Biology subjects

Kinjo, Y.

Publications and source records attributed to Kinjo, Y..

8 recordsLinked to original sources

bioRxiv2026

The ancestral endosymbiont Blattabacterium was lost ten times independently in Blattellidae, Pseudophyllodromiidae and Anaplectidae cockroaches

Most cockroaches and the termite Mastotermes darwiniensis are associated with Blattabacterium, an ancient obligate endosymbiont that participates in the nitrogen metabolism of its host. Blattabacterium has been vertically transmitted since it was acquired by the common ancestor of cockroaches and termites and was reportedly lost twice, once in the cockroach genus Nocticola and once in all termites except Mastotermes darwiniensis. Here, we acquired cockroach specimens spanning most of the cockroach phylogenetic tree to study Blattabacterium using shotgun sequencing. We found no traces of Blattabacterium in 64 specimens from ten independent lineages of cockroaches across three families: Blattellidae, Pseudophyllodromiidae, and Anaplectidae. The absence of Blattabacterium was confirmed with three PCR amplifications targeting the 16S and 23S ribosomal genes with primers specific to Blattabacterium. Notably, cockroaches lacking Blattabacterium were often infected by Rickettsia and Wolbachia, many of which were related to the mutualistic Wolbachia strain of Cimex lectularius, the common bed bug. These results indicate that cockroaches from Blattellidae, Pseudophyllodromiidae and Anaplectidae have lost their ancestral Blattabacterium endosymbiont at least ten times independently, with many of these losses possibly facilitated and compensated by new associations with mutualistic Wolbachia strains that may help provision the host with B vitamins.

evolutionary biology↗

bioRxiv2025

Horizontal gene transfers are widespread across termite genomes but do not confer metabolic innovations

Horizontal gene transfer (HGT), the transmission of genetic material across species, is an important innovation source in prokaryotes. In contrast, its significance is unclear in many eukaryotes, including insects. Here, we used high-quality genomes of 45 termites and two cockroaches to investigate HGTs across blattodean genomes. We identified 289 genes and 2,494 pseudogenes classified into 168 orthologous groups originating from an estimated 281 HGT events. Wolbachia represented the primary HGT source, while termite gut bacteria and the cockroach endosymbiont Blattabacterium did not contribute meaningfully to HGTs. Most horizontally acquired genes descended from recent and species-specific HGTs, experienced frequent duplications and pseudogenizations, and accumulated substitutions faster than synonymous sites of native protein-coding genes. Genes frequently transferred horizontally to termite genomes included mobile genetic elements and genetic information processing genes. Our results indicate that termites continuously acquired genes through HGT, which they soon lost, leaving few horizontally acquired genes conserved across lineages.

genomics↗

bioRxiv2025

Lysyl-phosphatidylglycerol promotes cell-to-cell interaction and biofilm formation of Staphylococcus aureus as a biofilm matrix component

Biofilms formed by Staphylococcus aureus contribute significantly to persistent infections and antibiotic resistance, driven by the unique composition of their extracellular matrix. While previous studies highlighted extracellular DNA, proteins, and polysaccharides as key components, the role of phospholipids in biofilm architecture remains underexplored. This study identifies extracellular phospholipids, including lysyl-phosphatidylglycerol (Lys-PG), phosphatidylglycerol, and cardiolipin (CL), as critical structural elements in S. aureus biofilms. Bacterial phospholipase A1 (PLA1) that cleaves the acyl ester bond at the sn-1 position of phospholipids effectively dispersed pre-formed biofilms and prevented new biofilm formation by hydrolyzing extracellular phospholipids, without affecting bacterial growth or exhibiting cytotoxicity. Microscopy analyses confirmed that PLA1 disrupts membranous nanostructures, including extracellular vesicles and nanofilaments, integral to biofilm stability. Lipidomic analysis revealed an enrichment of Lys-PG and CL in the biofilm matrix. Lys-PG promotes bacterial aggregation by acting as a molecular glue, mediated through electrostatic and hydrophobic interactions. Deletion of the mprF gene, responsible for Lys-PG synthesis, significantly impaired biofilm formation, confirming its essential role. These findings reveal a "moonlighting" function of phospholipids in biofilm architecture, providing insights into biofilm biology and presenting PLA1 as a promising tool for biofilm control. SignificanceBiofilms, dense bacterial communities, pose significant challenges across medical, industrial, and daily life contexts. Understanding their formation mechanisms is crucial for developing effective strategies against them. We investigated biofilm matrix components in S. aureus biofilms, focusing on phospholipids. Our study reveals the presence and significance of Lys-PG in the biofilm matrix, acting as a crucial factor in biofilm formation and maintenance. Through biochemical, lipidomic, and genetic analyses, we demonstrate the role of Lys-PG in facilitating cell-to-cell contacts, contributing to the robustness and thickness of S. aureus biofilms. These findings shed light on the physiological function of extracellular phospholipids in bacterial biofilms and suggest targeting Lys-PG and its synthetic mechanism as a promising strategy for biofilm control.

microbiology↗

bioRxiv2024

Periplasmic serine protease Prc is responsible for amyloid subunit CsgA degradation and proteostasis in Escherichia coli

Escherichia coli synthesizes curli amyloid fibers extracellularly during biofilm formation and host colonization. The proteostasis network regulates the major curli subunit, CsgA, to prevent intracellular amyloid aggregation, yet the degradation mechanism remains elusive. Here, through a comprehensive investigation employing genetically engineered E. coli, multi-copy-suppressor screening, and biochemical analyses, we identify periplasmic serine protease Prc as a key player in CsgA degradation. Prc directly degrades CsgA through internal cleavage, differing from canonical tail-specific proteases. Although the bacterial HtrA homologs DegP and DegQ exhibit limited CsgA degradation activity in vitro in the presence of the suicide activator YjfN, deletion of these proteases did not affect native CsgA degradation in vivo. Instead, Prc, in coordination with the periplasmic chaperone CsgC, prevents the periplasmic accumulation of CsgA amyloid-like aggregates. Additionally, disruptions in secretion efficiency and proteolytic systems reduce csg operon expression through activation of the Rcs and Cpx two-component systems. These findings reveal a dual-layered strategy employed by E. coli to prevent intracellular accumulation of extracellular amyloids at both protein degradation and transcriptional regulation levels. This study provides insights into the mechanisms ensuring cellular homeostasis during curli biogenesis.

microbiology↗

bioRxiv2023

Pervasive relaxed selection in termite genomes

The genetic changes that enabled the evolution of eusociality have long captivated biologists. In recent years, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we sequenced genomes from three of their non-eusocial cockroach relatives. Using a phylogenomic approach, we found that termite genomes experienced lower rates of synonymous mutations than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of nonsynonymous mutations in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24-31% of the genes analysed) compared with the latter (2-4%). We infer that this is due to a reduction in effective population size, rather than gene-specific effects (e.g., indirect selection of caste-biased genes). We found no obvious signature of increased genetic load in termites, and postulate efficient purging at the colony level. Additionally, we identified genomic adaptations that may underpin caste formation, such as genes involved in post-translational modifications. Our results provide insights into the evolution of termites and the genomic consequences of eusociality more broadly.

evolutionary biology↗

bioRxiv2023

Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life

Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient-poor diet. To investigate if host biology has impacted Blattabacterium at the genomic level, we sequenced and analysed 25 genomes from Australian soil-burrowing cockroaches (Blaberidae: Panesthiinae) which have undergone at least seven independent subterranean transitions from above-ground, wood-feeding ancestors. We find at least three independent instances of genome erosion have occurred in Blattabacterium strains exclusive to Australian soil-burrowing cockroaches. Such shrinkages have involved the repeated inactivation of genes involved in amino acid biosynthesis and nitrogen recycling, the core role of Blattabacterium in the host-symbiont relationship. The most drastic of these erosions have occurred in hosts thought to have transitioned underground the earliest relative to other lineages. As Blattabacterium is unable to fulfil its core function in such host groups, our findings suggest soil-burrowing cockroaches must acquire these nutrients from novel sources. Our study represents one of the first cases, to our knowledge, of parallel host adaptations leading to concomitant parallelism in their mutualistic symbionts, further underscoring the intimate relationship between these two partners.

genomics↗

bioRxiv2021

The functional evolution of termite gut microbiota

Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species, but remains largely unknown in other taxa. We intend to feel this gap and provide a global understanding of the functional evolution of termite gut microbiota. We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that key nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared [~]150 million years ago. Therefore, the "world smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception.

evolutionary biology↗

bioRxiv2020

Hierarchical Model for the Role of J-Domain Proteins in Distinct Cellular Functions

In Escherichia coli, the major bacterial Hsp70 system consists of DnaK, three J-domain proteins (JDPs: DnaJ, CbpA, and DjlA), and one nucleotide exchange factor (NEF: GrpE). JDPs determine substrate specificity for the Hsp70 system; however, knowledge on their specific role in bacterial cellular functions is limited. In this study, we demonstrated the role of JDPs in bacterial survival during heat stress and the DnaK-regulated formation of curli--extracellular amyloid fibers involved in E. coli biofilm formation. Genetic analysis with a complete set of JDP-null mutant strains demonstrated that only DnaJ is essential for survival at high temperature, while DnaJ and CbpA are indispensable in DnaK regulation of curli production. Additionally, we found that DnaJ and CbpA are involved in the expression of the master regulator CsgD through the folding of MlrA; this keeps CsgA in a translocation-competent state by preventing its aggregation in the cytoplasm. Our findings support a hierarchical model wherein the role of JDPs in the Hsp70 system differs according to individual cellular functions.

molecular biology↗