DNA sequence, organization and regulation of the qa gene cluster of Neurospora crassa

Geever, Robert F.; Huiet, Layne; Baum, James A.; Tyler, Brett M.; Patel, Virginia B.; Rutledge, Barbara J.; Case, Mary E.; Giles, Norman H.

doi:10.1016/0022-2836(89)90438-5

Cited by 153 publications

(94 citation statements)

References 38 publications

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“…1. The seven members that were used for calculation included SuhB, bovine inositol monophosphatase (4), CysQ (which is involved in sulfate assimilation in E. coli) (25), Qut-G and Qa-X (which are hypothetical gene products from open reading frames in Aspergillus nidulans and Neurospora crassa, respectively) (8,12), bovine inositol polyphosphate 1-phosphatase (which hydrolyzes the 1-position phosphate of inositol 1,3,4-triphosphate and inositol 1,4-bisphosphate) (41), and Met22 (which is involved in salt tolerance in Saccharomyces cerevisiae) (9). Not only do these proteins share two sequence motifs (26), but the similarity is found throughout the length of the SuhB sequence (except for long insertions in inositol polyphosphate 1-phosphatase, Met22, Qut-G, and Qa-X).…”

Section: Resultsmentioning

confidence: 99%

Inositol monophosphatase activity from the Escherichia coli suhB gene product

et al. 1995

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The suhB gene is located at 55 min on the Escherichia coli chromosome and encodes a protein of 268 amino acids. Mutant alleles of suhB have been isolated as extragenic suppressors for the protein secretion mutation (secY24), the heat shock response mutation (rpoH15), and the DNA synthesis mutation (dnaB121) (K. Shiba, K. Ito, and T. Yura, J. Bacteriol. 160:696-701, 1984; R. Yano, H. Nagai, K. Shiba, and T. Yura, J. Bacteriol. 172:2124-2130, 1990; S. Chang, D. Ng, L. Baird, and C. Georgopoulos, J. Biol. Chem. 266:3654-3660, 1991). These mutant alleles of suhB cause cold-sensitive cell growth, indicating that the suhB gene is essential at low temperatures. Little work has been done, however, to elucidate the role of the product of suhB in a normal cell and the suppression mechanisms of the suhB mutations in the aforementioned mutants. The sequence similarity shared between the suhB gene product and mammalian inositol monophosphatase has prompted us to test the inositol monophosphatase activity of the suhB gene product. We report here that the purified SuhB protein showed inositol monophosphatase activity. The kinetic parameters of SuhB inositol monophosphatase (K m ‫؍‬ 0.071 mM; V max ‫؍‬ 12.3 mol/min per mg) are similar to those of mammalian inositol monophosphatase. The ssyA3 and suhB2 mutations, which were isolated as extragenic suppressors for secY24 and rpoH15, respectively, had a DNA insertion at the 5 proximal region of the suhB gene, and the amount of SuhB protein within mutant cells decreased. The possible role of suhB in E. coli is discussed.The suhB gene was first identified as the locus for the ssyA3(Cs) mutation that was isolated as an extragenic suppressor for the secY24(Ts) mutant (31). The ssyA3 mutation restored the defect in protein secretion caused by the secY24 mutation (33) and rescued the temperature-sensitive cell growth of secY24 mutant cells. The ssyA3 mutation caused cold-sensitive cell growth by itself and impaired protein synthesis was observed in the ssyA3 mutant at low temperatures (31). The cold-sensitive growth of the ssyA3 mutant was rescued by introduction of the wild-type copy of suhB, indicating that ssyA3 is a mutant allele of suhB (40). The suhB2(Cs) mutation is another allele of suhB and was isolated as an extragenic suppressor of the rpoH15(Ts) mutation. The rpoH15 mutant gene produces an altered 32 protein and causes a defect in the induction of heat shock proteins at higher temperatures (42). The suhB2(Cs) mutation rescued the temperature-sensitive cell growth of the rpoH15 mutant and partially restored heat shock induction in the mutant cell (40). A coldsensitive mutation was also mapped in the suhB locus as an extragenic suppressor for the dnaB121(Ts) mutation that inhibits replication of phage (2). Thus, mutant alleles of suhB have effects on diverse cell activities, including protein export, stress response, and DNA replication.The suhB gene encodes a protein of 268 amino acids (40), and the primary structure of its translated product shows a high level of similarity t...

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Section: Resultsmentioning

confidence: 99%

Inositol monophosphatase activity from the Escherichia coli suhB gene product

et al. 1995

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“…(1-31) [6], the Aspergillus nidulans qutG gene (QutG) [7] and the E.schrrichiu co/i suhB (SuhB) [4] and nmtA [S] genes (AmtA), and to the C-terminal peptide fragment inferred from the 3'end of an ORF upstream from the Rhizobium kguminowrutn pss gene [8] yielded homology scores of 27, 35, 43, 21 and IO s.d. units, respectively.…”

Section: Mai)p------woecmdyav1'lagqagevvrealk--------------nemmentioning

confidence: 99%

“…Homologies between IMP and the products of the Neurospora crassa qa-x [6] and Aspergillus nidulans qutG [7] genes, which are both part of a cluster of genes involved in quinic acid utilization, have been reported previously [l]. A search of the GenBank database (release 67) using the FASTA program [3] uncovered a fifth homology to an open reading frame (ORF) upstream from the pss gene of Rhizobium leguminosarum [8] which is required for exopolysaccharide (EPS) synthesis and nodulation of peas.…”

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Diverse proteins homologous to inositol monophosphatase

Neuwald¹,

York²,

Majerus³

1991

FEBS Letters

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Bovine inositol monophosphatase (IMP) and several homologous proteins were found to share two sequence motifs with bovine inositol polyphosphate I-phosphatase (IPP). These motifs may correspond to binding sites within IMP and IPP for inositol phosphates or for lithium, since both substances are bound by these proteins. This suggests that the proteins homologous to IMP, which have diverse biological roles but whose function is not clear, may act by enhancing the synthesis or degradation of phosphorylated compounds.Amino acid sequence; Inositol phosphate; Signaling pathwayWe have found several proteins homologous to the inferred amino acid sequence of bovine inositol monophosphatase (IMP) [l], an enzyme of the inositol phosphate second messenger signaling pathway 121.A search of the PIR protein database (release 28.0) using the FASTA program of Pearson and Lipman [3] yielded homologies between IMP and 2 inferred Escherichia coli proteins: the products of the suhB and amtA genes, mutations which result in enhanced synthesis of the heat shock transcription sigma factor [4], and deficiency in ammonium transport [S], respectively. Homologies between IMP and the products of the Neurospora crassa qa-x [6] and Aspergillus nidulans qutG [7] genes, which are both part of a cluster of genes involved in quinic acid utilization, have been reported previously [l]. A search of the GenBank database (release 67) using the FASTA program [3] uncovered a fifth homology to an open reading frame (ORF) upstream from the pss gene of Rhizobium leguminosarum [8] which is required for exopolysaccharide (EPS) synthesis and nodulation of peas. (Only the 3' end of the sequence is known since the 5' end of this ORF was deleted during cloning of the fragment.)

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“…As described (14,23,24), the qa cluster is composed of five structural genes and two regulatory genes, as shown in Fig. 1.…”

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confidence: 99%

“…The qa gene cluster of Neurospora crassa and the GAL gene cluster of Saccharomyces cerevisiae in carbon metabolism have served as early paradigms for eukaryotic gene regulation (13,14) and are prime candidates for taking a genomic perspective on biological circuits. Mechanisms of regulation in the qa and GAL clusters with their transcriptional activator and repressors are also shared with many other regulatory networks.…”

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confidence: 99%

An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa

Battogtokh

Asch

Case

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

100

159

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A chemical reaction network for the regulation of the quinic acid (qa) gene cluster of Neurospora crassa is proposed. An efficient Monte Carlo method for walking through the parameter space of possible chemical reaction networks is developed to identify an ensemble of deterministic kinetics models with rate constants consistent with RNA and protein profiling data. This method was successful in identifying a model ensemble fitting available RNA profiling data on the qa gene cluster. With genome sequencing projects supplying an almost complete inventory of the building blocks of life, functional genomics is now facing the challenge of ''re-assembling the pieces'' (1, 2). Time-dependent mRNA (3) and protein profiling (4), protein-protein (5-8) and protein-DNA (9) interaction mapping, and the in vitro reconstruction of reaction networks (10, 11) are providing insight into the topology and kinetics of a living cell's full biochemical and gene regulatory circuitry. For the first time, it is now possible to place a particular biological circuit like those describing carbon metabolism, transcription, cell cycle, or the biological clock in simple eukaryotes in a larger context, and to examine the coupling of these circuits (12).New tools in computational biology are needed to identify these reaction networks by using well studied subcircuits like those for carbon metabolism, cell cycle, or the biological clock as a launch point into the entire circuit of a living cell. The qa gene cluster of Neurospora crassa and the GAL gene cluster of Saccharomyces cerevisiae in carbon metabolism have served as early paradigms for eukaryotic gene regulation (13,14) and are prime candidates for taking a genomic perspective on biological circuits. Mechanisms of regulation in the qa and GAL clusters with their transcriptional activator and repressors are also shared with many other regulatory networks. Because of their relative simplicity, they also provide an opportunity to test new genomic approaches to identifying chemical reaction networks or biological circuits that underlie many fundamental biological processes (15). Three opportunities exist now for identifying and refining biological circuits: the accumulation of transcriptional profiling data (3), a growing number of approaches to modeling gene regulation (11,(15)(16)(17)(18)(19)(20)(21), and the ability to carry out the in vitro reconstruction of biological circuits with a diversity of emergent properties including bistable (10) and oscillatory activity (11).However, initially, the profiling data will be scarce and the unknown parameters plentiful. Identification of the parameters in a reaction network is further complicated by the facts that the data are noisy and that our knowledge of the underlying reaction network's topology and of its participating molecular species is incomplete, even in well studied networks like those for the -switch, lac operon, trp operon, or GAL cluster. To circumvent these difficulties, we present a statistical modeling approach called the ensemble m...

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DNA sequence, organization and regulation of the qa gene cluster of Neurospora crassa

Cited by 153 publications

References 38 publications

Inositol monophosphatase activity from the Escherichia coli suhB gene product

Inositol monophosphatase activity from the Escherichia coli suhB gene product

Diverse proteins homologous to inositol monophosphatase

An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa

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