bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Aspergillus nidulans musN Gene Encodes a RecQ Helicase That Interacts With the PI-3K-Related Kinase UVSB
Authors: Hofmann Amy F , Harris Steven D 
Published: April 2021

Abstract
In Aspergillus nidulans, the uvsB gene encodes a member of the PI-3K-related kinase family of proteins. We have recently shown that UVSB is required for multiple aspects of the DNA damage response. Since the musN227 mutation is capable of partially suppressing defects caused by uvsB mutations, we sought to understand the mechanism underlying the suppression by cloning the musN gene. Here, we report that musN encodes a RecQ helicase with homology to S. pombe rqh1, S. cerevisiae sgs1, and human BLM and WRN. Phenotypic characterization of musN mutant alleles reveals that MUSN participates in the response to a variety of genotoxic agents. The slow growth and genotoxin sensitivity of a musN null mutant can be partially suppressed by a defect in homologous recombination caused by the uvsC114 mutation. In addition, we present evidence suggesting that MUSN may promote recovery from the DNA damage response. We suggest that a block to recovery caused by the musN227 mutation, coupled with the modest accumulation of recombination intermediates, can suppress defects caused by uvsB mutations. Finally, we report that another RecQ helicase, ORQA, performs a function that partially overlaps that of MUSN.
Molecular Characterization of Pax62Neu Through Pax610Neu: An Extension of the Pax6 Allelic Series and the Identification of Two Possible Hypomorph Alleles in the Mouse Mus musculus
Authors: Favor Jack , Peters Heiko , Hermann Thomas , Schmahl Wolfgang , Chatterjee Bimal , Neuhäuser-Klaus Angelika , Sandulache Rodica 
Published: April 2021

Abstract
Phenotype-based mutagenesis experiments will increase the mouse mutant resource, generating mutations at previously unmarked loci as well as extending the allelic series at known loci. Mapping, molecular characterization, and phenotypic analysis of nine independent Pax6 mutations of the mouse recovered in mutagenesis experiments is presented. Seven mutations result in premature termination of translation and all express phenotypes characteristic of null alleles, suggesting that Pax6 function requires all domains to be intact. Of major interest is the identification of two possible hypomorph mutations: Heterozygotes express less severe phenotypes and homozygotes develop rudimentary eyes and nasal processes and survive up to 36 hr after birth. Pax64Neu results in an amino acid substitution within the third helix of the homeodomain. Three-dimensional modeling indicates that the amino acid substitution interrupts the homeodomain recognition α-helix, which is critical for DNA binding. Whereas cooperative dimer binding of the mutant homeodomain to a paired-class DNA target sequence was eliminated, weak monomer binding was observed. Thus, a residual function of the mutated homeodomain may explain the hypomorphic nature of the Pax64Neu allele. Pax67Neu is a base pair substitution in the Kozak sequence and results in a reduced level of Pax6 translation product. The Pax64Neu and Pax67Neu alleles may be very useful for gene-dosage studies.
Gene Conversion Within Regulatory Sequences Generates Maize r Alleles With Altered Gene Expression
Authors: Li Ying , Bernot John P , Illingworth Charles , Lison Wyatt , Bernot Kelsie M , Eggleston William B , Fogle Keri J , DiPaola James E , Kermicle Jerry , Alleman Mary 
Published: April 2021

Abstract
The maize r locus encodes a transcription factor that regulates the developmental expression of the plant pigment anthocyanin. In an unusual example of gene regulatory diversity, the R-sc (Sc, strong seed color) and the R-p (P, plant color) alleles of r have nonoverlapping tissue specificity and nonhomologous 5′ flanking sequences. Heterozygotes between wild-type P and Sc mutants with Ds6 transposable element inserts (r-sc:m::Ds6 or sc:m) produce colored seed derivatives (Sc+) during meiotic recombination. The sc:m alleles with Ds6 insertion in 3′ regions of r produce crossover Sc+ derivatives. sc:m alleles with Ds6 elements inserted in 5′ regions produce rare Sc+ derivatives borne on nonrecombinant chromosomes. Among 52 such noncrossover Sc+ derivatives, 18 are indistinguishable from the Sc progenitor in phenotype and DNA sequence [Scp(+) alleles]. The remaining 34 derivatives have strong Sc+ expression, including darkly pigmented aleurone, scutellum, coleoptile, and scutellar node [Scp(e) alleles]. The coleoptile and scutellar node phenotypes are unique from either progenitor but are similar to those of some naturally occurring r alleles. Both classes of Sc+ derivatives are explained by gene conversion between the promoter region of Sc:124 and a homologous region located proximal to P. The recombinational intermediate formed between sc:m alleles and P results in deletion of the Ds6 element alone or both Ds6 and a nearby unrelated transposable element-like sequence.
Recombination, Balancing Selection and Phylogenies in MHC and Self-Incompatibility Genes
Authors: Schierup Mikkel H , Mikkelsen Anders M , Hein Jotun 
Published: April 2021

Abstract
Using a coalescent model of multiallelic balancing selection with recombination, the genealogical process as a function of recombinational distance from a site under selection is investigated. We find that the shape of the phylogenetic tree is independent of the distance to the site under selection. Only the timescale changes from the value predicted by Takahata's allelic genealogy at the site under selection, converging with increasing recombination to the timescale of the neutral coalescent. However, if nucleotide sequences are simulated over a recombining region containing a site under balancing selection, a phylogenetic tree constructed while ignoring such recombination is strongly affected. This is true even for small rates of recombination. Published studies of multiallelic balancing selection, i.e., the major histocompatibility complex (MHC) of vertebrates, gametophytic and sporophytic self-incompatibility of plants, and incompatibility of fungi, all observe allelic genealogies with unexpected shapes. We conclude that small absolute levels of recombination are compatible with these observed distortions of the shape of the allelic genealogy, suggesting a possible cause of these observations. Furthermore, we illustrate that the variance in the coalescent with recombination process makes it difficult to locate sites under selection and to estimate the selection coefficient from levels of variability.
The Roles of Klenow Processing and Flap Processing Activities of DNA Polymerase I in Chromosome Instability in Escherichia coli K12 Strains
Authors: Nagata Yuki , Mashimo Kazumi , Kawata Masakado , Yamamoto Kazuo 
Published: April 2021

Abstract
The sequences of spontaneous mutations occurring in the endogenous tonB gene of Escherichia coli in the ΔpolA and polA107 mutant strains were compared. Five categories of mutations were found: (1) deletions, (2) minus frameshifts, (3) plus frameshifts, (4) duplications, and (5) other mutations. The ΔpolA strain, which is deficient in both Klenow domain and 5′ → 3′ exonuclease domain of DNA polymerase I, shows a marked increase in categories 1–4. The polA107 strain, which is deficient in the 5′ → 3′ exonuclease domain but proficient in the Klenow domain, shows marked increases in categories 3 and 4 but not in 1 or 2. Previously, we reported that the polA1 strain, which is known to be deficient in the Klenow domain but proficient in the 5′ → 3′ exonuclease domain, shows increases in categories 1 and 2 but not in 3 or 4. The 5′ → 3′ exonuclease domain of DNA polymerase I is a homolog of the mammalian FEN1 and the yeast RAD27 flap nucleases. We therefore proposed the model that the Klenow domain can process deletion and minus frameshift mismatch in the nascent DNA and that flap nuclease can process plus frameshift and duplication mismatch in the nascent DNA.
Maternal Effect for DNA Mismatch Repair in the Mouse
Authors: Gurtu Vanessa E , Verma Shelly , Grossmann Allie H , Liskay R Michael , Skarnes William C , Baker Sean M 
Published: April 2021

Abstract
DNA mismatch repair (DMR) functions to maintain genome stability. Prokaryotic and eukaryotic cells deficient in DMR show a microsatellite instability (MSI) phenotype characterized by repeat length alterations at microsatellite sequences. Mice deficient in Pms2, a mammalian homolog of bacterial mutL, develop cancer and display MSI in all tissues examined, including the male germ line where a frequency of ~10% was observed. To determine the consequences of maternal DMR deficiency on genetic stability, we analyzed F1 progeny from Pms2−/− female mice mated with wild-type males. Our analysis indicates that MSI in the female germ line was ~9%. MSI was also observed in paternal alleles, a surprising result since the alleles were obtained from wild-type males and the embryos were therefore DMR proficient. We propose that mosaicism for paternal alleles is a maternal effect that results from Pms2 deficiency during the early cleavage divisions. The absence of DMR in one-cell embryos leads to the formation of unrepaired replication errors in early cell divisions of the zygote. The occurrence of postzygotic mutation in the early mouse embryo suggests that Pms2 deficiency is a maternal effect, one of a limited number identified in the mouse and the first to involve a DNA repair gene.
Arabidopsis Cytochrome P450cyp83B1Mutations Activate the Tryptophan Biosynthetic Pathway
Authors: Smolen Gromoslaw , Bender Judith 
Published: April 2021

AbstractIn plants, the tryptophan biosynthetic pathway provides a number of important secondary metabolites including the growth regulator indole-3-acetic acid (IAA) and indole glucosinolate defense compounds. Genes encoding tryptophan pathway enzymes are transcriptionally induced by a variety of stress signals, presumably to increase the production of both tryptophan and secondary metabolites during defense responses. To understand the mechanism of transcriptional induction, we isolated altered tryptophan regulation (atr) mutants in Arabidopsis thaliana with activated transcription of tryptophan genes. One atr complementation group consisted of mutations in the cytochrome P450 gene CYP83B1. Mutant plants had constitutively activated expression of the ATR1 Myb factor gene, which was identified as a positive regulator of tryptophan genes via the atr mutant screen. cyp83B1 mutants were previously characterized as having defects in IAA homeostasis due to perturbation of secondary tryptophan metabolism. Our findings indicate that the upregulation of tryptophan pathway genes might also contribute to the overaccumulation of IAA in mutant plants. Moreover, we show that cyp83B1 mutants have lesion-mimic phenotypes, suggesting that multiple stress pathways are activated by loss of CYP83B1 function.
Patterns of Genetic Variation at a Chromosome 4 Locus of Drosophila melanogaster and D. simulans
Authors: Jensen Mark A , Charlesworth Brian , Kreitman Martin 
Published: April 2021

Abstract
DNA sequence surveys of Drosophila melanogaster populations show a strong positive correlation between the recombination rate experienced by a locus and its level of nucleotide polymorphism. In particular, surveys of the fourth chromosome gene ciD show greatly reduced levels of nucleotide variation; this observation was originally interpreted in terms of selective sweeps occurring on the nonrecombining fourth chromosome. Subsequent theoretical work has, however, uncovered several other selective processes that can reduce variation. In this study, we revisit the Drosophila fourth chromosome, investigating variation in 5–6 kb of the gene ankyrin in D. melanogaster and D. simulans. Silent nucleotide site diversity is ~5 × 10−4 for both species, consistent with the previous observations of low variation at ciD. Given the observed frequency spectra at ankyrin, coalescent simulations indicate that reduced diversity in the region is unlikely to be due to a selective sweep alone. We find evidence for recombinational exchange at this locus, and both species appear to be fixed for an insertion of the transposable element HB in an intron of ankyrin.
RNAi Triggered by Symmetrically Transcribed Transgenes in Drosophila melanogaster
Authors: Giordano Ennio , Rendina Rosaria , Peluso Ivana , Furia Maria 
Published: April 2021

Abstract
Specific silencing of target genes can be induced in a variety of organisms by providing homologous double-stranded RNA molecules. In vivo, these molecules can be generated either by transcription of sequences having an inverted-repeat (IR) configuration or by simultaneous transcription of sense-antisense strands. Since IR constructs are difficult to prepare and can stimulate genomic rearrangements, we investigated the silencing potential of symmetrically transcribed sequences. We report that Drosophila transgenes whose sense-antisense transcription was driven by two convergent arrays of Gal4-dependent UAS sequences can induce specific, dominant, and heritable repression of target genes. This effect is not dependent on a mechanism based on homology-dependent DNA/DNA interactions, but is directly triggered by transcriptional activation and is accompanied by specific depletion of the endogenous target RNA. Tissue-specific induction of these transgenes restricts the target gene silencing to selected body domains, and spreading phenomena described in other cases of post-transcriptional gene silencing (PTGS) were not observed. In addition to providing an additional tool useful for Drosophila functional genomic analysis, these results add further strength to the view that events of sense-antisense transcription may readily account for some, if not all, PTGS-cosuppression phenomena and can potentially play a relevant role in gene regulation.
Molecular and Phenotypic Analysis of 25 Recessive, Homozygous-Viable Alleles at the Mouse agouti Locus
Authors: Miltenberger Rosalynn J , Wakamatsu Kazumasa , Ito Shosuke , Woychik Richard P , Russell Liane B , Michaud Edward J 
Published: April 2021

Abstract
Agouti is a paracrine-acting, transient antagonist of melanocortin 1 receptors that specifies the subapical band of yellow on otherwise black hairs of the wild-type coat. To better understand both agouti structure/function and the germline damage caused by chemicals and radiation, an allelic series of 25 recessive, homozygous-viable agouti mutations generated in specific-locus tests were characterized. Visual inspection of fur, augmented by quantifiable chemical analysis of hair melanins, suggested four phenotypic categories (mild, moderate, umbrous-like, severe) for the 18 hypomorphs and a single category for the 7 amorphs (null). Molecular analysis indicated protein-coding alterations in 8 hypomorphs and 6 amorphs, with mild-moderate phenotypes correlating with signal peptide or basic domain mutations, and more devastating phenotypes resulting from C-terminal lesions. Ten hypomorphs and one null demonstrated wild-type coding potential, suggesting that they contain mutations elsewhere in the ≥125-kb agouti locus that either reduce the level or alter the temporal/spatial distribution of agouti transcripts. Beyond the notable contributions to the field of mouse germ cell mutagenesis, analysis of this allelic series illustrates that complete abrogation of agouti function in vivo occurs most often through protein-coding lesions, whereas partial loss of function occurs slightly more frequently at the level of gene expression control.
Maize Mu Transposons Are Targeted to the 5′ Untranslated Region of the gl8 Gene and Sequences Flanking Mu Target-Site Duplications Exhibit Nonrandom Nucleotide Composition Throughout the Genome
Authors: Dietrich Charles R , Cui Feng , Packila Mark L , Li Jin , Ashlock Daniel A , Nikolau Basil J , Schnable Patrick S 
Published: April 2021

Abstract
The widespread use of the maize Mutator (Mu) system to generate mutants exploits the preference of Mu transposons to insert into genic regions. However, little is known about the specificity of Mu insertions within genes. Analysis of 79 independently isolated Mu-induced alleles at the gl8 locus established that at least 75 contain Mu insertions. Analysis of the terminal inverted repeats (TIRs) of the inserted transposons defined three new Mu transposons: Mu10, Mu11, and Mu12. A large percentage (&gt;80%) of the insertions are located in the 5′ untranslated region (UTR) of the gl8 gene. Ten positions within the 5′ UTR experienced multiple independent Mu insertions. Analyses of the nucleotide composition of the 9-bp TSD and the sequences directly flanking the TSD reveals that the nucleotide composition of Mu insertion sites differs dramatically from that of random DNA. In particular, the frequencies at which C's and G's are observed at positions −2 and +2 (relative to the TSD) are substantially higher than expected. Insertion sites of 315 RescueMu insertions displayed the same nonrandom nucleotide composition observed for the gl8-Mu alleles. Hence, this study provides strong evidence for the involvement of sequences flanking the TSD in Mu insertion-site selection.
Linkage Disequilibrium in Domestic Sheep
Authors: McRae A F , McEwan J C , Dodds K G , Wilson T , Crawford A M , Slate J 
Published: April 2021

Abstract
The last decade has seen a dramatic increase in the number of livestock QTL mapping studies. The next challenge awaiting livestock geneticists is to determine the actual genes responsible for variation of economically important traits. With the advent of high density single nucleotide polymorphism (SNP) maps, it may be possible to fine map genes by exploiting linkage disequilibrium between genes of interest and adjacent markers. However, the extent of linkage disequilibrium (LD) is generally unknown for livestock populations. In this article microsatellite genotype data are used to assess the extent of LD in two populations of domestic sheep. High levels of LD were found to extend for tens of centimorgans and declined as a function of marker distance. However, LD was also frequently observed between unlinked markers. The prospects for LD mapping in livestock appear encouraging provided that type I error can be minimized. Properties of the multiallelic LD coefficient D′ were also explored. D′ was found to be significantly related to marker heterozygosity, although the relationship did not appear to unduly influence the overall conclusions. Of potentially greater concern was the observation that D′ may be skewed when rare alleles are present. It is recommended that the statistical significance of LD is used in conjunction with coefficients such as D′ to determine the true extent of LD.
Selection, Load and Inbreeding Depression in a Large Metapopulation
Authors: Whitlock Michael C 
Published: April 2021

AbstractThe subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient FST and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.
An Estimator for Pairwise Relatedness Using Molecular Markers
Authors: Wang Jinliang 
Published: April 2021

Abstract
I propose a new estimator for jointly estimating two-gene and four-gene coefficients of relatedness between individuals from an outbreeding population with data on codominant genetic markers and compare it, by Monte Carlo simulations, to previous ones in precision and accuracy for different distributions of population allele frequencies, numbers of alleles per locus, actual relationships, sample sizes, and proportions of relatives included in samples. In contrast to several previous estimators, the new estimator is well behaved and applies to any number of alleles per locus and any allele frequency distribution. The estimates for two- and four-gene coefficients of relatedness from the new estimator are unbiased irrespective of the sample size and have sampling variances decreasing consistently with an increasing number of alleles per locus to the minimum asymptotic values determined by the variation in identity-by-descent among loci per se, regardless of the actual relationship. The new estimator is also robust for small sample sizes and for unknown relatives being included in samples for estimating allele frequencies. Compared to previous estimators, the new one is generally advantageous, especially for highly polymorphic loci and/or small sample sizes.
Predicting Evolutionary Potential:In VitroEvolution Accurately Reproduces Natural Evolution of the TEM β-Lactamase
Authors: Barlow Miriam , Hall Barry G 
Published: April 2021

AbstractTo evaluate the validity of our in vitro evolution method as a model for natural evolutionary processes, the TEM-1 β-lactamase gene was evolved in vitro and was selected for increased resistance to cefotaxime, cefuroxime, ceftazadime, and aztreonam, i.e., the “extended-spectrum” phenotype. The amino acid substitutions recovered in 10 independent in vitro evolvants were compared with the amino acid substitutions in the naturally occurring extended-spectrum TEM alleles. Of the nine substitutions that have arisen multiple times in naturally occurring extended-spectrum TEM alleles, seven were recovered multiple times in vitro. We take this result as evidence that our in vitro evolution technique accurately mimics natural evolution and can therefore be used to predict the results of natural evolutionary processes. Additionally, our results predict that a phenotype not yet observed among TEM β-lactamases in nature—resistance to cefepime—is likely to arise in nature.
Telomeric and rDNA Silencing in Saccharomyces cerevisiae Are Dependent on a Nuclear NAD+ Salvage Pathway
Authors: Sandmeier Joseph J , Celic Ivana , Boeke Jef D , Smith Jeffrey S 
Published: April 2021

Abstract
The Sir2 protein is an NAD+-dependent protein deacetylase that is required for silencing at the silent mating-type loci, telomeres, and the ribosomal DNA (rDNA). Mutations in the NAD+ salvage gene NPT1 weaken all three forms of silencing and also cause a reduction in the intracellular NAD+ level. We now show that mutation of a highly conserved histidine residue in Npt1p results in a silencing defect, indicating that Npt1p enzymatic activity is required for silencing. Deletion of another NAD+ salvage pathway gene called PNC1 caused a less severe silencing defect and did not significantly reduce the intracellular NAD+ concentration. However, silencing in the absence of PNC1 was completely dependent on the import of nicotinic acid from the growth medium. Deletion of a gene in the de novo NAD+ synthesis pathway BNA1 resulted in a significant rDNA silencing defect only on medium deficient in nicotinic acid, an NAD+ precursor. By immunofluorescence microscopy, Myc-tagged Bna1p was localized throughout the whole cell in an asynchronously growing population. In contrast, Myc-tagged Npt1p was highly concentrated in the nucleus in ~40% of the cells, indicating that NAD+ salvage occurs in the nucleus in a significant fraction of cells. We propose a model in which two components of the NAD+ salvage pathway, Pnc1p and Npt1p, function together in recycling the nuclear nicotinamide generated by Sir2p deacetylase activity back into NAD+.