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Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria.

Ugalde JA, Podell S, Narasingarao P, Allen EE - Biol. Direct (2011)

Bottom Line: Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized.We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea.Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.

View Article: PubMed Central - HTML - PubMed

Affiliation: Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.

ABSTRACT
Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.

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Protein alignment of key amino acid segments. Sequences include all xenorhodopsin homologs plus selected representatives of previously characterized microbial rhodopsin functional classes; bacteriorhodopsin (BR), halorhodopsin (HR) and sensory rhodopsins I (SR-I), II (SR-II) and III (SR-III). Shaded boxes indicate conserved residues involved in retinal binding [3]. The black box in Helix G shows a conserved Asp to Pro substitution in all xenorhodopsin proteins at this position. Retinal Schiff base proton acceptor (closed triangle) and proton donor (open triangle) residues are marked in Helix C.
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Figure 2: Protein alignment of key amino acid segments. Sequences include all xenorhodopsin homologs plus selected representatives of previously characterized microbial rhodopsin functional classes; bacteriorhodopsin (BR), halorhodopsin (HR) and sensory rhodopsins I (SR-I), II (SR-II) and III (SR-III). Shaded boxes indicate conserved residues involved in retinal binding [3]. The black box in Helix G shows a conserved Asp to Pro substitution in all xenorhodopsin proteins at this position. Retinal Schiff base proton acceptor (closed triangle) and proton donor (open triangle) residues are marked in Helix C.

Mentions: Amino acid alignments of residues known to determine function for previously characterized microbial rhodopsins are inconsistent with proton or chloride transporting activity for xenorhodopsins, suggesting a possible sensory role (see Additional File 2 for full alignment). Figure 2 shows that residues required to bind the retinal chromophore molecule are conserved across all xenorhodopsin group members. Ion transporting rhodopsins can be distinguished from sensory rhodopsins by comparing the residues that serve as the retinal Schiff base proton donor and proton acceptor during the photocycle [2,13]. These residues correspond to Asp98 (acceptor) and Asp109 (donor) in the H. salinarum bacteriorhodopsin (Helix C). Consistent with previously described sensory rhodopsins, ASR and all other xenorhodopsin homologs lack the canonical Asp residue at the donor position, a hallmark of proton translocating rhodopsins. Likewise, known sensory rhodopsins and xenorhodopsins both lack the Thr (acceptor) and Ala (donor) configuration diagnostic of chloride pumps (Figure 2).


Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria.

Ugalde JA, Podell S, Narasingarao P, Allen EE - Biol. Direct (2011)

Protein alignment of key amino acid segments. Sequences include all xenorhodopsin homologs plus selected representatives of previously characterized microbial rhodopsin functional classes; bacteriorhodopsin (BR), halorhodopsin (HR) and sensory rhodopsins I (SR-I), II (SR-II) and III (SR-III). Shaded boxes indicate conserved residues involved in retinal binding [3]. The black box in Helix G shows a conserved Asp to Pro substitution in all xenorhodopsin proteins at this position. Retinal Schiff base proton acceptor (closed triangle) and proton donor (open triangle) residues are marked in Helix C.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3198991&req=5

Figure 2: Protein alignment of key amino acid segments. Sequences include all xenorhodopsin homologs plus selected representatives of previously characterized microbial rhodopsin functional classes; bacteriorhodopsin (BR), halorhodopsin (HR) and sensory rhodopsins I (SR-I), II (SR-II) and III (SR-III). Shaded boxes indicate conserved residues involved in retinal binding [3]. The black box in Helix G shows a conserved Asp to Pro substitution in all xenorhodopsin proteins at this position. Retinal Schiff base proton acceptor (closed triangle) and proton donor (open triangle) residues are marked in Helix C.
Mentions: Amino acid alignments of residues known to determine function for previously characterized microbial rhodopsins are inconsistent with proton or chloride transporting activity for xenorhodopsins, suggesting a possible sensory role (see Additional File 2 for full alignment). Figure 2 shows that residues required to bind the retinal chromophore molecule are conserved across all xenorhodopsin group members. Ion transporting rhodopsins can be distinguished from sensory rhodopsins by comparing the residues that serve as the retinal Schiff base proton donor and proton acceptor during the photocycle [2,13]. These residues correspond to Asp98 (acceptor) and Asp109 (donor) in the H. salinarum bacteriorhodopsin (Helix C). Consistent with previously described sensory rhodopsins, ASR and all other xenorhodopsin homologs lack the canonical Asp residue at the donor position, a hallmark of proton translocating rhodopsins. Likewise, known sensory rhodopsins and xenorhodopsins both lack the Thr (acceptor) and Ala (donor) configuration diagnostic of chloride pumps (Figure 2).

Bottom Line: Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized.We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea.Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.

View Article: PubMed Central - HTML - PubMed

Affiliation: Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.

ABSTRACT
Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.

Show MeSH
Related in: MedlinePlus