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Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis.

Tan X, Meyers BC, Kozik A, West MA, Morgante M, St Clair DA, Bent AF, Michelmore RW - BMC Plant Biol. (2007)

Bottom Line: Evidence for alternative splicing was found for at least 12 genes, 11 of which encode TIR-NBS-LRR proteins.Most were present at low levels and exhibited tissue-specific expression patterns.Expression data are consistent with most Arabidopsis NBS-LRR-encoding and related genes functioning in plant defense responses but do not preclude other biological roles.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Genome Center, University of California, Davis, California 95616, USA. xpitan@ucdavis.edu

ABSTRACT

Background: Nucleotide binding site-leucine rich repeat (NBS-LRR)-encoding genes comprise the largest class of plant disease resistance genes. The 149 NBS-LRR-encoding genes and the 58 related genes that do not encode LRRs represent approximately 0.8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes.

Results: We analyzed the expression patterns of approximately 170 NBS-LRR-encoding and related genes in Arabidopsis Col-0 using multiple analytical approaches: expressed sequenced tag (EST) representation, massively parallel signature sequencing (MPSS), microarray analysis, rapid amplification of cDNA ends (RACE) PCR, and gene trap lines. Most of these genes were expressed at low levels with a variety of tissue specificities. Expression was detected by at least one approach for all but 10 of these genes. The expression of some but not the majority of NBS-LRR-encoding and related genes was affected by salicylic acid (SA) treatment; the response to SA varied among different accessions. An analysis of previously published microarray data indicated that ten NBS-LRR-encoding and related genes exhibited increased expression in wild-type Landsberg erecta (Ler) after flagellin treatment. Several of these ten genes also showed altered expression after SA treatment, consistent with the regulation of R gene expression during defense responses and overlap between the basal defense response and salicylic acid signaling pathways. Enhancer trap analysis indicated that neither jasmonic acid nor benzothiadiazole (BTH), a salicylic acid analog, induced detectable expression of the five NBS-LRR-encoding genes and one TIR-NBS-encoding gene tested; however, BTH did induce detectable expression of the other TIR-NBS-encoding gene analyzed. Evidence for alternative mRNA polyadenylation sites was observed for many of the tested genes. Evidence for alternative splicing was found for at least 12 genes, 11 of which encode TIR-NBS-LRR proteins. There was no obvious correlation between expression pattern, phylogenetic relationship or genomic location of the NBS-LRR-encoding and related genes studied.

Conclusion: Transcripts of many NBS-LRR-encoding and related genes were defined. Most were present at low levels and exhibited tissue-specific expression patterns. Expression data are consistent with most Arabidopsis NBS-LRR-encoding and related genes functioning in plant defense responses but do not preclude other biological roles.

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The expression level of 162 NBS-LRR-encoding and related genes in five different tissues of Arabidopsis wild-type Col-0. All NBS-LRR-encoding and related genes are ordered according to their At numbers along the X axis. Each Arabidopsis chromosome is indicated below each graph. Y-axis indicates the relative expression level of each probe set after scaling the mean intensity of each ATH1 microarray to 500.
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Figure 1: The expression level of 162 NBS-LRR-encoding and related genes in five different tissues of Arabidopsis wild-type Col-0. All NBS-LRR-encoding and related genes are ordered according to their At numbers along the X axis. Each Arabidopsis chromosome is indicated below each graph. Y-axis indicates the relative expression level of each probe set after scaling the mean intensity of each ATH1 microarray to 500.

Mentions: Five of the mRNA samples that were used to generate the Arabidopsis MPSS libraries described above (LEF, CAF, INF, ROF, and SIF MPSS libraries; [75-77]) were also analyzed using ATH1 arrays to cross-validate the two approaches. The expression patterns of the NBS-LRR-encoding and related genes detected in the microarray experiment were generally consistent with the MPSS data (Table 2; Additional file 1). These 162 genes showed different expression levels in different tissues. For example, both the MPSS data and Affymetrix array data indicated that At4g16990 has its highest expression in leaf, lower expression in flowers and siliques, and its lowest expression in callus and root. Most genes were usually the most highly expressed in callus; expression levels in flowers and siliques were similar (Figure 1). Forty-six of the 67 genes with undetectable levels of expression in the leaf sample in the microarray analysis had 0 MPSS tags in the leaf MPSS library (LEF), while 75 of the 95 genes detected by microarray analysis had more than one tag in the MPSS leaf library. For 88 NBS-LRR-encoding and related genes which are represented by unique MPSS tags and probe sets on the ATH1 array, Spearman rank correlation test showed a good correlation between MPSS data and Affymetrix array data generated from the same leaf tissue (correlation coefficient 0.74357, P-value < 0.001).


Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis.

Tan X, Meyers BC, Kozik A, West MA, Morgante M, St Clair DA, Bent AF, Michelmore RW - BMC Plant Biol. (2007)

The expression level of 162 NBS-LRR-encoding and related genes in five different tissues of Arabidopsis wild-type Col-0. All NBS-LRR-encoding and related genes are ordered according to their At numbers along the X axis. Each Arabidopsis chromosome is indicated below each graph. Y-axis indicates the relative expression level of each probe set after scaling the mean intensity of each ATH1 microarray to 500.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2175511&req=5

Figure 1: The expression level of 162 NBS-LRR-encoding and related genes in five different tissues of Arabidopsis wild-type Col-0. All NBS-LRR-encoding and related genes are ordered according to their At numbers along the X axis. Each Arabidopsis chromosome is indicated below each graph. Y-axis indicates the relative expression level of each probe set after scaling the mean intensity of each ATH1 microarray to 500.
Mentions: Five of the mRNA samples that were used to generate the Arabidopsis MPSS libraries described above (LEF, CAF, INF, ROF, and SIF MPSS libraries; [75-77]) were also analyzed using ATH1 arrays to cross-validate the two approaches. The expression patterns of the NBS-LRR-encoding and related genes detected in the microarray experiment were generally consistent with the MPSS data (Table 2; Additional file 1). These 162 genes showed different expression levels in different tissues. For example, both the MPSS data and Affymetrix array data indicated that At4g16990 has its highest expression in leaf, lower expression in flowers and siliques, and its lowest expression in callus and root. Most genes were usually the most highly expressed in callus; expression levels in flowers and siliques were similar (Figure 1). Forty-six of the 67 genes with undetectable levels of expression in the leaf sample in the microarray analysis had 0 MPSS tags in the leaf MPSS library (LEF), while 75 of the 95 genes detected by microarray analysis had more than one tag in the MPSS leaf library. For 88 NBS-LRR-encoding and related genes which are represented by unique MPSS tags and probe sets on the ATH1 array, Spearman rank correlation test showed a good correlation between MPSS data and Affymetrix array data generated from the same leaf tissue (correlation coefficient 0.74357, P-value < 0.001).

Bottom Line: Evidence for alternative splicing was found for at least 12 genes, 11 of which encode TIR-NBS-LRR proteins.Most were present at low levels and exhibited tissue-specific expression patterns.Expression data are consistent with most Arabidopsis NBS-LRR-encoding and related genes functioning in plant defense responses but do not preclude other biological roles.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Genome Center, University of California, Davis, California 95616, USA. xpitan@ucdavis.edu

ABSTRACT

Background: Nucleotide binding site-leucine rich repeat (NBS-LRR)-encoding genes comprise the largest class of plant disease resistance genes. The 149 NBS-LRR-encoding genes and the 58 related genes that do not encode LRRs represent approximately 0.8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes.

Results: We analyzed the expression patterns of approximately 170 NBS-LRR-encoding and related genes in Arabidopsis Col-0 using multiple analytical approaches: expressed sequenced tag (EST) representation, massively parallel signature sequencing (MPSS), microarray analysis, rapid amplification of cDNA ends (RACE) PCR, and gene trap lines. Most of these genes were expressed at low levels with a variety of tissue specificities. Expression was detected by at least one approach for all but 10 of these genes. The expression of some but not the majority of NBS-LRR-encoding and related genes was affected by salicylic acid (SA) treatment; the response to SA varied among different accessions. An analysis of previously published microarray data indicated that ten NBS-LRR-encoding and related genes exhibited increased expression in wild-type Landsberg erecta (Ler) after flagellin treatment. Several of these ten genes also showed altered expression after SA treatment, consistent with the regulation of R gene expression during defense responses and overlap between the basal defense response and salicylic acid signaling pathways. Enhancer trap analysis indicated that neither jasmonic acid nor benzothiadiazole (BTH), a salicylic acid analog, induced detectable expression of the five NBS-LRR-encoding genes and one TIR-NBS-encoding gene tested; however, BTH did induce detectable expression of the other TIR-NBS-encoding gene analyzed. Evidence for alternative mRNA polyadenylation sites was observed for many of the tested genes. Evidence for alternative splicing was found for at least 12 genes, 11 of which encode TIR-NBS-LRR proteins. There was no obvious correlation between expression pattern, phylogenetic relationship or genomic location of the NBS-LRR-encoding and related genes studied.

Conclusion: Transcripts of many NBS-LRR-encoding and related genes were defined. Most were present at low levels and exhibited tissue-specific expression patterns. Expression data are consistent with most Arabidopsis NBS-LRR-encoding and related genes functioning in plant defense responses but do not preclude other biological roles.

Show MeSH
Related in: MedlinePlus