The chloroplast genome

Sugiura, Masahiro

doi:10.1007/bf00015612

Cited by 593 publications

(374 citation statements)

References 124 publications

(109 reference statements)

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“…The gene content and sequence of the Z. latifolia cp genome are relatively conserved, with many characteristics in common with land plant cp genomes (Sugiura, 1992;Raubeson and Jansen, 2005). It encodes 130 predicted protein-coding genes; 110 are unique and 20 are duplicated in the IR regions.…”

Section: Resultsmentioning

confidence: 99%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

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Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and non-coding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.

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Section: Resultsmentioning

confidence: 99%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

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“…At least a few of the enzymes involved in this pathway and their genes have been identified in cyanobacteria, such as Plectonema boryanum (Fujita et al, 1991), in green algae, such as Chlamydomonas reinhardtii (Roitgrund and Mets, 1990;Suzuki and Bauer, 1992), in conifers, such as pine (Lidholm and Gustafsson, 1991), and in liverwort Ohyama et al, 1988;., 1989). One of the genes studied in detail is the algal chlL (Suzuki and Bauer, 1992) and its counterpart in the plastid genome of liverwort, frxC (Sugiura, 1992). A similarfrxc locus has also been suggested to occur in the plastid DNA of conifers (Lidholm and Gustafsson, 1991) but it appears to be absent from the plastid DNAs from tobacco and rice (Sugiura, 1992).…”

Section: This Review)mentioning

confidence: 99%

“…One of the genes studied in detail is the algal chlL (Suzuki and Bauer, 1992) and its counterpart in the plastid genome of liverwort, frxC (Sugiura, 1992). A similarfrxc locus has also been suggested to occur in the plastid DNA of conifers (Lidholm and Gustafsson, 1991) but it appears to be absent from the plastid DNAs from tobacco and rice (Sugiura, 1992). All chlL (fyxc) genes studied thus far encode proteins that are related to the bchL gene product of R. capsulatus, which is involved in the synthesis of bacteriochlorophyll a.…”

Section: This Review)mentioning

confidence: 99%

The Regulation of Enzymes Involved in Chlorophyll Biosynthesis

Reinbothe

1996

European Journal of Biochemistry

126

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All living organisms contain tetrapyrroles. In plants, chlorophyll (chlorophyll a plus chlorophyll b) is the most abundant and probably most important tetrapyrrole. It is involved in light absorption and energy transduction during photosynthesis. Chlorophyll is synthesized from the intact carbon skeleton of glutamate via the C, pathway. This pathway takes place in the chloroplast. It is the aim of this review to summarize the current knowledge on the biochemistry and molecular biology of the C,-pathway enzymes, their regulated expression in response to light, and the impact of chlorophyll biosynthesis on chloroplast development. Particular emphasis will be placed on the key regulatory steps of chlorophyll biosynthesis in higher plants, such as 5-aminolevulinic acid formation, the production of Mg*+-protoporphyrin IX, and light-dependent protochlorophyllide reduction.

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“…Sequencing of different chloroplastic higher plant genomes has revealed the existence of a set of genes showing significant homologies with genes coding for subunits of the mitochondrial NADH dehydrogenase complex [1,2]. These chloroplastic genes, named ndh, have been shown to be transcribed [3] and the polypeptide products of three of them (NDH H, NDH I and NDH K) have been found in thylakoid membranes [4,5,6].…”

Section: Introductionmentioning

confidence: 99%

Evidence for an association of ndh B, ndh J gene products and ferredoxin‐NADP‐reductase as components of a chloroplastic NAD(P)H dehydrogenase complex

et al. 1996

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Using non-denaturing gel electrophoresis and staining with nitro-blue tetrazolium, we reveal the presence of two NAD(P)H oxidoreductase activity bands within thylakoids membranes of Solanum tuberosum L. Second dimension SDS-PAGE and Western analysis show that one of the activity bands contains several polypeptides, two of them being recognized by antibodies directed against peptides corresponding to conserved domains of chloroplastic genes products NDH B and NDH J (at 32 and 18 kDa, respectively). Both activity bands also contain a polypeptide (around 36 kDa) recognized by an antibody directed against ferredoxin-NADP+-reductase (FNR). We conclude from these results that both chloroplastic ndh B and ndh J gene products are components of a thylakoid NAD(P)H dehydrogenase complex. The association with FNR is suggested to allow the complex to use NADPH instead of NADH as a preferential substrate.

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The chloroplast genome

Cited by 593 publications

References 124 publications

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

The Regulation of Enzymes Involved in Chlorophyll Biosynthesis

Evidence for an association of ndh B, ndh J gene products and ferredoxin‐NADP‐reductase as components of a chloroplastic NAD(P)H dehydrogenase complex

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