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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 distribution of TIR-NBS-LRR-encoding and related genes analyzed on neighbor-joining tree generated by Meyers et al. [7]. The genes studied by RACE are indicated by black arrows, the genes analyzed using RT-PCR are displayed in bold italic, and NBS-LRR-encoding and related genes with enhancer trap insertions are marked in bold. Other figure denotations are as described in Meyers et al. [7].
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Figure 3: The distribution of TIR-NBS-LRR-encoding and related genes analyzed on neighbor-joining tree generated by Meyers et al. [7]. The genes studied by RACE are indicated by black arrows, the genes analyzed using RT-PCR are displayed in bold italic, and NBS-LRR-encoding and related genes with enhancer trap insertions are marked in bold. Other figure denotations are as described in Meyers et al. [7].

Mentions: The Cold Spring Harbor database of flanking sequences for Arabidopsis Gene Trap lines [85] and the database of the Ds insertion lines from Singapore IMA (Institute of Molecular Agrobiology, [86]) were searched in 2002 for insertions in NBS-LRR-encoding and related genes using BLAST. Ten enhancer trap lines and three gene trap lines were identified with insertions into NBS-LRR-encoding or related genes. The insertion sites and orientations were confirmed for seven enhancer trap lines with insertions into five NBS-LRR-encoding genes and two TIR-NBS-encoding genes (Table 5, Figures 2 and 3). No gene trap lines were confirmed.


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 distribution of TIR-NBS-LRR-encoding and related genes analyzed on neighbor-joining tree generated by Meyers et al. [7]. The genes studied by RACE are indicated by black arrows, the genes analyzed using RT-PCR are displayed in bold italic, and NBS-LRR-encoding and related genes with enhancer trap insertions are marked in bold. Other figure denotations are as described in Meyers et al. [7].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The distribution of TIR-NBS-LRR-encoding and related genes analyzed on neighbor-joining tree generated by Meyers et al. [7]. The genes studied by RACE are indicated by black arrows, the genes analyzed using RT-PCR are displayed in bold italic, and NBS-LRR-encoding and related genes with enhancer trap insertions are marked in bold. Other figure denotations are as described in Meyers et al. [7].
Mentions: The Cold Spring Harbor database of flanking sequences for Arabidopsis Gene Trap lines [85] and the database of the Ds insertion lines from Singapore IMA (Institute of Molecular Agrobiology, [86]) were searched in 2002 for insertions in NBS-LRR-encoding and related genes using BLAST. Ten enhancer trap lines and three gene trap lines were identified with insertions into NBS-LRR-encoding or related genes. The insertion sites and orientations were confirmed for seven enhancer trap lines with insertions into five NBS-LRR-encoding genes and two TIR-NBS-encoding genes (Table 5, Figures 2 and 3). No gene trap lines were confirmed.

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