Comparative analysis of differential proteome-wide protein-protein interaction network of Methanobrevibacter ruminantium M1

A proteome-wide protein-protein interaction (PPI) network of Methanobrevibacter ruminantium M1 (MRU), a predominant rumen methanogen, was constructed from its metabolic genes using a gene neighborhood algorithm and then compared with closely related rumen methanogens Using proteome-wide PPI approach, we constructed network encompassed 2194 edges and 637 nodes interacting with 634 genes. Network quality and robustness of functional modules were assessed with gene ontology terms. A structure-function-metabolism mapping for each protein has been carried out with efforts to extract experimental PPI concomitant information from the literature. The results of our study revealed that some topological properties of its network were robust for sharing homologous protein interactions across heterotrophic and hydrogenotrophic methanogens. MRU proteome has shown to establish many PPI sub-networks for associated metabolic subsystems required to survive in the rumen environment. MRU genome found to share interacting proteins from its PPI network involved in specific metabolic subsystems distinct to heterotrophic and hydrogenotrophic methanogens. Across these proteomes, the interacting proteins from differential PPI networks were shared in common for the biosynthesis of amino acids, nucleosides, and nucleotides and energy metabolism in which more fractions of protein pairs shared with Methanosarcina acetivorans. Our comparative study expedites our knowledge to understand a complex proteome network associated with typical metabolic subsystems of MRU and to improve its genome-scale reconstruction in the future.

The transcriptome response of the ruminal methanogen Methanobrevibacter ruminantium strain M1 to the inhibitor lauric acid

Objective

Lauric acid (C₁₂) is a medium-chain fatty acid that inhibits growth and production of the greenhouse gas methane by rumen methanogens such as Methanobrevibacter ruminantium. To understand the inhibitory mechanism of C₁₂, a transcriptome analysis was performed in M. ruminantium strain M1 (DSM 1093) using RNA-Seq.

Results

Pure cell cultures in the exponential growth phase were treated with 0.4 mg/ml C₁₂, dissolved in dimethyl sulfoxide (DMSO), for 1 h and transcriptomic changes were compared to DMSO-only treated cells (final DMSO concentration 0.2%). Exposure to C₁₂ resulted in differential expression of 163 of the 2280 genes in the M1 genome (maximum log₂-fold change 6.6). Remarkably, C₁₂ hardly affected the expression of genes involved in methanogenesis. Instead, most affected genes encode cell-surface associated proteins (adhesion-like proteins, membrane-associated transporters and hydrogenases), and proteins involved in detoxification or DNA-repair processes. Enrichment analysis on the genes regulated in the C₁₂-treated group showed a significant enrichment for categories ‘cell surface’ and ‘mobile elements’ (activated by C₁₂), and for the categories ‘regulation’ and ‘protein fate’ (represssed). These results are useful to generate and test specific hypotheses on the mechanism how C₁₂ affects rumen methanogens.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3242-8) contains supplementary material, which is available to authorized users.

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau

Several natural anaerobic fungus-methanogen co-cultures have been isolated from rumen and feces source of herbivores with strong fiber degrading ability. In this study, we isolated 7 Neocallimastix with methanogen co-cultures from the rumen of yaks grazing on the Qinghai Tibetan Plateau. Based on morphological characteristics and internal transcribed spacer 1 sequences (ITS1), all the fungi were identified as Neocallimastix frontalis. The co-cultures were confirmed as the one fungus - one methanogen pattern by the PCR-denatured gradient gel electrophoresis (DGGE) assay. All the methanogens were identified as Methanobrevibacter ruminantium by 16s rRNA gene sequencing. We investigated the biodegrading capacity of the co-culture (N. frontalis + M. ruminantium) Yaktz1 on wheat straw, corn stalk and rice straw in a 7 days-incubation. The in vitro dry matter digestibility (IVDMD), acid detergent fiber digestibility (ADFD) and neural detergent fiber digestibility (NDFD) values of the substrates in the co-culture were significantly higher than those in the mono-culture N. frontalis Yaktz1. The co-culture exhibited high polysaccharide hydrolase (xylanase and FPase) and esterase activities. The xylanase in the co-culture reached the highest activity of 12500 mU/ml on wheat straw at the day 3 of the incubation. At the end of the incubation, 3.00 mmol-3.29 mmol/g dry matter of methane were produced by the co-culture. The co-culture also produced high level of acetate (40.00 mM-45.98 mM) as the end-product during the biodegradation. Interestingly, the N. frontalis Yaktz1 mono-culture produced large amount of lactate (8.27 mM-11.60 mM) and ethanol (163.11 mM-242.14 mM), many times more than those recorded in the previously reported anaerobic fungi. Our data suggests that the (N. frontalis + M. ruminantium) Yaktz1 co-culture and the N. frontalis Yaktz1 mono-culture both have great potentials for different industrial use.

A high-throughput screening assay for identification of inhibitors of the A1AO-ATP synthase of the rumen methanogen Methanobrevibacter ruminantium M1

We report the development of a high-throughput screening platform to identify inhibitors of the membrane-bound A1Ao-ATP synthase from the rumen methanogen Methanobrevibacter ruminantium M1. Inhibitors identified in the screen were tested against growing cultures of M. ruminantium, validating the approach to identify new inhibitors of methanogens.

Inhibition of methyl-CoM Reductase from Methanobrevibacter ruminantium by 2-bromoethanesulfonate

Cattle husbandry is a major contributor to atmospheric methane, which is considered as an important greenhouse gas. Moreover, the generation of methane in the intestine of domestic ruminants by methanogenic bacteria is a drag on feed efficacy. Studies on methanogenesis have typically implied model organisms that are, however, not relevant in the ruminant gut. This paper shows that methyl-CoM reductase catalyzing the final step of methanogenesis in Methanobrevibacter ruminantium, a major participant in methane production by cattle, is inhibited by 2-bromoethanesulfonate, a compound often used as a model in animal agriculture, with an apparent IC50 of 0.4 ± 0.04 μM.