New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions

Abstract

Background: The great metabolic versatility of the purple non-sulfur bacteria is of particular interest in green technology. Rhodospirillum rubrum S1H is an α-proteobacterium that is capable of photoheterotrophic assimilation of volatile fatty acids (VFAs). Butyrate is one of the most abundant VFAs produced during fermentative biodegradation of crude organic wastes in various applications. While there is a growing understanding of the photoassimilation of acetate, another abundantly produced VFA, the mechanisms involved in the photoheterotrophic metabolism of butyrate remain poorly studied. Results: In this work, we used proteomic and functional genomic analyses to determine potential metabolic pathways involved in the photoassimilation of butyrate. We propose that a fraction of butyrate is converted to acetyl-CoA, a reaction shared with polyhydroxybutyrate metabolism, while the other fraction supplies the ethylmalonyl-CoA (EMC) pathway used as an anaplerotic pathway to replenish the TCA cycle. Surprisingly, we also highlighted a potential assimilation pathway, through isoleucine synthesis and degradation, allowing the conversion of acetyl-CoA to propionyl-CoA. We tentatively named this pathway the methylbutanoyl-CoA pathway (MBC). An increase in isoleucine abundance was observed during the early growth phase under butyrate condition. Nevertheless, while the EMC and MBC pathways appeared to be concomitantly used, a genome-wide mutant fitness assay highlighted the EMC pathway as the only pathway strictly required for the assimilation of butyrate. Conclusion: Photoheterotrophic growth of Rs. rubrum with butyrate as sole carbon source requires a functional EMC pathway. In addition, a new assimilation pathway involving isoleucine synthesis and degradation, named the methylbutanoyl-CoA (MBC) pathway, could also be involved in the assimilation of this volatile fatty acid by Rs. rubrum.

Photoheterotrophic Assimilation of Valerate and Associated Polyhydroxyalkanoate Production by Rhodospirillum rubrum

“…2). The implication of the BCAA biosynthesis and degradation pathways has already been proposed as potential assimilation pathways in the presence of butyrate (14) or acetate (11,12). Recently, a sudden increase in light intensity highlighted that isoleucine biosynthesis may be implicated in high light intensity tolerance (15), further reinforcing the implication of this pathway in managing the redox balance, as previously proposed (53,54).…”

“…Our whole-metabolism analyses reveal that a fully functional methylmalonyl-CoA pathway is mandatory for the photoheterotrophic assimilation of valerate and that the ethylmalonyl-CoA pathway is not necessary for the assimilation of acetyl-CoA issued from valerate cleavage. We suggest that other pathways, such as those for pyruvate ferredoxin oxidoreductase (PFOR) or isoleucine biosynthesis, may take part in this assimilation process as has already been suggested by our previous studies (11,12,14,15). We also investigated PHA production by R. rubrum, highlighting the production of copolymers with an outstanding HV monomer percentage, even in conditions of full nutrient availability.…”

“…In order to first characterize the photoheterotrophic assimilation of valerate, R. rubrum S1H was cultivated with valerate as the sole source of carbon. Since bicarbonate ions are already known to act as a limiting factor in VFA assimilation such as acetate, propionate, or butyrate (12,14,(30)(31)(32), we tested the effect of an addition of a low and high concentration of bicarbonate ions (3 and 50 mM HCO 3 -) in the medium and used succinate as the control condition. Indeed, previous studies have demonstrated that bicarbonate ions are necessary during VFA assimilation to handle redox stress through the activation of a redox sink, namely, the Calvin-Benson-Bassham (CBB) cycle (31,33,34).…”

“…1B). The essentiality of bicarbonate ions for the assimilation of acetate, propionate, or butyrate has already been documented (14,15,31,35). Since the valerate constitutes the most reduced VFA compared to the biomass (redox state valerate, -2.5; biomass, Ϫ0.5) (36, 37), the requirement of bicarbonates ions could be linked to the redox stress induced by the photoheterotrophic assimilation of valerate.…”

“…The role of this pathway was first characterized by Alber and coworkers (9,10). In addition to the EMC pathway, the use of additional metabolic routes, such as the isoleucine biosynthesis and degradation pathways (MBC pathway) or the pyruvate ferredoxin oxydoreductase (PFOR) pathway, remains obscure, and further studies are still needed to attest to their involvement in acetate assimilation (11,12,14,15).…”