Identifying Mutations in Duplicated Functions in Saccharomyces cerevisiae: Recessive Mutations in Hmg-Coa Reductase Genes

The two yeast genes for 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, HMG1 and HMG2, each encode a functional isozyme. Although cells bearing null mutations in both genes are inviable, cells bearing a null mutation in either gene are viable. This paper describes a method of screening for recessive mutations in the HMG1 gene, the gene encoding the majority of HMG-CoA reductase activity in the cell. This method should be applicable to the isolation of mutations in other recovered in HMG1. These mutations exhibited intragenic complementation: one allele is in one complementation group and three alleles are in a second complementation group. Assays of HMG-CoA reductase activity indicated that the point mutations destroy most if not all of the activity encoded by HMG1. Intragenic complementation occurred with partial restoration of enzymatic activity. HMG1 was mapped to the left arm of chromosome XIII near SUP79, and HMG2 was mapped to the right arm of chromosome XII near SST2. A slight deleterious effect of a null mutation in either HMG-CoA reductase gene was detected by a co-cultivation experiment involving the wild-type strain and the two single mutants.     

Functional organization and evolution of mammalian hexokinases: mutations that caused the loss of catalytic activity in N-terminal halves of type I and type III isozymes.

Mammalian hexokinases are believed to have evolved from a 100-kDa hexokinase which itself is a product of duplication and fusion of an ancestral gene encoding a 50-kDa glucose 6-phosphate-sensitive hexokinase. Type II hexokinase has been shown to possess two distinct functional active sites, one in each half, which functionally resemble the original 100-kDa hexokinase, whereas type I and III isozymes possess only one active site in the C-terminal halves. This study was conducted to identify which mutations caused the loss of catalytic activity in the N-terminal halves of type I and III isozymes. Arg 174 and Ser 447 in type I isozyme and Asp 244 in type III isozyme are speculated to be the cause, because they reside adjacent to the "catalytic" site and corresponding residues, Gly 174, Asp 447, and Gly 231, are conserved in the N-terminal half of type II isozyme as well as all other 50-kDa units that possess catalytic activity. Mutations G174R and D447S in the N-terminal half of type II isozyme reduced specific activity by approximately 79 and 57%, respectively. Therefore, neither mutation alone can account for the inactivation of the N-terminal active site in type I isozyme. Either mutation, G174R or D447S, had moderate effects on Michaelis constants, K(m), for glucose and ATP. Mg(2+). Intriguingly, mutation D447S introduced a novel inhibition by unchelated ATP (K(i) = 68 microM ATP, competitive vs ATP. Mg(2+)) to the N-terminal active site of type II isozyme. Mutation G231D caused instability to type II hexokinase and near complete loss of catalytic activity (95%), suggesting that mutation G231D not only hinders catalysis at the N-terminal active site but also leads to structural instability in type II hexokinase.     

Comparison of the property of a novel isozyme E (formerly null mutant, O) with other isozymes of hemolymph acid phosphatase of the silkworm

1. A novel acid phosphatase isozyme E (formerly null mutant 0) was partially purified by ammonium sulfate fractionation, DEAE-Sephacel and Sephacryl S-200 column chromatography, and its properties were compared with those of other isozymes of the silkworm hemolymph. 2. The isozyme E was extremely heat labile and showed lower pH-stability than those of others. 3. Three isozymes hydrolyzed p-nitrophenyl phosphate, alpha-naphthyl phosphate, alpha-naphthyl phosphate and glucose-1-phosphate strongly. The isozyme E showed about 50% hydrolyzing activity for alpha-naphthyl phosphate as compared to those of A and B. 4. Activities of three isozymes were inhibited by tartaric acid, sodium fluoride, ammonium molybdate and potassium diphosphate. Inhibitory effects of Cu(2+) and HG(2+) were most remarkable against E isozyme.     

The membrane potential of mouse ascites-tumour cells studied with the fluorescent probe 3,3''-dipropyloxadicarbocyanine. Amplitude of the depolarization caused by amino acids.

1. The magnitude of the K+ gradient across the plasma membrane, which was in equilibrium with the membrane potential (E) of the tumour cells, was determined by the "null point" procedure of Hoffman & Laris (1974) [J. Physiol. (London) 239, 519--552] in which the fluorescence of the dye serves as an indicator of changes in the magnitude of E. 2. A mixture of oligomycin, 2,4-dinitrophenol and antimycin was used to stop the mitochondria from interfering with the fluorescence signal. Transport functions at the plasmalemma were maintained under these conditions in the presence of glucose. 3. Physiological circumstances were found in which incubation with glycine or with glucose changed the "null point" value of E within the range--20mV to--100mV. The fluorescence intensity at the "null point" was an approximately linear function of E over that range. The procedure enabled E to be inferred form the fluorescence intensity in circumstances where titration to the "null point" was not feasible. 4. The rapid depolarization caused by l-methionine or glycine was shown in this way to have a maximum amplitude of about 60mV. A mathematical model of this process was devised. 5. The electrogenic Na+ pump hyperpolarized the cells up to about --80mV when the cellular and extracellular concentrations of K+ were roughly equal. 6. The observations show that the factors generating the membrane potential represent a major source of energy available for the transport of amino acids in this system.     

Structural mutation in a major human aldehyde dehydrogenase gene results in loss of enzyme activity.

Most Caucasians have two major liver aldehyde dehydrogenase isozymes, ALDH1 and ALDH2, while approximately 50% of Orientals have only ALDH1 isozyme, missing the ALDH2 isozyme. A remarkably higher frequency of acute alcohol intoxication among Orientals than among Caucasians could be related to the absence of the ALDH2 isozyme, which has a low apparent Km for acetaldehyde. Examination of liver extracts by two-dimensional crossed immunoelectrophoresis revealed that an atypical Japanese liver, which had no ALDH2 isozyme, contained an enzymatically inactive but immunologically cross-reactive material corresponding to ALDH2, beside the active ALDH1 isozyme. Therefore, the absence of ALDH2 isozyme in atypical Orientals is not due to regulatory mutation, gene deletion, or nonsense mutation, but must be due to a structural mutation in a gene for the ALDH2 locus, resulting in synthesis of enzymatically inactive abnormal protein.     

The inheritance of rye seed peroxidases

Summary Genetic analyses were conducted on peroxidase of the embryo and endosperm of seeds of one open pollinated and six inbred lines of cultivated rye (Secale cereale L.), and one line of Secale vavilovii Grossh. The analyses of the individual parts of the S. cereale seed yield a total of 14 peroxidase isozymes. Isozymes m, a, b, c, d, e, f and g (in order from faster to slower migration) were found in the embryo plus scutellum, while isozymes 1, 2, 3, 4, 5 and 6 (also from faster to slower migration) were peculiar of the endosperm. S. vavilovii has isozymes m, c₁, d, e, f and g in its embryo plus scutellum, and isozyme 2 in the endosperm. Segregation data indicated that at least 13 different loci would be controlling the peroxidase of S. cereale. Isozymes a and b are controlled by alleles of the same locus, all the other loci have one active and dominant allele coding for one isozyme, and other null and recessive allele. The estimation of linkage relationships shows that five endosperm loci are linked, and tentative maps are shown. A possible dosage effect and the existence of controlling gene(s) for endosperm isozyme 4 is reported. All these data and the high frequency of null alleles found are discussed in relation to recent reports.     

Altered Circadian Period of Locomotor Activity in Carbonic Anhydrase II-Deficient Mice

This study finds lengthened circadian period in a congenic strain of mice homozygous for a null mutation in carbonic anhydrase isoenzyme-II gene on proximal Chromosome 3. Carbonic anhydrase II has the highest turnover rate of any constitutive enzyme. It catalyzes the reversible hydration of carbon dioxide to control intercellular acid/base balance. A strain of congenic mice has a carbonic anhydrase II null mutation within a DBA/2J inbred strain insert on a C57BL/6J inbred strain background. The locomotor activity levels and period of circadian rhythms were examined in the homozygous null mutants and their progenitors, mice heterozygous for the region around the carbonic anhydrase gene. The heterozygous mice siblings and the wild-type siblings served as the controls. During behavioral studies, male and female offspring and parents were housed singly in constant darkness. Locomotor activity was monitored using an infrared photobeam array. Mice homozygous for the carbonic anhydrase null mutation had a longer circadian period than either heterozygote or wild type littermates. Carbonic anhydrase null mutants also had low locomotor activity compared to either heterozygous or wild-type litter mates. This implies that either the physiological changes resulting from absence of carbonic anhydrase II isozyme or the presence of DBA/2J alleles around the carbonic anhydrase locus influence the circadian period and level of locomotor activity in laboratory mice.     

Altered Circadian Period of Locomotor Activity in Carbonic Anhydrase II-Deficient Mice

This study finds lengthened circadian period in a congenic strain of mice homozygous for a null mutation in carbonic anhydrase isoenzyme-II gene on proximal Chromosome 3. Carbonic anhydrase II has the highest turnover rate of any constitutive enzyme. It catalyzes the reversible hydration of carbon dioxide to control intercellular acid/base balance. A strain of congenic mice has a carbonic anhydrase II null mutation within a DBA/2J inbred strain insert on a C57BL/6J inbred strain background. The locomotor activity levels and period of circadian rhythms were examined in the homozygous null mutants and their progenitors, mice heterozygous for the region around the carbonic anhydrase gene. The heterozygous mice siblings and the wild-type siblings served as the controls. During behavioral studies, male and female offspring and parents were housed singly in constant darkness. Locomotor activity was monitored using an infrared photobeam array. Mice homozygous for the carbonic anhydrase null mutation had a longer circadian period than either heterozygote or wild type littermates. Carbonic anhydrase null mutants also had low locomotor activity compared to either heterozygous or wild-type litter mates. This implies that either the physiological changes resulting from absence of carbonic anhydrase II isozyme or the presence of DBA/2J alleles around the carbonic anhydrase locus influence the circadian period and level of locomotor activity in laboratory mice.     

Mapping actin surfaces required for functional interactions in vivo

An in vivo strategy to identify amino acids of actin required for functional interactions with actin-binding proteins was developed. This approach is based on the assumption that an actin mutation that specifically impairs the interaction with an actin-binding protein will cause a phenotype similar to a null mutation in the gene that encodes the actin-binding protein. 21 actin mutations were analyzed in budding yeast, and specific regions of actin subdomain 1 were implicated in the interaction with fimbrin, an actin filament-bundling protein. Mutations in this actin subdomain were shown to be, like a null allele of the yeast fimbrin gene (SAC6), lethal in combination with null mutations in the ABP1 and SLA2 genes, and viable in combination with a null mutation in the SLA1 gene. Biochemical experiments with act1-120 actin (E99A, E100A) verified a defect in the fimbrin-actin interaction. Genetic interactions between mutant alleles of the yeast actin gene and null alleles of the SAC6, ABP1, SLA1, and SLA2 genes also demonstrated that the effects of the 21 actin mutations are diverse and allowed four out of seven pseudo-wild-type actin alleles to be distinguished from the wild-type gene for the first time, providing evidence for functional redundancy between different surfaces of actin.     

Isozymes in nutrient medium of suspension-cultured apple cells (Malus sylvestris Mill.)

The time course of the activities of esterase, -galactosidase, and -glucosidase in cell sap and nutrient medium in in vitro cultured apple cells (Malus sylvestris Mill.) was studied. The corresponding isozyme patterns and the intracellular and extracellular isozyme patterns of acid phosphatase and polyphenol oxidase were compared using isozyme visualization methods adapted to ultra-thin-layer isoelectric focusing. Neither quantitative (total activity) nor qualitative (isozyme pattern) data were congruent for cell saps and nutrient media. Malate dehydrogenase, malic enzyme, and glutamate dehydrogenase occurred in cell sap only. The extracellular activities probably originate to a great part from a programmed release by intact cells. Nutrient media of plant cell cultures constitute a rich source of active plant isozymes.     

Loss of duplicate gene expression in tetraploid Chenopodium

Genetic analyses indicate that single-banded leucine aminopeptidase (LAP) phenotypes in tetraploid Chenopodium reflect homozygosity for null alleles at either locus of a polyduplicated pair. Other duplicated isozyme loci show simplification to the diploid phenotype. Loss of duplicate gene expression in the LAP system has occurred independently in putatively specialized taxa occupying the distributional periphery of a New World tetraploid complex. The geographic/taxonomic pattern of genetic variation suggests that fixation of null alleles is mediated by stochastic genetic phenomena associated with migration. Plants homozygous for null alleles at both LAP loci show no detetable activity in assays involving several exopeptidase substrates, although growth and fertility of double-null plants are not markedly reduced. Our data confirm that loss of duplicate gene expression can occur in isozyme systems of polyploid plant taxa. Thus, lack of electrophoretically detectable duplicate gene expression is not a certain indication of diploidy. However, loss of duplicate gene expression in population systems known to be of allopolyploid origin is a clear indication of phyletic derivation.     

Conditional (loxP-flanked) allele for the gene encoding the retinoic acid-synthesizing enzyme retinaldehyde dehydrogenase 2 (RALDH2)

Retinoic acid, the active vitamin A derivative, has pleiotropic functions during vertebrate development and postnatal life. Retinaldehyde dehydrogenase 2 (RALDH2) acts as the main retinoic acid-synthesizing enzyme during development. Mouse Raldh2 germline null mutants are early embryonic lethal and exhibit complex abnormalities that include defective heart looping morphogenesis. To investigate later functions of this enzyme, we have engineered a "floxed" (loxP-flanked) allele allowing Cre-mediated somatic gene inactivations. Mice heterozygous or homozygous for the floxed Raldh2 allele are viable and fertile. We tested whether the novel Raldh2 allele behaves as a null mutation after Cre-mediated in vivo excision by crossing the conditional mutants with CMV-Cre transgenic mice. An embryonic lethal phenotype indistinguishable from that of germline mutants was obtained. The conditional allele described herein is a genetic tool for studying tissue-specific, RALDH2-dependent functions of retinoic acid during development and in adult life.     

Phylogenetic signals from point mutations and polymorphic Alu

Allelic frequency data derived from five polymorphic Alu insertion loci and five point mutation polymorphic loci were compared to determine their ability to infer phylogenetic relationships among human populations. While point mutation polymorphisms inferred a monophyletic Caucasian clade that is corroborated by other studies, these data failed to support the generally accepted monophyly of Orientals with native Americans. In addition, there is less statistical bootstrap support for the maximum-likelihood tree derived from the point mutation polymorphisms as compared to those generated from either the Alu insertion data or the combined Alu insertion+point mutation data. The Alu data and the combined Alu insertion+point mutation data inferred a monophyletic relationship among the Oriental and native American populations. The Alu insertion data and the combined Alu insertion+point mutation data also displayed two separate, well defined, tight clusters of the Caucasian and the Oriental+native American populations which was not inferred from the point mutation data. These findings indicate greater phylogenetic information contained in Alu insertion frequencies than in allelic frequencies derived from point-mutations. This revised version was published online in July 2006 with corrections to the Cover Date.     

AbrB and Spo0E Control the Proper Timing of Sporulation in <Emphasis Type="Italic">Bacillus subtilis</Emphasis>

We have shown previously that Spo0AP-dependent sinIR operon expression was substantially down-regulated in abrB null mutant backgrounds. In this report, we show that loss of function mutations in abrB also cause phosphorelay gene expression to be down regulated. abrB null mutations caused diminished vegetative growth-associated sporulation and resulted in a significant reduction in sporulation frequencies at T₂₄. These mutants, however, sporulated at wild-type levels at T₄₈, indicating that sporulation timing was affected. The rvtA11 mutation in spo0A, a deletion mutation in spo0E, and a null mutation in hpr (scoC) rescued sporulation and Spo0AP-dependent gene expression in an abrB mutant background. These data indicate that AbrB and Spo0E may comprise a checkpoint system that regulates the progression of sporulation, allowing exploration of alternate cell states prior to the irrevocable commitment to sporulation.     

Increased mutation rate of E. coli K12 lambda cultures maintained in continuous logarithmic growth

Continuous logarithmic growth of E. coli K12 lambda in an automatic culture cell resulted in marked increases in the proportion of several mutants. The P1 phage-resistant cells increased 10 to 3000 times, the T2 phage-resistant cells 1 to 1000 times, the neomycin-resistant cells 1 to 10 times, and the virus-producing cells 30 to 70 times. No change occurred in the penicillin-resistant cells. Calculation of the growth curves and direct determination of the mutation rates by the null fraction method showed that the increases in the proportion of mutants were due to increases in the mutation rates.     

Myosin light chain-2 mutation affects flight, wing beat frequency, and indirect flight muscle contraction kinetics in Drosophila.

We have used a combination of classical genetic, molecular genetic, histological, biochemical, and biophysical techniques to identify and characterize a null mutation of the myosin light chain-2 (MLC-2) locus of Drosophila melanogaster. Mlc2E38 is a null mutation of the MLC-2 gene resulting from a nonsense mutation at the tenth codon position. Mlc2E38 confers dominant flightless behavior that is associated with reduced wing beat frequency. Mlc2E38 heterozygotes exhibit a 50% reduction of MLC-2 mRNA concentration in adult thoracic musculature, which results in a commensurate reduction of MLC-2 protein in the indirect flight muscles. Indirect flight muscle myofibrils from Mlc2E38 heterozygotes are aberrant, exhibiting myofilaments in disarray at the periphery. Calcium-activated Triton X-100-treated single fiber segments exhibit slower contraction kinetics than wild type. Introduction of a transformed copy of the wild type MLC-2 gene rescues the dominant flightless behavior of Mlc2E38 heterozygotes. Wing beat frequency and single fiber contraction kinetics of a representative rescued line are not significantly different from those of wild type. Together, these results indicate that wild type MLC-2 stoichiometry is required for normal indirect flight muscle assembly and function. Furthermore, these results suggest that the reduced wing beat frequency and possibly the flightless behavior conferred by Mlc2E38 is due in part to slower contraction kinetics of sarcomeric regions devoid or partly deficient in MLC-2.     

Inheritance of two independent isozyme variants in soybean plants derived from tissue culture

Summary Soybean [Glycine max (L.) Merr.] plants were regenerated via somatic embryogenesis from nine soybean cultivars. Our objective was to identify and characterize genetically novel mutations that would further our understanding of the soybean genome. Variant isozyme patterns were observed in two independent tissue culturederived lines. Genetic analyses were conducted on these two isozyme variants, and they were heritable. No variant isozyme patterns were evident in control (parental) soybean lines. In the cultivar BSR 101, a mutation of Aco2-b (aconitase) to a null allele was detected. The Aco2-bn mutant, Genetic Type T318, had not been previously observed in soybean. In the Chinese cultivar Jilin 3 (PI 427.099), a chlorophyll-deficient plant was identified that also lacked two mitochondrial malate-dehydrogenase (Mdh null) isozyme bands. These two mutant phenotypes, chlorophyll-deficient and Mdh null, were found to cosegregate. The Jilin 3 mutant, Mdh1-n (Ames 1) y20 (Ames 1) Genetic Type T317, was allelic to three chlorophyll-deficient, Mdh1 null mutants [Mdh1-n (Ames 2) y20 (Ames 2) (T323), Mdh1-n (Ames 3) y20 (Ames 3) (T324), and Mdh1-n (Ames 4) y20 (Ames 4) (T325)] previously identified from a transposon-containing soybean population, and to a chlorophyll-deficient, Mdh1 null mutant [Mdh1-n (Urbana) y20 (Urbana) k2, Genetic Type T253] which occurred spontaneously in soybean. The recovery of two isozyme variants from progeny of 185 soybean plants regenerated from somatic embryogenesis indicates the feasibility of selection for molecular variants.