Chih-Horng Kuo

Summary: Agrobacteria can deliver transfer DNA (T-DNA) into plant cells, causing tumorous growth. This process, agrobacteria-mediated transformation (AMT), underlies plant genetic engineering and has been regarded as an evolutionary innovation specific to these pathogens. By screening 63,759 alphaproteobacterial genomes for T-DNA border sequences, we identify mini-T-DNAs in diverse rhizobial genera. Each typically encodes a single cargo, a RolB/RolC family protein or a distant rhizobial homologue. We show that native rhizobia-mediated transformation (RMT) systems deliver these mini-T-DNAs into the root nodules of common bean, pea, and chickpea, where the cargo genes are expressed, with no signal in adjacent root tissue. RMT systems share VirG-dependent activation of the core virulence regulon but respond to distinct upstream signals. Our genome screen identifies many additional candidate T-DNA transfer systems, and phylogenetic analysis places their genes into two of the many type IV secretion system (T4SS) clades. RMT systems occur in both clades, together with other systems unrelated to T-DNA transfer, and typically have an ancestral-like T4SS configuration. In contrast, AMT systems occupy a single subclade, consistent with later acquisition of their T4SS module. AMT and RMT thus represent two specialized outcomes of an older, more widespread capability for bacteria-to-plant DNA transfer.

Vibrio campbellii strains PH1401 and PH1409 were isolated from shrimp ponds with documented mortality outbreaks in the Philippines. PH1401 and PH1409 share identity with V. campbellii strain BoB-53. Whole-genome analysis reveals full-length pirAB binary toxin genes in PH1401 . Both strains carry three type VI secretion systems.

Pyrroloquinoline quinone (PQQ) is a redox cofactor derived from prokaryotes that participates in various biological processes involving dehydrogenase enzymes. Previous field trials identified a PQQ‐producing endophyte, Burkholderia seminalis 869T2, which enhances banana growth and reduces Fusarium wilt incidence from 24.5% to 3.4%. While more recent studies have confirmed its agricultural benefits across multiple plant species, the underlying molecular mechanisms remain unclear. Here, integrated omics and imaging mass spectrometry were employed to investigate the role of PQQ in planta . Our results indicate that PQQ achieves these outcomes by modulating key aspects of plant energy metabolism, including the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, and NAD/NADP pathways. In addition, PQQ appears to influence phytohormone signalling pathways and trigger systemic plant resistance. Consistent with these molecular responses, exogenous PQQ enhanced root and shoot development and improved resistance to Fusarium infection. Collectively, these findings indicate that the endophyte functions as a biostimulant through PQQ production, coordinating plant metabolism and defence to counter pathogen invasion. This study provides mechanistic insight into plant–endophyte mutualism and highlights the potential of both PQQ and PQQ‐producing endophytes as biostimulants for sustainable agricultural applications.

Agrobacterium -mediated transient expression has revolutionized plant research, enabling numerous landmark discoveries across diverse areas of plant biology. Yet this powerful approach remains largely confined to solanaceous species, leaving most economically important crop families without a comparable rapid assay platform. Here, we show that an engineered Rhizobium rhizogenes strain, AS109, mediates efficient transient expression across diverse dicot species spanning multiple taxonomic families, consistently outperforming commonly used laboratory agrobacterial strains. Leveraging the broad host range of AS109, we establish a suite of functional assays in faba bean ( Vicia faba ), including protein localisation, RNA interference-mediated gene silencing, cell-surface elicitor recognition screens, nucleotide-binding leucine-rich repeat receptor (NLR) activation, and infection cell biology at the host-pathogen interface. We further demonstrate that both singleton NLRs and sensor-helper NLR pairs from Solanaceae retain effector recognition and cell death activity when transferred into faba bean, establishing a rapid platform for evaluating cross-family transferability of disease-resistance genes. AS109 thus provides an accessible and versatile chassis for functional genomics in non-model crops, bridging the widening gap between hypothesis generation and experimental validation across diverse plant species.

Type VI secretion system (T6SS) is a widespread bacterial nanomachine that mediates interbacterial antagonism and ecological competitiveness. Thirteen core type six secretion (Tss) proteins, including the outer membrane-anchoring protein TssJ, constitute the canonical T6SS. Yet, TssJ is absent from T6SSs in several lineages, raising the question of how their systems assemble and function without it. Using the TssJ-lacking T6SS of Agrobacterium C58 as a model, we describe a form of co-optive evolution in which a degenerated outer membrane polysaccharide transporter, TssX, functionally replaces TssJ. We delineated the assembly pathway of the agrobacterial T6SS and uncovered an assembly order in which TssX acts downstream of the membrane complex and prior to contractile sheath polymerization. Comparative genomic analyses of 32,414 complete proteobacterial genomes revealed that tssX defines a distinct T6SS subtype and is mutually exclusive with tssJ, indicating functional compensation through evolutionary replacement. Phylogenetic and synteny analyses revealed multiple independent losses of tssJ and subsequent co-option of tssX in α-proteobacterial lineages. Our work uncovers a novel T6SS outer membrane protein and shows that essential nanomachine elements can be replaced. The variation in both composition and assembly mechanisms exemplifies the remarkable flexibility in the evolution of protein complexes that are both structurally and functionally conserved.

We report the draft metagenome-assembled genome (MAG) of “ Candidatus Phytoplasma australasiaticum” strain TBB-AP, obtained from a symptomatic tomato plant collected in Andhra Pradesh, India. This assembly provides a genomic resource for functional and evolutionary studies of phytoplasmas associated with tomato big bud disease.

We report complete genome sequences of three Bradyrhizobium strains isolated from root nodules of peanut cultivar Tainan Select No. 9 collected in Taiwan. Hybrid assemblies using Nanopore and Illumina reads produced circular chromosome and plasmid contigs, providing high-quality genomic resources for future studies.

Phytoplasmas are insect-transmitted plant pathogens that manipulate host development through secreted effector proteins. While they are notorious for causing agricultural losses, in the ornamental plant poinsettia ( Euphorbia pulcherrima ), phytoplasma infection is uniquely harnessed to induce the commercially desirable free-branching trait. However, the effectors responsible for this phenotype have remained unknown. To address this question, we sequenced and analysed the 705,138 bp genome of ‘ Candidatus Phytoplasma pruni’ PR2021, a strain associated with the high-branching cultivar Princettia Pink. Comparative genomics confirmed its species assignment and revealed an unusual effector repertoire. PR2021 lacks most previously described effectors but encodes two distinct SAP11 homologues, a family of effectors known to induce plant branching. Genomic context analysis showed that one homologue is located within a potential mobile unit (PMU) and is nearly identical to the SAP11 of the distantly related ‘ Ca . P. asteris’, while the other is located outside PMU regions and is divergent in protein sequence (39.0% identity) and predicted structure. Functional assays using Agrobacterium -mediated transient expression in Nicotiana benthamiana demonstrated that each homologue independently induced significant branching, whereas co-expression did not enhance the phenotype, indicating overlapping functions. These findings establish a direct connection between poinsettia branching and SAP11-homologous effectors, providing the first experimental evidence linking phytoplasma effector activity to this horticulturally important trait. This work expands understanding of phytoplasma effector diversity and mobility, while offering a functional framework for developing pathogen-free strategies to modulate ornamental plant architecture.

Fire blight, caused by Erwinia amylovora, severely impacts global apple and pear production. Current control measures rely heavily on conventional antibiotics like streptomycin, oxytetracycline, and kasugamycin, which raise concerns regarding resistance development and environmental impacts. This research introduces RejuAgro A (RAA), an antimicrobial produced by Pseudomonas soli 0617-T307, showing potent activity against E. amylovora, including streptomycin-resistant strains. RAA demonstrates efficacy comparable to streptomycin in field trials, effectively reducing fire blight incidence. Studies on the antimicrobial mechanism reveal that RAA inhibits RNA, DNA, and protein synthesis, distinguishing from that of conventional antibiotics. Furthermore, RAA displays broad-spectrum activity against diverse plant bacterial and fungal pathogens. The RAA biosynthesis gene cluster in P. soli is identified, revealing key genes essential for its production. RAA presents an alternative to traditional antibiotics, potentially enhancing sustainable apple and pear production and addressing antibiotic resistance concerns.