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Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.

Hamacher K, Greiner T, Ogata H, Van Etten JL, Gebhardt M, Villarreal LP, Cosentino C, Moroni A, Thiel G - PLoS ONE (2012)

Bottom Line: To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced.However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium.Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Group, Technische Universit├Ąt Darmstadt, Darmstadt, Germany.

ABSTRACT
Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.

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Related in: MedlinePlus

Consensus, unrooted tree obtained by Bayesian estimates of phylogenies for the amino acid and nucleotide sequences, as well as for a protein parsimony approach.All clades showed a statistical support of 1 (=100%) with reference to the six independent trees computed (Bayesian estimate). The same holds for the statistical support with reference to the 1,000 replicas fed into the protpars program (protein parsimony). The branch length in this tree is arbitrary. The only difference between these is a weaker support in one of the clades (50% support, as indicated by the red star). Note that all phylogenetic approaches resulted in the same tree. Red entries indicate algae channels, while blue entries are viral channels.
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pone-0038826-g006: Consensus, unrooted tree obtained by Bayesian estimates of phylogenies for the amino acid and nucleotide sequences, as well as for a protein parsimony approach.All clades showed a statistical support of 1 (=100%) with reference to the six independent trees computed (Bayesian estimate). The same holds for the statistical support with reference to the 1,000 replicas fed into the protpars program (protein parsimony). The branch length in this tree is arbitrary. The only difference between these is a weaker support in one of the clades (50% support, as indicated by the red star). Note that all phylogenetic approaches resulted in the same tree. Red entries indicate algae channels, while blue entries are viral channels.

Mentions: Next we analyzed the phylogenetic relationship of the channels from C. variabilis and viruses using Bayesian estimates. Fig. 6 shows the consensus tree of phylogenies obtained by Bayesian estimation from nucleotide and amino acid sequences, as well as by a protein maximum parsimony method. This analysis indicated that the viral channels form a clade, which is clearly separate from the second clade containing the algal channels. A K+ channel (CrK) from another unicellular green alga, C. reinhardtii, grouped with a homolog from C. variabilis. The clear separation between the viral K+ channels and the algal channels occurs even when the amino acid or nucleotide sequences were analyzed individually; this separation is evident in spite of the large diversity on the nucleotide level (Fig. S3). Furthermore, the same results are obtained using different statistical methods (see Materials and Methods).


Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.

Hamacher K, Greiner T, Ogata H, Van Etten JL, Gebhardt M, Villarreal LP, Cosentino C, Moroni A, Thiel G - PLoS ONE (2012)

Consensus, unrooted tree obtained by Bayesian estimates of phylogenies for the amino acid and nucleotide sequences, as well as for a protein parsimony approach.All clades showed a statistical support of 1 (=100%) with reference to the six independent trees computed (Bayesian estimate). The same holds for the statistical support with reference to the 1,000 replicas fed into the protpars program (protein parsimony). The branch length in this tree is arbitrary. The only difference between these is a weaker support in one of the clades (50% support, as indicated by the red star). Note that all phylogenetic approaches resulted in the same tree. Red entries indicate algae channels, while blue entries are viral channels.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369850&req=5

pone-0038826-g006: Consensus, unrooted tree obtained by Bayesian estimates of phylogenies for the amino acid and nucleotide sequences, as well as for a protein parsimony approach.All clades showed a statistical support of 1 (=100%) with reference to the six independent trees computed (Bayesian estimate). The same holds for the statistical support with reference to the 1,000 replicas fed into the protpars program (protein parsimony). The branch length in this tree is arbitrary. The only difference between these is a weaker support in one of the clades (50% support, as indicated by the red star). Note that all phylogenetic approaches resulted in the same tree. Red entries indicate algae channels, while blue entries are viral channels.
Mentions: Next we analyzed the phylogenetic relationship of the channels from C. variabilis and viruses using Bayesian estimates. Fig. 6 shows the consensus tree of phylogenies obtained by Bayesian estimation from nucleotide and amino acid sequences, as well as by a protein maximum parsimony method. This analysis indicated that the viral channels form a clade, which is clearly separate from the second clade containing the algal channels. A K+ channel (CrK) from another unicellular green alga, C. reinhardtii, grouped with a homolog from C. variabilis. The clear separation between the viral K+ channels and the algal channels occurs even when the amino acid or nucleotide sequences were analyzed individually; this separation is evident in spite of the large diversity on the nucleotide level (Fig. S3). Furthermore, the same results are obtained using different statistical methods (see Materials and Methods).

Bottom Line: To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced.However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium.Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Group, Technische Universit├Ąt Darmstadt, Darmstadt, Germany.

ABSTRACT
Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.

Show MeSH
Related in: MedlinePlus