Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)

Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘Alicyclobacillaceae’. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family ‘Alicyclobacillaceae’. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project.

[1]  Wolfgang Ludwig,et al.  Revised road map to the phylum Firmicutes , 2015 .

[2]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[3]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[4]  Lynne A. Goodwin,et al.  Complete genome sequence of Kytococcus sedentarius type strain (541T) , 2009, Standards in genomic sciences.

[5]  R. Witthuhn,et al.  Isolation, identification and typification of Alicyclobacillus acidoterrestris and Alicyclobacillus acidocaldarius strains from orchard soil and the fruit processing environment in South Africa. , 2009, Food microbiology.

[6]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[7]  M. Rossi,et al.  A novel thermoacidophilic cellulase from Alicyclobacillus acidocaldarius. , 2008, Protein and peptide letters.

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

[9]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[10]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[11]  E. Bakker,et al.  New type of kdp region with a split sensor-kinase kdpD gene located within two divergent kdp operons from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius. , 2006, Biochimica et biophysica acta.

[12]  M. Rossi,et al.  Characterization of a β-glycosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius , 2006, Extremophiles.

[13]  Sang-Jae Lee,et al.  Characterization of a Thermoacidophilic l-Arabinose Isomerase from Alicyclobacillus acidocaldarius: Role of Lys-269 in pH Optimum , 2005, Applied and Environmental Microbiology.

[14]  Kersten S. Rabe,et al.  The esterase from Alicyclobacillus acidocaldarius as a reporter enzyme and affinity tag for protein biosynthesis , 2005, FEBS letters.

[15]  Akira Yokota,et al.  Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess omega-alicyclic fatty acids, and emended description of the genus Alicyclobacillus. , 2003, International journal of systematic and evolutionary microbiology.

[16]  Keiichi Goto,et al.  Alicyclobacillus acidiphilus sp. nov., a novel thermo-acidophilic, omega-alicyclic fatty acid-containing bacterium isolated from acidic beverages. , 2002, International journal of systematic and evolutionary microbiology.

[17]  K. Inagaki,et al.  Identification of thermoacidophilic bacteria and a new Alicyclobacillus genomic species isolated from acidic environments in Japan , 2002, Extremophiles.

[18]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[19]  G. Manco,et al.  Residues at the Active Site of the Esterase 2 fromAlicyclobacillus acidocaldarius Involved in Substrate Specificity and Catalytic Activity at High Temperature* , 2001, The Journal of Biological Chemistry.

[20]  F. M. Silva,et al.  Alicyclobacillus acidoterrestris spores in fruit products and design of pasteurization processes , 2001 .

[21]  F. Scheffel,et al.  Maltose and Maltodextrin Transport in the Thermoacidophilic Gram-Positive Bacterium Alicyclobacillus acidocaldarius Is Mediated by a High-Affinity Transport System That Includes a Maltose Binding Protein Tolerant to Low pH , 2000, Journal of bacteriology.

[22]  S. Condón,et al.  Heat resistance of Alicyclobacillus acidocaldarius in water, various buffers, and orange juice. , 2000, Journal of food protection.

[23]  E. Schneider,et al.  Erratum to: “Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodextrinase (neopullulanase) from Alicyclobacillus acidocaldarius, reclassification of a group of enzymes”[FEMS Microbiol. Lett. 183 (2000) 55–61] , 2000 .

[24]  E. Schneider,et al.  Erratum to: “Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodextrinase (neopullulanase) from Alicyclobacillus acidocaldarius, reclassification of a group of enzymes”: [FEMS Microbiol. Lett. 183 (2000) 55–61]1 , 2000 .

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

[26]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[27]  E. Schneider,et al.  Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodextrinase (neopullulanase) from Alicyclobacillus acidocaldarius, reclassification of a group of enzymes. , 2000, FEMS microbiology letters.

[28]  A. Gambacorta,et al.  Alicyclobacilli from an unexplored geothermal soil in Antarctica: Mount Rittmann , 1998, Polar Biology.

[29]  E. Bakker,et al.  Acidostable and acidophilic proteins: the example of the alpha-amylase from Alicyclobacillus acidocaldarius. , 1997, Comparative biochemistry and physiology. Part A, Physiology.

[30]  B. Liliensiek,et al.  Purification, properties and structural aspects of a thermoacidophilic alpha-amylase from Alicyclobacillus acidocaldarius atcc 27009. Insight into acidostability of proteins. , 1994, European journal of biochemistry.

[31]  G. Fox,et al.  Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov. , 1992, International journal of systematic bacteriology.

[32]  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.

[33]  A. Siebers,et al.  The high‐affinity K+‐translocating ATPase complex from Bacillus acidocaldarius consists of three subunits , 1989, Molecular microbiology.

[34]  K. Poralla,et al.  Bacillus acidoterrestris sp. nov., a New Thermotolerant Acidophile Isolated from Different Soils , 1987 .

[35]  K. Altendorf,et al.  High-affinity potassium uptake system in Bacillus acidocaldarius showing immunological cross-reactivity with the Kdp system from Escherichia coli , 1987, Journal of bacteriology.

[36]  E. Bakker,et al.  Low-affinity potassium uptake system in Bacillus acidocaldarius , 1987, Journal of bacteriology.

[37]  E. Bakker,et al.  Generation of a large, protonophore-sensitive proton motive force and pH difference in the acidophilic bacteria Thermoplasma acidophilum and Bacillus acidocaldarius , 1985, Journal of bacteriology.

[38]  K. Poralla,et al.  Effect of temperature and pH on the hopanoid content of Bacillus acidocaldarius , 1984 .

[39]  M. de Rosa,et al.  Effects of pH and Temperature on the Fatty Acid Composition of Bacillus acidocaldarius , 1974, Journal of bacteriology.

[40]  M. de Rosa,et al.  The formation of -cyclohexyl-fatty acids from shikimate in an acidophilic thermophilic bacillus. A new biosynthetic pathway. , 1972, The Biochemical journal.

[41]  T. D. Brock,et al.  Bacillus acidocaldarius sp.nov., an Acidophilic Thermophilic Spore-forming Bacterium , 1971 .

[42]  A. Prévot,et al.  Dictionnaire des Bactéries pathogènes pour l'homme , 1953 .

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

[44]  W. Wade,et al.  Bergey’s Manual of Systematic Bacteriology , 2012 .

[45]  Lynne A. Goodwin,et al.  Complete genome sequence of Kytococcus sedentarius type strain (541 T ) , 2009 .

[46]  R. Witthuhn,et al.  Isolation and identification of species of Alicyclobacillus from orchard soil in the Western Cape, South Africa , 2007, Extremophiles.

[47]  James R. Cole,et al.  Taxonomic Outline of the Bacteria and Archaea , Release 7 . 7 March 6 , 2007 . Part 9 – The Bacteria : Phylum “ Firmicutes ” : Class “ Bacilli ” , 2007 .

[48]  M. Rossi,et al.  Characterization of a β-glycosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius , 2007, Extremophiles.

[49]  A. Pretorius,et al.  Short communication Isolation and identification of Alicyclobacillus acidocaldarius by 16S rDNA from mango juice and concentrate , 2005 .

[50]  H. Matsubara,et al.  Alicyclobacillus herbarius sp. nov., a novel bacterium containing omega-cycloheptane fatty acids, isolated from herbal tea. , 2002, International journal of systematic and evolutionary microbiology.

[51]  G. Barrow,et al.  Cowan and Steel's Manual for the identification of medical bacteria: The Bacteriological Code , 1993 .

[52]  Sp Lapage,et al.  International Code of Nomenclature of Bacteria , 1992 .

[53]  Pha Sneath,et al.  International code of nomenclature of bacteria (1990 revision). , 1992 .

[54]  R J Roberts,et al.  Restriction and modification enzymes and their recognition sequences. , 1983, Nucleic acids research.

[55]  P. Sneath,et al.  Approved lists of bacterial names. , 1980, The Medical journal of Australia.

[56]  G. D. Mercer,et al.  Isolation and Characterization of Unusual Bacterial Amylases , 1979 .

[57]  R. Murray,et al.  Proposals Concerning the Higher Taxa of Bacteria , 1978 .