34Both type III effector proteins and non-ribosomal peptide toxins play important 35 roles for Pseudomonas syringae pathogenicity in host plants, but whether and how 36 these virulence pathways interact to promote infection remains unclear. Genomic 37 evidence from one clade of P. syringae suggests a tradeoff between the total number of 38 type III effector proteins and presence of syringomycin, syringopeptin, and syringolin A 39 toxins. Here we report the complete genome sequence from P. syringae CC1557, 40 which contains the lowest number of known type III effectors to date and has also 41 acquired genes similar to sequences encoding syringomycin pathways from other 42 strains. We demonstrate that this strain is pathogenic on Nicotiana benthamiana and 43 that both the type III secretion system and a new type III effector family, hopBJ1, 44 contribute to virulence. We further demonstrate that virulence activity of HopBJ1 is 45 dependent on similar catalytic sites as the E. coli CNF1 toxin. Taken together, our 46 results provide additional support for a negative correlation between type III effector 47 repertoires and the potential to produce syringomycin-like toxins while also highlighting 48 how genomic synteny and bioinformatics can be used to identify and characterize novel 49 virulence proteins. 50 51 Introduction 52
18Phage tail-like bacteriocins (tailocins) are bacterially-produced protein toxins that can mediate 19 competitive interactions between co-colonizing bacteria. Both theoretical and empirical research 20 has shown there are intransitive interactions between bacteriocin-producing, bacteriocin-21 sensitive, and bacteriocin-resistant populations, whereby producers outcompete sensitive, 22 escape the trap of fitness trade-offs associated with gaining de novo tailocin resistance, and 41 expands our understanding of how sensistive bacterial populations can persist in the presence of 42 lethal competitors. 43 44
Background. The bacterial plant pathogenic Ralstonia species belong to the betaproteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a "species complex"," gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. T3Es are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology). Methods. Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors. Results. We curated the T3E repertoires of 12 plant pathogenic Ralstoniastrains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.PeerJ reviewing PDF | Abstract 22 Background. The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria 23 class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range 24 of plant hosts. These bacteria form a heterogeneous group considered as a "species complex"," 25 gathering three newly defined species. Like many other Gram negative plant pathogens, 26 Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a 27 large repertoire of type III effectors into their plant host cells. T3Es are thought to participate in 28 generating a favorable environment for the pathogen (countering plant immunity and modifying 29 the host metabolism and physiology).Manuscript to be reviewed 31 Methods. Expert genome annotation, followed by specific type III-dependent secretion, allowed 32 us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III 33 effectors. 34 35 Results. We curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a 36 total of 12 strains spread over the different groups of the species complex. This generated a 37 pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we 38 scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant 39 pathogenic Ralstonia strains isolated from different host plants in different areas of the globe....
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
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