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Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus.

Schlesner M, Miller A, Streif S, Staudinger WF, Müller J, Scheffer B, Siedler F, Oesterhelt D - BMC Microbiol. (2009)

Bottom Line: Deletion of the second DUF439 protein had only minimal effects.Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context.Altogether, these results demonstrate that, in the archaeal domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling to the flagellar apparatus.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. schlesne@biochem.mpg.de

ABSTRACT

Background: Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown.

Results: Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che) proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla) proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a) photophobic responses were measured by a computer-based cell tracking system b) flagellar rotational bias was determined by dark-field microscopy, and c) chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea sequenced so far, but not in those of other archaeal species. Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context.

Conclusion: Altogether, these results demonstrate that, in the archaeal domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling to the flagellar apparatus.

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Phylogenetic analysis of DUF439 proteins. Unrooted phylogenetic tree by neighbor-joining, calculated from the multiple alignment shown in Figure 6. Species can be derived from the prefix of the protein identifier as explained in the legend of Figure 6.
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Figure 7: Phylogenetic analysis of DUF439 proteins. Unrooted phylogenetic tree by neighbor-joining, calculated from the multiple alignment shown in Figure 6. Species can be derived from the prefix of the protein identifier as explained in the legend of Figure 6.

Mentions: Two or more copies of DUF439 proteins were only found in the motile haloarchaea H. salinarum, N. pharaonis, and H. marismortui. All three species contain a second homolog in or adjacent to the che gene region (OE2404R in H. salinarum). These second homologs lack several residues conserved in all other proteins of the family DUF439 (see boxes in Figure 6), and probably fulfill a different function than the main group of DUF439 proteins. This is consistent with the phenotypic results obtained for the deletions: the deletion of OE2404R resulted, other than the deletion of OE2402F, only in a weak phenotype. Phylogenetic analysis (Figure 7) revealed that the second homologs in the che gene region of the haloarchaea (OE2404R, NP2162A, rrnAC2213) form a separate branch in the phylogenetic tree, indicating that they probably arose by a gene duplication prior to the divergence of the haloarchaea. H. marismortui contains two additional DUF439 homologs located apart from the che gene region. These two paralogs resemble more the main group of DUF439 proteins than the second homolog of the haloarchaea, as can be seen in the multiple alignment and the phylogenetic tree. If they also fulfill a function in taxis signaling, it remains elusive.


Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus.

Schlesner M, Miller A, Streif S, Staudinger WF, Müller J, Scheffer B, Siedler F, Oesterhelt D - BMC Microbiol. (2009)

Phylogenetic analysis of DUF439 proteins. Unrooted phylogenetic tree by neighbor-joining, calculated from the multiple alignment shown in Figure 6. Species can be derived from the prefix of the protein identifier as explained in the legend of Figure 6.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666748&req=5

Figure 7: Phylogenetic analysis of DUF439 proteins. Unrooted phylogenetic tree by neighbor-joining, calculated from the multiple alignment shown in Figure 6. Species can be derived from the prefix of the protein identifier as explained in the legend of Figure 6.
Mentions: Two or more copies of DUF439 proteins were only found in the motile haloarchaea H. salinarum, N. pharaonis, and H. marismortui. All three species contain a second homolog in or adjacent to the che gene region (OE2404R in H. salinarum). These second homologs lack several residues conserved in all other proteins of the family DUF439 (see boxes in Figure 6), and probably fulfill a different function than the main group of DUF439 proteins. This is consistent with the phenotypic results obtained for the deletions: the deletion of OE2404R resulted, other than the deletion of OE2402F, only in a weak phenotype. Phylogenetic analysis (Figure 7) revealed that the second homologs in the che gene region of the haloarchaea (OE2404R, NP2162A, rrnAC2213) form a separate branch in the phylogenetic tree, indicating that they probably arose by a gene duplication prior to the divergence of the haloarchaea. H. marismortui contains two additional DUF439 homologs located apart from the che gene region. These two paralogs resemble more the main group of DUF439 proteins than the second homolog of the haloarchaea, as can be seen in the multiple alignment and the phylogenetic tree. If they also fulfill a function in taxis signaling, it remains elusive.

Bottom Line: Deletion of the second DUF439 protein had only minimal effects.Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context.Altogether, these results demonstrate that, in the archaeal domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling to the flagellar apparatus.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. schlesne@biochem.mpg.de

ABSTRACT

Background: Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown.

Results: Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che) proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla) proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a) photophobic responses were measured by a computer-based cell tracking system b) flagellar rotational bias was determined by dark-field microscopy, and c) chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea sequenced so far, but not in those of other archaeal species. Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context.

Conclusion: Altogether, these results demonstrate that, in the archaeal domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling to the flagellar apparatus.

Show MeSH
Related in: MedlinePlus