bluuebunny/crossref_metadata_2025 huggingface dataset:
Fission Yeast cdc24+ Encodes a Novel Replication Factor Required for Chromosome Integrity
Authors: Gould Kathleen L , Burns C Geoffrey , Feoktistova Anna , Hu Ching-Pei , Pasion Sally G , Forsburg Susan L
Published: April 2021

A mutation within the Schizosaccharomyces pombe cdc24+ gene was identified previously in a screen for cell division cycle mutants and the cdc24+ gene was determined to be essential for S phase in this yeast. We have isolated the cdc24+ gene by complementation of a new temperature-sensitive allele of the gene, cdc24-G1. The DNA sequence predicts the presence of an open reading frame punctuated by six introns which encodes a pioneer protein of 58 kD. A cdc24 null mutant was generated by homologous recombination. Haploid cells lacking cdc24+ are inviable, indicating that cdc24+ is an essential gene. The transcript of cdc24+ is present at constant levels throughout the cell cycle. Cells lacking cdc24+ function show a checkpoint-dependent arrest with a 2N DNA content, indicating a block late in S phase. Arrest is accompanied by a rapid loss of viability and chromosome breakage. An S. pombe homolog of the replicative DNA helicase DNA2 of S. cerevisiae suppresses cdc24. These results suggest that Cdc24p plays a role in the progression of normal DNA replication and is required to maintain genomic integrity.
The PBN1 Gene of Saccharomyces cerevisiae: An Essential Gene That Is Required for the Post-translational Processing of the Protease B Precursor
Authors: Naik Rajesh R , Jones Elizabeth W
Published: April 2021

The vacuolar hydrolase protease B in Saccharomyces cerevisiae is synthesized as an inactive precursor (Prb1p). The precursor undergoes post-translational modifications while transiting the secretory pathway. In addition to N- and O -linked glycosylations, four proteolytic cleavages occur during the maturation of Prb1p. Removal of the signal peptide by signal peptidase and the autocatalytic cleavage of the large aminoterminal propeptide occur in the endoplasmic reticulum (ER). Two carboxy-terminal cleavages of the post regions occur in the vacuole: the first cleavage is catalyzed by protease A and the second results from autocatalysis. We have isolated a mutant, pbn1-1, that exhibits a defect in the ER processing of Prb1p. The autocatalytic cleavage of the propeptide from Prb1p does not occur and Prb1p is rapidly degraded in the cytosol. PBN1 was cloned and is identical to YCL052c on chromosome III. PBN1 is an essential gene that encodes a novel protein. Pbn1p is predicted to contain a sub-C-terminal transmembrane domain but no signal sequence. A functional HA epitope-tagged Pbn1p fusion localizes to the ER. Pbn1p is N-glycosylated in its amino-terminal domain, indicating a lumenal orientation despite the lack of a signal sequence. Based on these results, we propose that one of the functions of Pbn1p is to aid in the autocatalytic processing of Prb1p.
Evaluating Gene Flow Using Selected Markers: A Case Study
Authors: Lenormand Thomas , Guillemaud Thomas , Bourguet Denis , Raymond Michel
Published: April 2021

The extent to which an organism is locally adapted in an environmental pocket depends on the selection intensities inside and outside the pocket, on migration, and on the size of the pocket. When two or more loci are involved in this local adaptation, measuring their frequency gradients and their linkage disequilbria allows one to disentangle the forces—migration and selection—acting on the system. We apply this method to the case of a local adaptation to organophosphate insecticides in the mosquito Culex pipiens pipiens in southern France. The study of two different resistance loci allowed us to estimate with support limits gene flow as well as selection pressure on insecticide resistance and the fitness costs associated with each locus. These estimates permit us to pinpoint the conditions for the maintenance of this pocket of adaptation as well as the effect of the interaction between the two resistance loci.
Chromosome Rearrangements Induce Both Variegated and Reduced, Uniform Expression of Heterochromatic Genes in a Development-Specific Manner
Authors: Weiler Karen S , Wakimoto Barbara T
Published: April 2021

In Drosophila melanogaster, chromosome rearrangements that juxtapose euchromatin and heterochromatin can result in position effect variegation (PEV), the variable expression of heterochromatic and euchromatic genes in the vicinity of the novel breakpoint. We examined PEV of the heterochromatic light (lt) and concertina (cta) genes in order to investigate potential tissue or developmental differences in chromosome structure that might be informative for comparing the mechanisms of PEV of heterochromatic and euchromatic genes. We employed tissue pigmentation and in situ hybridization to RNA to assess expression of lt in individual cells of multiple tissues during development. Variegation of lt was induced in the adult eye, larval salivary glands and larval Malpighian tubules for each of three different chromosome rearrangements. The relative severity of the effect in these tissues was not tissue-specific but rather was characteristic of each rearrangement. Surprisingly, larval imaginal discs did not exhibit variegated lt expression. Instead, a uniform reduction of the lt transcript was observed, which correlated in magnitude with the degree of variegation. The same results were obtained for cta expression. These two distinct effects of rearrangements on heterochromatic gene expression correlated with the developmental stage of the tissue. These results have implications for models of heterochromatin formation and the nuclear organization of chromosomes during development and differentiation.
Linkage Relationships and Haplotype Polymorphism Among Cichlid Mhc Class II B Loci
Authors: Málaga-Trillo Edward , Zaleska-Rutczynska Zofia , McAndrew Brendan , Vincek Vladimir , Figueroa Felipe , Sültmann Holger , Klein Jan
Published: April 2021

The species flocks of cichlid fishes in the Great East African Lakes are paradigms of adaptive radiation and hence, of great interest to evolutionary biologists. Phylogenetic studies of these fishes have, however, been hampered by the lack of suitable polymorphic markers. The genes of the major histocompatibility complex hold the promise to provide, through their extensive polymorphism, a large number of such markers, but their use has been hampered by the complexity of the genetic system and the lack of definition of the individual loci. In this study we take the first substantial step to alleviate this problem. Using a combination of methods, including the typing of single sperm cells, gyno- or androgenetic individuals, and haploid embryos, as well as sequencing of class II B restriction fragments isolated from gels for Southern blots, we identify the previously characterized homology groups as distinct loci. At least 17 polymorphic class II B loci, all of which are presumably transcribed, have been found among the different species studied. Most of these loci are shared across the various cichlid species and genera. The number of loci per haplotype varies from individual to individual, ranging from 1 to 13. A total of 21 distinct haplotypes differing in the number of loci they carry has thus far been identified. All the polymorphic loci are part of the same cluster in which, however, distances between at least some of the loci (as indicated by recombination frequencies) are relatively large. Both the individual loci and the haplotypes can now be used to study phylogenetic relationships among the members of the species flocks and the mode in which speciation occurs during adaptive radiation.
Characterization of an Unstable Allele of the Arabidopsis HY4 Locus
Authors: Bruggemann Edward P , Doan Bernard , Handwerger Korie , Storz Gisela
Published: April 2021

The Arabidopsis HY4 gene encodes the nonessential blue light photoreceptor CRY1. Loss-of-function hy4 mutants have an elongated hypocotyl phenotype after germination under blue light. We previously analyzed 20 independent hy4 alleles produced by fast neutron mutagenesis. These alleles were grouped into two classes based on their genetic behavior and corresponding deletion size: (1) null hy4 alleles that were semidominant over wild type and contained small or moderate-sized deletions at HY4 and (2) null hy4 alleles that were recessive lethal and contained large HY4 deletions. Here we describe one additional fast neutron hy4 mutant, B144, that did not fall into either of these two classes. Mutant B144 was isolated as a heterozygote with an intermediate hy4 phenotype. One allele from this mutant, hy4-B144Δ, contains a large deletion at HY4 and is recessive lethal. The other allele from this mutant, HY4-B144*, appears to be intact and functional but is unstable and spontaneously converts to a nonfunctional hy4 allele. In addition, HY4-B144* is lethal in homozygotes and suppresses local recombination. We discuss genetic and epigenetic mechanisms that may account for the unusual behavior of the HY4-B144* allele.
In Vivo Identification of Intermediate Stages of the DNA Inversion Reaction Catalyzed by the Salmonella Hin Recombinase
Authors: Nanassy Oliver Z , Hughes Kelly T
Published: April 2021

The Hin recombinase catalyzes a site-specific recombination reaction that results in the reversible inversion of a 1-kbp segment of the Salmonella chromosome. The DNA inversion reaction catalyzed by the Salmonella Hin recombinase is a dynamic process proceeding through many intermediate stages, requiring multiple DNA sites and the Fis accessory protein. Biochemical analysis of this reaction has identified intermediate steps in the inversion reaction but has not yet revealed the process by which transition from one step to another occurs. Because transition from one reaction step to another proceeds through interactions between specific amino acids, and between amino acids and DNA bases, it is possible to study these transitions through mutational analysis of the proteins involved. We isolated a large number of mutants in the Hin recombinase that failed to carry out the DNA exchange reaction. We generated genetic tools that allowed the assignment of these mutants to specific transition steps in the recombination reaction. This genetic analysis, combined with further biochemical analysis, allowed us to define contributions by specific amino acids to individual steps in the DNA inversion reaction. Evidence is also presented in support of a model that Fis protein enhances the binding of Hin to the hixR recombination site. These studies identified regions within the Hin recombinase involved in specific transition steps of the reaction and provided new insights into the molecular details of the reaction mechanism.
Efficient Repair of All Types of Single-Base Mismatches in Recombination Intermediates in Chinese Hamster Ovary Cells: Competition Between Long-Patch and G-T Glycosylase-Mediated Repair of G-T Mismatches
Authors: Bill Colin A , Duran Walter A , Miselis Nathan R , Nickoloff Jac A
Published: April 2021

Repair of all 12 single-base mismatches in recombination intermediates was investigated in Chinese hamster ovary cells. Extrachromosomal recombination was stimulated by double-strand breaks in regions of shared homology. Recombination was predicted to occur via single-strand annealing, yielding heteroduplex DNA (hDNA) with a single mismatch. Nicks were expected on opposite strands flanking hDNA, equidistant from the mismatch. Unlike studies of covalently closed artificial hDNA substrates, all mismatches were efficiently repaired, consistent with a nick-driven repair process. The average repair efficiency for all mispairs was 92%, with no significant differences among mispairs. There was significant strand-independent repair of G-T → G-C, with a slightly greater bias in a CpG context. Repair of C-A was also biased (toward C-G), but no A-C → G-C bias was found, a possible sequence context effect. No other mismatches showed evidence of biased repair, but among hetero-mismatches, the trend was toward retention of C or G vs. A or T. Repair of both T-T and G-T mismatches was much less efficient in mismatch repair-deficient cells (~25%), and the residual G-T repair was completely biased toward G-C. Our data indicate that single-base mismatches in recombination intermediates are substrates for at least two competing repair systems.
Mapping Quantitative Trait Loci for Milk Production and Health of Dairy Cattle in a Large Outbred Pedigree
Authors: Zhang Qin , Boichard Didier , Hoeschele Ina , Ernst Cynthia , Eggen Andre , Murkve B , Pfister-Genskow Margaret , Witte LaRee A , Grignola Fernando E , Uimari Pekka , Thaller Georg , Bishop Michael D
Published: April 2021

Quantitative trait loci (QTL) affecting milk production and health of dairy cattle were mapped in a very large Holstein granddaughter design. The analysis included 1794 sons of 14 sires and 206 genetic markers distributed across all 29 autosomes and flanking an estimated 2497 autosomal cM using Kosambi's mapping function. All families were analyzed jointly with least-squares (LS) and variance components (VC) methods. A total of 6 QTL exceeding approximate experiment-wise significance thresholds, 24 QTL exceeding suggestive thresholds, and 34 QTL exceeding chromosome-wise thresholds were identified. Significance thresholds were determined via data permutation (for LS analysis) and chi-square distribution (for VC analysis). The average bootstrap confidence interval for the experiment-wise significant QTL was 48 cM. Some chromosomes harbored QTL affecting several traits, and these were always in coupling phase, defined by consistency with genetic correlations among traits. Chromosome 17 likely harbors 2 QTL affecting milk yield, and some other chromosomes showed some evidence for 2 linked QTL affecting the same trait. In each of these cases, the 2 QTL were in repulsion phase in those families appearing to be heterozygous for both QTL, a finding which supports the build-up of linkage disequilibrium due to selection.
Effects of Differential Selection in the Sexes on Cytonuclear Dynamics: Life Stages With Sex Differences
Authors: Babcock Christina S , Asmussen Marjorie A
Published: April 2021

We extend our investigation of cytonuclear selection by determining when differential selection between the sexes will generate allele frequency changes or cytonuclear disequilibria in populations with constant viability selection and an adult census. We demonstrate analytically that there can be a cytonuclear hitchhiking effect upon a selectively neutral marker in either sex provided the other marker is selected in that sex and there is allelic disequilibrium between the loci in females. Cytonuclear disequilibria are generated de novo in both sexes when both loci affect fitness in females and there is a nonmultiplicative fitness interaction between them. Similar fitness interactions in males generate male disequilibria only. Through numerical analyses, we investigate the potential magnitude of such disequilibria, their qualitative dynamics, the expected frequency of detectable disequilibria under particular patterns or strengths of selection, and the possible disequilibrium sign patterns resulting from selection. These adult/viability results subsume those for populations with a gamete census and either constant fertility or viability selection. Although previous work suggests that the disequilibria generated by cytonuclear selection may be difficult to detect experimentally, this study shows that cytonuclear disequilibria at life stages with sex differences can be useful markers of the presence and strength of selection.
Germline Bottlenecks and the Evolutionary Maintenance of Mitochondrial Genomes
Authors: Bergstrom Carl T , Pritchard Jonathan
Published: April 2021

Several features of the biology of mitochondria suggest that mitochondria might be susceptible to Muller's ratchet and other forms of evolutionary degradation: Mitochondria have predominantly uniparental inheritance, appear to be nonrecombining, and have high mutation rates producing significant deleterious variation. We demonstrate that the persistence of mitochondria may be explained by recent data that point to a severe “bottleneck” in the number of mitochondria passing through the germline in humans and other mammals. We present a population-genetic model in which deleterious mutations arise within individual mitochondria, while selection operates on assemblages of mitochondria at the level of their eukaryotic hosts. We show that a bottleneck increases the efficacy of selection against deleterious mutations by increasing the variance in fitness among eukaryotic hosts. We investigate both the equilibrium distribution of deleterious variation in large populations and the dynamics of Muller's ratchet in small populations. We find that in the absence of the ratchet, a bottleneck leads to improved mitochondrial performance and that, over a longer time scale, a bottleneck acts to slow the progression of the ratchet.
Molecular Evolution of the Cecropin Multigene Family in Drosophila: Functional Genes vs. Pseudogenes
Authors: Ramos-Onsins Sebastián , Aguadé Montserrat
Published: April 2021

Approximately 4 kb of the Cecropin cluster region have been sequenced in nine lines of Drosophila melanogaster and one line of the sibling species D. simulans, D. mauritiana, and D. sechellia. This region includes three functional genes (CecA1, CecA2, and CecB), which are involved in the insect immune response, and two pseudogenes (CecΨ1 and CecΨ2). The level of silent polymorphism in the three Cec genes is rather high (0.028), and there is no excess of nonsynonymous polymorphism. There is no evidence of gene conversion in the history of these genes. The interspecific comparison has revealed that in the three species of the simulans cluster the CecA2 gene is partially deleted and has therefore lost its function and become a pseudogene; in each of the species, subsequent deletions have accumulated. Divergence estimates indicate that the CecΨ1 and CecΨ2 pseudogenes are highly diverged, both between themselves and relative to the other three Cec genes. However, both CecΨ1 and CecΨ2 have conserved transcriptional signals and splice sites, and they present an open reading frame; also, correctly spliced transcripts have been detected for both CecΨ1 and CecΨ2. The data support that these genes are either active genes with some null alleles or young pseudogenes.
Identification of Functional Connections Between Calmodulin and the Yeast Actin Cytoskeleton
Authors: Sekiya-Kawasaki Mariko , Botstein David , Ohya Yoshikazu
Published: April 2021

One of four intragenic complementing groups of temperature-sensitive yeast calmodulin mutations, cmd1A, results in a characteristic functional defect in actin organization. We report here that among the complementing mutations, a representative cmd1A mutation (cmd1-226: F92A) is synthetically lethal with a mutation in MYO2 that encodes a class V unconventional myosin with calmodulin-binding domains. Gel overlay assay shows that a mutant calmodulin with the F92A alteration has severely reduced binding affinity to a GST-Myo2p fusion protein. Random replacement and site-directed mutagenesis at position 92 of calmodulin indicate that hydrophobic and aromatic residues are allowed at this position, suggesting an importance of hydrophobic interaction between calmodulin and Myo2p. To analyze other components involved in actin organization through calmodulin, we isolated and characterized mutations that show synthetic lethal interaction with cmd1-226; these “cax” mutants fell into five complementation groups. Interestingly, all the mutations themselves affect actin organization. Unlike cax2, cax3, cax4, and cax5 mutations, cax1 shows allele-specific synthetic lethality with the cmd1A allele. CAX1 is identical to ANP1/GEM3/MCD2, which is involved in protein glycosylation. CAX4 is identical to the ORF YGR036c, and CAX5 is identical to MNN10/SLC2/BED1. We discuss possible roles for Cax proteins in the regulation of the actin cytoskeleton.
Statistical Analysis of Ordered Tetrads
Authors: Zhao Hongyu , Speed Terence P
Published: April 2021

Ordered tetrad data yield information on chromatid interference, chiasma interference, and centromere locations. In this article, we show that the assumption of no chromatid interference imposes certain constraints on multilocus ordered tetrad probabilities. Assuming no chromatid interference, these constraints can be used to order markers under general chiasma processes. We also derive multilocus tetrad probabilities under a class of chiasma interference models, the chi-square models. Finally, we compare centromere map functions under the chi-square models with map functions proposed in the literature. Results in this article can be applied to order genetic markers and map centromeres using multilocus ordered tetrad data.
P-Element Insertion at the polyhomeotic Gene Leads to Formation of a Novel Chimeric Protein That Negatively Regulates yellow Gene Expression in P-Element-Induced Alleles of Drosophila melanogaster
Authors: Belenkaya Tatiana , Soldatov Alexey , Nabirochkina Elena , Birjukova Inna , Georgieva Sofia , Georgiev Pavel
Published: April 2021

Polyhomeotic is a member of the Polycomb group (Pc-G) of homeotic repressors. The proteins encoded by the Pc-G genes form repressive complexes on the polycomb group response element sites. The phP1 mutation was induced by insertion of a 1.2-kb P element into the 5′ transcribed nontranslated region of the proximal polyhomeotic gene. The phP1 allele confers no mutant phenotype, but represses transcription of P-element-induced alleles at the yellow locus. The phP1 allele encodes a chimeric P-PH protein, consisting of the DNA-binding domain of the P element and the PH protein lacking 12 amino-terminal amino acids. The P-PH, Polycomb (PC), and Posterior sex combs (PSC) proteins were immunohistochemically detected on polytene chromosomes in the regions of P-element insertions.
Y-Linked Male Sterile Mutations Induced by P Element in Drosophila melanogaster
Authors: Zhang Ping , Stankiewicz Rebecca L
Published: April 2021

The Y chromosome in Drosophila melanogaster is composed of highly repetitive sequences and is essential only in the male germ line. We employed P-element insertional mutagenesis to induce male sterile mutations in the Y chromosome. By using a combination of two modifiers of position effect variegation, adding an extra Y chromosome and increasing temperature, we isolated 61 P(ry+) elements in the Y chromosome. Six of these Y-linked insertions (approximately 10%) induced male sterile mutations that are mapped to two genes on the long and one on the short arms of the Y chromosome. These mutations are revertible to the wild type in a cell-autonomous and germ-line-dependent manner, consistent with previously defined Y-linked gene functions. Phenotypes associated with these P-induced mutations are similar to those resulting from deletions of the Y chromosome regions corresponding to the male fertility genes. Three alleles of the kl-3 gene on the Y long arm result in loss of the axonemal outer dynein arms in the spermatid tail, while three ks-2 alleles on the Y short arm induce defects at early postmeiotic stages. The recovery of the ms(Y) mutations induced by single P-element insertions will facilitate our effort to understand the structural and functional properties of the Y chromosome.
Accumulation of mRNA Coding for the Ctf13p Kinetochore Subunit of Saccharomyces cerevisiae Depends on the Same Factors That Promote Rapid Decay of Nonsense mRNAs
Authors: Dahlseid Jeffrey N , Puziss John , Shirley Renee L , Atkin Audrey L , Hieter Philip , Culbertson Michael R
Published: April 2021

The CTF13 gene codes for a subunit of the kinetochore in Saccharomyces cerevisiae. The temperature-sensitive mutation ctf13-30, which confers reduced fidelity of chromosome transmission, is a G → A transition causing an amino acid substitution of Lys for Glu146. Strains carrying one chromosomal copy of ctf13-30 fail to grow at the restrictive temperature, whereas a haploid strain carrying two copies of ctf13-30 can grow. Four genes, UPF1, UPF2, UPF3, and ICK1, were represented among extragenic suppressors of ctf13-30. The UPF genes encode proteins that promote rapid decay of pre-mRNAs and mRNAs containing a premature stop codon. Suppressor mutations in these genes restore kinetochore function by causing increased accumulation of ctf13-30 mRNA. They also cause increased accumulation of CYH2 pre-mRNA, which is a natural target of UPF-mediated decay. Mutations in ICK1 restore kinetochore function but have no effect on ctf13-30 mRNA or CYH2 pre-mRNA accumulation. Most importantly, loss of UPF1 function causes increased accumulation of wild-type CTF13 mRNA but has no effect on the mRNA half-life. We propose that UPF-mediated decay modulates the mRNA level of one or more factors involved in CTF13 mRNA expression.
Functions of the Caenorhabditis elegans Regulatory Myosin Light Chain Genes mlc-1 and mlc-2
Authors: Rushforth Alice M , White Claudia Cummins , Anderson Philip
Published: April 2021

Caenorhabditis elegans contains two muscle regulatory myosin light chain genes, mlc-1 and mlc-2. To determine their in vivo roles, we identified deletions that eliminate each gene individually and both genes in combination. Functions of mlc-1 are redundant to those of mlc-2 in both body-wall and pharyngeal muscle. mlc-1(0) mutants are wild type, but mlc-1(0) mlc-2(0) double mutants arrest as incompletely elongated L1 larvae, having both pharyngeal and body-wall muscle defects. Transgenic copies of either mlc-1(+) or mlc-2(+) rescue all defects of mlc-1(0) mlc-2(0) double mutants. mlc-2 is redundant to mlc-1 in body-wall muscle, but mlc-2 performs a nearly essential role in the pharynx. Approximately 90% of mlc-2(0) hermaphrodites arrest as L1 larvae due to pharyngeal muscle defects. Lethality of mlc-2(0) mutants is sex specific, with mlc-2(0) males being essentially wild type. Four observations suggest that hermaphrodite-specific lethality of mlc-2(0) mutants results from insufficient expression of the X-linked mlc-1(+) gene in the pharynx. First, mlc-1(0) mlc-2(0) double mutants are fully penetrant L1 lethals in both hermaphrodites and males. Second, in situ localization of mlc mRNAs demonstrates that both mlc-1 and mlc-2 are expressed in the pharynx. Third, transgenic copies of either mlc-1(+) or mlc-2(+) rescue the pharyngeal defects of mlc-1(0) mlc-2(0) hermaphrodites. Fourth, a mutation of the dosage compensation gene sdc-3 suppresses hermaphrodite-specific lethality of mlc-2(0) mutants.
The Male-Sterility Polymorphism of Silene vulgaris: Analysis of Genetic Data From Two Populations and Comparison With Thymus vulgaris
Authors: Charlesworth D , Laporte Valérie
Published: April 2021

Results are given of genetic studies of male sterility using plants from two natural populations from Sussex, England. Both populations have substantial frequencies of females, ∼0.25 in population 1 and 0.60 in population 3. As in the few other gynodioecious populations studied in detail, many genetic factors are present. In population 1, there are at least two, and more likely three, different cytoplasmic types, one of which appears to produce male sterility in progeny from any hermaphrodite pollen donor; in other words restorer alleles for this cytoplasm are rare or absent from the population. The other two populations can be carried in hermaphrodites that have the dominant restorers. In population 1, there are also probably three restorer loci with complementary recessive male-sterility alleles, as well as a locus with duplicate action, which cannot produce male sterility unless the plant is also homozygous for the recessive allele at another locus. The results from population 3 are quite similar, though there was no evidence in this population for an unrestored sterility cytoplasm. A similar joint nucleocytoplasmic model with multiple restorers fits data from Thymus vulgaris.
Novel Mutations in the RAD3 and SSL1 Genes Perturb Genome Stability by Stimulating Recombination Between Short Repeats in Saccharomyces cerevisiae
Authors: Maines Silvina , Negritto M Cristina , Wu Xuli , Manthey Glenn M , Bailis Adam M
Published: April 2021

Maintaining genome stability requires that recombination between repetitive sequences be avoided. Because short, repetitive sequences are the most abundant, recombination between sequences that are below a certain length are selectively restricted. Novel alleles of the RAD3 and SSL1 genes, which code for components of a basal transcription and UV-damage-repair complex in Saccharomyces cerevisiae, have been found to stimulate recombination between short, repeated sequences. In double mutants, these effects are suppressed, indicating that the RAD3 and SSL1 gene products work together in influencing genome stability. Genetic analysis indicates that this function is independent of UV-damage repair and mutation avoidance, supporting the notion that RAD3 and SSL1 together play a novel role in the maintenance of genome integrity.
Detecting Linkage Disequilibrium in Bacterial Populations
Authors: Haubold Bernhard , Travisano Michael , Rainey Paul B , Hudson Richard R
Published: April 2021

The distribution of the number of pairwise differences calculated from comparisons between n haploid genomes has frequently been used as a starting point for testing the hypothesis of linkage equilibrium. For this purpose the variance of the pairwise differences, VD, is used as a test statistic to evaluate the null hypothesis that all loci are in linkage equilibrium. The problem is to determine the critical value of the distribution of VD. This critical value can be estimated either by Monte Carlo simulation or by assuming that VD is distributed normally and calculating a one-tailed 95% critical value for VD, L, L = E(VD) + 1.645 Var(VD), where E(VD) is the expectation of VD, and Var(VD) is the variance of VD. If VD (observed) > L, the null hypothesis of linkage equilibrium is rejected. Using Monte Carlo simulation we show that the formula currently available for Var(VD) is incorrect, especially for genetically highly diverse data. This has implications for hypothesis testing in bacterial populations, which are often genetically highly diverse. For this reason we derive a new, exact formula for Var(VD). The distribution of VD is examined and shown to approach normality as the sample size increases. This makes the new formula a useful tool in the investigation of large data sets, where testing for linkage using Monte Carlo simulation can be very time consuming. Application of the new formula, in conjunction with Monte Carlo simulation, to populations of Bradyrhizobium japonicum, Rhizobium leguminosarum, and Bacillus subtilis reveals linkage disequilibrium where linkage equilibrium has previously been reported.
Negative Covariance Suggests Mutation Bias in a Two-Locus Microsatellite System in the Fish Sparus aurata
Authors: Dermitzakis Emmanouil T , Clark Andrew G , Batargias Costas , Magoulas Antonios , Zouros Eleftherios
Published: April 2021

Constraints on microsatellite length appear to vary in a species-specific manner. We know very little about the nature of these constraints and why they should vary among species. While surveying microsatellite variation in the Mediterranean gilthead sea bream, Sparus aurata, we discovered an unusual pattern of covariation between two closely linked microsatellite loci. One- and two-locus haplotypes were scored from PCR amplification products of each locus separately and both loci together. In a sample of 211 fish, there was a strong negative covariance in repeat number between the two loci, which suggests a mechanism that maintains the combined length below a constrained size. In addition, there were two clusters of the same combined haplotype length, one consisting of a long repeat array at one locus and a short array at the other and vice versa. We demonstrate that several models of biased mutation or natural selection, in theory, could generate this pattern of covariance. The common feature of all the models is the idea that tightly linked microsatellites do not evolve in complete independence, and that whatever size dependence there is to the process, it appears to “read” the combined size of the two loci.
Genetic Components of Variation in Nemophila menziesii Undergoing Inbreeding: Morphology and Flowering Time
Authors: Shaw Ruth G , Byers Diane L , Shaw Frank H
Published: April 2021

The standard approaches to estimation of quantitative genetic parameters and prediction of response to selection on quantitative traits are based on theory derived for populations undergoing random mating. Many studies demonstrate, however, that mating systems in natural populations often involve inbreeding in various degrees (i.e., self matings and matings between relatives). Here we apply theory developed for estimating quantitative genetic parameters for partially inbreeding populations to a population of Nemophila menziesii recently obtained from nature and experimentally inbred. Two measures of overall plant size and two of floral size expressed highly significant inbreeding depression. Of three dominance components of phenotypic variance that are defined under partial inbreeding, one was found to contribute significantly to phenotypic variance in flower size and flowering time, while the remaining two components contributed only negligibly to variation in each of the five traits considered. Computer simulations investigating selection response under the more complete genetic model for populations undergoing mixed mating indicate that, for parameter values estimated in this study, selection response can be substantially slowed relative to predictions for a random mating population. Moreover, inbreeding depression alone does not generally account for the reduction in selection response.
The Levels of the RoRNP-Associated Y RNA Are Dependent Upon the Presence of ROP-1, the Caenorhabditis elegans Ro60 Protein
Authors: Labbé Jean-Claude , Hekimi Siegfried , Rokeach Luis A
Published: April 2021

The Ro ribonucleoproteins (RoRNP) consist of at least one major protein of 60 kD, Ro60, and one small associated RNA, designated Y RNA. Although RoRNP have been found in all vertebrate species examined so far, their function remains unknown. The Caenorhabditis elegans rop-1 gene previously has been identified as encoding a Ro60 homologue. We report here the phenotypic characterization of a C. elegans strain in which rop-1 has been disrupted. This is the first report regarding the inactivation of a major RoRNP constituent in any organism. The rop-1 mutant worms display no visible defects. However, at the molecular level, the disruption of rop-1 results in a dramatic decrease in the levels of the ROP-1-associated RNA (CeY RNA). Moreover, transgenic expression of wild-type rop-1 partially rescues the levels of CeY RNA. Considering that transgenes are poorly expressed in the germline, the fact that the rescue is only partial is most likely related to the high abundance of the CeY RNA in the adult germline and in embryos. The developmental expression pattern and localization of CeY RNA suggest a role for this molecule during embryogenesis. We conclude that, under laboratory culture conditions, ROP-1 does not play a crucial role in C. elegans.
The Amylase Gene Cluster on the Evolving Sex Chromosomes of Drosophila miranda
Authors: Steinemann Sigrid , Steinemann Manfred
Published: April 2021

On the basis of chromosomal homology, the Amylase gene cluster in Drosophila miranda must be located on the secondary sex chromosome pair, neo-X (X2) and neo-Y, but is autosomally inherited in all other Drosophila species. Genetic evidence indicates no active amylase on the neo-Y chromosome and the X2-chromosomal locus already shows dosage compensation. Several lines of evidence strongly suggest that the Amy gene cluster has been lost already from the evolving neo-Y chromosome. This finding shows that a relatively new neo-Y chromosome can start to lose genes and hence gradually lose homology with the neo-X. The X2-chromosomal Amy1 is intact and Amy2 contains a complete coding sequence, but has a deletion in the 3′-flanking region. Amy3 is structurally eroded and hampered by missing regulatory motifs. Functional analysis of the X2-chromosomal Amy1 and Amy2 regions from D. miranda in transgenic D. melanogaster flies reveals ectopic AMY1 expression. AMY1 shows the same electrophoretic mobility as the single amylase band in D. miranda, while ectopic AMY2 expression is characterized by a different mobility. Therefore, only the Amy1 gene of the resident Amy cluster remains functional and hence Amy1 is the dosage compensated gene.
Statistical Methods for Mapping Quantitative Trait Loci From a Dense Set of Markers
Authors: Dupuis Josée , Siegmund David
Published: April 2021

Lander and Botstein introduced statistical methods for searching an entire genome for quantitative trait loci (QTL) in experimental organisms, with emphasis on a backcross design and QTL having only additive effects. We extend their results to intercross and other designs, and we compare the power of the resulting test as a function of the magnitude of the additive and dominance effects, the sample size and intermarker distances. We also compare three methods for constructing confidence regions for a QTL: likelihood regions, Bayesian credible sets, and support regions. We show that with an appropriate evaluation of the coverage probability a support region is approximately a confidence region, and we provide a theroretical explanation of the empirical observation that the size of the support region is proportional to the sample size, not the square root of the sample size, as one might expect from standard statistical theory.
Role of Saccharomyces cerevisiae Chromatin Assembly Factor-I in Repair of Ultraviolet Radiation Damage in Vivo
Authors: Game John C , Kaufman Paul D
Published: April 2021

In vitro, the protein complex Chromatin Assembly Factor-I (CAF-I) from human or yeast cells deposits histones onto DNA templates after replication. In Saccharomyces cerevisiae, the CAC1, CAC2, and CAC3 genes encode the three CAF-I subunits. Deletion of any of the three CAC genes reduces telomeric gene silencing and confers an increase in sensitivity to killing by ultraviolet (UV) radiation. We used double and triple mutants involving cac1Δ and yeast repair gene mutations to show that deletion of the CAC1 gene increases the UV sensitivity of cells mutant in genes from each of the known DNA repair epistasis groups. For example, double mutants involving cac1Δ and excision repair gene deletions rad1Δ or rad14Δ showed increased UV sensitivity, as did double mutants involving cac1Δ and deletions of members of the RAD51 recombinational repair group. cac1Δ also increased the UV sensitivity of strains with defects in either the error-prone (rev3Δ) or error-free (pol30-46) branches of RAD6-mediated postreplicative DNA repair but did not substantially increase the sensitivity of strains carrying null mutations in the RAD6 or RAD18 genes. Deletion of CAC1 also increased the UV sensitivity and rate of UV-induced mutagenesis in rad5Δ mutants, as has been observed for mutants defective in error-free postreplicative repair. Together, these data suggest that CAF-I has a role in error-free postreplicative damage repair and may also have an auxiliary role in other repair mechanisms. Like the CAC genes, RAD6 is also required for gene silencing at telomeres. We find an increased loss of telomeric gene silencing in rad6Δ cac1Δ and rad18Δ cac1Δ double mutants, suggesting that CAF-I and multiple factors in the postreplicative repair pathway influence chromosome structure.
A Mutation of the Yeast Gene Encoding PCNA Destabilizes Both Microsatellite and Minisatellite DNA Sequences
Authors: Kokoska Robert J , Stefanovic Lela , Buermeyer Andrew B , Liskay R Michael , Petes Thomas D
Published: April 2021

The POL30 gene of the yeast Saccharomyces cerevisiae encodes the proliferating cell nuclear antigen (PCNA), a protein required for processive DNA synthesis by DNA polymerase δ and ϵ. We examined the effects of the pol30-52 mutation on the stability of microsatellite (1- to 8-bp repeat units) and minisatellite (20-bp repeat units) DNA sequences. It had previously been shown that this mutation destabilizes dinucleotide repeats 150-fold and that this effect is primarily due to defects in DNA mismatch repair. From our analysis of the effects of pol30-52 on classes of repetitive DNA with longer repeat unit lengths, we conclude that this mutation may also elevate the rate of DNA polymerase slippage. The effect of pol30-52 on tracts of repetitive DNA with large repeat unit lengths was similar, but not identical, to that observed previously for pol3-t, a temperature-sensitive mutation affecting DNA polymerase δ. Strains with both pol30-52 and pol3-t mutations grew extremely slowly and had minisatellite mutation rates considerably greater than those observed in either single mutant strain.
The Use of Microsatellite Variation to Infer Population Structure and Demographic History in a Natural Model System
Authors: Goldstein David B , Roemer Gary W , Smith Deborah A , Reich David E , Bergman Aviv , Wayne Robert K
Published: April 2021

To assess the reliability of genetic markers it is important to compare inferences that are based on them to a priori expectations. In this article we present an analysis of microsatellite variation within and among populations of island foxes (Urocyon littoralis) on California's Channel Islands. We first show that microsatellite variation at a moderate number of loci (19) can provide an essentially perfect description of the boundaries between populations and an accurate representation of their historical relationships. We also show that the pattern of variation across unlinked microsatellite loci can be used to test whether population size has been constant or increasing. Application of these approaches to the island fox system indicates that microsatellite variation may carry considerably more information about population history than is currently being used.
Molecular Population Genetics of Floral Homeotic Loci: Departures From the Equilibrium-Neutral Model at the APETALA3 and PISTILLATA Genes of Arabidopsis thaliana
Authors: Purugganan Michael D , Suddith Jane I
Published: April 2021

Molecular variation in genes that regulate development provides insights into the evolutionary processes that shape the diversification of morphogenetic pathways. Intraspecific sequence variation at the APETALA3 and PISTILLATA floral homeotic genes of Arabidopsis thaliana was analyzed to infer the extent and nature of diversity at these regulatory loci. Comparison of AP3 and PI diversity with three previously studied genes revealed several features in the patterning of nucleotide polymorphisms common between Arabidopsis nuclear loci, including an excess of low-frequency nucleotide polymorphisms and significantly elevated levels of intraspecific replacement variation. This pattern suggests that A. thaliana has undergone recent, rapid population expansion and now exists in small, inbred subpopulations. The elevated intraspecific replacement levels may thus represent slightly deleterious polymorphisms that differentiate distinct ecotypes. The distribution of replacement and synonymous changes in AP3 and PI core and noncore functional domains also indicates differences in the patterns of molecular evolution between these interacting floral regulatory genes.
Identification and Characterization of Genes Required for Hyphal Morphogenesis in the Filamentous Fungus Aspergillus nidulans
Authors: Harris Steven D , Hofmann Amy F , Tedford Hugo W , Lee Maurice P
Published: April 2021

In the filamentous fungus Aspergillus nidulans, germination of an asexual conidiospore results in the formation of a hyphal cell. A key feature of spore germination is the switch from isotropic spore expansion to polarized apical growth. Here, temperature-sensitive mutations are used to characterize the roles of five genes (sepA, hypA, podB-podD) in the establishment and maintenance of hyphal polarity. Evidence that suggests that the hypA, podB, and sepA genes are required for multiple aspects of hyphal morphogenesis is presented. Notably, podB and sepA are needed for organization of the cytoskeleton at sites of polarized growth. In contrast, podC and podD encode proteins that appear to be specifically required for the establishment of hyphal polarity during spore germination. The role of sepA and the pod genes in controlling the spatial pattern of polarized morphogenesis in germinating spores is also described. Results obtained from these experiments indicate that the normal pattern of germ-tube emergence is dependent upon the integrity of the actin cytoskeleton.
Genome Reduction in a Hemiclonal Frog Rana esculenta From Radioactively Contaminated Areas
Authors: Vinogradov Alexander E , Chubinishvili Alexander T
Published: April 2021

A decrease in genome size was found in the hemiclonal hybridogenetic frog Rana esculenta (R. ridibunda × R. lessonae) from areas of radioactive contamination that resulted from the Chernobyl fallout. This genome reduction was of up to 4% and correlated with the background level of gamma-radiation (linear regression corresponded on average to -0.4% per doubling of radiation level). No change in genome size was observed in the coexisting parental species R. lessonae. There was no correlation between genome size and body mass in R. esculenta froglets, which have metamorphosed in the year of the study. The hemiclonal forms may become a suitable object for study on biological significance of individual DNA sequences (and of genome size as a whole) because mutant animals with deletions in a specified genome can arise after a low radiation dose. The proneness to genetic damage makes such forms also a prospective bioindicator of radioactive (and possibly other mutagenic) pollution with the effects of genetic damage conveniently and rapidly monitored by DNA flow cytometry.
A Method for Estimating Nucleotide Diversity From AFLP Data
Authors: Innan Hideki , Terauchi Ryohei , Kahl Günter , Tajima Fumio
Published: April 2021

A method for estimating the nucleotide diversity from AFLP data is developed by using the relationship between the number of nucleotide changes and the proportion of shared bands. The estimation equation is based on the assumption that GC-content is 0.5. Computer simulations, however, show that this method gives a reasonably accurate estimate even when GC-content deviates from 0.5, as long as the number of nucleotide changes per site (nucleotide diversity) is small. As an example, the nucleotide diversity of the wild yam, Dioscorea tokoro, was estimated. The estimated nucleotide diversity is 0.0055, which is larger than estimations from nucleotide sequence data for Adh and Pgi.
Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae
Authors: Jordan I King , McDonald John F
Published: April 2021

The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.