Biology subjects

Nojiri, H.

Publications and source records attributed to Nojiri, H..

5 recordsLinked to original sources

bioRxiv2026

Complete genome sequence of Comamonas testosteroni TA441 and comparative analysis of steroid degradation gene clusters across Proteobacteria and Actinomycetota

Comamonas testosteroni TA441 is a model aerobic steroid-degrading bacterium whose sterane degradation pathway has been elucidated in greater detail than that of any other bacterium to date. Similar pathways have been identified in many bacterial genera, including members of Proteobacteria and Actinomycetota, such as Mycobacterium tuberculosis. Steroid degradation genes in TA441 form an approximately 120-kb mega-cluster, and 40 genes involved mainly in the degradation of the sterane structure and the C20?C22 portion of the side chain at C17 have been identified. Here, we present the complete genome sequence of TA441 together with our findings on its steroid degradation genes. We also compare the genes in the mega-cluster with corresponding genes in other Comamonas strains, ?-Proteobacteria other than Comamonas, ?-Proteobacteria, ?-Proteobacteria, and Actinomycetota using CAGECAT to analyze similarities and differences in steroid degradation genes among these bacteria.

microbiology↗

bioRxiv2024

INCOMPATIBILITY GROUPS OF PSEUDOMONAS PLASMIDS REVISITED: COMPREHENSIVE ANALYSIS OF R-FACTORS AND THEIR REPLICONS

Plasmids are the most influential engines of bacterial evolution and horizontal gene transfer, fueling the global spread of traits such as antimicrobial resistance. Their deep evolutionary relationships, however, remain difficult to resolve because current classification schemes are constrained by host range and nucleotide similarity. Replication initiation proteins (RIPs), which govern plasmid persistence and diversification, also remain poorly annotated across public databases. Here we establish PInc, a curated and experimentally grounded replicon classification framework anchored in historically defined incompatibility groups of Pseudomonas plasmids. Homology searches beyond PInc revealed that most replication initiators analyzed here share a conserved winged-helix (WH) domain, defining a broad WH RIP superfamily. Using the conserved WH region, we reconstructed a large-scale phylogeny that linked WH RIPs to over 100,000 plasmids, representing approximately half of those analyzed across public databases. This phylogeny resolved eight major clades and the deep split between the single- and double-winged-helix superclades, while revealing clade-specific host and environmental distributions and substantial RIP diversity not captured by current typing tools or annotation schemes. Together, these results overcome the historical host bias of plasmid typing and provide a replication-centered view of plasmid diversification across bacterial lineages and environments.

microbiology↗

bioRxiv2024

Evolutionary conserved cis-trans regulation machinery for diterpenoid phytoalexin production in Poaceae

O_LIMomilactones and phytocassanes are diterpenoid phytoalexins involved in plant chemical defense. These metabolites, along with biosynthetic gene clusters (BGCs), are conserved in wild rice. However, the mechanisms by which phytoalexins are regulated in wild rice are unclear. Thus, we aimed to investigate the regulatory mechanisms for biosynthetic genes within the BGCs of diterpenoid phytoalexins. C_LIO_LIWe conducted a transcriptome analysis of five wild rice species, Oryza rufipogon, Oryza punctata, Oryza officinalis, Oryza brachyantha, and Leersia perrieri, after CuCl2 treatment. C_LIO_LIAmong the CuCl2-responsive transcription factors, diterpenoid phytoalexin factor (DPF), which regulates phytoalexin production in cultivated rice (Oryza sativa), was broadly conserved in wild rice and showed phytoalexin-inducing activity when introduced into cultivated rice. Highly conserved genomic regions containing N-boxes (5'-CACGAG-3'), the potential binding motif of DPF, were found. CRISPR/Cas9 genome editing to remove these regions showed that biosynthetic gene expression and phytoalexin production were significantly attenuated after CuCl2 treatment in the leaves of the edited plants. Thus, the cis-trans factor combination of DPF and N-boxes is a key determinant of regulation. C_LIO_LIDPF has evolved as a strong cis-trans regulatory system for diterpenoid phytoalexin production, with N-boxes generated within the cluster region during the evolution from wild rice to cultivated rice. C_LI

plant biology↗

bioRxiv2024

Evolution and diversification of the momilactone biosynthetic gene cluster in the genus Oryza

Plants are master chemists and collectively are able to produce hundreds of thousands of different organic compounds. The genes underlying the biosynthesis of many specialized metabolites are organized in biosynthetic gene clusters (BGCs), which is hypothesized to ensure their faithful co-inheritance and to facilitate their coordinated expression. In rice, momilactones are diterpenoids that act in plant defence and various organismic interactions. Many of the genes essential for momilactone biosynthesis are grouped in a BGC. Here, we apply comparative genomics of diploid and allotetraploid Oryza species to reconstruct the species-specific architecture, evolutionary trajectory, and sub-functionalisation of the momilactone biosynthetic gene cluster (MBGC) in the Oryza genus. Our data show that the evolution of the MBGC is marked by lineage-specific rearrangements and gene copy number variation, as well as by occasional cluster loss. We identified a distinct cluster architecture in O. coarctata, which represents the first instance of an alternative architecture of the MBGC in Oryza and strengthens the idea of a common origin of the cluster in Oryza and the distantly related genus Echinochloa. Our research illustrates the evolutionary and functional dynamics of a biosynthetic gene cluster within a plant genus.

plant biology↗

bioRxiv2022

Horizontal Transfers Lead to the Birth of Momilactone Biosynthetic Gene Clusters in Grass

Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in biosynthesis of momilactone A are found in clusters, i.e., MABGCs (Momilactone A biosynthetic gene clusters), in the rice and barnyardgrass genomes. How MABGCs originate and evolve is still not clear. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC-like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC-like cluster in Triticeae (BOP clade) via horizontal gene transfer (HGT) and followed by recruitment of MAS and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another HGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter being originated from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate HGT-mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.

evolutionary biology↗