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NADH: ubiquinone oxidoreductase from bovine heart mitochondria. A fourth nuclear encoded subunit with a homologue encoded in chloroplast genomes.

The amino acid sequence has been determined of the precursor of a nuclear encoded 20 kDa subunit of complex I from bovine heart mitochondria. The sequence of the mature protein is related to a protein of uncertain function, hitherto known as psbG, encoded in the chloroplast genomes of higher plants. Open reading frames encoding homologues of psbG have also been detected in bacteria and in the mitochondrial genome of Paramecium tetraurelia. The chloroplast psbG gene is found between ndhC and ndhJ, which encode homologues of ND3, a hydrophobic subunit of complex I encoded in the bovine mitochondrial genome, and of the nuclear encoded 30 kDa subunit of complex I. This 20 kDa protein is the eleventh out of the forty or more subunits of bovine complex I with a chloroplast encoded homologue, and its sequence provides further support for the presence in chloroplasts of a multisubunit enzyme related to complex I that could be involved in chlororespiration. The strict conservation of three cysteines suggests that the subunit might be an iron-sulphur protein.

Amino Acid Sequence

Assembly of NADH: ubiquinone reductase (complex I) in Neurospora mitochondria. Independent pathways of nuclear-encoded and mitochondrially encoded subunits.

NADH:ubiquinone reductase, the respiratory chain complex I of mitochondria, consists of some 25 nuclear-encoded and seven mitochondrially encoded subunits, and contains as redox groups one FMN, probably one internal ubiquinone and at least four iron-sulphur clusters. We are studying the assembly of the enzyme in Neurospora crassa. The flux of radioactivity in cells that were pulse-labelled with [35S]methionine was followed through immunoprecipitable assembly intermediates into the holoenzyme. Labelled polypeptides were observed to accumulate transiently in a Mr 350,000 intermediate complex. This complex contains all mitochondrially encoded subunits of the enzyme as well as subunits encoded in the nucleus that have no homologous counterparts in a small, merely nuclear-encoded form of the NADH:ubiquinone reductase made by Neurospora crassa cells poisoned with chloramphenicol. With regard to their subunit compositions, the assembly intermediate and small NADH:ubiquinone reductase complement each other almost perfectly to give the subunit composition of the large complex I. These results suggest that two pathways exist in the assembly of complex I that independently lead to the preassembly of two major parts, which subsequently join to form the complex. One preassembled part is related to the small form of NADH:ubiquinone reductase and contributes most of the nuclear-encoded subunits, FMN, three iron-sulphur clusters and the site for the internal ubiquinone. The other part is the assembly intermediate and contributes all mitochondrially encoded subunits, one iron-sulphur cluster and the catalytic site for the substrate ubiquinone. We discuss the results with regard to the evolution of the electron pathway through complex I.

Amino Acid Sequence

Differential regulation of the transcript levels of some nuclear-encoded and mitochondrial-encoded respiratory-chain components in response to growth activation.

Biogenesis of mammalian mitochondria requires the participation of both nuclear and mitochondrial genes. In order to study the expression and coordination of these two sets of genes, serum-deprived, quiescent NIH 3T3 cells were activated by serum addition. The steady-state levels of the transcripts for two growth-response genes (the mitochondrial adenine-nucleotide translocator and non-mitochondrial beta-actin), one nuclear-encoded respiratory-chain component (F1-ATPase beta-subunit) and the mitochondrial-encoded subunit I of cytochrome oxidase decreased significantly in quiescent cells and were rapidly restored with similar kinetics after addition of serum. The transcripts for two additional nuclear-encoded mitochondrial genes (cytochrome c1 and cytochrome oxidase subunit IV) did not respond to serum deprivation or growth activation. These results imply that mitochondrial biogenesis is at least partially regulated through growth-dependent mechanisms. Furthermore, the expression of nuclear genes encoding mitochondrial respiratory-chain components does not appear to be tightly coordinated, suggesting the existence of multiple control circuits.

3T3 Cells

Multiple regulatory elements for the glpA operon encoding anaerobic glycerol-3-phosphate dehydrogenase and the glpD operon encoding aerobic glycerol-3-phosphate dehydrogenase in Escherichia coli: further characterization of respiratory control.

In Escherichia coli, sn-glycerol-3-phosphate can be oxidized by two different flavo-dehydrogenases, an anaerobic enzyme encoded by the glpACB operon and an aerobic enzyme encoded by the glpD operon. These two operons belong to the glp regulon specifying the utilization of glycerol, sn-glycerol-3-phosphate, and glycerophosphodiesters. In glpR mutant cells grown under conditions of low catabolite repression, the glpA operon is best expressed anaerobically with fumarate as the exogenous electron acceptor, whereas the glpD operon is best expressed aerobically. Increased anaerobic expression of glpA is dependent on the fnr product, a pleiotropic activator of genes involved in anaerobic respiration. In this study we found that the expression of a glpA1(Oxr) (oxygen-resistant) mutant operon, selected for increased aerobic expression, became less dependent on the FNR protein but more dependent on the cyclic AMP-catabolite gene activator protein complex mediating catabolite repression. Despite the increased aerobic expression of glpA1(Oxr), a twofold aerobic repressibility persisted. Moreover, anaerobic repression by nitrate respiration remained normal. Thus, there seems to exist a redox control apart from the FNR-mediated one. We also showed that the anaerobic repression of the glpD operon was fully relieved by mutations in either arcA (encoding a presumptive DNA recognition protein) or arcB (encoding a presumptive redox sensor protein). The arc system is known to mediate pleiotropic control of genes of aerobic function.

Anaerobiosis

Exons 1-10 of the rat LH receptor encode a high affinity hormone binding site and exon 11 encodes G-protein modulation and a potential second hormone binding site.

We have reported that the rat LH receptor is encoded by 11 exons of a single copy gene. Exons 1-10 encode the N-terminal half and exon 11 the C-terminal half. Since exon splice sites often mark structural transitions of multiexon molecules, we have attempted to define the function of the exons by generating mutant receptors with missing exons. As a first step, we have constructed two LH mutant receptors, one containing exons 1-10 (LH receptor (exon)1-10) and the other containing exon 1 and exon 11 (LH receptor(exon)1&11). These mutant receptors were functionally expressed in Cos 7A cells. The LH mutant receptor(exon)1-10, which lacks the membrane associated C-terminal half of the receptor, showed a high affinity for hCG. Surprisingly, the LH mutant receptor(exon)1&11 recognized hCG with a low affinity and stimulated G-proteins and cAMP production. The results demonstrate that exons 1-10 encode a high affinity hCG binding site and proves an important hypothesis that exon 11 encodes the site for receptor-modulation to activate G-proteins. Furthermore, the results raises an intriguing possibility of a second hormone binding site in the C-terminal half and multistep hormone binding.

Animals

Nucleotide sequence of cDNA clones encoding the beta subunit of mitochondrial ATP synthase from the green alga Chlamydomonas reinhardtii: the precursor protein encoded by the cDNA contains both an N-terminal presequence and a C-terminal extension.

cDNA and genomic clones encoding the beta subunit of mitochondrial ATP synthase from Chlamydomonas reinhardtii have been isolated using heterologous DNA probes from the photosynthetic bacterium Rhodospirillum rubrum. The protein encoded by the cDNA is 79-83% identical to corresponding proteins from higher-plant and mammalian mitochondria, and 75% identical to the R. rubrum protein. It contains both an N-terminal presequence and a unique C-terminal extension. The presequence, which is the first mitochondrial presequence determined in C. reinhardtii, is similar in structure to mitochondrial presequences from other organisms. As chloroplast presequences from C. reinhardtii also share features with mitochondrial presequences from other organisms (L.-G. Franzén et al., FEBS Lett 260 (1990) 165-168), this raises interesting questions about protein targeting to chloroplasts and mitochondria in C. reinhardtii. The possibility that the C-terminal extension is involved in targeting the protein to the mitochondrion is discussed. Southern blot analysis indicates that the protein is encoded by a single-copy gene.

Amino Acid Sequence

Mammalian mRNAs encoding protein closely related to ubiquitin-conjugating enzyme encoded by yeast DNA repair gene RAD6.

A clone of about 1 kb has been isolated from a human brain cDNA library. The clone possesses a 151 amino acid open reading frame that exhibits 72% amino acid identity with the E2 ubiquitin-conjugating enzyme encoded by the RAD6 gene of Saccharomyces cerevisiae. A 90% amino acid identity was observed in a central sequence surrounding a cysteine, which most likely contributes the sulfhydryl group involved in the formation of the ubiquitin-E2 thiolester linkage. Northern hybridization analyses have identified a poly(A)-containing mRNA of about 1 kb encoding the E2-like sequence in human CEM lymphoblastoid and HeLa cells, Novikoff rat hepatoma cells and S49 mouse leukemia cells. Southern hybridization analyses indicate the presence of a single gene encoding this sequence in both human cell lines, but of two or more related genes in the rodent cell lines.

Amino Acid Sequence

A general method for the induction and screening of antisera for cDNA-encoded polypeptides: antibodies specific for a coronavirus putative polymerase-encoding gene.

A prokaryotic vector, pGE374, containing the recA and lacZ genes, out-of-frame, was used for the expression of cDNA derived from the putative polymerase-encoding gene of the coronavirus mouse hepatitis virus strain A59 (MHV-A59). The pGE374/viral recombinant vector generates a tripartite bacterial/viral protein composed of a segment of the RecA protein at the N terminus, the coronaviral sequences in the middle, and an enzymatically active beta-galactosidase at the C terminus. Rabbits immunized with such recombinant proteins generated antibodies to the MHV-A59 portion of the tripartite protein. Because the MHV-A59 polymerase proteins have been difficult to identify during infection, we used a novel method to demonstrate the viral specificity of the antiserum. The viral cDNA was excised from the expression vector, and transferred to a pGem vector, downstream from and in-frame with a portion of the cat gene. This construct contained a bacteriophage RNA polymerase promoter that enabled the cell-free synthesis of a fusion protein that was used to verify that antibodies were generated to the expressed viral DNA. This strategy was shown to successfully result in the specific generation of antibodies to the encoded information of the viral cDNA. Furthermore, this method has general applicability in the generation and characterization of antibodies directed against proteins encoded in cDNAs.

Animals

Evidence for three genes encoding class-I alcohol dehydrogenase subunits in baboon and analysis of the 5' region of the gene encoding the ADH beta subunit.

Five alcohol dehydrogenases (ADH; alcohol: NAD+ oxidoreductase; EC 1.1.1.1) have been identified in the baboon. All are homodimers of five distinct ADH subunits, with the two class-I ADH subunits being differentially expressed in the liver (the beta-subunit) and kidney. We have hybridized restriction-enzyme-digested baboon DNA to a 30-bp probe or a 337-bp DNA fragment, to reveal the presence of three genes encoding class-I ADH subunits in the baboon genome. This result was confirmed by the amplification of three different baboon ADH (bADH) nucleotide (nt) sequences, corresponding to exon 5 in the human gene encoding ADH beta (hADHB) from baboon DNA. Two of these sequences are identical to previously isolated liver and kidney cDNA nt sequences. These results are consistent with a phylogenetic analysis of the nt sequences of class-I hADH and bADH genes. Then, using primers based on the nt sequence of hADHB, we amplified a 336-bp DNA fragment, from genomic DNA, encoding the 5' region of the bADHB gene. In a 49-bp region of overlap, the nt sequence of this DNA fragment was identical to the sequence of a cDNA fragment amplified from baboon liver mRNA, whereas there were seven differences between this DNA fragment and the sequence of a cDNA amplified from baboon kidney mRNA. We used primer extension analysis to identify three adjacent transcriptional start points (tsp) for bADHB mRNA. Initiation of transcription at the most 5' bp leaves a 72-bp untranslated region. Examination of the sequence upstream from the tsp reveals a number of conserved putative regulatory sequence elements.

Alcohol Dehydrogenase

The oac gene encoding a lipopolysaccharide O-antigen acetylase maps adjacent to the integrase-encoding gene on the genome of Shigella flexneri bacteriophage Sf6.

Lysogens of Shigella flexneri harbouring the temperate bacteriophage, Sf6, have been previously shown to undergo a serotype conversion due to O-acetylation of the O-antigen of the lipopolysaccharide. A partial physical map of the phage genome has been constructed. Analysis of the phage DNA suggests that the phage packages by a headful mechanism and that the mature DNA molecules are terminally redundant. Cloning of the PstI fragments of Sf6 enabled the region encoding the serotype conversion to be localized, showing that this was clearly phage-encoded. The gene was further localized by mutagenesis with Tn5 and the nucleotide sequence of the entire 2693-bp PstI fragment was determined. Two major open reading frames (ORFs) were found capable of encoding proteins of 44.1 and 37.2 kDa. The latter corresponds to the O-antigen acetylase and its gene has been designated oac. The oac gene is capable of converting Sh. flexneri serotypes X, Y, 1a and 4a to 3a, 3b, 1b and 4b, respectively. The Oac protein bears a high degree of homology to the NodX protein of Rhizobium leguminosarum suggesting that it, too, may be a sugar acetylase. The second ORF immediately upstream from oac corresponds to the bacteriophage Sf6 integrase responsible for chromosomal integration and is highly homologous to the integrases of Escherichia coli bacteriophages P4 and phi 80, but less closely related to those of P1, P2, P22, 186 and lambda.

Acetylesterase

Co-expression of a Saccharomyces diastaticus glucoamylase-encoding gene and a Bacillus amyloliquefaciens alpha-amylase-encoding gene in Saccharomyces cerevisiae.

A glucoamylase-encoding gene (STA2) from Saccharomyces diastaticus and an alpha-amylase-encoding gene (AMY) from Bacillus amyloliquefaciens were cloned separately into a yeast-integrating shuttle vector (YIp5), generating recombinant plasmids pSP1 and pSP2, respectively. The STA2 and AMY genes were jointly cloned into YIp5, generating plasmid pSP3. Subsequently, the dominant selectable marker APH1, encoding resistance to Geneticin G418 (GtR), was cloned into pSP3, resulting in pSP4. For enhanced expression of GtR, the APH1 gene was fused to the GAL10 promoter and terminated by the URA3 terminator, resulting in pSP5. Plasmid pSP5 was converted to a circular minichromosome (pSP6) by the addition of the ARS1 and CEN4 sequences. Laboratory strains of Saccharomyces cerevisiae transformed with plasmids pSP1 through pSP6, stably produced and secreted glucoamylase and/or alpha-amylase. Brewers' and distillers' yeast transformed with pSP6 were also capable of secreting amylolytic enzymes. Yeast transformants containing pSP1, pSP2 and pSP3 assimilated soluble starch with an efficiency of 69%, 84% and 93%, respectively. The major starch hydrolysis products produced by crude amylolytic enzymes found in the culture broths of the pSP1-, pSP2- and pSP3-containing transformants, were glucose, glucose and maltose (1:1), and glucose and maltose (3:1), respectively. These results confirmed that co-expression of the STA2 and AMY genes synergistically enhanced starch degradation.

Bacillus

The herpes simplex virus 1 protein kinase encoded by the US3 gene mediates posttranslational modification of the phosphoprotein encoded by the UL34 gene.

Earlier studies have shown that a herpes simplex virus 1 (HSV-1) open reading frame, US3, encodes a novel protein kinase and have characterized the cognate amino acid sequence which is phosphorylated by this enzyme. This report identifies an apparently essential viral phosphoprotein whose posttranslational processing involves the viral protein kinase. Analyses of viral proteins phosphorylated in the course of productive infection revealed a phosphoprotein whose mobility was viral protein kinase and serotype dependent. Thus, the corresponding HSV-1 and HSV-2 phosphoproteins differ in their electrophoretic mobilities, and the phosphoprotein specified by the HSV-1 mutant deleted in US3 (R7041) differs from that of the corresponding HSV-1 and HSV-2 proteins. Analyses of HSV-1 x HSV-2 recombinants mapped the phosphoprotein between 0.42 and 0.47 map units on the prototype HSV-1 DNA map. Within this region, the UL34 open reading frame was predicted to encode a protein of appropriate molecular weight which would also contain the consensus target site for phosphorylation by the viral protein kinase as previously defined with synthetic peptides. Replacement of the native UL34 gene with a UL34 gene tagged with a 17-amino-acid epitope from the alpha 4 protein identified this gene as encoding the phosphoprotein. Finally, mutagenesis of the predicted phosphorylation site on UL34 in the viral genome, and specifically the substitution of threonine or serine with alanine in the product of the UL34 gene, yielded phosphoproteins whose electrophoretic mobilities could not be differentiated from that of the US3- mutant. We conclude that the posttranslational processing of the UL34 gene product to its wild-type phenotype requires the participation of the viral protein kinase. While the viral protein kinase is not essential for viral replication in cells in culture, the UL34 gene product itself may not be dispensable.

Amino Acid Sequence

Thyroid hormone and dexamethasone increase the levels of a messenger ribonucleic acid for a mitochondrially encoded subunit but not for a nuclear-encoded subunit of cytochrome c oxidase.

The nuclear genome is the primary locus of activity for thyroid hormone and dexamethasone; however, one well described secondary effect of treatment with these hormones is increased mitochondrial respiratory activity. To examine the mechanism of the increase in respiration, we have treated a rat hepatoma cell line, HTC cells, with thyroid hormone and dexamethasone and measured their effects on the activity of a respiratory chain enzyme and on mitochondrial (mt) RNA and mtDNA levels. Thyroid hormone, but not dexamethasone, increased cytochrome c oxidase activity in HTC cells; the increase in activity was nearly 2-fold over control values. To determine whether this increased activity was the result of coordinate increases in expression of nuclear and cytoplasmic genes for this enzyme, we measured changes in the levels of messenger RNAs for both nuclear and mitochondrially encoded cytochrome oxidase subunits. Treatment of HTC cells with thyroid hormone and/or dexamethasone resulted in 3- to 4-fold increases in the levels of several RNAs encoded in the mt genome, including subunit II of cytochrome c oxidase. In contrast, this treatment had no effect on the messenger RNA encoding a nuclear subunit of this same enzyme. Neither of these hormones had any effect on cell number or on the level of mtDNA. Dose response and time course of thyroid hormone and dexamethasone administration on mtRNA levels were consistent with these hormones acting through their nuclear hormone receptors. Increased expression of the mt genome by alteration of transcription or RNA stability is a likely candidate for a mechanism by which these hormones can regulate mitochondrial activity.

Animals

Ubiquitin-encoding mRNA and mRNA recognized by genes encoding ubiquitin-conjugating enzymes are differentially expressed in division-synchronized cultures of Chlamydomonas reinhardtii.

Cells of Chlamydomonas reinhardtii were synchronized by a light/dark illumination cycle of 14:10 h. All cells divided within the first 2 h of the dark period, the synchronization index was calculated as 0.916. RNA was isolated every 2 h and hybridized to 32P-labeled probes encoding (i) ubiquitin from Chlamydomonas reinhardtii (UBM) and (ii) two different ubiquitin-conjugating enzymes from Saccharomyces cerevisiae (UBC2 and UBC3). Sequences with homology to yeast UBC2 and UBC3, which are required for sporulation/DNA repair and G1/S transition in yeast, respectively, were detected in C. reinhardtii. In the algae, the relative abundance of transcripts encoding ubiquitin fusion proteins and UBC2 homologues is most prominent at the end of the light phase and throughout the dark. The highest amount of a putative polyubiquitin encoding transcript was detected during the dark phase of the synchronized culture. A high amount of this transcript is also present during the 8th hour of the light phase which may imply that the transcription of polyubiquitin gene is not only restricted to stress conditions in C. reinhardtii. The relative abundance of transcripts with homology to UBC3 is most pronounced within the light period corresponding to G1 and S phases of the C. reinhardtii cell cycle.

Animals

Isolation and characterization of a gene encoding a chlorophyll a/b-binding protein from mustard and the targeting of the encoded protein to the thylakoid membrane of pea chloroplasts in vitro.

Three independent clones carrying a mustard gene coding for the chlorophyll a/b-binding protein were isolated by screening a genomic library of mustard with a heterologous cDNA probe from pea. All of them encode the same CAB gene, which, as shown by sequence analysis and comparison with published CAB sequences, belongs to the family of type I PSII CAB genes, encoding a precursor protein of 266 amino acids. Several conserved sequence motifs are observed in the 5' and 3' non-coding region of the gene. The putative transcription start site could be localized to 60 bp upstream of SA-CAB1 initiator codon by S1 mapping. Plasmids were constructed which allow in vitro transcription and translation of the whole chlorophyll a/b-binding protein and of truncated species which lack increasing portions of the C-terminus. Whereas the in vitro import into pea chloroplasts is not affected by these C-terminal deletions, targeting to the thylakoid membrane is abolished by the removal of the C-terminal helical domain. Accordingly, the 54 amino acids which contain the C-terminal membrane-spanning helix and flanking regions is an essential component of the thylakoid targeting signal.

Amino Acid Sequence

Responses against antigens encoded by the H-3 histocompatibility locus: antigens stimulating class I MHC- and class II MHC-restricted T cells are encoded by separate genes.

The purpose of this work was to study the genetic basis of histocompatibility antigens encoded by the mouse minor histocompatibility (H) locus H-3. Both class I major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL) and class II MHC-restricted helper T cells (TH) specific for antigens encoded by genes within the H-3 locus were isolated and analyzed. Typing a number of mouse strains for expression of antigens recognized by these TH and CTL suggested that there was a different strain distribution pattern of expression of the antigens recognized by TH compared with those recognized by CTL. Separation of the genes whose products stimulate TH from those whose products stimulate CTL was suggested by: (1) analysis of the strain B10.FS(92NX)/Grf that has undergone recombination within the H-3 region; (2) genetic segregation studies of (B10.UW-H-3b/Sn x C57BL/10Sn)F2 mice; and (3) F1 complementation studies in which CTL specific for products of the TH-defined gene(s) could not be detected, even in the absence of immune responses to products of the CTL-defined genes. Taken together, these data suggest that in addition to two genes (B2m and Cd-1) within the H-3 region whose products typically stimulate class I MHC-restricted CTL, there is at least one additional gene whose product selectively stimulates class II MHC-restricted TH. This new gene is located telomeric from the CTL-defined genes and between the loci we and un on chromosome 2. These data demonstrate a novel degree of complexity of the H-3 "locus" and suggest selective presentation of minor H gene products in the context of class I or class II MHC proteins.

Animals

The autocatalytic protease p29 encoded by a hypovirulence-associated virus of the chestnut blight fungus resembles the potyvirus-encoded protease HC-Pro.

Gene expression by a viral-like double-stranded RNA genetic element associated with reduced virulence (hypovirulence) of the chestnut blight fungus was recently shown to involve an autoproteolytic event which resulted in the release of an encoded protease, designated p29, from a polyprotein during translation. Mutational analysis of p29, described in this report, revealed that residues Cys-162 and His-215 are essential for autocatalytic cleavage. The results were also consistent with previous predictions that cleavage occurs between Gly-248 and Gly-249. Interestingly, p29 bears a striking resemblance to the potyvirus-encoded protease HC-Pro. Both proteases autocatalytically cleave at glycine dipeptides. In addition, there is a significant degree of similarity in the amino acid sequences flanking the essential Cys and His residues of the two proteases and in the spacing of these residues from their respective cleavage sites.

Amino Acid Sequence

Characterization of the gene encoding mouse serum amyloid P component. Comparison with genes encoding other pentraxins.

A CBA/J-strain mouse serum amyloid P component (SAP) genomic clone was isolated and analysed. The clone contains the entire SAP gene and specifies a primary transcript of 1065 nucleotide residues. This comprises a first exon of 206 nucleotide residues containing the mRNA 5'-untranslated region and sequence encoding the pre-SAP leader peptide and the first two amino acid residues of mature SAP separated by a single 110-base intron from a 749-nucleotide-residue second exon containing sequence encoding the bulk of the mature SAP and specifying the mRNA 3'-untranslated region. The overall organization is similar to that of the human SAP gene, and the coding region and intron sequences are highly conserved. The SAP RNA cap site was defined by primer extension analysis of polyadenylated acute-phase liver RNA. The 5'-region of the mouse SAP gene contains modified CAAT and TATA promoter elements preceded by a putative hepatocyte-nuclear-factor-1-recognition site; these structures are in a region that is highly homologous to the corresponding region of the human SAP gene. Comparisons of the mouse SAP gene structure and derived amino acid sequence with those of other mammalian pentraxins were made.

Acute-Phase Proteins