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PubMed1988

Pilin-gene phase variation of Moraxella bovis is caused by an inversion of the pilin genes.

Moraxella bovis Epp63 can express either of two different pilin proteins, called alpha and beta. We have previously cloned and sequenced the beta-pilin gene and now report that DNAs isolated from bacteria expressing alpha pilin have hybridization patterns consistently different from those of bacteria expressing beta pilin. The phase variation between alpha- and beta-pilin gene expression appears to be associated with an inversion of about 2 kilobases of DNA, whose endpoints occur within the coding region of the expressed pilin gene. Comparisons of the beta-pilin gene sequence with those of well-studied bacterial inversion systems revealed a stretch of 58% sequence similarity (21 of 36 base pairs) between the left inverted repeat of the Salmonella typhimurium flagellar hin control region and the amino-terminal portion of the beta-pilin gene.

Bacterial Outer Membrane Proteins↗
PubMed1997

Genetic analysis of chlorophyll biosynthesis.

During this decade, there have been major advancements in the understanding of genetic loci involved in synthesis of the family of Mg-tetrapyrroles known as chlorophylls and bacteriochlorophylls. Molecular genetic analysis of Mg-tetrapyrrole biosynthesis was initiated by the performance of detailed sequence and mutational analysis of the photosynthesis gene cluster from Rhodobacter capsulatus. These studies provided the first detailed understanding of genes involved in bacteriochlorophyll a biosynthesis. In the short time since these studies were initiated, most of the chlorophyll biosynthesis genes have been identified by virtue of their ability to complement bacteriochlorophyll a biosynthesis mutants as well as by sequence homology comparisons. This review is centered on a discussion of our current understanding of bacterial, algal, and plant genes that code for enzymes in the Mg-branch of the tetrapyrrole biosynthetic pathway that are responsible for synthesis of chlorophylls and bacteriochlorophylls.

Chlorophyll↗
PubMed1993

Insect immunity. Two 17 bp repeats nesting a kappa B-related sequence confer inducibility to the diptericin gene and bind a polypeptide in bacteria-challenged Drosophila.

The Drosophila diptericin gene codes for a 9 kDa antibacterial peptide and is rapidly and transiently expressed in larvae and adults after bacterial challenge. It is also induced in a tumorous Drosophila blood cell line by the addition of lipopolysaccharide (LPS). The promoter of this gene contains two 17 bp repeats located closely upstream of the TATA-box and harbouring a decameric kappa B-related sequence. This study reports that the replacement of the two 17 bp repeats by random sequences abolishes bacteria inducibility in transgenic fly lines. In transfected tumorous blood cells, the replacement of both or either of the 17 bp motifs reduces dramatically LPS inducibility, whereas multiple copies significantly increase the level of transcriptional activation by LPS challenge. A specific DNA-protein binding activity is evidenced in cytoplasmic and nuclear extracts of induced blood cells and fat body. It is absent in controls. It is proposed that induction of the diptericin gene mediated by the two 17 bp repeats occurs via a mechanism similar to that of mammalian NF-kappa B.

Animals↗
PubMed1999

Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes.

Recognition of transcription regulation sites (operators) is a hard problem in computational molecular biology. In most cases, small sample size and low degree of sequence conservation preclude the construction of reliable recognition rules. We suggest an approach to this problem based on simultaneous analysis of several related genomes. It appears that as long as a gene coding for a transcription regulator is conserved in the compared bacterial genomes, the regulation of the respective group of genes (regulons) also tends to be maintained. Thus a gene can be confidently predicted to belong to a particular regulon in case not only itself, but also its orthologs in other genomes have candidate operators in the regulatory regions. This provides for a greater sensitivity of operator identification as even relatively weak signals are likely to be functionally relevant when conserved. We use this approach to analyze the purine (PurR), arginine (ArgR) and aromatic amino acid (TrpR and TyrR) regulons of Escherichia coli and Haemophilus influenzae. Candidate binding sites in regulatory regions of the respective H.influenzae genes are identified, a new family of purine transport proteins predicted to belong to the PurR regulon is described, and probable regulation of arginine transport by ArgR is demonstrated. Differences in the regulation of some orthologous genes in E.coli and H.influenzae, in particular the apparent lack of the autoregulation of the purine repressor gene in H.influenzae, are demonstrated.

Arginine↗
PubMed1991

A gene required for RNase P activity in Candida (Torulopsis) glabrata mitochondria codes for a 227-nucleotide RNA with homology to bacterial RNase P RNA.

We have mapped a gene in the mitochondrial DNA of Candida (Torulopsis) glabrata and shown that it is required for 5' end maturation of mitochondrial tRNAs. It is located between the tRNAfMet and tRNAPro genes, the same tRNA genes that flank the mitochondrial RNase P RNA gene in the yeast Saccharomyces cerevisiae. The gene is extremely AT rich and codes for AU-rich RNAs that display some sequence homology with the mitochondrial RNase P RNA from S. cerevisiae, including two regions of striking sequence homology between the mitochondrial RNAs and the bacterial RNase P RNAs. RNase P activity that is sensitive to micrococcal nuclease has been detected in mitochondrial extracts of C. glabrata. An RNA of 227 nucleotides that is one of the RNAs encoded by the gene that we mapped cofractionated with this mitochondrial RNase P activity on glycerol gradients. The nuclease sensitivity of the activity, the cofractionation of the RNA with activity, and the homology of the RNA with known RNase P RNAs lead us to propose that the 227-nucleotide RNA is the RNA subunit of the C. glabrata mitochondrial RNase P enzyme.

Base Sequence↗
PubMed1983

Gene fusions using the ompA gene coding for a major outer-membrane protein of Escherichia coli K12.

It has been shown previously that fragments of the Escherichia coli major outer membrane protein OmpA lacking CO2H-terminal parts can be incorporated into this membrane in vivo [Bremer et al. (1982) Eur. J. Biochem. 122, 223-231]. The possibility that these fragments can be used, via gene fusions, as vehicles to transport other proteins to the outer membrane has been investigated. To test whether fragments of a certain size were optimal for this purpose a set of plasmids was prepared encoding 160, 193, 228, 274, and 280 NH2-terminal amino acids of the 325-residue OmpA protein. The 160-residue fragment was not assembled into the outer membrane whereas the others were all incorporated with equal efficiencies. Thus, if any kind of OmpA-associated stop transfer is required during export the corresponding signal might be present between residues 160 and 193 but not CO2H-terminal to 193. The ompA gene was fused to the gene (tet) specifying tetracycline resistance and the gene for the major antigen (vp1) of foot-and-mouth disease virus. In the former case a 584-residue chimeric protein is encoded consisting NH2-terminally of 228 OmpA residues followed by 356 CO2H-terminal residues of the 396-residue 'tetracycline resistance protein'. In the other case the same part of OmpA is followed by 250 CO2H-terminal residues of the 213-residue Vp1 plus 107 residues partly derived from another viral protein and from the vector. Full expression of both hybrids proved to be lethal. Lipophilic sequences bordered by basic residues, present in the non-OmpA parts of both hybrids were considered as candidates for the lethal effect. A plasmid was constructed which codes for 280 OmpA residues followed by a 31-residue tail containing the sequence: -Phe-Val-Ile-Met-Val-Ile-Ala-Val-Ser-Cys-Lys-. Expression of this hybrid gene was lethal but by changing the reading frame for the tail to encode another, 30-residue sequence the deleterious effect was abolished. It is possible that the sequence incriminated acts as a stop signal for transfer through the plasma membrane thereby jamming export sites for other proteins and causing lethality. If so, OmpA appears to cross the plasma membrane completely during export.

Aphthovirus↗
PubMed1982

Structural and functional analysis of an rRNA operon and its flanking tRNA genes from Zea mays chloroplasts.

The complete analysis of an rRNA operon from Zea mays chloroplasts and its comparison with other plastidic or bacterial rRNA operons is presented. The maize operon contains structural genes for 16S, 23S and 4.5S rRNA species, a leader region proximal to the 16S rRNA gene and a 2.4 kb spacer between the 16S and 23S rRNA genes. Within the spacer DNA sequence are two tRNA genes which code for a tRNAIle and tRNAAla species but each gene is split by large intervening sequences of 949 and 806 bp, respectively. 4.5S rRNA is a structural equivalent of the 3' terminal region of bacterial 23S rRNA. The operon is flanked at its 5' side by a tRNAVal gene and at its 3' side by a 5S rRNA gene. Both these genes are probably not included in the large, primary precursor rRNA transcript.

Base Sequence↗
PubMed1989

Heterologous signal peptide processing in fusion interferon synthesis by engineered L-forms of Proteus mirabilis.

A recombinant DNA Proteus mirabilis L-form expression system, LVI (pJS127), was used to synthesize human fusion interferon alpha 1 (f-IFN-alpha 1). In the expression plasmid used, the complete coding sequence of IFN-alpha 1 was linked to the streptococcal speA promoter and the 5' end of the speA structural gene including its signal sequence coding region. LVI (pJS127) was capable of complete secretion into the culture medium of biologically active f-IFN-alpha 1 whose identity was confirmed by immunological and chemical evidence. In particular, bacterial L-forms were for the first time shown to be capable of correct signal peptide processing, as determined by N-terminal sequencing of the secreted f-IFN.

Amino Acids↗
PubMed2001

Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome.

With increases in the amounts of available DNA sequence data, it has become increasingly important to develop tools for comprehensive systematic analysis and comparison of species-specific characteristics of protein-coding sequences for a wide variety of genomes. In the present study, we used a novel neural-network algorithm, a self-organizing map (SOM), to efficiently and comprehensively analyze codon usage in approximately 60,000 genes from 29 bacterial species simultaneously. This SOM makes it possible to cluster and visualize genes of individual species separately at a much higher resolution than can be obtained with principal component analysis. The organization of the SOM can be explained by the genome G+C% and tRNA compositions of the individual species. We used SOM to examine codon usage heterogeneity in the E. coli O157 genome, which contains 'O157-unique segments' (O-islands), and showed that SOM is a powerful tool for characterization of horizontally transferred genes.

Algorithms↗
PubMed1983

[Functioning of amino acid operons in Escherichia coli strains with an altered transcription and translation apparatus. II. The effect of mutations in genes coding ribosomal protein S5 and translation elongation factor G on the functioning of the ilv operon].

It has been shown in our previous study that mutations in genes relA, relC and rpsL result in the delay in Escherichia coli ilv operon derepression; the complete inhibition of derepression of the ilv operon is observed in the double mutants having alterations in rpsL and relA or relC genes. At present, some mutations occurring in the fus gene and altering the structure of the translational elongation G factor have been also found to delay derepression of E. coli ilv operon and complete inhibition in fusr and rel double mutants. Phenotypical ile and val auxotrophy is also detected in the double E. coli mutants with spectinomycin resistance mutation in rpsE gene coding for the structure of ribosomal S5 protein and mutations in relA or relC genes. The suggestion of participation of the ilv operon in regulation of other E. coli amino acid operons expression is discussed.

Amino Acid Sequence↗
PubMed1988

Bacterial synthesis of active rat stearyl-CoA desaturase lacking the 26-residue amino-terminal amino acid sequence.

Two clones containing inserts in pBR322 that together include the entire 1074-base open reading frame coding for the 358 amino acids of rat liver stearyl-CoA desaturase have been used to construct expression vectors for residues 3-358 and 27-358 fused to the first 6 residues of beta-galactosidase and several amino acids of the multiple cloning site of pUC8. Growth of transformed Escherichia coli under conditions for suppression of the lac promoter, followed by subsequent induction of these cultures results in the synthesis of higher levels of desaturase proteins than those found in induced rat liver. The proteins are almost completely associated with the membrane fraction of cell homogenates. Posttranslational iron insertion into the apoproteins, either in vitro with membrane preparations or by iron addition during induction, results in the formation of active holoenzyme which can be reconstituted with NADH cytochrome b5 reductase and cytochrome b5 to form an active stearyl-CoA desaturase system. The deletion of the first 26 amino-terminal amino acid residues does not affect either enzyme activity or membrane binding. Therefore, the unusual sequence of 11 residues containing 10 amino acids with hydroxyl groups plays no apparent significant role in either protein insertion into membranes or iron chelation. Since the protein product for residues 3-358 is processed even further to delete the initial 33 amino-terminal residues, the limiting polypeptide primary structure required for an active membrane-bound catalyst is even smaller than this initial deletion mutation indicates.

Amino Acid Sequence↗
PubMed1992

Multidegenerate DNA recognition by the OxyR transcriptional regulator.

The Escherichia coli OxyR protein, a regulator of hydrogen peroxide-inducible genes, is a potent stimulator of transcription in its oxidized form but not in its reduced form. OxyR protein purified in its oxidized form was found to bind four of its non-homologous, functional DNA-binding sites with over 10(6)-fold higher affinity than random DNA sequences. A similarly high DNA binding specificity was observed for the reduced (transcriptionally inactive) form of OxyR, consistent with a model in which the OxyR protein is bound to its recognition sequences even in the absence of an oxidative stress. Alignment of five functional OxyR-binding sites revealed a marked lack of perfectly conserved positions, yet an unusually high number of degenerate homologies (positions at which only two of the four possible base pairs are represented). Methylation interference assays on two OxyR-binding sites showed that OxyR contacts its recognition sequences predominantly at positions of degenerate homology. These results suggest that the OxyR protein specifically recognizes seemingly dissimilar sequences through the use of a multidegenerate recognition code. The chemical basis for a plausible degenerate recognition system is discussed.

Bacterial Proteins↗
PubMed2005

Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines.

Introgression in Festulolium is a potentially powerful tool to isolate genes for a large number of traits which differ between Festuca pratensis Huds. and Lolium perenne L. Not only are hybrids between the two species fertile, but the two genomes can be distinguished by genomic in situ hybridisation and a high frequency of recombination occurs between homoeologous chromosomes and chromosome segments. By a programme of introgression and a series of backcrosses, L. perenne lines have been produced which contain small F. pratensis substitutions. This material is a rich source of polymorphic markers targeted towards any trait carried on the F. pratensis substitution not observed in the L. perenne background. We describe here the construction of an F. pratensis BAC library, which establishes the basis of a map-based cloning strategy in L. perenne. The library contains 49,152 clones, with an average insert size of 112 kbp, providing coverage of 2.5 haploid genome equivalents. We have screened the library for eight amplified fragment length polymorphism (AFLP) derived markers known to be linked to an F. pratensis gene introgressed into L. perenne and conferring a staygreen phenotype as a consequence of a mutation in primary chlorophyll catabolism. While for four of the markers it was possible to identify bacterial artificial chromosome (BAC) clones, the other four AFLPs were too repetitive to enable reliable identification of locus-specific BACs. Moreover, when the four BACs were partially sequenced, no obvious coding regions could be identified. This contrasted to BACs identified using cDNA sequences, when multiple genes were identified on the same BAC.

Blotting, Southern↗
PubMed2002

Transient requirement of the PrrA-PrrB two-component system for early intracellular multiplication of Mycobacterium tuberculosis.

Adaptive regulation of gene expression in response to environmental changes is a general property of bacterial pathogens. By screening an ordered transposon mutagenesis library of Mycobacterium tuberculosis, we have identified three mutants containing a transposon in the coding sequence or in the 5' regions of genes coding for two-component signal transduction systems (trcS, regX3, prrA). The intracellular multiplication capacity of the three mutants was investigated in mouse bone marrow-derived macrophages. Only the prrA mutant showed a defect in intracellular growth during the early phase of infection, and this defect was fully reverted when the mutant was complemented with prrA-prrB wild-type copies. The mutant phenotype was transient, as after 1 week this strain recovered full growth capacity to reach levels similar to that of the wild type at day 9. Moreover, a transient induction of prrA promoter activity was observed during the initial phase of macrophage infection, as shown by a prrA promoter-gfp fusion in M. bovis BCG infecting the mouse macrophages. The concordant transience of the prrA mutant phenotype and prrA promoter activity indicates that the PrrA-PrrB two-component system is involved in the environmental adaptation of M. tuberculosis, specifically in an early phase of the intracellular growth, and that, similar to other facultative intracellular parasites, M. tuberculosis can use genes temporarily required at different stages in the course of macrophage infection.

Animals↗
PubMed1975

Determinant of cistron specificity in bacterial ribosomes.

The sequence of the 3'-terminus of 16S RNA from different bacteria has been determined. Complementarity relationships between this sequence and a purine-rich tract in the ribosome binding site of different bacterial mRNAs suggest that the 3'-end of 16S RNA determines the intrinsic capacity of ribosomes to translate a particular cistron.

Bacillus↗