Biology subjects

Nishioka, N.

Publications and source records attributed to Nishioka, N..

2 recordsLinked to original sources

bioRxiv2023

Deciphering the Genomes of Motility-Deficient Mutants of Vibrio alginolyticus 138-2

The motility of Vibrio species plays a pivotal role in their survival and adaptation to diverse environments, and is intricately associated with pathogenicity in both humans and aquatic animals. Numerous mutant strains of Vibrio alginolyticus have been generated using UV or EMS mutagenesis to probe flagellar motility using molecular genetic approaches. Identifying these mutations promises to yield valuable insights into motility at the protein structural physiology level. In this study, we conducted an exhaustive analysis of the genomic structures of laboratory Vibrio strains that served as reference specimens. This assemblage notably encompassed the progenitor strain V. alginolyticus 138-2, alongside two strains displaying deficiencies in the lateral flagella (VIO5 and YM4) and one evincing a deficiency in the polar flagella (YM19). Subsequently, we meticulously ascertained the specific mutation sites within the 18 motility-deficient strains whose parents could be traced back to VIO5 or YM4. The identified mutations were conclusively localized within well-established flagella-related genes, providing a coherent rationale for the phenotypic traits exhibited by each motility-deficient mutant. In addition to these motility-related mutations, an average of 20 additional mutations was detected in each mutant strain. Genomic analysis of many mutants is a highly effective tool for comprehensively identifying genes related to specific phenotypes using forward genetics. IMPORTANCEBacteria of the Vibrio species rely on their motility for survival, adaptation, and pathogenicity. Identifying specific changes in the genome of non-motile mutants can help understand the genes that regulate flagella and motility in these bacteria. Herin, we sequenced the genome of Vibrio alginolyticus 138-2 strain and other motility defective strains and identified most of the mutations to be within genes encoding flagella. Additionally, we also provide a coherent rationale for the motility deficiency in these mutants. We believe that this study could provide a framework for genome sequencing-based methods for studying molecular functions in bacteria.

microbiology↗

bioRxiv2019

Unfolded protein-independent IRE1 activation contributes to multifaceted developmental processes in Arabidopsis

As an initial step for the unfolded protein response (UPR) pathway, the luminal domain of inositol requiring enzyme 1 (IRE1) senses unfolded proteins in the endoplasmic reticulum (ER). Recent findings in yeast and metazoans suggest alternative IRE1 activation without the sensor domain, although its mechanism and physiological significance remain to be elucidated. In Arabidopsis, the IRE1A and IRE1B double mutant (ire1a/b) is unable to activate cytoplasmic splicing of bZIP60 mRNA and regulated IRE1-dependent decay (RIDD) under ER stress, while the mutant does not exhibit severe developmental defects and is fertile under non-stress conditions. In this study, we focused on a third Arabidopsis IRE1 gene, designated as IRE1C, whose product lacks a sensor domain. We found that even though ire1c and ire1a/c mutants did not exhibit defective bZIP60 splicing and RIDD under ER stress, the ire1a/b/c triple mutant is lethal. Heterozygous IRE1C (ire1c/+) mutation in the ire1a/b mutants resulted in growth defects and reduction of the number of pollen grains. Genetic analysis revealed that IRE1C is required for male gametophyte development in the ire1a/b mutant background. Expression of a mutant form of IRE1B that lacks the luminal sensor domain ({Delta}LD) in the ire1a/b mutant did not complement defects in ER stress-dependent bZIP60 splicing and RIDD. Nevertheless, expression of {Delta}LD complemented a developmental defect in the male gametophyte in ire1a/b/c haplotype. In vivo, the {Delta}LD protein was activated by glycerol treatment that increases the composition of saturated lipid and was able to activate RIDD but not bZIP60 splicing. Phenotypes of IRE1B mutants lacking the sensor domain produced by CRISPR/Cas9-mediated gene editing in the ire1a/c mutant background were essentially same as those of {Delta}LD-expressing ire1a/b mutant. These observations suggest that IRE1 contributes to plant development, especially male gametogenesis, using an alternative activation mechanism that bypasses the unfolded protein-sensing luminal domain.

plant biology↗