Complete genome sequence of Halorhodospira halophila SL1

Halorhodospira halophila is among the most halophilic organisms known. It is an obligately photosynthetic and anaerobic purple sulfur bacterium that exhibits autotrophic growth up to saturated NaCl concentrations. The type strain H. halophila SL1 was isolated from a hypersaline lake in Oregon. Here we report the determination of its entire genome in a single contig. This is the first genome of a phototrophic extreme halophile. The genome consists of 2,678,452 bp, encoding 2,493 predicted genes as determined by automated genome annotation. Of the 2,407 predicted proteins, 1,905 were assigned to a putative function. Future detailed analysis of this genome promises to yield insights into the halophilic adaptations of this organism, its ability for photoautotrophic growth under extreme conditions, and its characteristic sulfur metabolism.

[1]  G. Garrity,et al.  Gammaproteobacteria class. nov. , 2015 .

[2]  J. Ruan [Bergey's Manual of Systematic Bacteriology (second edition) Volume 5 and the study of Actinomycetes systematic in China]. , 2013, Wei sheng wu xue bao = Acta microbiologica Sinica.

[3]  Douglas W. Raiford,et al.  An Extremely Halophilic Proteobacterium Combines a Highly Acidic Proteome with a Low Cytoplasmic Potassium Content* , 2012, The Journal of Biological Chemistry.

[4]  Peter Williams,et al.  IMG: the integrated microbial genomes database and comparative analysis system , 2011, Nucleic Acids Res..

[5]  Cliff Han,et al.  Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing Bacterium Halanaerobium hydrogeniformans , 2011, Journal of bacteriology.

[6]  Sean D. Hooper,et al.  Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii , 2009, PloS one.

[7]  A. Xie,et al.  Identification of Six New Photoactive Yellow Proteins—Diversity and Structure–Function Relationships in a Bacterial Blue Light Photoreceptor † , 2008, Photochemistry and photobiology.

[8]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[9]  F Pfeiffer,et al.  Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. , 2008, Genomics.

[10]  Marie-Christine Brun,et al.  TreeDyn: towards dynamic graphics and annotations for analyses of trees , 2006, BMC Bioinformatics.

[11]  Friedhelm Pfeiffer,et al.  The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity , 2006, BMC Genomics.

[12]  H. Kamikubo,et al.  Cloning and characterization of nif structural and regulatory genes in the purple sulfur bacterium, Halorhodospira halophila. , 2006, Journal of bioscience and bioengineering.

[13]  W. Doolittle,et al.  The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Friedhelm Pfeiffer,et al.  Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. , 2005, Genome research.

[15]  J. Euzéby Validation of publication of new names and new combinations previously effectively published outside the IJSEM. , 2005, International journal of systematic and evolutionary microbiology.

[16]  J. Alric,et al.  Study of the high-potential iron sulfur protein in Halorhodospira halophila confirms that it is distinct from cytochrome c as electron carrier. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Min Pan,et al.  Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. , 2004, Genome research.

[18]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[19]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[20]  T. Meyer,et al.  Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism. , 2003, Biochemistry.

[21]  Klaas J. Hellingwerf,et al.  Photoactive Yellow Protein, A New Type of Photoreceptor Protein: Will This "Yellow Lab" Bring Us Where We Want to Go? | , 2003 .

[22]  V. Thorsson,et al.  Genome sequence of Halobacterium species NRC-1. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[23]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[24]  J. Imhoff,et al.  The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses , 1996, Archives of Microbiology.

[25]  J. García,et al.  Anaerobic bacteria from hypersaline environments. , 1994, Microbiological reviews.

[26]  J P Armitage,et al.  The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein , 1993, Journal of bacteriology.

[27]  K. Hellingwerf,et al.  Abundance, subunit composition, redox properties, and catalytic activity of the cytochrome bc1 complex from alkaliphilic and halophilic, photosynthetic members of the family Ectothiorhodospiraceae , 1993, Journal of bacteriology.

[28]  K. Hellingwerf,et al.  Characterization of reaction center/antenna complexes from bacteriochlorophyll a containing Ectothiorhodospiraceae , 1991 .

[29]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[30]  G. Tollin,et al.  Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin. , 1987, Biochemistry.

[31]  T. Meyer,et al.  Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila. , 1985, Biochimica et biophysica acta.

[32]  J. Imhoff Reassignment of the Genus Ectothiorhodospira Pelsh 1936 to a New Family, Ectothiorhodospiraceae fam. nov., and Emended Description of the Chromatiaceae Bavendamm 1924 , 1984 .

[33]  G. Garrity Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.

[34]  N. Frigaard,et al.  Sulfur metabolism in phototrophic sulfur bacteria. , 2009, Advances in microbial physiology.

[35]  W. R. Sistrom,et al.  The isolation and preliminary characterization of a halophilic photosynthetic bacterium , 2004, Archiv für Mikrobiologie.

[36]  W. R. Sistrom,et al.  Ectothiorhodospira halophila: A new species of the genus Ectothiorhodospira , 2004, Archiv für Mikrobiologie.

[37]  J. Willison,et al.  Isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of Mediterranean salterns: description of Halorhodospira neutriphila sp. nov. and emendation of the genus Halorhodospira. , 2003, International journal of systematic and evolutionary microbiology.

[38]  DSMZ-Deutsche Dsm,et al.  Validation of publication of new names and new combinations previously effectively published outside the IJSEM. , 2003, International journal of systematic and evolutionary microbiology.

[39]  Strain Cip Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 65. , 1998, International journal of systematic bacteriology.

[40]  Strain Cip,et al.  Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 40. , 1992, International journal of systematic bacteriology.

[41]  * Joint first authors. , 2022 .