clean energy source that can be produced from cheap and abundantly available lignocellulose biomass. However, the complex structure of lignocellulose requires various physicochemical and biological pretreatments, as it exhibits significant resistance to microbial degradation. Biosurfactants can play a vital role in facilitating the microbial degradation of lignocellulose and inducing enzymatic hydrolysis. In addition, they can lower the surface tension to impede lignin-cellulase interactions and alter the lignin characteristics. Indeed, the application of lipopeptide biosurfactants to enhance hydrogen production from lignocellulose biomass is poorly studied. Thus, this study investigates the influence of lipopeptide biosurfactants on biohydrogen enhancement from lignocellulose biomass and their impact on short-chain fatty acid generation during anaerobic dark fermentation. Subsequently, Illumina HiSeq 2500 sequencing was employed to analyze the structure of microbial community and diversity significantly affected by the presence or absence of aided biosurfactants. Results revealed that the lipopeptide biosurfactant significantly improved the cumulative biogas and hydrogen production. The maximum cumulative hydrogen yield was achieved in lipopeptide-assisted bioreactors including BioR_3, BioR_2, and BioR_4 (i.e., 4.68, 4.56, and 4.50 mmol/2 g of substrate, respectively), showing an increase of 30.79% to 36.03% higher than BioR_1 (3.44 mmol). In addition, lipopeptide biosurfactants also impacted the short-chain fatty acid generation, where acetic acid, propionic acid, and isobutyric acid were found as major acids. On the other hand, various bacterial phyla, including Firmicutes, Proteobacteria, Actinobacteria, Chloroflexi, Planctomycetota, and Acidobacteriota, were detected in all bioreactors. Among the phyla, Firmicutes were predominated (54.74% to 86.38%) in lipopeptide-assisted bioreactors, indicating that biosurfactants substantially influenced the microbial community structure during hydrogen production. Besides, Ruminiclostridium and Bacillus were significantly promoted in lipopeptide-assisted bioreactors, representing efficient lignocellulose-degrading and hydrogen-producing genera. Conclusively, this study offers valuable insights into the underlying mechanism through which lipopeptide biosurfactants actively participate in biohydrogen production and illuminates the variations occurring within microbial communities.

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Studying Gene Regulation in Methanogenic Archaea

Cited by 12 publications

References 73 publications

High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea

High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea

Disruption and complementation of the selenocysteine biosynthesis pathway reveals a hierarchy of selenoprotein gene expression in the archaeon Methanococcus maripaludis

Lipopeptide Biosurfactants Enhanced Biohydrogen Evolution from Lignocellulose Biomass and Shaped the Microbial Community and Diversity

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