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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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Genomic neighborhood of xenorhodopsin (XR) genes. Functional annotations were obtained from NCBI [23] and IMG [22]. Similar gene functions are color-coded. Hypothetical proteins are unlabeled and shown in gray.
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Figure 3: Genomic neighborhood of xenorhodopsin (XR) genes. Functional annotations were obtained from NCBI [23] and IMG [22]. Similar gene functions are color-coded. Hypothetical proteins are unlabeled and shown in gray.

Mentions: An important element of previously characterized sensory rhodopsins in halophilic Archaea is the presence of a signal transduction mechanism, most often genetically encoded in a genomic position adjacent to the rhodopsin gene [18]. In Anabaena (Nostoc) sp. PCC 7120, the proposed soluble transducer protein ASRT (Anabaena sensory rhodopsin transducer) is encoded by a gene in the same operon as ASR [18] (Figure 3). Consistent with its putative role in light-activated sensory transduction, the ASRT protein has been shown to bind DNA, specifically the promoter region of genes involved in the synthesis of light-harvesting accessory pigments [19]. However, no homologs of ASRT were identified in other genomes containing a xenorhodopsin gene, suggesting the ASR-ASRT association is a specific feature of Anabaena (Nostoc) sp. PCC 7120. Moreover, the identification of ASRT homologs in numerous bacterial and archaeal genomes that lack an ASR (xenorhodopsin) homolog suggests the ASRT protein family is not specific to photosensory signal transduction processes.


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)

Genomic neighborhood of xenorhodopsin (XR) genes. Functional annotations were obtained from NCBI [23] and IMG [22]. Similar gene functions are color-coded. Hypothetical proteins are unlabeled and shown in gray.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Genomic neighborhood of xenorhodopsin (XR) genes. Functional annotations were obtained from NCBI [23] and IMG [22]. Similar gene functions are color-coded. Hypothetical proteins are unlabeled and shown in gray.
Mentions: An important element of previously characterized sensory rhodopsins in halophilic Archaea is the presence of a signal transduction mechanism, most often genetically encoded in a genomic position adjacent to the rhodopsin gene [18]. In Anabaena (Nostoc) sp. PCC 7120, the proposed soluble transducer protein ASRT (Anabaena sensory rhodopsin transducer) is encoded by a gene in the same operon as ASR [18] (Figure 3). Consistent with its putative role in light-activated sensory transduction, the ASRT protein has been shown to bind DNA, specifically the promoter region of genes involved in the synthesis of light-harvesting accessory pigments [19]. However, no homologs of ASRT were identified in other genomes containing a xenorhodopsin gene, suggesting the ASR-ASRT association is a specific feature of Anabaena (Nostoc) sp. PCC 7120. Moreover, the identification of ASRT homologs in numerous bacterial and archaeal genomes that lack an ASR (xenorhodopsin) homolog suggests the ASRT protein family is not specific to photosensory signal transduction processes.

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