Gene_locus Report for: arath-clh2

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

The Arabidopsis gene ATHCOR1, which encodes the CORI1 (coronatine-induced) protein, was expressed in bacterial cells. Soluble recombinant CORI1 was purified and shown to possess chlorophyllase (Chlase) activity in vitro. To determine its activity in vivo, wild-type Arabidopsis and coi1 mutant, which lacks ATHCOR1 transcripts, were transformed with sense and antisense forms of the gene. Wild-type and coi1 plants overexpressing ATHCOR1 showed increased contents of chlorophyllide (Chlide) without a substantial change in the total amount of the extractable chlorophyll (Chl). These plants presented high Chlide to Chl ratios in leaves, whereas antisense plants and nontransformed coi1 mutant showed undetectable ATHCOR1 mRNA and significantly lower Chlide to Chl ratios, relative to wild-type control. Overexpression of ATHCOR1 caused an increased breakdown of Chl a, as revealed by the Chlide a to b ratio, which was significantly higher in sense than wild-type, coi1 mutant, and antisense plants. This preferential activity of CORI1 toward Chl a was further supported by in vitro analyses using the purified protein. Increased Chlase activity was detected in developing flowers, which correlated to the constitutive expression of ATHCOR1 in this organ. Flowers of the antisense plant showed reduced Chlide to Chl ratio, suggesting a role of CORI1 in Chl breakdown during flower senescence. The results show that ATHCOR1 has Chlase activity in vivo, however, because coi1 flowers have no detectable ATHCOR1 mRNA and present Chlide to Chl ratios comparable with the wild type, an additional Chlase is likely to be active in Arabidopsis. In accordance, transcripts of a second Arabidopsis Chlase gene, AtCLH2, were detected in both normal and mutant flowers.

Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyzes the hydrolysis of ester bond to yield chlorophyllide and phytol. In the present study, we isolated the Chlase cDNA. We synthesized degenerate oligo DNA probes based on the internal amino acid sequences of purified Chlase from Chenopodium album, screened the C. album cDNA library, and cloned a cDNA (CaCLH, C. album chlorophyll-chlorophyllido hydrolase). The deduced amino acid sequence (347 aa residues) had a lipase motif overlapping with an ATP/GTP-binding motif (P-loop). CaCLH possibly was localized in the extraplastidic part of the cell, because a putative signal sequence for endoplasmic reticulum is at the N terminus. The amino acid sequence shared 37% identity with a function-unknown gene whose mRNA is inducible by coronatine and methyl jasmonate (MeJA) in Arabidopsis thaliana (AtCLH1). We expressed the gene products of AtCLH1 and of CaCLH in Escherichia coli, and they similarly exhibited Chlase activity. Moreover, we isolated another full-length cDNA based on an Arabidopsis genomic fragment and expressed it in E. coli, demonstrating the presence of the second Arabidopsis CLH gene (AtCLH2). No typical feature of signal sequence was identified in AtCLH1, whereas AtCLH2 had a typical signal sequence for chloroplast. AtCLH1 mRNA was induced rapidly by a treatment of MeJA, which is known to promote senescence and Chl degradation in plants, and a high mRNA level was maintained up to 9 h. AtCLH2, however, did not respond to MeJA.

We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3x dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis.

One important reaction of chlorophyll (chl) breakdown during plant senescence is the removal of the lipophilic phytol moiety by chlorophyllase. AtCLH1 and AtCLH2 were considered to be required for this reaction in Arabidopsis thaliana. Here we present evidence against this assumption. Using green fluorescent protein fusions, neither AtCLH isoform localizes to chloroplasts, the predicted site of chlorophyll breakdown. Furthermore, clh1 and clh2 single and double knockout lines are still able to degrade chlorophyll during senescence. From our data we conclude that AtCLHs are not required for senescence-related chlorophyll breakdown in vivo and propose that genuine chlorophyllase has not yet been molecularly identified.

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

The Arabidopsis gene ATHCOR1, which encodes the CORI1 (coronatine-induced) protein, was expressed in bacterial cells. Soluble recombinant CORI1 was purified and shown to possess chlorophyllase (Chlase) activity in vitro. To determine its activity in vivo, wild-type Arabidopsis and coi1 mutant, which lacks ATHCOR1 transcripts, were transformed with sense and antisense forms of the gene. Wild-type and coi1 plants overexpressing ATHCOR1 showed increased contents of chlorophyllide (Chlide) without a substantial change in the total amount of the extractable chlorophyll (Chl). These plants presented high Chlide to Chl ratios in leaves, whereas antisense plants and nontransformed coi1 mutant showed undetectable ATHCOR1 mRNA and significantly lower Chlide to Chl ratios, relative to wild-type control. Overexpression of ATHCOR1 caused an increased breakdown of Chl a, as revealed by the Chlide a to b ratio, which was significantly higher in sense than wild-type, coi1 mutant, and antisense plants. This preferential activity of CORI1 toward Chl a was further supported by in vitro analyses using the purified protein. Increased Chlase activity was detected in developing flowers, which correlated to the constitutive expression of ATHCOR1 in this organ. Flowers of the antisense plant showed reduced Chlide to Chl ratio, suggesting a role of CORI1 in Chl breakdown during flower senescence. The results show that ATHCOR1 has Chlase activity in vivo, however, because coi1 flowers have no detectable ATHCOR1 mRNA and present Chlide to Chl ratios comparable with the wild type, an additional Chlase is likely to be active in Arabidopsis. In accordance, transcripts of a second Arabidopsis Chlase gene, AtCLH2, were detected in both normal and mutant flowers.

Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyzes the hydrolysis of ester bond to yield chlorophyllide and phytol. In the present study, we isolated the Chlase cDNA. We synthesized degenerate oligo DNA probes based on the internal amino acid sequences of purified Chlase from Chenopodium album, screened the C. album cDNA library, and cloned a cDNA (CaCLH, C. album chlorophyll-chlorophyllido hydrolase). The deduced amino acid sequence (347 aa residues) had a lipase motif overlapping with an ATP/GTP-binding motif (P-loop). CaCLH possibly was localized in the extraplastidic part of the cell, because a putative signal sequence for endoplasmic reticulum is at the N terminus. The amino acid sequence shared 37% identity with a function-unknown gene whose mRNA is inducible by coronatine and methyl jasmonate (MeJA) in Arabidopsis thaliana (AtCLH1). We expressed the gene products of AtCLH1 and of CaCLH in Escherichia coli, and they similarly exhibited Chlase activity. Moreover, we isolated another full-length cDNA based on an Arabidopsis genomic fragment and expressed it in E. coli, demonstrating the presence of the second Arabidopsis CLH gene (AtCLH2). No typical feature of signal sequence was identified in AtCLH1, whereas AtCLH2 had a typical signal sequence for chloroplast. AtCLH1 mRNA was induced rapidly by a treatment of MeJA, which is known to promote senescence and Chl degradation in plants, and a high mRNA level was maintained up to 9 h. AtCLH2, however, did not respond to MeJA.