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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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Related in: MedlinePlus

Growth curves for wild-type and alanine-related mutant M. maripaludis cultures on lactate. The error bars indicate s.d. of triplicate cultures.
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fig4: Growth curves for wild-type and alanine-related mutant M. maripaludis cultures on lactate. The error bars indicate s.d. of triplicate cultures.

Mentions: Transcript levels for alanine dehydrogenase (ald) and alanine racemase (alr) genes in the methanogen (both involved in alanine utilization) were greatly elevated during syntrophic growth, with corresponding increases in protein abundances in the case of ald (Tables 2 and 3, Figure 2). The associated alanine transport gene, annotated as a sodium:alanine symporter (alsT, Mmp1511), exhibited a significant downregulation at the transcript level that may have resulted from repression by the nrpR nitrogen-regulation gene (Xia et al., 2009). AlsT was not identified in the proteomics data set. Previous characterization of the agcS (alsT) and ald deletion mutants indicated that these genes are essential when alanine is the sole source of nitrogen (Moore and Leigh 2005). However, in an ammonia-containing lactate medium, no significant differences in growth rate or cell density were observed for either deletion mutant in coculture as compared with wild type (Figure 4). Nonetheless, because the alanine dehydrogenase and racemase transcripts were among those most highly elevated in coculture, we further examined intra- and extracellular concentrations of alanine and its conversion product, pyruvate. Concentrations were determined for both cocultures and monocultures of the ΔalsT mutant and wild-type M. maripaludis. Values for cocultures reflect aggregate contributions from both D. vulgaris and M. maripaludis. Notably for both co- and monocultures, the cultures containing the mutant strain had significantly higher intra- and extracellular concentrations of both alanine and pyruvate (Table 4). Additionally, higher internal concentrations of both metabolites were observed in wild-type monocultures of M. maripaludis when compared with equivalent amounts of coculture cells.


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)

Growth curves for wild-type and alanine-related mutant M. maripaludis cultures on lactate. The error bars indicate s.d. of triplicate cultures.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Growth curves for wild-type and alanine-related mutant M. maripaludis cultures on lactate. The error bars indicate s.d. of triplicate cultures.
Mentions: Transcript levels for alanine dehydrogenase (ald) and alanine racemase (alr) genes in the methanogen (both involved in alanine utilization) were greatly elevated during syntrophic growth, with corresponding increases in protein abundances in the case of ald (Tables 2 and 3, Figure 2). The associated alanine transport gene, annotated as a sodium:alanine symporter (alsT, Mmp1511), exhibited a significant downregulation at the transcript level that may have resulted from repression by the nrpR nitrogen-regulation gene (Xia et al., 2009). AlsT was not identified in the proteomics data set. Previous characterization of the agcS (alsT) and ald deletion mutants indicated that these genes are essential when alanine is the sole source of nitrogen (Moore and Leigh 2005). However, in an ammonia-containing lactate medium, no significant differences in growth rate or cell density were observed for either deletion mutant in coculture as compared with wild type (Figure 4). Nonetheless, because the alanine dehydrogenase and racemase transcripts were among those most highly elevated in coculture, we further examined intra- and extracellular concentrations of alanine and its conversion product, pyruvate. Concentrations were determined for both cocultures and monocultures of the ΔalsT mutant and wild-type M. maripaludis. Values for cocultures reflect aggregate contributions from both D. vulgaris and M. maripaludis. Notably for both co- and monocultures, the cultures containing the mutant strain had significantly higher intra- and extracellular concentrations of both alanine and pyruvate (Table 4). Additionally, higher internal concentrations of both metabolites were observed in wild-type monocultures of M. maripaludis when compared with equivalent amounts of coculture cells.

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