Carbohydrate Metabolism and Carbon Fixation in Roseobacter denitrificans OCh114

Abstract

The Roseobacter clade of aerobic marine proteobacteria, which compose 10–25% of the total marine bacterial community, has been reported to fix CO2, although it has not been determined what pathway is involved. In this study, we report the first metabolic studies on carbohydrate utilization, CO2 assimilation, and amino acid biosynthesis in the phototrophic Roseobacter clade bacterium Roseobacter denitrificans OCh114. We develop a new minimal medium containing defined carbon source(s), in which the requirements of yeast extract reported previously for the growth of R. denitrificans can be replaced by vitamin B12 (cyanocobalamin). Tracer experiments were carried out in R. denitrificans grown in a newly developed minimal medium containing isotopically labeled pyruvate, glucose or bicarbonate as a single carbon source or in combination. Through measurements of 13C-isotopomer labeling patterns in protein-derived amino acids, gene expression profiles, and enzymatic activity assays, we report that: (1) R. denitrificans uses the anaplerotic pathways mainly via the malic enzyme to fix 10–15% of protein carbon from CO2; (2) R. denitrificans employs the Entner-Doudoroff (ED) pathway for carbohydrate metabolism and the non-oxidative pentose phosphate pathway for the biosynthesis of histidine, ATP, and coenzymes; (3) the Embden-Meyerhof-Parnas (EMP, glycolysis) pathway is not active and the enzymatic activity of 6-phosphofructokinase (PFK) cannot be detected in R. denitrificans; and (4) isoleucine can be synthesized from both threonine-dependent (20% total flux) and citramalate-dependent (80% total flux) pathways using pyruvate as the sole carbon source.

Retraction: Characterization of giant spheroplasts generated from the aerobic anoxygenic photosynthetic marine bacterium <i>Roseobacter litoralis</i>

“…In addition, the culture media of 9 samples of normal cells under light and 9 samples in the dark were measured as a control at 0, 6, 12, and 18 h of growth. absorption spectra of the normal R. litoralis cells and the spheroplasts at 0 h of growth showed peaks comparable to those previously reported for bacteriochlorophyll a (at 807 nm and 878 nm) (Shiba, 1991;Tang et al, 2009); however, no peaks were observed for the giant spheroplasts (Fig. 3).…”

Both Forward and Reverse TCA Cycles Operate in Green Sulfur Bacteria

“…Together, previ-ous and our studies suggest that the CO 2 -anaplerotic pathway is active during phototrophic growth of GSBs. The contribution of the CO 2 -anaplerotic pathway to the carbon metabolism of photoheterotrophic bacteria has also been identified experimentally (14,15). Thus, in addition to being required for the RTCA cycle, CO 2 is essential for assimilating pyruvate and acetate through the CO 2 -anaplerotic pathway and incorporating acetate through the catalysis of pyruvate:ferredoxin oxidoreductase (acetyl-CoA ϩ CO 2 ϩ 2Fd red ϩ 2H ϩ 3 pyruvate ϩ CoA ϩ 2Fd ox ) (Fig.…”

“…The methods used to extract RNA and perform QRT-PCR were described previously (14,15,18). QRT-PCR was performed to profile the gene expression under different growth conditions of C. tepdium.…”

Evolutionary Ecology of the Marine Roseobacter Clade

“…1). For all phototrophic roseobacters, genes for carbon fixation are absent, and thus, these processes may produce energy but do not directly provide fixed carbon; there has been speculation, however, of heightened anaplerotic pathways fueled by light (55). Nonobligate chemolithotrophy is also a common signature in Roseobacter genomes.…”