Haloferax volcanii an overview sciencedirect topics. Haloferax volcanii ss0101 is a halophilic archaeon isolated from salt farms in thailand. Crispr clustered regularly interspaced short palindromic repeat is an adaptive immune system that provides protection against mobile genetic elements viruses, transposable elements and conjugative plasmids. Haloferax volcanii strain atcc 29605 dsm 3757 ifo 14742 ncimb 2012 ds2 is a moderate halophilic archaeon isolated from bottom sediment from the dead sea.
Haloferax volcanii, a halophilic archaeon, is a tractable model to study prokaryotic genome plasticity and the evolution of new chromosomes mullakhanbhai and larsen 1975. Haloferax volcanii is an obligate halophilic archaeon with its origin in the dead sea. For example, haloferax volcanii contains one major chromosome and three minor chromosomes hartman et al. By the approach described here, all of the orf calls produced during those genome sequencing projects were automatically reconciled with the hfx. Isolated from the dead sea in 1975, haloferax volcanii thrives in high salt. Pdf the complete genome sequence of haloferax volcanii ds2. Genes for the initiator protein cdc6orc1, which are commonly located adjacent to archaeal origins of dna replication, are found on all replicons except plasmid phv2. Dna was isolated using a qiagen kit and used for genome sequencing. In midnovember2009 the community started haloferaxwiki, a wiki for community annotation of the haloferax volcanii ds2 genome. Genomic transposon insertion site loci were identified by using ncbi blastn suite and the publicly available genome sequence of h. This, in combination with its biochemical and genetic tractability, has made hfx. The genome has been completely sequenced and a paper discussing it was published in 2010.
For a statistical representation of the haloarchaeal genome, the conditions for partial cleavage were optimized and a fragment mixture with a size distribution of 35 kbp was isolated. The sequencing data were processed by phredphrapconsed software to assemble the whole genome sequence, using the genome sequence of haloferax volcanii ds2 as a reference. The genome was shown to encode at least 64 predicted rna including 3 rrna, 57 trna, 4 miscellaneous rna and 3911 proteincoding genes. The information in this wiki is freely accessible for everbody. Development of a gene knockout system for the halophilic. More than 40 nitrate respirationdeficient mutants of haloferax volcanii belonging to three different phenotypic classes were isolated.
Posttranscriptional modification of rna modification pattern of trnas. Hartman al, norais c, badger jh, delmas s, haldenby s, madupu r, robinson j, khouri h, ren q, lowe tm, et al. Haloarchaea are adapted to highsalt environments and accumulate equally high salt concentrations in the cytoplasm. Halophilic enzymes of potential interest to biotechnology have opened up the application of this organism in biocatalysis, bioremediation, nanobiotechnology. Haloferax volcanii s genome has officially been completely sequenced, however it is not yet available in full in annotated form. It is named in honour of benjamin volcani who pioneered the microbiology of the dead sea. This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. Grb contig maps reveals extensive volcanii ds2 and halobacterium salinarium.
Isolated from the dead sea in 1975, haloferax volcanii thrives in high salt environments and has emerged as an important archaeal model system. Transcriptome and proteome analyses have been established for halobacterium salinarum and haloferax volcanii. Useful derivatives of strain ds2 include strain hfx. Dna sequence determination was performed at the sequencing facility of the turku centre for biotechnology by using 3xl genetic analyzer pittsburgh, pa waltham, ma, usa. The genome sequence of haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for. It was isolated from the dead sea in 1975 and has been studied ever since. Peptostreptococcus anaerobius atcc 49031added 01282020. These results are generally consistent with the original genetic map of hfx. The most recent genome sequence draft was performed in april of 2007 by the institute for genomic research. Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. The extremely halophilic archaeon haloferax volcanii has two very different dihydrofolate reductases. The genome of haloferax volcanii, strain d2 4,012,900 nt comprises one chromosome 2,847,757 bp in several identical copies up to 20 and four smaller plasmids phv1. The complete genome sequence of haloferax volcanii ds2, a model. Genome sequence and description of haloferax massiliense.
Ds2 is found to have one chromosome and four plasmids. The genome sequence of haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, rna modifications, small noncoding rnas, and ubiquitinlike small archaeal modifier proteins. Comparative genomic analysis of the haloferax volcanii ds2. Genetic identification of three abc transporters as essential. The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of hfx. For the random shotgunsequencing phase, libraries with average sizes of 1. Functional genomic and advanced genetic studies reveal. Complete genome sequence of the metabolically versatile. Simple laboratory culture conditions and a wide range of genetic tools have made it a model organism for studying haloarchaeal cell biology. Draft genome sequence of haloferax volcanii ss0101. The complete genome sequence of haloferax volcanii ds2, a model archaeon amber l. The extremely halophilic archaeon haloferax volcanii is an obligate halophile that was first isolated from the dead sea. Wildtype copies of mutated genes were recovered from complemented mutants using two different approaches.
The complete genome sequence of haloferax volcanii ds2, a model archaeon. Bioinformatic and genetic characterization of three genes. Halobacterium volcanii encyclopedia article citizendium. Genetic identification of three abc transporters as. The full range of functional genomic methods has been established and results from transcriptomic, proteomic and. Genome sequence and description of haloferax massiliense sp. The complete genome sequence of chlorobium tepidum tls, a photosynthetic, anaerobic, greensulfur bacterium. Crispr clusters are transcribed and processed into crispr rna crrna. A previous study examined the genomic dna methylation patterns methylome of the halophilic archaeonhaloferax volcanii, a model archaeal system which can be easily manipulated in laboratory settings, via singlemolecule realtime smrt sequencing and deletion of. Haloferax volcanii s genome consists of a large 4 mb, multicopy chromosome and several megaplasmids. In this paper we describe the development of pyre based positive selection and counterselection systems to generate an efficient gene knockout system. Genomewide identification of transcriptional start sites.
So far, the extremely halophilic archaeon haloferax volcanii has the best genetic tools among the archaea. A previous study examined the genomic dna methylation patterns methylome of the halophilic archaeon haloferax volcanii, a model archaeal system which can be easily manipulated in laboratory settings, via singlemolecule realtime smrt sequencing and deletion of. Dec 20, 2019 haloferax volcanii is an obligate halophilic archaeon with its origin in the dead sea. The halophilic archaeon haloferax volcanii has a multireplicon genome, consisting of a main chromosome, three secondary chromosomes, and a plasmid. Genomewide identification of transcriptional start sites in. Gene table the haloferax volcanii genome database haloweb. Characterizing the dna methyltransferases of haloferax. Long stretches of short tandem repeats are present in the. Download fullsize image in this infographic we present the main tools available for the halophilic archaeon haloferax volcanii, which have enabled successful research on its biology, including its genetics, proteostasis, cell surface structures, metabolic pathways, and adaptation to high salt environments. Aug 06, 2010 haloferax volcanii s genome has officially been completely sequenced, however it is not yet available in full in annotated form.
The full range of functional genomic methods has been established and results from transcriptomic. We would like to show you a description here but the site wont allow us. The genomes of representatives of six haloarchaeal genera have been fully or partially sequenced, allowing the analysis of haloarchaeal properties in silico. The complete genome sequence of haloferax volcanii ds2. We report the presence of long stretches of tandem repeats in the genome of the halophilic archaea haloferax mediterranei and haloferax volcanii a 30 bp sequence with dyad symmetry including 5 bp inverted repeats was repeated in tandem, interspersed with 3339 bp unique sequences. The complete genome sequencing revealed a genome size of 3,094,203 bp with a circular chromosome and a gc content of 65.
Cgc and upon total digestion cleaves the gcrich genome of h. Development of additional selectable markers for the. Pdf the complete genome sequence of haloferax volcanii. Based on gene annotation, 3191 cdss, 6 rrna genes, and 76 trna genes were identified. Complete genome sequencing together with postgenomic studies provide the opportunity for a comprehensive systems biology understanding of model organisms. The complete genome sequence of haloferax volcanii ds2, a. Accelerated growth in the absence of dna replication origins.
All 15 mutants of the null phenotype were complemented with a genomic library of the wild type. Haloferax volcanii ds2 atcc29605, isolated from shore mud of the dead sea, is diskor cupshaped, and sometimes pleiomorphic. A large number of haloferax genomes have been sequenced 86, 87, and some are extremely similar to hfx. Functional genomic and advanced genetic studies reveal novel. For maximum effectiveness, an integrated database containing genomic, transcriptomic, and proteomic data is necessary. Search the haloferax volcanii genome database haloweb. Rnomics and modomics in the halophilic archaea haloferax. The leub gene, encoding 3isopropylmalate dehydrogenase, was chosen for development as a genetic marker, since it is the terminal gene in the operon and a deletion would not have a polar effect on transcription of leuc and. The complete genome sequence of the archaeal isolate. Crispr clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. However, the lack of an efficient gene knockout system for this organism has hampered further genetic studies. Nov 17, 2018 isolated from the dead sea in 1975, haloferax volcanii thrives in high salt environments and has emerged as an important archaeal model system. To improve data access and facilitate functional genomic studies on haloarchaea in our laboratory, a dedicated. Only one strain of haloferax volcanii haloferax volcanii ds2 has a mapped genome.
Moreover, 28 genes were annotated as related to salt tolerance, ammonium assimilation, and a truncated denitrification pathway. A comprehensive collection of highquality microbial genomics reference data. Prior to genome sequencing these minor chromosomes had been denoted as megaplasmids and, hence, got the names phv1, phv3 and phv4, but because of the organization of their replication origins they are now regarded to be bona fide. Dec 01, 2019 download one protein sequence per gene fasta. Citeseerx document details isaac councill, lee giles, pradeep teregowda. Genome 1 kegg genome 1 gene 6 refgene 4 ncbiproteinid 1 oc 1 protein sequence 1 uniprot 1 all databases 8 download rdf. Haloferax volcanii strain atcc 29605 dsm 3757 jcm 8879. The complete genome sequence was determined using the wholegenome shotgun method. Figure 1a shows their distribution identity and location in the general 2dcloverleaf structure of trna, while figure 1b. Genome 1 kegg genome 1 gene 6 refgene 4 ncbiproteinid 1 oc 1 protein sequence 1 uniprot 1 all databases 8 download rdf dbget integrated database retrieval system. Draft genome sequence of haloferax volcanii ss0101, isolated. Haloferax volcanii formerly halobacterium volcanii was first identified in the 1930s by microbiologist benjamin elazari volcani, for whom the species is named.
Strain archr t represents the th genome sequenced in the haloferax genus. It is a moderate halophile and a mesophile, in addition to being mildly acidophilic, and can be found living in the sediment of the dead sea, a salt lake in israel. Genetic and physical mapping of dna replication origins in. An operon containing the leucine biosynthesis genes leub, leuc, and leud was identified in the h. Generation of comprehensive transposon insertion mutant. Pcramplified 16s rrna gene of strain archrt yielded a 99. Its main chromosome has three origins, oric1, oric2, and oric3 norais et al.
Proteomes haloferax volcanii strain atcc 29605 dsm 3757 jcm 8879. It is a very versatile species that can grow in synthetic medium with a variety of carbon sources. Haloferax volcanii is a moderatly halophilic archaeon that grows optimally at a salt concentration around 2. Haloferax volcanii strain ds2 was obtained from atcc atcc 29605 and grown in the recommended media.
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