Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria

Abstract

Proteorhodopsin (PR) is present in half of surface ocean bacterioplankton, where its light-driven proton pumping provides energy to cells. Indeed, PR promotes growth or survival in different bacteria. However, the metabolic pathways mediating the light responses remain unknown. We analyzed growth of the PR-containing Dokdonia sp. MED134 (where light-stimulated growth had been found) in seawater with low concentrations of mixed [yeast extract and peptone (YEP)] or single (alanine, Ala) carbon compounds as models for rich and poor environments. We discovered changes in gene expression revealing a tightly regulated shift in central metabolic pathways between light and dark conditions. Bacteria showed relatively stronger light responses in Ala compared with YEP. Notably, carbon acquisition pathways shifted toward anaplerotic CO 2 fixation in the light, contributing 31 ± 8% and 24 ± 6% of the carbon incorporated into biomass in Ala and YEP, respectively. Thus, MED134 was a facultative double mixotroph, i.e., photo-and chemotrophic for its energy source and using both bicarbonate and organic matter as carbon sources. Unexpectedly, relative expression of the glyoxylate shunt genes (isocitrate lyase and malate synthase) was >300-fold higher in the light-but only in Ala-contributing a more efficient use of carbon from organic compounds. We explored these findings in metagenomes and metatranscriptomes and observed similar prevalence of the glyoxylate shunt compared with PR genes and highest expression of the isocitrate lyase gene coinciding with highest solar irradiance. Thus, regulatory interactions between dissolved organic carbon quality and central metabolic pathways critically determine the fitness of surface ocean bacteria engaging in PR phototrophy. microbial ecology | gene expression regulation | quantitative PCR

Expression of holo-proteorhodopsin in Synechocystis sp. PCC 6803

“…A similar growth-phase dependence of PR expression was observed in the naturally PRcontaining Dokdonia sp. MED134 (6). The drop in PR content during the stationary phase may be in part due to the promoter we selected, because it is known that psbA2 expression and transcript stability are light-intensity dependent (68)(69)(70)(71)(72)(73), and so is heterologous expression driven by this promoter (74,75).…”

“…The drop in PR content during the stationary phase may be in part due to the promoter we selected, because it is known that psbA2 expression and transcript stability are light-intensity dependent (68)(69)(70)(71)(72)(73), and so is heterologous expression driven by this promoter (74,75). It is worth noting that several of the recently discovered proteorhodopsins in 'chemotrophic', often psychrophilic, bacteria only contribute detectably to growth rate or cell yield when the cells are stressed and/or in stationary phase (6,(14)(15)(16)(18)(19)(20).…”

“…To show that PR is able to make a contribution to light-energy conversion in Synechocystis, we also made use of starvation/stressful conditions, just like it was initially done in E. coli (21) and in some of the organisms in which it is endogenously present (6,(14)(15)(16)(18)(19)(20). However, no fully consistent data have been obtained under these conditions so far.…”

“…Since then, PRs have turned out to be highly abundant in the oceans (6)(7)(8)(9), and organisms containing them, including a cyanobacterium (10) can be found in many other habitats as well (7,(11)(12)(13). In vivo experiments have shown that pumping of protons by PR can lead to increases in growth rate under nutrient-limited conditions (6,14,15), production of ATP (16), increased fixation of CO 2 (6,17), and/or survival under starvation or stress conditions (16,(18)(19)(20). However, these enhancements generally require nutrient-limitation or stress conditions before they exceed experimental error.…”

Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria

“…Dokdonia MED134 was the first bacterium shown to divide faster in the light compared to the dark under low organic carbon concentrations (Gómez-Consarnau et al, 2007). Subsequent studies on the same strain have shown that growth stimulation by PR in the light is linked to changes in central metabolism (Palovaara et al, 2014) and/or transcriptional changes associated with Na + pumping (Kimura et al, 2011). Recently, another flavobacterium, Nonlabens marinus S1-08, containing three different rhodopsin types (H + , Na + and Cl − pumps) has been described.…”