Limits...
MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum.

Ouyang S, Park G, Atamian HS, Han CS, Stajich JE, Kaloshian I, Borkovich KA - PLoS Pathog. (2014)

Bottom Line: One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen.The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response.Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.

ABSTRACT
MicroRNAs (miRNAs) suppress the transcriptional and post-transcriptional expression of genes in plants. Several miRNA families target genes encoding nucleotide-binding site-leucine-rich repeat (NB-LRR) plant innate immune receptors. The fungus Fusarium oxysporum f. sp. lycopersici causes vascular wilt disease in tomato. We explored a role for miRNAs in tomato defense against F. oxysporum using comparative miRNA profiling of susceptible (Moneymaker) and resistant (Motelle) tomato cultivars. slmiR482f and slmiR5300 were repressed during infection of Motelle with F. oxysporum. Two predicted mRNA targets each of slmiR482f and slmiR5300 exhibited increased expression in Motelle and the ability of these four targets to be regulated by the miRNAs was confirmed by co-expression in Nicotiana benthamiana. Silencing of the targets in the resistant Motelle cultivar revealed a role in fungal resistance for all four genes. All four targets encode proteins with full or partial nucleotide-binding (NB) domains. One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen. The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs.

Show MeSH

Related in: MedlinePlus

Properties of miRNAs expressed in resistant and susceptible tomato cultivars treated with water or the fungal pathogen Fusarium oxysporum.In total, four small RNA libraries were subjected to deep sequencing: susceptible tomato cultivar Moneymaker treated with water; Moneymaker treated with Fusarium oxysporum f. sp. lycopersici (F. oxysporum); resistant tomato cultivar Motelle treated with water and Motelle treated with F. oxysporum. The sequence length of small RNAs (A) for the combined data from the four libraries was determined as described in the Materials and Methods. Relative expression levels of known miRNAs (B) were determined by dividing normalized reads for F. oxysporum treatment by those for water treatment for each cultivar. The red bracket indicates the miRNAs that were negatively regulated in Motelle, but not Moneymaker, after F. oxysporum infection. Putative roles/targets of miRNAs in various plant species (information from miRBase.org): miR156, miR156c, miR156kj and miR157d: Squamosa-promoter Binding Protein (SBP)-like transcription factors; miR166glmf: HD-Zip transcription factors, including Phabulosa (PHB) and Phavoluta (PHV) that regulate axillary meristem initiation and leaf development; miR167b, miR167d and miR167fijeghac: Auxin Response Factors (ARF transcription factors); miR396abcd: Growth Regulating Factor (GRF) transcription factors, rhodenase-like proteins, and kinesin-like protein B; miR394ab, F-box proteins; miR827abc: Unknown; miR403bdf: Virus defense; miR162 and miR162abc: Unknown; miR530: Unknown; miR398abc: copper superoxide dismutases and cytochrome C oxidase subunit V; miR482f: NB domain proteins; miR5300, Unknown.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4199772&req=5

ppat-1004464-g001: Properties of miRNAs expressed in resistant and susceptible tomato cultivars treated with water or the fungal pathogen Fusarium oxysporum.In total, four small RNA libraries were subjected to deep sequencing: susceptible tomato cultivar Moneymaker treated with water; Moneymaker treated with Fusarium oxysporum f. sp. lycopersici (F. oxysporum); resistant tomato cultivar Motelle treated with water and Motelle treated with F. oxysporum. The sequence length of small RNAs (A) for the combined data from the four libraries was determined as described in the Materials and Methods. Relative expression levels of known miRNAs (B) were determined by dividing normalized reads for F. oxysporum treatment by those for water treatment for each cultivar. The red bracket indicates the miRNAs that were negatively regulated in Motelle, but not Moneymaker, after F. oxysporum infection. Putative roles/targets of miRNAs in various plant species (information from miRBase.org): miR156, miR156c, miR156kj and miR157d: Squamosa-promoter Binding Protein (SBP)-like transcription factors; miR166glmf: HD-Zip transcription factors, including Phabulosa (PHB) and Phavoluta (PHV) that regulate axillary meristem initiation and leaf development; miR167b, miR167d and miR167fijeghac: Auxin Response Factors (ARF transcription factors); miR396abcd: Growth Regulating Factor (GRF) transcription factors, rhodenase-like proteins, and kinesin-like protein B; miR394ab, F-box proteins; miR827abc: Unknown; miR403bdf: Virus defense; miR162 and miR162abc: Unknown; miR530: Unknown; miR398abc: copper superoxide dismutases and cytochrome C oxidase subunit V; miR482f: NB domain proteins; miR5300, Unknown.

Mentions: Using Illumina sequencing, we obtained a total of more than 27 million high quality small RNA sequences from the four libraries that could be mapped to the tomato genome. Of these, 5,743,067 were from MM_H2O, 5,492,955 from MM_Foxy, 4,392,583 from Mot_H2O and 5,497,730 from Mot_Foxy (Table S1). Among all size classes, 24-, 21- and 22-nt small RNA species were the three most abundant (Fig. 1A). These sizes are similar to those previously identified in tomato [22], [23]. Within the miRNA population of sequences, more than 98% of the reads began with a uracil. It has been demonstrated that Argonuate proteins recruit small RNAs based on the 5′ terminal nucleotide: AGO2 and AGO4 recruit small RNAs with 5′ terminal adenosine, whereas AGO1 and AGO5 recruit small RNAs with a 5′ terminal uracil and cytosine, respectively [33], [34], [35]. We identified 82 predicted miRNAs with at least one raw sequence read in one of the four libraries (Table S2). miRNAs were considered for further analysis if there were at least 12 raw sequence reads and at least a two-fold change between the F. oxysporum-infected and control plant libraries. Based on these criteria, we identified 18 unique miRNA sequences corresponding to plant disease resistance, stress responses, transcription factors, and others (Fig. 1B). Notably, among all of the regulated miRNAs identified, miR403 and miR398 are associated with disease resistance in other plant species [36], [37]. miR398 is also implicated in the regulatory network for additional abiotic stresses, including salinity, water deficit, oxidative stress, high levels of abscisic acid, ultraviolet light, copper and phosphate deficiency and high sucrose [11], [38], [39], [40], [41], [42], [43], [44]. In contrast to the other regulated miRNAs, functions for miR5300 have not been previously reported in any plant species, including tomato.


MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum.

Ouyang S, Park G, Atamian HS, Han CS, Stajich JE, Kaloshian I, Borkovich KA - PLoS Pathog. (2014)

Properties of miRNAs expressed in resistant and susceptible tomato cultivars treated with water or the fungal pathogen Fusarium oxysporum.In total, four small RNA libraries were subjected to deep sequencing: susceptible tomato cultivar Moneymaker treated with water; Moneymaker treated with Fusarium oxysporum f. sp. lycopersici (F. oxysporum); resistant tomato cultivar Motelle treated with water and Motelle treated with F. oxysporum. The sequence length of small RNAs (A) for the combined data from the four libraries was determined as described in the Materials and Methods. Relative expression levels of known miRNAs (B) were determined by dividing normalized reads for F. oxysporum treatment by those for water treatment for each cultivar. The red bracket indicates the miRNAs that were negatively regulated in Motelle, but not Moneymaker, after F. oxysporum infection. Putative roles/targets of miRNAs in various plant species (information from miRBase.org): miR156, miR156c, miR156kj and miR157d: Squamosa-promoter Binding Protein (SBP)-like transcription factors; miR166glmf: HD-Zip transcription factors, including Phabulosa (PHB) and Phavoluta (PHV) that regulate axillary meristem initiation and leaf development; miR167b, miR167d and miR167fijeghac: Auxin Response Factors (ARF transcription factors); miR396abcd: Growth Regulating Factor (GRF) transcription factors, rhodenase-like proteins, and kinesin-like protein B; miR394ab, F-box proteins; miR827abc: Unknown; miR403bdf: Virus defense; miR162 and miR162abc: Unknown; miR530: Unknown; miR398abc: copper superoxide dismutases and cytochrome C oxidase subunit V; miR482f: NB domain proteins; miR5300, Unknown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4199772&req=5

ppat-1004464-g001: Properties of miRNAs expressed in resistant and susceptible tomato cultivars treated with water or the fungal pathogen Fusarium oxysporum.In total, four small RNA libraries were subjected to deep sequencing: susceptible tomato cultivar Moneymaker treated with water; Moneymaker treated with Fusarium oxysporum f. sp. lycopersici (F. oxysporum); resistant tomato cultivar Motelle treated with water and Motelle treated with F. oxysporum. The sequence length of small RNAs (A) for the combined data from the four libraries was determined as described in the Materials and Methods. Relative expression levels of known miRNAs (B) were determined by dividing normalized reads for F. oxysporum treatment by those for water treatment for each cultivar. The red bracket indicates the miRNAs that were negatively regulated in Motelle, but not Moneymaker, after F. oxysporum infection. Putative roles/targets of miRNAs in various plant species (information from miRBase.org): miR156, miR156c, miR156kj and miR157d: Squamosa-promoter Binding Protein (SBP)-like transcription factors; miR166glmf: HD-Zip transcription factors, including Phabulosa (PHB) and Phavoluta (PHV) that regulate axillary meristem initiation and leaf development; miR167b, miR167d and miR167fijeghac: Auxin Response Factors (ARF transcription factors); miR396abcd: Growth Regulating Factor (GRF) transcription factors, rhodenase-like proteins, and kinesin-like protein B; miR394ab, F-box proteins; miR827abc: Unknown; miR403bdf: Virus defense; miR162 and miR162abc: Unknown; miR530: Unknown; miR398abc: copper superoxide dismutases and cytochrome C oxidase subunit V; miR482f: NB domain proteins; miR5300, Unknown.
Mentions: Using Illumina sequencing, we obtained a total of more than 27 million high quality small RNA sequences from the four libraries that could be mapped to the tomato genome. Of these, 5,743,067 were from MM_H2O, 5,492,955 from MM_Foxy, 4,392,583 from Mot_H2O and 5,497,730 from Mot_Foxy (Table S1). Among all size classes, 24-, 21- and 22-nt small RNA species were the three most abundant (Fig. 1A). These sizes are similar to those previously identified in tomato [22], [23]. Within the miRNA population of sequences, more than 98% of the reads began with a uracil. It has been demonstrated that Argonuate proteins recruit small RNAs based on the 5′ terminal nucleotide: AGO2 and AGO4 recruit small RNAs with 5′ terminal adenosine, whereas AGO1 and AGO5 recruit small RNAs with a 5′ terminal uracil and cytosine, respectively [33], [34], [35]. We identified 82 predicted miRNAs with at least one raw sequence read in one of the four libraries (Table S2). miRNAs were considered for further analysis if there were at least 12 raw sequence reads and at least a two-fold change between the F. oxysporum-infected and control plant libraries. Based on these criteria, we identified 18 unique miRNA sequences corresponding to plant disease resistance, stress responses, transcription factors, and others (Fig. 1B). Notably, among all of the regulated miRNAs identified, miR403 and miR398 are associated with disease resistance in other plant species [36], [37]. miR398 is also implicated in the regulatory network for additional abiotic stresses, including salinity, water deficit, oxidative stress, high levels of abscisic acid, ultraviolet light, copper and phosphate deficiency and high sucrose [11], [38], [39], [40], [41], [42], [43], [44]. In contrast to the other regulated miRNAs, functions for miR5300 have not been previously reported in any plant species, including tomato.

Bottom Line: One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen.The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response.Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.

ABSTRACT
MicroRNAs (miRNAs) suppress the transcriptional and post-transcriptional expression of genes in plants. Several miRNA families target genes encoding nucleotide-binding site-leucine-rich repeat (NB-LRR) plant innate immune receptors. The fungus Fusarium oxysporum f. sp. lycopersici causes vascular wilt disease in tomato. We explored a role for miRNAs in tomato defense against F. oxysporum using comparative miRNA profiling of susceptible (Moneymaker) and resistant (Motelle) tomato cultivars. slmiR482f and slmiR5300 were repressed during infection of Motelle with F. oxysporum. Two predicted mRNA targets each of slmiR482f and slmiR5300 exhibited increased expression in Motelle and the ability of these four targets to be regulated by the miRNAs was confirmed by co-expression in Nicotiana benthamiana. Silencing of the targets in the resistant Motelle cultivar revealed a role in fungal resistance for all four genes. All four targets encode proteins with full or partial nucleotide-binding (NB) domains. One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen. The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs.

Show MeSH
Related in: MedlinePlus