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Functional responses of methanogenic archaea to syntrophic growth.

Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA - ISME J (2012)

Bottom Line: These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis.A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)).The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis.

View Article: PubMed Central - PubMed

Affiliation: Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.

ABSTRACT
Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)). The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.

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Quantitative proteomic data. Analysis of coculture protein samples using iTRAQ labeling and shotgun liquid chromatography–mass spectrometry methods identified 82 proteins from M. maripaludis (out of 207 total coculture proteins) by at least two unique, high-confidence peptides in replicate runs. Among these 82 M. maripaludis proteins (Supplementary Table S1), 8 exhibited significant abundance increases (Table 3). Plot shows log2 ratios of the iTRAQ ratios of proteins from coculture versus the synthetic blend. The synthetic blend contains a 50:50 mixture of D. vulgaris to M. maripaludis, whereas the coculture is a 80:20 mixture of the same. Normalized data was used. For complete data see Supplementary Table S1.
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fig2: Quantitative proteomic data. Analysis of coculture protein samples using iTRAQ labeling and shotgun liquid chromatography–mass spectrometry methods identified 82 proteins from M. maripaludis (out of 207 total coculture proteins) by at least two unique, high-confidence peptides in replicate runs. Among these 82 M. maripaludis proteins (Supplementary Table S1), 8 exhibited significant abundance increases (Table 3). Plot shows log2 ratios of the iTRAQ ratios of proteins from coculture versus the synthetic blend. The synthetic blend contains a 50:50 mixture of D. vulgaris to M. maripaludis, whereas the coculture is a 80:20 mixture of the same. Normalized data was used. For complete data see Supplementary Table S1.

Mentions: The most general change associated with syntrophic growth was a decrease in transcripts for energy-consuming biosynthetic functions (for example, pyruvate oxidoreductase (Por), acetyl-CoA decarbonylase/synthase and energy-conserving hydrogenase B (Ehb), see Figure 1 for enzymatic reaction depictions) and an increase in transcripts in the energy-generating methanogenesis pathway (see Table 2 and Supplementary Tables S2 and S4; Supplementary Figure S1) plots transcriptional changes according to function as defined by clusters of orthologous groups). Figure 1 illustrates the differential expression of transcripts observed in coculture compared with hydrogen-limited M. maripaludis monocultures. However, compared with growth in monoculture under hydrogen limitation, transcript levels for isofunctional genes often diverged, with transcripts of one variant significantly increasing, whereas the other was little changed or significantly decreased in their relative abundances. A common feature was an apparent increase in transcripts for functions using H2 directly as reductant, versus those using the reduced deazaflavin (coenzyme F420). In several cases, the proteins were confidently identified (Table 3 and Figure 2) and the corresponding changes generally corroborated the observations at the transcript level. The greater importance of direct reduction by H2 was supported by improved syntrophic growth of a deletion mutant in an F420-dependent dehydrogenase of M. maripaludis (described in more detail below). Metabolite, transcript and proteomic analyses also pointed to a unique, although undefined, role for alanine utilization within this syntrophic coupling.


Functional responses of methanogenic archaea to syntrophic growth.

Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA - ISME J (2012)

Quantitative proteomic data. Analysis of coculture protein samples using iTRAQ labeling and shotgun liquid chromatography–mass spectrometry methods identified 82 proteins from M. maripaludis (out of 207 total coculture proteins) by at least two unique, high-confidence peptides in replicate runs. Among these 82 M. maripaludis proteins (Supplementary Table S1), 8 exhibited significant abundance increases (Table 3). Plot shows log2 ratios of the iTRAQ ratios of proteins from coculture versus the synthetic blend. The synthetic blend contains a 50:50 mixture of D. vulgaris to M. maripaludis, whereas the coculture is a 80:20 mixture of the same. Normalized data was used. For complete data see Supplementary Table S1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475374&req=5

fig2: Quantitative proteomic data. Analysis of coculture protein samples using iTRAQ labeling and shotgun liquid chromatography–mass spectrometry methods identified 82 proteins from M. maripaludis (out of 207 total coculture proteins) by at least two unique, high-confidence peptides in replicate runs. Among these 82 M. maripaludis proteins (Supplementary Table S1), 8 exhibited significant abundance increases (Table 3). Plot shows log2 ratios of the iTRAQ ratios of proteins from coculture versus the synthetic blend. The synthetic blend contains a 50:50 mixture of D. vulgaris to M. maripaludis, whereas the coculture is a 80:20 mixture of the same. Normalized data was used. For complete data see Supplementary Table S1.
Mentions: The most general change associated with syntrophic growth was a decrease in transcripts for energy-consuming biosynthetic functions (for example, pyruvate oxidoreductase (Por), acetyl-CoA decarbonylase/synthase and energy-conserving hydrogenase B (Ehb), see Figure 1 for enzymatic reaction depictions) and an increase in transcripts in the energy-generating methanogenesis pathway (see Table 2 and Supplementary Tables S2 and S4; Supplementary Figure S1) plots transcriptional changes according to function as defined by clusters of orthologous groups). Figure 1 illustrates the differential expression of transcripts observed in coculture compared with hydrogen-limited M. maripaludis monocultures. However, compared with growth in monoculture under hydrogen limitation, transcript levels for isofunctional genes often diverged, with transcripts of one variant significantly increasing, whereas the other was little changed or significantly decreased in their relative abundances. A common feature was an apparent increase in transcripts for functions using H2 directly as reductant, versus those using the reduced deazaflavin (coenzyme F420). In several cases, the proteins were confidently identified (Table 3 and Figure 2) and the corresponding changes generally corroborated the observations at the transcript level. The greater importance of direct reduction by H2 was supported by improved syntrophic growth of a deletion mutant in an F420-dependent dehydrogenase of M. maripaludis (described in more detail below). Metabolite, transcript and proteomic analyses also pointed to a unique, although undefined, role for alanine utilization within this syntrophic coupling.

Bottom Line: These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis.A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)).The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis.

View Article: PubMed Central - PubMed

Affiliation: Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.

ABSTRACT
Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)). The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.

Show MeSH
Related in: MedlinePlus