bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation of Acetate Auxotrophs of the Methane-Producing Archaeon Methanococcus maripaludis by Random Insertional Mutagenesis
Authors: Kim Wonduck , Whitman William B 
Published: April 2021

Abstract
To learn more about autotrophic growth of methanococci, we isolated nine conditional mutants of Methanococcus maripaludis after transformation of the wild type with a random library in pMEB.2, a suicide plasmid bearing the puromycin-resistance cassette pac. These mutants grew poorly in mineral medium and required acetate or complex organic supplements such as yeast extract for normal growth. One mutant, JJ104, was a leaky acetate auxotroph. A plasmid, pWDK104, was recovered from this mutant by electroporation of a plasmid preparation into Escherichia coli. Transformation of wild-type M. maripaludis with pWDK104 produced JJ104-1, a mutant with the same phenotype as JJ104, thus establishing that insertion of pWDK104 into the genome was responsible for the phenotype. pWDK104 contained portions of the methanococcal genes encoding an ABC transporter closely related to MJ1367-MJ1368 of M. jannaschii. Because high levels of molybdate, tungstate, and selenite restored growth to wild-type levels, this transporter may be specific for these oxyanions. A second acetate auxotroph, JJ117, had an absolute growth requirement for either acetate or cobalamin, and wild-type growth was observed only in the presence of both. Cobinamide, 5′,6′-dimethylbenzimidazole, and 2-aminopropanol did not replace cobalamin. This phenotype was correlated with tandem insertions in the genome but not single insertions and appeared to have resulted from an indirect effect on cobamide metabolism. Plasmids rescued from other mutants contained portions of ORFs denoted in M. jannaschii as endoglucanase (MJ0555), transketolase (MJ0681), thiamine biosynthetic protein thiI (MJ0931), and several hypothetical proteins (MJ1031, MJ0835, and MJ0835.1).
Dependence of the Regulation of Telomere Length on the Type of Subtelomeric Repeat in the Yeast Saccharomyces cerevisiae
Authors: Craven Rolf J , Petes Thomas D 
Published: April 2021

Abstract
In the yeast Saccharomyces cerevisiae, chromosomes terminate with ∼400 bp of a simple repeat poly(TG1-3). Based on the arrangement of subtelomeric X and Y′ repeats, two types of yeast telomeres exist, those with both X and Y′ (Y′ telomeres) and those with only X (X telomeres). Mutations that result in abnormally short or abnormally long poly(TG1-3) tracts have been previously identified. In this study, we investigated telomere length in strains with two classes of mutations, one that resulted in short poly(TG1-3) tracts (tel1) and one that resulted in elongated tracts (pif1, rap1-17, rif1, or rif2). In the tel1 pif1 strain, Y′ telomeres had about the same length as those in tel1 strains and X telomeres had lengths intermediate between those in tel1 and pif1 strains. Strains with either the tel1 rap1-17 or tel1 rif2 genotypes had short tracts for all chromosome ends examined, demonstrating that the telomere elongation characteristic of rap1-17 and rif2 strains is Tel1p-dependent. In strains of the tel1 rif1 or tel1 rif1 rif2 genotypes, telomeres with Y′ repeats had short terminal tracts, whereas most of the X telomeres had long terminal tracts. These results demonstrate that the regulation of telomere length is different for X and Y′ telomeres.
Origination of Ds Elements From Ac Elements in Maize: Evidence for Rare Repair Synthesis at the Site of Ac Excision
Authors: Yan Xianghe , Martínez-Férez Isabel M , Kavchok Steven , Dooner Hugo K 
Published: April 2021

Abstract
Although it has been known for some time that the maize transposon Ac can mutate to Ds by undergoing internal deletions, the mechanism by which these mutations arise has remained conjectural. To gain further insight into this mechanism in maize we have studied a series of Ds elements that originated de novo from Ac elements at known locations in the genome. We present evidence that new, internally deleted Ds elements can arise at the Ac donor site when Ac transposes to another site in the genome. However, internal deletions are rare relative to Ac excision footprints, the predominant products of Ac transposition. We have characterized the deletion junctions in five new Ds elements. Short direct repeats of variable length occur adjacent to the deletion junction in three of the five Ds derivatives. In the remaining two, extra sequences or filler DNA is inserted at the junction. The filler DNAs are identical to sequences found close to the junction in the Ac DNA, where they are flanked by the same sequences that flank the filler DNA in the deletion. These findings are explained most simply by a mechanism involving error-prone DNA replication as an occasional alternative to end-joining in the repair of Ac-generated double-strand breaks.
Functional Overlap Between the mec-8 Gene and Five sym Genes in Caenorhabditis elegans
Authors: Davies Andrew G , Spike Caroline A , Shaw Jocelyn E , Herman Robert K 
Published: April 2021

Abstract
Earlier work showed that the Caenorhabditis elegans gene mec-8 encodes a regulator of alternative RNA splicing and that mec-8 null mutants have defects in sensory neurons and body muscle attachment but are generally viable and fertile. We have used a genetic screen to identify five mutations in four genes, sym-1–sym-4, that are synthetically lethal with mec-8 loss-of-function mutations. The phenotypes of sym single mutants are essentially wild type. mec-8; sym-1 embryos arrest during embryonic elongation and exhibit defects in the attachment of body muscle to extracellular cuticle. sym-1 can encode a protein containing a signal sequence and 15 contiguous leucine-rich repeats. A fusion of sym-1 and the gene for green fluorescent protein rescued the synthetic lethality of mec-8; sym-1 mutants; the fusion protein was secreted from the apical hypodermal surface of the embryo. We propose that SYM-1 helps to attach body muscle to the extracellular cuticle and that another gene that is dependent upon mec-8 for pre-mRNA processing overlaps functionally with sym-1. RNA-mediated interference experiments indicated that a close relative of sym-1 functionally overlaps both sym-1 and mec-8 in affecting muscle attachment. sym-2, sym-3, and sym-4 appear to provide additional functions that are essential in the absence of mec-8(+).
A Genetic Screen for Modifiers of E2F in Drosophila melanogaster
Authors: Staehling-Hampton Karen , Ciampa Phillip J , Brook Adam , Dyson Nicholas 
Published: April 2021

Abstract
The activity of the E2F transcription factor is regulated in part by pRB, the protein product of the retinoblastoma tumor suppressor gene. Studies of tumor cells show that the p16ink4a/cdk4/cyclin D/pRB pathway is mutated in most forms of cancer, suggesting that the deregulation of E2F, and hence the cell cycle, is a common event in tumorigenesis. Extragenic mutations that enhance or suppress E2F activity are likely to alter cell-cycle control and may play a role in tumorigenesis. We used an E2F overexpression phenotype in the Drosophila eye to screen for modifiers of E2F activity. Coexpression of dE2F and its heterodimeric partner dDP in the fly eye induces S phases and cell death. We isolated 33 enhancer mutations of this phenotype by EMS and X-ray mutagenesis and by screening a deficiency library collection. The majority of these mutations sorted into six complementation groups, five of which have been identified as alleles of brahma (brm), moira (mor) osa, pointed (pnt), and polycephalon (poc). osa, brm, and mor encode proteins with homology to SWI1, SWI2, and SWI3, respectively, suggesting that the activity of a SWI/SNF chromatin-remodeling complex has an important impact on E2F-dependent phenotypes. Mutations in poc also suppress phenotypes caused by p21CIP1 expression, indicating an important role for polycephalon in cell-cycle control.
Inferences on the Genome Structure of Progenitor Maize Through Comparative Analysis of Rice, Maize and the Domesticated Panicoids
Authors: Wilson William A , Harrington Sandra E , Woodman Wendy L , Lee Michael , Sorrells Mark E , McCouch Susan R 
Published: April 2021

Abstract
Corn and rice genetic linkage map alignments were extended and refined by the addition of 262 new, reciprocally mapped maize cDNA loci. Twenty chromosomal rearrangements were identified in maize relative to rice and these included telomeric fusions between rice linkage groups, nested insertion of rice linkage groups, intrachromosomal inversions, and a nonreciprocal translocation. Maize genome evolution was inferred relative to other species within the Panicoideae and a progenitor maize genome with eight linkage groups was proposed. Conservation of composite linkage groups indicates that the tetrasomic state arose during maize evolution either from duplication of one progenitor corn genome (autoploidy) or from a cross between species that shared the composite linkages observed in modern maize (alloploidy). New evidence of a quadruplicated homeologous segment on maize chromosomes 2 and 10, and 3 and 4, corresponded to the internally duplicated region on rice chromosomes 11 and 12 and suggested that this duplication in the rice genome predated the divergence of the Panicoideae and Oryzoideae subfamilies. Charting of the macroevolutionary steps leading to the modern maize genome clarifies the interpretation of intercladal comparative maps and facilitates alignments and genomic cross-referencing of genes and phenotypes among grass family members.
Genetic Study of Interactions Between the Cytoskeletal Assembly Protein Sla1 and Prion-Forming Domain of the Release Factor Sup35 (eRF3) in Saccharomyces cerevisiae
Authors: Bailleul Peggy A , Newnam Gary P , Steenbergen Judith N , Chernoff Yury O 
Published: April 2021

Abstract
Striking similarities between cytoskeletal assembly and the “nucleated polymerization” model of prion propagation suggest that similar or overlapping sets of proteins may assist in both processes. We show that the C-terminal domain of the yeast cytoskeletal assembly protein Sla1 (Sla1C) specifically interacts with the N-terminal prion-forming domain (Sup35N) of the yeast release factor Sup35 (eRF3) in the two-hybrid system. Sla1C and several other Sup35N-interacting proteins also exhibit two-hybrid interactions with the poly-Gln-expanded N-proximal fragment of human huntingtin, which promotes Huntington disease-associated aggregation. The Sup35N-Sla1C interaction is inhibited by Sup35N alterations that make Sup35 unable to propagate the [PSI+] state and by the absence of the chaperone protein Hsp104, which is essential for [PSI] propagation. In a Sla1– background, [PSI] curing by dimethylsulfoxide or excess Hsp104 is increased, while translational readthrough and de novo [PSI] formation induced by excess Sup35 or Sup35N are decreased. These data show that, in agreement with the proposed function of Sla1 during cytoskeletal formation, Sla1 assists in [PSI] formation and propagation, but is not required for these processes. Sla1– strains are sensitive to some translational inhibitors, and some sup35 mutants, obtained in a Sla1– background, are sensitive to Sla1, suggesting that the interaction between Sla1 and Sup35 proteins may play a role in the normal function of the translational apparatus. We hypothesize that Sup35N is involved in regulatory interactions with intracellular structural networks, and [PSI] prion may be formed as a by-product of this process.
The TamA Protein Fused to a DNA-Binding Domain Can Recruit AreA, the Major Nitrogen Regulatory Protein, to Activate Gene Expression in Aspergillus nidulans
Authors: Small Anna J , Hynes Michael J , Davis Meryl A 
Published: April 2021

Abstract
The areA gene of Aspergillus nidulans encodes a GATA zinc finger transcription factor that activates the expression of a large number of genes subject to nitrogen metabolite repression. The amount and activity of the AreA protein under different nitrogen conditions is modulated by transcriptional, post-transcriptional, and post-translational controls. One of these controls of AreA activity has been proposed to involve the NmrA protein interacting with the DNA-binding domain and the extreme C terminus of AreA to inhibit DNA binding under nitrogen sufficient conditions. In contrast, mutational evidence suggests that the tamA gene has a positive role together with areA in regulating the expression of genes subject to nitrogen metabolite repression. This gene was identified by the selection of mutants resistant to toxic nitrogen source analogues, and a number of nitrogen metabolic activities have been shown to be reduced in these mutants. To investigate the role of this gene we have used constructs encoding the TamA protein fused to the DNA-binding domain of either the FacB or the AmdR regulatory proteins. These hybrid proteins have been shown to activate expression of the genes of acetate or GABA utilization, respectively, as well as the amdS gene. Strong activation was shown to require the AreA protein but was not dependent on AreA binding to DNA. The homologous areA gene of A. oryzae and nit-2 gene of Neurospora crassa can substitute for A. nidulans areA in this interaction. We have shown that the same C-terminal region of AreA and NIT-2 that is involved in the interaction with NmrA is required for the TamA-AreA interaction. However, it is unlikely that TamA requires the same residues as NmrA within the GATA DNA-binding domain of AreA.
A Requirement for Recombinational Repair in Saccharomyces cerevisiae Is Caused by DNA Replication Defects of mec1 Mutants
Authors: Merrill Bradley J , Holm Connie 
Published: April 2021

Abstract
To examine the role of the RAD52 recombinational repair pathway in compensating for DNA replication defects in Saccharomyces cerevisiae, we performed a genetic screen to identify mutants that require Rad52p for viability. We isolated 10 mec1 mutations that display synthetic lethality with rad52. These mutations (designated mec1-srf for synthetic lethality with rad-fifty-two) simultaneously cause two types of phenotypes: defects in the checkpoint function of Mec1p and defects in the essential function of Mec1p. Velocity sedimentation in alkaline sucrose gradients revealed that mec1-srf mutants accumulate small single-stranded DNA synthesis intermediates, suggesting that Mec1p is required for the normal progression of DNA synthesis. sml1 suppressor mutations suppress both the accumulation of DNA synthesis intermediates and the requirement for Rad52p in mec1-srf mutants, but they do not suppress the checkpoint defect in mec1-srf mutants. Thus, it appears to be the DNA replication defects in mec1-srf mutants that cause the requirement for Rad52p. By using hydroxyurea to introduce similar DNA replication defects, we found that single-stranded DNA breaks frequently lead to double-stranded DNA breaks that are not rapidly repaired in rad52 mutants. Taken together, these data suggest that the RAD52 recombinational repair pathway is required to prevent or repair double-stranded DNA breaks caused by defective DNA replication in mec1-srf mutants.
A Mutation in a Methionine tRNA Gene Suppresses the prp2-1 Ts Mutation and Causes a Pre-mRNA Splicing Defect in Saccharomyces cerevisiae
Authors: Kim Dong-Ho , Edwalds-Gilbert Gretchen , Ren Chengzhen , Lin Ren-Jang 
Published: April 2021

Abstract
The PRP2 gene in Saccharomyces cerevisiae encodes an RNA-dependent ATPase that activates spliceosomes for the first transesterification reaction in pre-mRNA splicing. We have identified a mutation in the elongation methionine tRNA gene EMT1 as a dominant, allele-specific suppressor of the temperature-sensitive prp2-1 mutation. The EMT1-201 mutant suppressed prp2-1 by relieving the splicing block at high temperature. Furthermore, EMT1-201 single mutant cells displayed pre-mRNA splicing and cold-sensitive growth defects at 18°. The mutation in EMT1-201 is located in the anticodon, changing CAT to CAG, which presumably allowed EMT1-201 suppressor tRNA to recognize CUG leucine codons instead of AUG methionine codons. Interestingly, the prp2-1 allele contains a point mutation that changes glycine to aspartate, indicating that EMT1-201 does not act by classical missense suppression. Extra copies of the tRNALeu(UAG) gene rescued the cold sensitivity and in vitro splicing defect of EMT1-201. This study provides the first example in which a mutation in a tRNA gene confers a pre-mRNA processing (prp) phenotype.
Genome Rearrangements by Nonlinear Transposons in Maize
Authors: Zhang Jianbo , Peterson Thomas 
Published: April 2021

Abstract
Transposable elements have long been considered as potential agents of large-scale genome reorganization by virtue of their ability to induce chromosomal rearrangements such as deletions, duplications, inversions, and reciprocal translocations. Previous researchers have shown that particular configurations of transposon termini can induce chromosome rearrangements at high frequencies. Here, we have analyzed chromosomal rearrangements derived from an unstable allele of the maize P1 (pericarp color) gene. The progenitor allele contains both a full-length Ac (Activator) transposable element and an Ac terminal fragment termed fAc (fractured Ac) inserted in the second intron of the P1-rr gene. Two rearranged alleles were derived from a classical maize ear twinned sector and were found to contain a large inverted duplication and a corresponding deficiency. The sequences at the junctions of the rearrangement breakpoints indicate that the duplication and deletion structures were produced by a single transposition event involving Ac and fAc termini located on sister chromatids. Because the transposition process we describe involves transposon ends located on different DNA molecules, it is termed nonlinear transposition (NLT). NLT can rapidly break and rejoin chromosomes and thus could have played an important role in generating structural heterogeneity during genome evolution.
Insights Into Genome Differentiation: Pheromone-Binding Protein Variation and Population History in the European Corn Borer (Ostrinia nubilalis)
Authors: Willett Christopher S , Harrison Richard G 
Published: April 2021

Abstract
Examination of sequence variation at nuclear loci can give insights into population history and gene flow that cannot be derived from other commonly used molecular markers, such as allozymes. Here, we report on sequence variation at a single nuclear locus, the pheromone-binding protein (PBP) locus, in the European corn borer (Ostrinia nubilalis). The European corn borer has been divided into three races in New York State on the basis of differences in pheromone communication and life history. Previous allozyme data have suggested that there is a small but significant amount of genetic differentiation between these races. The PBP does not appear to be involved in the pheromone differences between these races. Examination of variation at the PBP locus in the three races reveals no fixed differences between races despite high levels of polymorphism. There also appears to have been considerable recombination in the history of the pheromone-binding protein alleles. Observation of both recombination between alleles and lack of significant nucleotide or insertion/deletion divergence between races leads us to suggest that these populations are either recently diverged or have continued to exchange genetic material subsequent to divergence in pheromone communication and life history.
A Comparison of the Genetic Basis of Wing Size Divergence in Three Parallel Body Size Clines of Drosophila melanogaster
Authors: Gilchrist A Stuart , Partridge Linda 
Published: April 2021

AbstractBody size clines in Drosophila melanogaster have been documented in both Australia and South America, and may exist in Southern Africa. We crossed flies from the northern and southern ends of each of these clines to produce F1, F2, and first backcross generations. Our analysis of generation means for wing area and wing length produced estimates of the additive, dominance, epistatic, and maternal effects underlying divergence within each cline. For both females and males of all three clines, the generation means were adequately described by these parameters, indicating that linkage and higher order interactions did not contribute significantly to wing size divergence. Marked differences were apparent between the clines in the occurrence and magnitude of the significant genetic parameters. No cline was adequately described by a simple additive-dominance model, and significant epistatic and maternal effects occurred in most, but not all, of the clines. Generation variances were also analyzed. Only one cline was described sufficiently by a simple additive variance model, indicating significant epistatic, maternal, or linkage effects in the remaining two clines. The diversity in genetic architecture of the clines suggests that natural selection has produced similar phenotypic divergence by different combinations of gene action and interaction.
Nonequilibrium Migration in Human History
Authors: Wakeley John 
Published: April 2021

Abstract
A nonequilibrium migration model is proposed and applied to genetic data from humans. The model assumes symmetric migration among all possible pairs of demes and that the number of demes is large. With these assumptions it is straightforward to allow for changes in demography, and here a single abrupt change is considered. Under the model this change is identical to a change in the ancestral effective population size and might be caused by changes in deme size, in the number of demes, or in the migration rate. Expressions for the expected numbers of sites segregating at particular frequencies in a multideme sample are derived. A maximum-likelihood analysis of independent polymorphic restriction sites in humans reveals a decrease in effective size. This is consistent with a change in the rates of migration among human subpopulations from ancient low levels to present high ones.
Genotype-Environment Interaction for Quantitative Trait Loci Affecting Life Span in Drosophila melanogaster
Authors: Vieira Cristina , Pasyukova Elena G , Zeng Zhao-Bang , Hackett J Brant , Lyman Richard F , Mackay Trudy F C 
Published: April 2021

Abstract
The nature of genetic variation for Drosophila longevity in a population of recombinant inbred lines was investigated by estimating quantitative genetic parameters and mapping quantitative trait loci (QTL) for adult life span in five environments: standard culture conditions, high and low temperature, and heat-shock and starvation stress. There was highly significant genetic variation for life span within each sex and environment. In the analysis of variance of life span pooled over sexes and environments, however, the significant genetic variation appeared in the genotype × sex and genotype × environment interaction terms. The genetic correlation of longevity across the sexes and environments was not significantly different from zero in these lines. We estimated map positions and effects of QTL affecting life span by linkage to highly polymorphic roo transposable element markers, using a multiple-trait composite interval mapping procedure. A minimum of 17 QTL were detected; all were sex and/or environment-specific. Ten of the QTL had sexually antagonistic or antagonistic pleiotropic effects in different environments. These data provide support for the pleiotropy theory of senescence and the hypothesis that variation for longevity might be maintained by opposing selection pressures in males and females and variable environments. Further work is necessary to assess the generality of these results, using different strains, to determine heterozygous effects and to map the life span QTL to the level of genetic loci.