Korea Research Institute of Bioscience and Biotechnology
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The velvet regulator VosA governs survival and secondary metabolism of sexual spores in Aspergillus nidulans
No full textThe velvet regulator VosA plays a pivotal role in asexual sporulation in the model filamentous fungus Aspergillus nidulans. In the present study, we characterize the roles of VosA in sexual spores (ascospores) in A. nidulans. During ascospore maturation, the deletion of vosA causes a rapid decrease in spore viability. The absence of vosA also results in a lack of trehalose biogenesis and decreased tolerance of ascospores to thermal and oxidative stresses. RNA-seq-based genome-wide expression analysis demonstrated that the loss of vosA leads to elevated expression of sterigmatocystin (ST) biosynthetic genes and a slight increase in ST production in ascospores. Moreover, the deletion of vosA causes upregulation of additional gene clusters associated with the biosynthesis of other secondary metabolites, including asperthecin, microperfuranone, and monodictyphenone. On the other hand, the lack of vosA results in the downregulation of various genes involved in primary metabolism. In addition, vosA deletion alters mRNA levels of genes associated with the cell wall integrity and trehalose biosynthesis. Overall, these results demonstrate that the velvet regulator VosA plays a key role in the maturation and the cellular and metabolic integrity of sexual spores in A. nidulans.
Overexpression of Chlamydomonas reinhardtii LCIA (CrLCIA) gene increases growth of Nannochloropsis salina CCMP1776
No full textMost aquatic photosynthetic organisms have developed inorganic carbon-concentrating mechanisms (CCMs) to compensate for the kinetic constraints of CO2 concentration in the vicinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), which functions in the first steps of carbon fixation. CCMs, which are widespread in various types of algae, evolved independently among algal lineages and accordingly play a fundamental role in algal photosynthesis, metabolism, growth, and biomass production. Nannochloropsis, a marine eustigmatophycean microalga, is a candidate organism for biofuel production due to its high lipid content; however, inorganic carbon (Ci) availability in Nannochloropsis cells is not sufficient for complete carbon fixation due to inherently weak CCM machinery, including a CO2-leaking HCO3？ pump. CrLCIA, a member of the formate-nitrite transporter family, functions as a HCO3？ transporter in Chlamydomonas reinhardti. Thus, in this study, we overexpressed the CrLCIA gene heterologously in N. salina CCMP1776 in an attempt to reinforce its bicarbonate transport activity. CrLCIA expression in N. salina increased intracellular Ci and carbonic anhydrase (CA) activity, resulting in increased growth (30%) and biomass (2-fold). These results indicate that constitutively expressed CrLCIA leads to increased Ci uptake and CA activity, contributing to high availability of CO2 for photosynthesis under low CO2 conditions. The total fatty acid (FA) per cell mass in the transgenic lines was similar to that of wild-type Nannochloropsis cells, indicating that total FA productivity in the transgenic lines is increased approximately 2-fold. These findings will be useful to improve the CCM function for high biomass and lipid production using genetic modification tools in Nannochloropsis species, contributing to improved biodiesel production.
Regulation of reticulophagy by the N-degron pathway
No full textCellular homeostasis requires selective autophagic degradation of damaged or defective organelles, including the endoplasmic reticulum (ER). Previous studies have shown that specific ER transmembrane receptors recruit LC3 on autophagic membranes by using LC3-interacting domains. In this study, we showed that the N-degron pathway mediates ubiquitin (Ub)-dependent reticulophagy. During this 2-step process, the ER transmembrane E3 ligase TRIM13 undergoes auto-ubiquitination via lysine 63 (K63) linkage chains and acts as a ligand for the autophagic receptor SQSTM1/p62 (sequestosome 1). In parallel, ER-residing molecular chaperones, such as HSPA5/GRP78/BiP, are relocated to the cytosol and conjugated with the amino acid L-arginine (Arg) at the N-termini by ATE1 (arginyltransferase 1). The resulting N-terminal Arg (Nt-Arg) binds the ZZ domain of SQSTM1, inducing oligomerization of SQSTM1-TRIM13 complexes and facilitating recruitment of LC3 on phagophores to the sites of reticulophagy. We developed small molecule ligands to the SQSTM1 ZZ domain and demonstrate that these chemical mimics of Nt-Arg facilitate reticulophagy and autophagic protein quality control of misfolded aggregates in the ER.
The tumor suppressor, p53, negatively regulates non-canonical NF-κB signaling through miRNA-induced silencing of NF-κB-inducing kinase
No full textNF-κB signaling through both canonical and non-canonical pathways plays a central role in immune responses and inflammation. NF-κB-inducing kinase (NIK) stabilization is a key step in activation of the non-canonical pathway and its dysregulation implicated in various hematologic malignancies. The tumor suppressor, p53, is an established cellular gatekeeper of proliferation. Abnormalities of the TP53 gene have been detected in more than half of all human cancers. While the non-canonical NF-κB and p53 pathways have been explored for several decades, no studies to date have documented potential cross-talk between these two cancer-related mechanisms. Here, we demonstrate that p53 negatively regulates NIK in an miRNA-dependent manner. Overexpression of p53 decreased the levels of NIK, leading to inhibition of the non-canonical NF-κB pathway. Conversely, its knockdown led to increased levels of NIK, IKKα phosphorylation, and p100 processing. Additionally, miR-34b induced by nutlin-3 directly targeted the coding sequences (CDS) of NIK. Treatment with anti-miR-34b-5p augmented NIK levels and subsequent non-canonical NF-κB signaling. Our collective findings support a novel cross-talk mechanism between non-canonical NF-κB and p53.
mpCRISTAR: multiple plasmid approach for CRISPR/Cas9 and TAR-mediated multiplexed refactoring of natural product biosynthetic gene clusters
No full textMultiplexed refactoring provides a tool for rapid transcriptional optimization of biosynthetic gene clusters (BGCs) through simultaneous replacement of multiple native promoters with synthetic counterparts. Here, we present the mpCRISTAR, a multiple plasmid-based CRISPR/Cas9 and TAR (transformation-associated recombination), that enables a rapid and highly efficient, multiplexed refactoring of natural product BGCs in yeast. A series of CRISPR plasmids with different auxotrophic markers that could be stably maintained in yeast cells were constructed to express multiple gRNAs simultaneously. We demonstrated the multiplexing capacity of mpCRISTAR using the actinorhodin biosynthetic gene cluster as a model cluster. mpCRISTAR1, in which each CRISPR plasmid expresses one gRNA, allows for simultaneous replacement of up to four promoter sites with nearly 100% efficiency. By expressing two gRNAs from one CRISPR plasmid, termed mpCRISTAR2, we simultaneously replaced a total of six and eight promoter sites with 68% and 32% efficiency, respectively. The mpCRISTAR could be performed iteratively using two different auxotrophic markers, allowing for refactoring of any type of BGC regardless of their operon complexities. The mpCRISTAR platform we report here would become a useful tool for the discovery of new natural products from transcriptionally silent biosynthetic gene clusters present in microbial genomes.
Dengue virus-polymersome hybrid nanovesicles for advanced drug screening using real-time single nanoparticle-virus tracking
No full textDengue virus (DENV) is a major infectious viral pathogen that affects millions of individuals worldwide every year, causing a potentially fatal syndrome, while no commercial antiviral drugs are yet available. To develop an antiviral against dengue fever, it is necessary to understand the relationship between DENV and host cells, which could provide a basis for viral dynamics and identification of inhibitory drug targets. In this study, we designed DiD-loaded and BODIPY-ceramide-encapsulated DENV-polymersome hybrid nanovesicles (DENVSomes) prepared by an extrusion method, which trigger red fluorescence in the endosome and green in the Golgi. DENVSome monitors the dynamics of host cell-virus interaction and tracking in living cells with novel state-of-the-art imaging technologies that show images at high resolution. Also, DENVSome can be exploited to screen whether candidate antiviral drugs interact with DENVs. Consequently, we successfully demonstrated that DENVSome is an efficient tool for tracking and unraveling the mechanisms of replication and drug screening for antiviral drugs of DENV.
Discovery and biochemical characterization of a methanol dehydrogenase from Lysinibacillus xylanilyticus
No full textBioconversion of C1 chemicals such as methane and methanol into higher carbon-chain chemicals has been widely studied. Methanol oxidation catalyzed by methanol dehydrogenase (Mdh) is one of the key steps in methanol utilization in bacterial methylotrophy. In bacteria, few NAD+-dependent Mdhs have been reported that convert methanol to formaldehyde. In this study, an uncharacterized Mdh gene from Lysinibacillus xylanilyticus (Lxmdh) was cloned and expressed in Escherichia coli. The maximum alcohol oxidation activity of the recombinant enzyme was observed at pH 9.5 and 55°C in the presence of 10 mM Mg2+. To improve oxidation activity, rational approach-based, site-directed mutagenesis of 16 residues in the putative active site and NAD+-binding region was performed. The mutations S101V, T141S, and A164F improved the enzyme's specific activity toward methanol compared to that of the wild-type enzyme. These mutants show a slightly higher turnover rate than that of wild-type, although their K M values were increased compared to that of wild-type. Consequently, according the kinetic results, S101, T141, and A164 positions may related to the catalytic activity in the active site for methanol dehydrogenation. It should be further studied other mutant variants with high activity for methanol. In conclusion, we characterized a new Lxmdh and its variants that may be potentially useful for the development of synthetic methylotrophy in the future.
Paraconexibacter algicola gen. nov., sp. nov., a novel actinobacterium isolated from a eutrophic lake during the end of cyanobacterial harmful algal blooms, and proposal of Paraconexibacteraceae fam. nov. in the order Solirubrobacterales
No full textA novel bacterium, strain Seoho-28T, was isolated from a shallow eutrophic lake during the end of cyanobacterial harmful algal blooms and was characterized taxonomically and phylogenetically. Strain Seoho-28T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0？% NaCl and at 25-30？°C on Reasoner's 2A medium. The phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the order Solirubrobacterales, but sequence similarities to known species were less than 94.7？%. The genomic DNA G+C content of the strain Seoho-28T was 74.2？mol%. Genomic comparisons of strain Seoho-28T with families in the order Solirubrobacterales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤14.9, ≤73.5 and ≤57.8？%, respectively). Strain Seoho-28T contained C16？:？0-iso, C18？:？1 ？ω9c and C16？:？0 as major fatty acids and MK-7 (H4) as the major quinone. Strain Seoho-28T contained diphosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid as major polar lipids. Meso- and ll-diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. Based on the genotypic, chemotaxonomic and phenotypic results, strain Seoho-28T represents a novel genus and species, Paraconexibacter algicola gen. nov., sp. nov., which belongs to a new family Paraconexibacteraceae in the order Solirubrobacterales and the class Thermoleophilia. The type strain is Seoho-28T (=KCTC 39791T=JCM 31881T).
Structure of the MICU1-MICU2 heterodimer provides insights into the gatekeeping threshold shift
No full textMitochondrial calcium uptake proteins 1 and 2 (MICU1 and MICU2) mediate mitochondrial Ca2+ influx via the mitochondrial calcium uniporter (MCU). Its molecular action for Ca2+ uptake is tightly controlled by the MICU1-MICU2 heterodimer, which comprises Ca2+ sensing proteins which act as gatekeepers at low [Ca2+] or facilitators at high [Ca2+]. However, the mechanism underlying the regulation of the Ca2+ gatekeeping threshold for mitochondrial Ca2+ uptake through the MCU by the MICU1-MICU2 heterodimer remains unclear. In this study, we determined the crystal structure of the apo form of the human MICU1-MICU2 heterodimer that functions as the MCU gatekeeper. MICU1 and MICU2 assemble in the face-to-face heterodimer with salt bridges and me-thio-nine knobs stabilizing the heterodimer in an apo state. Structural analysis suggests how the heterodimer sets a higher Ca2+ threshold than the MICU1 homodimer. The structure of the heterodimer in the apo state provides a framework for understanding the gatekeeping role of the MICU1-MICU2 heterodimer.
Reclassification of Gyrodinium flavescens Kofoid & Swezy as Torquentidium flavescens comb. nov. (Ceratoperidiniaceae, Dinophyceae), based on morphology and phylogeny
No full textA Cochlodinium-like species was isolated from the Korean coast and examined by light microscopy and scanning electron microscopy (SEM). The species was characterised by cellular torsion, cingulum with 1.25 turns and sulcus with 0.25 turn, and a hemispherical hypocone. The nucleus was curved, and sausage-shaped, and there were small, dark grains distributed at the cell periphery, which were also reported in the original description of Gyrodinium flavescens by Kofoid & Swezy (1921). SEM observations revealed that the apical structure complex of the species formed a complete circle surrounding the cell apex, consisting of three parallel rows of vesicles; and that the outer rows, composed of small vesicles, were visible along the sides of cingulum. These morphological features were identical to those of Torquentidium convolutum. Phylogeny-based on small subunit and large subunit rDNA sequences, confirmed that the species was closely related to T. convolutum within the family Ceratoperidiniaceae. However, the species was distinct from T. convolutum by differences in cingulum and sulcus turn numbers, shape of hypocone in dorsal view and size. Based on morphological and phylogenetic analyses, we propose Torquentidium flavescens comb. nov. nested within the family Ceratoperidiniaceae. ⓒ 2020, ⓒ 2020 International Phycological Society.