Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea

Abstract

We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a halophilic archaeal isolate from the Dead Sea. The genome is organized into nine circular replicons of varying G+C compositions ranging from 54% to 62%. Comparison of the genome architectures of Halobacterium sp. NRC-1 and H. marismortui suggests a common ancestor for the two organisms and a genome of significantly reduced size in the former. Both of these halophilic archaea use the same strategy of high surface negative charge of folded proteins as means to circumvent the salting-out phenomenon in a hypersaline cytoplasm. A multitiered annotation approach, including primary sequence similarities, protein family signatures, structure prediction, and a protein function association network, has assigned putative functions for at least 58% of the 4242 predicted proteins, a far larger number than is usually achieved in most newly sequenced microorganisms. Among these assigned functions were genes encoding six opsins, 19 MCP and/or HAMP domain signal transducers, and an unusually large number of environmental response regulators-nearly five times as many as those encoded in Halobacterium sp. NRC-1-suggesting H. marismortui is significantly more physiologically capable of exploiting diverse environments. In comparing the physiologies of the two halophilic archaea, in addition to the expected extensive similarity, we discovered several differences in their metabolic strategies and physiological responses such as distinct pathways for arginine breakdown in each halophile. Finally, as expected from the larger genome, H. marismortui encodes many more functions and seems to have fewer nutritional requirements for survival than does Halobacterium sp. NRC-1.

Evolution of a Protein-Folding Machine: Genomic and Evolutionary Analyses Reveal Three Lineages of the Archaeal hsp70(dnaK) Gene

“…All of the organisms with Type III Locus I were extreme halophiles and showed a diversity in locus organization that was not observed in the other two Locus I Types. This diversity parallels other kinds of variations observed in haloarchaeal genomes, suggesting that these genomes are somewhat variable by comparison with other archaeal groups, e.g., the methanogens (Ng et al 2000;Baliga et al 2004). …”

“…For H. mediterranei, no sequence is available upstream of grpE. Not shown is the locus from Haloarcula marismortui (whose genome has recently been sequenced [Baliga et al 2004; http://halo.systemsbiology.net; for sequence, data, annotations, and analyses, http://www.ebi.ac.uk/interpro/READ-ME1.html; InterProScan, http://www.genome.ad.jp/kegg-bin/ srch_orth_html; KEGG database, http://ncbi.nih.gov/COG]), in which the dnaJ gene is not in the dnaK locus but is separated from the latter by 3266 bp, with other genes between them. grpE and dnaK are consecutive genes (no other gene between them), separated by 165 bp.…”

Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain

“…As P. wickerhamii is haploid, crossover of 18S rRNA genes by homologous recombination is not to be expected. The origin of different types of SSU rRNA gene in a single genome has been explained by either (1) divergent evolution following gene duplication (Mylvaganam & Dennis, 1992;Baliga et al, 2004) or (2) Fig. 4.…”

The methylaspartate cycle in haloarchaea and its possible role in carbon metabolism

“…Mutant construction was performed using the pop-in/pop-out method Figure 2 Genomic region of Haloarcula marismortui and H. hispanica coding for the enzymes of the methylaspartate cycle (Baliga et al, 2004;Liu et al, 2011b). MamAB, glutamate mutase; Mal, methylaspartate ammonia lyase; Mct, mesaconate CoA-transferase; Mch, mesaconyl-CoA hydratase; Mcl, β-methylmalyl-CoA lyase.…”