Blocking, Bending, and Binding: Regulation of Initiation of Chromosome Replication During the Escherichia coli Cell Cycle by Transcriptional Modulators That Interact With Origin DNA

Genome duplication is a critical event in the reproduction cycle of every cell. Because all daughter cells must inherit a complete genome, chromosome replication is tightly regulated, with multiple mechanisms focused on controlling when chromosome replication begins during the cell cycle. In bacteria, chromosome duplication starts when nucleoprotein complexes, termed orisomes, unwind replication origin (oriC) DNA and recruit proteins needed to build new replication forks. Functional orisomes comprise the conserved initiator protein, DnaA, bound to a set of high and low affinity recognition sites in oriC. Orisomes must be assembled each cell cycle. In Escherichia coli, the organism in which orisome assembly has been most thoroughly examined, the process starts with DnaA binding to high affinity sites after chromosome duplication is initiated, and orisome assembly is completed immediately before the next initiation event, when DnaA interacts with oriC’s lower affinity sites, coincident with origin unwinding. A host of regulators, including several transcriptional modulators, targets low affinity DnaA-oriC interactions, exerting their effects by DNA bending, blocking access to recognition sites, and/or facilitating binding of DnaA to both DNA and itself. In this review, we focus on orisome assembly in E. coli. We identify three known transcriptional modulators, SeqA, Fis (factor for inversion stimulation), and IHF (integration host factor), that are not essential for initiation, but which interact directly with E. coli oriC to regulate orisome assembly and replication initiation timing. These regulators function by blocking sites (SeqA) and bending oriC DNA (Fis and IHF) to inhibit or facilitate cooperative low affinity DnaA binding. We also examine how the growth rate regulation of Fis levels might modulate IHF and DnaA binding to oriC under a variety of nutritional conditions. Combined, the regulatory mechanisms mediated by transcriptional modulators help ensure that at all growth rates, bacterial chromosome replication begins once, and only once, per cell cycle.

Clinical Features of de novo Pure 16q21q24.1 Chromosome Duplication

Pure partial duplications of the long arm of chromosome 16 are rare and few cases are described with delineation by chromosomal microarray. Data about clinical abnormalities of pure partial 16q duplications are incomplete because many individuals die during the perinatal period. We describe the clinical features of a 47-month-old Brazilian girl with 16q21q24.1 duplication. To the best of our knowledge, she is the first person with this specific chromosome segment duplication, and we compare her phenotype with the only reported individual alive with intermediate–distal pure 16q duplication.

Pengaruh Konsentrasi Dan Lama Inkubasi Kolkisin Terhadap Duplikasi Kromosom Planlet Terung (Solanum melongena L.) Haploid Galur Aksesi Hasil Kultur Antera

The purpose of this study was to determine the effect of colchicine on chromosome duplication and to determine the best colchicine concentration and incubation time for haploid eggplant chromosome duplication results from anther culture. Laboratory experiments have been carried out at PT. East West Seed Indonesia, Benteng Village, Campaka District, Purwakarta from March to June 2020. With an altitude of 69 m above sea level. The environmental design used in this study was a completely randomized design consisting of 7 treatments and repeated 4 times. Colchicine treatment design A = Control, B = colchicine 0.05% 24 hours incubation, C = colchicine 0.05% 48 hours incubation, D = colchicine 0.1% 24 hours incubation, E = colchicine 0.1% 48 hours incubation, F = kolkisisn 0.15% incubation 24 hours, G = colchicine 0.15% incubation 48 hours. The responses observed were contamination, callous plantlets, rooted plantlets, live plantlets, haploid plantlets, double haploid plantlets, triploid plantets and unreadable ploidy check results. The results showed that the colchysis concentration and incubation time had an effect on the duplication of haploid eggplant plantlet chromosomes resulting from anther culture. And giving colchicine at a concentration of 0.05% with an incubation time of 48 hours and a colchicine concentration of 0.1% with an incubation time of 48 hours had a significant effect on the double haploid plantet of 23.44%.

Genetic variation in aneuploidy prevalence and tolerance across the Saccharomyces cerevisiae phylogeny

Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual's genetic makeup influences its tolerance of karyotypic imbalance. Here we took a population genetics perspective to investigate the selective forces influencing aneuploidy prevalence in Saccharomyces cerevisiae populations as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The phylogenetic context of lineages showing high aneuploidy rates suggests that increased aneuploidy frequency arose multiple times in S. cerevisiae evolution. Separate from aneuploidy frequency, analyzing growth phenotypes reveals that some backgrounds – such as European Wine strains – show fitness costs upon chromosome duplication, whereas other clades with high aneuploidy rates show little evidence of major deleterious effects. Our analysis confirms that chromosome amplification can produce phenotypic benefits that can influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.

Chromosome doubling in Cattleya tigrina A. Rich

Chromosome doubling induction in orchids may benefit their production for resulting in flowers of higher commercial value, larger size and higher content of substances that intensify the color and fragrance when compared with diploid orchids. This work aimed to induce and confirm artificial polyploidization, using flow cytometry and stomatal analysis. Explants were treated with colchicine at concentrations of 0, 2.5, 7.5, and 12.5 mM, for 24 and 48 hours and with oryzalin, at concentrations of 0, 10, 30, and 50 μM, for three and six days. For the flow cytometric analysis, a sample of leaf tissue was removed from each plant, crushed to release the nuclei and stained with propidium iodide. In addition to flow cytometry, the ploidy of the antimitotic treated plants was evaluated by stomata analysis. Young leaves were used where the density, functionality and stomatal index were evaluated. Colchicine provided induction of satisfactory polyploidy in C. tigrina at all concentrations and times of exposure, obtaining a greater number of polyploid individuals in the concentration of 12.5 mM for 48 hours. Oryzalin did not induce chromosome duplication at the tested concentrations.

Identification of Double-Haploid Maize Plants One Generation After the Chromosomes Doubling

The objectives in the present work were to identify maize double haploids one generation after chromosome duplication through the evaluation of phenotypic characteristics in thr field, flow cytometry and molecular markers SSR. The seeds used in the present study were obtained from a cross between four simple hybrids (DKB393, GNS 3225, GNS 3264, GNS 3032) and the KEMS inducer of gymnogenetic haploidy, used as a male parent. Seeds from this crossing were selected according to the R-Navajo marker and those considered haploid, were submitted to two different chromosome duplication protocols. Plants that survived to the chromosome duplication protocols were acclimatized in greenhouse and later transplanted to the field. After self-fertilization of the DH0 plants, the DH1 seeds obtained were seeded in the field, divided into treatments according to the parental and duplication protocols. At the vegetative stage V4 of the DH1 seedlings, leaf tissue samples were collected to identify ploidy via flow cytometry and DNA analyzes using microsatellite markers. These results were confronted with the morphological characteristics of the future DH1 plants developed in the field, evaluated with the use of descriptive tools. Statistical analyzes were performed using the generalized linear modeling approach and the exploratory and inferential analyzes of datas, by the use of graphical resources, barplot and boxplot. For the analysis of variance, were used the Student-Newman-Keuls test, and the Pearson's correlations. It was not observed uniformity of phenotypic characteristics of plants subjected to duplication protocols in the field and the use of descriptive tools in the morphological analysis of adult maize plants must be done carefully to avoid the wrong classification of determined genotypes related to the ployd. Flow cytometry must be used as screening in the identification of possible DH´s and the molecular markers SSR can be used to prove the genetically inherited KEMS lineage and also to identify the double-haploid corn plants.

Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts

Conflicts between the replication and transcription machineries have profound effects on chromosome duplication, genome organization, as well as evolution across species. Head-on conflicts (lagging strand genes) are significantly more detrimental than co-directional conflicts (leading strand genes). The source of this fundamental difference is unknown. Here, we report that topological stress underlies this difference. We find that head-on conflict resolution requires the relaxation of positive supercoils DNA gyrase and Topo IV. Interestingly, we find that after positive supercoil resolution, gyrase introduces excessive negative supercoils at head-on conflict regions, driving pervasive R-loop formation. The formation of these R-Loops through gyrase activity is most likely caused by the diffusion of negative supercoils through RNA polymerase spinning. Altogether, our results address a longstanding question regarding replication-transcription conflicts by revealing the fundamental mechanistic difference between the two types of encounters.

Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community

Mutualisms can be promoted by pleiotropic win-win mutations which directly benefit self (self-serving) and partner (partner-serving). Intuitively, partner-serving phenotype could be quantified as an individual’s benefit supply rate to partners. Here, we demonstrate the inadequacy of this thinking, and propose an alternative. Specifically, we evolved well-mixed mutualistic communities where two engineered yeast strains exchanged essential metabolites lysine and hypoxanthine. Among cells that consumed lysine and released hypoxanthine, a chromosome duplication mutation seemed win-win: it improved cell’s affinity for lysine (self-serving), and increased hypoxanthine release rate per cell (partner-serving). However, increased release rate was due to increased cell size accompanied by increased lysine utilization per birth. Consequently, total hypoxanthine release rate per lysine utilization (defined as ‘exchange ratio’) remained unchanged. Indeed, this mutation did not increase the steady state growth rate of partner, and is thus solely self-serving during long-term growth. By extension, reduced benefit production rate by an individual may not imply cheating.