bluuebunny/crossref_metadata_2025 huggingface dataset:
The Detection and Measurement of Recombination From Sequence Data
Authors: Smith J Maynard
Published: April 2021

There are two types of recombination that we may wish to detect: rare recombinants between members of different populations or species and repeated recombination within a population. Methods appropriate in the former context are inappropriate in the latter because they depend on recognizing the existence of runs of nucleotides with similar ancestry. If recombination is sufficiently frequent, no such runs will be present. Several methods, including the homoplasy test and the incompatibility test, are described that are appropriate for detecting repeated recombination and for measuring its importance, relative to mutation, in causing genetic change. The sensitivity of these tests is investigated by simulating populations with varying frequencies of mutation and recombination and calculating the various statistics on samples.
Molecular Evolution of the Escherichia coli Chromosome. V. Recombination Patterns Among Strains of Diverse Origin
Authors: Milkman Roger , Raleigh Elisabeth A , McKane Melissa , Cryderman Diane , Bilodeau Patricia , McWeeny Kerri
Published: April 2021

Incorporation patterns of donor DNA into recipient chromosomes following transduction or conjugation have been studied in the progeny of a variety of Escherichia coli crosses in which donor and recipient nucleotide sequences differ by 1-3%. Series of contiguous or variously spaced PCR fragments have been amplified from each recombinant chromosome and digested with a commercial restriction endonuclease previously shown to distinguish the respective parents in a given fragment. We conclude that entering donor DNA fragments are frequently abridged (cut and shortened) before incorporation, the cutting being due to restriction systems, and the shortening presumably due to exonuclease activity. Analysis of several backcrosses confirms, and extends to conjugation, the importance of restriction in E. coli recombination in nature. The transmission patterns in conjugation are similar to those of transduction, but (as expected) on a much larger scale. Asymmetric results of reciprocal crosses imply that mismatch frequency is not a major factor. Marked differences among the results of simple crosses according to parental strain combinations are consistent with observations that E. coli strains in nature vary dramatically in their restriction-modification systems.
The Evolution of Age-Specific Mortality Rates in Drosophila melanogaster: Genetic Divergence Among Unselected Lines
Authors: Pletcher Scott D , Houle David , Curtsinger James W
Published: April 2021

Age-specific effects of spontaneous mutations on mortality rates in Drosophila are inferred from three large demographic experiments. Data were collected from inbred lines that were allowed to accumulate spontaneous mutations for 10, 19, and 47 generations. Estimates of age-specific mutational variance for mortality were based on data from all three experiments, totalling ∼225,000 flies, using a model developed for genetic analysis of age-dependent traits (the character process model). Both within- and among-generation analyses suggest that the input of genetic variance is greater for early life mortality rates than for mortality at older ages. In females, age-specific mutational variances ranged over an order of magnitude from 5.96 × 10-3 at 2 wk posteclosion to 0.02 × 10-3 at 7 wk. The male data show a similar pattern. Age-specific genetic variances were substantially less at generation 47 than at generation 19—an unexplained observation that is likely due to block effects. Mutational correlations among mortality rates at different ages tend to increase with the accumulation of new mutations. Comparison of the mutation-accumulation lines at generations 19 and 47 with their respective control lines suggests little age-specific mutational bias.
stress sensitive B Encodes an Adenine Nucleotide Translocase in Drosophila melanogaster
Authors: Zhang Yong Q , Roote John , Brogna Saverio , Davis Andrew W , Barbash Daniel A , Nash David , Ashburner Michael
Published: April 2021

Adenine nucleotide translocases (ANT) are required for the exchange of ADP and ATP across the inner mitochondrial membrane. They are essential for life, and most eukaryotes have at least two different Ant genes. Only one gene had been described from Drosophila, and this had not been characterized genetically. We show that mutations in this gene correspond to the previously described loci, sesB and l(1)9Ed. Immediately adjacent to this gene is another encoding a second ANT protein, which has 78% identity to that encoded by sesB/l(1)9Ed. These two genes are transcribed from a common promoter, and their mRNAs are produced by differential splicing. Hutter and Karch suggested that the sesB ANT gene corresponded to Hmr, a gene identified by an allele that rescues otherwise inviable interspecific hybrids between Drosophila melanogaster and its sibling species. This hypothesis is not supported by our study of the ANT genes of D. melanogaster.
Linkage Analysis of Molecular Markers and Quantitative Trait Loci in Populations of Inbred Backcross Lines of Brassica napus L.
Authors: Butruille David V , Guries Raymond P , Osborn Thomas C
Published: April 2021

Backcross populations are often used to study quantitative trait loci (QTL) after they are initially discovered in balanced populations, such as F2, BC1, or recombinant inbreds. While the latter are more powerful for mapping marker loci, the former have the reduced background genetic variation necessary for more precise estimation of QTL effects. Many populations of inbred backcross lines (IBLs) have been developed in plant and animal systems to permit simultaneous study and dissection of quantitative genetic variation introgressed from one source to another. Such populations have a genetic structure that can be used for linkage estimation and discovery of QTL. In this study, four populations of IBLs of oilseed Brassica napus were developed and analyzed to map genomic regions from the donor parent (a winter-type cultivar) that affect agronomic traits in spring-type inbreds and hybrids. Restriction fragment length polymorphisms (RFLPs) identified among the IBLs were used to calculate two-point recombination fractions and LOD scores through grid searches. This information allowed the enrichment of a composite genetic map of B. napus with 72 new RFLP loci. The selfed and hybrid progenies of the IBLs were evaluated during two growing seasons for several agronomic traits. Both pedigree structure and map information were incorporated into the QTL analysis by using a regression approach. The number of QTL detected for each trait and the number of effective factors calculated by using biometrical methods were of similar magnitude. Populations of IBLs were shown to be valuable for both marker mapping and QTL analysis.
Fine Mapping and Characterization of Linked Quantitative Trait Loci Involved in the Transition of the Maize Apical Meristem From Vegetative to Generative Structures
Authors: Vlăduţu Cristian , McLaughlin John , Phillips Ronald L
Published: April 2021

Quantitative trait locus (QTL) mapping has detected two linked QTL in the 8L chromosome arm segment introgressed from Gaspé Flint (a Northern Flint open-pollinated population) into the background of N28 (a Corn Belt Dent inbred line). Homozygous recombinant lines, with a variable length of the introgressed segment, confirmed the presence of the two previously identified, linked QTL. In the N28 background, Gaspé Flint QTL alleles at both loci induce a reduction in node number, height, and days to anthesis (pollen shed). Given the determinate growth pattern of maize, the phenotypic effects indicate that the two QTL are involved in the transition of the apical meristem from vegetative to generative structures. Relative to the effects of the two QTL in the background of N28, we distinguish two general developmental factors affecting the timing of pollen shed. The primary factor is the timing of the transition of the apical meristem. The second, derivative factor is the global extent of internode elongation. Having separated the two linked QTL, we have laid the foundation for the positional cloning of the QTL with a larger effect.
spp42, Identified as a Classical Suppressor of prp4-73, Which Encodes a Kinase Involved in Pre-mRNA Splicing in Fission Yeast, Is a Homologue of the Splicing Factor Prp8p
Authors: Schmidt Henning , Richert Kathrin , Drakas Robert A , Käufer Norbert F
Published: April 2021

We have identified two classical extragenic suppressors, spp41 and spp42, of the temperature sensitive (ts) allele prp4-73. The prp4+ gene of Schizosaccharomyces pombe encodes a protein kinase. Mutations in both suppressor genes suppress the growth and the pre-mRNA splicing defect of prp4-73ts at the restrictive temperature (36°). spp41 and spp42 are synthetically lethal with each other in the presence of prp4-73ts, indicating a functional relationship between spp41 and spp42. The suppressor genes were mapped on the left arm of chromosome I proximal to the his6 gene. Based on our mapping data we isolated spp42 by screening PCR fragments for functional complementation of the prp4-73ts mutant at the restrictive temperature. spp42 encodes a large protein (p275), which is the homologue of Prp8p. This protein has been shown in budding yeast and mammalian cells to be a bona fide pre-mRNA splicing factor. Taken together with other recent genetic and biochemical data, our results suggest that Prp4 kinase plays an important role in the formation of catalytic spliceosomes.
Quantitative Trait Loci Affecting Survival and Fertility-Related Traits in Caenorhabditis elegans Show Genotype-Environment Interactions, Pleiotropy and Epistasis
Authors: Shook David R , Johnson Thomas E
Published: April 2021

We have identified, using composite interval mapping, quantitative trait loci (QTL) affecting a variety of life history traits (LHTs) in the nematode Caenorhabditis elegans. Using recombinant inbred strains assayed on the surface of agar plates, we found QTL for survival, early fertility, age of onset of sexual maturity, and population growth rate. There was no overall correlation between survival on solid media and previous measures of survival in liquid media. Of the four survival QTL found in these two environments, two have genotype-environment interactions (GEIs). Epistatic interactions between markers were detected for four traits. A multiple regression approach was used to determine which single markers and epistatic interactions best explained the phenotypic variance for each trait. The amount of phenotypic variance accounted for by genetic effects ranged from 13% (for internal hatching) to 46% (for population growth). Epistatic effects accounted for 9–11% of the phenotypic variance for three traits. Two regions containing QTL that affected more than one fertility-related trait were found. This study serves as an example of the power of QTL mapping for dissecting the genetic architecture of a suite of LHTs and indicates the potential importance of environment and GEIs in the evolution of this architecture.
The Mcp Element From the Drosophila melanogaster Bithorax Complex Mediates Long-Distance Regulatory Interactions
Authors: Muller Martin , Hagstrom Kirsten , Gyurkovics Henrik , Pirrotta Vincenzo , Schedl Paul
Published: April 2021

In the studies reported here, we have examined the properties of the Mcp element from the Drosophila melanogaster bithorax complex (BX-C). We have found that sequences from the Mcp region of BX-C have properties characteristic of Polycomb response elements (PREs), and that they silence adjacent reporters by a mechanism that requires trans-interactions between two copies of the transgene. However, Mcp trans-regulatory interactions have several novel features. In contrast to classical transvection, homolog pairing does not seem to be required. Thus, trans-regulatory interactions can be observed not only between Mcp transgenes inserted at the same site, but also between Mcp transgenes inserted at distant sites on the same chromosomal arm, or even on different arms. Trans-regulation can even be observed between transgenes inserted on different chromosomes. A small 800-bp Mcp sequence is sufficient to mediate these long-distance trans-regulatory interactions. This small fragment has little silencing activity on its own and must be combined with other Polycomb-Group-responsive elements to function as a “pairing-sensitive” silencer. Finally, this pairing element can also mediate long-distance interactions between enhancers and promoters, activating mini-white expression.
Mapping of Hybrid Incompatibility Loci in Nasonia
Authors: Gadau Jürgen , Page Robert E , Werren John H
Published: April 2021

According to theory, F2 hybrid breakdown (lethality or sterility) is due to incompatibilities between interacting genes of the different species (i.e., the breaking up of coadapted gene complexes). Detection of such incompatibilities is particularly straightforward in haplodiploid species, because virgin F1 hybrid females will produce haploid recombinant F2 males. This feature allows for screening of the complete genome for recessive genetic incompatibilities. Crosses were performed between Nasonia vitripennis (v) and its sibling species N. giraulti (g). First, a linkage map was produced using RAPD markers. RAPD markers showed an overall bias toward vitripennis alleles, a pattern not predicted by the basic two-interactor Dobzhansky-Muller model. Recovery patterns of visible markers were consistent with those of linked RAPD markers. If particular genetic interactions between two loci are causing hybrid lethality, then those genotypes should be underrepresented or absent among adult F2 males. Four sets of significant incompatibilities were detected by performing pairwise comparisons of markers on different chromosomes. Likely explanations for the observed patterns are maternal effect-zygotic gene incompatibilities or clustering of incompatibility loci. Due to the short generation time, advantages of haplodiploidy, and availability of markers, Nasonia promises to be a productive system for investigating the genetics of hybrid inviability.
Sex-ratio Meiotic Drive in Drosophila simulans Is Related to Equational Nondisjunction of the Y Chromosome
Authors: Cazemajor Michel , Joly Dominique , Montchamp-Moreau Catherine
Published: April 2021

The sex-ratio trait, an example of naturally occurring X-linked meiotic drive, has been reported in a dozen Drosophila species. Males carrying a sex-ratio X chromosome produce an excess of female offspring caused by a deficiency of Y-bearing sperm. In Drosophila simulans, such males produce ~70–90% female offspring, and 15–30% of the male offspring are sterile. Here, we investigate the cytological basis of the drive in this species. We show that the sex-ratio trait is associated with nondisjunction of Y chromatids in meiosis II. Fluorescence in situ hybridization (FISH) using sex-chromosome-specific probes provides direct evidence that the drive is caused by the failure of the resulting spermatids to develop into functional sperm. XYY progeny were not observed, indicating that few or no YY spermatids escape failure. The recovery of XO males among the progeny of sex-ratio males shows that some nullo-XY spermatids become functional sperm and likely explains the male sterility. A review of the cytological data in other species shows that aberrant behavior of the Y chromosome may be a common basis of sex-ratio meiotic drive in Drosophila and the signal that triggers differential spermiogenesis failure.
Evolutionary Reversals During Viral Adaptation to Alternating Hosts
Authors: Crill W D , Wichman H A , Bull J J
Published: April 2021

Experimental adaptation of the bacteriophage ϕX174 to a Salmonella host depressed its ability to grow on the traditional Escherichia host, whereas adaptation to Escherichia did not appreciably affect growth on Salmonella. Continued host switching consistently exhibited this pattern. Growth inhibition on Escherichia resulted from two to three substitutions in the major capsid gene. When these phages were forced to grow again on Escherichia, fitness recovery occurred predominantly by reversions at these same sites, rather than by second-site compensatory changes, the more frequently observed mechanism in most microbial systems. The affected residues lie on the virion surface and they alter attachment efficiency, yet they occur in a region distinct from a putative binding region previously identified from X-ray crystallography. These residues not only experienced high rates of evolution in our experiments, but also exhibited high levels of radical amino acid variation among ϕX174 and its known relatives, consistent with a history of adaptation involving these sites.
Male-Offspring-Specific, Haplotype-Dependent, Nonrandom Cosegregation of Alleles at Loci on Two Mouse Chromosomes
Authors: de Villena Fernando Pardo-Manuel , de la Casa-Esperón Elena , Briscoe Tammi L , Malette Jan-Michel , Sapienza Carmen
Published: April 2021

F1 backcrosses involving the DDK and C57BL/6 inbred mouse strains show transmission ratio distortion at loci on two different chromosomes, 11 and X. Transmission ratio distortion on chromosome X is restricted to female offspring while that on chromosome 11 is present in offspring of both sexes. In this article we investigate whether the inheritance of alleles at loci on one chromosome is independent of inheritance of alleles on the other. A strong nonrandom association between the inheritance of alleles at loci on both chromosomes is found among male offspring, while independent assortment occurs among female offspring. We also provide evidence that the mechanism by which this phenomenon occurs involves preferential cosegregation of nonparental chromatids of both chromosomes at the second meiotic divison, after the ova has been fertilized by a C57BL/6 sperm bearing a Y chromosome. These observations confirm the influence of the sperm in the segregation of chromatids during female meiosis, and indicate that a locus or loci on the Y chromosome are involved in this instance of meiotic drive.
The Probability of Duplicate Gene Preservation by Subfunctionalization
Authors: Lynch Michael , Force Allan
Published: April 2021

It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members of the pair are preserved as one acquires a mutation with a beneficial function and the other retains the original function. However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under this model, and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We consider the ways in which the probability of duplicate-gene preservation by such complementary mutations is modified by aspects of gene structure, degree of linkage, mutation rates and effects, and population size. Even if most mutations cause complete loss-of-subfunction, the probability of duplicate-gene preservation can be appreciable if the long-term effective population size is on the order of 105 or smaller, especially if there are more than two independently mutable subfunctions per locus. Even a moderate incidence of partial loss-of-function mutations greatly elevates the probability of preservation. The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.
A Genetic Test of the Mechanism of Wolbachia-Induced Cytoplasmic Incompatibility in Drosophila
Authors: Presgraves Daven C
Published: April 2021

Cytoplasmic bacteria of the genus Wolbachia are best known as the cause of cytoplasmic incompatibility (CI): many uninfected eggs fertilized by Wolbachia-modified sperm from infected males die as embryos. In contrast, eggs of infected females rescue modified sperm and develop normally. Although Wolbachia cause CI in at least five insect orders, the mechanism of CI remains poorly understood. Here I test whether the target of Wolbachia-induced sperm modification is the male pronucleus (e.g., DNA or pronuclear proteins) or some extranuclear factor from the sperm required for embryonic development (e.g., the paternal centrosome). I distinguish between these hypotheses by crossing gynogenetic Drosophila melanogaster females to infected males. Gynogenetic females produce diploid eggs whose normal development requires no male pronucleus but still depends on extranuclear paternal factors. I show that when gynogenetic females are crossed to infected males, uniparental progeny with maternally derived chromosomes result. This finding shows that Wolbachia impair the male pronucleus but no extranuclear component of the sperm.
BALB/c Alleles at Modifier Loci Increase the Severity of the Maternal Effect of the “DDK Syndrome”
Authors: Le Bras Stéphanie , Cohen-Tannoudji Michel , Kress Chantal , Vandormael-Pournin Sandrine , Babinet Charles , Baldacci Patricia
Published: April 2021

The Om locus was first described in the DDK inbred mouse strain: DDK mice carry a mutation at Om resulting in a parental effect lethality of F1 embryos. When DDK females are mated with males of other (non-DDK) inbred strains, e.g., BALB/c, they exhibit a low fertility, whereas the reciprocal cross, non-DDK females × DDK males, is fertile (as is the DDK intrastrain cross). The low fertility is due to the death of (DDK × non-DDK)F1 embryos at the late-morula to blastocyst stage, which is referred to as the “DDK syndrome.” The death of these F1 embryos is caused by an incompatibility between a DDK maternal factor and the non-DDK paternal pronucleus. Previous genetic studies showed that F1 mice have an intermediate phenotype compared to parental strains: crosses between F1 females and non-DDK males are semisterile, as are crosses between DDK females and F1 males. In the present studies, we have examined the properties of mice heterozygous for BALB/c and DDK Om alleles on an essentially BALB/c genetic background. Surprisingly, we found that the females are quasi-sterile when mated with BALB/c males and, thus, present a phenotype similar to DDK females. These results indicate that BALB/c alleles at modifier loci increase the severity of the DDK syndrome.
Quantitative Trait Loci and Candidate Gene Mapping of Bud Set and Bud Flush in Populus
Authors: Frewen Barbara E , Chen Tony H H , Howe Glenn T , Davis Joel , Rohde Antje , Boerjan Wout , Bradshaw H D
Published: April 2021

The genetic control of bud phenology in hybrid poplar was studied by mapping quantitative trait loci (QTL) affecting the timing of autumn bud set and spring bud flush. The founders of the mapping pedigree were collected from widely separated latitudes to maximize segregating variation for dormancy-related traits in the F2 generation—the female Populus trichocarpa parent is from Washington State (48°N) and the male P. deltoides parent is from Texas (31°N). Bud set and bud flush timing were measured on the F2 generation in a replicated clonal field trial. Using a linkage map constructed of AFLP and microsatellite markers, three QTL controlling bud set and six QTL controlling bud flush were detected. Additionally, five candidate genes believed to be involved in perception of photoperiod (PHYB1, PHYB2) or transduction of abscisic acid response signals (ABI1B, ABI1D, and ABI3) were placed on the QTL map. PHYB2 and ABI1B were found to be coincident with QTL affecting bud set and bud flush.
A Genetic Map of Tomato Based on BC1 Lycopersicon esculentum × Solanum lycopersicoides Reveals Overall Synteny but Suppressed Recombination Between These Homeologous Genomes
Authors: Chetelat Roger T , Meglic Vladimir , Cisneros Pedro
Published: April 2021

F1 hybrids between the cultivated tomato (Lycopersicon esculentum) and the wild nightshade Solanum lycopersicoides are male sterile and unilaterally incompatible, breeding barriers that impede further crosses to tomato. Meiosis is disrupted in 2× hybrids, with reduced chiasma formation and frequent univalents, but is normal in allotetraploid hybrids, indicating the genomes are homeologous. In this study, a partially male-fertile F1 was backcrossed to tomato, producing the first BC1 population suitable for genetic mapping from this cross. BC1 plants were genotyped at marker loci to study the transmission of wild alleles and to measure rates of homeologous recombination. The pattern of segregation distortion, in favor of homozygotes on chromosomes 2 and 5 and heterozygotes on chromosomes 6 and 9, suggested linkage to a small number of loci under selection on each chromosome. Genome ratios nonetheless fit Mendelian expectations. Resulting genetic maps were essentially colinear with existing tomato maps but showed an overall reduction in recombination of ~27%. Recombination suppression was observed for all chromosomes except 9 and 12, affected both proximal and distal regions, and was most severe on chromosome 10 (70% reduction). Recombination between markers on the long arm of this chromosome was completely eliminated, suggesting a lack of colinearity between S. lycopersicoides and L. esculentum homeologues in this region. Results are discussed with respect to phylogenetic relationships between the species and their potential use for studies of homeologous pairing and recombination in a diploid plant genome.
Analysis of Sir2p Domains Required for rDNA and Telomeric Silencing in Saccharomyces cerevisiae
Authors: Cockell Moira M , Perrod Severine , Gasser Susan M
Published: April 2021

Silent information regulator (Sir) 2 is a limiting component of the Sir2/3/4 complex, which represses transcription at subtelomeric and HM loci. Sir2p also acts independently of Sir3p and Sir4p to influence chromatin organization in the rDNA locus. Deleted and mutated forms of Sir2p have been tested for their ability to complement and/or to disrupt silencing. The highly conserved C-terminal domain of Sir2p (aa 199–562) is insufficient to restore repression at either telomeric or rDNA reporters in a sir2Δ background and fails to nucleate silencing when targeted to an appropriate reporter gene. However, its expression in an otherwise wild-type strain disrupts telomeric repression. Similarly, a point mutation (P394L) within this conserved core inactivates the full-length protein but renders it dominant negative for all types of silencing. Deletion of aa 1–198 from Sir2394L eliminates its dominant negative effect. Thus we define two distinct functional domains in Sir2p, both essential for telomeric and rDNA repression: the conserved core domain found within aa 199–562 and a second domain that encompasses aa 94–198. Immunolocalization and two-hybrid studies show that aa 94–198 are required for the binding of Sir2p to Sir4p and for the targeting of Sir2p to the nucleolus through another ligand. The globular core domain provides an essential silencing function distinct from that of targeting or Sir complex formation that may reflect its reported mono-ADP-ribosyl transferase activity.
Compensatory Mutations, Antibiotic Resistance and the Population Genetics of Adaptive Evolution in Bacteria
Authors: Levin Bruce R , Perrot Véronique , Walker Nina
Published: April 2021

In the absence of the selecting drugs, chromosomal mutations for resistance to antibiotics and other chemotheraputic agents commonly engender a cost in the fitness of microorganisms. Recent in vivo and in vitro experimental studies of the adaptation to these “costs of resistance” in Escherichia coli, HIV, and Salmonella typhimurium found that evolution in the absence of these drugs commonly results in the ascent of mutations that ameliorate these costs, rather than higher-fitness, drug-sensitive revertants. To ascertain the conditions under which this compensatory evolution, rather than reversion, will occur, we did computer simulations, in vitro experiments, and DNA sequencing studies with low-fitness rpsL (streptomycin-resistant) mutants of E. coli with and without mutations that compensate for the fitness costs of these ribosomal protein mutations. The results of our investigation support the hypothesis that in these experiments, the ascent of intermediate-fitness compensatory mutants, rather than high-fitness revertants, can be attributed to higher rates of compensatory mutations relative to that of reversion and to the numerical bottlenecks associated with serial passage. We argue that these bottlenecks are intrinsic to the population dynamics of parasitic and commensal microbes and discuss the implications of these results to the problem of drug resistance and adaptive evolution in parasitic and commmensal microorganisms in general.
Autoregulated Expression of Schizosaccharomyces pombe Meiosis-Specific Transcription Factor Mei4 and a Genome-Wide Search for Its Target Genes
Authors: Abe Hiroko , Shimoda Chikashi
Published: April 2021

The Schizosaccharomyces pombe mei4+ gene encoding a forkhead transcription factor is necessary for the progression of meiosis and sporulation. We searched for novel meiotic genes, the expression of which is dependent on Mei4p, since only the spo6+ gene has been assigned to its targets. Six known genes responsible for meiotic recombination were examined by Northern blotting, but none were Mei4 dependent for transcription. We determined the important cis-acting element, designated FLEX, to which Mei4p can bind. The S. pombe genome sequence database (The Sanger Centre, UK) was scanned for the central core heptamer and its flanking 3′ sequence of FLEX composed of 17 nucleotides, and 10 candidate targets of Mei4 were selected. These contained a FLEX-like sequence in the 5′ upstream nontranslatable region within 1 kb of the initiation codon. Northern blotting confirmed that 9 of them, named mde1+ to mde9+, were transcriptionally induced during meiosis and were dependent on mei4+. Most mde genes have not been genetically defined yet, except for mde9+, which is identical to spn5+, which encodes one of the septin family of proteins. mde3+ and a related gene pit1+ encode proteins related to Saccharomyces cerevisiae Ime2. The double disruptant frequently produced asci having an abnormal number and size of spores, although it completed meiosis. We also found that the forkhead DNA-binding domain of Mei4p binds to the FLEX-like element in the putative promoter region of mei4 and that the maximum induction level of mei4 mRNA required functional mei4 activity. Furthermore, expression of a reporter gene driven by the authentic mei4 promoter was induced in vegetative cells by ectopic overproduction of Mei4p. These results suggest that mei4 transcription is positively autoregulated.
quick-to-court, a Drosophila Mutant With Elevated Levels of Sexual Behavior, Is Defective in a Predicted Coiled-Coil Protein
Authors: Gaines Peter , Tompkins Laurie , Woodard Craig T , Carlson John R
Published: April 2021

Remarkably little is known about the molecular mechanisms that drive sexual behavior. We have identified a new gene, quick-to-court (qtc), whose mutations cause males to show high levels of male-male courtship. qtc males also show a novel phenotype: when placed in the presence of a virgin female, they begin courtship abnormally quickly. qtc mutations are striking in their specificity, in that many aspects of male sexual behavior are normal. We have cloned the qtc gene and found that it encodes a predicted coiled-coil protein and is expressed in the olfactory organs, central nervous system, and male reproductive tract.
A General Procedure for Predicting Rates of Inbreeding in Populations Undergoing Mass Selection
Authors: Bijma Piter , Van Arendonk Johan A M , Woolliams John A
Published: April 2021

Predictions of rates of inbreeding (ΔF), based on the concept of long-term genetic contributions assuming the infinitesimal model, are developed for populations with discrete or overlapping generations undergoing mass selection. Phenotypes of individuals are assumed to be recorded prior to reproductive age and to remain constant over time. The prediction method accounts for inheritance of selective advantage both within and between age classes and for changing selection intensities with age. Terms corresponding to previous methods that assume constant selection intensity with age are identified. Predictions are accurate (relative errors ≤8%), except for cases with extreme selection intensities in females in combination with high heritability. With overlapping generations ΔF reaches a maximum when parents are equally distributed over age classes, which is mainly due to selection of the same individuals in consecutive years. ΔF/year decreases much more slowly compared to ΔF/generation as the number of younger individuals increases, whereas the decrease is more similar as the number of older individuals increases. The minimum ΔF (per year or per generation) is obtained when most parents were in the later age classes, which is mainly due to an increased number of parents per generation. With overlapping generations, the relationship between heritability and ΔF is dependent on the age structure of the population.
Genetic Modifiers of the Drosophila NSF Mutant, comatose, Include a Temperature-Sensitive Paralytic Allele of the Calcium Channel α1-Subunit Gene, cacophony
Authors: Dellinger Bonnie , Felling Ryan , Ordway Richard W
Published: April 2021

The N-ethylmaleimide-sensitive fusion protein (NSF) has been implicated in vesicle trafficking in perhaps all eukaryotic cells. The Drosophila comatose (comt) gene encodes an NSF homolog, dNSF1. Our previous work with temperature-sensitive (TS) paralytic alleles of comt has revealed a function for dNSF1 at synapses, where it appears to prime synaptic vesicles for neurotransmitter release. To further examine the molecular basis of dNSF1 function and to broaden our analysis of synaptic transmission to other gene products, we have performed a genetic screen for mutations that interact with comt. Here we report the isolation and analysis of four mutations that modify TS paralysis in comt, including two intragenic modifiers (one enhancer and one suppressor) and two extragenic modifiers (both enhancers). The intragenic mutations will contribute to structure-function analysis of dNSF1 and the extragenic mutations identify gene products with related functions in synaptic transmission. Both extragenic enhancers result in TS behavioral phenotypes when separated from comt, and both map to loci not previously identified in screens for TS mutants. One of these mutations is a TS paralytic allele of the calcium channel α1-subunit gene, cacophony (cac). Analysis of synaptic function in these mutants alone and in combination will further define the in vivo functions and interactions of specific gene products in synaptic transmission.
The Mitochondrial Genome of the Brachiopod Laqueus rubellus
Authors: Noguchi Yasuhiro , Endo Kazuyoshi , Tajima Fumio , Ueshima Rei
Published: April 2021

The complete nucleotide sequence of the 14,017-bp mitochondrial (mt) genome of the articulate brachiopod Laqueus rubellus is presented. Being one of the smallest of known mt genomes, it has an extremely compact gene organization. While the same 13 polypeptides, two rRNAs, and 22 tRNAs are encoded as in most other animal mtDNAs, lengthy noncoding regions are absent, with the longest apparent intergenic sequence being 54 bp in length. Gene-end sequence overlaps are prevalent, and several stop codons are abbreviated. The genes are generally shorter, and three of the protein-coding genes are the shortest among known homologues. All of the tRNA genes indicate size reduction in either or both of the putative TΨC and DHU arms compared with standard tRNAs. Possession of a TV (TΨC arm-variable loop) replacement loop is inferred for tRNA(R) and tRNA(L-tag). The DHU arm appears to be unpaired not only in tRNA(S-tct) and tRNA(S-tga), but also in tRNA(C), tRNA(I), and tRNA(T), a novel condition. All the genes are encoded in the same DNA strand, which has a base composition rich in thymine and guanine. The genome has an overall gene arrangement drastically different from that of any other organisms so far reported, but contains several short segments, composed of 2–3 genes, which are found in other mt genomes. Combined cooccurrence of such gene assortments indicates that the Laqueus mt genome is similar to the annelid Lumbricus, the mollusc Katharina, and the octocoral Sarcophyton mt genomes, each with statistical significance. Widely accepted schemes of metazoan phylogeny suggest that the similarity with the octocoral could have arisen through a process of convergent evolution, while it appears likely that the similarities with the annelid and the mollusc reflect phylogenetic relationships.
Evidence for Recent Invasion of the Medaka Fish Genome by the Tol2 Transposable Element
Authors: Koga Akihiko , Shimada Atsuko , Shima Akihiro , Sakaizumi Mitsuru , Tachida Hidenori , Hori Hiroshi
Published: April 2021

Tol2 is a transposable element of the terminal-inverted-repeat class, residing in the genome of the medaka fish Oryzias latipes. The genus Oryzias contains more than 10 species for which phylogenetic relationships have previously been estimated. To infer the history of Tol2 in this genus we performed genomic Southern blots and PCR analyses of 10 of the species. It was revealed that Tol2 occurs in 2 of the 10 species (O. curvinotus and O. latipes) and that the length and the restriction map structure of Tol2 are identical in the two cases. Further, sequencing analysis revealed an extremely low level of divergence compared with that in a nuclear gene. These results suggest recent incorporation of Tol2 into one or both of the two species, implying horizontal transfer of Tol2 from one species to the other or into them both from a common source.
Inhibition of mRNA Turnover in Yeast by an xrn1 Mutation Enhances the Requirement for eIF4E Binding to eIF4G and for Proper Capping of Transcripts by Ceg1p
Authors: Brown Justin T , Yang Xianmei , Johnson Arlen W
Published: April 2021

Null mutants of XRN1, encoding the major cytoplasmic exoribonuclease in yeast, are viable but accumulate decapped, deadenylated transcripts. A screen for mutations synthetic lethal with xrn1Δ identified a mutation in CDC33, encoding eIF4E. This mutation (glutamate to glycine at position 72) affected a highly conserved residue involved in interaction with eIF4G. Synthetic lethality between xrn1 and cdc33 was not relieved by high-copy expression of eIF4G or by disruption of the yeast eIF4E binding protein Caf20p. High-copy expression of a mutant eIF4G defective for eIF4E binding resulted in a dominant negative phenotype in an xrn1 mutant, indicating the importance of this interaction in an xrn1 mutant. Another allele of CDC33, cdc33-1, along with mutations in CEG1, encoding the nuclear guanylyltransferase, were also synthetic lethal with xrn1Δ, whereas mutations in PRT1, encoding a subunit of eIF3, were not. Mutations in CDC33, CEG1, PRT1, PAB1, and TIF4631, encoding eIF4G1, have been shown to lead to destabilization of mRNAs. Although such destabilization in cdc33, ceg1, and pab1 mutants can be partially suppressed by an xrn1 mutation, we observed synthetic lethality between xrn1 and either cdc33 or ceg1 and no suppression of the inviability of a pab1 null mutation by xrn1Δ. Thus, the inhibition of mRNA turnover by blocking Xrn1p function does not suppress the lethality of defects upstream in the turnover pathway but it does enhance the requirement for 7mG caps and for proper formation of the eIF4E/eIF4G cap recognition complex.
Fine Mapping of Quantitative Trait Loci Using Linkage Disequilibria With Closely Linked Marker Loci
Authors: Meuwissen T H E , Goddard M E
Published: April 2021

A multimarker linkage disequilibrium mapping method was developed for the fine mapping of quantitative trait loci (QTL) using a dense marker map. The method compares the expected covariances between haplotype effects given a postulated QTL position to the covariances that are found in the data. The expected covariances between the haplotype effects are proportional to the probability that the QTL position is identical by descent (IBD) given the marker haplotype information, which is calculated using the genedropping method. Simulation results showed that a QTL was correctly positioned within a region of 3, 1.5, or 0.75 cM in 70, 62, and 68%, respectively, of the replicates using markers spaced at intervals of 1, 0.5, and 0.25 cM, respectively. These results were rather insensitive to the number of generations since the QTL occurred and to the effective population size, except that 10 generations yielded rather poor estimates of the QTL position. The position estimates of this multimarker disequilibrium mapping method were more accurate than those from a single marker transmission disequilibrium test. A general approach for identifying QTL is suggested, where several stages of disequilibrium mapping are used with increasingly dense marker spacing.
Loss of Rhb1, a Rheb-Related GTPase in Fission Yeast, Causes Growth Arrest With a Terminal Phenotype Similar to That Caused by Nitrogen Starvation
Authors: Mach Kathleen E , Furge Kyle A , Albright Charles F
Published: April 2021

The Rheb GTPase is most similar in primary sequence to the Ras, Rap, R-Ras, and Ral GTPases, which regulate cell growth and differentiation in many cell types. A likely fission yeast homologue of mammalian Rheb, which we designated Rhb1, was identified by genome sequencing. Our investigation of rhb1 showed that rhb1− cells arrested cell growth and division with a terminal phenotype similar to that of nitrogenstarved cells. In particular, cells depleted of Rhb1 arrested as small, round cells with 1N DNA content, arrested more quickly in low-nitrogen medium, and induced expression of fnx1 and mei2 mRNA, two mRNAs that were normally induced by nitrogen starvation. Since mammalian Rheb binds and may regulate Raf-1, a Ras effector, we tested for functional overlap between Ras1 and Rhb1 in fission yeast. This analysis showed that Ras1 overexpression did not suppress rhb1− mutant phenotypes, Rhb1 overexpression did not suppress ras1− mutant phenotypes, and ras1−  rhb1− double mutants had phenotypes equal to the sum of the corresponding single-mutant phenotypes. Hence, there is no evidence for overlapping functions between Ras1 and Rhb1. On the basis of this study, we hypothesize that Rhb1 negatively regulates entry into stationary phase when extracellular nitrogen levels are adequate for growth. If this hypothesis is correct, then Rhb1 and Ras1 regulate alternative responses to limiting nutrients.
Co-expression of the Mating-Type Genes Involved in Internuclear Recognition Is Lethal in Podospora anserina
Authors: Coppin Evelyne , Debuchy Robert
Published: April 2021

In the heterothallic filamentous fungus Podospora anserina, four mating-type genes encoding transcriptional factors have been characterized: FPR1 in the mat+ sequence and FMR1, SMR1, and SMR2 in the alternative mat− sequence. Fertilization is controlled by FPR1 and FMR1. After fertilization, male and female nuclei, which have divided in the same cell, form mat+/mat− pairs during migration into the ascogenous hyphae. Previous data indicate that the formation of mat+/mat− pairs is controlled by FPR1, FMR1, and SMR2. SMR1 was postulated to be necessary for initial development of ascogenous hyphae. In this study, we investigated the transcriptional control of the mat genes by seeking mat transcripts during the vegetative and sexual phase and fusing their promoter to a reporter gene. The data indicate that FMR1 and FPR1 are expressed in both mycelia and perithecia, whereas SMR1 and SMR2 are transcribed in perithecia. Increased or induced vegetative expression of the four mat genes has no effect when the recombined gene is solely in the wild-type strain. However, the combination of resident FPR1 with deregulated SMR2 and overexpressed FMR1 in the same nucleus is lethal. This lethality is suppressed by the expression of SMR1, confirming that SMR1 operates downstream of the other mat genes.
Histone Acetylation and Gene Expression Analysis of Sex lethal Mutants in Drosophila
Authors: Bhadra Utpal , Pal-Bhadra Manika , Birchler James A
Published: April 2021

The evolution of sex determination mechanisms is often accompanied by reduction in dosage of genes on a whole chromosome. Under these circumstances, negatively acting regulatory genes would tend to double the expression of the genome, which produces compensation of the single-sex chromosome and increases autosomal gene expression. Previous work has suggested that to reduce the autosomal expression to the female level, these dosage effects are modified by a chromatin complex specific to males, which sequesters a histone acetylase to the X. The reduced autosomal histone 4 lysine 16 (H4Lys16) acetylation results in lowered autosomal expression, while the higher acetylation on the X is mitigated by the male-specific lethal complex, preventing overexpression. In this report, we examine how mutations in the principal sex determination gene, Sex lethal (Sxl), impact the H4 acetylation and gene expression on both the X and autosomes. When Sxl expression is missing in females, we find that the sequestration occurs concordantly with reductions in autosomal H4Lys16 acetylation and gene expression on the whole. When Sxl is ectopically expressed in SxlM mutant males, the sequestration is disrupted, leading to an increase in autosomal H4Lys16 acetylation and overall gene expression. In both cases we find relatively little effect upon X chromosomal gene expression.
Sojourn Times and Substitution Rate at Overdominant and Linked Neutral Loci
Authors: Ohashi Jun , Tokunaga Katsushi
Published: April 2021

The sojourn times until fixation of an overdominant allele were investigated based on the diffusion equation. Furthermore, the rate of accumulation of mutations, or the substitution rate, was predicted from the mean extinction time of a common overdominant allele. The substitution rate calculated theoretically agreed well with that determined by computer simulation. Overdominant selection enhances the polymorphism at linked loci, while its effect on the sojourn times and the substitution rate at linked loci has not been studied yet. To solve these problems, a model that assumed two linked loci, each with infinite alleles, was examined by computer simulation. A decrease in the recombination rate between two loci markedly changed the distribution of sojourn times of a neutral allele. Although overdominant selection obviously increased the sojourn times and the polymorphism at a linked locus, the rate of nucleotide substitution at the neutral locus was not influenced significantly even if complete linkage was assumed. These results suggest that, in regions containing overdominant genes, linked neutral loci will exhibit elevated levels of polymorphism, but their rate of molecular evolution remains that predicted by neutral theory.