Transcriptional induction of purple membrane and gas vesicle synthesis in the archaebacterium Halobacterium halobium is blocked by a DNA gyrase inhibitor

Yang, Chin-Fen; DasSarma, Shiladitya

doi:10.1128/jb.172.7.4118-4121.1990

Cited by 51 publications

(64 citation statements)

References 40 publications

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“…The bacterio-opsin gene bop displayed the highest up-regulation (15-fold) of all ORFs. The strong differential expression of the bop gene is consistent with its regulation by the oxygenor redox-sensing activator Bat (2,3,40,41). Genes involved in aerobic respiration in NRC-1 were not down-regulated in the absence of oxygen.…”

Section: Fig 3 Rt-pcr Analysis Of the Dms Operon Insupporting

confidence: 49%

“…strain NRC-1 under anaerobic conditions. Previous work utilized a combination of genetic and genomic studies to establish the purple membrane regulon, which leads to coordinate synthesis of bacterio-opsin and its chromophore, retinal, to allow for light-driven proton pumping (2,8,40,41). The previous work led to the identification of a novel positive regulator, Bat, which controls the expression of the bacterio-opsin (bop) gene, as well as the first and last steps in the retinal biosynthetic pathway.…”

Section: Discussionmentioning

confidence: 99%

“…Finally, the induction of gvp genes, resulting in increased gas vesicle formation under anaerobic conditions, would enable Halobacterium sp. strain NRC-1 to float to aerobic zones in the water column (40).…”

Section: Discussionmentioning

confidence: 99%

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Genomic Analysis of Anaerobic Respiration in the ArchaeonHalobacteriumsp. Strain NRC-1: Dimethyl Sulfoxide and TrimethylamineN-Oxide as Terminal Electron Acceptors

2005

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We have investigated anaerobic respiration of the archaeal model organism Halobacterium sp. strain NRC-1 by using phenotypic and genetic analysis, bioinformatics, and transcriptome analysis. NRC-1 was found to grow on either dimethyl sulfoxide (DMSO) or trimethylamine N-oxide (TMAO) as the sole terminal electron acceptor, with a doubling time of 1 day. An operon, dmsREABCD, encoding a putative regulatory protein, DmsR, a molybdopterin oxidoreductase of the DMSO reductase family (DmsEABC), and a molecular chaperone (DmsD) was identified by bioinformatics and confirmed as a transcriptional unit by reverse transcriptase PCR analysis. dmsR, dmsA, and dmsD in-frame deletion mutants were individually constructed. Phenotypic analysis demonstrated that dmsR, dmsA, and dmsD are required for anaerobic respiration on DMSO and TMAO. The requirement for dmsR, whose predicted product contains a DNA-binding domain similar to that of the Bat family of activators (COG3413), indicated that it functions as an activator. A cysteine-rich domain was found in the dmsR gene, which may be involved in oxygen sensing. Microarray analysis using a wholegenome 60-mer oligonucleotide array showed that the dms operon is induced during anaerobic respiration. Comparison of dmsR؉ and ⌬dmsR strains by use of microarrays showed that the induction of the dmsEABCD operon is dependent on a functional dmsR gene, consistent with its action as a transcriptional activator. Our results clearly establish the genes required for anaerobic respiration using DMSO and TMAO in an archaeon for the first time.Extremely halophilic archaea (haloarchaea) generally grow heterotrophically under aerobic conditions in hypersaline environments, although they possess facultative anaerobic capabilities (9). These anaerobic capabilities are important since the high salt concentrations and elevated temperatures the organisms encounter, together with high cell densities promoted by aerobic growth and flotation, reduce the availability of molecular oxygen. Although haloarchaeal microorganisms frequently encounter microaerobic or even anoxic conditions, detailed knowledge regarding the extent of haloarchaeal anaerobic growth is still only beginning to emerge. Some species of haloarchaea can carry out primary energy conservation in the absence of molecular oxygen via photophosphorylation (13), substrate-level phosphorylation (13), and anaerobic respiration using nitrate (references 9 and 42 and references therein). In addition, two previous reports described the ability to use dimethyl sulfoxide (DMSO) and trimethylamine-N-oxide (TMAO) (23), and to some extent fumarate (22), as alternative electron acceptors for growth enhancement for some haloarchaea.The molecular basis of the DMSO and TMAO respiratory systems has not been described for any member of the domain Archaea. By contrast, in various bacterial model organisms, DMSO reductases and the related TMAO reductases are well characterized as membrane-bound or periplasmic terminal reductases forming dimethyl sulfide or trimethyla...

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Section: Fig 3 Rt-pcr Analysis Of the Dms Operon Insupporting

confidence: 49%

Section: Discussionmentioning

confidence: 99%

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Genomic Analysis of Anaerobic Respiration in the ArchaeonHalobacteriumsp. Strain NRC-1: Dimethyl Sulfoxide and TrimethylamineN-Oxide as Terminal Electron Acceptors

2005

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“…Thus, the inhibitory function of NifL appears to lie in its C-terminal domain, which presumably interacts with NifA. The N-terminal domain of NifL contains a region of homology (ϳ30% amino acid identity over 130 residues) to the product of the bat gene from Halobacterium halobium (19,47,50). Since Bat is an oxygen-responsive activator of the synthesis of bacterio-opsin, it has been proposed that the region of homology may be involved in oxygen sensing.…”

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confidence: 99%

Iron is required to relieve inhibitory effects on NifL on transcriptional activation by NifA in Klebsiella pneumoniae

Schmitz

Kustu

1996

J Bacteriol

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In Klebsiella pneumoniae, products of the nitrogen fixation nifLA operon regulate transcription of the other nif operons. NifA activates transcription by 54 -holoenzyme. In vivo, NifL antagonizes the action of NifA under aerobic conditions or in the presence of combined nitrogen. In contrast to a previous report, we show that depletion of iron (Fe) from the growth medium with the chelating agent o-phenanthroline (20 M) mimics aerobiosis or combined nitrogen in giving rise to inhibition of NifA activity even under anaerobic, nitrogenlimiting conditions. Adding back Fe in only twofold molar excess over phenanthroline restores NifA activity, whereas adding other metals fails to do so. By using strains that lack NifL, we showed that NifA activity itself does not require Fe and is not directly affected by phenanthroline. In the free-living diazotroph Klebsiella pneumoniae, expression of nitrogen fixation (nif) genes is regulated by the products of the nifLA operon (3,8,14,32). NifA activates transcription of all nif genes (except nifLA) by the alternative holoenzyme form of RNA polymerase 54 -holoenzyme. NifA binds to an upstream activation sequence (34) and contacts promoterbound 54 -holoenzyme by means of a DNA loop (9). It catalyzes the ATP-dependent isomerization of closed complexes between 54 -holoenzyme and a nif promoter to transcriptionally productive open complexes (25,35). NifL, which is a negative regulator, inhibits NifA activity in vivo in response to molecular oxygen and/or combined nitrogen (22,32).NifL from K. pneumoniae is composed of two domains separated by a hydrophilic interdomain linker (Q-linker [12]). We showed recently that the C-terminal domain is sufficient to inhibit transcriptional activation by NifA in vitro and in vivo (37). Thus, the inhibitory function of NifL appears to lie in its C-terminal domain, which presumably interacts with NifA. The N-terminal domain of NifL contains a region of homology (ϳ30% amino acid identity over 130 residues) to the product of the bat gene from Halobacterium halobium (19,47,50). Since Bat is an oxygen-responsive activator of the synthesis of bacterio-opsin, it has been proposed that the region of homology may be involved in oxygen sensing. The mechanism(s) by which NifL senses oxygen and/or combined nitrogen is not understood.The N-terminal domain of NifL contains one CysXXCys motif (Cys-184-Ala-Asp-Cys-187). The similarity of this motif to sequences involved in binding metal clusters in proteins such as ferrodoxins and rubredoxins (1, 4, 24) suggested a possible metal-binding role of this region in NifL (21). On the basis of this prediction, Henderson et al. (21) examined the influence of metal ion deficiency on NifL activity. They concluded that iron (Fe) deficiency reduced the inhibitory activity of NifL expressed at high levels in Escherichia coli.To further study the function of a possible metal ion or iron-sulfur (Fe-S) cluster in oxygen-sensing by NifL, we examined the effect of Fe deficiency on NifL inhibition of NifA activity in vivo in a stra...

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“…The brp gene is part of a gene cluster (Fig. 1) that includes bop, which encodes BO; bat, which encodes a transacting factor (Bat) that contains a region homologous to the PAS domain of the oxygen sensor NifL (19,20) and activates bop expression under microaerobic conditions (21,22); and blp, a gene of unknown function (23). Insertions in brp greatly decrease BR and bop mRNA levels (15)(16)(17)(18).…”

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confidence: 99%

brp and blh Are Required for Synthesis of the Retinal Cofactor of Bacteriorhodopsin in Halobacterium salinarum

Peck

Echávarri-Erasun²,

Johnson

et al. 2001

Journal of Biological Chemistry

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Bacteriorhodopsin, the light-driven proton pump of Halobacterium salinarum, consists of the membrane apoprotein bacterioopsin and a covalently bound retinal cofactor. The mechanism by which retinal is synthesized and bound to bacterioopsin in vivo is unknown. As a step toward identifying cellular factors involved in this process, we constructed an in-frame deletion of brp, a gene implicated in bacteriorhodopsin biogenesis. In the ⌬brp strain, bacteriorhodopsin levels are decreased ϳ4.0-fold compared with wild type, whereas bacterioopsin levels are normal. The probable precursor of retinal, ␤-carotene, is increased ϳ3.8-fold, whereas retinal is decreased by ϳ3.7-fold. These results suggest that brp is involved in retinal synthesis. Additional cellular factors may substitute for brp function in the ⌬brp strain because retinal production is not abolished. The in-frame deletion of blh, a brp paralog identified by analysis of the Halobacterium sp. NRC-1 genome, reduced bacteriorhodopsin accumulation on solid medium but not in liquid. However, deletion of both brp and blh abolished bacteriorhodopsin and retinal production in liquid medium, again without affecting bacterioopsin accumulation. The level of ␤-carotene increased ϳ5.3-fold. The simplest interpretation of these results is that brp and blh encode similar proteins that catalyze or regulate the conversion of ␤-carotene to retinal.Rhodopsins are integral membrane proteins containing seven transmembrane ␣-helices and a covalently bound molecule of retinal. Two distinct rhodopsin families are known: the visual rhodopsins, which bind 11-cis retinal or related compounds and function as photoreceptors in vertebrates (1) and invertebrates (2), and the archaeal rhodopsins, which bind all-trans-retinal and function as light-driven ion pumps and phototaxis receptors in archaea (3). Archaeal rhodopsin orthologs have been found recently in bacteria (4) and fungi (5), suggesting that retinal-based pigments are of widespread significance. Despite their importance, the biogenesis of these molecules is not fully understood. In particular, relatively little is known about how retinal is assembled with the opsin apoprotein in vivo. Thus, a goal in elucidating rhodopsin biogenesis is to identify the cellular factors that mediate the biosynthesis or uptake of retinal, the transport of retinal in the cell, and the binding of retinal to the corresponding opsin.To this end, we have studied the biogenesis of bacteriorhodopsin (BR), 1 a light-driven proton pump in the archaeon Halobacterium salinarum. BR consists of the membrane protein bacterioopsin (BO) and all-trans-retinal. Under microaerobic conditions, BR is induced ϳ50-fold (6) and forms a twodimensional crystal known as the purple membrane. This system has served as a model for studying key steps in membrane protein biogenesis, including protein insertion into the membrane (7,8) and the assembly of protein-lipid complexes (9, 10). H. salinarum is genetically tractable, and the genome sequence of a closely related organism, Halo...

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Transcriptional induction of purple membrane and gas vesicle synthesis in the archaebacterium Halobacterium halobium is blocked by a DNA gyrase inhibitor

Cited by 51 publications

References 40 publications

Genomic Analysis of Anaerobic Respiration in the ArchaeonHalobacteriumsp. Strain NRC-1: Dimethyl Sulfoxide and TrimethylamineN-Oxide as Terminal Electron Acceptors

Genomic Analysis of Anaerobic Respiration in the ArchaeonHalobacteriumsp. Strain NRC-1: Dimethyl Sulfoxide and TrimethylamineN-Oxide as Terminal Electron Acceptors

Iron is required to relieve inhibitory effects on NifL on transcriptional activation by NifA in Klebsiella pneumoniae

brp and blh Are Required for Synthesis of the Retinal Cofactor of Bacteriorhodopsin in Halobacterium salinarum

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