Limits...
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.

Show MeSH

Related in: MedlinePlus

Phylogenetic tree of microbial rhodopsin proteins showing diversity of functional classes. Tree is based on a total of 34 sequences (205 amino acid positions) using maximum likelihood and Bayesian inference methods. Numbers at nodes represent posterior probablities inferred by MrBayes (first value) and maximum likelihood bootstrap values using RaxML (second value). Only values greater than 50% are shown. GenBank accession numbers are shown in parentheses for each protein except H. roseosalivarus (IMG-ER database gene object ID) [22]. Sequences CV1 and CV2 were recovered by PCR amplification of environmental DNA from a solar saltern in Chula Vista, California, USA, using Nanohaloarchaeal-specific xenorhodopsin primers (see Additional File 1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3198991&req=5

Figure 1: Phylogenetic tree of microbial rhodopsin proteins showing diversity of functional classes. Tree is based on a total of 34 sequences (205 amino acid positions) using maximum likelihood and Bayesian inference methods. Numbers at nodes represent posterior probablities inferred by MrBayes (first value) and maximum likelihood bootstrap values using RaxML (second value). Only values greater than 50% are shown. GenBank accession numbers are shown in parentheses for each protein except H. roseosalivarus (IMG-ER database gene object ID) [22]. Sequences CV1 and CV2 were recovered by PCR amplification of environmental DNA from a solar saltern in Chula Vista, California, USA, using Nanohaloarchaeal-specific xenorhodopsin primers (see Additional File 1).

Mentions: Figure 1 shows a phylogenetic analysis using maximum likelihood and Bayesian inference methods for the ASR homologs, together with a set of representative protein sequences from all previously recognized functional microbial rhodopsin classes. Methods and experimental procedures are provided in Additional File 1. The phylogenetic tree also includes additional sequences we obtained by PCR amplification using primers specifically targeting Nanohaloarchaeal rhodopsin genes. These sequences were recovered from a hypersaline environment (South Bay Salt Works, Chula Vista, California, USA) that is geographically distant from the original isolation site of the Nanohaloarchaea genomes (Lake Tyrrell, Victoria, Australia). Tree topology shows robust clustering of all ASR homologs as a single clade, distinct from other rhodopsin types. We propose the name "xenorhodopsins" to describe this class of rhodopsin proteins, articulating the wide taxonomic diversity of its members.


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)

Phylogenetic tree of microbial rhodopsin proteins showing diversity of functional classes. Tree is based on a total of 34 sequences (205 amino acid positions) using maximum likelihood and Bayesian inference methods. Numbers at nodes represent posterior probablities inferred by MrBayes (first value) and maximum likelihood bootstrap values using RaxML (second value). Only values greater than 50% are shown. GenBank accession numbers are shown in parentheses for each protein except H. roseosalivarus (IMG-ER database gene object ID) [22]. Sequences CV1 and CV2 were recovered by PCR amplification of environmental DNA from a solar saltern in Chula Vista, California, USA, using Nanohaloarchaeal-specific xenorhodopsin primers (see Additional File 1).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Phylogenetic tree of microbial rhodopsin proteins showing diversity of functional classes. Tree is based on a total of 34 sequences (205 amino acid positions) using maximum likelihood and Bayesian inference methods. Numbers at nodes represent posterior probablities inferred by MrBayes (first value) and maximum likelihood bootstrap values using RaxML (second value). Only values greater than 50% are shown. GenBank accession numbers are shown in parentheses for each protein except H. roseosalivarus (IMG-ER database gene object ID) [22]. Sequences CV1 and CV2 were recovered by PCR amplification of environmental DNA from a solar saltern in Chula Vista, California, USA, using Nanohaloarchaeal-specific xenorhodopsin primers (see Additional File 1).
Mentions: Figure 1 shows a phylogenetic analysis using maximum likelihood and Bayesian inference methods for the ASR homologs, together with a set of representative protein sequences from all previously recognized functional microbial rhodopsin classes. Methods and experimental procedures are provided in Additional File 1. The phylogenetic tree also includes additional sequences we obtained by PCR amplification using primers specifically targeting Nanohaloarchaeal rhodopsin genes. These sequences were recovered from a hypersaline environment (South Bay Salt Works, Chula Vista, California, USA) that is geographically distant from the original isolation site of the Nanohaloarchaea genomes (Lake Tyrrell, Victoria, Australia). Tree topology shows robust clustering of all ASR homologs as a single clade, distinct from other rhodopsin types. We propose the name "xenorhodopsins" to describe this class of rhodopsin proteins, articulating the wide taxonomic diversity of its members.

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