Functional responses of methanogenic archaea to syntrophic growth.

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

Mechanism for microbial population collapse in a fluctuating resource environment.

Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reduce

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

Genome-scale metabolic models have proven useful for answering fundamental questions about metabolic capabilities of a variety of microorganisms, as well as informing their metabolic engineering. However, only a few models are available for oxygenic photosynthetic microorganisms, particularly in cyanobacteria in which photosynthetic and respiratory electron transport chains (ETC) share components. We addressed the complexity of cyanobacterial ETC by developing a genome-scale model for the diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142. The resulting metabolic reconstruction, iCce806, consists of 806 genes associated with 667 metabolic reactions and includes a detailed representation of the ETC and a biomass equation based on experimental measurements. Both computational and experimental approaches were used to investigate light-driven metabolism in Cyanothece sp. ATCC 51142, with a particular focus on reductant production and partitioning within the ETC. The simulation results suggest that growth and metabolic flux distributions are substantially impacted by the relative amounts of light going into the individual photosystems. When growth is limited by the flux through photosystem I, terminal respiratory oxidases are predicted to be an important mechanism for removing excess reductant. Similarly, under photosystem II flux limitation, excess electron carriers must be removed via cyclic electron transport. Furthermore, in silico calculations were in good quantitative agreement with the measured growth rates whereas predictions of reaction usage were qualitatively consistent with protein and mRNA expression data, which we used to further improve the resolution of intracellular flux values

Predicted effects of varying photon uptake rates on growth and electron transport pathways.

<p>(A) 2-D phenotypic phase plane (PhPP) displaying maximum growth rates for varying photon uptake rates. The PhPP has 3 distinct regions – in regions 1 and 3, flux through a single photosystem limit growth rates, whereas in region 2 flux increases through either photosystem will increase growth rate. (B) Pathway maps of electron transfer reactions in different PhPP regions. PhPP flux variability analysis was performed to see which flux is always required (red arrows), optional (green arrows), and blocked (blue arrows) across each of the three PhPP regions.</p

Effect of nutrient limitation on biomass composition (normalized to ash-free dry weight).

<p>Effect of nutrient limitation on biomass composition (normalized to ash-free dry weight).</p

Effects of <i>in silico</i> reaction deletions on flux spans under light-limited conditions.

<p>(A) Effects of deletions are compared to the cases where no reactions were deleted (red bar), or TPD were used as constraints (green bar). The values represent the average flux span across all reactions in central metabolism. Only deletions which lower the flux span by at least >1 mmol·g⁻¹ AFDW·h⁻¹ are presented. (B) Changes in flux spans for specific reactions catalyzed by ribulose bisphosphate carboxylase (RBC) and phosphoglucose isomerase (PGI) between simulations that (i) use TPD data as a constraint (green bars), (ii) delete single reactions (blue and purple bars), (iii) delete two reactions (yellow bar) or (iv) impose no additional constraints (red bars). Reaction abbreviations match those listed in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002460#pcbi.1002460.s005" target="_blank">Table S1</a>.</p

Flux variability analysis for model simulations in light-limited and ammonium-limited chemostat conditions.

<p>Flux variability analysis for model simulations in light-limited and ammonium-limited chemostat conditions.</p

Impact of electron transport pathways on growth and metabolism of <i>Cyanothece</i> 51142.

<p>(A) Effects of removing cyclic photosynthesis (<i>via</i> NDH-1, NDH-2, FdPq, G3PD_PQ, and SUCD_PQ) and alternative reductant sinks (H₂ production, COX, QOX, and Mehler reactions). (B) Effect of removing alternative reductant sinks but including all routes for cyclic photosynthesis. Shaded regions indicate that multiple flux values can achieve maximal growth rate. (C) All photosynthetic and respiratory electron flow routes operate, except H₂ production.</p