DOI: 10.1046/j.1462-2920.2003.00501.x. Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern

Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern

10.1046/j.1462-2920.2003.00501.x

Crossref journal-article

Wiley

Environmental Microbiology (311)

Abstract

SummaryHaloarchaeal rhodopsins are a diverse group of transmembrane proteins that use light energy to drive several different cellular processes. Two rhodopsins, bacteriorhodopsin and halorhodopsins, are H+ and Cl– ion pumps, respectively, and two rhodopsins, sensory rhodopsin I and II, regulate phototaxis. Bacteriorhodopsin is of special interest as it is a non‐chlorophyll‐based type of phototrophy (i.e. generation of chemical energy from light energy). However, very little is known about the diversity and distribution of rhodopsin genes in hypersaline environments. Here, we have used environmental PCR and cloning techniques to directly retrieve rhodopsin genes from three different salinity ponds located in a sea salt manufacturing facility near Alicante, Spain. Our survey resulted in the discovery of previously concealed variation including what is hypothesized to be bacteriorhodopsin genes from the uncultivated square morphotype that dominates these environments. In some instances, identical genes were discovered in seemingly different habitats suggesting that some haloarchaea are present over widely varying concentrations of salt.

Bibliography

Papke, R. T., Douady, C. J., Doolittle, W. F., & RodrÃguezâValera, F. (2003). Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern. Environmental Microbiology, 5(11), 1039â1045. Portico.

Authors 4

R. Thane Papke (first)
Christophe J. Douady (additional)
W. Ford Doolittle (additional)
Francísco Rodríguez‐Valera (additional)

References 35 Referenced 25

10.1046/j.1462-2920.1999.00065.x
10.1073/pnas.192558999
10.1128/AEM.68.9.4486-4494.2002
10.1126/science.289.5486.1902
10.1016/S0723-2020(11)80418-2
10.1073/pnas.96.14.8034
10.1007/s00248-002-1000-9
10.1046/j.1462-2920.2002.00297.x
{'key': 'e_1_2_6_10_1', 'volume-title': 'PHYLIP (Phylogeny Inference Package)', 'author': 'Felsenstein J.', 'year': '2001'} / PHYLIP (Phylogeny Inference Package) by Felsenstein J. (2001)
10.1038/24297
10.1006/mpev.1993.1015
{'key': 'e_1_2_6_13_1', 'first-page': '294', 'volume-title': "Bergey's Manual of Systematic Bacteriology", 'author': 'Grant W.D.', 'year': '2001'} / Bergey's Manual of Systematic Bacteriology by Grant W.D. (2001)
10.1007/s00299-001-0399-7
{'key': 'e_1_2_6_15_1', 'first-page': '754', 'article-title': 'MRBAYES: Bayesian inference of phylogeny', 'volume': '17', 'author': 'Huelsenbeck J.P.', 'year': '2001', 'journal-title': 'Biometrics'} / Biometrics / MRBAYES: Bayesian inference of phylogeny by Huelsenbeck J.P. (2001)
10.1006/jmbi.1998.2286
10.4319/lo.1983.28.1.0153
10.1093/bioinformatics/8.3.275
10.1007/s007920050071
10.1007/s007920050040
10.1038/38323
10.1093/bioinformatics/17.6.573
10.1038/30965
10.1073/pnas.70.10.2853
10.1007/BF00411075
10.1128/aem.63.9.3600-3606.1997 / Appl Environ Microbiol / Diversity of ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities by Pichard S.L. (1997)
{'key': 'e_1_2_6_27_1', 'first-page': '27', 'volume-title': 'Microbiology and Biogeochemistry of Hypersaline Environments.', 'author': 'Rodríguez‐Valera F.', 'year': '1999'} / Microbiology and Biogeochemistry of Hypersaline Environments. by Rodríguez‐Valera F. (1999)
10.1146/annurev.cellbio.16.1.365
10.1128/jb.148.1.352-360.1981 / J Bacteriol / Walsby's square bacterium: fine structure of an orthogonal procaryote by Stoeckenius W. (1981)
10.1007/978-3-642-70290-7_16
10.1093/oxfordjournals.molbev.a025664
{'key': 'e_1_2_6_32_1', 'volume-title': 'PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods)', 'author': 'Swofford D.L.', 'year': '2002'} / PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) by Swofford D.L. (2002)
10.1128/AEM.63.11.4298-4303.1997
10.1038/283069a0
10.1128/MMBR.62.4.1353-1370.1998
10.1007/PL00010710

Dates

Type	When
Created	21 years, 10 months ago (Oct. 24, 2003, 3:55 a.m.)
Deposited	1 year, 10 months ago (Oct. 15, 2023, 1:10 a.m.)
Indexed	5 months ago (April 1, 2025, 1:21 p.m.)
Issued	21 years, 11 months ago (Sept. 8, 2003)
Published	21 years, 11 months ago (Sept. 8, 2003)
Published Online	21 years, 11 months ago (Sept. 8, 2003)
Published Print	21 years, 10 months ago (Nov. 1, 2003)

Funders 0

None

BibTeX

@article{Papke_2003, title={Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern}, volume={5}, ISSN={1462-2920}, url={http://dx.doi.org/10.1046/j.1462-2920.2003.00501.x}, DOI={10.1046/j.1462-2920.2003.00501.x}, number={11}, journal={Environmental Microbiology}, publisher={Wiley}, author={Papke, R. Thane and Douady, Christophe J. and Doolittle, W. Ford and Rodríguez‐Valera, Francísco}, year={2003}, month=sep, pages={1039–1045} }

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