cDNAs encoding spinach stromal and thylakoid‐bound ascorbate peroxidase, differing in the presence or absence of their 3′‐coding regions

Ishikawa, Takahiro; Sakai, Kosuke; Yoshimura, Kazuya; Takeda, Toru; Shigeoka, Shigeru

doi:10.1016/0014-5793(96)00332-8

Cited by 79 publications

(59 citation statements)

References 23 publications

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“…This alternative splicing is regulated by light, and the alternative splice site is 17 bp downstream of the predicted intron donor site. In spinach (Spinacia oleracea), there are two cDNA clones encoding stromal and thylakoid-bound ascorbate peroxidase isoenzymes (Ishikawa et al, 1996), which are produced by alternative splicing of two 3Ј-terminal exons (Ishikawa et al, 1997). In cauliflower (Brassica oleracea), a truncated SRK protein is specifically expressed in stigmata and translated from one of several transcripts, which are generated by a combination of alternative splicing and the use of alternative polyadenylation signals (Giranton et al, 1995).…”

Section: Analysis Of the Full-length Cdna Sequencesmentioning

confidence: 99%

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

Xiao¹,

Malik²,

Whitelaw³

et al. 2002

Plant Physiology

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About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein homologs from other species or expressed sequence matches from Arabidopsis. These are referred to as "hypothetical genes." On chromosome 2, sequenced by The Institute for Genomic Research, there are approximately 800 hypothetical genes among a total of approximately 4,100 genes. To test their expression under various growth conditions and in specific tissues, we used six cDNA populations prepared from cold-treated, heat-treated, and pathogen (Xanthomonas campestris pv campestris)-infected plants, callus, roots, and young seedlings. To date, 169 hypothetical genes were tested, and 138 of them are found to be expressed in one or more of the six cDNA populations. By sequencing multiple clones from each 5Ј-and 3Ј-rapid amplification of cDNA ends (RACE) product and assembling the sequences, we generated full-length sequences for 16 of these genes. For 14 genes, there was one full-length assembly that precisely supported the intron-exon boundaries of their gene predictions, adding only 5Ј-and 3Ј-untranslated region sequences. However, for three of these genes, the other assemblies represent additional exons and alternatively spliced or unspliced introns. For the remaining two genes, the cDNA sequences reveal major differences with predicted gene structures. In addition, a total of six genes displayed more than one polyadenylation site. These data will be used to update gene models in The Institute for Genomic Research annotation database ATH1.With the combined efforts of scientists from Europe, Japan, and the United States, the first higher plant genome-sequencing project, whole-genome sequencing of Arabidopsis has been completed. The sequences of chromosome 2 and 4 were first released in 1999 (Lin et al., 1999;Mayer et al., 1999), and the remaining three chromosomes were sequenced by the end of 2000 (Salanoubat et al., 2000;Tabata et al., 2000;Theologis et al., 2000). This provides scientists a wealth of information and knowledge with which to understand plant biology from a genomic perspective. The whole Arabidopsis genome encodes approximately 25,000 genes (The Arabidopsis Genome Initiative, 2000) and the functional analysis of these genes is a major challenge in this post-sequencing era. One approach to this, taken by several groups (Ceres, Stanford Genome Center, Salk Institute, Plant Gene Expression Center [in collaboration with RIKEN Genomic Sciences Center], and Institut National de la Recherche Agronomique/Genoplante) is to produce full-length cDNAs for all of the 25,000ϩ genes in the Arabidopsis genome, because these complete sequences are essential to fully understand their structure and function (Seki et al., 2001a(Seki et al., , 2001b. Recent comparison of full-length cDNAs from Ceres and SSP with previous genomic annotation revealed that the structures of about one-third of the genes could be improved based on c...

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Section: Analysis Of the Full-length Cdna Sequencesmentioning

confidence: 99%

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

Xiao¹,

Malik²,

Whitelaw³

et al. 2002

Plant Physiology

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“…RT-PCR and 5Ј/3ЈRACE-To amplify a chlAPX-specific partial cDNA fragment from tobacco, degenerate oligonucleotide primers (sense, 5Ј-TGGCA(C/T)GATGC(C/T)GG(A/T)ACTTA-3Ј; antisense, 5Ј-(C/T)-TCAT(A/C/G/T)GAATC(C/T)GA(A/C/T)AGCTC-3Ј) were designed from the common region of the amino acid sequences of tAPX and sAPX from higher plants described previously (4,13). RT-PCR was carried out with poly(A) ϩ RNA isolated from tobacco leaves as described previously (14).…”

Section: Methodsmentioning

confidence: 99%

“…We have previously demonstrated that, in spinach sAPX, the N-terminal 364 amino acids encoding the transit peptide and the catalytic domains are completely identical with those of tAPX, except for the Cterminal 50 amino acids, and that chloroplastic APX (chlAPX) isoenzymes, which are encoded by a single gene (ApxII), are produced by the alternative splicing of the 3Ј-terminal region of ApxII pre-mRNA in spinach (4,5). The ApxII contained 13 exons split by 12 introns.…”

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confidence: 99%

Identification of a cis Element for Tissue-specific Alternative Splicing of Chloroplast Ascorbate Peroxidase Pre-mRNA in Higher Plants

Yoshimura

Yabuta

Ishikawa

et al. 2002

Journal of Biological Chemistry

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Alternative splicing events in the 3-terminal region of chloroplast ascorbate peroxidase (chlAPX) pre-mRNA in spinach and tobacco, which produced four types of mRNA variants, one form (tAPX-I) encoding thylakoidbound APX (tAPX) and three forms (sAPX-I, -II, and -III) encoding stromal APX (sAPX), were regulated in a tissue-specific manner. The ratio of the level of sAPX mRNAs (sAPX-I, -II, and -III) to tAPX-I mRNA was close to 1 in leaf, whereas the ratio in root was greatly elevated due to an increase in sAPX-III and a decrease in tAPX-I resulting from the alternative excision of intron 11 and intron 12, respectively. A putative splicing regulatory cis element (SRE), which is highly conserved in the sequences of chlAPX genes of higher plants, was identified upstream of the acceptor site in intron 12. The deletion of the SRE sequence diminished the splicing efficiency of intron 12 in tobacco leaf in vivo. Gel-shift analysis showed that SRE interacts strongly with a nuclear protein from leaves but not those from the roots of spinach and tobacco. These results indicate that the tissue-specific alternative splicing of chlAPX pre-mRNA is regulated by the splicing enhancer SRE.

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“…sAPX and tAPX are encoded by a single gene in spinach, pumpkin, and tobacco plants, and this gene generates both isoenzymes by alternative splicing. 3,21,[86][87][88][89] Alternative splicing occurs in the 3′-terminal region of chlAPX pre-mRNA and is regulated in a tissue-specific manner. The ratio of sAPX mRNA to tAPX mRNA was found to be close to 1 in leaves, and was markedly elevated in roots.…”

Section: )mentioning

confidence: 99%

Cellular redox regulation, signaling, and stress response in plants

Shigeoka

Maruta

2014

Bioscience, Biotechnology, and Biochemistry

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Cellular and organellar redox states, which are characterized by the balance between oxidant and antioxidant pool sizes, play signaling roles in the regulation of gene expression and protein function in a wide variety of plant physiological processes including stress acclimation. Reactive oxygen species (ROS) and ascorbic acid (AsA) are the most abundant oxidants and antioxidants, respectively, in plant cells; therefore, the metabolism of these redox compounds must be strictly and spatiotemporally controlled. In this review, we provided an overview of our previous studies as well as recent advances in (1) the molecular mechanisms and regulation of AsA biosynthesis, (2) the molecular and genetic properties of ascorbate peroxidases, and (3) stress acclimation via ROS-derived oxidative/redox signaling pathways, and discussed future perspectives in this field.

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cDNAs encoding spinach stromal and thylakoid‐bound ascorbate peroxidase, differing in the presence or absence of their 3′‐coding regions

Cited by 79 publications

References 23 publications

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

Identification of a cis Element for Tissue-specific Alternative Splicing of Chloroplast Ascorbate Peroxidase Pre-mRNA in Higher Plants

Cellular redox regulation, signaling, and stress response in plants

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