Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii

Background: Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. Results: In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. Conclusions: Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied

Functional characterization of AWR affector proteins from the phytopathogen "R. solanacearum" (Caracterització funcional de les proteïnes efectores AWR del fitopatogen "R. solanacearum")

[eng] "R. solanacearum" is a devastating bacterial pathogen that infects "Solanaceae" spp. such as tomato, eggplant or banana. A functional T3SS is required for virulence and more than 70 putative effectors have been described, although only few have been studied. This thesis focuses on a five-member gene family of effectors named "awr". We demonstrated that awr gene family is extremely conserved among R. solanacearum strains but also present in other plant pathogens such as Acidovorax or Burkholderia spp. and even present in the human pathogen B. pseudomallei. Virulence of a Ralstonia mutant strain devoid of all awr genes was tested on tomato, eggplant and Aradidopsis. Plant growth of quintuple mutant strain was considerably reduced in natural hosts, indicating a role in virulence, but remained unchanged in Arabidopsis. Col-0 infection with Pseudomonas syringae DC3000 heterologously expressing each AWR was also performed. While presence of some AWRs in Pseudomonas did not have an effect on plant growth, others (like AWR5) dramatically reduced the pathogen multiplication, pointing out a possible plant detection. In order to unravel the functions of AWR proteins, they were transiently expressed by means of Agrobacterium in non-host Nicotiana spp. Upon AWR expression, necroses took place to different extents on the plant leaves. AWR5 induced the strongest necrosis, resembling an HR phenotype which was later confirmed by TB/DAB staining and by RT-PCR of specific HR marker genes. Furthermore, a strong reduction in yeast cells was experimented upon several AWR protein expressions which indicate that the mechanisms that might be altered by these effector proteins is conserved among eukaryotes and hence reinforces their role in virulence. AWR4 appeared not to be toxic in this model organism and for that reason we sought to decipher some of the plant targets of this AWR protein as a start point. Out of more than 60 interacting clones were sequenced after a yeast-two hybrid screening with Arabidopsis root cDNA from R. solanacearum challenged plants. Among them, several defense-related proteins were found: phenylalanine ammonia-lyase, MPK6, DMR6 or KIN10. In order to find other key genes for AWR activity, the AWRs that displayed a strong yeast toxicity were heterologously produced in both E. coli and R. solanacearum to be ready to be employed as a bait for plant protein complexes that will be analysed by mass spectrometry. In summary, AWR are highly conserved effectors that play an important role in both pathogenesis and plant recognition as they reduce P. syringae virulence and trigger an HR-like phenotype in non-host plants. Deciphering effector function will open promising avenues towards the design of new strategies to control R. solanacearum.[cat] R. solanacearum és un patogen bacterià capaç d’infectar diferents solanàcies com ara la tomaquera, la patatera, l’alberginiera o el plataner. Aquest fitopatogen injecta més de 70 proteïnes efectores en la cèl•lula vegetal hoste, tot i que només algunes han sigut ja estudiades. Aquesta tesi es centra en una família multigènica d’efectors: els AWRs. Els estudis científics duts a terme durant aquesta tesi van demostrar que la família de AWR no només estava altament conservada en el llinatge de R. solanacearum sinó que també es trobava present en altres fitopatògens o inclús en el patogen humà Burkholderia pseudomallei. A més a més, diferents assajos de patogenicitat en tomaquera i alberginiera van provar que els gens awr presentaven un paper clar en virulència per aquests hostes. Contràriament, la presència d’aquestes proteïnes en la planta model Arabidopsis thaliana produïen una disminució en la capacitat infectiva/multiplicativa. Això indicaria una dualitat dels efectors AWR depenent del context que ens trobem, ja sigui contribuint a la patogenicitat del bacteri o bé éssent reconeguts per la planta i així disminuint la patogenicitat bacteriana. Per tal de desentranyar les funcions de les proteïnes AWR, es van expressar de forma transitòria a la planta model no-hoste Nicotiana spp. L’expressió d’algunes proteïnes AWR va provocar una forta necrosi de les fulles que s’assemblaria a una resposta hipersensible. Mitjançant diferents tincions i assajos de PCR en temps real es va corroborar que l’AWR5 presentava aquest tipus de mort cel•lular programada. L’elevada toxicitat d’algunes AWRs es va demostrar també en llevat. En el transcurs d’aquesta tesi també s’ha realitzat un crivellatge en doble híbrid per tal de buscar proteïnes dianes de la planta per a l’AWR4 (la menys tòxica). A més a més, es va posar a punt l’expressió dels AWRs a E. coli o bé a R. solanacearum per tal d’abordar altres tècniques que permetin una millor cerca d’interactors en el futur

A chromosomal insertion toolbox for promoter probing, mutant complementation and pathogenicity studies in Ralstonia solanacearum

We describe here the construction of a delivery system for stable and directed insertion of gene constructs in a permissive chromosomal site of the bacterial wilt pathogen Ralstonia solanacearum. The system consists of a collection of suicide vectors the Ralstonia chromosome (pRC) series that carry an integration element flanked by transcription terminators and two sequences of homology to the chromosome of strain GMI1000, where the integration element is inserted through a double recombination event. Unique restriction enzyme sites and a GATEWAY cassette enable cloning of any promoter::gene combination in the integration element. Variants endowed with different selectable antibiotic resistance genes and promoter::gene combinations are described. We show that the system can be readily used in GMI1000 and adapted to other R. solanacearum strains using an accessory plasmid. We prove that the pRC system can be employed to complement a deletion mutation with a single copy of the native gene, and to measure transcription of selected promoters in monocopy both in vitro and in planta. Finally, the system has been used to purify and study secretion type III effectors. These novel genetic tools will be particularly useful for the construction of recombinant bacteria that maintain inserted genes or reporter fusions in competitive situations (i.e., during plant infection)

The awr gene family encodes a novel class of Ralstonia solanacearum type III effectors displaying virulence and avirulence activities

We present here the characterization of a new gene family, awr, found in all sequenced Ralstonia solanacearum strains and in other bacterial pathogens. We demonstrate that the five paralogues in strain GMI1000 encode type III-secreted effectors and that deletion of all awr genes severely impairs its capacity to multiply in natural host plants. Complementation studies show that the AWR (alanine-tryptophanarginine tryad) effectors display some functional redundancy, although AWR2 is the major contributor to virulence. In contrast, the strain devoid of all awr genes (¿awr1-5) exhibits enhanced pathogenicity on Arabidopsis plants. A gain-of-function approach expressing AWR in Pseudomonas syringae pv. tomato DC3000 proves that this is likely due to effector recognition, because AWR5 and AWR4 restrict growth of this bacterium in Arabidopsis. Transient overexpression of AWR in nonhost tobacco species caused macroscopic cell death to varying extents, which, in the case of AWR5, shows characteristics of a typical hypersensitive response. Our work demonstrates that AWR, which show no similarity to any protein with known function, can specify either virulence or avirulence in the interaction of R. solanacearum with its plant hosts

Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii

Background: Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. Results: In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. Conclusions: Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied