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Rates of evolution for cytochrome c over the past one billion years were calculated from a maximum parsimony dendrogram which approximates the phylogeny of 87 lineages. Two periods of evolutionary acceleration and deceleration apparently occurred for the cytochrome c molecule. The tempo of evolutionary change indicated by this analysis was compared to the patterns of acceleration and deceleration in the ancestry of several other proteins. The synchrony of these tempos of molecular change supports the notion that rapid genetic evolution accompanied periods of major adaptive radiations. Rates of change at different time in several structural-functional areas of cytochrome c were also investigated in order to test the Darwinian hypothesis that during periods of rapid evolution, functional sites accumulate proportionately more substitutions than areas with no known functions. Rates of change in four proposed functional groupings of sites were therefore compared to rates in areas of unknown function for several different time periods. This analysis revealed a significant increase in the rate of evolution for sites associated with the regions of cytochrome c oxidase and reductase interaction during the period between the emergence of the eutherian ancestor to the emergence of the anthropoid ancestor.
J Mol Evol 1981
PMID:Evolution of cytochrome C investigated by the maximum parsimony method. 626 11

By using electron microscopy of self-annealed DNA and restriction enzyme analysis, we have compared the physical maps of two group A streptococcal plasmids associated with conventional MLS resistance (pEL1; 20 Md) and zonal lincomycin resistance (pSM10419; 15 Md). Of their monomeric molecules, about 40% and 60%, respectively, are occupied by identical non-tandem inverted repeats containing sequences specifying putative replication functions. Sequence homology also exists between their resistance determinants which are located in unique DNA. Moreover, homology between additional regions of unknown function is so extensive and restriction fragment arrangement so similar that, formally, pSM10419 can be considered a deletion variant of pEL1. The results suggest that MLS and zonal lincomycin resistance have the same biochemical basis (i.e. methylation of 23S ribosomal RNA) and differ only quantitatively in the inducible control systems.
Mol Gen Genet 1982
PMID:Sequence relationships between plasmids associated with conventional MLS resistance and zonal lincomycin resistance in Streptococcus pyogenes. 629 65

The genes coding for the H3 and H4 histones of Saccharomyces cerevisiae have been isolated by recombinant DNA cloning. The genes were detected in a bacteriophage lambda library of the yeast genome by hybridization with plasmids containing the cloned Psammechinus miliaris sea urchin histone genes (pCH7) and the cloned Drosophila histone genes (cDM500). Two non-allelic sets of the H3 and H4 genes have been isolated. Each set consists of one H3 gene and one H4 gene arranged as a divergently transcribed pair separated by an intergene spacer DNA. The histone genes were located on the cloned yeast fragments by S1 nuclease mapping, as was a gene (SMT1) of unknown function that does not code for a histone but is closely linked to one of the histone sets. Sequence homology between the two non-allelic sets is confined to the coding regions of the respective genes while the flanking DNA and intergene spacer DNA are extensively divergent. Cellular RNA homologous to the histone genes, including transcribed non-coding sequences unique to each of the four genes, was detected by S1 mapping, thus demonstrating that all four genes are transcribed in vegetative cells.
J Mol Biol 1983 Sep 25
PMID:Yeast H3 and H4 histone messenger RNAs are transcribed from two non-allelic gene sets. 631 32

We examined the transcription of the hepatitis B virus surface antigen (HBsAg) gene in COS cells transfected with simian virus 40-based recombinant plasmids. When positioned behind the simian virus 40 late promoter, three transcripts were identified which hybridized to the HBsAg gene: a 2,000-nucleotide transcript colinear with a gene, a 1,100-nucleotide transcript representing a spliced molecule in which a major portion of the sequences encoding HBsAg were deleted, and an 800-nucleotide transcript derived primarily from sequences 3' to the HBsAg gene. The splice acceptor site utilized by the 1,100-nucleotide transcript is located immediately upstream of an open reading frame of unknown function contained within the 3' nontranslated region of the HBsAg gene. The HBsAg-specific mRNA species terminate 12 to 19 base pairs 3' of the sequence UAUAAA, similar to the concensus hexanucleotide which is thought to promote polyadenylation (AAUAAA). We constructed a series of plasmids with progressive deletions from the region surrounding where these transcripts terminate. Analysis of mRNA produced by cells transfected with these plasmids indicated that the signal hexanucleotide is in itself unable to promote the efficient processing of mRNA in the absence of downstream hepatitis B virus sequences. Processing proceeds properly, however, from plasmids containing an additional 30 nucleotides 3' of this signal.
Mol Cell Biol 1983 Dec
PMID:Analysis of processing and polyadenylation signals of the hepatitis B virus surface antigen gene by using simian virus 40-hepatitis B virus chimeric plasmids. 631 92

The gene II protein of bacteriophage f1 is a site-specific endonuclease required for initiation of phage viral strand DNA synthesis. Within gene II is another gene, X, encoding a protein of unknown function identical to the C-terminal 27% of the gene II protein, and separately translated from codon 300 (AUG) of gene II. By oligonucleotide mutagenesis, we constructed phage mutants in which this codon has been changed to UAG (amber) or UUG (leucine), and propagated them on cells carrying a cloned copy of gene X on a plasmid. The amber mutant makes no gene X protein, and cannot grow in the absence of the complementing plasmid; the leucine-inserting mutant can make gene X protein, and grows normally without the plasmid. Without gene X protein, phage DNA synthesis (particularly viral strand synthesis) is impaired. We discuss this finding in the context of other known in-frame overlapping genes (particularly genes A and A* of phage phi X174), many of which are also involved in the specific initiation of DNA synthesis, and suggest applications for the mutagenic strategy we employed.
J Mol Biol 1984 Sep 15
PMID:Gene X of bacteriophage f1 is required for phage DNA synthesis. Mutagenesis of in-frame overlapping genes. 633 12

The androgen-dependence of two mRNAs from rat ventral prostate coding for a 20 000 and an 11 000 dalton translation product has been investigated using complementary DNA cloned in the bacterial plasmid PBR322. One of the cloned insert DNAs from a recombinant plasmid, C-27, arrests the in vitro translation of C2 (Peeters et al. (1980) J. Biol. Chem. 255, 7017-7023). The other cloned insert DNA arrests the translation of a glycoprotein 20 000 daltons in size, with unknown function. The quantities of mRNA coding for the 20 000 and 11 000 dalton translation product were determined by hybridization of 32P-labeled inserts to filter-bound total RNA or poly(A+)-mRNA. Castration caused a decline in both mRNAs of 250-fold over 8 days. Stimulation with androgen of 5-week castrates restored the mRNA levels to 17% of intact for the 20 000 dalton translation product and 31% of intact for the 11 000 dalton translation product. The quantity of the two mRNAs found in the lateral poly(A+)-mRNA was about 1/10 that of the ventral level and the mRNAs were not detectable in the dorsal prostate, seminal vesicle or human prostate poly(A+)-mRNA populations. RNA from the ventral prostates of animals 10-21 days old contained mature levels of complementary sequences, suggesting a form of developmental posttranscriptional regulation for synthesis of the polypeptides which are not synthesized in mature quantities at this stage of development (Heyns et al. (1978) Endocrinology 103, 1090-1095; Kistler et al. (1981) Proc. Natl. Acad. Sci. (U.S.A.) 78, 737-741).
Mol Cell Endocrinol 1983 Aug
PMID:Developmental aspects of androgen-dependent mRNA from rat ventral prostate using cloned cDNA. 635 73

The nucleotide sequence of a 1622 base-pair segment of the broad host-range IncP plasmid RK2 (identical to RP1, RP4, R18 and R68) was determined. This region includes the trfA gene, encoding a trans-acting product essential for vegetative plasmid replication. The nucleotide sequence, together with the results described in the accompanying paper by Shingler & Thomas, indicates that the trfA gene encodes two polypeptide products (of 382 and 285 amino acids) by utilizing different translational start points within a single open reading frame. The region common to both trfA polypeptides includes a sequence with homology to a number of proteins that bind to double-stranded DNA. The trfA gene is preceded by another open reading frame, encoding a polypeptide of 116 amino acids of unknown function. Both cistrons are transcribed from a promoter outside the region of sequence reported here; however, much higher levels of the short polypeptide than of either of the trfA gene products are observed. Possible mechanisms for the control of the relative levels of the products of this operon are discussed, together with features of the trfA gene that may be important for its function in the diverse gram-negative bacterial species in which RK2 can be maintained.
J Mol Biol 1984 May 25
PMID:Nucleotide sequence of the trfA gene of broad host-range plasmid RK2. 637 58

The HSP90 gene of the yeast Saccharomyces cerevisiae encodes a heat shock-inducible protein with an Mr of 90,000 (hsp90) and unknown function. We fused DNA fragments of a known sequence (namely, either end of a 1.4-kilobase EcoRI fragment which contains the S. cerevisiae TRP1 gene) to an EcoRI site within the coding sequence of the HSP90 gene. When these fusions are introduced into S. cerevisiae they direct the synthesis of unique truncated hsp90 proteins. By determining the size and charge of these proteins we were able to deduce the translational reading frame at the (EcoRI) fusion site. This information allowed us to design and construct a well-defined in-frame fusion between the S. cerevisiae HSP90 gene and the Escherichia coli lacZ gene. When this fused gene is introduced into S. cerevisiae on a multicopy plasmid vector, it directs the heat shock-inducible synthesis of a fused protein, which is an enzymatically active beta-galactosidase. Thus, for the first time, it is possible to quantitate the heat shock response in a eucaryotic organism with a simple enzyme assay.
Mol Cell Biol 1983 Sep
PMID:Heat shock-regulated production of Escherichia coli beta-galactosidase in Saccharomyces cerevisiae. 641 4

Gamma-carboxyglutamic acid is an amino acid with a dicarboxylic acid side chain. This amino acid, with unique metal binding properties, confers metal binding character to the proteins into which it is incorporated. This amino acid has been discovered in blood coagulation proteins (prothrombin, Factor X, Factor IX, and Factor VII), plasma proteins of unknown function (Protein C, Protein S, and Protein Z), and proteins from calcified tissue (osteocalcin and bone-Gla protein). It has also been observed in renal calculi, atherosclerotic plaque, and the egg chorioallantoic membrane, among other tissues. Gamma-carboxyglutamic acid is synthesized by the post-translational modification of glutamic acid residues. This reaction, catalyzed by a hepatic carboxylase, requires reduced vitamin K, oxygen, and carbon dioxide. The function of gamma-carboxyglutamic acid is uncertain. In prothrombin gamma-carboxyglutamic acid residues bound to metal ions participate as an intramolecular non-covalent bridge to maintain protein conformation. Additionally, these amino acids participate in the calcium-dependent molecular assembly of proteins on membrane surfaces through intermolecular bridges involving gamma-carboxyglutamic acid and metal ions.
Mol Cell Biochem 1981 Sep 25
PMID:Gamma-carboxyglutamic acid. 645 61

Two methods have been used to identify the protein products of the Escherichia coli K-12 ilv region at 84 min and the flanking rrnC (counterclockwise) and rho (clockwise) loci. First, a set of lambda dilv specialized transducing phages, including some phages that carry rho and others that carry part of rrnC, was used to infect UV irradiated cells. The proteins produced by the infecting lambda dilv phage were selectively labelled with radioactivity amino acids and identified by SDS gel electrophoresis and autoradiography. Second, restriction enzyme fragments were cloned from the lambda dilv phage into pBR322 and the plasmid specific gene products produced in maxicells were similarly identified by SDS gel electrophoresis and autoradiography. The proteins produced were correlated with specific genes and restriction enzyme fragments present in the lambda dilv phage and the pBR322 derivatives. Several ilv gene products that have previously been refractory to protein purification attempts have been identified for the first time by this technique. The presence of mutations at the ilvO site is shown to activate the cryptic ilvG gene and to result in the production of a 62,000 dalton protein. A 15,000 dalton protein of unknown function is synthesized from a DNA segment between ilv and rrnC. The rho gene was cloned from lambda dilv phage into pBR322 and shown to be dominant to a rho mutation on the host chromosome. The rho gene product and four additional proteins coded by genes near or between rho and ilv have been detected.
Mol Gen Genet 1981
PMID:Identification of the protein products of the rrnC, ilv, rho region of the Escherichia coli K-12 chromosome. 646 Sep 9


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