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Imanaka T. Application of recombinant DNA technology to the production of useful biomaterials. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 33:1-27. [PMID: 2944355 DOI: 10.1007/bfb0002451] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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2
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Young JL, Jarai G, Fu YH, Marzluf GA. Nucleotide sequence and analysis of NMR, a negative-acting regulatory gene in the nitrogen circuit of Neurospora crassa. MOLECULAR & GENERAL GENETICS : MGG 1990; 222:120-8. [PMID: 2146484 DOI: 10.1007/bf00283032] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In Neurospora the expression of a set of unlinked structural genes, which allows utilization of various nitrogen-containing compounds, is controlled by the positive-acting nit-2 gene and the negative-acting nmr gene. The nucleotide sequence of the nmr gene has been determined and a long open reading frame which encodes a putative protein of 54854 daltons has been identified. A full-length cDNA clone was obtained and its the sequence revealed that the nmr gene contains no introns. The transcriptional start and stop sites have been mapped by S1 nuclease and primer extension. Site-directed mutagenesis was used to introduce stop codons at various locations in the nmr coding region. Transformation assays showed that the proteins lacking up to 16% of the carboxyl-terminus were still functional. Homology searches showed that the nmr protein is homologous to the yeast arginine regulatory gene AR-GRII.
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Affiliation(s)
- J L Young
- Department of Biochemistry, Ohio State University, Columbus 43210
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3
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Affiliation(s)
- R Bentley
- Department of Chemistry, University of Sheffield, U.K
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4
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Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V. Mol Cell Biol 1989. [PMID: 2540423 DOI: 10.1128/mcb.9.2.566] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.
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5
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Soliday CL, Dickman MB, Kolattukudy PE. Structure of the cutinase gene and detection of promoter activity in the 5'-flanking region by fungal transformation. J Bacteriol 1989; 171:1942-51. [PMID: 2703464 PMCID: PMC209843 DOI: 10.1128/jb.171.4.1942-1951.1989] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cutinase gene from Fusarium solani f. sp. pisi (Nectria hematococa) was cloned and sequenced. Sau3A fragments of genomic DNA from the fungus were cloned in a lambda Charon 35 vector. When restriction fragments generated from the inserts were screened with 5' and 3' probes from cutinase cDNA, a 5.5-kilobase SstI fragment hybridized with both probes, suggesting the presence of the entire cutinase gene. A 2,818-base pair segment was sequenced, revealing a 690-nucleotide open reading frame that was identical to that found in the cutinase cDNA with a single 51-base pair intron. Transformation vectors were constructed containing a promoterless gene for hygromycin resistance, which was translationally fused to flanking sequences of the cutinase gene. When protoplasts and mycelia were transformed with these vectors, hygromycin-resistant transformants were obtained. Successful transformation was assessed by Southern blot analysis by using radiolabeled probes for the hygromycin resistance gene and the putative promoter. The results of Southern blot analysis indicated that the plasmid had integrated into the Fusarium genome and that the antibiotic resistance was a manifestation of the promoter activity of the cutinase flanking sequences. Transformation of Colletotrichum capsici with the same construct confirmed the promoter activity of the flanking region and the integration of the foreign DNA. Transformation and deletion analysis showed that promoter activity resided within the 360 nucleotides immediately 5' to the cutinase initiation codon.
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Affiliation(s)
- C L Soliday
- Ohio State Biotechnology Center, Ohio State University, Columbus, 43210
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6
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Sachs MS, Bertrand H, Metzenberg RL, RajBhandary UL. Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V. Mol Cell Biol 1989; 9:566-77. [PMID: 2540423 PMCID: PMC362633 DOI: 10.1128/mcb.9.2.566-577.1989] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.
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Affiliation(s)
- M S Sachs
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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7
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McNally MT, Free SJ. Isolation and characterization of a Neurospora glucose-repressible gene. Curr Genet 1988; 14:545-51. [PMID: 2977301 DOI: 10.1007/bf00434079] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Using differential hybridization, the cDNA copy of a Neurospora gene coding for an abundant glucose-repressible mRNA (grg-1) has been isolated. The cDNA was used to clone the genomic copy, and both were sequenced. The cDNA is nearly full length and contains putative translational start and termination codons. Conceptual translation indicates that grg-1 mRNA could direct the synthesis of a 7,000 molecular weight polypeptide. The genomic clone, contained in an 1,888 bp PvuII fragment, encompasses the entire cDNA as well as 838 bp of 5' and 369 bp of 3' flanking sequence. Comparison of the cDNA and genomic clones revealed the presence of two short introns in potential protein-coding sequences. grg-1 message levels were found to increase within minutes following the onset of glucose deprivation and rise 50 fold during the first 90 min of derepression.
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Affiliation(s)
- M T McNally
- Department of Biological Sciences, State University of New York, Buffalo 14260
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8
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Aaronson LR, Hager KM, Davenport JW, Mandala SM, Chang A, Speicher DW, Slayman CW. Biosynthesis of the plasma membrane H+-ATPase of Neurospora crassa. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68255-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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9
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Anton IA, Coggins JR. Sequencing and overexpression of the Escherichia coli aroE gene encoding shikimate dehydrogenase. Biochem J 1988; 249:319-26. [PMID: 3277621 PMCID: PMC1148705 DOI: 10.1042/bj2490319] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The Escherichia coli aroE gene encoding shikimate dehydrogenase was sequenced. The deduced amino acid sequence was confirmed by N-terminal amino acid sequencing and amino acid analysis of the overproduced protein. The complete polypeptide chain has 272 amino acid residues and has a calculated Mr of 29,380. E. coli shikimate dehydrogenase is homologous to the shikimate dehydrogenase domain of the fungal arom multifunctional enzymes and to the catabolic quinate dehydrogenase of Neurospora crassa.
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Affiliation(s)
- I A Anton
- Department of Biochemistry, University of Glasgow, Scotland, U.K
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10
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Abstract
We investigated the functional organization of the Aspergillus nidulans trpC promoter by the sequential removal of sequences upstream of the major trpC mRNA cap site (+1). DNA fragments containing promoter mutations were fused to the Escherichia coli lacZ gene, and a novel method was used to select for integration of the fusion gene at the Aspergillus argB locus. beta-Galactosidase assays and S1 nuclease protection experiments demonstrated that the promoter mutations affected gene expression in three ways: (i) 5' deletions up to -82 resulted in variable increases in beta-galactosidase activity, depending on the growth conditions; (ii) a deletion from -67 to -11 did not alter the level of beta-galactosidase activity, but did give rise to mRNAs with aberrant 5' ends; and (iii) a 5' deletion with an endpoint at -11 and an internal deletion from -142 to -11 abolished gene expression. These results indicate that sequences upstream of -82 reduce transcription of the trpC gene and that distinct DNA sequence elements are required for expression versus correct initiation of transcription of the trpC gene. The sequences essential for trpC expression do not include the common eucaryotic promoter elements CCAAT and TATAAA. To our knowledge, this is the first functional analysis of a promoter from a fungus other than Saccharomyces cerevisiae.
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11
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Kleene R, Pfanner N, Pfaller R, Link TA, Sebald W, Neupert W, Tropschug M. Mitochondrial porin of Neurospora crassa: cDNA cloning, in vitro expression and import into mitochondria. EMBO J 1987; 6:2627-33. [PMID: 2960519 PMCID: PMC553683 DOI: 10.1002/j.1460-2075.1987.tb02553.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
cDNA encoding porin of Neurospora crassa, the major protein component of the outer mitochondrial membrane, was isolated and the nucleotide sequence was determined. The deduced protein sequence consists of 283 amino acids (29,979 daltons) and shows sequence homology of around 43% to yeast porin; however, no significant homology to bacterial porins was apparent. According to secondary structure predictions, mitochondrial porin consists mainly of membrane-spanning sided beta-sheets. Porin was efficiently synthesized in vitro from the cDNA; this allowed us to study in detail its import into mitochondria. Thereby, three characteristics of import were defined: (i) import depended on the presence of nucleoside triphosphates; (ii) involvement of a proteinaceous receptor-like component on the surface of the mitochondria was demonstrated; (iii) insertion into the outer membrane was resolved into at least two distinct steps: specific binding to high-affinity sites and subsequent assembly to the mature form.
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Affiliation(s)
- R Kleene
- Institut für Physiologische Chemie, Universität München, FRG
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12
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Duncan K, Edwards RM, Coggins JR. The pentafunctional arom enzyme of Saccharomyces cerevisiae is a mosaic of monofunctional domains. Biochem J 1987; 246:375-86. [PMID: 2825635 PMCID: PMC1148286 DOI: 10.1042/bj2460375] [Citation(s) in RCA: 109] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nucleotide sequence of the Saccharomyces cerevisiae ARO1 gene which encodes the arom multifunctional enzyme has been determined. The protein sequence deduced for the pentafunctional arom polypeptide is 1588 amino acids in length and has a calculated Mr of 174555. Functional regions within the polypeptide chain have been identified by comparison with the sequences of the five monofunctional Escherichia coli enzymes whose activities correspond with those of the arom multifunctional enzyme. The observed homologies demonstrate that the arom polypeptide is a mosaic of functional domains and are consistent with the hypothesis that the ARO1 gene evolved by the linking of ancestral E. coli-like genes.
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Affiliation(s)
- K Duncan
- Department of Biochemistry, University of Glasgow, U.K
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13
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Abstract
We investigated the functional organization of the Aspergillus nidulans trpC promoter by the sequential removal of sequences upstream of the major trpC mRNA cap site (+1). DNA fragments containing promoter mutations were fused to the Escherichia coli lacZ gene, and a novel method was used to select for integration of the fusion gene at the Aspergillus argB locus. beta-Galactosidase assays and S1 nuclease protection experiments demonstrated that the promoter mutations affected gene expression in three ways: (i) 5' deletions up to -82 resulted in variable increases in beta-galactosidase activity, depending on the growth conditions; (ii) a deletion from -67 to -11 did not alter the level of beta-galactosidase activity, but did give rise to mRNAs with aberrant 5' ends; and (iii) a 5' deletion with an endpoint at -11 and an internal deletion from -142 to -11 abolished gene expression. These results indicate that sequences upstream of -82 reduce transcription of the trpC gene and that distinct DNA sequence elements are required for expression versus correct initiation of transcription of the trpC gene. The sequences essential for trpC expression do not include the common eucaryotic promoter elements CCAAT and TATAAA. To our knowledge, this is the first functional analysis of a promoter from a fungus other than Saccharomyces cerevisiae.
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14
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Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain. Mol Cell Biol 1987. [PMID: 2951591 DOI: 10.1128/mcb.7.3.1256] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The qa-1F regulatory gene of Neurospora crassa encodes an activator protein required for quinic acid induction of transcription in the qa gene cluster. This activator protein was expressed in insect cell culture with a baculovirus expression vector. The activator binds to 13 sites in the gene cluster that are characterized by a conserved 16-base-pair sequence of partial dyad symmetry. One site is located between the divergently transcribed qa-1F and qa-1S regulatory genes, corroborating prior evidence that qa-1F is autoregulated and controls expression of the qa-1S repressor. Multiple upstream sites located at variable positions 5' to the qa structural genes appear to allow for greater transcriptional control by qa-1F. Full-length and truncated activator peptides were synthesized in vitro, and the DNA-binding domain was localized to the first 183 amino acids. A 28-amino acid sequence within this region shows striking homology to N-terminal sequences from other lower-eucaryotic activator proteins. A qa-1F(Ts) mutation is located within this putative DNA-binding domain.
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15
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Römisch J, Tropschug M, Sebald W, Weiss H. The primary structure of cytochrome c1 from Neurospora crassa. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 164:111-5. [PMID: 3030747 DOI: 10.1111/j.1432-1033.1987.tb11000.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The primary structure of the cytochrome c1 subunit of ubiquinol-cytochrome-c reductase from mitochondria of Neurospora crassa was determined by sequencing the cDNA of a bank cloned in Escherichia coli. From the coding region the sequence of 332 amino acids, corresponding to the molecular mass of 36,496 Da, was derived for the precursor protein. The mature protein, the N terminus of which was previously sequenced [Tsugita et al. (1979) in Cytochrome oxidase (King, T. E. et al., eds) pp. 67-77, Elsevier, New York], consists of 262 amino acids and has the molecular mass of 29,908 Da including the heme. The sequence contains an N-terminal hydrophilic part of 211 residues, which carries the heme, a hydrophobic stretch of 15 residues, which is assumed to anchor the protein to the membrane, and a C-terminal hydrophilic part of 36 residues. The N-terminal presequence of 70 amino acids contains 9 positive charges but only 1 negative charge and is characterized by a stretch of 20 uncharged residues.
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Baum JA, Geever R, Giles NH. Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain. Mol Cell Biol 1987; 7:1256-66. [PMID: 2951591 PMCID: PMC365200 DOI: 10.1128/mcb.7.3.1256-1266.1987] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The qa-1F regulatory gene of Neurospora crassa encodes an activator protein required for quinic acid induction of transcription in the qa gene cluster. This activator protein was expressed in insect cell culture with a baculovirus expression vector. The activator binds to 13 sites in the gene cluster that are characterized by a conserved 16-base-pair sequence of partial dyad symmetry. One site is located between the divergently transcribed qa-1F and qa-1S regulatory genes, corroborating prior evidence that qa-1F is autoregulated and controls expression of the qa-1S repressor. Multiple upstream sites located at variable positions 5' to the qa structural genes appear to allow for greater transcriptional control by qa-1F. Full-length and truncated activator peptides were synthesized in vitro, and the DNA-binding domain was localized to the first 183 amino acids. A 28-amino acid sequence within this region shows striking homology to N-terminal sequences from other lower-eucaryotic activator proteins. A qa-1F(Ts) mutation is located within this putative DNA-binding domain.
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17
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Abstract
Recombinant DNA technology enables the creation of well-defined alterations in the genetic material of an organism. Methods to manipulate recombinant DNA in the filamentous fungi (a group of microorganisms that includes species of academic as well as commercial interest) have recently been developed. This has been the result of adaptation of procedures successfully employed in the manipulation of other microorganisms. There are a number of similarities in the behavior of recombinant DNA in different fungi, but a number of differences have also been observed between the filamentous and the nonfilamentous fungi. Such differences include the ability to identify DNA replication origins and the host range of expression of fungal genes.
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Affiliation(s)
- D J Ballance
- Department of Microbiology, University of Bristol, U.K
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Da Silva AJ, Whittington H, Clements J, Roberts C, Hawkins AR. Sequence analysis and transformation by the catabolic 3-dehydroquinase (QUTE) gene from Aspergillus nidulans. Biochem J 1986; 240:481-8. [PMID: 2949740 PMCID: PMC1147441 DOI: 10.1042/bj2400481] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The induction of catabolic 3-dehydroquinase by quinic acid in Aspergillus nidulans has been shown to involve transcriptional control and yields a single major 0.8 kb mRNA. The nucleotide sequence of the catabolic 3-dehydroquinase QUTE gene has been determined and contains a single uninterrupted open reading frame of 462 bases encoding a 16,505 Da protein of 153 residues. Comparison with the corresponding QA2 gene of Neurospora crassa reveals the absence of 75 nucleotides encoding 25 amino acids from the centre of the QUTE gene of A. nidulans and the presence of 21 additional nucleotides at its 3' end. There is no nucleotide or amino acid homology between these two elements. A 16 bp inverted repeat (5' GGCAGAGCGTTCTGCC) shows similarity to such repeats found in other fungal promoters. The functional integrity of the QUTE gene was demonstrated by the transformation of a qutE mutant strain which regains growth on quinic acid as sole carbon source. Four of the twelve transformed strains examined contained vector sequences integrated at the qutE locus, and these strains all exhibited normal regulation of 3-dehydroquinase even when 16 copies of the QUTE gene were present.
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20
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Addison R. Primary structure of the Neurospora plasma membrane H+-ATPase deduced from the gene sequence. Homology to Na+/K+-, Ca2+-, and K+-ATPase. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66801-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Abstract
In Neurospora crassa, the qa-1F regulatory gene positively controls transcription of all genes in the quinic acid (qa) gene cluster. qa-1F is transcribed at a low, uninduced level but is subject to strong (50-fold), autogenous regulation as well as to control by the negative regulatory gene, qa-1S, and the inducer quinic acid. Cloned qa-1F DNA sequences hybridize to two related mRNAs of 2.9 and 3.0 kilobases. When wild-type (qa-1F+) cultures are transferred to inducing conditions, qa-1F mRNA increases for 4 h, remains somewhat level, and decreases after 8 to 10 h. That this control is autogenous, i.e., that the qa-1F gene controls the synthesis of its own mRNA, is indicated by the presence of approximately the same low level of qa-1F mRNA in poly(A)+ RNA from noninducible qa-1F- mutant cultures under inducing conditions as that observed in uninduced wild-type cultures. The qa-1S gene also regulates the transcription of qa-1F, since a qa-1S- mutant, whether in noninducing or inducing conditions, contains a level of qa-1F mRNA that corresponds to the low level observed in uninduced wild-type cultures. These results corroborate the hypothesis (M. E. Case and N. H. Giles, Proc. Natl. Acad. Sci. USA 72:553-557, 1975; V. B. Patel, M. Schweizer, C. C. Dykstra, S. R. Kushner, and N. H. Giles, Proc. Natl. Acad. Sci. USA 78:5783-5787, 1981; L. Huiet, Proc. Natl. Acad. Sci. USA 81:1174-1178, 1984) that the qa-1F gene encodes an activator protein and acts positively in controlling transcription of itself and the other qa genes.
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Duncan K, Chaudhuri S, Campbell MS, Coggins JR. The overexpression and complete amino acid sequence of Escherichia coli 3-dehydroquinase. Biochem J 1986; 238:475-83. [PMID: 3541912 PMCID: PMC1147159 DOI: 10.1042/bj2380475] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The enzyme 3-dehydroquinase was purified in milligram quantities from an overproducing strain of Escherichia coli. The amino acid sequence was deduced from the nucleotide sequence of the aroD gene and confirmed by determining the amino acid composition of the overproduced enzyme and its N-terminal amino acid sequence. The complete polypeptide chain consists of 240 amino acid residues and has a calculated subunit Mr of 26,377. Transcript mapping revealed that aroD is a typical monocistronic gene.
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23
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Huiet L, Giles NH. The qa repressor gene of Neurospora crassa: wild-type and mutant nucleotide sequences. Proc Natl Acad Sci U S A 1986; 83:3381-5. [PMID: 3010294 PMCID: PMC323517 DOI: 10.1073/pnas.83.10.3381] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The qa-1S gene, one of two regulatory genes in the qa gene cluster of Neurospora crassa, encodes the qa repressor. The qa-1S gene together with the qa-1F gene, which encodes the qa activator protein, control the expression of all seven qa genes, including those encoding the inducible enzymes responsible for the utilization of quinic acid as a carbon source. The nucleotide sequence of the qa-1S gene and its flanking regions has been determined. The deduced coding sequence for the qa-1S protein encodes 918 amino acids with a calculated molecular weight of 100,650 and is interrupted by a single 66-base-pair intervening sequence. Both constitutive and noninducible mutants occur in the qa-1S gene and two different mutations of each type have been cloned and sequenced. All four mutations occur within the predicted coding region of the qa-1S gene. This result strongly supports the hypothesis that the qa-1S gene encodes a repressor. All four mutations are located within codons for the last 300 amino acids of the qa-1S protein. The mutations in three of the mutants involve amino acid substitutions, while the fourth mutant, which has a constitutive phenotype, contains a frameshift mutation. The two constitutive mutations occur in the most distal region of the gene, possibly implicating the COOH-terminal region of the qa repressor in binding to its target. The two noninducible mutations occur in a region proximal to the constitutive mutations, possibly implicating this region of the qa repressor in binding the inducer.
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24
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Beltzer JP, Chang LF, Hinkkanen AE, Kohlhaw GB. Structure of yeast LEU4. The 5' flanking region contains features that predict two modes of control and two productive translation starts. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)89228-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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25
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Abstract
In Neurospora crassa, the qa-1F regulatory gene positively controls transcription of all genes in the quinic acid (qa) gene cluster. qa-1F is transcribed at a low, uninduced level but is subject to strong (50-fold), autogenous regulation as well as to control by the negative regulatory gene, qa-1S, and the inducer quinic acid. Cloned qa-1F DNA sequences hybridize to two related mRNAs of 2.9 and 3.0 kilobases. When wild-type (qa-1F+) cultures are transferred to inducing conditions, qa-1F mRNA increases for 4 h, remains somewhat level, and decreases after 8 to 10 h. That this control is autogenous, i.e., that the qa-1F gene controls the synthesis of its own mRNA, is indicated by the presence of approximately the same low level of qa-1F mRNA in poly(A)+ RNA from noninducible qa-1F- mutant cultures under inducing conditions as that observed in uninduced wild-type cultures. The qa-1S gene also regulates the transcription of qa-1F, since a qa-1S- mutant, whether in noninducing or inducing conditions, contains a level of qa-1F mRNA that corresponds to the low level observed in uninduced wild-type cultures. These results corroborate the hypothesis (M. E. Case and N. H. Giles, Proc. Natl. Acad. Sci. USA 72:553-557, 1975; V. B. Patel, M. Schweizer, C. C. Dykstra, S. R. Kushner, and N. H. Giles, Proc. Natl. Acad. Sci. USA 78:5783-5787, 1981; L. Huiet, Proc. Natl. Acad. Sci. USA 81:1174-1178, 1984) that the qa-1F gene encodes an activator protein and acts positively in controlling transcription of itself and the other qa genes.
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Giles NH, Case ME, Baum J, Geever R, Huiet L, Patel V, Tyler B. Gene organization and regulation in the qa (quinic acid) gene cluster of Neurospora crassa. Microbiol Rev 1985. [PMID: 2931582 DOI: 10.1128/mmbr.49.3.338-358.1985] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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Giles NH, Case ME, Baum J, Geever R, Huiet L, Patel V, Tyler B. Gene organization and regulation in the qa (quinic acid) gene cluster of Neurospora crassa. Microbiol Rev 1985; 49:338-58. [PMID: 2931582 PMCID: PMC373038 DOI: 10.1128/mr.49.3.338-358.1985] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Harnisch U, Weiss H, Sebald W. The primary structure of the iron-sulfur subunit of ubiquinol-cytochrome c reductase from Neurospora, determined by cDNA and gene sequencing. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 149:95-9. [PMID: 2986972 DOI: 10.1111/j.1432-1033.1985.tb08898.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The primary structure of the iron-sulfur subunit of ubiquinol-cytochrome c reductase from Neurospora mitochondria was determined by cDNA and genomic DNA sequencing. A first cDNA was identified from a cDNA bank cloned in Escherichia coli by hybridization selection of mRNA, cell-free protein synthesis and immunoadsorption. Further cDNA and geonomic DNA were identified by colony filter hybridization. The N-terminal sequence of the mature protein was determined by automated Edman degradation. From the sequence a molecular mass of 24749 Da results for the precursor protein and of 21556 Da for the mature protein. The presequence consists of 32 amino acids with four arginines as the only charged residues. The mature protein consists of 199 amino acids. It is characterized by a small N-terminal hydrophilic part of 29 residues, a hydrophobic stretch of 25 residues and a large C-terminal hydrophilic domain of 145 residues. The only four cysteines of the protein, which are assumed to bind the 2 Fe-2S cluster, are located in a moderate hydrophobic region of this large domain. Cysteines 3 and 4 are unusually arranged in that they are separated by only one proline. From sequence data the arrangement of the subunit in the membrane is deduced.
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Mullaney EJ, Hamer JE, Roberti KA, Yelton MM, Timberlake WE. Primary structure of the trpC gene from Aspergillus nidulans. MOLECULAR & GENERAL GENETICS : MGG 1985; 199:37-45. [PMID: 3158796 DOI: 10.1007/bf00327506] [Citation(s) in RCA: 161] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have determined the structure and complete nucleotide sequence of the trifunctional trpC gene from the Ascomycetous fungus Aspergillus nidulans. Results from RNA gel blot analyses showed that this gene encodes two size classes of polyribosomal, poly (A)+RNAs with approximate lengths of 2,400 and 2,600 nucleotides. S1 nuclease protection studies demonstrated that the distribution into the two size classes is due to selection of alternative sites for polyadenylation. The transcription units contain a single open translation reading frame of 2,304 nucleotides. The sequence of this reading frame is approximately 40% divergent from the sequence of the functionally analogous trp-1 gene from Neurospora crassa (Schechtman, M.G. and Yanofsky, C., J. Mol. Appl. Gen. 2:83-99). The predicted amino acid sequence of the A. nidulans trpC polypeptide is also 40% divergent from the predicted amino acid sequence of the N. crassa trp-1 polypeptide. The A. nidulans gene has considerably less bias in codon selection than observed for the N. crassa gene. Discrete regions of DNA homology were also found in similar positions in the 5' and 3' flanking sequences of the Aspergillus and Neurospora genes. Similar regions of homology were not observed in other Aspergillus or Neurospora genes that have been sequenced. Thus, if these evolutionarily conserved sequences act as signals for transcription initiation or polyadenylation, or are involved in gene regulation, their functions are restricted to a subset of protein coding genes in these two closely related fungi.
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Transformation of Neurospora crassa with recombinant plasmids containing the cloned glutamate dehydrogenase (am) gene: evidence for autonomous replication of the transforming plasmid. Mol Cell Biol 1985. [PMID: 6095037 DOI: 10.1128/mcb.4.10.2041] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have characterized Neurospora crassa transformants obtained with plasmid pJR2, which consists of the Neurospora glutamate dehydrogenase (am) gene cloned in pUC8 and an am132 host strain which contains a deletion encompassing the cloned fragment. Every one of 33 transformants tested showed extreme meiotic instability: less than 1 or 2% am+ progeny were obtained in initial or successive backcrosses between am+ transformants and am132 or in intercrosses between am+ progeny. Furthermore, am+ progeny from backcrosses gave a high proportion of auxotrophic (am) mitotic segregants during vegetative growth. These results indicate that the am+ character is not stably integrated into chromosomal DNA in any of the transformants tested. Nuclear DNAs from six transformants were analyzed by Southern hybridization. All six transformants contained sequences homologous to pJR2. Four showed restriction fragments expected for unmodified pJR2, but most showed additional bands. Southern blots of undigested DNAs showed that the plasmid sequences are present predominantly in high-molecular-weight form (larger than 20 kilobases). Southern blots showed that auxotrophic (am) progeny from a backcross to am132 had lost restriction bands corresponding to free plasmid but retained additional bands, apparently integrated into chromosomal DNA in a nonfunctional manner. Considered together, these results are most reasonably interpreted as follows: recombinant plasmids containing the am+ gene can replicate autonomously in N. crassa, the free plasmids are present in oligomeric or modified form or both, and plasmid sequences also integrate at multiple sites in the deletion host but in a nonfunctional manner. An alternate interpretation--that tandem repeats of the plasmid are integrated into chromosomal DNA but eliminated during meiosis--cannot be completely excluded. However, stable integration of the am gene can be obtained under a variety of other conditions, viz., using the am gene cloned in a phage lambda vector (J. A. Kinsey and J. A. Rambosek, Mol. Cell. Biol. 4:117-122, 1984), using derivatives of pJR2, or using pJR2 to transform a frameshift mutant.
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Grant DM, Lambowitz AM, Rambosek JA, Kinsey JA. Transformation of Neurospora crassa with recombinant plasmids containing the cloned glutamate dehydrogenase (am) gene: evidence for autonomous replication of the transforming plasmid. Mol Cell Biol 1984; 4:2041-51. [PMID: 6095037 PMCID: PMC369021 DOI: 10.1128/mcb.4.10.2041-2051.1984] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We have characterized Neurospora crassa transformants obtained with plasmid pJR2, which consists of the Neurospora glutamate dehydrogenase (am) gene cloned in pUC8 and an am132 host strain which contains a deletion encompassing the cloned fragment. Every one of 33 transformants tested showed extreme meiotic instability: less than 1 or 2% am+ progeny were obtained in initial or successive backcrosses between am+ transformants and am132 or in intercrosses between am+ progeny. Furthermore, am+ progeny from backcrosses gave a high proportion of auxotrophic (am) mitotic segregants during vegetative growth. These results indicate that the am+ character is not stably integrated into chromosomal DNA in any of the transformants tested. Nuclear DNAs from six transformants were analyzed by Southern hybridization. All six transformants contained sequences homologous to pJR2. Four showed restriction fragments expected for unmodified pJR2, but most showed additional bands. Southern blots of undigested DNAs showed that the plasmid sequences are present predominantly in high-molecular-weight form (larger than 20 kilobases). Southern blots showed that auxotrophic (am) progeny from a backcross to am132 had lost restriction bands corresponding to free plasmid but retained additional bands, apparently integrated into chromosomal DNA in a nonfunctional manner. Considered together, these results are most reasonably interpreted as follows: recombinant plasmids containing the am+ gene can replicate autonomously in N. crassa, the free plasmids are present in oligomeric or modified form or both, and plasmid sequences also integrate at multiple sites in the deletion host but in a nonfunctional manner. An alternate interpretation--that tandem repeats of the plasmid are integrated into chromosomal DNA but eliminated during meiosis--cannot be completely excluded. However, stable integration of the am gene can be obtained under a variety of other conditions, viz., using the am gene cloned in a phage lambda vector (J. A. Kinsey and J. A. Rambosek, Mol. Cell. Biol. 4:117-122, 1984), using derivatives of pJR2, or using pJR2 to transform a frameshift mutant.
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Huiet L, Tyler BM, Giles NH. A leucine tRNA gene adjacent to the QA gene cluster of Neurospora crassa. Nucleic Acids Res 1984; 12:5757-65. [PMID: 6235483 PMCID: PMC320028 DOI: 10.1093/nar/12.14.5757] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A single tRNALeu gene has been localized and sequenced from Neurospora crassa. It is located only 375 bp from the qa gene cluster and it is the only tRNA or 5S rRNA gene within this cloned 37 kb region. The gene encodes a tRNALeu with the anti-codon AAG, and unlike the other nuclear eukaryotic tRNALeu (AAG) gene sequenced (from C. elegans), contains an intervening sequence of 27 bp. The Neurospora tRNALeu (AAG) is 84% and 73% homologous respectively to the C. elegans and bovine tRNALeu (AAG), and is 84% homologous to a Drosophila tRNALeu (CAA). However, it is only 65% homologous to a yeast tRNALeu (CAA) and there is little conservation of intervening sequences or V-loop regions. The gene hybridizes to at least 16 other DNA fragments in the Neurospora genome. Its expression does not seem to be linked to that of the qa genes.
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Abstract
The GAL4 gene encodes a positive regulator of the galactose-inducible genes in Saccharomyces cerevisiae. Recently, GAL4 has been cloned and its 2.8-kilobase mRNA has been identified. We report here the DNA sequence of GAL4 and the mapping of the 5' and 3' ends of its transcripts. The region sequenced contains a single open reading frame, 881 codons long, which could encode a 99,350-dalton protein. The 5' ends of the GAL4 transcripts fall into two clusters. Transcripts which begin at the upstream cluster would encode the 99,350-dalton protein, whereas those starting at the downstream cluster may result in the synthesis of a shorter, 91,600-dalton protein. The putative GAL4 proteins contain an amino acid sequence near their amino termini which resembles a DNA-binding motif found in bacterial and phage repressors and gene activator proteins.
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Abstract
The GAL4 gene encodes a positive regulator of the galactose-inducible genes in Saccharomyces cerevisiae. Recently, GAL4 has been cloned and its 2.8-kilobase mRNA has been identified. We report here the DNA sequence of GAL4 and the mapping of the 5' and 3' ends of its transcripts. The region sequenced contains a single open reading frame, 881 codons long, which could encode a 99,350-dalton protein. The 5' ends of the GAL4 transcripts fall into two clusters. Transcripts which begin at the upstream cluster would encode the 99,350-dalton protein, whereas those starting at the downstream cluster may result in the synthesis of a shorter, 91,600-dalton protein. The putative GAL4 proteins contain an amino acid sequence near their amino termini which resembles a DNA-binding motif found in bacterial and phage repressors and gene activator proteins.
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Geever RF, Case ME, Tyler BM, Buxton F, Giles NH. Point mutations and DNA rearrangements 5' to the inducible qa-2 gene of Neurospora allow activator protein-independent transcription. Proc Natl Acad Sci U S A 1983; 80:7298-302. [PMID: 6316356 PMCID: PMC390042 DOI: 10.1073/pnas.80.23.7298] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Expression of the qa-2 gene of Neurospora crassa normally requires a functional activator protein encoded by qa-1F. Twelve transcriptional mutants of the qa-2 gene have been isolated in qa-1F- strains, and these allow partial expression of qa-2 (1-45% of induced wild type) in the absence of functional activator protein. All 12 mutants have been characterized by genomic (Southern) blot hybridization and the DNAs of 5 have been cloned and sequenced. Eight mutations consist of large DNA rearrangements within a 500-base-pair region 5' to the qa-2 gene. One large rearrangement mutation, located 378 base pairs before the normal site of transcription initiation, causes exceptional levels of qa-2 transcription (45% of induced wild type) from near the normal initiation site. Two of the other four mutations cloned involve tandem duplications (68 and 84 base pairs) of the same upstream region (centered at nucleotide - 145), and two involve "point" mutations (at nucleotides -200 and -95) that closely flank the duplicated region. With one possible exception, none of the mutations appears to involve changes directly associated with RNA polymerase II binding and hence they differ from analogous mutations in comparable prokaryotic systems. The overall results suggest that at least some of the large DNA rearrangement mutations may be acting as upstream activator elements, possibly by juxtaposing enhancer-like sequences, whereas the duplications and point mutations may define a region of qa-2 regulation, for instance at the level of RNA polymerase II access.
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Buxton FP, Radford A. Cloning of the structural gene for orotidine 5'-phosphate carboxylase of Neurospora crassa by expression in Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1983; 190:403-5. [PMID: 6308396 DOI: 10.1007/bf00331067] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A Neurospora gene bank in plasmid pRK9 was used to complement pyrimidine auxotrophs in E. coli. Two plasmids were obtained that complement a pyrF mutant of E. coli. These plasmids hybridise to Neurospora DNA and transform a pyr-4 strain of Neurospora. The promoter used in expressing the orotidine 5'-monophosphate carboxylase in E. coli is within the Neurospora sequence.
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Mahler HR. The exon:intron structure of some mitochondrial genes and its relation to mitochondrial evolution. INTERNATIONAL REVIEW OF CYTOLOGY 1983; 82:1-98. [PMID: 6352548 DOI: 10.1016/s0074-7696(08)60823-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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