Abortive activity of Topoisomerase I: a challenge for genome integrity? Abstract Single-strand breaks (SSB) are discontinuities in one strand of the DNA double helix and are the most common type of damages that arise in cells. SSBs arise mainly from direct attack by intracellular metabolites, however, also essential nuclear processes generate SSBs as intermediates. During the catalytic cycle of DNA topoisomerase I (Top1) a SSB is generated, which is normally transient and rapidly resealed by the enzyme. However, several situations can stabilize a Top1-generated SSB, and this poses the risk of converting the SSB into a double strand break (DSB) if encountered by the replication machinery. A DSB is a more serious treat for cells as it can fuel chromosomal rearrangements and thus jeopardize genome stability and cause cells to become cancerous. In this perspective, we discuss the cellular consequences of Top1-generated damage during DNA replication with focus on the differences between endogenous Top1-generated damage and Top1 damage generated due to the use of the drug camptothecin.

Regulation of the protein entry gate assembly by mitochondrial porin Abstract Mitochondrial biogenesis and functions rely on transport of their resident proteins as well as small molecules/ions across their membranes. The TOM complex functions as a protein entry gate for most mitochondrial proteins and mitochondrial porin facilitates transport of small-molecule metabolites and ions. We recently found a novel role of porin in regulation of the TOM complex assembly, the dynamic exchange between the dimer and trimer, and different substrate specificities of the dimer and trimer. Using distinct assembly forms customized for different client proteins, the TOM complex can handle ~ 1000 different mitochondrial protein for their import into mitochondria.

Cla4 PAK-like kinase is required for pathogenesis, asexual/sexual development and polarized growth in Bipolaris maydis Abstract PAK (p21-activated protein kinases)-like kinases are master regulators of development and morphogenesis, which were conserved among eukaryotes, including fungi. In budding yeast, two types of PAK-like kinases, Ste20 and Cla4 have distinct but shared roles in the regulation of pseudohyphal development, budding and mating. In this study, to examine the broad functions of PAK-like kinases in growth, pathogenicity and asexual/sexual reproduction in filamentous fungi, we identified and characterized two PAK-like kinases, Ste20 and Cla4 in Bipolaris maydis. A single mutant of both Ste20 and Cla4 gene was viable, while the double mutant was not available, possibly because of lethality. In growth, conidiation, and pathogenicity, Δste20 strains showed phenotypes similar to those of the wild-type, while Δcla4 strains showed severely defected phenotypes. In this study, we also clarified that Ste20 is partially involved in pseudothecium development but is dispensable for maternity, while Cla4 is essential for maternal pseudothecium development and also involve in ascospore development in paternal pseudothecium. Fluorescent microscopy visualized the disorder in cell polarity at the hyphal tip in Δcla4. These results suggested that not Ste20 but Cla4 is a master regulator of growth, pathogenicity and asexual/sexual development in B. maydis. In addition, we successfully visualized alternation of branching pattern and distribution of Spitzenkörper at the hyphal tip in Δcla4 strains.

The evolution of peptide mating pheromones in fission yeast Abstract In fungi, sexual reproduction primarily depends on the interaction between peptide pheromones and their receptors. Most ascomycete fungi produce two classes of peptide mating pheromones, a simple peptide and a modified peptide. These peptides are recognized by their corresponding receptors on the surface of cells of the opposite mating type to induce the mating reaction. Pheromone diversification may be associated with reproductive isolation, which restricts gene flow among populations; thus, it remains unclear how pheromones diversify without loss of successful mating. Here, I provide a brief review of recent findings on the ‘asymmetric’ diversification of peptide pheromones in the fission yeast Schizosaccharomyces pombe, and discuss evolution of the mating pheromones in fission yeast.

The Bax inhibitor UvBI-1, a negative regulator of mycelial growth and conidiation, mediates stress response and is critical for pathogenicity of the rice false smut fungus Ustilaginoidea virens Abstract Bax inhibitor-1 (BI-1), an evolutionarily conserved protein, is a suppressor of cell death induced by the proapoptotic protein Bax and is involved in the response to biotic and abiotic stress in animals, plants and yeast. Rice false smut caused by Ustilaginoidea virens is one of the destructive rice diseases worldwide. Although BI-1 proteins are widely distributed across filamentous fungi, few of them are functionally characterized. In this study, we identified a BI-1 protein in U. virens, UvBI-1, which contains a predicted Bax inhibitor-1-like family domain and could suppress the cell death induced by Bax. By co-transformation of the CRISPR/Cas9 construct along with donor DNA fragment containing the hygromycin resistance gene, we successfully generated Uvbi-1 deletion mutants. The UvBI-1 deletion showed an increase in mycelia vegetative growth and conidiation, suggesting this gene acts as a negative regulator of the growth and conidiation. In addition, the Uvbi-1 mutants exhibited higher sensitivity to osmotic and salt stress, hydrogen peroxide stress, and cell wall or membrane stress than the wild-type strain. Furthermore, UvBI-1 deletion was found to cause increased production of secondary metabolites and loss of pathogenicity of U. virens. Taken together, our results demonstrate that UvBI-1 plays a negative role in mycelial growth and conidiation, and is critical for stress tolerance, cell wall integrity, secondary metabolites production and pathogenicity of U. virens. Therefore, this study provides new evidence on the conserved function of BI-1 among fungal organisms and other species.

Transcriptional silencing of centromere repeats by heterochromatin safeguards chromosome integrity Abstract The centromere region of chromosomes consists of repetitive DNA sequences, and is, therefore, one of the fragile sites of chromosomes in many eukaryotes. In the core region, the histone H3 variant CENP-A forms centromere-specific nucleosomes that are required for kinetochore formation. In the pericentromeric region, histone H3 is methylated at lysine 9 (H3K9) and heterochromatin is formed. The transcription of pericentromeric repeats by RNA polymerase II is strictly repressed by heterochromatin. However, the role of the transcriptional silencing of the pericentromeric repeats remains largely unclear. Here, we focus on the chromosomal rearrangements that occur at the repetitive centromeres, and highlight our recent studies showing that transcriptional silencing by heterochromatin suppresses gross chromosomal rearrangements (GCRs) at centromeres in fission yeast. Inactivation of the Clr4 methyltransferase, which is essential for the H3K9 methylation, increased GCRs with breakpoints located in centromeric repeats. However, mutations in RNA polymerase II or the transcription factor Tfs1/TFIIS, which promotes restart of RNA polymerase II following its backtracking, reduced the GCRs that occur in the absence of Clr4, demonstrating that heterochromatin suppresses GCRs by repressing the Tfs1-dependent transcription. We also discuss how the transcriptional restart gives rise to chromosomal rearrangements at centromeres.

TORC1 specifically inhibits microautophagy through ESCRT-0 Abstract Nutrient starvation induces the degradation of specific plasma membrane proteins through the multivesicular body (MVB) sorting pathway and of vacuolar membrane proteins through microautophagy. Both of these processes require the gateway protein Vps27, which recognizes ubiquitinated cargo proteins at phosphatidylinositol 3-phosphate-rich membranes as part of a heterodimeric complex coined endosomal sorting complex required for transport 0. The target of rapamycin complex 1 (TORC1), a nutrient-activated central regulator of cell growth, directly phosphorylates Vps27 to antagonize its function in microautophagy, but whether this also serves to restrain MVB sorting at endosomes is still an open question. Here, we show that TORC1 inhibits both the MVB pathway-driven turnover of the plasma membrane-resident high-affinity methionine permease Mup1 and the inositol transporter Itr1 and the microautophagy-dependent degradation of the vacuolar membrane-associated v-ATPase subunit Vph1. Using a Vps277D variant that mimics the TORC1-phosphorylated state of Vps27, we further show that cargo sorting of Vph1 at the vacuolar membrane, but not of Mup1 and Itr1 at endosomes, is sensitive to the TORC1-controlled modifications of Vps27. Thus, TORC1 specifically modulates microautophagy through phosphorylation of Vps27, but controls MVB sorting through alternative mechanisms.

Identification and functional characterization of Candida albicans mannose–ethanolamine phosphotransferase (Mcd4p) Abstract Glycosylphosphatidylinositol (GPI) is an important compound for the growth of fungi, because GPI-anchored proteins including glycosyltransferases and adhesins are involved in cell-wall integrity, adhesion, and nutrient uptake in this organism. In this study, we examined orf19.5244 in the genome database of the pathogenic fungus Candida albicans, a homologue of the Saccharomyces cerevisiae mannose–ethanolamine phosphotransferase gene, MCD4, which plays a role in GPI synthesis. Expression of this homologue, designated CaMCD4, restored cell growth in a defective conditional mcd4 mutant of S. cerevisiae, Scmcd4t, in which expression of native MCD4 was repressed in the presence of doxycycline (Dox). Analysis of radiolabeled lipids showed that the accumulation of abnormal GPI anchor precursors in Scmcd4t decreased markedly upon expression of CaMCD4. Moreover, we constructed a single mutant (Camcd4/CaMCD4) and a conditional double mutant (Camcd4/Camcd4t) at the MCD4 locus of C. albicans. Repression of CaMCD4 expression by Dox led to a decrease in growth and appearance of abnormal morphology in C. albicans, both in vitro and in a silkworm infection model. These results suggest that CaMcd4p is indispensable for growth of C. albicans both in vitro and in infected hosts and a candidate target for the development of new antifungals.

Interaction studies on bacterial stringent response protein RelA with uncharged tRNA provide evidence for its prerequisite complex for ribosome binding Abstract The bacterial stringent response is regulated by the synthesis of (p)ppGpp which is mediated by RelA in a complex with uncharged tRNA and ribosome. We intended to probe RelA–uncharged tRNA interactions off the ribosome to understand the sequential activation mechanism of RelA. Stringent response is a key regulatory pleiotropic mechanism which allows bacteria to survive in unfavorable conditions. Since the discovery of RelA, it has been believed that it is activated upon binding to ribosomes which already have uncharged tRNA on acceptor site (A-site). However, uncharged tRNA occupied in the A-site of the ribosome prior to RelA binding could not be observed; therefore, recently an alternate model for RelA activation has been proposed in which RelA first binds to uncharged tRNA and then RelA–uncharged tRNA complex is loaded on to the ribosome to synthesize (p)ppGpp. To explore the alternate hypothesis, we report here the in vitro binding of uncharged tRNA to RelA in the absence of ribosome using formaldehyde cross-linking, fluorescence spectroscopy, surface plasmon resonance, size-exclusion chromatography, and hydrogen–deuterium exchange mass spectrometry. Altogether, our results clearly indicate binding between RelA and uncharged tRNA without the involvement of ribosome. Moreover, we have analyzed their binding kinetics and mapping of tRNA-interacting regions of RelA structure. We have also co-purified TGS domain in complex with tRNA to further establish in vivo RelA–tRNA binding. We have observed that TGS domain recognizes all types of uncharged tRNA similar to EF-Tu and tRNA interactions. Altogether, our results demonstrate the complex formation between RelA and uncharged tRNA that may be loaded to the ribosome for (p)ppGpp synthesis.

(p)ppGpp: the magic governor of bacterial growth economy Abstract A fundamental question in microbiology is how bacterial cells manage to coordinate gene expression with cell growth during adapting to various environmental conditions. Although the cellular responses to changing environments have been extensively studied using transcriptomic and proteomic approaches, it remains poorly understood regarding the molecular strategy enabling bacteria to manipulate the global gene expression patterns. The alarmone (p)ppGpp is a key secondary messenger involved in regulating various biochemical and physiological processes of bacterial cells. However, despite of the extensive studies of (p)ppGpp signaling in stringent response during the past 50 years, the connection between (p)ppGpp and exponential growth remains poorly understood. Our recent work demonstrates that (p)ppGpp is strongly involved in regulating cell growth of Escherichia coli through balancing the cellular investment on metabolic proteins and ribosomes, highlighting itself as a magic governor of bacterial global resource allocation. In this mini-review, we briefly summarize some historical perspectives and current progress of the relation between (p)ppGpp and bacterial exponential growth. Two important future directions are also highlighted: the first direction is to elucidate the cellular signal that triggers (p)ppGpp accumulation during poor growth conditions; the second direction is to investigate the relation between (p)ppGpp and exponential growth for bacterial species other than E. coli.