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The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions.

Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT - PLoS ONE (2010)

Bottom Line: Technologies to reduce these emissions are lacking.To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed.It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.

View Article: PubMed Central - PubMed

Affiliation: Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.

ABSTRACT

Background: Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed.

Methodology/principal findings: The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H(2)) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species.

Conclusions/significance: The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.

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Methanogenesis pathway.The predicted pathway of methane formation in M1 based on the scheme of Thauer et al. [15] for methanogens without cytochromes is shown. The diagram is divided into three parts to show the capture of reductant, the reduction of CO2, and conservation of energy at the methyltransfer step. The main reactions are indicated by thick arrows and enzymes catalysing each step are coloured green. Protein subunits coloured red signify the corresponding genes that were up-regulated during co-culture with Butyrivibrio proteoclasticus. Cofactor participation is indicated with thin arrows. For simplicity, protons are not shown and the overall reaction is not balanced. Membrane-located proteins are contained in light brown boxes and potential vaccine and chemogenomic targets are labelled with a circled V or C, respectively. Full gene names and corresponding locus tag numbers can be found in Table S1. H4MPT; tetrahydromethanopterin; MF, methanofuran; F420, coenzyme F420 oxidised; F420H2, coenzyme F420 reduced; Fdox?, unknown oxidised ferredoxin; Fdred?, unknown reduced ferredoxin; HSCoM, reduced coenzyme M; HSCoB, reduced coenzyme B, CoMS-SCoB, coenzyme B-coenzyme M heterodisulphide; NADP+, nicotinamide adenosine dinucleotide phosphate non-reduced; NADPH, nicotinamide adenosine dinucleotide phosphate reduced.
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pone-0008926-g002: Methanogenesis pathway.The predicted pathway of methane formation in M1 based on the scheme of Thauer et al. [15] for methanogens without cytochromes is shown. The diagram is divided into three parts to show the capture of reductant, the reduction of CO2, and conservation of energy at the methyltransfer step. The main reactions are indicated by thick arrows and enzymes catalysing each step are coloured green. Protein subunits coloured red signify the corresponding genes that were up-regulated during co-culture with Butyrivibrio proteoclasticus. Cofactor participation is indicated with thin arrows. For simplicity, protons are not shown and the overall reaction is not balanced. Membrane-located proteins are contained in light brown boxes and potential vaccine and chemogenomic targets are labelled with a circled V or C, respectively. Full gene names and corresponding locus tag numbers can be found in Table S1. H4MPT; tetrahydromethanopterin; MF, methanofuran; F420, coenzyme F420 oxidised; F420H2, coenzyme F420 reduced; Fdox?, unknown oxidised ferredoxin; Fdred?, unknown reduced ferredoxin; HSCoM, reduced coenzyme M; HSCoB, reduced coenzyme B, CoMS-SCoB, coenzyme B-coenzyme M heterodisulphide; NADP+, nicotinamide adenosine dinucleotide phosphate non-reduced; NADPH, nicotinamide adenosine dinucleotide phosphate reduced.

Mentions: Many of the enzymes involved in the methanogenesis pathway are strongly conserved and found only among methanogens. Although this pathway has been well studied in methanogens from a range of other environments [15] the M1 genome shows for the first time details of this pathway in a rumen methanogen. M1 can grow with H2 plus CO2 and formate [16] and encodes the enzymes, and most of the cofactors, required for conversion of these substrates through to methane according to the metabolic scheme presented in Figure 2. Consistent with this hydrogenotrophic lifestyle, M1 lacks the methanophenazine-reducing [Ni-Fe] hydrogenase (VhoACG) and methanophenazine-dependent heterodisulphide reductase (HdrDE) found in methanophenazine-containing species within the order Methanosarcinales [17].


The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions.

Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT - PLoS ONE (2010)

Methanogenesis pathway.The predicted pathway of methane formation in M1 based on the scheme of Thauer et al. [15] for methanogens without cytochromes is shown. The diagram is divided into three parts to show the capture of reductant, the reduction of CO2, and conservation of energy at the methyltransfer step. The main reactions are indicated by thick arrows and enzymes catalysing each step are coloured green. Protein subunits coloured red signify the corresponding genes that were up-regulated during co-culture with Butyrivibrio proteoclasticus. Cofactor participation is indicated with thin arrows. For simplicity, protons are not shown and the overall reaction is not balanced. Membrane-located proteins are contained in light brown boxes and potential vaccine and chemogenomic targets are labelled with a circled V or C, respectively. Full gene names and corresponding locus tag numbers can be found in Table S1. H4MPT; tetrahydromethanopterin; MF, methanofuran; F420, coenzyme F420 oxidised; F420H2, coenzyme F420 reduced; Fdox?, unknown oxidised ferredoxin; Fdred?, unknown reduced ferredoxin; HSCoM, reduced coenzyme M; HSCoB, reduced coenzyme B, CoMS-SCoB, coenzyme B-coenzyme M heterodisulphide; NADP+, nicotinamide adenosine dinucleotide phosphate non-reduced; NADPH, nicotinamide adenosine dinucleotide phosphate reduced.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2812497&req=5

pone-0008926-g002: Methanogenesis pathway.The predicted pathway of methane formation in M1 based on the scheme of Thauer et al. [15] for methanogens without cytochromes is shown. The diagram is divided into three parts to show the capture of reductant, the reduction of CO2, and conservation of energy at the methyltransfer step. The main reactions are indicated by thick arrows and enzymes catalysing each step are coloured green. Protein subunits coloured red signify the corresponding genes that were up-regulated during co-culture with Butyrivibrio proteoclasticus. Cofactor participation is indicated with thin arrows. For simplicity, protons are not shown and the overall reaction is not balanced. Membrane-located proteins are contained in light brown boxes and potential vaccine and chemogenomic targets are labelled with a circled V or C, respectively. Full gene names and corresponding locus tag numbers can be found in Table S1. H4MPT; tetrahydromethanopterin; MF, methanofuran; F420, coenzyme F420 oxidised; F420H2, coenzyme F420 reduced; Fdox?, unknown oxidised ferredoxin; Fdred?, unknown reduced ferredoxin; HSCoM, reduced coenzyme M; HSCoB, reduced coenzyme B, CoMS-SCoB, coenzyme B-coenzyme M heterodisulphide; NADP+, nicotinamide adenosine dinucleotide phosphate non-reduced; NADPH, nicotinamide adenosine dinucleotide phosphate reduced.
Mentions: Many of the enzymes involved in the methanogenesis pathway are strongly conserved and found only among methanogens. Although this pathway has been well studied in methanogens from a range of other environments [15] the M1 genome shows for the first time details of this pathway in a rumen methanogen. M1 can grow with H2 plus CO2 and formate [16] and encodes the enzymes, and most of the cofactors, required for conversion of these substrates through to methane according to the metabolic scheme presented in Figure 2. Consistent with this hydrogenotrophic lifestyle, M1 lacks the methanophenazine-reducing [Ni-Fe] hydrogenase (VhoACG) and methanophenazine-dependent heterodisulphide reductase (HdrDE) found in methanophenazine-containing species within the order Methanosarcinales [17].

Bottom Line: Technologies to reduce these emissions are lacking.To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed.It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.

View Article: PubMed Central - PubMed

Affiliation: Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.

ABSTRACT

Background: Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed.

Methodology/principal findings: The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H(2)) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species.

Conclusions/significance: The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.

Show MeSH
Related in: MedlinePlus