Article

Complete genome sequence of Haloterrigena turkmenica type strain (4kT)

Standards in Genomic Sciences (Impact Factor: 3.17). 02/2010; 2(1):107-16. DOI: 10.4056/sigs.681272
Source: PubMed

ABSTRACT Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is the type species of the genus Haloterrigena in the euryarchaeal family Halobacteriaceae. It is of phylogenetic interest because of the yet unclear position of the genera Haloterrigena and Natrinema within the Halobacteriaceae, which created some taxonomic problems historically. H. turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme halophile, requiring at least 2 M NaCl for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Haloterrigena, but the eighth genome sequence from a member of the family Halobacteriaceae. The 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Download full-text

Full-text

Available from: Jonathan A Eisen, Sep 03, 2015
1 Follower
 · 
194 Views
 · 
61 Downloads
  • Source
    • "asiatica strain ATCC 700177 has been reported [21]. The genome of Haloterrigena turkmenica strain DSM 5511, a halophilic archaeon isolated from sulfate saline soil in Turkmenistan, is complete and contains 5,287 protein coding genes [22]. Furthermore, the complete genome of Natronomonas pharaonis DSM 2160, a haloalkaliphilic archaeon isolated from a soda lake in Egypt, contains 2,843 protein coding genes [23]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is a dual extremophile requiring alkaline conditions and hypersalinity for optimal growth. The genome sequence of Nab. magadii type strain ATCC 43099 was deciphered to obtain a comprehensive insight into the genetic content of this haloarchaeon and to understand the basis of some of the cellular functions necessary for its survival. The genome of Nab. magadii consists of four replicons with a total sequence of 4,443,643 bp and encodes 4,212 putative proteins, some of which contain peptide repeats of various lengths. Comparative genome analyses facilitated the identification of genes encoding putative proteins involved in adaptation to hypersalinity, stress response, glycosylation, and polysaccharide biosynthesis. A proton-driven ATP synthase and a variety of putative cytochromes and other proteins supporting aerobic respiration and electron transfer were encoded by one or more of Nab. magadii replicons. The genome encodes a number of putative proteases/peptidases as well as protein secretion functions. Genes encoding putative transcriptional regulators, basal transcription factors, signal perception/transduction proteins, and chemotaxis/phototaxis proteins were abundant in the genome. Pathways for the biosynthesis of thiamine, riboflavin, heme, cobalamin, coenzyme F420 and other essential co-factors were deduced by in depth sequence analyses. However, approximately 36% of Nab. magadii protein coding genes could not be assigned a function based on Blast analysis and have been annotated as encoding hypothetical or conserved hypothetical proteins. Furthermore, despite extensive comparative genomic analyses, genes necessary for survival in alkaline conditions could not be identified in Nab. magadii. Based on genomic analyses, Nab. magadii is predicted to be metabolically versatile and it could use different carbon and energy sources to sustain growth. Nab. magadii has the genetic potential to adapt to its milieu by intracellular accumulation of inorganic cations and/or neutral organic compounds. The identification of Nab. magadii genes involved in coenzyme biosynthesis is a necessary step toward further reconstruction of the metabolic pathways in halophilic archaea and other extremophiles. The knowledge gained from the genome sequence of this haloalkaliphilic archaeon is highly valuable in advancing the applications of extremophiles and their enzymes.
    BMC Genomics 05/2012; 13:165. DOI:10.1186/1471-2164-13-165 · 4.04 Impact Factor
  • Source
    • "Nucleotide and protein sequences were obtained for completed haloarchaeal genomes from NCBI: Halobacterium sp. NRC-1 ATCC 700922 (NRC-1) [8], Haloarcula marismortui ATCC 43049 (Hma) [43], Natronomonas pharaonis DSM 2160 (Nph) [44], Haloquadratum walsbyi DSM 16790 (Hwa) [45], Halorubrum lacusprofundi ATCC 49239 (Hla) [46], Halogeometricum borinquense DSM 11551 (Hbo) [47], Halomicrobium mukohataei DSM 12286 (Hmu) [48], Halorhabdus utahensis DSM 12940 (Hut) [49], Haloferax volcanii DS2 (Hvo) [50], Haloterrigena turkmenica DSM 5511 (Htu) [51], Natrialba magadii ATCC 43099 (Nma) [52], Halalkalicoccus jeotgali B3 (Hje) [53], and Halopiger xanaduensis SH-6 (Hxa) [54]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Since the first genome of a halophilic archaeon was sequenced in 2000, biologists have been advancing the understanding of genomic characteristics that allow for survival in the harsh natural environments of these organisms. An increase in protein acidity and GC-bias in the genome have been implicated as factors in tolerance to extreme salinity, desiccation, and high solar radiation. However, few previous attempts have been made to identify novel genes that would permit survival in such extreme conditions. With the recent release of several new complete haloarchaeal genome sequences, we have conducted a comprehensive comparative genomic analysis focusing on the identification of unique haloarchaeal conserved proteins that likely play key roles in environmental adaptation. Using bioinformatic methods, we have clustered 31,312 predicted proteins from nine haloarchaeal genomes into 4,455 haloarchaeal orthologous groups (HOGs). We assigned likely functions by association with established COG and KOG databases in NCBI. After identifying homologs in four additional haloarchaeal genomes, we determined that there were 784 core haloarchaeal protein clusters (cHOGs), of which 83 clusters were found primarily in haloarchaea. Further analysis found that 55 clusters were truly unique (tucHOGs) to haloarchaea and qualify as signature proteins while 28 were nearly unique (nucHOGs), the vast majority of which were coded for on the haloarchaeal chromosomes. Of the signature proteins, only one example with any predicted function, Ral, involved in desiccation/radiation tolerance in Halobacterium sp. NRC-1, was identified. Among the core clusters, 33% was predicted to function in metabolism, 25% in information transfer and storage, 10% in cell processes and signaling, and 22% belong to poorly characterized or general function groups. Our studies have established conserved groups of nearly 800 protein clusters present in all haloarchaea, with a subset of 55 which are predicted to be accessory proteins that may be critical or essential for success in an extreme environment. These studies support core and signature genes and proteins as valuable concepts for understanding phylogenetic and phenotypic characteristics of coherent groups of organisms.
    BMC Genomics 01/2012; 13(1):39. DOI:10.1186/1471-2164-13-39 · 4.04 Impact Factor
  • Source
    • "Sequencing and annotation of H. borinquense, H. mukohataei, H. utahensis, and H. turkmenica have been previously described [16]–[19]. A publication describing the sequencing and annotation of H. lacusprofundi is in preparation. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis. We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses. These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.
    PLoS ONE 05/2011; 6(5):e20237. DOI:10.1371/journal.pone.0020237 · 3.23 Impact Factor
Show more