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B A Sherf

Publications and source records attributed to B A Sherf.

8 recordsLinked to original sources
PubMed1992

Protein expression from an Escherichia coli/Bacillus subtilis multifunctional shuttle plasmid with synthetic promoter sequences.

A plasmid shuttle vector (pSP10) was designed and constructed to simplify screening of cloned DNA and to facilitate expression of the protein products. The plasmid contained the following features: (i) a selection gene, chloramphenicol acetyltransferase; (ii) an indicator gene encoding beta-galactosidase for visual identification of colonies containing DNA inserts; (iii) a cloning region immediately upstream from the indicator gene; (iv) origins of replication recognized by both Escherichia coli and Bacillus subtilis; and (v) a synthetic DNA expression control sequence, including -35 and -10 regions, ribosomal binding site, and transcriptional and translational start sites. The promoter region is a synthetic consensus sequence derived from published B. subtilis promoters. The plasmid has been shown to replicate actively in E. coli and B. subtilis and to confer chloramphenicol resistance to both hosts. DNA inserted at the cloning region inactivates the indicator gene, resulting in white colonies on 5'-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside plates. beta-Galactosidase has been expressed from pSP10 in both E. coli and B. subtilis. A comparison was made of the expression levels of beta-galactosidase from the same plasmid which had been modified to contain: (i) the synthetic control region, (ii) no promoter region, (iii) the synthetic control region cloned in the opposite orientation, or (iv) the tac promoter.

Bacillus subtilis↗
PubMed1990

Identification of the mcrD gene product and its association with component C of methyl coenzyme M reductase in Methanococcus vannielii.

A mcrD-lacZ gene fusion has been constructed and expressed under lacP control in Escherichia coli. Antibodies raised against the product of this gene fusion have been used in Western blotting (immunoblotting) to demonstrate the gene product of mcrD (gpmcrD) in Methanococcus vannielii. The alpha, beta, and gamma subunit polypeptides of component C of methyl coenzyme M reductase (MR) were coprecipitated with gpmcrD when bound by antibodies raised either against MR or against gpmcrD-lacZ. This association of MR and gpmcrD did not withstand polyacrylamide gel electrophoresis under nondenaturing conditions.

Amino Acid Sequence↗
PubMed1989

An archaebacterial promoter sequence assigned by RNA polymerase binding experiments.

To identify an archaebacterial promoter sequence, nuclease protection studies with the purified RNA polymerase of Methanococcus vannielii were performed. The enzyme binds specifically both at protein-encoding (hisA and methyl CoM reductase, component C) and tRNA-rRNA genes. The binding region of the RNA polymerase extends from 30 base pairs (bp) upstream (-30) to 20 bp downstream (+20) from the in vivo transcription start site. This finding indicates that the archaebacterial enzyme recognizes promoters without transacting transcription factors. The DNA segment protected from nuclease digestion by bound RNA polymerase contains an octanucleotide sequence centered at -25, which is conserved between the protein-encoding and the stable RNA genes. According to the specific binding of the enzyme to only DNA-fragments harbouring this motif, we propose the sequence TTTATATA as the major recognition signal of the Methanococcus RNA polymerase. Comparison of this motif with published archaebacterial DNA sequences revealed the presence of homologous sequences at the same location upstream of 36 genes. We therefore consider the overall consensus TTTATAATA as a general element of promoters in archaebacteria. In spite of the specific binding of the enzyme, most preparations of the Methanococcus vannielii RNA polymerase are unable to initiate transcription at the correct sites in vitro. Here we present first evidence for the possible existence of a transcription factor conferring the ability to the enzyme to initiate and terminate transcription specifically in vitro.

Archaea↗
PubMed1989

A comparison of the methyl reductase genes and gene products.

The DNA sequences encoding component C of methyl coenzyme M reductase (mcr genes) in Methanothermus fervidus, Methanobacterium thermoautotrophicum, Methanococcus vannielii, and Methanosarcina barkeri have been published. Comparisons of transcription initiation and termination sites and of the amino acid sequences of the mcr gene products are presented. Structural features conserved within the amino acid sequences are identified and a comparison of methyl reductase with other disulfide bond synthesizing enzymes is presented.

Amino Acid Sequence↗
PubMed1988

Structure and comparative analysis of the genes encoding component C of methyl coenzyme M reductase in the extremely thermophilic archaebacterium Methanothermus fervidus.

A 6-kilobase-pair (kbp) region of the genome of the extremely thermophilic arachaebacterium Methanothermus fervidus which encodes the alpha, beta, and gamma subunit polypeptides of component C of methyl coenzyme M reductase was cloned and sequenced. Genes encoding the beta (mcrB) and gamma (mcrG) subunits were separated by two open reading frames (designated mcrC and mcrD) which encode unknown gene products. The M. fervidus genes were preceded by ribosome-binding sites, separated by short A + T-rich intergenic regions, contained unexpectedly few NNC codons, and exhibited inflexible codon usage at some locations. Sites of transcription initiation and termination flanking the mcrBDCGA cluster of genes in M. fervidus were identified. The sequences of the genes, the encoded polypeptides, and transcription regulatory signals in M. fervidus were compared with the functionally equivalent sequences from two mesophilic methanogens (Methanococcus vannielii and Methanosarcina barkeri) and from a moderate thermophile (Methanobacterium thermoautotrophicum Marburg). The amino acid sequences of the polypeptides encoded by the mcrBCGA genes in the two thermophiles were approximately 80% identical, whereas all other pairs of these gene products contained between 50 and 60% identical amino acid residues. The mcrD gene products have diverged more than the products of the other mcr genes. Identification of highly conserved regions within mcrA and mcrB suggested oligonucleotide sequences which might be developed as hybridization probes which could be used for identifying and quantifying all methanogens.

Amino Acid Sequence↗
PubMed1988

RNA polymerase-binding and transcription initiation sites upstream of the methyl reductase operon of Methanococcus vannielii.

RNA polymerase, purified from Methanococcus vannielii, was shown by exonuclease III footprinting to bind to a 49-base-pair (bp) region of DNA in the intergenic region upstream of mcrB. S1 nuclease protection experiments demonstrated that transcription initiation in vivo occurs within this region at 32 or 33 bp 5' to the ATG translation initiation codon of mcrB and 19 or 20 bp 3' to a TATA box.

Base Sequence↗
PubMed1987

Structure and expression of the genes, mcrBDCGA, which encode the subunits of component C of methyl coenzyme M reductase in Methanococcus vannielii.

The genes that encode the alpha, beta, and gamma subunits of component C of methyl coenzyme M reductase (mcrA, mcrB, and mcrG) in Methanococcus vannielii have been cloned and sequenced, and their expression in Escherichia coli has been demonstrated. These genes are organized into a five-gene cluster, mcrBDCGA, which contains two genes, designated mcrC and mcrD, with unknown functions. The mcr genes are separated by very short intergenic regions that contain multiple translation stop codons and strong ribosomebinding sequences. Although the genome of M. vannielii is 69 mol% A+T, there is a very strong preference in the mcrA, mcrB, and mcrG genes for the codon with a C in the wobble position in the codon pairs AA(U) (C) (asparagine), GA(U) (C) (aspartic acid), CA(U) (C) (histidine), AU(U) (C) (isoleucine), UU(U) (C) (phenylalanine), and UA(U) (C) (tyrosine). The mcrC and mcrD genes do not show this codon preference and frequently have U or A in the wobble position. As the codon pairs listed above are likely to be translated by the same tRNA with a G in the first anticodon position, the presence of C in the wobble position might ensure maximum efficiency of translation of transcripts of these very highly expressed genes.

Journal Article↗