Restoration of enzyme activity by recessive missense suppressors in the fungus Coprinus.

Summary The acu-1 locus in Coprinus is the structural gene for acetyl-CoA synthetase. Five suppressor gene mutations, which suppress the acu-1,34 missense allele, were induced by mutagen treatment. All five suppressors were shown to have properties expected for tRNA structural gene mutations: they are recessive, they show a gene dosage effect in any doubly heterozygous combination of two sup ⁺ mutations and they are allele specific in action.Crosses between suppressed mutants established that at least four suppressor loci were represented. Doubly suppressed mutants derived from these crosses were used to show that the gene dosage effect is maintained when two sup ⁺ mutations are in cis as well as trans combinations in the two nuclei of the basidiomycete dikaryon.Extracts of the unsuppressed acu-1.34 mutant contained less than 2% of wild type acetyl-CoA synthetase activity whereas extracts of four of the five suppressor strains showed activities ranging from 28 to 37% of wild type. Only a slight increase in activity was detected in the fifth suppressor strain but this was associated with a temperature sensitive sup ⁺ phenotype. All five sup ⁺ mutations restored the ability of the acu-1.34 mutant to induce isocitrate lyase, an enzyme which, under the conditions of growth used, can only be induced when acetyl-CoA synthetase activity is present. Thus all five suppressors act to restore normal acu-1 protein function.     

Acetate-nonutilizing mutants of Neurospora crassa: acu-6, the structural gene for PEP carboxykinase and inter-allelic complementation at the acu-6 locus

Summary Revertants of an acu-6 mutant of Neurospora crassa have been isolated. One revertant, which showed temperature-sensitive growth on acetate (Fig. 2), was found to possess an abnormally thermolabile PEP carboxykinase (Fig. 3). The temperature-sensitive property mapped at, or extremely close to, the site of the original mutation, confirming that acu-6 is the structural gene for PEP carboxykinase.A group of acu-6 mutants were examined by polyacrylamide gel electrophoresis for the presence of a protein migrating in the same position as PEP carboxykinase. Two of the seven mutants examined were found to possess such protein and both of these show inter-allelic complementation. When grown on acetate the complementing heterokaryons showed about 5% of the wild type level of PEP carboxykinase activity. This activity was more thermolabile than that in wild type (Fig. 6) and the heterokaryons showed temperature-sensitive growth on acetate (Fig. 5).     

Gene cloning and transformation in the basidiomycete fungus Coprinus cinereus: Isolation and expression of the isocitrate lyase gene (acu-7)

Summary The cloned isocitrate lyase structural gene of Aspergillus nidulans (acuD) was shown to hybridize under reduced stringency conditions to unique sequences in genomic DNA digests of the basidiomycete fungus Coprinus cinereus. A gene library of C. cinereus was constructed in the lambda replacement vector L47 and screened for sequences hybridizing to the A. nidulans gene. A recombinant phage was isolated which contained the hybridizing sequence on a 5.6-kb BamHI fragment. This fragment was subcloned into pUC13 to give plasmid pHIONA1 and shown to contain a functional C. cinereus isocitrate lyase gene (acu-7) by transformation of an acu-7 mutant. Direct selection for Acu⁺ transformants was not possible because of the toxicity of the acetate selection medium. Acu⁺ transformants were obtained as cotransformants by transforming an acu-7 trp-1 double mutant, having mutations in both the isocitrate lyase and tryptophan synthetase structural genes, with a plasmid containing the trp-1 gene and either pHIONA1 or the original lambda clone. Up to 47.5% of the selected Trp⁺ transformants were cotransformed to Acu⁺. A physical analysis of 40 Acu⁺ transformants showed that the acu-7 gene had integrated at non-homologous and often multiple sites in the genome. Meiotic stability of the integrated gene was demonstrated by genetic crosses.     

Complementation of anAspergillus nidulans mutation by a gene from the basidiomyceteCoprinus cinereus

TheCoprinus cinereus acu-7 gene, encoding isocitrate lyase, has been cotransformed into strains ofAspergillus nidulans carrying anacuD mutation in the corresponding structural gene. Transformants with high copy numbers of integratedacu-7 sequences were able to grow on acetate as the sole carbon source, indicating complementation of theacuD mutation. Northern blot analysis showed that theC. cinereus gene was transcribed constitutively and not regulated normally by acetate.     

Genetic interaction between the Ras-CAMP pathway and the Dis2s1/Glc7 protein phosphatase in Saccharomyces cerevisiae

The Saccharomyces cerevisiae DIS2S1/GLC7 gene encodes a type 1 protein phosphatase indispensable for cell proliferation. We found that introduction of a multicopy DIS2S1 plasmid impaired growth of cells with reduced activity of the cAMP-dependent protein kinase. In order to understand further the interaction between the two enzymes, a temperature-sensitive mutation in the DIS2S1 gene was isolated. The mutant accumulated less glycogen than wild type at the permissive temperature, indicating that activity of the Dis2s1 protein phosphatase is attenuated by the mutation. Furthermore, the dis2s1 ^ts mutation was shown to be suppressed by a multicopy plasmid harboring PDE2, a gene for cAMP phosphodiesterase. These results indicate that the Ras-cAMP pathway interacts genetically with the DIS2S1/GLC7 gene.     

Major factors affecting isocitrate lyase activity in <Emphasis Type="Italic">Rhodobacter capsulatus</Emphasis> B10 under phototrophic conditions

External factors affecting the activity of isocitrate lyase (ICL) in Rhodobacter capsulatus B10 grown under controlled photoheterotrophic anaerobic conditions were investigated. The activity of this enzyme was found to depend on the history of the inoculum and on the growth phase on acetate medium. Intracellular degradation of ICL under unfavorable conditions was shown. However, transition of the growing culture from acetate to lactate did not result in active degradation of the enzyme. When transferred to acetate, Rba. capsulatus could grow without the lag phase and did not exhibit ICL activity, suggesting another anaplerotic pathway in Rba. capsulatus cells. Since emergence of the ICL activity in the cells grown on acetate results in an increase in its growth rate, the glyoxylate bypass plays an important role in acetate metabolism of Rba. Capsulatus.     

Acetate-nonutilizing Mutants of Neurospora crassa II. Biochemical Deficiencies and the Roles of Certain Enzymes

The levels of Krebs cycle, glyoxylate cycle, and certain other enzymes were measured in a wild-type strain and in seven groups of acetate-nonutilizing (acu) mutants of Neurospora crassa, both after growth on a medium containing sucrose and after a subsequent 6-hr incubation in a similar medium, containing acetate as the sole source of carbon. In the wild strain, incubation in acetate medium caused a rise in the levels of isocitrate lyase, malate synthase, phosphoenolpyruvate carboxykinase, acetyl-coenzyme A synthetase, nicotinamide adenine dinucleotide phosphate-linked isocitrate dehydrogenase, citrate synthase, and fumarate hydratase. Isocitrate lyase activity was absent in acu-3 mutants; acu-5 mutants lacked acetyl-coenzyme A synthetase activity; and no oxoglutarate dehydrogenase activity (or only low levels) could be detected in acu-2 and acu-7 mutants. In acu-6 mutants, phosphoenolpyruvate carboxykinase activity was either very low or absent. No specific biochemical deficiencies could be attributed to the acu-1 and acu-4 mutations. The role of several of these enzymes during growth on acetate is discussed.     

Gel mobility shift scanning of the acetate-inducible promoters fromNeurospora crassa reveals a common co-inducible DNA-binding protein

The promoter regions of four acetate-inducible genes ofNeurospora crassa, acu-3, acu-5, acu-8 andacu-9, have been sequenced. Using a scanning gel mobility shift assay particular DNA regions in each promoter have been shown specifically to bind partially purified protein extracted from acetate-induced mycelia. The protein-binding regions so defined have common sequence motifs, elements of which are similar to those required for acetate induction inAspergillus nidulans.     

Genetic interaction between the Ras-CAMP pathway and the Dis2s1/Glc7 protein phosphatase in Saccharomyces cerevisiae

The Saccharomyces cerevisiae DIS2S1/GLC7 gene encodes a type 1 protein phosphatase indispensable for cell proliferation. We found that introduction of a multicopy DIS2S1 plasmid impaired growth of cells with reduced activity of the cAMP-dependent protein kinase. In order to understand further the interaction between the two enzymes, a temperature-sensitive mutation in the DIS2S1 gene was isolated. The mutant accumulated less glycogen than wild type at the permissive temperature, indicating that activity of the Dis2s1 protein phosphatase is attenuated by the mutation. Furthermore, the dis2s1 ^ts mutation was shown to be suppressed by a multicopy plasmid harboring PDE2, a gene for cAMP phosphodiesterase. These results indicate that the Ras-cAMP pathway interacts genetically with the DIS2S1/GLC7 gene.     

Premeiotic disruption of the Neurospora crassa malate synthase gene by native and divergent DNAs

Summary Repeat-induced point mutation (RIP) has been used to generate new mutations in the previously uncharacterised gene for malate synthase in Neurospora crassa. Molecular clones carrying the am (NADP-glutamate dehydrogenase) gene and the malate synthase gene from either N. crassa or Aspergillus nidulans have been introduced into Neurospora as ectopic duplicate copies by transformation, selecting for the am function in a deletion host. A number of meiotic progeny derived from these transformants were unable to use acetate as sole carbon source, yielded no detectable malate synthase activity and demonstrated extensive cytosine methylation of their duplicated sequences. The new locus has been designated acu-9 and has been assigned to linkage group VII.     

Enzyme profiles of Thiobacillus versutus after aerobic and denitrifying growth: Regulation of isocitrate lyase

The specific activities of the tricarboxylic acid (TCA) cycle enzymes in Thiobacillus versutus were invariably lower after aerobic growth as compared to denitrifying growth in acetate- or succinate-limited chemostat cultures. Of the glyoxylate cycle enzymes, isocitrate lyase (ICL) activity was nil during aerobic and 76 nmol·min^-1·mg^-1 protein during denitrifying growth on acetate whereas malate synthase (MS) did not change. In succinate-grown cells ICL was always near nil. The change in ICL and MS was followed after pulse additions of acetate and nitrate to an aerobic acetate-limited chemostat culture made anaerobic prior to the first pulse. ICL remained nil during denitrifying growth after the first pulse but increased to 47 and 81 nmol ·min^-1·mg^-1 protein after the second and third pulse, respectively. MS remained unaltered. The appearance of ICL was dependent upon de novo protein synthesis. During transition in a steady state culture on acetate from oxygen to nitrate as terminal electron acceptor, denitrifying growth started after 0.6 volume replacements. The resumption of growth was concomitant with an increase in TCA cycle enzyme activities. ICL was observed only after two volume replacements. During the reverse transition, ICL disappeared at a rate twice the dilution rate. SDS polyacrylamide gelectrophoresis of cell-free extracts containing ICL showed a major protein band with a R_f value identical to purified ICL and a mol·wt. of 60,000. ICL from T. versutus was inhibited by 1.5 mM itaconate but not by 10 mM phosphoenolpyruvate. Its activity was dependent upon the presence of Mg²⁺ and cysteine.Abbreviations TCA Tricarboxylic acid - ICL isocitrate lyase - MS malate synthase - FPLC fast protein liquid chromatography - maximum specific oxygen consumption rate     

Cloning of the isocitrate lyase gene (ICL1) from Yarrowia lipolytica and characterization of the deduced protein

The ICL1 gene encoding isocitrate lyase was cloned from the dimorphic fungus Yarrowia lipolytica by complementation of a mutation (acuA3) in the structural gene of isocitrate lyase of Escherichia coli. The open reading frame of ICL1 is 1668 by long and contains no introns in contrast to currently sequenced genes from other filamentous fungi. The ICL1 gene encodes a deduced protein of 555 amino acids with a molecular weight of 62 kDa, which fits the observed size of the purified monomer of isocitrate lyase from Y. lipolytica. Comparison of the protein sequence with those of known pro- and eukaryotic isocitrate lyases revealed a high degree of homology among these enzymes. The isocitrate lyase of Y. lipolytica is more similar to those from Candida tropicalis and filamentous fungi than to Sacharomyces cerevisiae. This enzyme of Y. lipolytica has the putative glyoxysomal targeting signal S-K-L at the carboxy-terminus. It contains a partial repeat which is typical for eukaryotic isocitrate lyases but which is absent from the E. coli enzyme. Surprisingly, deletion of the ICL1 gene from the genome not only inhibits the utilization of acetate, ethanol, and fatty acids, but also reduces the growth rate on glucose.     

Acetate-nonutilizing Mutants of Neurospora crassa I. Mutant Isolation, Complementation Studies, and Linkage Relationships

Sixty mutants of Neurospora crassa unable to grow on acetate as sole source of carbon, but able to utilize sucrose, were isolated. On the basis of complementation tests, they were divided into seven groups, each group representing a different gene. Six of the genes have been mapped; no two are closely linked. These loci have been designated acu-1 to acu-7. Mutations at four of these loci result in poor germination of ascospores.     

Quorum sensing is a key regulator for the antifungal and biocontrol activity of chitinase‐producing Chromobacterium sp. C61

Chromobacterium sp. strain C61 has strong biocontrol activity; however, the genetic and biochemical determinants of its plant disease suppression activity are not well understood. Here, we report the identification and characterization of two new determinants of its biocontrol activity. Transposon mutagenesis was used to identify mutants that were deficient in fungal suppression. One of these mutants had an insertion in a homologue of depD, a structural gene in the dep operon, that encodes a protein involved in non‐ribosomal peptide synthesis. In the second mutant, the insertion was in a homologue of the luxI gene, which encodes a homoserine lactone synthase. The luxI^– and depD^– mutants had no antifungal activity in vitro and a dramatically reduced capacity to suppress various plant diseases in planta. Antifungal production and biocontrol were restored by complementation of the luxI^– mutant. Other phenotypes associated with effective biological control, including motility and lytic enzyme secretion, were also affected by the luxI mutation. Biochemical analysis of ethyl acetate extracts of culture filtrates of the mutant and wild‐type strains showed that a key antifungal compound, chromobactomycin, was produced by wild‐type C61 and the complemented luxI^– mutant, but not by the luxI^– or depD^– mutant. These data suggest that multiple biocontrol‐related phenotypes are regulated by homoserine lactones in C61. Thus, quorum sensing plays an essential role in the biological control potential of diverse bacterial lineages.     

Improving the expression yield of Candida antarctica lipase B in Escherichia coli by mutagenesis

Increasing the expression yield of active Candida antarctica lipase B (CAL-B) in Escherichia coli was achieved by using a codon-optimized synthetic gene and by mutagenesis to introduce hydrophilic residues on the surface of CAL-B. Five residues (four leucines and one isoleucine) on the surface of CAL-B were selected and changed with aspartate after codon optimization. While the codon-optimized synthetic gene of CAL-B did not increase the expression yield, the mutation increased the activity of the enzyme three-fold (3.3 mg/l of culture) compared to the wild type. The mutant enzyme had similar hydrolytic activity toward hydrolysis of p-nitrophenyl acetate or p-nitrophenyl butyrate and enantioselectivity toward hydrolysis of (R, S)-1-phenylethyl acetate compared to the wild-type enzyme. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Dual autogenous regulatory role of threonine deaminase in Escherichia coli K-12.

Summary We describe the regulatory properties of two strains carrying either the ilvA624 or the ilvA625 mutations, located in the structural gene for threonine deaminase. Crude extracts of both these strains possess a threonine deaminase activity migrating on polyacrylamide gels, differently from the wild type enzyme. Growth studies demonstrate that these mutations do not cause a limitation of isoleucine biosynthesis, suggesting normal catalytic activity of deaminase.A regulatory consequence of the ilvA624 allele is a derepression of the isoleucine-valine biosynthetic enzymes, which is recessive to an ilvA ⁺ allele. The ilvA625 mutation causes a derepression which is dominant in an ilvA625/ilvA ⁺ diploid. We interpret these data assuming that threonine deaminase, previously shown to be an autogenous regulator of the ilv genes, lacks a repressor function in the ilvA624 mutant, while in the ilvA625 mutant it is a better activator than wild type threonine deaminase.The data are discussed in terms of a model requiring that threonine deaminase, or a precursor of it, is in equilibrium between two forms, one being an activator of gene expression and the other being a repressor.     

Dominant and recessive informational suppressors of a missense mutation in Coprinus

Summary Twenty-one suppressor gene mutations which suppress the met-5.1 missense mutation of Coprinus were separated into six groups (A-F) on the basis of dominance or recessiveness, linkage to the met-5 locus, comlementation in heterozygous cells and growth behaviour. The actual number of suppressor loci could not be determined because crosses between suppressed mutants were inviable. The allele specificity of group A, C, D and F suppressors was confirmed by appropriate crosses. Group B and E suppressors were not tested because of close linkage to the met-5 locus. No evidence for functional suppression of met-5 mutations was obtained thus it is likely that all the suppressors cause translational corelation of met-5.1. Suppressors in four groups (C-F) have properties expected of tRNA structural gene mutations: the group C mutation is dominant, the other mutations are recessive but do not complement in heterozygous cells. The relative efficiencies of the tRNA species involved was assessed by comparing the degree to which the different sup ⁺ mutations depressed the growth rate on methionine supplemented medium. The dominant mutation depressed growth to the greatest extent and is, therefore, the most efficient suppressor. The least efficient suppressors did not depress growth at all. When growth was compared on minimal medium it was found that the more efficient the suppressor the less well it restored growth. The mutations in groups A and B depressed growth more than the tRNA mutations but affect some other component in translation because they are recessive and complement normally. It is suggested that they may act to alter tRNA modifying enzymes.     

A mutation in Aspergillus nidulans which affects the regulation of nitrite reductase and is tightly linked to its structural gene.

Summary The selection of nis-5, a mutation which is tightly linked to the structural genes for nitrate reductase (niaD) and nitrite reductase (niiA) but which only affects nitrite reductase activities, is described. nis-5 single mutants have only 40% of the wild type activity of nitrite reductase after induction by nitrate and, for this reason, grow poorly on nitrate and nitrite. Nitrate reductase activity is not affected, and nis-5 is shown to complement with a niaD^- mutation but not with a niiA^- mutation.When grown without inducer, nis-5 strains have higher than the non-induced wild type activity of nitrite reductase. This low, constitutive activity is insensitive to repression by ammonium. These facts explain why the nis-5 mutation weakly suppresses many nirA^- and areA^r mutations for utilization of nitrite.Three of the possible explanations of this unusual phenotype are considered. Studies of nitrite reductase in cell-free extracts provided no evidence for the already unlikely possibility that nis-5 is a structural gene mutation resulting in the observed phenotype because of alteration in the catalytic activity and/or stability of the nitrite reductase.A more plausible explanation is that it defines a receptor site for either the nirA gene product and/or the areA gene product. However, no evidence for this has yet been obtained from a study of double mutants carrying nis-5 and areA or nirA mutations.A third possibility is that nis-5 creates a new, but inefficient promoter or initiator, which is not subject to the normal control systems (and therefore causes constitutive, deprepressed synthesis) but whose physical presence reduces maximal enzyme synthesis. The presence of a translocation in nis-5 strains suggests a means by which niiA could come to be under the control of another promoter/initiator.     

Involvement of IS1 in the dissociation of the r-determinant and RTF components of the plasmid R100.1

Summary Detailed mapping localized the PHO 1 mutation between the OLI 2 and OLI 4 loci on mitochondrial DNA of Saccharomyces cerevisiae.In its mitochondrially integrated form, the PHO 1-ATPase³ was difficult to identify either immunologically or by specific inhibitors like oligomycin and DCCD. Solubilization by Triton X-100 allowed unambiguuous identification of this enzyme as an authentic mitochondrial ATPase. However, Triton extraction produced a 2 to 3 fold enhancement of the PHO 1-ATPase activity which also became drastically cold-sensitive. The wild type ATPase was neither activated nor made cold-labile by solubilization, and retained full sensitivity to oligomycin and DCCD.Sucrose gradient analysis of the Triton-extracted ATPase from wild type, PHO 1 mutant and rho ^- strains showed a density difference between the solubilized PHO 1-and wild type ATPase, and similarity between solubilized PHO 1-and rho ^- ATPase (F₁).Whole cells of the PHO 1 mutant present considerably increased respiration rates.Comparison of oligomycin-sensitivity in whole cells, coupled isolated mitochondria and membrane-bound ATPase indicates a contrast between oligomycin-resistance of the ATPase and oligomycin-sensitivity of in vivo or in vitro coupling systems, which might characterize the products of this region of mitochondrial DNA.