Phosphoglucose Isomerase Expression in Species of Clarkia with and without a Duplication of the Coding Gene

The duplication of the nuclear gene specifying the cytosolic isozyme of phosphoglucose isomerase (PGI; EC 5.3.1.9) arose within Clarkia, a genus of annual plants native to California, and now characterizes about half of the diploid species of this genus. Evidence obtained by immunological inhibition and titration of crude leaf extracts demonstrated that species with and without the duplication have the same levels of cytosolic to total PGI (the sum of the cytosolic and plastid PGI activities). The immunological studies were carried out with a specific anticytosolic PGI antiserum and were fully supported by a densitometric analysis of the electrophoretically separated isozymes. Densitometric examination of electrophoretically separated PGIs in 11 vegetable species revealed only two levels of cytosolic to total PGI activities, one of which was the same as in Clarkia. This suggests that only certain levels of the cytosolic isozyme are compatible with proper operation of the cytosolic PGI reaction and make it likely that some form of genic or metabolic regulation has evolved that compensates for the PGI duplication.     

Evidence for duplication and divergence of the structural gene for phosphoglucoisomerase in diploid species of clarkia

Formal genetic analysis of the mode of inheritance of the electrophoretic phenotypes for phosphoglucoisomerase (PGI) in the annual plants Clarkia rubicunda and C. xantiana showed that these diploid species have two and three genes, respectively, that specify PGI subunits. Electrophoretic examination of seven other diploid species of Clarkia revealed that species assigned to ancestral sections in the current taxonomy have two PGI genes, whereas more specialized species have three PGI genes. Together with evidence that diploid species in two closely related genera have two PGI genes, this suggests the third PGI gene arose within Clarkia. Intergenic heterodimers are formed between polypeptides specified by the third gene and one of the other PGI genes, indicating they have a high degree of structural similarity. The combined genetic, biochemical, and phylogenetic evidence suggests that the third PGI gene resulted from a process of gene duplication. The apparent Michaelis constants (F6P to G6P) of the most common electrophoretic variants of the ancestral gene in C. xantiana and in C. rubicunda are closely similar, but that of the duplicate enzyme is much higher. The intergenic heteromer has an intermediate value. Four alleles have been identified for the duplicate PGI gene in C. xantiana, including a null allele which eliminates the activity of its product. This allele is one of the few examples of a "silenced" duplicate gene. The ancestral and duplicate genes assort independently in C. xantiana. In conjunction with the substantial chromosomal rearrangements that characterize species of Clarkia, this may mean that the duplicate PGI marks a duplicated chromosomal segment that originated from a cross between partially overlapping reciprocal translocations rather than from unequal crossing over.     

Evidence for duplication of the structural genes coding plastid and cytosolic isozymes of triose phosphate isomerase in diploid species of clarkia

Formal genetic analyses of the mode of inheritance of the multiple plastid and cytosolic isozymes of triose phosphate isomerase (TPI, EC 5.3.1.1) in annual diploid species of Clarkia (Onagraceae), native to California, suggest that each set of isozymes is specified by duplicate structural genes. In contrast, most diploid plant species possess one plastid and one cytosolic TPI isozyme each coded by a single locus. Linkage tests revealed that the two genes coding the plastid TPIs assort independently. Although the number of individuals sampled per species was small, the plastid isozymes were electrophoretically more variable than the cytosolic isozymes. The two gene duplications are the first reported that characterize an entire plant genus. Initial electrophoretic surveys of TPI in other genera of Onagraceae revealed that the duplication of the gene coding the plastid isozyme is apparently restricted to Clarkia, whereas that of the gene coding the cytosolic isozyme is present in most genera of the family. The separate phylogenetic distributions of the two duplications suggest that the processes that gave rise to them were unrelated.     

Duplicated phosphoglucose isomerase genes in avocado

Summary Avocado (Persea americana) cultivars were assayed for phosphoglucose isomerase (PGI) isozymes using starch gel electrophoresis. Three PGI genes were identified: one monomorphic locus, Pgi-I, coding for the plastid isozyme and two independently assorting loci, Pgi-2 and Pgi-3, coding for the cytosolic isozymes. The genetic analysis was based on comparisons of PGI zymograms from somatic and pollen tissue and on Mendelian analysis of progeny from selfed trees. The isozymic variability for PGI can be used for cultivar identification and for differentiating between hybrid and selfed progeny in avocado breeding.     

Molecular Characterization of Duplicate Cytosolic Phosphoglucose Isomerase Genes in Clarkia and Comparison to the Single Gene in Arabidopsis

The nucleotide sequence of PgiC1-a which encodes a cytosolic isozyme of phosphoglucose isomerase (PGIC; EC 5.3.1.9) in Clarkia lewisii, a wildflower native to California, is described and compared to the previously published sequence of the duplicate PgiC2-a from the same genome. Both genes have the same structure of 23 exons and 22 introns located in identical positions, and they encode proteins of 569 amino acids. Exon and inferred protein sequences of the two genes are 96.4% and 97.2% identical, respectively. Intron sequences are 88.2% identical. The high nucleotide similarity of the two genes is consistent with previous genetic and biosystematic findings that suggest the duplication arose within Clarkia. A partial sequence of PgiC2-b was also obtained. It is 99.5% identical to PgiC2-a in exons and 99.7% in introns. The nucleotide sequence of the single PgiC from Arabidopsis thaliana was also determined for comparison to the Clarkia genes. The A. thaliana PgiC has 21 introns located at positions identical to those in Clarkia PgiC1 and PgiC2, but lacks the intron that divides Clarkia exons 21 and 22. The A. thaliana PGIC protein is shorter, with 560 amino acids, and differs by about 17% from the Clarkia PGICs. The PgiC in A. thaliana was mapped to a site 20 cM from restriction fragment length polymorphism marker 331 on chromosome 5.     

A recently silenced, duplicate PgiC locus in Clarkia

Previous electrophoretic analysis showed that 17 diploid species of the wildflower Clarkia (Onagraceae) have two cytosolic isozymes of phosphoglucose isomerase (PGIC; EC 5.3.1.9), whereas 15 other diploid species have a single PGIC. Molecular studies revealed that the two isozymes in the former species are encoded by duplicate genes, PgiC1 and PgiC2, whereas the single isozyme in the latter is always encoded by PgiC1. Phylogenetic analysis of the nucleotide sequences implied that PgiC2 was silenced four times independently in the genus. Here we describe a psi PgiC2 from C. mildrediae, a species in which only PgiC1 is expressed. The discovery of the psi PgiC2 is significant because it confirms a formal prediction of the phylogenetic analysis. The psi PgiC2 includes 5,039 nucleotides corresponding to 18 of the 23 exons of PgiC, as well as the intervening introns and 3' nontranslated region. The absence of an increase of nucleotide substitutions in its "exons" suggests that the gene was silenced recently. The present study appears to be the first to establish that a specific duplicate gene locus regularly expressed in a group of related plant species has been silenced in one of them. The multiple independent silencings of PgiC2 suggest that it remained functional but inessential in ancestral lineages. We discuss the possibility that PgiC2 may have been preserved in these lineages by selection against mutants causing defective PGIC1- PGIC2 heterodimers.      

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.     

Subunit hybridization and immunological studies of duplicated phosphoglucose isomerase isozymes

We examined structural and functional properties of the recently duplicated cytosolic isozymes of phosphoglucose isomerase (PGI) (EC 5.3.1.9) of the wild plant Clarkia xantiana and related species. A new purification protocol yielded PGIs with high specific activities. The duplicated PGI isozymes showed similar substrate affinities (apparent Km) in both catalytic directions. A newly devised competitive enzyme-linked immunosorbent assay (ELISA), using polyclonal antibodies, distinguished sodium dodecyl sulfate (SDS)-denatured PGIs coded by the duplicated loci but did not discriminate between allelic products of one of the loci. In vitro dissociation and reassociation experiments revealed that the duplicated subunits differed in their efficiency of reassociation. The difference was closely correlated with differences between the isozymes in their in vivo accumulation. In contrast, allelic subunits in species with or without the duplication were able to reassociate with similar efficiency. The duplicated PGI isozymes have diverged more in structural properties than kinetic ones. The total evidence suggests that mechanisms have evolved which reduce the potential consequences of the duplication.     

Phosphoglucose isomerase isozymes and allozymes of the brown trout, Salmo trutta L

1. In brown trout the Pgi-1 and Pgi-2 loci are predominantly expressed in white skeletal muscle; Pgi-3 being mainly expressed in most other tissues. 2. Total PGI activity determinations revealed that the allele formerly designated Pgi-2(65) is a null allele, Pgi-2(n). 3. Enzyme kinetic studies on the partially purified PGI homodimeric isozymes revealed that from 5 to 25 degrees C both PGI-1 and PGI-2 had significantly higher mean Km(F6P) values compared to PGI-3. 4. Distinct metabolic roles for the "muscle" (PGI-1, PGI-2) and "liver" (PGI-3) isozymes are proposed. 5. Significant Km (F6P) differences were found among the PGI-2 allozymes and among the PGI-3 allozymes.     

Reduced-activity mutants of phosphoglucose isomerase in the cytosol and chloroplast of Clarkia xantiana

(i) We have studied the influence of reduced phosphoglucose-isomerase (PGI) activity on photosynthetic carbon metabolism in mutants of Clarkia xantiana Gray (Onagraceae). The mutants had reduced plastid (75% or 50% of wildtype) or reduced cytosolic (64%, 36% or 18% of wildtype) PGI activity. (ii) Reduced plastid PGI had no significant effect on metabolism in low light. In high light, starch synthesis decreased by 50%. There was no corresponding increase of sucrose synthesis. Instead glycerate-3-phosphate, ribulose-1,5-bisphosphate, reduction of Q_A (the acceptor for photosystem II) and energy-dependent chlorophyll-fluorescence quenching increased, and O₂ evolution was inhibited by 25%. (iii) Decreased cytosolic PGI led to lower rates of sucrose synthesis, increased fructose-2,6-bisphosphate, glycerate-3-phosphate and ribulose-1,5-bisphosphate, and a stimulation of starch synthesis, but without a significant inhibition of O₂ evolution. Partitioning was most affected in low light, while the metabolite levels changed more at saturating irradiances. (iv) These results provide decisive evidence that fructose-2,6-bisphosphate can mediate a feedback inhibition of sucrose synthesis in response to accumulating hexose phosphates. They also provide evidence that the ensuing stimulation of starch synthesis is due to activation of ADP-glucose pyrophosphorylase by a rising glycerate-3-phosphate: inorganic phosphate ratio, and that this can occur without any loss of photosynthetic rate. However the effectiveness of these mechanisms varies, depending on the conditions. (v) These results are analysed using the approach of Kacser and Burns (1973, Trends Biochem. Sci. 7, 1149–1161) to provide estimates for the elasticities and flux-control coefficient of the cytosolic fructose-1,6-bisphosphatase, and to estimate the gain in the fructose-2,6-bisphosphate regulator cycle during feedback inhibition of sucrose synthesis.Abbreviations and symbols Chl chlorophyll - Fru6P fructose-6-phosphate - Frul,6bisP fructose-1,6-bisphosphate - Fru-1,6Pase fructose-1,6-bisphosphatase - Fru2,6bisP fructose-2,6-bisphosphate - Fru2,6Pase fructose-2,6-bisphosphatase - Glc6P glucose-6-phosphate - PGI phosphoglucose isomerase - Pi inorganic phosphate - Q_A acceptor for photosystem II - Ru1,5bisP ributose-1,5-bisphosphate - SPS sucrose-phosphate synthase     

Silencing of duplicate genes: a null allele polymorphism for lactate dehydrogenase in brown trout (Salmo trutta)

A previously described isozyme polymorphism at one of two skeletal muscle LdhA loci in brown trout is due to a null allele, Ldh1(n), producing no detectable catalytic activity. Homozygotes for this allele have approximately only 56% of the LDH activity in skeletal muscle relative to homozygotes for the active allele. The remaining activity results from enzyme subunits produced by other LDH loci. The Ldh1(n) allele is common and widespread throughout brown trout populations in Sweden and is also found in populations from Ireland. The persistence of duplicate gene expression for the LdhA loci in almost all salmonid species is best explained by natural selection against individuals containing null alleles. However, there is no indication of natural selection against brown trout with the Ldh1(n) allele: We suggest that the selection against individuals containing null alleles that is apparently responsible for the persistence of duplicate LdhA loci in salmonids occurs only under certain environmental conditions.      

Genetic differentiation in populations of the polymorphic fernCeratopteris thalictroides in Japan

Analysis of isozyme variation was carried out for 27 natural populations ofCeratopteris thalictroides in Japan. Of fifteen enzyme loci examined, eight loci were genetically polymorphic. At six loci,Lap, Pgi-2, Pgm-3, Pgm-4, Idh-2, and Skd-2, a marked genetic differentiation was observed between populations to the south of Okinawa Island and those to the north of the island. Okinawa Island contained a mixture of both southern and northern variants. Thus, two genetically distinct types (the south type and the north type) ofC. thalictroides occur allopatrically in Japan. Nei's genetic identity (I) between the two was 0.64, which was within the range of the I values between congeneric pteridophyte species. Regional fixation of a null allele was detected for one duplicated PGI locus in the north type ofC. thalictroides. This finding supports the recent hypothesis of genetic diploidization of polyploids through gene silencing.     

Central cell nuclear-cytoplasmic incongruity:a mechanism for segregation distortion in advanced backcross and selfed generations of (Allium cepa L. x Allium fistulosum L.) x A. cepa interspecific hybrid derivatives

A model is presented as an explanation for an anomaly observed in germination and establishment and isozyme segregation patterns in Allium cepa x A. fistulosum F2BC3 populations generated in an introgression-breeding program. The F1BC3 parent of these populations was selected for its heterozygous PGI phenotype, Pgi-1(2/3); Pgi-1(2) was inherited from an A. cepa (Ac) seed parent and Pgi-1(3) from an A. fistulosum (Af) pollen parent. Germination and establishment was recorded for the F2BC3 progeny population. Segregation of Ac and Af Pgi-1 alleles was investigated in F2BC3 seeds and embryo and endosperm tissue was isolated and tested for isozyme expression. A pooled goodness-of-fit test of the segregation of Pgi-1 alleles in the populations to the expected Mendelian 1:2:1 ratio using the chi-square statistic gave a chi2 = 185.9, well beyond the accepted limits at 2 degrees of freedom. The 1:2:1 ratio expected for simple Mendelian inheritance was rejected, while a pooled chi-square goodness-of-fit test of the segregation of Pgi-1 alleles in the populations fit a 1:1 ratio with a chi2 = 0.203, based on the incongruity model. We present here the central cell nuclear-cytoplasmic incongruity hypothesis to explain the observed anomalies.     

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.     

Isozymes of glucosephosphate isomerase (PGI) in fishes of the subclass actinopterygii

A compilation of the species of fishes of the subclass Actinopterygii for the study of the PGI isozyme system is given. PGI appears to be codified by more than one locus in fishes; 65% of the species analysed here have two loci for PGI. PGI duplication in fishes and the relationship of isozymes of PGI with temperature and metabolism are discussed.     

Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution

Gene duplication is the primary source of new genes. Duplicate genes that are stably preserved in genomes usually have divergent functions. The general rules governing the functional divergence, however, are not well understood and are controversial. The neofunctionalization (NF) hypothesis asserts that after duplication one daughter gene retains the ancestral function while the other acquires new functions. In contrast, the subfunctionalization (SF) hypothesis argues that duplicate genes experience degenerate mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We here show that neither NF nor SF alone adequately explains the genome-wide patterns of yeast protein interaction and human gene expression for duplicate genes. Instead, our analysis reveals rapid SF, accompanied by prolonged and substantial NF in a large proportion of duplicate genes, suggesting a new model termed subneofunctionalization (SNF). Our results demonstrate that enormous numbers of new functions have originated via gene duplication.     

KlADH3, a gene encoding a mitochondrial alcohol dehydrogenase, affects respiratory metabolism and cytochrome content in Kluyveromyces lactis

A Kluyveromyces lactis strain, harbouring KlADH3 as the unique alcohol dehydrogenase (ADH) gene, was used in a genetic screen on allyl alcohol to isolate mutants deregulated in the expression of this gene. Here we report the characterization of some mutants that lacked or had highly reduced amounts of KlAdh3p activity; in addition, these mutants showed alterations in glucose metabolism, reduced respiration and reduced cytochrome content. Our results confirm that the KlAdh3p activity contributes to the reoxidation of cytosolic NAD(P)H feeding the respiratory chain through KlNdi1p, the mitochondrial internal transdehydrogenase. The low levels of KlAdh3p in two of the mutants were associated with mutations in KlSDH1, one of the genes of complex II, suggesting signalling between the respiratory chain and expression of the KlADH3 gene.     

Evidence from subunit molecular weight suggests hybridization was the source of the phosphoglucose isomerase gene duplication in Clarkia

Summary The apparent molecular weight of cytosolic phosphoglucose isomerase (PGI) subunits was evaluated in 18 species of Clarkia which have or do not have duplicated genes specifying this glycolytic enzyme. Species that lack the duplication had subunits of 59,000 or 60,400 whereas species with the duplication generally possessed two types of PGI subunits with these or closely similar molecular weights. The additive pattern in the species with the duplication suggests that the molecular weight divergence preceded the origin of the duplication, and that the duplication arose following hybridization between taxa that represented different lineages within Clarkia.     

Molecular trajectories leading to the alternative fates of duplicate genes

Gene duplication generates extra gene copies in which mutations can accumulate without risking the function of pre-existing genes. Such mutations modify duplicates and contribute to evolutionary novelties. However, the vast majority of duplicates appear to be short-lived and experience duplicate silencing within a few million years. Little is known about the molecular mechanisms leading to these alternative fates. Here we delineate differing molecular trajectories of a relatively recent duplication event between humans and chimpanzees by investigating molecular properties of a single duplicate: DNA sequences, gene expression and promoter activities. The inverted duplication of the Glutathione S-transferase Theta 2 (GSTT2) gene had occurred at least 7 million years ago in the common ancestor of African great apes and is preserved in chimpanzees (Pan troglodytes), whereas a deletion polymorphism is prevalent in humans. The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion. In contrast, selective constraint preserved duplicate divergence in chimpanzees. The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones. Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.     

A novel family of yeast chaperons involved in the distribution of V-ATPase and other membrane proteins.

Null mutations in genes encoding V-ATPase subunits in Saccharomyces cerevisiae result in a phenotype that is unable to grow at high pH and is sensitive to high and low metal-ion concentrations. Treatment of these null mutants with ethylmethanesulfonate causes mutations that suppress the V-ATPase null phenotype, and the mutant cells are able to grow at pH 7.5. The suppressor mutants were denoted as svf (suppressor of V-ATPase function). The frequency of svf is relatively high, suggesting a large target containing several genes for the ethylmethanesulfonate mutagenesis. The suppressors' frequency is dependent on the individual genes that were inactivated to manifest the V-ATPase null mutation. The svf mutations are recessive, because crossing the svf mutants with their corresponding V-ATPase null mutants resulted in diploid strains that are unable to grow at pH 7.5. A novel gene family in which null mutations cause pleiotropic effects on metal-ion resistance or sensitivity and distribution of membrane proteins in different targets was discovered. The family was defined as VTC (Vacuolar Transporter Chaperon) and it contains four genes in the S. cerevisiae genome. Inactivation of one of them, VTC1, in the background of V-ATPase null mutations resulted in svf phenotype manifested by growth at pH 7.5. Deletion of the VTC1 gene (DeltaVTC1) results in a reduced amount of V-ATPase in the vacuolar membrane. These mutant cells fail to accumulate quinacrine into their vacuoles, but they are able to grow at pH 7.5. The VTC1 null mutant also results in a reduced amount of the plasma membrane H(+)-ATPase (Pma1p) in membrane preparations and possibly mis-targeting. This observation may provide an explanation for the svf phenotype in the double disruptant mutants of DeltaVTC1 and DeltaVMA subunits.