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Saccharomyces cerevisiae and Schizosaccharomyces pombe have served as uncontested unicellular model organisms, as major discoveries made in the field of genome biology using yeast genetics have proved to be relevant from yeast to humans. The yeast Candida albicans has attracted much attention because of its ability to switch between a harmless commensal and a dreaded human pathogen. C. albicans bears unique features regarding its life cycle, genome structure, and dynamics, and their links to cell biology and adaptation to environmental challenges. Examples include a unique reproduction cycle with haploid, diploid, and tetraploid forms; a distinctive organisation of chromosome hallmarks; a highly dynamic genome, with extensive karyotypic variations, including aneuploidies, isochromosome formation, and loss-of-heterozygosity; and distinctive links between the response to DNA alterations and cell morphology. These features have made C. albicans emerge as a new and attractive unicellular model to study genome biology and dynamics in eukaryotes. Highlights C. albicans is a major human pathogen, with features that distinguish it from other yeast species. Rather than meiosis, ploidy reduction upon mating occurs by a parasexual process of concerted chromosome loss. Centromeres have unique organisation and are epigenetically regulated. Neither centromeres nor the DNA replication origins share any common defining DNA sequence. Loss-of-heterozygosity events are frequent and widespread in the genome of C. albicans. The DNA damage response is coupled to morphogenetic shifts. C. albicans emerges as a new unicellular model to study eukaryotic genome biology and dynamics. [ABSTRACT FROM AUTHOR]

Human papillomaviruses have 8kbp DNA episomal genomes that replicate autonomously from host DNA. During initial infection, the virus increases its copy number to 20–50 copies per cell, causing torsional stress on the replicating DNA. This activates the DNA damage response (DDR) and HPV replicates its genome, at least in part, using homologous recombination. An active DDR is on throughout the HPV life cycle. Two viral proteins are required for replication of the viral genome; E2 binds to 12bp palindromic sequences around the A/T rich origin of replication and recruits the viral helicase E1 via a protein–protein interaction. E1 forms a di-hexameric complex that replicates the viral genome in association with host factors. Transient replication assays following transfection with E1–E2 expression plasmids, along with an origin containing plasmid, allow monitoring of E1-E2 replication activity. Incorporating a bacterial lacZ gene into the origin plasmid allows for the determination of replication fidelity. Here we describe how we exploited this system to investigate replication and repair in mammalian cells, including using damaged DNA templates. We propose that this system has the potential to enhance the understanding of cellular components involved in DNA replication and repair.

Albinism has been used for new variety screening in some edible mushrooms and the underlying mechanisms are fascinating. Albino fruiting body of Cordyceps militaris, a well-known edible fungus and model organism for Cordyceps, has the potential to be a nutraceutical or functional food due to its high content of metabolites and antioxidant activities. In this study, a spontaneous albino mutant strain (505) of C. militaris was obtained. In comparison to its normal sibling strain (498), the albino strain stably remained white in response to light and had significantly decreased conidia and carotenoid production but accumulated more cordycepin. Transcriptome analysis of both strains revealed that all the seven photoreceptors were expressed similarly in response to light. However, many more genes in the albino strain were differentially expressed in response to light than its sibling strain. The significantly enriched pathways in 498L vs. 505L were mainly associated with replication and repair. Some secondary metabolite backbone genes including those encoding DMAT, two NRPS-like proteins, three NPRS, and lanosterol synthase were differentially expressed in the albino when compared with that of the normal strains. Transcriptome and real-time quantitative PCR analyses indicated that some cytochrome P450s and methyltransferases might be related to the phenotypic differences observed between the two strains. This study compared the genome-wide transcriptional responses to light irradiation in a spontaneous albino mutant and its normal sibling strain of an edible fungus, and these findings potentially pave the way for further investigation of the pigment biosynthetic pathway.

Mitochondrial DNA (mtDNA) mutations are found in several human pathologies and are associated with aging. Deletion mutations in mtDNA result in the loss of essential genes for mitochondrial function. Over 250 deletion mutations have been reported and the common deletion is the most frequent mtDNA deletion linked to disease. This deletion removes 4977 base pairs of mtDNA. It has previously been shown that exposure to UVA radiation can promote the formation of the common deletion. Furthermore, aberrations in mtDNA replication and repair are associated with formation of the common deletion. However, molecular mechanisms describing the formation of this deletion are poorly characterized. This chapter describes a method to irradiate human skin fibroblasts with physiological doses of UVA and the subsequent detection of the common deletion by quantitative PCR analysis., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Human papillomaviruses have 8kbp DNA episomal genomes that replicate autonomously from host DNA. During initial infection, the virus increases its copy number to 20–50 copies per cell, causing torsional stress on the replicating DNA. This activates the DNA damage response (DDR) and HPV replicates its genome, at least in part, using homologous recombination. An active DDR is on throughout the HPV life cycle. Two viral proteins are required for replication of the viral genome; E2 binds to 12bp palindromic sequences around the A/T rich origin of replication and recruits the viral helicase E1 via a protein–protein interaction. E1 forms a di-hexameric complex that replicates the viral genome in association with host factors. Transient replication assays following transfection with E1–E2 expression plasmids, along with an origin containing plasmid, allow monitoring of E1-E2 replication activity. Incorporating a bacterial lacZ gene into the origin plasmid allows for the determination of replication fidelity. Here we describe how we exploited this system to investigate replication and repair in mammalian cells, including using damaged DNA templates. We propose that this system has the potential to enhance the understanding of cellular components involved in DNA replication and repair. [ABSTRACT FROM AUTHOR]

The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.

Albinism has been used for new variety screening in some edible mushrooms and the underlying mechanisms are fascinating. Albino fruiting body of Cordyceps militaris , a well-known edible fungus and model organism for Cordyceps, has the potential to be a nutraceutical or functional food due to its high content of metabolites and antioxidant activities. In this study, a spontaneous albino mutant strain (505) of C. militaris was obtained. In comparison to its normal sibling strain (498), the albino strain stably remained white in response to light and had significantly decreased conidia and carotenoid production but accumulated more cordycepin. Transcriptome analysis of both strains revealed that all the seven photoreceptors were expressed similarly in response to light. However, many more genes in the albino strain were differentially expressed in response to light than its sibling strain. The significantly enriched pathways in 498L vs. 505L were mainly associated with replication and repair. Some secondary metabolite backbone genes including those encoding DMAT, two NRPS-like proteins, three NPRS, and lanosterol synthase were differentially expressed in the albino when compared with that of the normal strains. Transcriptome and real-time quantitative PCR analyses indicated that some cytochrome P450s and methyltransferases might be related to the phenotypic differences observed between the two strains. This study compared the genome-wide transcriptional responses to light irradiation in a spontaneous albino mutant and its normal sibling strain of an edible fungus, and these findings potentially pave the way for further investigation of the pigment biosynthetic pathway.

Genome maintenance is ensured by a variety of biochemical sensors and pathways that repair accumulated damage. During mitosis, the mechanisms that sense and resolve DNA damage remain elusive. Studies have demonstrated that damage accumulated on lagging chromosomes can activate the spindle assembly checkpoint. However, there is little known regarding damage to DNA after anaphase onset. In this study, we demonstrate that laser-induced damage to chromosome tips (presumptive telomeres) in anaphase of Potorous tridactylis cells (PtK2) inhibits cytokinesis. In contrast, equivalent irradiation of non-telomeric chromosome regions or control irradiations in either the adjacent cytoplasm or adjacent to chromosome tips near the spindle midzone during anaphase caused no change in the eventual completion of cytokinesis. Damage to only one chromosome tip caused either complete absence of furrow formation, a prolonged delay in furrow formation, or furrow regression. When multiple chromosome tips were irradiated in the same cell, the cytokinesis defects increased, suggesting a potential dose-dependent mechanism. These results suggest a mechanism in which dysfunctional telomeres inhibit mitotic exit.