bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Divergence and Fitness Convergence Under Uniform Selection in Experimental Populations of Bacteria
Authors: Korona Ryszard
Published: January 2021

Replicate populations of bacteria were propagated for 1000 generations in the laboratory. The growth substrate was periodically renewed, so that during most generations (cell doublings) it was not limiting. The final clones demonstrated about a 40% fitness increase when competed against their common ancestor. This increase was uniform both among and within populations despite extensive differentiation in correlated traits: cell size, resistance to starvation and dry mass of culture. It is suggested that genetic diversity developed because selection promoted any changes directing cell activity toward a higher maximum growth rate. Evolution of this trait halted at a similar level when some basic constraints on bacterial metabolism were met. The selective values of emerging mutations must have depended on the genetic background. They would be beneficial early in evolution but ineffective near the limit of adaptation. This hypothesis was tested for one mutation that affected both fitness and colony morphology. In some clones it was the first adaptive mutation and provided a third of the total fitness increase, but it was not assimilated by the clones that reached the adaptive ceiling in some other way. Near the limit of adaptation, epistasis levels off the fitnesses of genetically variable clones.
A Novel Drosophila Minute Locus Encodes Ribosomal Protein S13
Authors: Saeboe-Larssen Stein , Lambertsson Andrew
Published: January 2021

Minutes comprise >50 phenotypically similar Drosophila mutations believed to affect ribosomal protein genes. Common traits of the Minute phenotype are short and thin bristles, slow development, and recessive lethality. To further investigate the proposed Minute to ribosomal protein correspondence, loss-of-function Minute mutations were induced by P-element mutagenesis. Here, we report a previously undescribed Minute locus that maps to 32A on chromosome 2L; this Minute allele is named P{lac-W}M(2)32A1 and the gene M(2)32A. Flies heterozygous for P{lacW}M(2)32A1 have a medium Minute phenotype. The gene interrupted by the P-element insertion was cloned. Sequence analyses revealed that it encodes the Drosophila homologue of eukaryotic ribosomal protein S13. It is a singlecopy gene and the level of RPS13 transcript is reduced to ~50% in P{lacW}M(2)32A1 heterozygotes. Both transcript level and phenotype are restored to wild type by remobilizing the P element, demonstrating that the mutation is caused by insertion of the P-element construct. These results further strengthen the notion that Minutes encode ribosomal proteins and demonstrate that P-element mutagenesis is a fruitful approach to use in these studies.
The Om(1E) Mutation in Drosophila ananassae Causes Compound Eye Overgrowth due to tom Retrotransposon-Driven Overexpression of a Novel Gene
Authors: Juni Naoto , Awasaki Takeshi , Yoshida Kiyohito , Hori Samuel H
Published: January 2021

Optic morphology (Om) mutations in Drosophila ananassae are a group of retrotransposon (tom)-induced gain-of-function mutations that map to at least 22 independent loci and exclusively affect the compound eye morphology. In marked contrast to other Om mutations, which are characterized by fewer-than-normal and disorganized ommatidia, the Om(1E) mutation exhibits a peculiar phenotype as enlarged eyes with regularly arrayed normal ommatidia. To characterize the Om(1E) mutation, we have carried out molecular analyses. A putative Om(1E) locus cloned by tom tagging and chromosome walking contained two transcribed regions in the vicinity of tom insertion sites of the Om(1E) mutant alleles, and one of these regions was shown to be the Om(1E) gene by Pelement-mediated transformation experiments with D. melanogaster. The Om(1E) gene encodes a novel protein having potential transmembrane domain(s). In situ hybridization analyses demonstrated that the Om(1E) gene is expressed ubiquitously in embryonic cells, imaginal discs, and the cortex of the central nervous system of third instar larvae, and specifically in lamina precursor cells. Artificially induced ubiquitous overexpression of Om(1E) affected morphogenesis of wing imaginal disc derivatives or large bristle formation. These findings suggest that the Om(1E) gene is involved in a variety of developmental processes.
The hobo Transposable Element Excises and Has Related Elements in Tephritid Species
Authors: Handler Alfred M , Gomez Sheilachu P
Published: January 2021

Function of the Drosophila melanogaster hobo transposon in tephritid species was tested in transient embryonic excision assays. Wild-type and mutant strains of Anastrepha suspensa, Bactrocera dorsalis, B. cucurbitae, Ceratitis capitata, and Toxotrypana curvicauda all supported hobo excision or deletion both in the presence and absence of co-injected hobo transposase, indicating a permissive state for hobo mobility and the existence of endogenous systems capable of mobilizing hobo. In several strains hobo helper reduced excision. Excision depended on hobo sequences in the indicator plasmid, though almost all excisions were imprecise and the mobilizing systems appear mechanistically different from hobo. hobe-related sequences were identified in all species except T. curvicauda. Parsimony analysis yielded a subgroup including the B. cucurbitae and C. capitata sequences along with hobo and Hermes, and a separate, more divergent subgroup including the A. suspensa and B. dorsalis sequences. All of the sequences exist as multiple genomic elements, and a deleted form of the B. cucurbitae element exists in B. dorsalis. The hobo-related sequences are probably members of the hAT transposon family with some evolving from distant ancestor elements, while others may have originated from more recent horizontal transfers.
Doing the Conjugative Two-step: Evidence of Recipient Autonomy in Retrotransfer
Authors: Heinemann Jack A , Scott Heidi E , Williams Meredith
Published: January 2021

Bidirectional exchange of genetic information, called retrotransfer, during bouts of bacterial conjugation has drawn the interest of those concerned with the risk of releasing genetically engineered microbes, the fluidity of genes among species, and the mechanism of DNA transport between cells. The phenomenon has generated two models in explanation, both of which yield highly testable predictions. The first model, called the one-step, predicts that the flow of genes from recipient bacteria to donor bacteria is mechanistically distinct from, but dependent on, conjugation between donors and recipients. The second model, called the two-step, predicts that the same genetic requirements and mechanistic constraints apply to the process of gene flow from recipients to donors as for gene flow from donors to recipients. The requirement for expression of at least 10 plasmid-encoded genes in recipients, sensitivity of the reverse flow (recipient to donor) to restriction of DNA transferring from the donor, and the requirement of an additional 30–90 min for DNA to flow from recipients back to donors are predictions of the two-step model and directly refute the one-step model. Retrotransfer of genes to donors during conjugation remains genetically and physically indistinguishable from two successive rounds of conjugation between neighbors.
Mutations in the SPT4, SPT5, and SPT6 Genes Alter Transcription of a Subset of Histone Genes in Saccharomyces cerevisiae
Authors: Compagnone-Post Patricia A , Osley Mary Ann
Published: January 2021

The SPT4, SPT5, and SPT6 gene products define a class of transcriptional repressors in Saccharomyces cermisiae that are thought to function through their effects on chromatin assembly or stability. Mutations in these genes confer a similar range of phenotypes to mutations in HIR genes, which encode transcriptional repressors that regulate expression of many of the core histone genes. Here we show that mutations in the three SPTgenes also affect transcription of the histone genes that reside at the HTA1-HTB1 locus. HTA1-lacZ transcription was reduced in each spt mutant background, an effect that required a negative site in the HTA1 promoter. The transcriptional effect could be reversed by the overproduction of histones H2A and H2B in an spt4 mutant and histones H3 and H4 in all three spt mutants. Suppression of the spt4 transcriptional defect was dependent on the overproduction of both histones H2A and H2B, and required the presence of N-terminal amino acids in both histones. The results are consistent with the idea that the effects of the spt mutations on nucleosome assembly and/or stability activate repressors of HTA1 transcription.
Timing of Expression of a Gene in the Adult Drosophila Is Regulated by Mechanisms Independent of Temperature and Metabolic Rate
Authors: Rogina Blanka , Helfand Stephen L
Published: January 2021

The examination of β-galactosidase (β-gal) expression in the third segment of the antenna of the 2216 enhancer trap line in Drosophila melanogaster reveals two distinct spatial and temporal regulatory patterns of expression during adult life. Type I expression is characterized by a decline in the level of β-gal expression with increasing age. Starting from a maximal level of expression at the time of adult emergence, there is a decrease in the number of cells that express β-gal so that by 40-50 days of adult life few cells express β-gal. Varying the ambient temperature and using hyperactivity mutants (Hyperkznetic1, Shaker5) demonstrates that the rate of this decline is independent of temperature and metabolic rate. Type II expression is distinctly different in spatial distribution and temporal regulation from the first pattern. Type II expression is restricted in the antenna to a small (<20–30) set of cells whose level of expression changes in a periodic manner with time. The regulation of this periodicity appears to be linked to ambient temperature.
Genetics of a Difference in Male Cuticular Hydrocarbons Between Two Sibling Species, Drosophila simulans and D. sechellia
Authors: Coyne Jerry A
Published: January 2021

In seven of the eight species of the Drosophila melanogaster group, the predominant cuticular hydrocarbon of males is Ftricosene, but in the island endemic species D. sechellia it is 6-tricosene. The phylogeny of the group implies that the novel hydrocarbon profile of D. sechellia is a derived character. Genetic analysis of hybrids between D. sechellia and its close relative D. simulans show that each of the five major chromosome arms carries at least one gene affecting the ratio of the two tricosene isomers, with the right arm of the third chromosome having the largest effect. The species difference in this character is therefore polygenic with the effects of the different chromosome arms generally additive, although there is some epistasis among third-chromosome genes. Observations of courtship by males who have been coated with foreign hydrocarbons suggest that a male's hydrocarbon profile may slightly affect the degree of sexual isolation in one of the reciprocal hybridizations between these species, but that this role is small compared to that played by hydrocarbon differences between females.
Characterization of a Meiotic Crossover in Maize Identified by a Restriction Fragment Length Polymorphism-Based Method
Authors: Timmermans Marja C P , Das O Prem , Messing Joachim
Published: January 2021

Genetic map lengths do not correlate directly with genome size, suggesting that meiotic recombination is not uniform throughout the genome. Further, the abundance of repeated sequences in plant genomes requires that crossing over is restricted to particular genomic regions. We used a physical mapping approach to identify these regions without the bias introduced by phenotypic selection. This approach is based on the detection of nonparental polymorphisms formed by recombination between polymorphic alleles. In an F2 population of 48 maize plants, we identified a crossover at two of the seven restriction fragment length polymorphism loci tested. Characterization of one recombination event revealed that the crossover mapped within a 534bp region of perfect homology between the parental alleles embedded in a 2773-bp unique sequence. No transcripts from this region could be detected. Sequences immediately surrounding the crossover site were not detectably methylated, except for an SstI site probably methylated via non-CpG or CpXpG cytosine methylation. Parental methylation patterns at this SstI site and at the flanking repetitive sequences were faithfully inherited by the recombinant allele. Our observations suggest that meiotic recombination in maize occurs between perfectly homologous sequences, within unmethylated, nonrepetitive regions of the genome.
Genetic Markers and Quantitative Genetic Variation in Medicago truncatula (Leguminosae): A Comparative Analysis of Population Structure
Authors: Bonnin Isabelle , Prosperi Jean-Marie , Olivieri Isabelle
Published: January 2021

Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations.
Specificity of Chromosome Damage Caused by the Rex Element of Drosophila melanogaster
Authors: Robbins Leonard G
Published: January 2021

Rex is a multicopy genetic element that maps within an X-linked ribosomal RNA gene (rDNA) array of D. melanogaster. Acting maternally, Rex causes recombination between rDNA arrays in a few percent of early embryos. With target chromosomes that contain two rDNA arrays, the exchanges either delete all of the material between the two arrays or invert the entire intervening chromosomal segment. About a third of the embryos produced by Rex homozygotes have cytologically visible chromosome damage, nearly always involving a single chromosome. Most of these embryos die during early development, displaying a characteristic apoptosis-like phenotype. An experiment that tests whether the cytologically visible damage is rDNA-specific is reported here. In this experiment, females heterozygous for Rex and an rDNA-deficient X chromosome were crossed to males of two genotypes. Some of the progeny from the experimental cross entirely lacked rDNA, while all of the progeny from the control cross had at least one rDNA array. A significantly lower frequency of early-lethal embryos in the experimental cross, proportionate to the fraction of rDNA-deficient embryos, demonstrates that Rex preferentially damages rDNA.
Multiple Versions of the A Mating Type Locus of Coprinus cinereus are Generated by Three Paralogous Pairs of Multiallelic Homeobox Genes
Authors: Pardo Eneida H , O'Shea Suzanne F , Casselton Lorna A
Published: January 2021

The A mating type locus of Coprinus cinereus determines mating compatibility by regulating essential steps in sexual development. Each A locus contains several genes separated into two functionally independent complexes termed Aα and Aβ, and the multiple alleles of these genes generate an estimated 160 A mating specificities. The genes encode two classes of homeodomain-containing proteins designated HD1 and HD2. In this report we describe two newly cloned loci, A2 and A5, and compare them with A42, A43 and A6 that we have described previously. An Aβ-null locus, retaining just a single active HD1 gene from the α-complex, was generated by mutation. Using this as a transformation host, gene combinations that promote A-regulated development were identified. We demonstrate that each A locus contains members of three paralogous pairs of HD1 and HD2 genes. Different allelic versions of gene pairs are compatible but paralogous genes are incompatible. The genes present in four uncloned A loci were deduced using Southern analyses and transformations with available cloned genes. The combined analysis of nine A factors identifies sufficient A gene alleles to generate at least 72 A mating specificities.
Escape From het-6 Incompatibility in Neurospora crassa Partial Diploids Involves Preferential Deletion Within the Ectopic Segment
Authors: Smith Myron L , Yang Christopher J , Mehenberg Robert L , Glass N Louise
Published: January 2021

Self-incompatible het-6  OR/het-6  PA partial diploids of Neurospora crassa were selected from a cross involving the translocation strain, T(IIL → IIIR)AR18, and a normal sequence strain. About 25% of the partial diploids exhibited a marked increase in growth rate after 2 weeks, indicating that “escape” from het-6 incompatibility had occurred. Near isogenic tester strains with different alleles (het-6  OR and het-6  PA) were constructed and used to determine that 80 of 96 escape strains tested were het-6  PA, retaining the het-6 allele found in the normal-sequence LGII position; 16 were het-6  OR, retaining the allele in the translocated position. Restriction fragment length polymorphisms in 45 escape strains were examined with probes made from cosmids that spanned the translocated region. Along with electrophoretic analysis of chromosomes from three escape strains, RFLPs showed that escape is associated with deletion of part of one or the other of the duplicated DNA segments. Deletions ranged in size from ~70 kbp up to putatively the entire 270-kbp translocated region but always included a 35-kbp region wherein we hypothesize het-6 is located. The deletion spectrum at het-6 thus resembles other cases where mitotic deletions occur such as of tumor suppressor genes and of the hprt gene (coding for hypoxanthine-guanine phosphoribosyl-transferase) in humans.
Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of tra-1 and Its Functional Consequences
Authors: de Bono Mario , Hodgkin Jonathan
Published: January 2021

The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra-1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(nul1) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defines several conserved regions likely to be important for tra-1 function. The phenotypic differences between Ce-tra-1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex.
Recognition of Homeology by the Wheat Ph1 Locus
Authors: Luo Ming-Cheng , Dubcovsky Jorge , Dvořák Jan
Published: January 2021

Chromosome 1Am of Triticum monococcum is closely homeologous to T. aestivum chromosome 1A but recombines with it little in the presence of the wheat suppressor of homeologous chromosome pairing, Ph1. In the absence of Ph1, the two chromosomes recombine as if they were completely homologous. Chromosomes having either terminal or interstitial segments of chromosome 1Am in 1A were constructed and their recombination with 1A was investigated in the presence of Ph1. No recombination was detected in the homeologous (1Am/1A) segments, irrespective of whether terminally or interstitially positioned in a chromosome, whereas the levels of recombination in the juxtaposed homologous (1A/1A) segments was normal or close to normal relative to completely homologous 1A chromosomes. These observations show that Ph1 does not regulate chromosome pairing by premeiotic chromosome alignment and a mitotic spindle-centromere interaction, as has been suggested, but processes homology along the entire length of chromosomes.
The Saccharomyces cerevisiae RTG2 Gene Is a Regulator of Aconitase Expression Under Catabolite Repression Conditions
Authors: Vélot Christian , Haviernik Peter , Lauquin Guy J-M
Published: January 2021

The ACO1 gene, encoding mitochondrial aconitase of Saccharomyces cerevisiae, is required both for oxidative metabolism and for glutamate prototrophy. This gene is subject to catabolite repression; the ACO1 mRNA level is further reduced when glutamate is supplied with glucose. To further explore regulation of ACO1 expression, we have screened for mutations that reduce expression of an ACO1-lacZ fusion borne on a multicopy vector. We identified a gene required for wild-type expression of ACO1 only under catabolite repression conditions. Sequencing of the corresponding cloned gene revealed that it is identical to RTG2 previously cloned as a pivotal gene in controlling interorganelle retrograde communication. Cells containing either the original rtg2-2 mutation or a null rtg2 allele are not petite but show a residual growth on minimum glucose medium with ammonium sulfate as the sole nitrogen source. This growth defect is partially restored by supplying aspartate or threonine, and fully with glutamate or proline supplement. Surprisingly, this phenotype is not observed on complete medium lacking either of these amino acids. In addition, a genetic analysis revealed an interaction between RTG2 and ASP5 (encoding aspartate amino transferase), thus supporting our hypothesis that RTG2 may be involved in the control of several anaplerotic pathways.
Saccharomyces cerevisiae S288C Has a Mutation in FL08, a Gene Required for Filamentous Growth
Authors: Liu Haoping , Styles Cora Ann , Fink Gerald R
Published: January 2021

Diploid strains of baker's yeast Saccharomyces cermisiae can grow in a cellular yeast form or in filaments called pseudohyphae. This dimorphic transition from yeast to pseudohyphae is induced by starvation for nitrogen. Not all laboratory strains are capable of this dimorphic switch; many grow only in the yeast form and fail to form pseudohyphae when starved for nitrogen. Analysis of the standard laboratory strain S288C shows that this defect in dimorphism results from a nonsense mutation in the FL08 gene. This defect in FL08 blocks pseudohyphal growth in diploids, haploid invasive growth, and flocculation. Since feral strains of S. cerevisiae are dimorphic and have a functional FL08 gene, we suggest that the fl08 mutation was selected during laboratory cultivation.
Dosage Suppressors of a Benomyl-Dependent Tubulin Mutant: Evidence for a Link Between Microtubule Stability and Cellular Metabolism
Authors: Machin Nathan A , Lee Janet M , Chamany Katayoun , Barnes Georjana
Published: January 2021

To identify factors important for the regulation of microtubule stability in yeast, dosage suppressors of the hyperstable microtubule phenotype of the budding yeast tub2-150 β-tubulin mutation were isolated. Of the two suppressors reported here, one (JSN2) encodes a tRNAVal, and the other (JSN3) is an antimorphic allele of the methionine biosynthesis transcription factor Met4p. Furthermore, growth of tub2-150 mutants and suppression of tub2-150 mutants by JSN3 are sensitive to levels of methionine in the growth medium. We explore several possible explanations for these findings, including the potential involvement of the general amino acid control and the involvement of Cbflp, a component of yeast kinetochores that is also necessary for Met4p-mediated transcription.
The Mitochondrial Genome Integrity Gene, MGI1, of Kluyveromyces lactis Encodes the β-Subunit of F1-ATPase
Authors: Chen Xin Jie , Clark-Walker G Desmond
Published: January 2021

In a previous report, we found that mutations at the mitochondrial genome integrity locus, MGI1, can convert Kluyveromyces lactis into a petite-positive yeast. In this report, we describe the isolation of the MGI1 gene and show that it encodes the β-subunit of the mitochondrial F1-ATPase. The site of mutation in four independently isolated mgi1 alleles is at Arg435, which has changed to Gly in three cases and Ile in the fourth isolate. Disruption of MGI1 does not lead to the production of mitochondrial genome deletion mutants, indicating that an assembled F1 complex is needed for the “gain-of-function” phenotype found in mgi1 point mutants. The location of Arg435 in the β-subunit, as deduced from the three-dimensional structure of the bovine F1-ATPase, together with mutational sites in the previously identified mgi2 and mgi5 alleles, suggests that interaction of the β- and α- (MGI2) subunits with the γ-subunit (MGI5) is likely to be affected by the mutations.
Genetic and Physical Mapping of the Mouse Ulnaless Locus
Authors: Peichel Catherine L , Abbott Catherine M , Vogt Thomas F
Published: January 2021

The mouse Ulnaless locus is a semidominant mutation which displays defects in patterning along the proximal-distal and anterior-posterior axes of all four limbs. The first Ulnaless homozygotes have been generated, and they display a similar, though slightly more severe, limb phenotype than the heterozygotes. To create a refined genetic map of the Ulnaless region using molecular markers, four backcrosses segregating Ulnaless were established. A 0.4-cM interval containing the Ulnaless locus has been defined on mouse chromosome 2, which has identified Ulnaless as a possible allele of a Hoxd cluster gene(s). With this genetic map as a framework, a physical map of the Ulnaless region has been completed. Yeast artificial chromosomes covering this region have been isolated and ordered into a 2 Mb contig. Therefore, the region that must contain the Ulnaless locus has been defined and cloned, which will be invaluable for the identification of the molecular nature of the Ulnaless mutation.
Characterization of Maternal and Zygotic D-raf Proteins: Dominant Negative Effects on Torso Signal Transduction
Authors: Radke Kori , Baek Kwang-Hyun , Ambrosio Linda
Published: January 2021

The maternal D-raf serine/threonine kinase acts downstream of Torso (Tor) for specification of cell fates at the embryonic termini. D-raf activity is also required in other signal transduction pathways and consistent with its pleiotropic role, we find accumulation of a 90-kD D-raf protein throughout embryonic development. We also characterize the accumulation of maternal D-raf proteins in 0–2-hr embryos derived from females with germ cells lacking D-raf activity. Accumulation of a 90-kD or truncated mutant D-raf protein is observed for some of these embryos, while others lack the maternal D-raf protein. Then, to determine whether rescue of the Tor pathway is influenced by pools of nonfunctional maternal D-raf, wild-type D-raf mRNA was injected into embryos that inherit maternal stores of inactive 90-kD or truncated D-raf protein. For embryos lacking the maternal D-raf protein, a high level of terminal rescue is obtained. In contrast, rescue is reduced or not observed for embryos that accumulate mutant maternal D-raf proteins. These findings suggest that mutant forms of D-raf may deplete the embryo of a positive activator and/or form inactive protein complexes that affect rescue of the Tor pathway.
Mutations in the Saccharomyces cerevisiae Type 2A Protein Phosphatase Catalytic Subunit Reveal Roles in Cell Wall Integrity, Actin Cytoskeleton Organization and Mitosis
Authors: Evans David R H , Stark Michael J R
Published: January 2021

Temperature-sensitive mutations were generated in the Saccharomyces cerevisiae PPH22 gene that, together with its homologue PPH21, encode the catalytic subunit of type 2A protein phosphatase (PP2A). At the restrictive temperature (37°), cells dependent solely on pph22ts alleles for PP2A function displayed a rapid arrest of proliferation. Ts–  pph22 mutant cells underwent lysis at 37°, showing an accompanying viability loss that was suppressed by inclusion of 1 m sorbitol in the growth medium. Ts–  pph22 mutant cells also displayed defects in bud morphogenesis and polarization of the cortical actin cytoskeleton at 37°. PP2A is therefore required for maintenance of cell integrity and polarized growth. On transfer from 24° to 37°, Ts–  pph22 mutant cells accumulated a 2N DNA content indicating a cell cycle block before completion of mitosis. However, during prolonged incubation at 37°, many Ts–  pph22 mutant cells progressed through an aberrant nuclear division and accumulated multiple nuclei. Ts–  pph22 mutant cells also accumulated aberrant microtubule structures at 37°, while under semi-permissive conditions they were sensitive to the microtubule-destabilizing agent benomyl, suggesting that PP2A is required for normal microtubule function. Remarkably, the multiple defects of Ts–  pph22 mutant cells were suppressed by a viable allele (SSD1-v1) of the polymorphic SSD1 gene.
Bayesian Statistical Analyses for Presence of Single Genes Affecting Meat Quality Traits in a Crossed Pig Population
Authors: Janss L L G , Van Arendonk J A M , Brascamp E W
Published: January 2021

Presence of single genes affecting meat quality traits was investigated in F2 individuals of a cross between Chinese Meishan and Western pig lines using phenotypic measurements on 11 traits. A Bayesian approach was used for inference about a mixed model of inheritance, postulating effects of polygenic background genes, action of a biallelic autosomal single gene and various nongenetic effects. Cooking loss, drip loss, two pH measurements, intramuscular fat, shearforce and back-fat thickness were traits found to be likely influenced by a single gene. In all cases, a recessive allele was found, which likely originates from the Meishan breed and is absent in the Western founder lines. By studying associations between genotypes assigned to individuals based on phenotypic measurements for various traits, it was concluded that cooking loss, two pH measurements and possibly backfat thickness are influenced by one gene, and that a second gene influences intramuscular fat and possibly shearforce and drip loss. Statistical findings were supported by demonstrating marked differences in variances of families of fathers inferred as carriers and those inferred as noncarriers. It is concluded that further molecular genetic research effort to map single genes affecting these traits based on the same experimental data has a high probability of success.
MDP1, a Saccharomyces cerevisiae Gene Involved in Mitochondrial/Cytoplasmic Protein Distribution, Is Identical to the Ubiquitin-Protein Ligase Gene RSP5
Authors: Żołądek Teresa , Tobiasz Anna , Vaduva Gabriela , Boguta Magda , Martin Nancy C , Hopper Anita K
Published: January 2021

Alteration of the subcellular distribution of Mod5p-I, a tRNA modification enzyme, member of the sorting isozyme family, affects tRNA-mediated nonsense suppression. Altered suppression efficiency was used to identify MDP genes, which, when mutant, change the mitochondrial/cytosolic distribution of Mod5p-I,KR6. MDP2 is the previously identified VRP1, which encodes verprolin, required for proper organization of the actin cytoskeleton. MDP3 is identical to PAN1, which encodes a protein involved in initiation of translation and actin cytoskeleton organization. We report here the cloning and characterization of wild-type and mutant MDP1 alleles and the isolation and characterization of a multicopy suppressor of mdp1 mutations. MDP1 is identical to RSP5, which encodes ubiquitin-protein ligase, and mdp1 mutations are suppressed by high copy expression of ubiquitin. All four characterized mdp1 mutations cause missense changes located in the hect domain of Rsp5p that is highly conserved among ubiquitin-protein ligases. In addition to its well-known function in protein turnover, ubiquitination has been proposed to play roles in subcellular sorting of proteins via endocytosis and in delivery of proteins to peroxisomes, the endoplasmic reticulum and mitochondria. mdp1, as well as mdp2/vrp1 and mdp3/pan1 mutations, affect endocytosis. Further, mdp1 mutations show synthetic interactions with mdp2/vrp1 and mdp3/pan1. Identification of MDP1 as RSP5, along with our previous identification of MDP2/VRP1 and MDP3/PAN1, implicate interactions of the ubiquitin system, the actin cytoskeleton and protein synthesis in the subcellular distribution of proteins.
Alanine-Scanning Mutagenesis of Protein Phosphatase Type 1 in the Yeast Saccharomyces cerevisiae
Authors: Baker Stefanie H , Frederick Debra L , Bloecher Andrew , Tatchell Kelly
Published: January 2021

Protein phosphatase type 1, encoded by GLC7 in Saccharomyces cerevisiae, is an essential serine/threonine phosphatase implicated in the regulation of a diverse array of physiological functions. We constructed and examined 20 mutant alleles of GLC7 in which codons encoding clusters of charged residues were changed to alanine codons. Three of 20 mutant alleles alter residues in the active site of the phosphatase and are unable to rescue the lethality of a glc7::LEU2 disruption. The 17 alleles that support growth confer a range of mutant traits including cell cycle arrest, 2-deoxyglucose resistance, altered levels of glycogen, sensitivity to high salt, and sporulation defects. For some traits, such as 2-deoxyglucose resistance and cell cycle arrest, the mutated residues map to specific regions of the protein whereas the mutated residues in glycogen-deficient mutants and sporulation-defective mutants are more widely distributed over the protein surface. Many mutants have complex phenotypes, each displaying a diverse range of defects. The wide range of phenotypes identified from the collection of mutant alleles is consistent with the hypothesis that Glc7p-binding proteins, which are thought to regulate the specificity of Glc7p, have overlapping binding sites on the surface of Glc7p. This could account for the high level of sequence conservation found among type 1 protein phosphatases from different species.
Molecular Characterization of Two High Affinity Sulfate Transporters in Saccharomyces cerevisiae
Authors: Cherest Hélène , Davidian Jean-Claude , Thomas Dominique , Benes Vladimir , Ansorge Wilhelm , Surdin-Kerjan Yolande
Published: January 2021

Strains resistant to the toxic analogues of sulfate, selenate and chromate have been isolated. Their genetic analysis allowed us to identify four genes. One, called MET28, encodes a transcriptional factor. The three other genes, called SUL1, SUL2 and SUL3, encode proteins involved in sulfate transport. The sequence of Sul1p and Sul2p indicate that they are integral membrane proteins exhibiting, respectively, 11 and 10 transmembrane domains. Moreover, Sul1p and Sul2p share a high degree of similarity. Sulfate transport kinetic studies made with parental and mutant strains show that, as expected from genetic results, Saccharomyces cerevisiae has two high affinity sulfate transport systems. Sul3p has been shown to be involved in the transcriptional regulation of the SUL2 gene.
Structural and Functional Differences in the Promoter and 5′ Flanking Region of Ldh-B Within and Between Populations of the Teleost Fundulus heteroclitus
Authors: Schulte Patricia M , Gómez-Chiarri Marta , Powers Dennis A
Published: January 2021

We have investigated the mechanisms underlying differences in the transcriptional regulation of lactate dehydrogenase-B (Ldh-B) between northern and southern populations of a teleost fish, Fundulus heteroclitus. A 1-kb region immediately 5′ of the gene was sequenced from populations throughout the species range. There were two major allele classes in the sample, one containing alleles from Maine and another containing those from Florida. Populations from intermediate localities contained both allele classes. Some individuals from Georgia had sequences intermediate between the two classes, representing either ancestral alleles or recombinants. Tests of neutrality were applied to determine whether observed variation was consistent with neutral expectations. Significant deviations from neutral expectations were detected for the 5′ flanking region, but not for other loci. The functional consequences of flanking sequence variation were assessed by transfection of reporter gene constructs into cultured cells and injection into living fish. Consistent with observed variation in Ldh-B transcription rate between populations, significant differences in reporter gene activity were driven by flanking regions from northern and southern populations both in cell culture and in vivo. This functional differentiation, coupled with departures from neutral expectations, suggests that selection may have acted on the regulation of Ldh-B in F. heteroclitus.
A Method of Estimating the Numbers of Human and Mouse Immunoglobulin V-Genes
Authors: Johnson George , Wu Tai T
Published: January 2021

Mutations in immunoglobulin V-genes can be due to gene multiplication, allelic variations, mutations induced by antigens or somatic mutations, etc., and various combinations of these. Since the number of different mouse lambda light V-gene nucleotide sequences is relatively small, a pairwise comparison between these sequences can provide a rough idea as to the contributions of the above mechanisms to the number of nucleotide differences between sequences. A plot of occurrences against the number of differences suggests that differences between one to five can be attributed to somatic mutations. Six to 12 differences can be allelic. Thirteen to 17 may be due to allelic variations together with somatic mutations. Differences >17 appear to be derived from gene multiplication. Although these numbers are most likely somewhat different in humans, they can nevertheless provide a rough guide to sort out the effect of gene multiplication. Estimations of human heavy, kappa and lambda light chain immunoglobulin V-genes are in reasonably good agreement with recent experimental studies. For mouse kappa light and heavy chains, our estimations can provide some insight to future analyses by direct sequencing of these gene segments.
The Geographic Distribution of Human Y Chromosome Variation
Authors: Hammer M F , Spurdle A B , Karafet T , Bonner M R , Wood E T , Novelletto A , Malaspina P , Mitchell R J , Horai S , Jenkins T , Zegura S L
Published: January 2021

We examined variation on the nonrecombining portion of the human Y chromosome to investigate human evolution during the last 200,000 years. The Y-specific polymorphic sites included the Y Alu insertional polymorphism or “YAP” element (DYS287), the poly(A) tail associated with the YAP element, three point mutations in close association with the YAP insertion site, an A-G polymorphic transition (DYS271), and a tetranucleotide microsatellite (DYS19). Global variation at the five bi-allelic sites (DYS271, DYS287, and the three point mutations) gave rise to five “YAP haplotypes” in 60 populations from Africa, Europe, Asia, Australasia, and the New World (n = 1500). Combining the multi-allelic variation at the microsatellite loci (poly(A) tail and DYS19) with the YAP haplotypes resulted in a total of 27 “combination haplotypes”. All five of the YAP haplotypes and 21 of the 27 combination haplotypes were found in African populations, which had greater haplotype diversity than did populations from other geographical locations. Only subsets of the five YAP haplotypes were found outside of Africa. Patterns of observed variation were compatible with a variety of hypotheses, including multiple human migrations and range expansions.
A Coalescent Estimator of the Population Recombination Rate
Authors: Hey Jody , Wakeley John
Published: January 2021

Population genetic models often use a population recombination parameter 4Nc, where N is the effective population size and c is the recombination rate per generation. In many ways 4Nc is comparable to 4Nu, the population mutation rate. Both combine genome level and population level processes, and together they describe the rate of production of genetic variation in a population. However, 4Nc is more difficult to estimate. For a population sample of DNA sequences, historical recombination can only be detected if polymorphisms exist, and even then most recombination events are not detectable. This paper describes an estimator of 4Nc, hereafter designated γ (gamma), that was developed using a coalescent model for a sample of four DNA sequences with recombination. The reliability of γ was assessed using multiple coalescent simulations. In general γ has low to moderate bias, and the reliability of γ is comparable, though less, than that for a widely used estimator of 4Nu. If there exists an independent estimate of the recombination rate (per generation, per base pair), γ can be used to estimate the effective population size or the neutral mutation rate.
Competition Between Different Variegating Rearrangements for Limited Heterochromatic Factors in Drosophila melanogaster
Authors: Lloyd Vett K , Sinclair Donald A , Grigliatti Thomas A
Published: January 2021

Position effect variegation (PEV) results from the juxtaposition of a euchromatic gene to heterochromatin. In its new position the gene is inactivated in some cells and not in others. This mosaic expression is consistent with variability in the spread of heterochromatin from cell to cell. As many components of heterochromatin are likely to be produced in limited amounts, the spread of heterochromatin into a normally euchromatic region should be accompanied by a concomitant loss or redistribution of the protein components from other heterochromatic regions. We have shown that this is the case by simultaneously monitoring variegation of a euchromatic and a heterochromatic gene associated with a single chromosome rearrangement. Secondly, if several heterochromatic regions of the genome share limited components of heterochromatin, then some variegating rearrangements should compete for these components. We have examined this hypothesis by testing flies with combinations of two or more different variegating rearrangements. Of the nine combinations of pairs of variegating rearrangements we studied, seven showed nonreciprocal interactions. These results imply that many components of heterochromatin are both shared and present in limited amounts and that they can transfer between chromosomal sites. Consequently, even nonvariegation portions of the genome will be disrupted by re-allocation of heterochromatic proteins associated with PEV. These results have implications for models of PEV.
Embryonic Expression and Evolution of Duplicated E-Protein Genes in Xenopus laevis: Parallels With Ancestral E-Protein Genes
Authors: Shah Daniel H , Neuman Toomas , Zuber Mauricio X
Published: January 2021

E-proteins comprise a subfamily of helix-loop-helix transcription factors that have been identified in arthropods and several chordate taxa. In mammals, there are three classes of E-protein genes (E2A, E2-2, and HEB) that encode related, and often interchangeable, gene products. We have determined that the clawed frog Xenopus laevis contains twice the number of transcriptionally active E-protein genes when compared with other vertebrate species. Based upon genomic Southern blots and nucleotide sequence comparisons, it is likely that the additional X. laevis genes arose from tetraploidization. During embryogenesis, XE2A (homologue of mammalian E2A) transcripts were broadly expressed in anterior and posterior regions of the embryo while homologues of E2-2 (XE2.2) and HEB (XE1.2) appeared in vertebrate-specific structures including the pineal gland, olfactory bulb, and brachial arches. A phylogenetic analysis of these genes and other known metazoan E-proteins suggests that there were two periods of marked E-protein gene expansion; one that predated the radiation of vertebrates, and the other that coincided with Xenopus tetraploidization. Both of these periods were characterized by the rapid evolution of E2-2 and HEB-class genes, but not of E2A. We propose that the former genes acquired new or specialized roles during early chordate evolution and also more recently in Xenopus, as reflected by the stereotypic expression patterns of these genes during X. laevis development.
Linkage Mapping in Experimental Crosses: The Robustness of Single-Gene Models
Authors: Wright Fred A , Kong Augustine
Published: January 2021

The robustness of parametric linkage mapping against model misspecification is considered in experimental breeding designs, with a focus on localization of the gene. By examining the expected LOD across the genome, it is shown that single-gene models are quite robust, even for polygenic traits. However, when the marker map is of low resolution, linked polygenes can give rise to an apparent “ghost” gene, mapped to an incorrect interval. The results apply equally well to quantitative traits or qualitative (categorical) traits. The results are derived for backcross populations, with a discussion of extensions to intercross populations and relative-pair mapping in humans.
Meiotic Crossing Over Between Nonhomologous Chromosomes Affects Chromosome Segregation in Yeast
Authors: Jinks-Robertson Sue , Sayeed Shariq , Murphy Tamara
Published: January 2021

Meiotic recombination between artificial repeats positioned on nonhomologous chromosomes occurs efficiently in the yeast Saccharomyces cerevisiae. Both gene conversion and crossover eventS have been observed, with crossovers yielding reciprocal translocations. In the current study, 5.5-kb ura3 repeats positioned on chromosomes V and XV were used to examine the effect of ectopic recombination on meiotic chromosome segregation. Ura+ random spores were selected and gene conversion vs. crossover events were distinguished by Southern blot analysis. Approximately 15% of the crossover events between chromosomes V and XV were associated with missegregation of one of these chromosomes. The missegregation was manifest as hyperploid spores containing either both translocations plus a normal chromosome, or both normal chromosomes plus one of the translocations. In those cases where it could be analyzed, missegregation occurred at the first meiotic division. These data are discussed in terms of a model in which ectopic crossovers compete efficiently with normal allelic crossovers in directing meiotic chromosome segregation.