Biology subjects

Coutinho, T.

Publications and source records attributed to Coutinho, T..

5 recordsLinked to original sources

bioRxiv2024

Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans

Pantoea agglomerans is one of four Pantoea species for which strains have been reported in the United States to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Genome assemblies were generated for 87 P. agglomerans strains that showed a range in onion virulence phenotypes. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies identified two well-represented and well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion leaves and bulbs were only identified in Phylogroup II and encoded the HiVir biosynthetic cluster for the phytotoxin pantaphos, supporting the role of HiVir as a crucial pathogenicity factor. Using a MASH-based plasmid classification system, the P. agglomerans HiVir cluster was determined to be encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes of P. agglomerans revealed that the pOnion plasmids harbored alt genes responsible for encoding tolerance to the thiosulfinate defensive chemistry in Allium spp. Additionally, many of these pOnion plasmids harbored cop gene clusters, which confer resistance to copper. However, the pOnion plasmids encoded the HiVir cluster less frequently. We demonstrated that the pOnion plasmid pCB1C, encoding HiVir and alt clusters as well as an intact conjugative type IV secretion system (T4SS), can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.

microbiology↗

bioRxiv2023

Pantailocins: Phage-derived Bacteriocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes

Phage-derived bacteriocins are highly specific and effective antimicrobial molecules which have successfully been used as prophylactic treatments to prevent phytopathogen infections. Given the specificity of tailocins, a necessary step for broadening the tailocin catalog and for extending applicability across systems and diseases is the screening of new clades of phytopathogens for production of molecules with tailocin-like killing activity. Here, we describe production by and sensitivity of strains to tailocins produced by Pantoea ananatis and Pantoea stewartii subsp. indologenes. Phylogenetic evidence suggests that these tailocins are derived from Myoviridae family phage like many previously described R type syringacins and R type pyocins, but also suggests that cooption from phage occurred independently of previously described tailocins. Since these tailocin encoding loci are present in the same genomic locations across multiple strains of both species and display a level of divergence that is consistent with other shared regions between the genomes and with vertical inheritance of the locus, we refer to them broadly as pantailocins.

microbiology↗

bioRxiv2022

A novel biosynthetic gene cluster across the Pantoea species complex is important for pathogenicity in onion

Onion center rot is caused by at least four species of Pantoea (P. ananatis, P. agglomerans, P. allii, and P. stewartii subsp. indologenes). Critical onion pathogenicity determinants for P. ananatis were recently described but whether those determinants are common among other onion-pathogenic Pantoea species remains unknown. In this work, we report onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. We identified two distinct secondary metabolite biosynthetic gene clusters in different strains of onion pathogenic P. stewartii subsp. indologenes. One cluster is similar to the previously described HiVir phosphonate biosynthetic cluster of P. ananatis and another is a novel putative phosphonate biosynthetic gene cluster, which we name "Halophos". The Halophos gene cluster was also identified in P. allii strains. Both clusters are predicted to be phosphonate biosynthetic clusters based on the presence of a characteristic phosphenolpyruvate phosphomutase (pepM) gene. The deletion of pepM gene from either the P. stewartii subsp. indologenes HiVir or Halophos clusters caused loss of necrosis on onion leaves and red onion scales, and resulted in significantly lower bacterial populations compared to the corresponding wildtype and complemented strains. Seven (halB-halH) out of eleven genes (halA-halK) in the Halophos gene cluster are required for onion necrosis phenotypes. The onion non-pathogenic strain PNA15-2 gained the capacity to cause foliar necrosis on onion via exogenous expression of a minimal seven gene Halophos cluster (halB -halH). Furthermore, cell-free culture filtrates of PNA14-12 expressing the intact Halophos-gene cluster caused necrosis on onion leaves consistent with the presence of a secreted toxin. Together, these observations indicated that pepM genes in both phosphonate biosynthetic gene clusters (HiVir and Halophos) are important for Pantoea spp. onion pathogenicity and the biosynthetic product of the Halophos cluster causes necrosis on onion leaf tissue. Overall, this is the first report of onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. Author summaryOnion center rot is caused by multiple Pantoea species including P. stewartii subsp. indologenes and P. allii. We identified two distinct secondary metabolite biosynthetic clusters associated with onion pathogenic strains, the validated HiVir phosphonate cluster and a putative phosphonate biosynthetic cluster that we named as Halophos based on the associated "halo" phenotype on the red onion scales. We found that pepM genes from each cluster (HiVir and Halophos) are required for onion infection by P. stewartii subsp. indologenes and P. allii but not for millet infection by P. stewartii subsp. indologenes. Conversely, the T3SS was important for millet infection by P. stewartii subsp. indologenes but not onion infection. Induction of the intact Halophos cluster was associated with the accumulation of a necrosis-inducing factor in culture, which suggests it might be a secreted phytotoxin. Seven of the eleven Halophos cluster genes are required for onion necrosis phenotypes and expression of this minimal cluster conferred a limited onion necrosis phenotype to an onion-non-pathogenic Pantoea strain. We provide evidence of a Halophos biosynthetic gene cluster to be associated with onion pathogenicity in strains of P. stewartii subsp. indologenes and P. allii.

microbiology↗

bioRxiv2020

The distribution of onion virulence gene clusters among Pantoea spp.

Pantoea ananatis is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and alt, associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of a predicted small molecule toxin. The alt gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other Pantoea species suggest that these gene clusters are present outside of P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains of Pantoea spp. were phenotyped using the red onion scale necrosis (RSN) assay and were assayed using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 Pantoea species, 41 isolation sources, and 23 countries, collected from 1946-2019, were tested. There is a significant association between the alt PCR assay and Pantoea strains recovered from symptomatic onion (P<0.001). There is also a significant association of a positive HiVir PCR and RSN assay among P. ananatis strains but not among Pantoea spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural alt positive [RSN+/HiVir+/alt+] P. ananatis strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to alt negative [RSN+/HiVir+/alt-] P. ananatis strains. A combination of assays that include PCR of virulence genes [HiVir and alt] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic P. ananatis strains.

plant biology↗

bioRxiv2019

Transfer of Xanthomonas campestris pv. arecae, and Xanthomonas campestris pv. musacearum to Xanthomonas vasicola (Vauterin) as Xanthomonas vasicola pv. arecae comb. nov., and Xanthomonas vasicola pv. musacearum comb. nov. and description of Xanthomonas vasicola pv. vasculorum pv. nov.

LETTER TO THE EDITOR LETTER TO THE EDITOR EMENDED DESCRIPTION OF... REFERENCES Members of the genus Xanthomonas, within the gamma-Proteobacteria, collectively cause disease on more than 400 plant species (Hayward 1993), though some members are apparently non-pathogenic (Vauterin et al. 1996) and some have been isolated from clinical samples such as skin microbiota (Seite, Zelenkova, and Martin 2017). Historically, taxonomy of Xanthomonas was tied to the host of isolation (Starr 1981; Wernham 1948), with the genus being split into large numbers of species, each defined by this single phenotypic feature (Dye 1962). Subsequently, most of the species were transferred (lumped) into a single species, X. campestris, and designated as nomenspec ...

microbiology↗