Characterization of the plastid-encoded carboxyltransferase subunit (accD) gene of potato

Plant Cell and Molecular Biology Research Unit, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
Molecules and Cells (Impact Factor: 2.09). 07/2004; 17(3):422-9.
Source: PubMed


The plastid accD gene encoding the carboxyltransferase b subunit of acetyl-coenzyme A carboxylase (ACCase) was cloned from potato. Potato accD (saccD) is 2487 bp in length with a 614 bp 5 cent upstream promoter region and an ORF of 1524 bp, corresponding to a polypeptide of 507 amino acids. The N-terminal region lacks recognizable motifs, while the C-terminal regions contains five motifs. Among these is motif II, PLIIVCASGGARMQE, the sole motif present in all available accD sequences of plants and animals, and of E. coli, suggesting that this motif may correspond to the catalytic site. saccD has the typical prokaryotic promoter signatures, TTGACA and TATCAA, which are -35 and -10-like sequences for plastid-encoded RNA polymerase (PEP), at positions -184 and -160, respectively. However, it seems to be transcribed by the nucleus-encoded RNA polymerase because it is expressed in tuber and root, and in the dark (under crippled PEP conditions) and its transcription initiation sites do not correspond to those of PEP. saccD is expressed in all potato tissues, i.e., leaf, stem, root, and tuber, and its transcript is produced at a similar rate in the light and dark, at different developmental stages, and during growth in the presence of different sugars and carbon sources. Taken together, our results suggest that potato accD is a housekeeping gene constitutively expressed in both chloroplast and amyloplast.

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Available from: Jae-Wook Bang, Oct 04, 2015
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    • "Interestingly, the reading frame in the accD genes has been conserved, suggesting that the genes are functional. In the potato plastid accD, three functionally relevant sites were identified: a putative acetyl-CoA binding site, a CoA-carboxylation catalytic site and a carboxybiotin-binding site.24 Each of the sites is clustered at the C-terminus of the protein, and they are conserved in all M. truncatula accessions (Fig. 5). "
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    ABSTRACT: We fully sequenced four and partially sequenced six additional plastid genomes of the model legume Medicago truncatula. Three accessions, Jemalong 2HA, Borung and Paraggio, belong to ssp. truncatula, and R108 to ssp. tricycla. We report here that the R108 ptDNA has a ∼45-kb inversion compared with the ptDNA in ssp. truncatula, mediated by a short, imperfect repeat. DNA gel blot analyses of seven additional ssp. tricycla accessions detected only one of the two alternative genome arrangements, represented by three and four accessions each. Furthermore, we found a variable number of repeats in the essential accD and ycf1 coding regions. The repeats within accD are recombinationally active, yielding variable-length insertions and deletions in the central part of the coding region. The length of ACCD was distinct in each of the 10 sequenced ecotypes, ranging between 650 and 796 amino acids. The repeats in the ycf1 coding region are also recombinationally active, yielding short indels in 10 regions of the reading frames. Thus, the plastid genome variability we report here could be linked to repeat-mediated genome rearrangements. However, the rate of recombination was sufficiently low, so that no heterogeneity of ptDNA could be observed in populations maintained by single-seed descent.
    DNA Research 03/2014; 21(4). DOI:10.1093/dnares/dsu007 · 5.48 Impact Factor
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    • "While the coding sequences of T. aureum and T. grandiflorum share pairwise identity of 75.4% over their entire length (not shown), at the protein level local identity reached well into the 90% range. The C-terminal catalytic domain (PLI- IVCASGGARMQE; Lee et al., 2004) required for ACCase function is present and contained within a larger block of 80 residues with 91.3% identity between the two Trifolium species and 90.4% among the two and the Cicer arietinum pt-accD (Figure S3). Extensive searching of public genomic resources (see methods) revealed the presence of an accD open reading frame in the nuclear genomes of Medicago truncatula and Cicer arietinum. "
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    ABSTRACT: Land plant plastid genomes (plastomes) provide a tractable model for evolutionary study in that they are relatively compact and gene dense. Among the groups that display an appropriate level of variation for structural features, the inverted-repeat-lacking clade (IRLC) of papilionoid legumes presents the potential to advance general understanding of the mechanisms of genomic evolution. Here, are presented six complete plastome sequences from economically important species of the IRLC, a lineage previously represented by only five completed plastomes. A number of characters are compared across the IRLC including gene retention and divergence, synteny, repeat structure and functional gene transfer to the nucleus. The loss of clpP intron 2 was identified in one newly sequenced member of IRLC, Glycyrrhiza glabra. Using deeply sequenced nuclear transcriptomes from two species helped clarify the nature of the functional transfer of accD to the nucleus in Trifolium, which likely occurred in the lineage leading to subgenus Trifolium. Legumes are second only to cereal crops in agricultural importance based on area harvested and total production. Genetic improvement via plastid transformation of IRLC crop species is an appealing proposition. Comparative analyses of intergenic spacer regions emphasize the need for complete genome sequences for developing transformation vectors for plastid genetic engineering of legume crops.
    Plant Biotechnology Journal 03/2014; 12(6). DOI:10.1111/pbi.12179 · 5.75 Impact Factor
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    • "Within the Campanulaceae, the 39 end of n-accD that corresponds to the accD carboxylase domain is highly conserved compared with the 59 end of the gene, consistent with it also encoding a functional domain in this nuclear gene. Second, the carboxyltransferase domain of the nuclear protein maintains the " PLIIVCASGGARMQE " motif that is considered to be the accD putative catalytic site (Lee et al., 2004). Figure 6. "
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    ABSTRACT: Eukaryotic cells originated when an ancestor of the nucleated cell engulfed bacterial endosymbionts that gradually evolved into the mitochondrion and the chloroplast. Soon after these endosymbiotic events, thousands of ancestral prokaryotic genes were functionally transferred from the endosymbionts to the nucleus. This process of functional gene relocation, now rare in eukaryotes, continues in angiosperms. In this article, we show that the chloroplastic accD gene that is present in the plastome of most angiosperms has been functionally relocated to the nucleus in the Campanulaceae. Surprisingly, the nucleus-encoded accD transcript is considerably smaller than the plastidic version, consisting of little more than the carboxylase domain of the plastidic accD gene fused to a coding region encoding a plastid targeting peptide. We verified experimentally the presence of a chloroplastic transit peptide by showing that the product of the nuclear accD fused to GFP was imported in the chloroplasts. The nuclear gene regulatory elements that enabled the erstwhile plastidic gene to become functional in the nuclear genome were identified and the evolution of the intronic and exonic sequences in the nucleus is described. Relocation and truncation of the accD gene is a remarkable example of the processes underpinning endosymbiotic evolution.
    Plant physiology 02/2013; 161(4). DOI:10.1104/pp.113.214528 · 6.84 Impact Factor
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