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PubMed2006

The 160-kilobase genome of the bacterial endosymbiont Carsonella.

Previous studies have suggested that the minimal cellular genome could be as small as 400 kilobases. Here, we report the complete genome sequence of the psyllid symbiont Carsonella ruddii, which consists of a circular chromosome of 159,662 base pairs, averaging 16.5% GC content. It is by far the smallest and most AT-rich bacterial genome yet characterized. The genome has a high coding density (97%) with many overlapping genes and reduced gene length. Genes for translation and amino acid biosynthesis are relatively well represented, but numerous genes considered essential for life are missing, suggesting that Carsonella may have achieved organelle-like status.

Amino Acids↗

PubMed1991

Non-radioactively labelled polynucleotide and oligonucleotide DNA probes, for selectively detecting Escherichia coli strains producing Vero cytotoxins VT1, VT2 and VT2 variant.

Vero cytotoxin producing Escherichia coli (VTEC) were detected in faecal specimens and bacterial isolates, using non-radioactively labelled polynucleotide and oligonucleotide DNA probes specific for Vero cytotoxin (VT) genes. VT1 and VT2 structural gene sequences, previously cloned and used for radioactive probes, were labelled with digoxigenin or biotin. Oligonucleotide gene sequences coding for the A subunit of VT1, VT2 and VT2 variant were labelled with digoxigenin. The VT1 and VT2 probes were specific for detecting VT1 and VT2 gene sequences and gave very similar results to those obtained using the radioactive label 35S as a standard. The VT2 variant probe hybridized only with the strains of porcine origin. For the range of isolates tested, there was little significant difference in specificity and sensitivity between the digoxigenin-labelled polynucleotide and oligonucleotide probes. The biotin system gave rise to more non-specific effects, particularly with some non-E. coli strains, and was therefore less reliable. All of the digoxigenin-labelled probes gave satisfactory results after several times re-use, which is of importance when considering cost.

Bacterial Toxins↗

PubMed1993

The VirD2 protein of Agrobacterium tumefaciens carries nuclear localization signals important for transfer of T-DNA to plant.

Agrobacterium tumefaciens is able to transfer a piece of DNA, the T-DNA, to the nucleus of the plant cell. The VirD2 protein is required for the production of the T-DNA, it is tightly linked to the T-DNA and it is thought to direct it to the plant genome. Two nuclear localization signals (NLS), one in the N-terminal part and one in the C-terminal part of the VirD2 protein, have been shown to be able to target marker proteins to the plant nucleus. Here we analyze nuclear entry of the T-DNA complex using a new and very sensitive assay for T-DNA transfer. We show that optimal T-DNA transfer requires the VirD2 NLS located in the C-terminal part of the protein, whereas mutations in the N-terminal NLS coding sequence seem to have no effect on T-DNA transfer.

Agrobacterium tumefaciens↗

PubMed2004

The light-responsive promoter of cyanobacterial ORF76 gene overlaps with the htpG terminator.

A Synechococcus PCC7942 gene, encoding 76 amino acids of an unknown protein (designated ORF76), is located at the same orientation and downstream of the htpG gene. The processed site of ORF76 transcripts is located at position +39 with respect to the true transcription initiation site. The non-E. colisigma70-like basal promoter of ORF76 (-51 to -9) is controlled by three cis-acting elements: positively acting element (-160 to -86), negative regulatory element (-86 to -51) and light-responsive element (-51 to +63) that, together, respond to high light induction at transcriptional level. The ORF76 gene is expressed as monocistronic transcript. The promoter elements of ORF76 gene overlap with the coding sequence and 3' end formation signal of htpG gene.

Amino Acid Sequence↗

PubMed1984

Rhizobium japonicum nitrogenase Fe protein gene (nifH).

A 12.1-kilobase PstI fragment from Rhizobium japonicum, which contains homology to both the Klebsiella pneumoniae and the Rhizobium meliloti nifH genes, was cloned into vector pHE3 . The nifH -homologous region was localized on the restriction enzyme cleavage map by Southern blot hybridization experiments. DNA fragments overlapping the R. japonicum nifH gene were subcloned into plasmid vectors to allow the expression of this region in Escherichia coli minicells. The nifH gene product (the polypeptide of the nitrogenase Fe protein) was thus found to have a molecular weight of 33,000. The complete nucleotide sequence of the nifH gene was established, and the amino acid sequence of its gene product was deduced. The reading frame is 882 nucleotides long, corresponding to 294 amino acids which add up to a polypeptide with a molecular weight of 31,525. There was extensive sequence homology with nifH genes or gene products from other nitrogen-fixing bacteria. The transcription initiation site of the R. japonicum nifH gene was found to lie 153 nucleotides upstream from the coding region and was preceded by a characteristic promoter sequence. A potential terminator region was located 13 nucleotides downstream from the coding region.

Amino Acid Sequence↗

PubMed1992

Precorrin-6x reductase from Pseudomonas denitrificans: purification and characterization of the enzyme and identification of the structural gene.

Precorrin-6x reductase, which catalyzes the NADPH-dependent reduction of precorrin-6x to a dihydro derivative named precorrin-6y, was purified 14,300-fold to homogeneity with an 8% yield from extracts of a recombinant strain of Pseudomonas denitrificans. Precorrin-6y was identified by fast atom bombardment-mass spectrometry. It was converted in high yield (90%) to hydrogenobyrinic acid by cell-free protein preparations from P. denitrificans. For the purification and characterization of precorrin-6x reductase, a coupled-enzyme radioenzymatic assay was developed in which precorrin-6y was methylated in situ by the cobL gene product (F. Blanche, A. Famechon, D. Thibaut, L. Debussche, B. Cameron, J. Crouzet, J. Bacteriol. 174:1050-1052, 1992) in the presence of [methyl-3H]S-adenosyl-L-methionine. Molecular weights of precorrin-6x reductase obtained by gel filtration (Mr congruent to 27,000) and by analytical sodium dodecyl sulfate-polyacrylamide gel electrophoresis (Mr congruent to 31,000) were consistent with the enzyme being a monomer. Km values of 3.6 +/- 0.2 microM for precorrin-6x and 23.5 +/- 3.5 microM for NADPH and a Vmax value of 17,000 U mg-1 were obtained at pH 7.7. The N-terminal sequence (six amino acids) and three internal sequences obtained after tryptic digestion of the enzyme were determined by microsequencing and established that precorrin-6x reductase is encoded by the cobK gene, located on a previously described 8.7-kb EcoRI fragment (J. Crouzet, B. Cameron, L. Cauchois, S. Rigault, M.-C. Rouyez, F. Blanche, D. Thibaut, and L. Debussche, J. Bacteriol. 172:5980-5990, 1990). However, the coding sequence was shown to be on the strand complementary to the one previously proposed as the coding strand.

Amino Acid Sequence↗

PubMed1994

An amplifiable DNA region from the Mycoplasma hyorhinis genome.

A novel amplifiable genomic region that displays variability in the number of tandem copies of a 1,368-bp DNA sequence (designated RS-2) was discovered among individual clonal derivatives within Mycoplasma hyorhinis broth-grown cell populations. Clonal isolates representing variant subpopulations from the original broth culture were of a single size variant, and although continued culture under a variety of growth conditions did not result in further amplification of RS-2, evidence for deletion events which reduced RS-2 copy number, presumably by homologous recombination, was obtained. RS-2 homologous sequences were identified in all M. hyorhinis strains tested, but only the tissue culture-derived strains GDL-1 and GDL-2 showed variability in genomic dosage. The RS-2 nucleotide sequence established that each tandem copy is flanked by direct repeats of a 20-bp sequence and suggested a possible mechanism for its original duplication as the initial phase of a genetic amplification process. The coding strand was defined by PCR amplification of a reverse transcriptase-generated cDNA, and its sequence revealed that RS-2 encodes a 456-residue internal, highly cysteine-rich domain of a larger M. hyorhinis protein whose coding sequence initiates and terminates in unique genomic sequences several hundred base pairs from RS-2 on either side of it. Changes in RS-2 copy number maintain the reading frame, and therefore the coding capacity, for this predicted size-variant protein.

Amino Acid Sequence↗

PubMed1996

Cloning, expression and properties of the alpha' subunit of casein kinase 2 from zebrafish (Danio rerio).

The protein kinase casein kinase 2 (CK2) is ubiquitous in eukaryotic cells and is apparently involved in the control of cell division. The holoenzyme is a tetramer composed of two catalytic subunits (alpha and/or alpha') and regulatory subunits (beta 2). The alpha and alpha' subunits are encoded by different genes but are very similar in amino acid sequence, except that alpha' is normally considerably shorter. There have been extensive biochemical studies with recombinant alpha and beta subunits of many species, but only one previous description of the activity of an isolated recombinant alpha' subunit from human CK2 (Bodenbach, L., Fauss, J., Robitzki, A., Krehan, A., Lorenz, P., Lozeman, F. J. & Pyerin, W. (1994) Recombinant human casein kinase II. A study with the complete set of subunits (alpha, alpha', and beta), site-directed autophosphorylation mutants and a bicistronically expressed holoenzyme, Eur. J. Biochem. 220, 263-273). In the present work, the isolation and bacterial expression of a cDNA coding for the alpha' subunit of zebrafish (Danio rerio) is reported. The clone covers the complete coding region that generates a protein of 348 amino acids that is 86% identical to the alpha' subunits of human and chicken, and 82% identical to the sequenced portion of the CK2 alpha subunit of zebrafish. The recombinant alpha' subunit has apparent K(m) values for ATP (6 microM), GTP (20 microM), casein (2.0 mg/ml) and the model peptide RRRDDDSEDD (0.3 mM) which are very similar to those of the recombinant alpha subunit of Xenopus laevis. The alpha' subunit kcat was 7.2 min-1 which is again similar to that of Xenopus laevis alpha subunit (7.5 min-1). The alpha' subunit also behaved similarly to CK2 alpha with regard to optimal concentrations for Mg+2 or Mn+2 and to the inhibition by heparin and the poly(Glu80Tyr20) peptide. However alpha' kinase activity was less sensitive to poly(U) inhibition than alpha, it was more heat stable than alpha, and alpha' was slightly more sensitive to KCl inhibition than alpha. The difference in salt sensitivity, however, was enhanced by the presence of the regulatory beta subunit which shifted the optimal salt concentration of the phosphorylating activity. The alpha' 2 beta 2 holoenzyme was inhibited by KCl concentrations above 100 mM, while the alpha 2 beta 2 enzyme was stimulated by KCl concentrations up to 150 mM and required 180 mM for inhibition. Another important difference between alpha and alpha' is seen in the degree of the stimulation of casein phosphorylation activity in the presence of the regulatory beta subunit. When assayed at 100 mM KCl stoichiometric amounts of CK2 beta produced maximal stimulation of both alpha' (D. rerio) and alpha (X. laevis), however the activity levels with alpha' were stimulated 20-fold by beta while the addition of beta stimulated alpha (X. laevis) only 7-8-fold.

Amino Acid Sequence↗

PubMed2003

Genetic variation and activity of mouse Nod2, a susceptibility gene for Crohn's disease.

Genetic variation in human Nod2 has been associated with susceptibility to Crohn's disease. The mouse Nod2 locus is located at chromosome 8 and composed of 12 exons, 11 of which encode the Nod2 protein. Sequence analysis of Nod2 from 45 different strains of Mus musculus and Mus spretus revealed extensive polymorphism involving all exons of Nod2. Of the 140 polymorphic sites identified, 68 were located in the coding region, of which 28 created amino acid substitutions in Nod2. Expression of mouse Nod2 activated NF-kappaB and conferred responsiveness to bacterial components, an activity that was deficient in mutants corresponding to those associated with susceptibility to Crohn's disease. These studies demonstrate a conserved role for Nod2 in the response to bacterial components and suggest that selective evolutionary pressure exerted by pathogens may have contributed to the high level of variability of Nod2 sequences in both humans and mice.

Amino Acid Sequence↗

PubMed2001

Identification and characterization of two novel human mitochondrial elongation factor genes, hEFG2 and hEFG1, phylogenetically conserved through evolution.

Rapid progress in the sequencing of the genome of man and other species allows for the comparative analysis of their genetic structure and content. We have used a combined biochemical and computer-based approach to characterize a 146 kb human genomic bacterial artificial chromosome clone from chromosome 5q13 and discovered a novel human elongation-factor gene, hEFG2. The complete human EFG2 cDNA sequence is 3033 bp and contains 21 exons with conserved exon-intron splice junctions encompassing 45 kb of the genomic sequence with its 5'-end residing within a CpG island, characteristic of a housekeeping gene. The complete size of the hEFG2 cDNA was confirmed by Northern blot and reverse transcription/polymerase chain reaction analysis, which showed a single transcript of 3.2 kb ubiquitously expressed in various human tissues. The hEFG2 protein shows significant homology to several bacterial EF-G proteins, including that of Thermus thermophilus, and to the yeast Saccharomyces cerevisiae mitochondrial elongation factor-G ( MEF2). Multiple alignments reveal a novel gene family of mitochondrial EF-G proteins that can by divided into two subgroups, EF-G1 and EF-G2, in several eukaryotic species including S. pombe, Caenorhabditis elegans and Drosophila melanogaster. Using the information contained in the public databases, we also identified and cloned the complete coding sequence of the human EFG1 gene on chromosome 3q25. The cloning and characterization of these human mitochondrial elongation factor genes should permit us to address their role in the regulation of normal mitochondrial function and in various disease states.

Amino Acid Sequence↗

PubMed1991

Molecular considerations in the evolution of bacterial genes.

Synonymous and nonsynonymous substitution rates at the loci encoding glyceraldehyde-3-phosphate dehydrogenase (gap) and outer membrane protein 3A (ompA) were examined in 12 species of enteric bacteria. By examining homologous sequences in species of varying degrees of relatedness and of known phylogenetic relationships, we analyzed the patterns of synonymous and nonsynonymous substitutions within and among these genes. Although both loci accumulate synonymous substitutions at reduced rates due to codon usage bias, portions of the gap and ompA reading frames show significant deviation in synonymous substitution rates not attributable to local codon bias. A paucity of synonymous substitutions in portions of the ompA gene may reflect selection for a novel mRNA secondary structure. In addition, these studies allow comparisons of homologous protein-coding sequences (gap) in plants, animals, and bacteria, revealing differences in evolutionary constraints on this glycolytic enzyme in these lineages.

Amino Acid Sequence↗

PubMedDate not supplied

Sequence comparison of the EcoHK31I and EaeI restriction-modification systems suggests an intergenic transfer of genetic material.

The genes coding for the EcoHK31I and EaeI restriction-modification (R-M) systems from Escherichia coli strain HK31 and Enterobacter aerogenes, respectively, have been cloned and sequenced. Both ENases recognize and cleave Y/GGCCR leaving 4 nucleotide 5'-protruding ends, while the MTases modify the internal cytosine. The systems were isolated on a 2.3kb AseI fragment for EcoHK31I, and a 4.6 kb HindIII fragment for EaeI. The R and M genes of both systems converge and overlap by 14 nucleotides. Previously, we found that M.EcoHK31I consisted of two subunits, (alpha and beta), with the beta subunit being translated from an alternative open reading frame within the gene encoding the alpha subunit. Sequence comparison between the EcoHK31I and EaeI systems reveals striking similarity. The eaeIM gene also encodes alpha and beta polypeptides of 309 and 176 amino acids which share 96% and 97% identity, respectively, with those of ecoHK31IM. ecoHK31IR and eaeIR encode proteins of 318 and 315 aa, respectively, which share 92% identity but are otherwise unique in the GenBank database. The EaeI and the EcoHK31I R-M systems were found to be flanked by genes coding for integrases. It is possible that these integrases have facilitated the transfer of this system among different bacterial species.

Amino Acid Sequence↗

PubMed1981

Termination of DNA replication in vitro at a sequence-specific replication terminus.

The replication terminus of the drug resistance factor R6K has been cloned into the plasmid vectors pBR313 and pBR322. When the exogenously added DNA is replicated in vitro using cell extracts prepared from Escherichia coli, the plasmid replication terminus temporarily arrests the progression of the unidirectionally moving replication fork at or near the cloned terminator sequence. When the relative location of the terminator sequence is changed with respect to the replication origin, the point of arrest of the replication fork shifts correspondingly to the new location of the terminator. Termination of replication takes place in vitro regardless of whether the cell extracts used in the in vitro reaction are prepared from E. coli with a resident terminus sequence containing plasmid. From these observations we conclude that the termination of replication in vitro is identical or very similar to that observed in vivo, membrane association is not necessary for the activity of the replication terminus and the terminus sequence does not code for a transacting factor necessary for termination of replication. Therefore, any transacting factor which may be needed for the termination of replication must be coded by the host chromosome.

Base Sequence↗

PubMed1986

Structure of the uvrB gene of Escherichia coli. Homology with other DNA repair enzymes and characterization of the uvrB5 mutation.

The complete nucleotide sequence of the Escherichia coli uvrB gene has been determined. The coding region of the uvrB gene consists of 2019 nucleotides which direct the synthesis of a 673 amino-acid long polypeptide with a calculated molecular weight of 76.614 daltons. Comparison of the UvrB protein sequence to other known DNA repair enzymes revealed that 2 domains of the UvrB protein (domain I = 6 amino acids, domain II = 14 amino acids) are also present in the protein sequence of the uvrC gene. We show that the structural homologies between UvrB and UvrC are as well reflected by the cross-reactivity of anti-uvrB and anti-uvrC antibodies with UvrC and UvrB protein respectively. In the N-terminal part of UvrB, domain III (17 amino acids) shows a strong homology with one part of the AlkA gene product. Adjacent to domain III, an ATP binding site consensus sequence is found in domain IV. The uvrB5 mutant gene from strain AB1885 has been cloned on plasmid pBL01. We show that the uvrB5 mutation is due to a point deletion of a CG basepair and results in the synthesis of an 18 kD protein composed of the 113 N-terminal amino acids of the wild type uvrB gene and a 43 amino acid long tail coded in the -1 frame.

Amino Acid Sequence↗

PubMed1991

Genetic and physical analysis of the nodD3 region of Rhizobium meliloti.

The nodulation (nod) genes of the symbiont Rhizobium meliloti are transcriptionally controlled by protein activators in the nodD gene family. While NodD1 and NodD2 act in concert with small molecular weight inducers provided by the host legume plant, NodD3 is an inducer-independent activator of the nod promoters. We determined the sequence of the nodD3 gene, confirmed the expression of a 35 kDa protein in vitro, and determined the insertion points of five Tn5 insertions in the region of the nodD3 gene. We found the NodD3 amino acid sequence to be markedly diverged from the sequences of NodD1 and NodD2, which were more similar to the inducer-dependent NodD of another species, Rhizobium leguminosarum biovar viciae. The expression of nodD3 is not well understood, but involves at least SyrM, another positive activator related to the LysR-NodD family. One of the phenotypically mutant Tn5 insertions used in genetic studies of NodD3-dependent nod regulation lacks NodD3 protein as determined by Western blots, but another expresses about 50-60% of the wild type level. The location of these Tn5 insertions substantially upstream of the open reading frame for NodD3 suggests importance of relatively distant regulatory sequences for nodD3 expression. An insertion that did not cause a NodD3- phenotype is located in the extreme C-terminus of the protein coding region.

Amino Acid Sequence↗

PubMed1990

Nucleotide sequences and genomic constitution of five tryptophan genes of Lactobacillus casei.

Five trp genes, trpD, trpC, trpF, trpB, and trpA, of Lactobacillus casei were cloned by transformation of tryptophan auxotrophic mutants of the respective trp genes in Escherichia coli. These trp genes appear to constitute an operon and are located in the above order in a segment of DNA of 6,468 base pairs. The entire nucleotide sequence of this DNA segment was determined. Five contiguous open reading frames in this segment can encode proteins consisting of 341, 260, 199, 406, and 266 amino acids, respectively, in the same direction. The amino acid sequences of these proteins exhibit 25.5-50.2% homology with the amino acid sequences of the corresponding trp enzymes of E. coli. Two trp genes, trpC and trpF, from L. casei can complement mutant alleles of the corresponding genes of E. coli. However, neither the trpA gene nor the trpB gene of L. casei can complement mutations in the E. coli trpA gene and the trpB gene, respectively, suggesting that the protein products of the L. casei and E. coli trpA and trpB genes, respectively, cannot form heterodimers of tryptophan synthetase with activity. Other features of the coding and flanking regions of the trp genes are also described.

Amino Acid Sequence↗

PubMed1988

Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomyces coelicolor A3(2).

The nucleotide sequence of 2.5 kb of the Streptomyces coelicolor A3(2) rRNA gene set rrnD, extending from upstream of the 16S rRNA gene to the putative 5' end of the 23S rRNA gene, has been determined (Baylis and Bibb, 1987; this paper). In addition to locating the 5' end of the 16S rRNA gene, nuclease S1 mapping identified seven RNA 5' end-points upstream of the 16S rRNA gene; four of these were coincident with transcriptional initiation points for S. coelicolor A3(2) RNA polymerase in vitro and were consequently regarded as in vivo transcription start points for promoters p1 to p4. One end-point identified by nuclease S1 mapping localized a putative processing site analogous to those found upstream of 16S rRNA genes in other eubacteria. Sequence motifs similar to those discovered in low G+C Gram-positive bacteria were found associated with two of the promoters and the processing site. A probable protein coding region was observed upstream of the promoter region.

Base Sequence↗

PubMed1988

Nucleotide sequence of the structural gene for class I pilin from Neisseria meningitidis: homologies with the pilE locus of Neisseria gonorrhoeae.

The nucleotide sequence has been determined for the expressed pilin (pilE) locus of Neisseria meningitidis strain C311 which produces class I pili that are antigenically and structurally similar to those of gonococci. The deduced amino acid sequence of the N. meningitidis pilE translation product contains a 7 amino acid N-terminal pre-pilin leader sequence which is identical to that found in gonococcal pilin and which is characteristic of N-methylphenylalanine pili in general. The succeeding N-terminal 53 amino acids are identical to those found in the equivalent position in antigenically variant gonococcal pilins and confirm direct peptide sequencing of the amino-terminus of at least one type of meningococcal pilin. Other regions that are conserved in variant pilin polypeptides from Neisseria gonorrhoeae are conserved at the amino acid level in the class I meningococcal pilin but the coding DNA contains numerous base substitutions when compared with the equivalent gonococcal pil sequence. Sequences extending downstream for about 140 bp on the 3' side of the coding region for both pilin genes are only about 85% homologous.

Amino Acid Sequence↗