Highlights

Ali Diyapoglu, Yu-You Liu, Alican Abay, Kuan-Hung Lin, I-Wen Lo, Chi-Fon Chang, Yi-Ping Huang, Chi-Ting Chung, Tsung-Lin Li, Menghsiao Meng; The Crucial Role of LTTR_0390 in Burkholderia gladioli BBB-01 in Orchestrating Antibiotic Production, Quorum-Sensing Responses, and Pathogenicity on Mushrooms. J. Agric. Food Chem. 8 April 2026; 74 (13): 11271–11284. https://doi.org/10.1021/acs.jafc.5c12363

Burkholderia gladioli strain BBB-01, classified as B. gladioli pv agaricicola, displays broad antagonism against diverse pathogens. We investigated the regulatory role of the LysR-type transcriptional regulator LTTR_0390 and its potential involvement in pathogenicity toward the cultivated button mushroom (Agaricus bisporus). Using insertional mutagenesis, metabolite profiling, transcriptomic analysis, and phenotypic assays, we found that disruption of the lttr_0390 gene extensively reprograms secondary metabolism, for example, upregulating the gladiostatin biosynthetic gene cluster while downregulating the gladiolin cluster. Although this gene disruption did not affect production of quorum-sensing (QS) autoinducers, the mutant exhibited reduced QS-linked behaviors, including motility and biofilm formation. Additionally, disruption of lttr_0390 markedly diminished soft rot symptoms on A. bisporus fruiting bodies. Together, these findings identify LTTR_0390 as a global regulator that coordinates secondary metabolism and QS-linked behaviors while decoupling antifungal activity from mushroom damage.

Lopez-Agudelo, J.C., Goh, F.-J., Tchabashvili, S., Huang, Y.-S., Huang, C.-Y., Lee, K.-T., Wang, Y.-C., Wu, Y., Chang, H.-X., Kuo, C.-H., Lai, E.-M. and Wu, C.-H. (2026), Rhizobium rhizogenes A4-derived strains mediate hyper-efficient transient gene expression in Nicotiana benthamiana and other solanaceous plants. Plant Biotechnol. J, 24: 131-144. https://doi.org/10.1111/pbi.70083

Agrobacteria are widely used in plant biotechnology because of their natural ability to transfer DNA into plant cells. This ability allows researchers to rapidly introduce genes into plants through a technique called agroinfiltration, which is commonly used to study gene function and produce valuable proteins. However, most laboratory strains used for this purpose are derived from a limited number of bacterial isolates, leaving much of the natural diversity of agrobacteria unexplored.

In this study, we screened 47 agrobacterial strains to identify bacteria with improved ability to deliver DNA into plants. We found that Rhizobium rhizogenes strain A4 was particularly effective, producing substantially stronger transient gene expression than commonly used laboratory strains in Nicotiana benthamiana. Building on this finding, we developed a disarmed A4-derived strain, AS109, that can be safely used for plant transformation while retaining its high DNA-delivery efficiency.

We further demonstrated that AS109 performs particularly well in older plants and across a broad range of plant species. Compared with conventional laboratory strains, AS109 produced stronger transient gene expression in several economically important crops, including tomato, pepper and eggplant. These results demonstrate that agrobacterial diversity can provide new and improved tools for plant biotechnology.

Our work highlights the potential of exploring naturally diverse bacterial strains to overcome limitations of existing transformation systems. The molecular mechanisms underlying the exceptional performance of A4-derived strains remain to be determined, and understanding these mechanisms could enable the development of even more efficient and versatile tools for plant genetic engineering.

Yu Wu, Hsin-Yi Chang, Chih-Hang Wu, Erh-Min Lai, Chih-Horng Kuo* (2025). Comparative transcriptomics reveals context- and strain-specific regulatory programmes of Agrobacterium during plant colonization. Microbial Genomics, 11(8):001485. doi: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001485

Agrobacterium is a genus of plant-associated bacteria capable of transferring DNA into host genomes to induce tumourigenesis. The process has been primarily studied in a few model strains, particularly C58, and developed into Agrobacterium-mediated transformation for genetic manipulation. However, the diversity of wild-type strains and their context-specific regulatory responses remains poorly characterized. Here, we evaluated five wild-type strains and identified 1D1108 as superior in tumourigenesis on legumes and transient transformation in Nicotiana benthamiana. Under in vitro virulence induction with acetosyringone, we identified 126 differentially expressed genes (DEGs) in 1D1108. Although the number of DEGs was comparable to those in C58 and the legume isolate 1D1609 under the same condition, only 22 DEGs, primarily within the vir regulon, were conserved, indicating extensive divergence among these Agrobacterium strains. Leaf infiltration of N. benthamiana revealed 1,134 DEGs specifically regulated in planta for 1D1108. These included genes involved in attachment, virulence regulation, type IV pilus, succinoglycan biosynthesis and diverse nutrient transporters, providing new evidence on expression regulation during colonization. Comparative analyses of in planta transcriptomes with C58 and Pseudomonas syringae DC3000 revealed distinct secretion systems required for pathogenesis, namely, type IV for Agrobacterium and type III for Pseudomonas, and only ~5–19% of DEGs were conserved. These limited transcriptomic overlaps underscore the importance of studying gene expression in strains and conditions directly relevant to the biological context, rather than relying on model systems. Together, this work reveals how environmental and host-associated cues shape transcriptional responses in plant-associated bacteria.

Negi A, Yadav BG, Kuo CW, Hazam PK, Lin WC, Teh OK, Chen JY (2025). A Deep-Sea probiotic platform: Dual-function biopreservation for aquaculture immunomodulation and meat shelf-life extension. Innovative Food Science & Emerging Technologies. 2025 Jul 2:104107. https://doi.org/10.1016/j.ifset.2025.104107

Two major challenges in the food industry include antibiotic overuse in aquaculture and reliance on synthetic preservatives to increase meat shelf-life. To address these challenges, we developed a dual-function platform using Lactococcus lactis L25_4, isolated from 312-m depth in Taiwan's Taimali region. As a feed additive, L. lactis L25_4 significantly enhanced Litopenaeus vannamei (whiteleg shrimp) survival against Vibrio vulnificus infection by modulating gut microbiota (e.g., enriching Rhodobacteraceae and Streptococcaceae and inhibiting Desulfovibrionaceae and Klebsiella) and improving gut membrane integrity. It also upregulated immune genes (e.g., HSP70, Lysozyme C, SOD and Tollo) and increased short chain fatty acids (SCFAs) levels in the shrimp intestinal region. Transcriptomic and microbiome analyses revealed immune priming and stress mitigation, with Spearman correlations linking beneficial bacteria to enhanced gut integrity and immune activation. The cell-free supernatant (CFS) of L. lactis L25_4 was incorporated into a chitosan-based hydrogel and applied as a surface coating on raw pork meat. Samples were inoculated with Shewanella putrefaciens (106 CFU/mL), a known meat spoilage bacterium, and the CFS–chitosan hydrogel inhibited bacterial growth by >99 % for up to 5 days at 4°C compared to untreated controls, as confirmed by CFU enumeration and Cryo-SEM imaging. L. lactis L25_4 demonstrated functional stability across aquaculture and chilled meat systems, supporting its dual application in biopreservation. By integrating multi-omics, biopolymer engineering, and pathogen inhibition assays, we present a scalable, nature-derived alternative to antibiotics and synthetic preservatives. This work advanced food science via a validated, application-ready platform aligned with One Health principles and offers a paradigm shift in sustainable biopreservation technologies.

TIGP 20th Certificate Conferral Ceremony

Congratulations to the TIGP-MBAS Graduation Awardees!

TIGP 2025 Research Performance Fellowship Award result

Congratulations to three MBAS awardees:

Chih-Ying Lu

Sanjay Prasad Selvaraj

Yu Wu

Wan-Yin Han, Bo-Han Hou, Wen-Chi Lee, Tze-Ching Chan, Tzu-Hsiang Lin, Ho-Ming Chen* (2023) Arabidopsis mRNA decay landscape shaped by XRN 5′-3′ exoribonucleases. The Plant Journal. (https://doi.org/10.1111/tpj.16181) (IF: 7.091)

Plant cells use a variety of exoribonucleases (XRNs) to remove mRNA processing remnants produced during mRNA maturation, or to clear damaged functional mRNA. Mining the substrates and products of XRNs can expand understanding of pre-mRNA processing and post-transcriptional regulation mechanism. By comparing the degradation fragments of Arabidopsis wild type and XRN mutants, we found that the nucleus-localized XRN3 is responsible for removing spliced introns and 3' fragments produced during pre-mRNA processing. In addition, the analysis of XRN3 substrates reveals that mRNA 3'-terminal cleavage often happens after an adenosine, which is contrast to the assumption of some previous studies. Through the comparison with the cytoplasmic exoribonuclease XRN4 mutant, we suggest that many degradation fragments highly accumulated in the wild type are products of XRN4 rather than its substrates. Further analysis of XRN4 substrates reveals a novel endonucleolytic cleavage mechanism in the 3' untranslated regions. Our findings provide a revised view regarding mRNA processing and degradation, and also demonstrate the application of analyzing decay intermediates to uncover mRNA post-transcriptional regulatory mechanism.

Keat Ying Chan, Ching-Cher Sanders Yan, Hsiao-Yuh Roan, Shao-Chun Hsu, Tzu-Lun Tseng, Chung-Der Hsiao, Chao-Ping Hsu, Chen-Hui Chen* (2022) Skin cells undergo asynthetic fission to expand body surfaces in zebrafish. Nature. (https://doi.org/10.1038/s41586-022-04641-0) (IF: 64.8)

As an animal’s surface area expands during development, skin cell populations must quickly respond to maintain sufficient epithelial coverage. Despite much progress in understanding of skin cell behaviours in vivo, it remains unclear how cells collectively act to satisfy coverage demands at an organismic level. Here we created a multicolour cell membrane tagging system, palmskin, to monitor the entire population of superficial epithelial cells (SECs) in developing zebrafish larvae. Using time-lapse imaging, we found that many SECs readily divide on the animal body surface; during a specific developmental window, a single SEC can produce a maximum of four progeny cells over its lifetime on the surface of the animal. Remarkably, EdU assays, DNA staining and hydroxyurea treatment showed that these terminally differentiated skin cells continue splitting despite an absence of DNA replication, causing up to 50% of SECs to exhibit reduced genome size. On the basis of a simple mathematical model and quantitative analyses of cell volumes and apical surface areas, we propose that ‘asynthetic fission’ is used as an efficient mechanism for expanding epithelial coverage during rapid growth. Furthermore, global or local manipulation of body surface growth affects the extent and mode of SEC division, presumably through tension-mediated activation of stretch-activated ion channels. We speculate that this frugal yet flexible mode of cell proliferation might also occur in contexts other than zebrafish skin expansion.

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