Bacterioopsin, haloopsin, and sensory opsin I of the halobacterial isolate Halobacterium sp. strain SG1: three new members of a growing family

Soppa, Jörg; Duschl, Jutta; Oesterhelt, Dieter

doi:10.1128/jb.175.9.2720-2726.1993

Cited by 52 publications

(32 citation statements)

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“…The excess of acidic amino acids (difference between the fractions of acidic and basic residues) is 14.7%, which is much higher than the value of 1.9% for proteins of enteric bacteria. This is a common feature of soluble halobacterial proteins (28,41) and is thought to be important for solubility at the high ionic strength found in the cytoplasm (3,12,13). A database search showed that the CK of P. aeruginosa is the only protein with significant similarity to the halobacterial enzyme.…”

Section: Resultsmentioning

confidence: 99%

Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster

1996

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Fermentative growth via the arginine deiminase pathway is mediated by the enzymes arginine deiminase, carbamate kinase, and catabolic ornithine transcarbamylase and by a membrane-bound arginine-ornithine antiporter. Recently we reported the characterization of catabolic ornithine transcarbamylase and the corresponding gene, arcB, from Halobacterium salinarium (formerly Halobacterium halobium). Upstream of the arcB gene, three additional open reading frames with halobacterial codon usage were found. They were identified as the arcC gene coding for carbamate kinase, the arcA gene coding for arginine deiminase, and a gene, tentatively termed arcR, coding for a putative regulatory protein. The identification of the arcC and arcA genes was verified, respectively, by heterologous expression of the enzyme in Haloferax volcanii and by protein isolation and N-terminal sequence determination of three peptides. The gene order arcRACB differs from the gene order arcDABC in Pseudomonas aeruginosa, the only other organism for which sequence information is available. Transcripts from H. salinarium cultures grown fermentatively or aerobically were characterized by Northern (RNA) blot and primer extension analyses. It was determined (i) that monocistronic transcripts corresponding to the four open reading frames exist and that there are three polycistronic transcripts, (ii) that the level of induction during fermentative growth differs for the various transcripts, and (iii) that upstream of the putative transcriptional start sites for the three structural genes there are sequences with similarities to the halobacterial consensus promoter. The data indicate that expression of the arc gene cluster and its regulation differ in H. salinarium and P. aeruginosa.The arginine deiminase pathway of fermentative arginine utilization consists of the three enzymes arginine deiminase (ADI, EC 3.5.3.6), catabolic ornithine transcarbamylase (cOTCase, EC 2.1.3.3), and carbamate kinase (CK, EC 2.7.2.2) and a membrane-bound arginine-ornithine antiporter. The degradation of arginine is coupled to the equimolar generation of ATP by substrate level phosphorylation. This pathway is found in a variety of phylogenetic groups within the domain Bacteria, e.g., Pseudomonas spp., Mycoplasma spp., Bacillus spp., and lactic bacteria (for a review, see reference 8). The pathway has been most extensively studied in Pseudomonas aeruginosa (21), the only species for which the sequences of the four genes have been determined (1,2,29). The genes are organized in an operon, and a polycistronic mRNA is transcribed from a single promoter and subsequently processed into a variety of smaller transcripts (17) in an RNase E-dependent reaction (18). The transcription of the arcDABC operon is under the positive control of the ANR protein (15, 22), a member of the FNR protein family.Within the domain Archaea, arginine-dependent anaerobic growth has only been reported for some halobacterial species (25,37). The consumption of arginine was coupled to the equimolar production o...

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Section: Resultsmentioning

confidence: 99%

Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster

1996

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“…In previous studies bacteria-opsin had been compared to some members of the GPCR family without finding similarities [ 191 and the retinal protein family was used to search for related sequences in protein sequence databases without success [13]. Of course this lack of sequence similarties does not exclude the development of the two protein families from a common ancestor.…”

Section: Discussionmentioning

confidence: 99%

“…During the last years, the primary structures of Bop, Hop and Sop I of different halobacterial species have been determined, so that today 10 non-identical sequences and a number of partial sequences are known [6-l 3]. These proteins are clearly homologous based on the similarities of the primary sequences as well as biochemical and biophysical properties [13,14]. Therefore, a hypothesis about the relationship of BR to the GPCRs is in fact a hypothesis about the relationship of two protein families.…”

Section: Bacteriorhodopsinmentioning

confidence: 99%

“…For membrane-spanning helices with most of the amino acids in contact with the lipid phase, alanine-leucine mismatches and valine-leucine mismatches seem to be equivalent and even alanine-tr~tophan mismatches are energetically not too unfavored, but the Table 2 Similarities between helices 1, 2 and 7 and the remaining part of the respective halobacterial retinal proteins Used for the search The alignments were done with the program, Gap [15]. The helix boundaries were taken from the structural model of H. halobium BR [2] and the alignment of the retinal proteins [13]. The helices were aligned to the remaining C-terminal (helices 1 and 2) or N-terminal (helix 7) sequence of the helix used.…”

Section: Evolution Of Br and Gpcrs From A Common Ancestor Involving Ementioning

confidence: 99%

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Two hypotheses ‐ one answer

Soppa

1994

FEBS Letters

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The structure of bacteriorhodopsin (BR) of Halobacterium halobium is known. Despite the lack of sequence similarities it is often taken as a model for eukaryotic G-protein~upl~ receptors (GPCRs). Recently two hypotheses were used to support the homology of BR and GPCRs, namly evolution by exon shuflling and evolution by gene duplication. BR is a member of a family of halobacterial retinal proteins. The sequences of eight members of this family were used to test the two hypotheses. Based on sequence comparison, no indication for an evolutionary linkage between the two protein families could be found.

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“…It codes for a protein of 295 amino acids with a calculated molecular mass of 32 kDa. The cOTCase has an amino acid composition which is characteristic of soluble halophilic proteins; i.e., it contains 20% acidic residues (DϩE), and the preference of acidic residues, DϩE minus KϩR, is 14%, compared with 2% for proteins of enteric bacteria (45). The great fraction of acidic residues leads to the difference between the calculated molecular mass (32 kDa) and the apparent molecular mass, determined by SDS-PAGE (41 kDa), which is typical of halophilic proteins.…”

Section: Resultsmentioning

confidence: 99%

Catabolic ornithine transcarbamylase of Halobacterium halobium (salinarium): purification, characterization, sequence determination, and evolution

et al. 1995

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Halobacterium halobium (salinarium) is able to grow fermentatively via the arginine deiminase pathway, which is mediated by three enzymes and one membrane-bound arginine-ornithine antiporter. One of the enzymes, catabolic ornithine transcarbamylase (cOTCase), was purified from fermentatively grown cultures by gel filtration and ammonium sulfate-mediated hydrophobic chromatography. It consists of a single type of subunit with an apparent molecular mass of 41 kDa. As is common for proteins of halophilic Archaea, the cOTCase is unstable below 1 M salt. In contrast to the cOTCase from Pseudomonas aeruginosa, the halophilic enzyme exhibits Michaelis-Menten kinetics with both carbamylphosphate and ornithine as substrates with K m values of 0.4 and 8 mM, respectively. The N-terminal sequences of the protein and four peptides were determined, comprising about 30% of the polypeptide. The sequence information was used to clone and sequence the corresponding gene, argB. It codes for a polypeptide of 295 amino acids with a calculated molecular mass of 32 kDa and an amino acid composition which is typical of halophilic proteins. The native molecular mass was determined to be 200 kDa, and therefore the cOTCase is a hexamer of identical subunits. The deduced protein sequence was compared to the cOTCase of P. aeruginosa and 14 anabolic OTCases, and a phylogenetic tree was constructed. The halobacterial cOTCase is more distantly related to the cOTCase than to the anabolic OTCase of P. aeruginosa. It is found in a group with the anabolic OTCases of Bacillus subtilis, P. aeruginosa, and Mycobacterium bovis.Fermentative arginine degradation via the arginine deiminase pathway is found in different groups of Bacteria (for reviews see references 1 and 8). The pathway consists of an arginine-ornithine antiporter and the enzymes arginine deiminase (ADI; EC 3.5.3.6), catabolic ornithine transcarbamylase (cOTCase; EC 2.1.3.3), and carbamate kinase (CK; EC 2.7.2.2). Arginine is degraded to ornithine, ammonia, and CO 2 , concomitantly generating 1 mol of ATP per mol of arginine degraded. An OTCase activity is also involved in arginine biosynthesis. Organisms capable of both arginine biosynthesis and fermentative arginine degradation possess two OTCases which are differentially regulated. The ADI pathway has been most extensively studied in Pseudomonas aeruginosa (2-5, 16, 17, 21, 29, 32, 58). In this organism, the genes are situated in an operon and are cotranscribed.Halobacteria are the only Archaea for which anaerobic growth using arginine has been reported (22). As arginine consumption was coupled to the equimolar occurrence of ornithine in the medium, it was proposed that Halobacterium halobium (salinarium) (H. halobium has recently been renamed H. salinarium, which is used for the rest of this article.) degrades arginine via the ADI pathway (22).To study this pathway and its regulation in an archaeon, the cOTCase from H. salinarium was isolated and characterized. The corresponding gene was cloned and sequenced, and the deduced protein...

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Bacterioopsin, haloopsin, and sensory opsin I of the halobacterial isolate Halobacterium sp. strain SG1: three new members of a growing family

Abstract: The genes coding for bacterioopsin, haloopsin, and sensory opsin I

Cited by 52 publications

References 51 publications

Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster

Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster

Two hypotheses ‐ one answer

Catabolic ornithine transcarbamylase of Halobacterium halobium (salinarium): purification, characterization, sequence determination, and evolution

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