Genome sequence of
            <i>Halobacterium</i>
            species NRC-1

Ng, Wailap Victor; Kennedy, Sean P.; Mahairas, Gregory G.; Berquist, Brian R.; Pan, Min; Shukla, Hem D.; Lasky, Stephen R.; Baliga, Nitin S.; Thórsson, Vésteinn; Sbrogna, Jennifer; Swartzell, Steven; Weir, D. M.; Hall, J. G.; Dahl, Timothy; Welti, Russell; Goo, Young Ah; Leithauser, Brent; Keller, Kim; Cruz, R. P.G.; Danson, Michael J.; Hough, David W.; Maddocks, Deborah G.; Jablonski, Peter E.; Krebs, Mark P.; Angevine, Christine M.; Dale, Heather; Isenbarger, Thomas A.; Peck, Ronald F.; Pohlschröder, Mechthild; Spudich, John L.; Jung, Kwang Hwan; Alam, Maqsudul; Freitas, Tracey; Hou, Shaobin; Daniels, Charles J.; Dennis, Patrick P.; Omer, Arina D.; Ebhardt, H. Alexander; Lowe, Todd M.; Liang, Ping; Riley, Matilda White; Hood, Leroy; DasSarma, Shiladitya

doi:10.1073/pnas.190337797

Cited by 674 publications

(592 citation statements)

References 74 publications

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“…As an adaptation to high salinity environments, the H. salinarum proteome is known to be unusually acidic, with an average pI of 5.1 [24,36]. Consequently, observed migration bands of acidic proteins in SDS-PAGE gels are well known to not correspond directly to their molecular weight (MW).…”

Section: Resultsmentioning

confidence: 99%

“…H. salinarum NRC-1 is a halophilic archaeon that thrives in 4.3 M NaCl environments and presents a salt-in strategy for osmoregulation, as well as a highly acidic proteome [24]. Global gene regulatory networks have been studied in this organism using diverse environmental and genetic perturbations [25], ranking H. salinarum as having one of the most extensively studied archaeal transcriptomes.…”

Section: Introductionmentioning

confidence: 99%

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Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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“…NRC-1, a sequenced (Ng et al 2000) and genetically tractable mesophilic halophile isolated from Solar salt, and H. lacusprofundi, a cold-adapted halophile isolated from Deep Lake, Antarctica (Franzmann et al 1988). The results for Halobacterium NRC-1 indicate that this halophile grows well between 15 and 48 xC (Fig.…”

Section: Growth Of Halophiles At Low Temperaturesmentioning

confidence: 94%

Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures

Reid¹,

Sparks²,

Lubow³

et al. 2006

International Journal of Astrobiology

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: Cold environments are common throughout the Galaxy. We are conducting a series of experiments designed to probe the low-temperature limits for growth in selected methanogenic and halophilic Archaea. This paper presents initial results for two mesophiles, a methanogen, Methanosarcina acetivorans, and a halophile, Halobacterium sp. NRC-1, and for two Antarctic coldadapted Archaea, a methanogen, Methanococcoides burtonii, and a halophile, Halorubrum lacusprofundi. Neither mesophile is active at temperatures below 5 xC, but both cold-adapted microorganisms show significant growth at sub-zero temperatures (x2 xC and x1 xC, respectively), extending previous lowtemperature limits for both species by 4-5 xC. At low temperatures, both H. lacusprofundi and M. burtonii form multicellular aggregates, which appear to be embedded in extracellular polymeric substances. This is the first detection of this phenomenon in Antarctic species of Archaea at cold temperatures. The low-temperature limits for both psychrophilic species fall within the temperature range experienced on present-day Mars and could permit survival and growth, particularly in subsurface environments. We also discuss the results of our experiments in the context of known exoplanet systems, several of which include planets that intersect the Habitable Zone. In most cases, those planets follow orbits with significant eccentricity, leading to substantial temperature excursions. However, a handful of the known gas giant exoplanets could potentially harbour habitable terrestrial moons.

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“…Both vac regions are related but not identical to the gvp1 (p-vac) and gvp2 (c-vac) gene clusters of Hbt. salinarum NRC-1 (Ng et al, 2000). A third vac region, mc-vac (mc, mediterranei chromosomal), is found in Hfx.…”

Section: Introductionmentioning

confidence: 99%

GvpD-induced breakdown of the transcriptional activator GvpE of halophilic archaea requires a functional p-loop and an arginine-rich region of GvpD

Scheuch

Pfeifer

2007

Microbiology

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The two proteins involved in the regulation of gas vesicle formation in Haloferax mediterranei, mcGvpE (activator) and mcGvpD (repressive function), are able to interact in vitro. It was also found that the respective proteins cGvpE and cGvpD of Halobacterium salinarum and the heterologous pairs mcGvpD-cGvpE and cGvpD-mcGvpE were able to interact. Previously constructed mcGvpD mutants with alterations in regions affecting the repressive function of GvpD (p-loop motif or the two arginine-rich regions bR1 and bR2) were tested for their ability to interact with GvpE, and all still bound GvpE. Even a deletion of or near the p-loop motif in GvpD did not affect this ability to interact. Further deletion variants lacking larger N-or C-terminal portions of mcGvpD yielded that neither the N-terminal region with the p-loop motif nor the C-terminal portion were important for the binding of GvpE, and suggested that the central portion is involved in GvpE binding. The GvpD protein also induces a reduction in the amount of GvpE in Haloferax volcanii transformants expressing both genes under fdx promoter control on a single plasmid. Such DE ex transformants contain GvpD, but no detectable GvpE, whereas large amounts of GvpE are found in DDE ex transformants that have incurred a deletion within the gvpD gene. A similar reduction was observed in D ex +E ex transformants harbouring both reading frames under fdx promoter control on two different plasmids. GvpD wild-type and also GvpD mutants were tested, and a significant reduction in the amount of GvpE was obtained in the case of GvpD wild-type and the super-repressor mutant GvpD 3-AAA . In contrast, transformants harbouring GvpD mutants with alterations in the p-loop motif or the bR1 region still contained GvpE. Since the amount of gvpE transcript was not reduced, the reduction occurred at the protein level. These results underlined that a functional p-loop and the arginine-rich region bR1 of GvpD were required for the GvpD-mediated reduction in the amount of GvpE.

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Genome sequence of Halobacterium species NRC-1

Cited by 674 publications

References 74 publications

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures

GvpD-induced breakdown of the transcriptional activator GvpE of halophilic archaea requires a functional p-loop and an arginine-rich region of GvpD

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