Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria

Abstract

Light-activated, ion-pumping rhodopsins are broadly distributed among many different bacteria and archaea inhabiting the photic zone of aquatic environments. Bacterial proton-or sodium-translocating rhodopsins can convert light energy into a chemiosmotic force that can be converted into cellular biochemical energy, and thus represent a widespread alternative form of photoheterotrophy. Here we report that the genome of the marine flavobacterium Nonlabens marinus S1-08 T encodes three different types of rhodopsins: Nonlabens marinus rhodopsin 1 (NM-R1), Nonlabens marinus rhodopsin 2 (NM-R2), and Nonlabens marinus rhodopsin 3 (NM-R3). Our functional analysis demonstrated that NM-R1 and NM-R2 are light-driven outward-translocating H + and Na + pumps, respectively. Functional analyses further revealed that the lightactivated NM-R3 rhodopsin pumps Cl − ions into the cell, representing the first chloride-pumping rhodopsin uncovered in a marine bacterium. Phylogenetic analysis revealed that NM-R3 belongs to a distinct phylogenetic lineage quite distant from archaeal inward Cl − -pumping rhodopsins like halorhodopsin, suggesting that different types of chloride-pumping rhodopsins have evolved independently within marine bacterial lineages. Taken together, our data suggest that similar to haloarchaea, a considerable variety of rhodopsin types with different ion specificities have evolved in marine bacteria, with individual marine strains containing as many as three functionally different rhodopsins.

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

“…While MED134 and DSW-1 T have one copy of the rhodopsin gene, PRO95 contains two different rhodopsin genes: a H + rhodopsin (PR) and a Na + rhodopsin (NaR), based on sequence comparison (Yoshizawa et al, 2014;Bertsova et al, 2015). This Abbreviation: bp, base pair.…”

“…Recently, another flavobacterium, Nonlabens marinus S1-08, containing three different rhodopsin types (H + , Na + and Cl − pumps) has been described. Similarly to MED134, this bacterium grows better in the light compared with dark in a low organic matter medium (Yoshizawa et al, 2014). In contrast to these two Dokdonia (S1-08 and MED134), another strain of the same genus, PRO95, has not yet shown enhanced growth or increased PR gene expression in the light compared to the dark (Riedel et al, 2010).…”

“…In contrast to these two Dokdonia (S1-08 and MED134), another strain of the same genus, PRO95, has not yet shown enhanced growth or increased PR gene expression in the light compared to the dark (Riedel et al, 2010). PRO95 also has more than one rhodopsin type and, according to sequence similarities, one functions to pump H + and the other one to pump Na + ions (Yoshizawa et al, 2014, Bertsova et al, 2015. Together, the studies of PR in cultured bacteria reflect a diversity of physiological responses that still cannot be predicted solely based on whole-genome sequence information, and therefore a combination of different research approaches are required to elucidate the specific mechanisms of PR photoheterotrophy.…”

On the role, ecology, phylogeny, and structure of dual-family immunophilins

“…Essentially, all Flavobacteria switch from rodshaped cells to long filaments that can intertwine to form clumps (Jooste and Hugo 1999). They also contain a variety of pigments such as yellow pigments (Verma and Rathore 2015) or proteorhodopsin and can be stimulated by light (Gómez-Consarnau et al 2007); Yoshizawa et al 2014). In another example, R. biformata forms characteristic rusty red pigmented colonies and, like many Flavobacteria, contains genes for the complex pathway of carotenoid biosynthesis (Oh et al, 2009).…”

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

“…A while after these discoveries, microbial rhodopsins were thought to be restricted to hypersaline environments. However, because of the recent developments in molecular biology techniques, three different functional rhodopsins, a light-driven H ϩ -pumping proteorhodopsin, a light-driven Na ϩ (sodium ion)-pumping rhodopsin, and a light-driven Cl Ϫ -pumping rhodopsin, were found in marine microorganisms (3)(4)(5). Now it is known that ion-translocating rhodopsins are widely distributed in a variety of microorganisms in all three domains of life (6 -8).…”