Ptr1 evolved convergently with RPS2 and Mr5 to mediate recognition of AvrRpt2 in diverse solanaceous species

SummaryThe Ptr1 (Pseudomonas tomato race 1) locus in Solanum lycopersicoides confers resistance to strains of Pseudomonas syringae pv. tomato expressing AvrRpt2 and Ralstonia pseudosolanacearum expressing RipBN. Here we describe the identification and phylogenetic analysis of the Ptr1 gene. A single recombinant among 585 F2 plants segregating for the Ptr1 locus was discovered that narrowed the Ptr1 candidates to eight nucleotide-binding leucine-rich repeat protein (NLR)-encoding genes. From analysis of the gene models in the S. lycopersicoides genome sequence and RNA-Seq data, two of the eight genes emerged as the strongest candidates for Ptr1. One of these two candidates was found to encode Ptr1 based on its ability to mediate recognition of AvrRpt2 and RipBN when it was transiently expressed with these effectors in leaves of Nicotiana glutinosa. The ortholog of Ptr1 in tomato and in Solanum pennellii is a pseudogene. However, a functional Ptr1 ortholog exists in N. benthamiana and potato and both mediate recognition of AvrRpt2 and RipBN. In apple and Arabidopsis, recognition of AvrRpt2 is mediated by the Mr5 and RPS2 proteins, respectively. Phylogenetic analysis places Ptr1 in a distinct clade compared to Mr5 and RPS2 and it therefore appears to have arisen by convergent evolution for recognition of AvrRpt2.

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The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2/RipBN

10.1101/518399 ◽

2019 ◽

Author(s):

Carolina Mazo-Molina ◽

Samantha Mainiero ◽

Sara R. Hind ◽

Christine M. Kraus ◽

Mishi Vachev ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Genetic Resistance ◽

Site Directed Mutagenesis ◽

Type Iii Effector ◽

Bacterial Speck ◽

Solanum Lycopersicoides ◽

Type Iii ◽

Bacterial Speck Disease ◽

Race 1 ◽

Ralstonia Pseudosolanacearum

AbstractRace 1 strains of Pseudomonas syringae pv. tomato, which causes bacterial speck disease of tomato, are becoming increasingly common and no simply-inherited genetic resistance to such strains is known. We discovered that a locus in Solanum lycopersicoides, termed Pseudomonas tomato race 1 (Ptr1), confers resistance to race 1 Pst strains by recognizing the type III effector AvrRpt2. In Arabidopsis, AvrRpt2 degrades the RIN4 protein thereby activating RPS2-mediated immunity. Ptr1 also recognized homologs of AvrRpt2 from diverse bacteria including one in Ralstonia pseudosolanacearum and this correlated with the ability of AvrRpt2 to degrade RIN4. Using site-directed mutagenesis of AvrRpt2 we found that Ptr1 and RPS2 recognize identical features of AvrRpt2. However, the genome sequence of S. lycopersicoides revealed no RPS2 homolog in the Ptr1 region. Ptr1 could play an important role in controlling bacterial speck disease and its future cloning may shed light on an example of convergent evolution for recognition of a widespread type III effector.

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The Ptr1 Locus of Solanum lycopersicoides Confers Resistance to Race 1 Strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by Recognizing the Type III Effectors AvrRpt2 and RipBN

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-01-19-0018-r ◽

2019 ◽

Vol 32 (8) ◽

pp. 949-960 ◽

Cited By ~ 10

Author(s):

Carolina Mazo-Molina ◽

Samantha Mainiero ◽

Sarah R. Hind ◽

Christine M. Kraus ◽

Mishi Vachev ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Genetic Resistance ◽

Site Directed Mutagenesis ◽

Type Iii Effector ◽

Bacterial Speck ◽

Solanum Lycopersicoides ◽

Type Iii ◽

Bacterial Speck Disease ◽

Race 1 ◽

Ralstonia Pseudosolanacearum

Race 1 strains of Pseudomonas syringae pv. tomato, which cause bacterial speck disease of tomato, are becoming increasingly common and no simply inherited genetic resistance to such strains is known. We discovered that a locus in Solanum lycopersicoides, termed Pseudomonas tomato race 1 (Ptr1), confers resistance to race 1 P. syringae pv. tomato strains by detecting the activity of type III effector AvrRpt2. In Arabidopsis, AvrRpt2 degrades the RIN4 protein, thereby activating RPS2-mediated immunity. Using site-directed mutagenesis of AvrRpt2, we found that, like RPS2, activation of Ptr1 requires AvrRpt2 proteolytic activity. Ptr1 also detected the activity of AvrRpt2 homologs from diverse bacteria, including one in Ralstonia pseudosolanacearum. The genome sequence of S. lycopersicoides revealed no RPS2 homolog in the Ptr1 region. Ptr1 could play an important role in controlling bacterial speck disease and its future cloning may shed light on an example of convergent evolution for recognition of a widespread type III effector.

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Different Sequevars of Ralstonia pseudosolanacearum Causing Bacterial Wilt of Bidens pilosa in China

Plant Disease ◽

10.1094/pdis-12-19-2738-sc ◽

2020 ◽

Vol 104 (11) ◽

pp. 2768-2773

Author(s):

Yonglin He ◽

Yixue Mo ◽

Dehong Zheng ◽

Qiqin Li ◽

Wei Lin ◽

...

Keyword(s):

Arachis Hypogaea ◽

Bacterial Wilt ◽

Geographical Origin ◽

Bidens Pilosa ◽

Invasive Weed ◽

High Virulence ◽

Race 1 ◽

Ralstonia Pseudosolanacearum ◽

Phylotype I

Bidens pilosa is an invasive weed that threatens the growth of crops and biodiversity in China. In 2017, suspected bacterial wilt of B. pilosa was discovered in Qinzhou and Beihai, Guangxi, China. A variety of weeds are considered as reservoirs harboring bacterial wilt pathogens, but most do not show obvious symptoms in the field. Identifying the classification status of the B. pilosa bacterial wilt pathogen and exploring its geographical origin might be helpful for clarifying the role of weeds in the circulation of the disease. Phylotyping, sequevar analysis, and cross inoculation of pathogens isolated from B. pilosa and nearby peanut (Arachis hypogaea), balsam gourd (Momordica charantia), and eucalyptus (Eucalyptus robusta) plants were carried out. Three isolates of B. pilosa (Bp01, Bp02, and Bp03) were identified as Ralstonia pseudosolanacearum, race 1, biovar 3, and phylotype I, and belonged to sequevars 17 and 44, and an unknown sequevar. The sequevars isolated from B. pilosa were not completely consistent with those of the nearby hosts, and the virulence of these isolates differed when cross inoculated. The Bp03 sequevar was different from peanut isolate sequevars in the same field and was not identical to any previously designated sequevars. The isolates from B. pilosa and other nearby hosts displayed low or no virulence toward their cross hosts (with wilt incidences less than 33.33%). An exception to this was the isolates from B. pilosa, which displayed high virulence toward eucalyptus (with a wilt incidence of 70.00 to 100.00%). This is the first report of different sequevars of R. pseudosolanacearum causing typical bacterial wilt symptoms in B. pilosa in the field.

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Pseudomonas syringae Effector AvrPphB Suppresses AvrB-Induced Activation of RPM1 but Not AvrRpm1-Induced Activation

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-08-14-0248-r ◽

2015 ◽

Vol 28 (6) ◽

pp. 727-735 ◽

Cited By ~ 24

Author(s):

Andrew R. Russell ◽

Tom Ashfield ◽

Roger W. Innes

Keyword(s):

Disease Resistance ◽

Protein Kinase ◽

Molecular Mechanism ◽

Pseudomonas Syringae ◽

Hypersensitive Response ◽

Hypersensitive Resistance ◽

Nicotiana Glutinosa ◽

Resistance Response ◽

Interacting Protein ◽

Soybean Plants

The Pseudomonas syringae effector AvrB triggers a hypersensitive resistance response in Arabidopsis and soybean plants expressing the disease resistance (R) proteins RPM1 and Rpg1b, respectively. In Arabidopsis, AvrB induces RPM1-interacting protein kinase (RIPK) to phosphorylate a disease regulator known as RIN4, which subsequently activates RPM1-mediated defenses. Here, we show that AvrPphB can suppress activation of RPM1 by AvrB and this suppression is correlated with the cleavage of RIPK by AvrPphB. Significantly, AvrPphB does not suppress activation of RPM1 by AvrRpm1, suggesting that RIPK is not required for AvrRpm1-induced modification of RIN4. This observation indicates that AvrB and AvrRpm1 recognition is mediated by different mechanisms in Arabidopsis, despite their recognition being determined by a single R protein. Moreover, AvrB recognition but not AvrRpm1 recognition is suppressed by AvrPphB in soybean, suggesting that AvrB recognition requires a similar molecular mechanism in soybean and Arabidopsis. In support of this, we found that phosphodeficient mutations in the soybean GmRIN4a and GmRIN4b proteins are sufficient to block Rpg1b-mediated hypersensitive response in transient assays in Nicotiana glutinosa. Taken together, our results indicate that AvrB and AvrPphB target a conserved defense signaling pathway in Arabidopsis and soybean that includes RIPK and RIN4.

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Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽

10.1186/s12864-021-07605-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qi Wu ◽

Yiming Luo ◽

Xiaoyong Wu ◽

Xue Bai ◽

Xueling Ye ◽

...

Keyword(s):

Expression Profiles ◽

Functional Characterization ◽

Chenopodium Quinoa ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Rna Seq ◽

Short Day ◽

Homologous Genes ◽

The Relationship ◽

Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

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Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

AMB Express ◽

10.1186/s13568-020-01134-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Maroua Oueslati ◽

Magdalena Mulet ◽

Mohamed Zouaoui ◽

Charlotte Chandeysson ◽

Jorge Lalucat ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Pseudomonas Syringae ◽

Ice Nucleation ◽

Phylogenetic Study ◽

Future Studies ◽

Citrus Orchards ◽

First Time ◽

New Cultivars

Abstract The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.

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Identification of QTLs controlling resistance to Pseudomonas syringae pv. tomato race 1 strains from the wild tomato, Solanum habrochaites LA1777

Theoretical and Applied Genetics ◽

10.1007/s00122-015-2463-7 ◽

2015 ◽

Vol 128 (4) ◽

pp. 681-692 ◽

Cited By ~ 22

Author(s):

Shree Prasad Thapa ◽

Eugene M. Miyao ◽

R. Michael Davis ◽

Gitta Coaker

Keyword(s):

Pseudomonas Syringae ◽

Wild Tomato ◽

Solanum Habrochaites ◽

Race 1

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Outbreak of Fusarium oxysporum f. sp. lycopersici race 3 in commercial fresh-market tomato fields in Rio de Janeiro State, Brazil

Horticultura Brasileira ◽

10.1590/s0102-05362007000300025 ◽

2007 ◽

Vol 25 (3) ◽

pp. 451-454 ◽

Cited By ~ 25

Author(s):

Ailton Reis ◽

Leonardo S Boiteux

Keyword(s):

Fusarium Oxysporum ◽

Rio De Janeiro ◽

Present Report ◽

Fresh Market ◽

Solanum Pennellii ◽

Espírito Santo ◽

Race 1 ◽

Serious Disease ◽

Espirito Santo ◽

Janeiro State

Fusarium wilt, caused by three races of Fusarium oxysporum f. sp. lycopersici, is one of the most important tomato diseases. In Brazil, all three races were reported, however, race 3 has been so far restricted only to Espírito Santo State. In the present work, seven F. oxysporum isolates obtained from wilted plants of the race 1 and 2-resistant tomato hybrids 'Giovana', 'Carmen' and 'Alambra' in São José de Ubá and Itaocara (Rio de Janeiro State, Brazil) were characterized at race level. Virulence assays were performed using a set of race differential cultivars: 'Ponderosa' (susceptible to all races), 'IPA-5' (resistant to race 1), 'Floradade' (resistant to races 1 and 2), 'BHRS-2,3' (resistant to all three races). Two wild tomato accessions (Solanum pennellii 'LA 716' e S. chilense 'LA 1967') previously reported as resistant to all Brazilian isolates of F. oxysporum f. sp. lycopersici were also evaluated. Isolates from São José de Ubá and Itaocara were highly virulent to 'Ponderosa', 'IPA-5' and 'Floradade'. They were also able to infect a few plants of 'BHRS-2,3', inducing vascular browning and wilt symptoms. Solanum pennellii and S. chilense accessions displayed an extreme (immune-like) resistant response. These results indicated that all seven isolates could be classified as F. oxysporum f. sp. lycopersici race 3, expanding the geographical distribution of this pathogen within Brazil. The hypothesis of transmission via contaminated seeds is reinforced after the present report, which confirms the almost simultaneous outbreak of race 3 in two geographically isolated tomato-growing areas in Brazil (Espirito Santo and Rio de Janeiro). Evaluation of commercial seed lots imported into Brazil for contamination with the pathogen would be necessary in order to avoid nation-wide spread of this serious disease.

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Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation

International Journal of Molecular Sciences ◽

10.3390/ijms23020746 ◽

2022 ◽

Vol 23 (2) ◽

pp. 746

Author(s):

Bo Li ◽

Xiangzhan Zhang ◽

Ruiwei Duan ◽

Chunhong Han ◽

Jian Yang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Developmental Stages ◽

Genomic Analysis ◽

Pyrus Communis ◽

Anthocyanin Content ◽

Anthocyanin Accumulation ◽

Rna Seq ◽

Virus Induced Gene Silencing ◽

Functional Identification ◽

Glutathione S Transferase

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding.

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