Nucleotide sequence of the rpoN (hno) gene region of Alcaligenes eutrophus: evidence for a conserved gene cluster

The nucleotide sequence of the rpoN gene, formerly designated hno, and flanking DNA regions of the aerobic hydrogen bacterium Alcaligenes eutrophus has been determined; rpoN codes for the RNA polymerase sigma factor sigma 54 involved in nitrogen regulation and diverse physiological functions of gram-negative bacteria. In A. eutrophus hydrogen metabolism is under control of rpoN. The Tn5-Mob insertion in a previously isolated pleiotropic mutant was mapped within the rpoN gene. The derived amino acid sequence of the A. eutrophus RpoN protein shows extensive homology to the RpoN proteins of other organisms. Sequencing revealed four other open reading frames: one upstream (ORF280) and three downstream (ORF130, ORF99 and ORF greater than 54) of the rpoN gene. A similar arrangement of homologous ORFs is found in the rpoN regions of other bacteria and is indicative of a conserved gene cluster.

The P gene of the porcine paramyxovirus LPMV encodes three possible polypeptides P, V and C: the P protein mRNA is edited

The nucleotide sequence of the P gene of the porcine paramyxovirus La-Piedad-Michoacan-Mexico virus (LPMV) was analysed. Three long open reading frames (ORFs) were found in the mRNA sense. Insertion of two G residues is necessary to obtain an ORF encoding the P protein, which gives a P protein of 404 amino acids with a calculated Mr of 42475. This form of editing was demonstrated, two non-templated G residues being added in a portion of the mRNA transcripts. The LPMV V protein, which has a conserved cysteine-rich C-terminal region, is encoded by an exact copy of the P gene. The third ORF has the capacity to encode a protein of 126 amino acids, which may resemble the C proteins found in some paramyxoviruses. The ORF starts from an AUG codon down-stream of the first AUG codon of the P/V ORF.

Conjugative transfer of Enterococcus faecalis plasmid pAD1: nucleotide sequence and transcriptional fusion analysis of a region involved in positive regulation

The Enterococcus faecalis plasmid pAD1 undergoes conjugative transfer in response to cAD1, a peptide sex pheromone emitted by potential bacterial recipients. Regulation of pAD1 transfer involves a number of plasmid-encoded determinants:iad, which determines a peptide-competitive inhibitor iAD1; signal sensing and transducing elements; and negative and positive regulators. The key positive regulator(s) of the pheromone response is believed to be encoded within a segment designated the E region of the plasmid. In this study, we analyzed the nucleotide sequence and transcription within the E region. An open reading frame designated traE1 was identified; its inferred protein consists of 118 amino acids. Insertional mutagenesis of traE1 resulted in a complete loss in plasmid transfer capability. Analysis of Tn917-lac insertions giving rise to transcriptional lacZ fusions showed that traE1 is transcribed only under cAD1 inducing conditions. Analysis of additional lacZ fusions within the region provided some insight into the roles of potential regulatory signals within and around the nucleotide sequences reported here. A regulatory role appearing to involve read-through of certain key transcription termination sequences seemed evident.

Duplication of a DNA sequence homologous to genes for immunoglobulin receptors and M proteins in Streptococcus pyogenes

The nucleotide sequence of an open reading frame of 355 amino acids downstream of the IgA-binding protein gene arp4 in Streptococcus pyogenes M-type 4 has been determined. Analysis of the deduced amino acid sequence for the open reading frame shows an extensive homology to streptococcal M proteins and immunoglobulin binding proteins. Expression of the open reading frame has not been detected and the function may be as a genetic reservoir in the generation of new immunoglobulin receptors and antigenic variants of M proteins.

Cloning and sequencing of Puumala virus Sotkamo strain S and M RNA segments: evidence for strain variation in hantaviruses and expression of the nucleocapsid protein

The prototype Puumala virus (PV) Sotkamo strain small (S) and medium (M) RNA genome segments were amplified by the polymerase chain reaction (PCR), cloned and sequenced. The S segment is 1830 nucleotides long with an open reading frame coding for 433 amino acids. The identity to the PV Hällnäs strain was 83% at the nucleotide and 96% at the amino acid level. The M segment in the Sotkamo strain is 3616 nucleotides long and contains one open reading frame of 1148 amino acids with 83% nucleotide and 94% amino acid identity to the Hällnäs strain. Most amino acid changes were conservative and the five predicted glycosylation sites are identical. The amino acid identity to the prototype hantavirus, Hantaan virus, was 62 and 54% for S and M segments, respectively. The coding region of the S segment was further amplified by PCR, ligated to pEX vectors and expressed in Escherichia coli as a beta-galactosidase fusion protein and was seen to be specifically detected by nephropathia epidemica sera in immunoblotting.

Recognition of correct reading frame by the ribosome

The translation frame-monitoring mechanism has been suggested earlier, based on transient complementary contacts, between mRNA and rRNA. Recent studies related to the frame-monitoring mechanism are reviewed. The mechanism is well supported by both new experimental and sequence analysis data. Experiments are suggested for further elucidation of the structural details of the mRNA-rRNA interaction in the ribosome.

Cloning, sequence analysis, and expression of the structural gene encoding glucose-fructose oxidoreductase from Zymomonas mobilis

The gene encoding glucose-fructose oxidoreductase (gfo) from Zymomonas mobilis was cloned in Escherichia coli and sequenced. An open reading frame of 439 amino acids encoded a protein of 49 kDa. A leader sequence of 52 amino acids preceded the N-terminal sequence of the enzyme, indicating cleavage of the precursor protein at an Ala-Ala site to give rise to an active form of the enzyme of 43 kDa. Processing of the glucose-fructose oxidoreductase leader sequence, although not complete, was demonstrated in an in vitro translation system. The two Z. mobilis promoters of the gfo gene show considerable homology to other highly expressed Z. mobilis genes (pdc, adhB, gap, and pgk) as well as to the E. coli consensus sequence. Although translation of the gfo gene was demonstrated in vitro in an E. coli S30 coupled transcription-translation system, a functional stable protein was not produced in the E. coli clone. However, the gfo gene cloned into a shuttle vector was shown to overexpress glucose-fructose oxidoreductase to levels of up to 6% of the soluble protein in Z. mobilis.

Sequence and expression pattern of pax-6 are highly conserved between zebrafish and mice

Despite obvious differences in the patterns of early embryonic development, vertebrates share a number of developmental mechanisms and control genes, suggesting that they use similar genetic programs at some stages of development. To examine this idea, we isolated and characterized one such gene, pax-6, a member of the pax gene family, from the zebrafish Brachydanio rerio and determined the evolutionary conservation in the structure and expression of this gene by comparison to its homolog in mice. We found two alternatively spliced forms of the zebrafish pax-6 message. Sequence and expression pattern of the zebrafish pax-6 gene are remarkably similar to its murine homolog. pax-6 expression begins during early neurulation. A stripe of cells in the neuroectoderm, including the prospective diencephalon and a part of the telencephalon, expresses pax-6 as well as the hindbrain and the ventral spinal cord extending from the level of the first rhombomere to the posterior end of the CNS. During later development more limited regions of the brain including the eye, the olfactory bulb and the pituitary gland express pax-6. Cells at the midbrain-hindbrain junction express eng genes and are separated from the neighboring pax-6 regions by several cells that express neither gene, indicating a complex subdivision of this region. pax-6 expression appears during processes when cell-to-cell signalling is thought to be important, for example during induction of the eye and regionalization of the spinal cord and brain, suggesting that it may be one component mediating the response to inductive interactions.

Cloning, nucleotide sequencing, and expression in Escherichia coli of a Rhizobium leguminosarum gene encoding a symbiotically repressed outer membrane protein

We describe the cloning of a gene from Rhizobium leguminosarum biovar viciae strain 248 encoding protein IIIa, the 36-kDa outer membrane protein forming a part of the outer membrane protein antigen group III. The expression of this antigen group is repressed in the bacteroid form during symbiosis (R. A. de Maagd, R. de Rijk, I. H. M. Mulders, and B. J. J. Lugtenberg, J. Bacteriol. 171:1136-1142, 1989). A cosmid clone expressing the strain 248-specific MAb38 epitope of this antigen group in a nonrelated strain was selected by a colony blot assay. Sequencing revealed one large open reading frame encoding a 39-kDa protein. N-terminal amino acid sequencing of the purified 36-kDa outer membrane protein IIIa revealed that the isolated gene, now designated ropA, is the structural gene for this protein and that the mature protein was formed by processing of the 22-residue N-terminal signal sequence. The gene is preceded by a promoter that was active in R. leguminosarum but not in Escherichia coli. This promoter, which showed no homology to known promoter sequences, was located approximately by determination of the transcription start site. The region upstream of the putative promoter was shown to contain two potential binding sites for integration host factor protein. Expression of protein IIIa under control of the inducible lac promoter in E. coli shows that, of its earlier described properties, the peptidoglycan linkage of protein IIIa is specific for R. leguminosarum but that outer membrane localization and calcium-stabilized oligomer formation can to a large extent also occur in E. coli.

Cloning, sequencing, expression, and functional studies of a 15,000-molecular-weight Haemophilus somnus antigen similar to Escherichia coli ribosomal protein S9

Haemophilus somnus is a gram-negative bacterium capable of causing a number of disease syndromes in cattle. This article describes the cloning and characterization of a gene coding for a 15,000-molecular-weight (15K) polypeptide which reacts strongly with antiserum against H. somnus. Analysis of plasmid-encoded polypeptides by polyacrylamide gel electrophoresis showed that the corresponding gene is the second in a transcriptional unit. The first gene codes for a protein with a molecular weight of approximately 17,000. Using antiserum against the two recombinant proteins, we could show that the natural proteins are predominantly present in purified ribosomes from H. somnus. The nucleotide sequence of both genes and flanking regions has been determined, and the deduced amino acid sequence of the two polypeptides was used to search for sequence homology in the GenBank data base. The 15K polypeptide showed 89% similarity to the Escherichia coli ribosomal protein S9, and the 17K polypeptide showed 94% similarity to the E. coli ribosomal protein L13. In E. coli, the corresponding genes constitute a bicistronic operon, with the same gene order as that found in H. somnus. A plasmid expressing the 15K protein was found to complement an E. coli rpsI mutation. When a frameshift mutation was introduced into the 15K protein gene, the resulting plasmid failed to complement this rpsI mutation, demonstrating functional homology between the 15K protein and S9 from E. coli. Downstream from the 15K protein gene is located another open reading frame, which could code for a polypeptide with a predicted molecular weight of 24,427. A protein with a similar molecular weight was detected in minicells containing the recombinant clone. This polypeptide is 69% similar to the stringent starvation protein (Ssp) of E. coli.

Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911

The proteins expressed by insertion sequence IS911, a member of the widespread IS3 family of elements, have been analyzed. The results indicate that three major species are produced from two consecutive reading frames. A protein of Mr 11,500, ORFA, is synthesized from an upstream reading frame. A larger protein, ORFAB, uses the same initiation codon and is produced by a -1 programmed translational frameshift between orfA and a downstream frame, orfB, whose amino acid sequence shows significant homology with retroviral integrase proteins. The orfB frame is also expressed independently in two alternative forms: the first uses a rare AUU initiation codon in the orfB phase whereas the second appears to initiate in the orfA phase and is produced by a -1 frameshift mechanism similar to that used in ORFAB expression. A specific IS911 integration reaction using a minimal active junction composed of 51 base-pairs of the right inverted repeat and a flanking phase lambda sequence resembling a second end in inverted orientation has been developed to analyze the functions of these proteins by transcomplementation in vivo. The orfA and orfB frames are shown to be essential and production of ORFAB is shown to stimulate integration in this system, suggesting that this fusion protein is the IS911 transposase.

Ribosomal frameshifting, jumping and readthrough

New examples of high-level ribosomal frameshift and readthrough events have been described over the past year and a half. These include -1 frameshifting at tandem codons and +1 frameshifting at neighboring slow codons. Several bizarre examples of ribosome jumping and multiple stop-codon readthrough continue to perplex investigators in this field.

Molecular cloning and transcriptional analysis of the cpeBA operon of the cyanobacterium Pseudanabaena species PCC7409

The cpeBA operon of the Group III chromatically adapting cyanobacterium Pseudanabaena species PCC 7409 was cloned, sequenced and characterized. The cpeBA genes are transcribed in green-light-grown cells as an abundant 1400-nucleotide mRNA which initiates 69 nucleotides upstream from the cpeB translation start. Extensive sequence identity, extending 70 nucleotides 5' to the transcription start, occurs among cpeBA promoters of Group II and III chromatic adapters. Cell extracts of green-light-grown Calothrix species PCC 7601 contain an activity which specifically binds a restriction fragment containing the Pseudanabanea species PCC 7409 cpeBA promoter. Green-light-dependent cpeBA transcription in Group II and III chromatically adapting cyanobacteria is suggested to be similarly controlled by a transcriptional activator.

Rat gastric H,K-ATPase beta-subunit gene: intron/exon organization, identification of multiple transcription initiation sites, and analysis of the 5'-flanking region

A rat genomic library was screened using a gastric H,K-ATPase beta-subunit cDNA probe, and two clones were identified. Restriction endonuclease mapping and Southern hybridization analyses indicated that each of these clones contains the entire H,K-ATPase beta-subunit gene. The nucleotide sequence was determined for the 8.75-kb transcription unit and 2.2 kb of the 5'-flanking region. The gene consists of seven exons and shows a high degree of similarity to the Na,K-ATPase beta 1-subunit gene. Primer extension and S1 nuclease protection analyses identified a major transcription initiation site 23 bases upstream of the translation start site and several minor transcription initiation sites located further upstream. The 5'-flanking region of the gene has two potential TATA sequences, each located 25-30 bases upstream of a transcription initiation site, and a number of potential promoter and regulatory elements. In addition, the 5'-flanking region contains nucleotide sequences that may regulate transcription through the formation of unusual DNA structures. These include a sequence that may form a triple helix and an adjacent sequence with the potential to form Z-DNA.

Mitochondrial inner membrane protease 1 of Saccharomyces cerevisiae shows sequence similarity to the Escherichia coli leader peptidase

The nuclear yeast mutant pet ts2858 is defective in the removal of pre-sequences from the mitochondrially encoded cytochrome oxidase subunit II (COXII) and the processing intermediate of cytochrome b2 (Cytb2), a nuclear gene product. In order to identify the genetic lesion in this mutant we have cloned and characterized a DNA region which complements the pet ts2858 mutation. The DNA sequence revealed three open reading frames, one of which is responsible for the complementation. A 570 bp reading frame represents the structural gene PET2858, as demonstrated by in vitro mutagenesis, gene expression from a foreign promoter, and allelism tests. PET2858 encodes a 21.4 kDa protein, which is essential for growth on non-fermentable carbon sources and for the proteolytic processing of COXII and the Cytb2 intermediate. When the N-terminus of the PET2858 protein is fused to a reporter protein, the resulting hybrid molecule is imported into mitochondria. Interestingly, the N-terminal half of the deduced PET2858 protein exhibits 30.7% amino acid identity to the leader peptidase of Escherichia coli. These results suggest that PET2858 codes for a mitochondrial inner membrane protease (IMP1) or at least a subunit of it. This protease is involved in protein processing and export from the mitochondrial matrix.

Structure of the bovine placental lactogen gene and alternative splicing of transcripts

Preliminary evidence for heterogeneity among bovine placental lactogen (bPL) transcripts prompted characterization of additional cDNA clones and isolation of the bPL gene. Nucleotide replacements were detected among sequenced cDNAs isolated from different animals at a total of 11 positions. Four of these predict amino acid substitutions, which are generally conservative in nature. In addition, truncated forms of bPL are predicted by the sequences of two cDNAs in which alternative splicing is evident. In one case, exon III is deleted with no effect on reading frame. However, in the other instance, a shifted reading frame resulting in a novel carboxyl terminus is generated by use of an alternative 5' splice donor site within exon IV. Nuclease protection analysis demonstrated that these variant transcripts comprise about 13% of the total bPL mRNA present in the midgestation placenta. Characterization of the bPL gene revealed that it is similar in structure to other members of this gene family. Sequence analysis demonstrated that the 5'-flanking region of the bPL gene has diverged considerably from the bovine prolactin and growth hormone genes, but shares homology with the previously characterized gene corresponding to bovine prolactin-related cDNAI (bPRCI). Primer extension as well as nuclease protection analysis indicated that a single transcription start site was utilized in the fetal placenta at midgestation. Exact matches to the consensus sequences for response elements for thyroid hormone and transcription factor AP-2 were located 50 and 70 bp, respectively, upstream from the transcription start site in cloned genomic 5'-flanking sequences. We conclude that the bovine placenta may express more than a single placental lactogen product, raising the possibility of alternative hormones with distinct biological properties, and that the bPL gene may share regulatory elements with the gene for the distinct prolactin-related product, bPRCI, based on similarities in the 5' regions of the corresponding genes.

Sendai virus P gene produces multiple proteins from overlapping open reading frames

The Sendai virus P gene contains overlapping open reading frames (ORFs), and several unusual mechanisms are used to produce multiple proteins from all three ORFs of this gene. These include the use of a non-AUG start codon, leaky ribosomal scanning, what appears to be scanning-independent ribosomal initiation and/or ribosomal jumping, and a form of mRNA editing.

Effects of elongation on the translation of a reovirus bicistronic mRNA

The S1 species of reovirus mRNA contains two overlapping open reading frames. Both are utilized in either virus-infected or S1 DNA transfected mammalian cells, resulting in two different polypeptides from a single mRNA. Consistent with ribosome scanning, expression of the downstream reading frame was increased by sequence changes that diminished the consensus around the upstream initiator site. However, the upstream product was not decreased by the same changes, suggesting that its synthesis is rate-limited at elongation. The results suggest a model for regulating bicistronic mRNA translation in which the ribosomes in one reading frame interfere with the movement of ribosomes in the other frame due to different rates of elongation.