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Keuter S, Rahav E, Herut B, Rinkevich B. Distribution patterns of bacterioplankton in the oligotrophic south-eastern Mediterranean Sea. FEMS Microbiol Ecol 2015; 91:fiv070. [DOI: 10.1093/femsec/fiv070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2015] [Indexed: 11/14/2022] Open
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Silveira CB, Cardoso AM, Coutinho FH, Lima JL, Pinto LH, Albano RM, Clementino MM, Martins OB, Vieira RP. Tropical aquatic Archaea show environment-specific community composition. PLoS One 2013; 8:e76321. [PMID: 24086729 PMCID: PMC3783403 DOI: 10.1371/journal.pone.0076321] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/23/2013] [Indexed: 11/18/2022] Open
Abstract
The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota, a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria.
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Affiliation(s)
- Cynthia B. Silveira
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexander M. Cardoso
- Centro Universitário Estadual da Zona Oeste - UEZO, Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Metrologia, Qualidade e Tecnologia, INMETRO, Duque de Caxias, Rio de Janeiro, Brazil
| | - Felipe H. Coutinho
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joyce L. Lima
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo H. Pinto
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho M. Albano
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, UERJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maysa M. Clementino
- Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando B. Martins
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo P. Vieira
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
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Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context. J Bacteriol 2013; 195:3834-44. [PMID: 23794616 DOI: 10.1128/jb.00412-13] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A stochastic, agent-based mathematical model of the coevolution of the archaeal and bacterial adaptive immunity system, CRISPR-Cas, and lytic viruses shows that CRISPR-Cas immunity can stabilize the virus-host coexistence rather than leading to the extinction of the virus. In the model, CRISPR-Cas immunity does not specifically promote viral diversity, presumably because the selection pressure on each single proto-spacer is too weak. However, the overall virus diversity in the presence of CRISPR-Cas grows due to the increase of the host and, accordingly, the virus population size. Above a threshold value of total viral diversity, which is proportional to the viral mutation rate and population size, the CRISPR-Cas system becomes ineffective and is lost due to the associated fitness cost. Our previous modeling study has suggested that the ubiquity of CRISPR-Cas in hyperthermophiles, which contrasts its comparative low prevalence in mesophiles, is due to lower rates of mutation fixation in thermal habitats. The present findings offer a complementary, simpler perspective on this contrast through the larger population sizes of mesophiles compared to hyperthermophiles, because of which CRISPR-Cas can become ineffective in mesophiles. The efficacy of CRISPR-Cas sharply increases with the number of proto-spacers per viral genome, potentially explaining the low information content of the proto-spacer-associated motif (PAM) that is required for spacer acquisition by CRISPR-Cas because a higher specificity would restrict the number of spacers available to CRISPR-Cas, thus hampering immunity. The very existence of the PAM might reflect the tradeoff between the requirement of diverse spacers for efficient immunity and avoidance of autoimmunity.
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Silveira CB, Vieira RP, Cardoso AM, Paranhos R, Albano RM, Martins OB. Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean. PLoS One 2011; 6:e17789. [PMID: 21408023 PMCID: PMC3052384 DOI: 10.1371/journal.pone.0017789] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 02/09/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. CONCLUSIONS/SIGNIFICANCE Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.
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Affiliation(s)
- Cynthia B. Silveira
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo P. Vieira
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexander M. Cardoso
- Instituto Nacional de Metrologia
Normalização e Qualidade Industrial, Rio de Janeiro,
Brazil
- * E-mail:
| | - Rodolfo Paranhos
- Instituto de Biologia, Universidade Federal do
Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho M. Albano
- Departamento de Bioquímica,
Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando B. Martins
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Varela MM, van Aken HM, Herndl GJ. Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic. Environ Microbiol 2008; 10:1903-11. [DOI: 10.1111/j.1462-2920.2008.01627.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Moisander PH, Morrison AE, Ward BB, Jenkins BD, Zehr JP. Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarray. Environ Microbiol 2008; 9:1823-35. [PMID: 17564615 DOI: 10.1111/j.1462-2920.2007.01304.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The distribution of nitrogen-fixing microorganisms in the Chesapeake Bay was investigated using fingerprints from a nifH microarray comprised of 706 60-mer oligonucleotide nifH probes representing cultivated organisms and environmental clones from different nifH clusters. Diverse nifH targets, amplified from samples using degenerate nifH primers, were detected in water column and sediment samples collected in April and October, 2001-2002. Total nifH richness and diversity (Simpson's and Shannon indices) were highest at the most riverine, oligohaline North Bay station. In most samples, the highest diversity was in nifH Cluster 3, which includes many anaerobes, while Cluster 1 (alpha-, beta- gamma- Proteobacteria, Cyanobacteria) targets had the greatest microarray signal intensities. In a multidimensional scaling analysis, deep water communities from April and October were similar within each of the sampling sites, while the surface communities had more variability. Diazotroph communities in the water column in the North Bay were distinct from the Mid- and South Bay communities, and there was a gradual change in sediment diazotroph assemblages from the North to the South Bay. Diazotrophic assemblages from the majority of the water column samples from the Mid- and South Bay clustered with the sediment assemblage in Mid-Bay. Dissolved inorganic nitrogen, salinity, dissolved organic carbon and dissolved organic phosphorus had a significant relationship with the diazotrophic bacterioplankton community. Higher diversity in the freshwater end of the system may reflect variability in disturbance rates and environmental conditions such as forms and concentrations of organic matter, nutrients and oxygen.
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Affiliation(s)
- Pia H Moisander
- Ocean Sciences Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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Logue JB, Bürgmann H, Robinson CT. Progress in the Ecological Genetics and Biodiversity of Freshwater Bacteria. Bioscience 2008. [DOI: 10.1641/b580205] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Vieira RP, Gonzalez AM, Cardoso AM, Oliveira DN, Albano RM, Clementino MM, Martins OB, Paranhos R. Relationships between bacterial diversity and environmental variables in a tropical marine environment, Rio de Janeiro. Environ Microbiol 2007; 10:189-99. [PMID: 17892478 DOI: 10.1111/j.1462-2920.2007.01443.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study is the first to apply a comparative analysis of environmental chemistry, microbiological parameters and bacterioplankton 16S rRNA clone libraries from different areas of a 50 km transect along a trophic gradient in the tropical Guanabara Bay ecosystem. Higher bacterial diversity was found in the coastal area, whereas lower richness was observed in the more polluted inner bay water. The significance of differences between clone libraries was examined with LIBSHUFF statistics. Paired reciprocal comparisons indicated that each of the libraries differs significantly from the others, and this is in agreement with direct interpretation of the phylogenetic tree. Furthermore, correspondence analyses showed that some taxa are related to specific abiotic, trophic and microbiological parameters in Guanabara Bay estuarine system.
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Affiliation(s)
- Ricardo P Vieira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, RJ, Brazil
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Pernthaler J, Amann R. Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol Mol Biol Rev 2005; 69:440-61. [PMID: 16148306 PMCID: PMC1197807 DOI: 10.1128/mmbr.69.3.440-461.2005] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major biogeochemical processes in the water columns of lakes and oceans are related to the activities of heterotrophic microbes, e.g., the mineralization of organic carbon from photosynthesis and allochthonous influx or its transport to the higher trophic levels. During the last 15 years, cultivation-independent molecular techniques have substantially contributed to our understanding of the diversity of the microbial communities in different aquatic systems. In parallel, the complexity of aquatic habitats at a microscale has inspired research on the ecophysiological properties of uncultured microorganisms that thrive in a continuum of dissolved to particulate organic matter. One possibility to link these two aspects is to adopt a"Gleasonian" perspective, i.e., to study aquatic microbial assemblages in situ at the population level rather than looking at microbial community structure, diversity, or function as a whole. This review compiles current knowledge about the role and fate of different populations of heterotrophic picoplankton in marine and inland waters. Specifically, we focus on a growing suite of techniques that link the analysis of bacterial identity with growth, morphology, and various physiological activities at the level of single cells. An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed.
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Affiliation(s)
- Jakob Pernthaler
- Limnological Station, Institute of Plant Biology, Seestrasse 187, CH-8802 Kilchberg, Switzerland.
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Sabehi G, Loy A, Jung KH, Partha R, Spudich JL, Isaacson T, Hirschberg J, Wagner M, Béjà O. New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol 2005; 3:e273. [PMID: 16008504 PMCID: PMC1175822 DOI: 10.1371/journal.pbio.0030273] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 06/06/2005] [Indexed: 11/19/2022] Open
Abstract
Proteorhodopsin phototrophy was recently discovered in oceanic surface waters. In an effort to characterize uncultured proteorhodopsin-exploiting bacteria, large-insert bacterial artificial chromosome (BAC) libraries from the Mediterranean Sea and Red Sea were analyzed. Fifty-five BACs carried diverse proteorhodopsin genes, and we confirmed the function of five. We calculate that proteorhodopsin-exploiting bacteria account for 13% of microorganisms in the photic zone. We further show that some proteorhodopsin-containing bacteria possess a retinal biosynthetic pathway and a reverse sulfite reductase operon, employed by prokaryotes oxidizing sulfur compounds. Thus, these novel phototrophs are an unexpectedly large and metabolically diverse component of the marine microbial surface water. Metagenomic analyses of the Mediterranean Sea and Red Sea estimate that proteorhodopsin genes are exploited by a surprisingly high percentage of bacteria. Experimental studies reveal metabolically diverse roles for these phototrophs.
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Affiliation(s)
- Gazalah Sabehi
- 1Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Alexander Loy
- 2Department of Microbial Ecology, University of Vienna, Austria
| | - Kwang-Hwan Jung
- 3Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas, United States of America
| | - Ranga Partha
- 3Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas, United States of America
| | - John L Spudich
- 3Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas, United States of America
| | - Tal Isaacson
- 4Department of Genetics, The Hebrew University of Jerusalem, Israel
| | | | - Michael Wagner
- 2Department of Microbial Ecology, University of Vienna, Austria
| | - Oded Béjà
- 1Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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Schweickert B, Moter A, Lefmann M, Göbel UB. Let them fly or light them up: matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry and fluorescence in situ hybridization (FISH). APMIS 2005; 112:856-85. [PMID: 15638841 DOI: 10.1111/j.1600-0463.2004.apm11211-1210.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review focuses on clinical bacteriology and by and large does not cover the detection of fungi, viruses or parasites. It discusses two completely different but complementary approaches that may either supplement or replace classic culture-based bacteriology. The latter view may appear provocative in the light of the actual market penetration of molecular genetic testing in clinical bacteriology. Despite its elegance, high specificity and sensitivity, molecular genetic diagnostics has not yet reached the majority of clinical laboratories. The reasons for this are manifold: Many microbiologists and medical technologists are more familiar with classical microbiological methods than with molecular biology techniques. Culture-based methods still represent the work horse of everyday routine. The number of available FDA-approved molecular genetic tests is limited and external quality control is still under development. Finally, it appears difficult to incorporate genetic testing in the routine laboratory setting due to the limited number of samples received or the lack of appropriate resources. However, financial and time constraints, particularly in hospitals as a consequence of budget cuts and reduced length of stay, lead to a demand for significantly shorter turnaround times that cannot be met by culture-dependent diagnosis. As a consequence, smaller laboratories that do not have the technical and personal equipment required for molecular genetic amplification techniques may adopt alternative methods such as fluorescence in situ hybridization (FISH) that combines easy-to-perform molecular hybridization with microscopy, a technique familiar to every microbiologist. FISH is hence one of the technologies presented here. For large hospital or reference laboratories with a high sample volume requiring massive parallel high-throughput testing we discuss matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) of nucleic acids, a technology that has evolved from the post-genome sequencing era, for high-throughput sequence variation analysis (1, 2).
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Affiliation(s)
- Birgitta Schweickert
- Institut für Mikrobiologie und Hygiene, Charité, Universitätsmedizin Berlin, Germany
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Caron DA, Countway PD, Brown MV. The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools. J Eukaryot Microbiol 2004; 51:38-48. [PMID: 15068264 DOI: 10.1111/j.1550-7408.2004.tb00159.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.
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Affiliation(s)
- David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371, USA.
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Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich EN, Spudich JL, Béjà O. Diversification and spectral tuning in marine proteorhodopsins. EMBO J 2003; 22:1725-31. [PMID: 12682005 PMCID: PMC154475 DOI: 10.1093/emboj/cdg183] [Citation(s) in RCA: 222] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2002] [Revised: 02/06/2003] [Accepted: 02/25/2003] [Indexed: 11/14/2022] Open
Abstract
Proteorhodopsins, ubiquitous retinylidene photoactive proton pumps, were recently discovered in the cosmopolitan uncultured SAR86 bacterial group in oceanic surface waters. Two related proteorhodopsin families were found that absorb light with different absorption maxima, 525 nm (green) and 490 nm (blue), and their distribution was shown to be stratified with depth. Using structural modeling comparisons and mutagenesis, we report here on a single amino acid residue at position 105 that functions as a spectral tuning switch and accounts for most of the spectral difference between the two pigment families. Furthermore, looking at natural environments, we found novel proteorhodopsin gene clusters spanning the range of 540-505 nm and containing changes in the same identified key switch residue leading to changes in their absorption maxima. The results suggest a simultaneous diversification of green proteorhodopsin and the new key switch variant pigments. Our observations demonstrate that this single-residue switch mechanism is the major determinant of proteorhodopsin wavelength regulation in natural marine environments.
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Affiliation(s)
- Dikla Man
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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