Biology subjects

Nakabachi, A.

Publications and source records attributed to Nakabachi, A..

7 recordsLinked to original sources

bioRxiv2026

Dynamic evolution of diaphorin biosynthetic genes against a background of genome conservation in Profftella

The Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera), a major agricultural pest, harbors the unusual obligate bacterial symbiont "Candidatus Profftella armatura" (Profftella), which is intimately integrated with its host yet devotes a remarkably large proportion of its highly reduced genome to the production of diaphorin, a bioactive polyketide. To gain insight into the evolution of this distinctive symbiont, we determined the genomes of Profftella and the co-resident nutritional symbiont "Candidatus Carsonella ruddii" (Carsonella) from Diaphorina lycii and compared them with previously characterized counterparts from D. citri and D. cf. continua. The Profftella and Carsonella chromosomes from D. lycii were 471 and 174 kb, respectively, and Profftella harbored an 8-kb plasmid. Genome organization and gene content were highly conserved across the three lineages. The diaphorin biosynthetic system likewise retained its overall organization, consistent with an important role for diaphorin in the Diaphorina symbiotic system. Remarkably, however, pronounced lineage-specific structural variation was observed in diaphorin synthases DipP and DipT, encoded by two of the 20 diaphorin biosynthetic genes. These synthases contained three extensively amplified tandem arrays of acyl carrier protein (ACP) domains that carry growing polyketide intermediates, with up to seven copies compared with one or two at corresponding positions in the related pederin synthases. All three regions of tandem ACP repeats showed copy-number variation among the Profftella lineages. This variation indicates that ACP amplification remains evolutionarily dynamic despite the otherwise highly constrained symbiotic genome. Together, our findings show that even highly integrated obligate symbionts retain evolutionary flexibility in specialized functional systems.

genomics↗

bioRxiv2026

Diaphorin induces extensive transcriptional remodeling of translation, transport, metabolism, and stress responses in Escherichia coli

Diaphorin is a pederin-family polyketide produced by the obligate bacterial symbiont "Candidatus Profftella armatura" (Betaproteobacteria) of the Asian citrus psyllid Diaphorina citri, in which it accumulates at millimolar concentrations. Diaphorin suppresses the growth of many bacterial species but promotes the growth and metabolic activity of Escherichia coli, highlighting the importance of elucidating the mechanisms underlying these contrasting effects. Although cell-free studies show that diaphorin directly affects bacterial translation, how E. coli transcription changes during growth promotion remains unclear. Here, we analyzed the transcriptome of E. coli after 7 h of exposure to 5 mM diaphorin, when its growth-promoting effect is most pronounced. Diaphorin altered the expression of 1,278 of 4,269 analyzed genes. Functional enrichment analyses revealed strong negative enrichment of translation- and ribosome-related functions, pathway-specific changes in metabolism, and enrichment of transport-, stress-response, and quorum-sensing-related functions. Ribosomal protein genes were broadly downregulated, whereas coordinated upregulation was observed in mdtEF, prpBCDE, the Gad system, and luxS/lsr genes. These findings indicate functionally structured transcriptional remodeling during diaphorin-enhanced growth. Together with previous cell-free evidence, the pronounced translation-related changes observed here highlight bacterial translation as a major process associated with the response of E. coli to diaphorin. One possible interpretation of the apparently contrasting observations is that an earlier stimulation of bacterial translation is followed by compensatory downregulation of translation-related genes as growth proceeds. More broadly, these transcriptional changes provide insight into diaphorin-enhanced growth in E. coli and offer a basis for understanding the strikingly different effects of this symbiont-derived polyketide among bacterial species.

microbiology↗

bioRxiv2025

Characterization of an enigmatic tubular ultrastructure in the bacterial defensive symbiont of the Asian citrus psyllid

"Candidatus Profftella armatura" (Betaproteobacteria) is a unique organelle-like defensive symbiont harbored intracellularly within the symbiotic organ of a devastating citrus pest, the Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera). Our previous two-dimensional transmission electron microscopy identified an unprecedented ultrastructure that appeared tubular in Profftella, but their detailed architecture, three-dimensional arrangement, and components were unknown. To address these issues, this study conducted serial block-face scanning electron microscopy, high-voltage electron tomography, and fluorescence in situ hybridization. The results revealed that highly elongated (2.8-136 {micro}m observed), string-shaped Profftella cells contain tubes of various numbers (1-43 per cell observed) and length (up to 45 m observed), depending on the cell length. The tubes were evenly distributed throughout the cells, occupying an average of 6.3% of the total cell volume. Each tube consisted of five or six thin fibers twisted into a right-handed helix, maintaining a consistent diameter of approximately 230 nm along its entire length. Even without fixation or embedding, the tubes retained their shape under high vacuum conditions in electron microscopes, demonstrating their remarkable stability and robustness. These findings suggest that the tubes may help provide mechanical stability to the highly elongated and potentially vulnerable Profftella cells. Further analysis showed that the tubes are closely associated with ribosomes, suggesting a role in protein synthesis. Overall, these results offer new insights into the structural and functional evolution of bacteria, with potential implications for developing novel pest control strategies. Significance statementBacteria generally have simple intracellular structures, lacking organelles. Here, we report a highly elongated, elaborate organelle-like structure with a tubular shape in a bacterial symbiont of an important agricultural pest. The tube, which exhibits high durability and robustness, may contribute to the mechanical stability of the notably elongated symbiont cell. They are closely associated with numerous ribosomes, suggesting a potential role in gene expression. These findings not only enhance our understanding of bacterial evolution but may also provide clues for developing novel strategies for pest control.

microbiology↗

bioRxiv2024

Highly reduced complementary genomes of dual bacterial symbionts in the mulberry psyllid Anomoneura mori

The genomes of obligately host-restricted bacteria suffer from accumulating mildly deleterious mutations, resulting in a drastic size reduction. Psyllids (Hemiptera) are phloem sap-sucking insects with a specialized organ called the bacteriome, which typically harbors two vertically transmitted bacterial symbionts: the primary symbiont "Candidatus Carsonella ruddii" (Gammaproteobacteria) and a secondary symbiont phylogenetically diverse among psyllid lineages. Genomes of several Carsonella lineages were revealed to be drastically reduced (158-174 kb), AT-rich (14.0-17.9% GC), and structurally conserved with similar gene inventories devoted for synthesizing essential amino acids scarce in the phloem sap. However, genomic information for secondary symbionts was limited. Hence, this study analyzed genomes of the bacteriome-associated dual symbionts, Secondary_AM (Gammaproteobacteria) and Carsonella_AM, in the mulberry psyllid Anomoneura mori (Psyllidae). This revealed that the Secondary_AM genome is as small and AT-rich (229,822 bp, 17.3% GC) as those of Carsonella, including Carsonella_AM (169,120 bp, 16.2% GC), implying that Secondary_AM is an evolutionarily ancient obligate mutualist like Carsonella. Phylogenomic analyses demonstrated that Secondary_AM is sister to "Candidatus Psyllophila symbiotica" of Cacopsylla spp. (Psyllidae), whose genomes (221-237 kb, 17.3-18.6% GC) were recently reported. The Secondary_AM and Psyllophila genomes showed highly conserved synteny, sharing all genes for complementing the incomplete tryptophan biosynthetic pathway of Carsonella and genes for synthesizing B vitamins. However, sulfur assimilation and carotenoid synthesizing genes were retained only in Secondary_AM and Psyllophila, respectively, indicating ongoing gene silencing. Average nucleotide identity, gene ortholog similarity, genome-wide synteny, and substitution rates suggested that the Secondary_AM/Psyllophila genomes are more labile than the Carsonella genomes.

genomics↗

bioRxiv2024

Microbiome of psyllids of the family Aphalaridae, including Aphalara itadori, a potential biocontrol agent against Reynoutria spp.

Several European and North American countries have started releasing the Japanese knotweed psyllid Aphalara itadori (Hemiptera: Aphalaridae) to control the Japanese knotweed Reynoutria japonica (Caryophyllales: Polygonaceae) and its relatives, which are among the worst invasive exotic plants. However, establishing populations of the current Kyushu and Hokkaido strains in the field has not been successful, desiring new lineages. Moreover, little is known about the microbiome of the current strains, which potentially impacts properties as biocontrol agents. Hence, this study analyzed the microbiota of an A. itadori strain newly collected on Honshu Island, along with related species of the family Aphalaridae, using amplicon sequencing of 16S rRNA genes. The A. itadori symbionts were further located using fluorescence in situ hybridization. The results demonstrated that the analyzed A. itadori strain has a dual symbiotic system with "Candidatus Carsonella ruddii" (Gammaproteobacteria: Oceanospirillales) and Sodalis sp. (Gammaproteobacteria: Enterobacterales) harbored in the bacteriome, suggesting their evolutionarily stable mutualistic relationships with A. itadori. The central area of the bacteriome harboring Sodalis appeared to comprise uninucleate bacteriocytes with nuclei larger than those of bacteriocytes for Carsonella, rather than a syncytium with smaller nuclei as previously reported for various psyllid lineages. No known plant pathogens or manipulators of insect reproduction were identified in the analyzed strain, indicating its suitability as a biocontrol agent, posing a minimum risk to the ecosystem. Besides distinct Carsonella lineages, the analysis identified Sodalis independently acquired by Craspedolepta miyatakeai, and an ambiguous Enterobacterales symbiont in Epheloscyta kalopanacis. Only Carsonella was identified in Togepsylla matsumurana.

molecular biology↗

bioRxiv2024

A limited concentration range of diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, promotes the in vitro gene expression with bacterial ribosomes

Diaphorin is a polyketide produced by "Candidatus Profftella armatura" (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a devastating agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Physiological concentrations of diaphorin, which D. citri contains at levels as high as 2-20 mM, are inhibitory to various eukaryotes and Bacillus subtilis (Firmicutes: Bacilli) but promote the growth and metabolic activity of Escherichia coli (Gammaproteobacteria: Enterobacterales). Our previous study demonstrated that five-millimolar diaphorin, which exhibits significant inhibitory and promoting effects on cultured B. subtilis and E. coli, respectively, inhibits in vitro gene expression utilizing purified B. subtilis and E. coli ribosomes. This suggested that the adverse effects of diaphorin on B. subtilis are partly due to its influence on gene expression. However, the result appeared inconsistent with the positive effects on E. coli. Moreover, the diaphorin concentration in bacterial cells, where genes are expressed in vivo, may be lower than in culture media. Therefore, the present study analyzed the effects of 50 and 500 M of diaphorin on bacterial gene expression using the same analytical method. The result revealed that this concentration range of diaphorin, in contrast to five-millimolar diaphorin, promotes the in vitro translation with the B. subtilis and E. coli ribosomes, suggesting that the positive effects of diaphorin on E. coli are due to its direct effects on translation. This study demonstrated for the first time that a pederin-type compound promotes gene expression, establishing a basis for utilizing its potential in pest management and industrial applications. ImportanceThis study revealed that a limited concentration range of diaphorin, a secondary metabolite produced by a bacterial symbiont of an agricultural pest, promotes cell-free gene expression utilizing substrates and proteins purified from bacteria. The unique property of diaphorin, which is inhibitory to various eukaryotes and Bacillus subtilis but promotes the growth and metabolic activity of Escherichia coli, may affect the microbial flora of the pest insect, potentially influencing the transmission of devastating plant pathogens. Moreover, the activity may be exploited to improve the efficacy of industrial production by E. coli, which is often used to produce various important materials, including pharmaceuticals, enzymes, amino acids, and biofuels. This study elucidated a part of the mechanism by which the unique activity of diaphorin is expressed, constructing a foundation for applying the unique property to pest management and industrial use.

microbiology↗

bioRxiv2022

Diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, inhibits the growth of Bacillus subtilis but promotes the growth of Escherichia coli

Diaphorin is a polyketide produced by Candidatus Profftella armatura (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). The analyses revealed that diaphorin inhibits the growth of B. subtilis but moderately promotes the growth of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host + symbionts) against some bacterial lineages but is beneficial for others, which potentially include obligate symbionts of D. citri. ImportanceCertain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of symbiosis between animal hosts and bacteria but may also potentially be exploited to promote the effectiveness of industrial material production by microorganisms.

microbiology↗