The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity

Bolhuis, Henk; Palm, Peter; Wende, Andy; Falb, Michaela; Rampp, Markus; Rodrı́guez-Valera, Francisco; Pfeiffer, Friedhelm; Oesterhelt, Dieter

doi:10.1186/1471-2164-7-169

Cited by 260 publications

(239 citation statements)

References 40 publications

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“…The noncyanobacterial matches are more phylogenetically diverse than for some of the other BOGUAY elements discussed here. For the GyrB intein, these include halophilic archaea (notably Haloquadratum walsbyi, "Walsby's square bacterium" [52]) and two species of sulfur-oxidizing gammaproteobacteria (Fig. 5A), while the BOGUAY DnaE intein is related to a planctomycete and a Bacteroidetes sequence (Fig.…”

Section: Resultsmentioning

confidence: 99%

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

MacGregor

Biddle

Teske

2013

Appl Environ Microbiol

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The draft genome sequence of a single orange Beggiatoa ("Candidatus Maribeggiatoa") filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to the fdxN excision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceae matches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

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Section: Resultsmentioning

confidence: 99%

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

MacGregor

Biddle

Teske

2013

Appl Environ Microbiol

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“…The transducer proteins HtrI for SRI and HtrII for SRII belong to a family of two transmembrane helical proteins similar to chemoreceptors Tar and Tsr in E. coli (31), and they are termed methyl-accepting chemotaxis proteins (31). It should be noted that no putative transducer protein genes were found, not only in the sequences downstream of HwBR or MR but in the whole genome of H. walsbyi (33).…”

Section: Two Microbial Rhodopsin Proteins In the Genome Of Hmentioning

confidence: 98%

“…1a and supplemental Fig. S1) and also one gene that encodes a halorhodopsin-like protein (33). The amino acid sequence of bopII (HwBR) is distantly related to BR from H. salinarum (ϳ52% identity) and contains all amino acid residues (Asp-85, Asp-96, Asp-201, Glu-194, and Glu-204 in BR) identified as necessary for its function (Fig.…”

Section: Two Microbial Rhodopsin Proteins In the Genome Of Hmentioning

confidence: 99%

A Microbial Rhodopsin with a Unique Retinal Composition Shows Both Sensory Rhodopsin II and Bacteriorhodopsin-like Properties

Sudo

Ihara

Kobayashi

et al. 2011

Journal of Biological Chemistry

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Rhodopsins possess retinal chromophore surrounded by seven transmembrane ␣-helices, are widespread in prokaryotes and in eukaryotes, and can be utilized as optogenetic tools. Although rhodopsins work as distinctly different photoreceptors in various organisms, they can be roughly divided according to their two basic functions, light-energy conversion and light-signal transduction. In microbes, light-driven proton transporters functioning as light-energy converters have been modified by evolution to produce sensory receptors that relay signals to transducer proteins to control motility. In this study, we cloned and characterized two newly identified microbial rhodopsins from Haloquadratum walsbyi. One of them has photochemical properties and a proton pumping activity similar to the well known proton pump bacteriorhodopsin (BR). The other, named middle rhodopsin (MR), is evolutionarily transitional between BR and the phototactic sensory rhodopsin II (SRII), having an SRII-like absorption maximum, a BR-like photocycle, and a unique retinal composition. The wild-type MR does not have a light-induced proton pumping activity. On the other hand, a mutant MR with two key hydrogen-bonding residues located at the interaction surface with the transducer protein HtrII shows robust phototaxis responses similar to SRII, indicating that MR is potentially capable of the signaling. These results demonstrate that color tuning and insertion of the critical threonine residue occurred early in the evolution of sensory rhodopsins. MR may be a missing link in the evolution from type 1 rhodopsins (microorganisms) to type 2 rhodopsins (animals), because it is the first microbial rhodopsin known to have 11-cis-retinal similar to type 2 rhodopsins.Rhodopsin molecules are photochemically active membrane-embedded proteins having seven transmembrane ␣-helices and retinal chromophore (vitamin A aldehyde) (1, 2). Rhodopsins are classified into two groups, microbial (type 1) and animal (type 2) rhodopsins (3). Type 1 rhodopsins are widespread in the microbial world in prokaryotes (bacteria and archaea) and in eukaryotes (fungi and algae) (1, 4 -7), and type 2 rhodopsins, such as visual pigments, are G-proteincoupled receptors, widespread in vertebrates and in invertebrates (3,8). An interesting feature of this photoactive protein family is a wide range of seemingly dissimilar functions performed by its members. Some rhodopsins are light-driven transporters, such as proton pumps bacteriorhodopsin (BR) 2 in haloarchaea, xanthorhodopsin in halophilic bacteria, proteorhodopsin in marine bacteria, and Leptosphaeria rhodopsin in fungi (1, 9 -13). Those proteins generate an electrochemical membrane potential upon light activation, which is utilized by ATP synthase to produce ATP (14). Other rhodopsins are light sensors, such as the phototaxis receptors sensory rhodopsins I (SRI) and II (SRII) in haloarchaea (1, 5) and mammalian rod rhodopsin and color visual pigments both in vertebrates and in invertebrates (3,8). These sensory receptors relay signals...

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“…These calculated values are remarkably lower than 0.60, which is the putative lower limit enabling life on Earth (Oren, 2008 ) . Of particular relevance is the ability of the haloarchaeon Haloquadratum walsbyi to live in low water activity environments, for which the presence of speci fi c proteins that are able to provide an effective protection against desiccation has been suggested (Bolhuis et al, 2006 ) .…”

Section: Water Activity: Habitability and Cell Densitiesmentioning

confidence: 99%

The Role of Terrestrial Analogs in the Exploration of the Habitability of Martian Evaporitic Environments

Barbieri

2013

Habitability of Other Planets and Satellites

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Roberto Barbieri is a professor of Paleontology at the University of Bologna, and his current research focuses on the geological role of microbes in small-scale processes and the microbes-sediment relationships in extreme environments. In particular, he works on (1) modern and fossil cold-seep (methane-related) ecosystems and their geological record and (2) the geomicrobiology of hypersaline continental environments (modern and fossil) from arid regions. He also has a strong interest in the exploration of the terrestrial analogs of Martian environments in an astrobiological perspective. He maintains an interest in the study of fossil foraminifera.

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The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity

Cited by 260 publications

References 40 publications

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

A Microbial Rhodopsin with a Unique Retinal Composition Shows Both Sensory Rhodopsin II and Bacteriorhodopsin-like Properties

The Role of Terrestrial Analogs in the Exploration of the Habitability of Martian Evaporitic Environments

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