Thermoregulation of Meningococcal fHbp, an Important Virulence Factor and Vaccine Antigen, Is Mediated by Anti-ribosomal Binding Site Sequences in the Open Reading Frame

The binding of MC1 protein, the major chromosomal protein of the archaebacterium Methanosarcina sp. CHTI 55, to the region preceding the strongly expressed genes encoding methyl coenzyme reductase in a closely related micro-organism has been investigated. By gel retardation and DNAase I footprinting assays, we identified a preferential binding sequence in an open reading frame of unknown function. The large area of DNA protected against DNAase I is interrupted by a strong cleavage enhancement site on each strand. By circular permutation assays, we showed that the DNA bends upon MC1 binding. Furthermore we observed that the presence of a sequence outside the binding site can induce an unusual electrophoretic behaviour in some complexes.

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Identification of the miaB Gene, Involved in Methylthiolation of Isopentenylated A37 Derivatives in the tRNA of Salmonella typhimurium andEscherichia coli

Journal of Bacteriology ◽

10.1128/jb.181.23.7256-7265.1999 ◽

1999 ◽

Vol 181 (23) ◽

pp. 7256-7265 ◽

Cited By ~ 63

Author(s):

Birgitta Esberg ◽

Hon-Chiu Eastwood Leung ◽

Ho-Ching Tiffany Tsui ◽

Glenn R. Björk ◽

Malcolm E. Winkler

Keyword(s):

Escherichia Coli ◽

Salmonella Typhimurium ◽

Binding Site ◽

Binding Sites ◽

Open Reading Frame ◽

Iron Binding ◽

Reading Frame ◽

Conserved Motif ◽

E Coli ◽

Weak Similarity

ABSTRACT The tRNA of the miaB2508::Tn10dCm mutant of Salmonella typhimurium is deficient in the methylthio group of the modified nucleosideN 6-(4-hydroxyisopentenyl)-2-methylthioadenosine (ms2io6A37). By sequencing, we found that the Tn10dCm of this strain had been inserted into thef474 (yleA) open reading frame, which is located close to the nag locus in both S. typhimurium and Escherichia coli. By complementation of the miaB2508::Tn10dCm mutation with a minimal subcloned f474 fragment, we showed thatf474 could be identified as the miaB gene, which is transcribed in the counterclockwise direction on the bacterial chromosome. Transcriptional studies revealed two promoters upstream ofmiaB in E. coli and S. typhimurium. A Rho-independent terminator was identified downstream of themiaB gene, at which the majority (96%) of themiaB transcripts terminate in E. coli, showing that the miaB gene is part of a monocistronic operon. A highly conserved motif with three cysteine residues was present in MiaB. This motif resembles iron-binding sites in other proteins. Only a weak similarity to an AdoMet-binding site was found, favoring the idea that the MiaB protein is involved in the thiolation step and not in the methylating reaction of ms2i(o)6A37 formation.

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Oligopeptidase B-2 from Leishmania amazonensis with an unusual C-terminal extension

Acta Parasitologica ◽

10.2478/s11686-008-0026-7 ◽

2008 ◽

Vol 53 (2) ◽

Cited By ~ 12

Author(s):

Herbert Matos Guedes ◽

Rafael Carvalho ◽

Daniel Oliveira Gomes ◽

Bartira Rossi-Bergmann ◽

Salvatore De-Simone

Keyword(s):

Leishmania Major ◽

Catalytic Triad ◽

Genome Project ◽

Leishmania Amazonensis ◽

Open Reading Frame ◽

Reading Frame ◽

Oligopeptidase B ◽

Major Genome ◽

Important Virulence Factor ◽

S2 Subsite

AbstractThe oligopeptidase B serine protease is an important virulence factor and therapeutic target in Trypanosoma infections. Recently, the Leishmania major Genome Project identified a new oligopeptidase B that was denominated oligopeptidase B-like, herein named oligopeptidase B-2. In this study, a complete open reading frame of oligopeptidase B-2 from Leishmania amazonensis (PH8 strain) was amplified by PCR using primers designed for the oligopeptidase B-2 gene of L. major. The 2,715 bp fragment coded for a protein of 905 amino acids with a predicted molecular mass of 103,918.9 Da and theoretical pI of 5.82. The encoded protein displayed ∼96% identity with L. major and ∼75% identity with Trypanosoma cruzi and T. brucei oligopeptidases B-2, and ∼21% identity with Escherichia coli and L. amazonensis classical oligopeptidase B. An unusual C-terminal extension was found in relation to the classical trypanosomatid oligopeptidase B. By sequence alignment, we determined a catalytic triad (Ser 629, Asp 717 and His 758), S1 subsite (Glu 674 and Glu 676) and suggest a difference in the S2 subsite of L. amazonensis oligopeptidase B-2. We also found that the oligopeptidase B-2 gene is expressed in all cycle stages of L. amazonensis. A phylogenetic analysis indicated that oligopeptidase B-2 is a new member of oligopeptidase B.

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Lipase 8 Affects the Pathogenesis of Candida albicans

Infection and Immunity ◽

10.1128/iai.00372-07 ◽

2007 ◽

Vol 75 (10) ◽

pp. 4710-4718 ◽

Cited By ~ 45

Author(s):

Attila Gácser ◽

Frank Stehr ◽

Cathrin Kröger ◽

László Kredics ◽

Wilhelm Schäfer ◽

...

Keyword(s):

Candida Albicans ◽

Open Reading Frame ◽

Infection Model ◽

Reading Frame ◽

Reverse Transcription Pcr ◽

Knockout Mutants ◽

Important Virulence Factor ◽

Actin Promoter ◽

Disruption Method

ABSTRACT The production of lipases can affect microbial fitness and virulence. We examined the role of the lipase 8 (LIP8) gene in the virulence of Candida albicans by constructing Δlip8 strains by the URA-blaster disruption method. Reverse transcription-PCR experiments demonstrated the absence of LIP8 expression in the homozygous knockout mutants. Reconstituted strains and overexpression mutants were generated by introducing a LIP8 open reading frame under control of a constitutive actin promoter. Knockout mutants produced more mycelium, particularly at higher temperatures and pH ≥7. Diminished LIP8 expression resulted in reduced growth in lipid-containing media. Mutants deficient in the LIP8 gene were significantly less virulent in a murine intravenous infection model. The results clearly indicate that Lip8p is an important virulence factor of C. albicans.

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Cloning, sequencing and analysis of the structural gene and regulatory region of the Pseudomonas aeruginosa chromosomal ampCβ-lactamase

Biochemical Journal ◽

10.1042/bj2720627 ◽

1990 ◽

Vol 272 (3) ◽

pp. 627-631 ◽

Cited By ~ 71

Author(s):

J M Lodge ◽

S D Minchin ◽

L J V Piddock ◽

S J W Busby

Keyword(s):

Pseudomonas Aeruginosa ◽

Binding Site ◽

Regulatory Protein ◽

Regulatory Region ◽

Open Reading Frame ◽

Beta Lactamase ◽

Chromosomal Gene ◽

Reading Frame ◽

Beta Lactamases ◽

Lactamase Gene

The chromosomal gene from Pseudomonas aeruginosa encoding beta-lactamase has been cloned, and the sequence determined and compared with corresponding sequences of beta-lactamases from members of the enterobacteriaceae. Upstream of the beta-lactamase gene is an open reading frame which we postulate encodes a regulatory protein, AmpR. We identified a helix-turn-helix region in AmpR and a putative AmpR-binding site.

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Identification and Characterization of thescl Gene Encoding a Group A StreptococcusExtracellular Protein Virulence Factor with Similarity to Human Collagen

Infection and Immunity ◽

10.1128/iai.68.12.6542-6553.2000 ◽

2000 ◽

Vol 68 (12) ◽

pp. 6542-6553 ◽

Cited By ~ 119

Author(s):

Slawomir Lukomski ◽

Kazumitsu Nakashima ◽

Iman Abdi ◽

Vincent J. Cipriano ◽

Robin M. Ireland ◽

...

Keyword(s):

Amino Acid ◽

Dna Sequence ◽

Structural Gene ◽

Virulence Factor ◽

Open Reading Frame ◽

Genomic Diversity ◽

Reading Frame ◽

Isogenic Mutant ◽

Group A ◽

Human Collagen

ABSTRACT Group A Streptococcus (GAS) expresses cell surface proteins that mediate important biological functions such as resistance to phagocytosis, adherence to plasma and extracellular matrix proteins, and degradation of host proteins. An open reading frame encoding a protein of 348 amino acid residues was identified by analysis of the genome sequence available for a serotype M1 strain. The protein has an LPATGE sequence located near the carboxy terminus that matches the consensus sequence (LPXTGX) present in many gram-positive cell wall-anchored molecules. Importantly, the central region of this protein contains 50 contiguous Gly-X-X triplet amino acid motifs characteristic of the structure of human collagen. The structural gene (designated scl for streptococcal collagen-like) was present in all 50 GAS isolates tested, which together express 21 different M protein types and represent the breadth of genomic diversity in the species. DNA sequence analysis of the gene in these 50 isolates found that the number of contiguous Gly-X-X motifs ranged from 14 in serotype M6 isolates to 62 in a serotype M41 organism. M1 and M18 organisms had the identical allele, which indicates very recent horizontal gene transfer. The gene was transcribed abundantly in the logarithmic but not stationary phase of growth, a result consistent with the occurrence of a DNA sequence with substantial homology with a consensus Mga binding site immediately upstream of the sclopen reading frame. Two isogenic mutant M1 strains created by nonpolar mutagenesis of the scl structural gene were not attenuated for mouse virulence as assessed by intraperitoneal inoculation. In contrast, the isogenic mutant derivative made from the M1 strain representative of the subclone most frequently causing human infections was significantly less virulent when inoculated subcutaneously into mice. In addition, both isogenic mutant strains had significantly reduced adherence to human A549 epithelial cells grown in culture. These studies identify a new extracellular GAS virulence factor that is widely distributed in the species and participates in adherence to host cells and soft tissue pathology.

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An upstream open reading frame (uORF) signals for cellular localization of the virulence factor implicated in pregnancy associated malaria

Nucleic Acids Research ◽

10.1093/nar/gky178 ◽

2018 ◽

Vol 46 (10) ◽

pp. 4919-4932 ◽

Cited By ~ 2

Author(s):

Yair Fastman ◽

Shany Assaraf ◽

Miriam Rose ◽

Elad Milrot ◽

Katherine Basore ◽

...

Keyword(s):

Virulence Factor ◽

Cellular Localization ◽

Open Reading Frame ◽

Upstream Open Reading Frame ◽

Reading Frame ◽

In Pregnancy

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Expression and base sequence of the citrate synthase gene of Acinetobacter anitratum

Biochemistry and Cell Biology ◽

10.1139/o87-121 ◽

1987 ◽

Vol 65 (11) ◽

pp. 930-938 ◽

Cited By ~ 8

Author(s):

Lynda J. Donald ◽

Harry W. Duckworth

Keyword(s):

Genomic Dna ◽

Citrate Synthase ◽

Open Reading Frame ◽

Base Sequence ◽

Negative Bacterium ◽

Terminal Sequence ◽

Base Pairs ◽

Reading Frame ◽

E Coli ◽

Ribosomal Binding Site

The sequence of 1895 base pairs of Acinetobacter anitratum genomic DNA, containing the structural gene for the allosteric citrate synthase of that Gram-negative bacterium, is presented. The sequence contains an open reading frame of 424 codons, the 5′ end of which is the same as the N-terminal sequence of A. anitratum citrate synthase, less the initiator methionine. The inferred amino acid sequence of the enzyme is about 70% identical with that of citrate synthase from Escherichia coli, which like the A. anitratum enzyme is sensitive to allosteric inhibition by NADH. There is also a more distant homology with the nonallosteric citrate synthases of pig heart and yeast. The gene contains sequences that strongly resemble those found in E. coli promoters, an E. coli type of ribosomal binding site, and a hyphenated dyad sequence at the 3′ end of the gene which resembles the rho-independent terminators found in some E. coli genes. The plasmid clone containing the A. anitratum citrate synthase gene pLJD1, originally isolated because it hybridized with the cloned E. coli citrate synthase gene under conditions of reduced stringency, produces large amounts of A. anitratum citrate synthase in an E. coli host which lacks citrate synthase. This work completes proof of the hypothesis that the three major kinds of citrate synthases are formed of similar subunits, although their functional properties are different.

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PRS5, the Fifth Member of the Phosphoribosyl Pyrophosphate Synthetase Gene Family inSaccharomyces cerevisiae, Is Essential for Cell Viability in the Absence of either PRS1 or PRS3

Journal of Bacteriology ◽

10.1128/jb.180.23.6404-6407.1998 ◽

1998 ◽

Vol 180 (23) ◽

pp. 6404-6407 ◽

Cited By ~ 17

Author(s):

Yolanda Hernando ◽

Adrian Parr ◽

Michael Schweizer

Keyword(s):

Gene Family ◽

Binding Site ◽

Sequence Similarity ◽

Cation Binding ◽

Open Reading Frame ◽

Phosphoribosyl Pyrophosphate ◽

Reading Frame ◽

Nucleotide Pools ◽

Cation Binding Site ◽

Phosphoribosyl Pyrophosphate Synthetase

ABSTRACT In Saccharomyces cerevisiae, an open reading frame, YOL061w, encodes a polypeptide with sequence similarity to the four known 5-phosphoribosyl-1(α)-pyrophosphate synthetase (PRS) genes since it contains a divalent cation binding site and a phosphoribosyl pyrophosphate binding site. We regard YOL061w as the fifth member of the PRS gene family, PRS5. Loss of Prs5p has a significant impact on PRS enzyme activity, causing it to be reduced by 84%. On the other hand, Δprs5 strains are not affected in growth or in the size of their nucleotide pools. However, simultaneous deletion of PRS1 and PRS5 orPRS3 and PRS5 rendered the strains inviable, which implies that PRS5 plays an important role in the maintenance of PRS function in S. cerevisiae.

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ComEB protein is dispensable for transformation but must be translated for optimal synthesis of ComEC

10.1101/2020.12.30.424838 ◽

2020 ◽

Author(s):

Micaela De Santis ◽

Jeanette Hahn ◽

David Dubnau

Keyword(s):

Bacillus Subtilis ◽

Transcriptional Control ◽

Cytidine Deaminase ◽

Open Reading Frame ◽

Common Mechanism ◽

Its Sequence ◽

Dna Uptake ◽

Reading Frame ◽

Ribosomal Binding Site

We show that the ComEB protein is not required for transformation in Bacillus subtilis, despite its expression from within the comE operon under competence control. We show further that the synthesis of the putative channel protein ComEC is translationally coupled to the upstream comEB open reading frame, so that translation of comEB and a suboptimal ribosomal binding site embedded in its sequence are needed for proper comEC expression. Translational coupling appears to be a common mechanism in three major competence operons for the adjustment of protein amounts independent of transcriptional control, probably ensuring the correct stoichiometries for assembly of the transformation machinery. comEB and comFC respectively encode cytidine deaminase and a protein resembling type 1 phosphoribosyl transferases and we speculate that nucleotide scavenging proteins are produced under competence control for efficient reutilization of the products of degradation of the non-transforming strand during DNA uptake.

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