| extremely halophilic bacteria in crystallizer ponds from solar salterns. | it is generally assumed that hypersaline environments with sodium chloride concentrations close to saturation are dominated by halophilic members of the domain archaea, while bacteria are not considered to be relevant in this kind of environment. here, we report the high abundance and growth of a new group of hitherto-uncultured bacteria in crystallizer ponds (salinity, from 30 to 37%) from multipond solar salterns. in the present study, these bacteria constituted from 5 to 25% of the total prok ... | 2000 | 10877805 |
| the contribution of halophilic bacteria to the red coloration of saltern crystallizer ponds(1). | analysis of the pigments extracted from solar saltern crystallizer ponds in santa pola near alicante and on the balearic island of mallorca, spain, showed that 5-7.5% of the total prokaryotic pigment absorbance could be attributed to a novel carotenoid or carotenoid-like compound. this unidentified pigment was identical to the sole pigment present in salinibacter ruber, the only described member of a newly discovered genus of red halophilic bacteria related to the cytophaga-flavobacterium-bacter ... | 2001 | 11451516 |
| salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the bacteria from saltern crystallizer ponds. | five brightly red-pigmented, motile, rod-shaped, extremely halophilic bacteria were isolated from saltern crystallizer ponds in alicante (two strains) and mallorca (three strains), spain. they grew optimally at salt concentrations between 20 and 30% and did not grow below 15% salts. thus, these isolates are among the most halophilic organisms known within the domain bacteria. the temperature optimum was 37-47 degrees c. a single, yet to be identified pigment was present, with an absorption maxim ... | 2002 | 11931160 |
| prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. | bacterial and archaeal assemblages have been studied in a multipond solar saltern using a range of microbial ecology techniques by four laboratories simultaneously. these include 16s rdna sequencing from both denaturing gradient gel electrophoresis (dgge) and clone libraries, and culturing methods. water samples from eight ponds were analysed, covering a salinity range from near sea water (4% salt) to saturated sodium chloride (37% salt; ponds called crystallizers). clone libraries focused on po ... | 2002 | 12071980 |
| amino acid composition of bulk protein and salt relationships of selected enzymes of salinibacter ruber, an extremely halophilic bacterium. | the extremely halophilic bacterium salinibacter ruber was previously shown to have a high intracellular potassium content, comparable to that of halophilic archaea of the family halobacteriaceae. the amino acid composition of its bulk protein showed a high content of acidic amino acids, a low abundance of basic amino acids, a low content of hydrophobic amino acids, and a high abundance of serine. we tested the level of four cytoplasmic enzymatic activities at different kcl and nacl concentration ... | 2002 | 12072957 |
| new c(40)-carotenoid acyl glycoside as principal carotenoid in salinibacter ruber, an extremely halophilic eubacterium. | the principal (>96% of total) carotenoid in the novel, extremely halophilic eubacterium salinibacter ruber, here called salinixanthin (1), has been assigned the structure (all-e,2's)-2'-hydroxy-1'-[6-o-(13-methyltetradecanoyl)-beta-d-glycopyranosyloxy]-3',4'-didehydro-1',2'-dihydro-beta,psi-caroten-4-one by spectrometric (vis, eims, (1)hnmr, cd, gcms) and chemical methods. | 2002 | 12350161 |
| intracellular ion and organic solute concentrations of the extremely halophilic bacterium salinibacter ruber. | salinibacter ruber is a red obligatory aerobic chemoorganotrophic extremely halophilic bacterium, related to the order cytophagales. it was isolated from saltern crystallizer ponds, and requires at least 150 g l(-1) salt for growth. the cells have an extremely high potassium content, the ratio k(+)/protein being in the same range as in halophilic archaea of the order halobacteriales. x-ray microanalysis in the electron microscope of cells grown in medium of 250 g l(-1) salt confirmed the high in ... | 2002 | 12486458 |
| metabolism of chloride in halophilic prokaryotes. | while much understanding has been achieved on the intracellular sodium and potassium concentrations of halophilic and halotolerant microorganisms and on their regulation, we know little on the metabolism of anions. archaea of the family halobacteriaceae contain molar concentrations of chloride, which is pumped into the cells by cotransport with sodium ions and/or using the light-driven primary chloride pump halorhodopsin. most halophilic and halotolerant representatives of the bacterial domain c ... | 2003 | 12728360 |
| sugar metabolism in the extremely halophilic bacterium salinibacter ruber. | growth of salinibacter ruber, a red, extremely halophilic bacterium phylogenetically affiliated with the flavobacterium/cytophaga branch of the domain bacteria, is stimulated by a small number of sugars (glucose, maltose, starch at 1 g l(-1)). glucose consumption starts after other substrates have been depleted. glucose metabolism proceeds via a constitutive, salt-inhibited hexokinase and a constitutive salt-dependent nicotinamide adenine dinucleotide phosphate (nadp)-linked glucose-6-phosphate ... | 2003 | 12799004 |
| substrate uptake in extremely halophilic microbial communities revealed by microautoradiography and fluorescence in situ hybridization. | the combination of fluorescence in situ hybridization and microautoradiography (fish-mar approach) was applied to brine samples of a solar saltern crystallizer pond from mallorca (spain) where the simultaneous occurrence of salinibacter spp. and the conspicuous square archaea had been detected. radioactively labeled bicarbonate, acetate, glycerol, and an amino acid mixture were tested as substrates for the microbial populations inhabiting such brines. the results indicated that hitherto uncultur ... | 2003 | 12820037 |
| characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (t-rflp). | the diversity of prokaryotes inhabiting solar saltern ponds was determined by thermal melting and reassociation of community dna. these measurements were compared with fingerprinting techniques such as terminal restriction fragment length polymorphisms (t-rflp) analysis, denaturant gradient gel electrophoresis (dgge), and cloning and sequencing approaches. three ponds with salinities of 22, 32, and 37% (nacl saturation) were studied. the combination of independent molecular techniques to estimat ... | 2003 | 12904916 |
| occurrence of two different glutamate dehydrogenase activities in the halophilic bacterium salinibacter ruber. | salinibacter ruber, an extremely halophilic member of the domain bacteria, has two different cytoplasmic glutamate dehydrogenase activities, marked as gdhi and gdhii. gdhi showed a strong dependence on high salt concentrations for stability, but not for activity, displaying maximal activity in the absence of salts. gdhii depended on high salt concentrations for both activity and stability. it catalyzed amination of 2-oxoglutarate with optimal activity in 3 m kcl at ph 8. no activating effect was ... | 2003 | 13129625 |
| glycerol metabolism in the extremely halophilic bacterium salinibacter ruber. | growth of salinibacter ruber, a red, extremely halophilic bacterium phylogenetically affiliated with the flavobacterium/cytophaga branch of the domain bacteria, is stimulated by glycerol. in contrast to glucose consumption, which starts only after more easily degradable substrates present in yeast extract have been depleted, glycerol is consumed during the earliest growth phases. when u-(14)c-labeled glycerol was added to the culture, up to 25% of the radioactivity was incorporated by the cells. ... | 2004 | 15033241 |
| molecular adaptation: the malate dehydrogenase from the extreme halophilic bacterium salinibacter ruber behaves like a non-halophilic protein. | malate dehydrogenase from the extreme halophilic bacterium, salinibacter ruber (sr maldh) was purified and characterised as a tetramer by sedimentation velocity measurements, showing the enzyme belongs to the ldh-like group of maldhs. in contrast to most other halophilic enzymes, which unfold when incubated at low salt concentration, sr maldh is completely stable in absence of salt. its amino acid composition does not display the strong acidic character specific of halophilic proteins. the enzym ... | 2004 | 15194233 |
| novel sulfonolipid in the extremely halophilic bacterium salinibacter ruber. | salinibacter ruber is an extremely halophilic bacterium, phylogenetically affiliated with the flavobacterium/cytophaga branch of the domain bacteria. electrospray mass analyses (negative ion) of the total lipid extract of a pure culture of s. ruber shows a characteristic peak at m/z 660 as the most prominent peak in the high-mass range of the spectrum. a novel sulfonolipid, giving rise to the molecular ion [m-h]- of m/z 660, has been identified. the sulfonolipid isolated and purified by thin-lay ... | 2004 | 15528534 |
| intraspecific comparative analysis of the species salinibacter ruber. | salinibacter ruber is the first extremely halophilic member of the bacteria domain of proven environmental relevance in hypersaline brines at or approaching nacl saturation, that has been brought to pure culture. a collection of 17 strains isolated from five different geographical locations (mallorca, alicante, ebro delta, canary islands, and peruvian andes) were studied following the currently accepted taxonomic approach. additionally, random amplification of genomic dna led to the phenetic ana ... | 2005 | 15841344 |
| xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. | energy transfer from light-harvesting carotenoids to chlorophyll is common in photosynthesis, but such antenna pigments have not been observed in retinal-based ion pumps and photoreceptors. here we describe xanthorhodopsin, a proton-pumping retinal protein/carotenoid complex in the eubacterium salinibacter ruber. the wavelength dependence of the rate of pumping and difference absorption spectra measured under a variety of conditions indicate that this protein contains two chromophores, retinal a ... | 2005 | 16179480 |
| the genome of salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. | saturated thalassic brines are among the most physically demanding habitats on earth: few microbes survive in them. salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. the phenotype of this bacterium is remarkably similar to that of the hyperhalophilic archaea (haloarchaea). the genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing ... | 2005 | 16330755 |
| ph-dependent transitions in xanthorhodopsin. | xanthorhodopsin (xr), the light-driven proton pump of the halophilic eubacterium salinibacter ruber, exhibits substantial homology to bacteriorhodopsin (br) of archaea and proteorhodopsin (pr) of marine bacteria, but unlike them contains a light-harvesting carotenoid antenna, salinixanthin, as well as retinal. we report here the ph-dependent properties of xr. the pka of the retinal schiff base is as high as in br, i.e. > or =12.4. deprotonation of the schiff base and the ensuing alkaline denatur ... | 2006 | 16649816 |
| induced chirality of the light-harvesting carotenoid salinixanthin and its interaction with the retinal of xanthorhodopsin. | in xanthorhodopsin, a retinal protein-carotenoid complex of salinibacter ruber, the carotenoid salinixanthin functions as a light-harvesting antenna in supplying additional excitation energy for retinal isomerization and proton transport. another retinal protein, archaerhodopsin, has been shown to contain a carotenoid, bacterioruberin, but without an antenna function. we report here that the binding site confers a chiral geometry on salinixanthin in xanthorhodopsin and confirm that the same is t ... | 2006 | 16953586 |
| phylogenetic position of salinibacter ruber based on concatenated protein alignments. | a total of 22 genes from the genome of salinibacter ruber strain m31 were selected in order to study the phylogenetic position of this species based on protein alignments. the selection of the genes was based on their essential function for the organism, dispersion within the genome, and sufficient informative length of the final alignment. for each gene, an individual phylogenetic analysis was performed and compared with the resulting tree based on the concatenation of the 22 genes, which rende ... | 2007 | 16971080 |
| functions of carotenoids in xanthorhodopsin and archaerhodopsin, from action spectra of photoinhibition of cell respiration. | the recent discovery of a carotenoid light-harvesting antenna in xanthorhodopsin, a retinal-based proton pump in salinibacter ruber, made use of photoinhibition of respiration in whole cells to obtain action spectra [balashov et al. science 309, (2005) 2061-2064]. here we provide further details of this phenomenon, and compare action spectra in three different systems where carotenoids have different functions or efficiencies of light-harvesting. the kinetics of light-induced inhibition of respi ... | 2006 | 17020745 |
| interrelationships between dunaliella and halophilic prokaryotes in saltern crystallizer ponds. | thanks to their often very high population densities and their simple community structure, saltern crystallizer ponds form ideal sites to study the behavior of halophilic microorganisms in their natural environment at saturating salt concentrations. the microbial community is dominated by square red halophilic archaea, recently isolated and described as haloquadratum walsbyi, extremely halophilic red rod-shaped bacteria of the genus salinibacter, and the unicellular green alga dunaliella as the ... | 2008 | 17186316 |
| phylogeny and molecular signatures (conserved proteins and indels) that are specific for the bacteroidetes and chlorobi species. | the bacteroidetes and chlorobi species constitute two main groups of the bacteria that are closely related in phylogenetic trees. the bacteroidetes species are widely distributed and include many important periodontal pathogens. in contrast, all chlorobi are anoxygenic obligate photoautotrophs. very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them. | 2007 | 17488508 |
| xanthorhodopsin: proton pump with a carotenoid antenna. | retinal proteins function as photoreceptors and ion pumps. xanthorhodopsin of salinibacter ruber is a recent addition to this diverse family. its novel and distinctive feature is a second chromophore, a carotenoid, which serves as light-harvesting antenna. here we discuss the properties of this carotenoid/retinal complex most relevant to its function (such as the specific binding site controlled by the retinal) and its relationship to other retinal proteins (bacteriorhodopsin, archaerhodopsin, p ... | 2007 | 17571211 |
| dihydroxyacetone metabolism in salinibacter ruber and in haloquadratum walsbyi. | the extremely halophilic bacterium salinibacter ruber inhabits saltern crystallizer ponds worldwide, together with the square archaeon haloquadratum walsbyi. cultures of salinibacter have been shown to convert up to 20% of the glycerol added to a not previously characterized overflow product. we here identify this product of incomplete glycerol oxidation by salinibacter as dihydroxyacetone. genomic information suggests that h. walsbyi possesses an efficient uptake system for dihydroxyacetone, an ... | 2008 | 17938852 |
| photoactive yellow protein from the halophilic bacterium salinibacter ruber. | a gene for photoactive yellow protein (pyp) was identified from the genome sequence of the extremely halophilic aerobic bacterium salinibacter ruber (sr). the sequence is distantly related to the prototypic pyp from halorhodospira halophila (hh) (37% identity) and contains most of the amino acid residues identified as necessary for function. however, the sr pyp gene is not flanked by its two biosynthetic genes as in other species. to determine as to whether the sr pyp gene encodes a functional p ... | 2008 | 18198898 |
| sensitivity of haloquadratum and salinibacter to antibiotics and other inhibitors: implications for the assessment of the contribution of archaea and bacteria to heterotrophic activities in hypersaline environments. | antibiotics and bile salts have been used to differentiate between heterotrophic activity of halophilic archaea and bacteria in saltern ponds. in nacl-saturated brines of crystallizer ponds, most activity was attributed to archaea. following the recent isolation of haloquadratum, the dominant archaeon in the salterns (reported to be sensitive to chloramphenicol and erythromycin), and the discovery of salinibacter, a representative of the bacteria, in the same ecosystem, reevaluation of the earli ... | 2008 | 18205815 |
| metabolic evidence for biogeographic isolation of the extremophilic bacterium salinibacter ruber. | the biogeography of prokaryotes and the effect of geographical barriers as evolutionary constraints are currently subjected to great debate. some clear-cut evidence for geographic isolation has been obtained by genetic methods but, in many cases, the markers used are too coarse to reveal subtle biogeographical trends. contrary to eukaryotic microorganisms, phenotypic evidence for allopatric segregation in prokaryotes has never been found. here we present, for the first time, a metabolomic approa ... | 2008 | 18239610 |
| adapting to environmental changes using specialized paralogs. | when a bacterial species survives under changing environmental circumstances (e.g. salinity or temperature), its proteins might not function in all physicochemical conditions. we propose that prokaryotes cope with this problem by having two or more copies of the genes affected by environmental fluctuations, each one performing the same function under different conditions (i.e. ecoparalog). we identify potential examples in the bacterium salinibacter ruber and in other species that experience wid ... | 2008 | 18325625 |
| novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline lake tebenquiche (salar de atacama). | lake tebenquiche is one of the largest saline water bodies in the salar de atacama at 2,500 m above sea level in northeastern chile. bacteria inhabiting there have to deal with extreme changes in salinity, temperature and uv dose (i.e., high environmental dissimilarity in the physical landscape). we analyzed the bacterioplankton structure of this lake by 16s rrna gene analyses along a spatio-temporal survey. the bacterial assemblage within the lake was quite heterogeneous both in space and time. ... | 2008 | 18347752 |
| chromophore interaction in xanthorhodopsin--retinal dependence of salinixanthin binding. | xanthorhodopsin is a light-driven proton pump in the extremely halophilic bacterium salinibacter ruber. its unique feature is that besides retinal it has a carotenoid, salinixanthin, with a light harvesting function. tight and specific binding of the carotenoid antenna is controlled by binding of the retinal. addition of all-trans retinal to xanthorhodopsin bleached with hydroxylamine restores not only the retinal chromophore absorption band, but causes sharpening of the salinixanthin bands refl ... | 2008 | 18399915 |
| identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor. | photoactive yellow proteins (pyp) are bacterial photoreceptors with a per-arnt-sim (pas) domain fold. we report the identification of six new pyps, thus nearly doubling the size of this protein family. this extends the taxonomic diversity of pyp-containing bacteria from photosynthetic to nonphotosynthetic bacteria, from aquatic to soil-dwelling organisms, and from proteobacteria to salinibacter ruber from the phylum bacteriodetes. the new pyps greatly increase the sequence diversity of the pyp f ... | 2008 | 18399917 |
| microbial life at high salt concentrations: phylogenetic and metabolic diversity. | halophiles are found in all three domains of life. within the bacteria we know halophiles within the phyla cyanobacteria, proteobacteria, firmicutes, actinobacteria, spirochaetes, and bacteroidetes. within the archaea the most salt-requiring microorganisms are found in the class halobacteria. halobacterium and most of its relatives require over 100-150 g/l salt for growth and structural stability. also within the order methanococci we encounter halophilic species. halophiles and non-halophilic r ... | 2008 | 18412960 |
| prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world. | araruama lagoon is an environment characterized by high salt concentrations. the low raining and high evaporation rates in this region favored the development of many salty ponds around the lagoon. in order to reveal the microbial composition of this system, we performed a 16s rrna gene survey. among archaea, most clones were related to uncultured environmental euryarchaeota. in lagoon water, we found some clones related to methanomicrobia and methanothermococcus groups, while in the saline pond ... | 2008 | 18427718 |
| xanthorhodopsin: a bacteriorhodopsin-like proton pump with a carotenoid antenna. | xanthorhodopsin is a light-driven proton pump like bacteriorhodopsin, but made more effective for collecting light by its second chromophore, salinixanthin, a carotenoid. action spectra for transport and fluorescence of the retinal upon excitation of the carotenoid indicate that the carotenoid functions as an antenna to the retinal. the calculated center-to-center distance and angle of the transition moments of the two chromophores are 11 a and 56 degrees , respectively. as expected from their p ... | 2008 | 18515067 |
| excitation energy-transfer and the relative orientation of retinal and carotenoid in xanthorhodopsin. | the cell membrane of salinibacter ruber contains xanthorhodopsin, a light-driven transmembrane proton pump with two chromophores: a retinal and the carotenoid, salinixanthin. action spectra for transport had indicated that light absorbed by either is utilized for function. if the carotenoid is an antenna in this protein, its excited state energy has to be transferred to the retinal and should be detected in the retinal fluorescence. from fluorescence studies, we show that energy transfer occurs ... | 2008 | 18515390 |
| prokaryotic diversity in tuz lake, a hypersaline environment in inland turkey. | tuz lake is an inland thalassohaline water body located in central anatolia that contributes to 60% of the total salt production in turkey per year. the microbiota inhabiting this lake has been studied by fish, denaturing gradient gel electrophoresis of pcr-amplified fragments of 16s rrna genes, and 16s rrna gene clone library analysis. total cell counts per milliliter (1.38 x 10(7)) were in the range of the values normally found for hypersaline environments. the proportion of bacteria to archae ... | 2008 | 18537839 |
| salinibacter sensory rhodopsin: sensory rhodopsin i-like protein from a eubacterium. | halobacterium salinarum sensory rhodopsin i (hssri), a dual receptor regulating both negative and positive phototaxis in haloarchaea, transmits light signals through changes in protein-protein interactions with its transducer, halobacterial transducer protein i (htri). haloarchaea also have another sensor pigment, sensory rhodopsin ii (srii), which functions as a receptor regulating negative phototaxis. compared with hssri, the signal relay mechanism of srii is well characterized because srii fr ... | 2008 | 18566451 |
| crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. | homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. we determined the structure of this eubacterial membrane protein-carotenoid complex by x-ray diffraction, to 1.9-a resolution. although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably diff ... | 2008 | 18922772 |
| distribution, abundance and diversity of the extremely halophilic bacterium salinibacter ruber. | since its discovery in 1998, representatives of the extremely halophilic bacterium salinibacter ruber have been found in many hypersaline environments across the world, including coastal and solar salterns and solar lakes. here, we review the available information about the distribution, abundance and diversity of this member of the bacteroidetes. | 2008 | 18957079 |
| structural changes of salinibacter sensory rhodopsin i upon formation of the k and m photointermediates. | sensory rhodopsin i (sri) is one of the most interesting photosensory receptors in nature because of its ability to mediate opposite signals depending on light color by photochromic one-photon and two-photon reactions. recently, we characterized sri from eubacterium salinibacter ruber (srsri). this protein allows more detailed information about the structure and structural changes of sri during its action to be obtained. in this paper, fourier transform infrared (ftir) spectroscopy is applied to ... | 2008 | 18991393 |
| characterization of polar membrane lipids of the extremely halophilic bacterium salinibacter ruber and possible role of cardiolipin. | the lipid composition of the extremely halophilic bacterium salinibacter ruber (bacteroidetes) was investigated by thin layer chromatography, gas chromatography, high performance liquid chromatography and electrospray ionization-mass spectrometry. polar lipids represent about 80% of the total lipid extract. the main polar lipids are a sulfonic acid analogue of ceramide (or capnine analogue), phosphatidylcholine, phosphatidylserine, dimethylphosphatidylethanolamine, phosphatidylglycerol, cardioli ... | 2009 | 18996223 |
| characterization of salicola sp. ic10, a lipase- and protease-producing extreme halophile. | in order to explore the diversity of extreme halophiles able to produce different hydrolytic enzymes (amylase, protease, lipase and dnase) in hypersaline habitats of south spain, a screening program was performed. a total of 43 extreme halophiles showing hydrolytic activities have been isolated and characterized. the isolated strains were able to grow optimally in media with 15-20% (w/v) total salts and in most cases, growth was detected up to 30% (w/v) total salts. most hydrolase producers were ... | 2009 | 19187212 |
| femtosecond carotenoid to retinal energy transfer in xanthorhodopsin. | xanthorhodopsin of the extremely halophilic bacterium salinibacter ruber represents a novel antenna system. it consists of a carbonyl carotenoid, salinixanthin, bound to a retinal protein that serves as a light-driven transmembrane proton pump similar to bacteriorhodopsin of archaea. here we apply the femtosecond transient absorption technique to reveal the excited-state dynamics of salinixanthin both in solution and in xanthorhodopsin. the results not only disclose extremely fast energy transfe ... | 2009 | 19289053 |
| characterization of halophiles isolated from solar salterns in baja california, mexico. | solar salterns are extreme hypersaline environments that are five to ten times saltier than seawater (150-300 g l(-1) salt concentration) and typically contain high numbers of halophiles adapted to tolerate such extreme hypersalinity. thirty-five halophile cultures of both bacteria and archaea were isolated from the exportadora de sal saltworks in guerrero negro, baja california, mexico. 16s rrna sequence analysis showed that these cultured isolates included members belonging to the halorubrum, ... | 2009 | 19418017 |
| effects of chloride ion binding on the photochemical properties of salinibacter sensory rhodopsin i. | microbial organisms utilize light not only as energy sources but also as signals by which rhodopsins (containing retinal as a chromophore) work as photoreceptors. sensory rhodopsin i (sri) is a dual photoreceptor that regulates both negative and positive phototaxis in microbial organisms, such as the archaeon halobacterium salinarum and the eubacterium salinibacter ruber. these organisms live in highly halophilic environments, suggesting the possibility of the effects of salts on the function of ... | 2009 | 19560470 |
| a photochromic photoreceptor from a eubacterium. | sensory rhodopsin i (sri) is one of the most interesting photo- sensory receptors because of its function in using the photochromic reaction to mediate opposing signals which depend on the color of light. it was initially thought that sri exists only in the archaea, but we recently reported for the first time a newly functional sri from a eubacterium, salinibacter ruber (srsri). the amino acid sequence of srsri shows 43% identity with the well-known sri (hssri) and contains most of the amino aci ... | 2008 | 19704876 |
| molecular ecology of extremely halophilic archaea and bacteria. | abstract water bodies with nacl concentrations approaching saturation are often populated by dense microbial communities. red halophilic archaea of the family halobacteriaceae dominate in such environments. the application of molecular biological techniques, in particular the use of approaches based on the characterization of ribosomal rna sequences, has greatly contributed to our understanding of the community structure of halophilic archaea in hypersaline ecosystems. analyses of lipids extract ... | 2002 | 19709178 |
| electronic coulombic coupling of excitation-energy transfer in xanthorhodopsin. | electronic coupling of excitation-energy transfer (eet) in a retinal (ret) protein, xanthorhodopsin (xr), was studied theoretically. the protein, functioning as a light driven proton pump, contains a carotenoid antenna, salinixanthin (sxn), to collect light energy for an ret chromophore through eet. the pseudo-coulombic interaction (pci) between the donor sxn and the acceptor ret molecules was calculated by a transition density fragment interaction (tdfi) method, which overcomes difficulty arisi ... | 2009 | 19772318 |
| characterization of a signaling complex composed of sensory rhodopsin i and its cognate transducer protein from the eubacterium salinibacter ruber. | sensory rhodopsin i (sri) exists in the cell membranes of microorganisms such as the archaeon halobacterium salinarum and is a photosensor responsible for positive and negative phototaxis. sri forms a signaling complex with its cognate transducer protein, htri, in the membrane. that complex transmits light signals to the flagellar motor through changes in protein-protein interactions with the kinase chea and the adaptor protein chew, which controls the direction of the rotation of the flagellar ... | 2009 | 19778064 |
| metagenomic islands of hyperhalophiles: the case of salinibacter ruber. | saturated brines are extreme environments of low diversity. salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. in order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain dsm 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. this kind of analysis reveals the presence of metagenomic islands, i.e. ... | 2009 | 19951421 |
| spectroscopic studies of a sensory rhodopsin i homologue from the archaeon haloarcula vallismortis. | sensory rhodopsin i (sri) functions as a dual receptor regulating both negative and positive phototaxis. it transmits light signals through changes in protein-protein interactions with its transducer protein, htri. the phototaxis function of halobacterium salinarum sri (hssri) has been well characterized using genetic and molecular techniques, whereas that of salinibacter ruber sri (srsri) has not. srsri has the advantage of high protein stability compared with hssri and, therefore, provided new ... | 2010 | 20067303 |
| low-temperature ftir study of multiple k intermediates in the photocycles of bacteriorhodopsin and xanthorhodopsin. | low-temperature ftir spectroscopy of bacteriorhodopsin and xanthorhodopsin was used to elucidate the number of k-like bathochromic states, their sequence, and their contributions to the photoequilibrium mixtures created by illumination at 80-180 k. we conclude that in bacteriorhodopsin the photocycle includes three distinct k-like states in the sequence br (hv)--> i* --> j --> k(0) --> k(e) --> l --> ..., and similarly in xanthorhodopsin. k(0) is the main fraction in the mixture at 77 k that is ... | 2010 | 20136108 |
| photoselective ultrafast investigation of xanthorhodopsin and its carotenoid antenna salinixanthin. | excited-state dynamics of xanthorhodopsin (xr) and of salinixanthin (sx) in ethanol were investigated by ultrafast pump-hyperspectral probe spectroscopy. following excitation to the strongly allowed s(2) state of the sx chromophore, transient spectra were recorded photoselectively in the range 430-850 nm. global kinetic analysis of these data shows the following. (1) efficient energy transfer from s(2) of the sx in xr to its retinal moiety is verified here. the lifetime of s(2) in sx is, however ... | 2010 | 20146526 |
| fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting salinibacter ruber strains. | genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. in this study, we compare the genomes, metabolomes and selected ecological traits of the strains m8 and m31 of the hyperhalophilic bacterium salinibacter ruber that contain ribosomal rna ... | 2010 | 20164864 |
| molecular factors controlling photosynthetic light harvesting by carotenoids. | carotenoids are naturally occurring pigments that absorb light in the spectral region in which the sun irradiates maximally. these molecules transfer this energy to chlorophylls, initiating the primary photochemical events of photosynthesis. carotenoids also regulate the flow of energy within the photosynthetic apparatus and protect it from photoinduced damage caused by excess light absorption. to carry out these functions in nature, carotenoids are bound in discrete pigment-protein complexes in ... | 2010 | 20446691 |
| the metavirome of a hypersaline environment. | hypersaline environments harbour the highest number of virus-like particles reported for planktonic systems. however, very little is known about the genomic diversity of these virus assemblages since most of the knowledge on halophages is based on the analysis of a few isolates infecting strains of hyperhalophilic archaea that may not be representatives of the natural microbiota. here, we report the characterization, through a metagenomic approach, of the viral assemblage inhabiting a crystalliz ... | 2010 | 20561021 |
| gradual adaptive changes of a protein facing high salt concentrations. | several experimental techniques were applied to unravel fine molecular details of protein adaptation to high salinity. we compared four homologous enzymes, which suggested a new halo-adaptive state in the process of molecular adaptation to high-salt conditions. together with comparative functional studies, the structure of malate dehydrogenase from the eubacterium salinibacter ruber shows that the enzyme shares characteristics of a halo-adapted archaea-bacterial enzyme and of non-halo-adapted en ... | 2010 | 20888835 |
| removal and reconstitution of the carotenoid antenna of xanthorhodopsin. | salinixanthin, a c(40)-carotenoid acyl glycoside, serves as a light-harvesting antenna in the retinal-based proton pump xanthorhodopsin of salinibacter ruber. in the crystallographic structure of this protein, the conjugated chain of salinixanthin is located at the protein-lipid boundary and interacts with residues of helices e and f. its ring, with a 4-keto group, is rotated relative to the plane of the π-system of the carotenoid polyene chain and immobilized in a binding site near the β-ionone ... | 2010 | 21104180 |
| investigating excited state dynamics of salinixanthin and xanthorhodopsin in the near-infrared. | excited state dynamics of native xanthorhodopsin (xr), of an xr sample with a reduced prosthetic group, and of the associated carotenoid (car) salinixanthin (sx) in ethanol were investigated by hyperspectral near infrared (nir) probing. global kinetic analysis shows that: (1) unlike the transient spectra recorded in the visible, fitting of the nir data requires only two phases of exponential spectral evolution, assigned to internal conversion from s(2) → s(1) and from s(1) → s(0) of the carotene ... | 2010 | 21183996 |
| spectral tuning in sensory rhodopsin i from salinibacter ruber. | organisms utilize light as energy sources and as signals. rhodopsins, which have seven transmembrane a-helices with retinal covalently linked to a conserved lys residue, are found in various organisms as distant in evolution as bacteria, archaea, and eukarya. one of the most notable properties of rhodopsin molecules is the large variation in their absorption spectrum. sensory rhodopsin i (sri) and sensory rhodopsin ii (srii) function as photosensors and have similar properties (retinal compositi ... | 2011 | 21288897 |
| characterization of heterotrophic prokaryote subgroups in the sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis. | here, we combined flow cytometry (fcm) and phylogenetic analyses after cell sorting to characterize the dominant groups of the prokaryotic assemblages inhabiting two ponds of increasing salinity: a crystallizer pond (ts) with a salinity of 390 g/l, and the non-crystallizer pond (m1) with a salinity of 200 g/l retrieved from the solar saltern of sfax in tunisia. as expected, fcm analysis enabled the resolution of high nucleic acid content (hna) and low nucleic acid content (lna) prokaryotes. next ... | 2011 | 21424516 |
| spectrally silent intermediates during the photochemical reactions of salinibacter sensory rhodopsin i. | salinibacter sensory rhodopsin i (srsri) is a microbial rhodopsin discovered from the eubacterium salinibacter ruber . it is thought to be a photoreceptor engaging the signal transductions for both positive and negative phototaxis. to elucidate the photoreactions of srsri in the presence and absence of chloride ions, we measured the refractive index change after the photoexcitation by the transient grating method. as a result, two spectrally silent processes were identified after the formation o ... | 2011 | 21449587 |
| response to adverse conditions in two strains of the extremely halophilic species salinibacter ruber. | we have studied the response of the two closest relative strains m8 and m31 of salinibacter ruber to environmental changes as the transition from exponential to stationary phase in a batch growth, and the submission to two different environmental stresses (dilution of the culture medium and temperature decrease). we monitored the changes in cultivability, ribosomal content by fluorescence in situ hybridization (fish), and metabolic changes with high-field ion cyclotron fourier transform mass spe ... | 2011 | 21461978 |
| metatranscriptomic analysis of extremely halophilic viral communities. | hypersaline environments harbour the highest number of viruses reported for aquatic environments. in crystallizer ponds from solar salterns, haloviruses coexist with extremely halophilic archaea and bacteria and present a high diversity although little is known about their activity. in this work, we analyzed the viral expression in one crystallizer using a metatranscriptomic approach in which clones from a metaviromic library were immobilized in a microarray and used as probes against total mrna ... | 2011 | 21490689 |
| structural characteristics around the β-ionone ring of the retinal chromophore in salinibacter sensory rhodopsin i. | organisms sense and respond to environmental stimuli through membrane-embedded receptors and transducers. sensory rhodopsin i (sri) and sensory rhodopsin ii (srii) are the photoreceptors for the positive and negative phototaxis in microorganisms, respectively. they form signaling complexes in the membrane with their cognate transducer proteins, htri and htrii, and these sri-htri and srii-htrii complexes transmit a light signal through their cytoplasmic sensory signaling system, inducing opposite ... | 2011 | 21545132 |
| prokaryotic diversity in aran-bidgol salt lake, the largest hypersaline playa in iran. | prokaryotic diversity in aran-bidgol salt lake, a thalasohaline lake in iran, was studied by fluorescence in situ hybridization (fish), cultivation techniques, denaturing gradient gel electrophoresis (dgge) of pcr-amplified fragments of 16s rrna genes and 16s rrna gene clone library analysis. viable counts obtained (2.5-4×10(6) cells ml(-1)) were similar to total cell abundance in the lake determined by dapi direct count (3-4×10(7) cells ml(-1)). the proportion of bacteria to archaea in the comm ... | 2011 | 22185719 |
| salinibacter iranicus sp. nov. and salinibacter luteus sp. nov., isolated from a salt lake, and emended descriptions of the genus salinibacter and salinibacter ruber. | two gram-staining-negative, red- and orange- pigmented, nonmotile, rod-shaped, extremely halophilic bacteria, designated strains cb7t and dgot, were isolated from aran-bidgol salt lake, iran. growth occurred between 2 and 5 m nacl and the isolates grew optimally at 3 m nacl. the optimum ph and temperature for growth of both strains were ph 7.5 and 37 °c, respectively, while they were able to grow over ph and temperature ranges of 6-8 and 25-50 °c, respectively. the predominant fatty acids of the ... | 2011 | 21856978 |