scholarly journals Cysteine Biosynthesis Pathway in the ArchaeonMethanosarcina barkeri Encoded by Acquired Bacterial Genes?

2000 ◽  
Vol 182 (1) ◽  
pp. 143-145 ◽  
Author(s):  
Makoto Kitabatake ◽  
Man Wah So ◽  
Debra L. Tumbula ◽  
Dieter Söll
Keyword(s):  
Sulfolobus Solfataricus ◽  
Methanosarcina Barkeri ◽  
Archaeoglobus Fulgidus ◽  
Biosynthesis Pathway ◽  
Cysteine Biosynthesis ◽  
Gene Encoding ◽  
Reading Frame ◽  
Genome Data ◽  
Genes Encoding ◽  
Bacterial Genes

ABSTRACT The pathway of cysteine biosynthesis in archaea is still unexplored. Complementation of a cysteine auxotrophic Escherichia coli strain NK3 led to the isolation of the Methanosarcina barkeri cysK gene [encoding O-acetylserine (thiol)-lyase-A], which displays great similarity to bacterialcysK genes. Adjacent to cysK is an open reading frame orthologous to bacterial cysE (serine transacetylase) genes. These two genes could account for cysteine biosynthesis in this archaeon. Analysis of recent genome data revealed the presence of bacteria-like cysM genes [encodingO-acetylserine (thiol)-lyase-B] in Pyrococcusspp., Sulfolobus solfataricus, and Thermoplasma acidophilum. However, no orthologs for these genes can be found in Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Archaeoglobus fulgidus, implying the existence of unrecognizable genes for the same function or a different cysteine biosynthesis pathway.

scholarly journals Clustered Genes Encoding the Methyltransferases of Methanogenesis from Monomethylamine

1998 ◽  
Vol 180 (13) ◽  
pp. 3432-3440 ◽  
Author(s):  
Stephen A. Burke ◽  
Sam L. Lo ◽  
Joseph A. Krzycki
Keyword(s):  
Transcriptional Start Site ◽  
Methanosarcina Barkeri ◽  
Open Reading Frame ◽  
Methionine Synthase ◽  
Binding Motif ◽  
Gene Encoding ◽  
Reading Frame ◽  
Genes Encoding ◽  
Translational Start ◽  
Monocistronic Transcript

ABSTRACT Coenzyme M (CoM) is methylated during methanogenesis from monomethyamine in a reaction catalyzed by three proteins. Using monomethylamine, a 52-kDa polypeptide termed monomethylamine methyltransferase (MMAMT) methylates the corrinoid cofactor bound to a second polypeptide, monomethylamine corrinoid protein (MMCP). Methylated MMCP then serves as a substrate for MT2-A, which methylates CoM. The genes for these proteins are clustered on 6.8 kb of DNA inMethanosarcina barkeri MS. The gene encoding MMCP (mtmC) is located directly upstream of the gene encoding MMAMT (mtmB). The gene encoding MT2-A (mtbA) was found 1.1 kb upstream of mtmC, but no obvious open reading frame was found in the intergenic region betweenmtbA and mtmC. A single monocistronic transcript was found for mtbA that initiated 76 bp from the translational start. Separate transcripts of 2.4 and 4.7 kb were detected, both of which carried mtmCB. The larger transcript also encoded mtmP, which is homologous to the APC family of cationic amine permeases and may therefore encode a methylamine permease. A single transcriptional start site was found 447 bp upstream of the translational start of mtmC. MtmC possesses the corrinoid binding motif found in corrinoid proteins involved in dimethylsulfide- and methanol-dependent methanogenesis, as well as in methionine synthase. The open reading frame ofmtmB was interrupted by a single in-frame, midframe, UAG codon which was also found in mtmB from M. barkeri NIH. A mechanism that circumvents UAG-directed termination of translation must operate during expression ofmtmB in this methanogen.

scholarly journals The carB Gene Encoding the Large Subunit of Carbamoylphosphate Synthetase from Lactococcus lactis Is Transcribed Monocistronically

1998 ◽  
Vol 180 (17) ◽  
pp. 4380-4386 ◽  
Author(s):  
Jan Martinussen ◽  
Karin Hammer
Keyword(s):  
Lactococcus Lactis ◽  
Large Subunit ◽  
Arginine Deiminase ◽  
Gene Encoding ◽  
Pyrimidine Nucleotides ◽  
Reading Frame ◽  
Glutathione Peroxidases ◽  
Carbamoylphosphate Synthetase ◽  
Genes Encoding ◽  
High Degree

ABSTRACT The biosynthesis of carbamoylphosphate is catalyzed by the heterodimeric enzyme carbamoylphosphate synthetase. The genes encoding the two subunits of this enzyme in procaryotes are normally transcribed as an operon, but the gene encoding the large subunit (carB) in Lactococcus lactis is shown to be transcribed as an isolated unit. Carbamoylphosphate is a precursor in the biosynthesis of both pyrimidine nucleotides and arginine. By mutant analysis,L. lactis is shown to possess only onecarB gene; the same gene product is thus required for both biosynthetic pathways. Furthermore, arginine may satisfy the requirement for carbamoylphosphate in pyrimidine biosynthesis through degradation by means of the arginine deiminase pathway. The expression of the carB gene is subject to regulation at the level of transcription by pyrimidines, most probably by an attenuator mechanism. Upstream of the carB gene, an open reading frame showing a high degree of similarity to those of glutathione peroxidases from other organisms was identified.

scholarly journals Clustering of the YNA1 gene encoding a Zn(II)2Cys6 transcriptional factor in the yeast Hansenula polymorpha with the nitrate assimilation genes YNT1, YNI1 and YNR1, and its involvement in their transcriptional activation

1998 ◽  
Vol 335 (3) ◽  
pp. 647-652 ◽  
Author(s):  
Julio ÁVILA ◽  
Celedonio GONZÁLEZ ◽  
Nélida BRITO ◽  
José M. SIVERIO
Keyword(s):  
Transcriptional Activation ◽  
Hansenula Polymorpha ◽  
Nitrate Assimilation ◽  
Transcriptional Factors ◽  
Gene Encoding ◽  
Reading Frame ◽  
Transcription Start Sites ◽  
The Family ◽  
Genes Encoding ◽  
Free Media

The genes encoding the nitrate transporter (YNT1), nitrite reductase (YNI1) and nitrate reductase (YNR1) are clustered in the yeast Hansenula polymorpha. In addition, DNA sequencing of the region containing these genes demonstrated that a new open reading frame called YNA1 (yeast nitrate assimilation) was located between YNR1 and YNI1. The YNA1 gene encodes a protein of 529 residues belonging to the family of Zn(II)2Cys6 fungal transcriptional factors, and has the highest similarity to the transcriptional factors encoded by nirA, and to a smaller extent to nit-4, involved in the nitrate induction of the gene involved in the assimilation of this compound in filamentous fungi. Northern blot analysis showed the presence of the YNA1 transcript in cells incubated in nitrate, nitrate plus ammonium, ammonium, and nitrogen-free media, with a decrease in its levels in those cells incubated in ammonium. In nitrate the strain Δyna1::URA3, with a disrupted YNA1 gene, neither grew nor expressed the genes YNT1, YNI1 and YNR1. In the gene cluster YNT1-YNI1-YNA1-YNR1, the four genes were transcribed independently in the YNT1 → YNR1 direction and the transcription start sites were determined by primer extension.

scholarly journals Genome Mining Reveals Two Missing CrtP and AldH Enzymes in the C30 Carotenoid Biosynthesis Pathway in Planococcus faecalis AJ003T

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5892
Author(s):  
Jun Ho Lee ◽  
Jin Won Kim ◽  
Pyung Cheon Lee
Keyword(s):  
Escherichia Coli ◽  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Gene Encoding ◽  
A Genome ◽  
Genes Encoding ◽  
Carotenoid Biosynthesis Pathway ◽  
Carotenoid Pathway

Planococcus faecalis AJ003T produces glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid as its main carotenoid. Five carotenoid pathway genes were presumed to be present in the genome of P. faecalis AJ003T; however, 4,4-diaponeurosporene oxidase (CrtP) was non-functional, and a gene encoding aldehyde dehydrogenase (AldH) was not identified. In the present study, a genome mining approach identified two missing enzymes, CrtP2 and AldH2454, in the glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid biosynthetic pathway. Moreover, CrtP2 and AldH enzymes were functional in heterologous Escherichia coli and generated two carotenoid aldehydes (4,4′-diapolycopene-dial and 4,4′-diaponeurosporene-4-al) and two carotenoid carboxylic acids (4,4′-diaponeurosporenoic acid and 4,4′-diapolycopenoic acid). Furthermore, the genes encoding CrtP2 and AldH2454 were located at a distance the carotenoid gene cluster of P. faecalis.

scholarly journals Identification of a New Gene Essential for Germinationof Bacillus subtilis Spores withCa2+-Dipicolinate

2003 ◽  
Vol 185 (7) ◽  
pp. 2315-2329 ◽  
Author(s):  
Katerina Ragkousi ◽  
Patrick Eichenberger ◽  
Christiaan van Ooij ◽  
Peter Setlow
Keyword(s):  
Bacillus Subtilis ◽  
Spore Germination ◽  
Function Analysis ◽  
Dipicolinic Acid ◽  
Functional Characterization ◽  
Lytic Enzyme ◽  
Spore Coat ◽  
Gene Encoding ◽  
Reading Frame ◽  
Genes Encoding

ABSTRACT Bacillus subtilis spores can germinate with a 1:1 chelate of Ca2+ and dipicolinic acid (DPA), a compound present at high levels in the spore core. Using a genetic screen to identify genes encoding proteins that are specifically involved in spore germination by Ca2+-DPA, three mutations were identified. One was in the gene encoding the cortex lytic enzyme, CwlJ, that was previously shown to be essential for spore germination by Ca2+-DPA. The other two were mapped to an open reading frame, ywdL, encoding a protein of unknown function. Analysis of ywdL expression showed that the gene is expressed during sporulation in the mother cell compartment of the sporulating cell and that its transcription is σE dependent. Functional characterization of YwdL demonstrated that it is a new spore coat protein that is essential for the presence of CwlJ in the spore coat. Assembly of YwdL itself into the spore coat is dependent on the coat morphogenetic proteins CotE and SpoIVA. However, other than lacking CwlJ, ywdL spores have no obvious defect in their spore coat. Because of the role for YwdL in a part of the spore germination process, we propose renaming ywdL as a spore germination gene, gerQ.

scholarly journals Prevalence of Antibiotic Resistance Genes in Subjects with Successful and Failing Dental Implants. A Pilot Study

2015 ◽  
Vol 8 (1) ◽  
pp. 257-263 ◽  
Author(s):  
Georgios Koukos ◽  
Christos Papadopoulos ◽  
Lazaros Tsalikis ◽  
Dimitra Sakellari ◽  
Minas Arsenakis ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Dental Implants ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Beta Lactams ◽  
Gene Encoding ◽  
Osseointegrated Implants ◽  
Genes Encoding ◽  
Bacterial Genes

Objectives :To investigate the prevalence of the bacterial genes encoding resistance to beta-lactams, tetracyclines and metronidazole respectively, in subjects with successful and failing dental implants and to assess the presence ofStaphylococcus aureusand themecAgene encoding for Methicillin ResistantStaphylococcus aureus(MRSA) in the same samples.Materials and Methodology:The subject sample included 20 participants with clinically healthy osseointegrated implants and 20 participants with implants exhibiting peri-implantitis. Clinical parameters were assessed with an automated probe, samples were collected from the peri-implant sulcus or pocket and analyzed with Polymerase Chain Reaction forblaTEM, tetM, tetQandnimgenes,S. aureusand MRSA using primers and conditions previously described in the literature.Results:Findings have shown high frequencies of detection for both groups for the tetracycline resistance genestetM(>30%),tetQ(>65%) with no statistical differences between them (z-test with Bonferroni corrections,p<0.05). TheblaTEMgene, which encodes resistance to beta-lactams, was detected in <15% of the samples. Thenimgene, which encodes resistance to metronidazole,S.aureusand themecAgene encoding for MRSA were not detected in any of the analyzed samples.Conclusions:Healthy peri-implant sulci and peri-implantitis cases often harbor bacterial genes encoding for resistance to the tetracyclines and less often for beta-lactams. Thus, the antimicrobial activity of the tetracyclines and to a lower extent to beta-lactams, might be compromised for treatment of peri-implantitis. Since no metronidazole resistance genes were detected in the present study, its clinical use is supported by the current findings.S.aureusmay not participate in peri-implant pathology.

scholarly journals H2O2-Forming NADH Oxidase with Diaphorase (Cytochrome) Activity from Archaeoglobus fulgidus

2001 ◽  
Vol 183 (24) ◽  
pp. 7007-7016 ◽  
Author(s):  
David W. Reed ◽  
Jack Millstein ◽  
Patricia L. Hartzell
Keyword(s):  
Nadh Oxidase ◽  
Specific Activity ◽  
Transcription Unit ◽  
Transfer Reactions ◽  
Archaeoglobus Fulgidus ◽  
Lactate Oxidation ◽  
Reading Frame ◽  
Sulfate Reducing ◽  
Diaphorase Activity ◽  
Genes Encoding

ABSTRACT An enzyme exhibiting NADH oxidase (diaphorase) activity was isolated from the hyperthermophilic sulfate-reducing anaerobeArchaeoglobus fulgidus. N-terminal sequence of the protein indicates that it is coded for by open reading frame AF0395 in theA. fulgidus genome. The gene AF0395 was cloned and its product was purified from Escherichia coli. Like the native NADH oxidase (NoxA2), the recombinant NoxA2 (rNoxA2) has an apparent molecular mass of 47 kDa, requires flavin adenine dinucleotide for activity, has NADH-specific activity, and is thermostable. Hydrogen peroxide is the product of bivalent oxygen reduction by rNoxA2 with NADH. The rNoxA2 is an oxidase with diaphorase activity in the presence of electron acceptors such as tetrazolium and cytochrome c. During purification NoxA2 remains associated with the enzyme responsible for d-lactate oxidation, thed-lactate dehydrogenase (Dld), and the genes encoding NoxA2 and Dld are in the same transcription unit. Together these results suggest that NADH oxidase may be involved in electron transfer reactions resulting in sulfate respiration.

scholarly journals A Highly Selective Oligopeptide Binding Protein from the Archaeon Sulfolobus Solfataricus

2010 ◽  
Vol 192 (12) ◽  
pp. 3123-3131 ◽  
Author(s):  
M. Gogliettino ◽  
M. Balestrieri ◽  
G. Pocsfalvi ◽  
I. Fiume ◽  
L. Natale ◽  
...  
Keyword(s):  
Cell Surface ◽  
Binding Protein ◽  
Sulfolobus Solfataricus ◽  
Binding Activity ◽  
Protein Accumulation ◽  
Reading Frame ◽  
Typical Sequence ◽  
Hybrid Complex ◽  
Genes Encoding ◽  
A Cell

ABSTRACT SSO1273 of Sulfolobus solfataricus was identified as a cell surface-bound protein by a proteomics approach. Sequence inspection of the genome revealed that the open reading frame of sso1273 is associated in an operon-like structure with genes encoding all the remaining components of a canonical protein-dependent ATP-binding cassette (ABC) transporter. sso1273 gene expression and SSO1273 protein accumulation on the cell surface were demonstrated to be strongly induced by the addition of a peptide mixture (tryptone) to the culture medium. The native protein was obtained in multimeric form, mostly hexameric, under the purification conditions used, and it was characterized as an oligopeptide binding protein, named S. solfataricus OppA (OppASs). OppaASs possesses typical sequence patterns required for glycosylphosphatidylinositol lipid anchoring, resulting in an N-linked glycoprotein with carbohydrate moieties likely composed of high mannose and/or hybrid complex carbohydrates. OppASs specifically binds oligopeptides and shows a marked selectivity for the amino acid composition of substrates when assayed in complex peptide mixtures. Moreover, a truncated version of OppASs, produced in recombinant form and including the putative binding domain, showed a low but significant oligopeptide binding activity.

scholarly journals Analysis of Genes Encoding an Alternative Nitrogenase in the Archaeon Methanosarcina barkeri227

2000 ◽  
Vol 182 (11) ◽  
pp. 3247-3253 ◽  
Author(s):  
Yueh-Tyng Chien ◽  
Victoria Auerbuch ◽  
Andrew D. Brabban ◽  
Stephen H. Zinder
Keyword(s):  
Amino Acid ◽  
Amino Acid Level ◽  
Sufficient Conditions ◽  
Methanosarcina Barkeri ◽  
Amino Acid Sequences ◽  
Gram Positive ◽  
Reading Frame ◽  
Genes Encoding ◽  
Alternative Nitrogenase ◽  
Diazotrophic Growth

ABSTRACT Methanosarcina barkeri 227 possesses two clusters of genes potentially encoding nitrogenases. We have previously demonstrated that one cluster, called nif2, is expressed under molybdenum (Mo)-sufficient conditions, and the deduced amino acid sequences for nitrogenase structural genes in that cluster most closely resemble those for the Mo nitrogenase of the gram-positive eubacteriumClostridium pasteurianum. The previously clonednifH1 from M. barkeri shows phylogenetic relationships with genes encoding components of eubacterial Mo-independent eubacterial alternative nitrogenases and other methanogen nitrogenases. In this study, we cloned and sequencednifD1 and part of nifK1 from M. barkeri 227. The deduced amino acid sequence encoded bynifD1 from M. barkeri showed great similarity with vnfD gene products from vanadium (V) nitrogenases, with an 80% identity at the amino acid level with the vnfDgene product from Anabaena variabilis. Moreover, there was a small open reading frame located between nifD1 andnifK1 with clear homology to vnfG, a hallmark of eubacterial alternative nitrogenases. Stimulation of diazotrophic growth of M. barkeri 227 by V in the absence of Mo was demonstrated. The unusual complement of nifgenes in M. barkeri 227, with one cluster resembling that from a gram-positive eubacterium and the other resembling a eubacterial V nitrogenase gene cluster, suggests horizontal genetic transfer of those genes.

scholarly journals Purification of the Pyruvate Dehydrogenase Multienzyme Complex of Zymomonas mobilis and Identification and Sequence Analysis of the Corresponding Genes

1998 ◽  
Vol 180 (6) ◽  
pp. 1540-1548 ◽  
Author(s):  
Ute Neveling ◽  
Ralf Klasen ◽  
Stephanie Bringer-Meyer ◽  
Hermann Sahm
Keyword(s):  
Sequence Analysis ◽  
Pyruvate Dehydrogenase ◽  
Zymomonas Mobilis ◽  
Specific Activity ◽  
Electron Microscopic ◽  
Gene Encoding ◽  
Reading Frame ◽  
Amino Terminal ◽  
Genes Encoding ◽  
Lipoyl Domain

ABSTRACT The pyruvate dehydrogenase (PDH) complex of the gram-negative bacterium Zymomonas mobilis was purified to homogeneity. From 250 g of cells, we isolated 1 mg of PDH complex with a specific activity of 12.6 U/mg of protein. Analysis of subunit composition revealed a PDH (E1) consisting of the two subunits E1α (38 kDa) and E1β (56 kDa), a dihydrolipoamide acetyltransferase (E2) of 48 kDa, and a lipoamide dehydrogenase (E3) of 50 kDa. The E2 core of the complex is arranged to form a pentagonal dodecahedron, as shown by electron microscopic images, resembling the quaternary structures of PDH complexes from gram-positive bacteria and eukaryotes. The PDH complex-encoding genes were identified by hybridization experiments and sequence analysis in two separate gene regions in the genome ofZ. mobilis. The genes pdhAα (1,065 bp) andpdhAβ (1,389 bp), encoding the E1α and E1β subunits of the E1 component, were located downstream of the gene encoding enolase. The pdhB (1,323 bp) and lpd (1,401 bp) genes, encoding the E2 and E3 components, were identified in an unrelated gene region together with a 450-bp open reading frame (ORF) of unknown function in the order pdhB-ORF2-lpd. Highest similarities of the gene products of the pdhAα,pdhAβ, and pdhB genes were found with the corresponding enzymes of Saccharomyces cerevisiae and other eukaryotes. Like the dihydrolipoamide acetyltransferases of S. cerevisiae and numerous other organisms, the product of thepdhB gene contains a single lipoyl domain. The E1β subunit PDH was found to contain an amino-terminal lipoyl domain, a property which is unique among PDHs.

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