Pea chloroplast genes encoding a 4kDa polypeptide of photosystem I and a putative enzyme of C1 metabolism

Smith, Alison G.; Wilson, Rebecca J.; Kaethner, T. M.; Willey, David L.; Gray, John C.

doi:10.1007/bf00309603

Cited by 24 publications

(17 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As reported previously (Nagano et al 1991a;Smith et al 1991), and shown by a dot-matrix plot in Supplemental Figure S2A, P. sativum accD contains several in-frame internal repeats of up to 37 codons long. L. sativus accD has a similarly repetitive structure, but the sections of the gene that are repeated are different in the two species (Supplemental Fig.…”

Section: Rapid Evolution Of Ycf4 In Legumessupporting

confidence: 83%

“…Newly sequenced regions were completed on both strands, and all the PstI sites used for cloning were confirmed by sequencing spanning PCR fragments. At the ycf4 locus, there is a 2-bp deletion in the sequence reported by Nagano et al (1991a), relative to the sequence reported by Smith et al (1991), both of which were obtained from the same cloned 17.3-kb PstI fragment from P. sativum cv. Alaska.…”

Section: Nucleotide Sequencingmentioning

confidence: 87%

“…Five instances of gene loss from the IRLC chloroplast genomes have been discovered. As well as the aforementioned gene transfers of rpl22 and infA and substitution of rps16 (Gantt et al 1991;Millen et al 2001;Ueda et al 2008), it has been reported that that accD is completely absent from Trifolium subterraneum (subclover) cpDNA, and that ycf4 in Pisum sativum (pea) is either absent or a pseudogene (Nagano et al 1991a;Smith et al 1991;Cai et al 2008). Slot-blot hybridization experiments suggested that ycf4 and rps16 may have been lost independently multiple times in different lineages of legumes (Doyle et al 1995).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Localized hypermutation and associated gene losses in legume chloroplast genomes

Magee¹,

Aspinall²,

Rice³

et al. 2010

Genome Res.

Self Cite

221

343

View full text Add to dashboard Cite

Point mutations result from errors made during DNA replication or repair, so they are usually expected to be homogeneous across all regions of a genome. However, we have found a region of chloroplast DNA in plants related to sweetpea (Lathyrus) whose local point mutation rate is at least 20 times higher than elsewhere in the same molecule. There are very few precedents for such heterogeneity in any genome, and we suspect that the hypermutable region may be subject to an unusual process such as repeated DNA breakage and repair. The region is 1.5 kb long and coincides with a gene, ycf4, whose rate of evolution has increased dramatically. The product of ycf4, a photosystem I assembly protein, is more divergent within the single genus Lathyrus than between cyanobacteria and other angiosperms. Moreover, ycf4 has been lost from the chloroplast genome in Lathyrus odoratus and separately in three other groups of legumes. Each of the four consecutive genes ycf4-psaI-accD-rps16 has been lost in at least one member of the legume ''inverted repeat loss'' clade, despite the rarity of chloroplast gene losses in angiosperms. We established that accD has relocated to the nucleus in Trifolium species, but were unable to find nuclear copies of ycf4 or psaI in Lathyrus. Our results suggest that, as well as accelerating sequence evolution, localized hypermutation has contributed to the phenomenon of gene loss or relocation to the nucleus.

show abstract

Section: Rapid Evolution Of Ycf4 In Legumessupporting

confidence: 83%

Section: Nucleotide Sequencingmentioning

confidence: 87%

mentioning

confidence: 99%

See 1 more Smart Citation

Localized hypermutation and associated gene losses in legume chloroplast genomes

Magee¹,

Aspinall²,

Rice³

et al. 2010

Genome Res.

Self Cite

221

343

View full text Add to dashboard Cite

show abstract

“…chll (frxC) and chlN are apparently located on the chloroplast genome of all plants except angiosperms, although chll also appears to be absent from the chloroplast genome of the fern Psilotum nudum (Suzuki and Bauer, 1992). accD, which was previously identified in pea chloroplast DNA as zpfA (Sasaki et al, 1989, but see Smith et al, 1991) on the basis of a single zinc finger motif (also as M. polymorpha ORF 316 [Ohyama et al, 19861 and tobacco ORF 512 [Shinozaki et al, 1986]), is homologous to E. colidedB (usg), which has recently been shown to encode the p subunit of acetyl-coenzyme A carboxylase carboxytransferase . In addition, two proteins involved in nitrogen assimilation, glutamate synthase (GOGAT), encoded by glt6, and a protein involved in the regulation of both the activity and transcription of glutamine synthetase (encoded by glnB), are encoded on the I ?…”

Section: Biosynthesis Genesmentioning

confidence: 97%

A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea.

1993

View full text Add to dashboard Cite

Extensive DNA sequencing of the chloroplast genome of the red alga Porphyra purpurea has resulted in the detection of more than 125 genes. Fifty-eight (approximately 46%) of these genes are not found on the chloroplast genomes of land plants. These include genes encoding 17 photosynthetic proteins, three tRNAs, and nine ribosomal proteins. In addition, nine genes encoding proteins related to biosynthetic functions, six genes encoding proteins involved in gene expression, and at least five genes encoding miscellaneous proteins are among those not known to be located on land plant chloroplast genomes. The increased coding capacity of the P. purpurea chloroplast genome, along with other characteristics such as the absence of introns and the consenration of ancestral operons, demonstrate the primitive nature of the f . purpurea chloroplast genome. In addition, evidence for a monophyletic origin of chloroplasts is suggested by the identification of two groups of genes that are clustered in chloroplast genomes but not in cyanobacteria. INTRODUCTIONThe complete DNA sequences of three photosynthetic land plant chloroplast genomes have revealed an enormous amount of functional and evolutionary information. The chloroplast genomes of tobacco (Shinozaki et al., 1986), rice (Hiratsuka et al., 1989), and the liverwort Marchantia polymorpha (Ohyama et al., 1986) have each been shown to contain 110 to 118 genes. The products of these genes are primarily involved in two processes: gene expresssion (59 to 60 genes) and photosynthesis (29 genes). In addition, 11 genes encoding subunits of NADPH dehydrogenase (Arizmendi et al., 1992) as well as a number of conserved open reading frames (ORFs) are contained on these genomes. The gene content of all land plant chloroplast genomes investigated is surprisingly conserved (for review, see Palmer, 1991).Alga1 chloroplast genomes, on the other hand, have not been so extensively characterized. Current information on the chloroplast genomes of chlorophyll a/b-containing algae suggest that their gene content is not too different from that of land plants, although a few genes that are absent from land plant chloroplast genomes (e.g., tufA in several species [Baldauf et al., 19901, rpl5 [Christopher and Hallick, 19891, and ccsA [Orsat et al., 19921 in Euglena gracilis) have been identified. Of greater significance, however, may be the observation of substantial genome rearrangements in green alga1 chloroplast genomes in the form of the splitting up of ancestral operons in several species of Chlamydomonas (e.g., Woessner et al., 1987) and the large number of introns, including introns within introns, To whom correspondence should be addressed. in E. gracilis (Christopher and Hallick, 1989; Copertino and Hallick, 1991). These observations are indicative of chloroplast genomes that are evolving under more relaxed constraints than land plant chloroplast genomes. lnformation about the gene content of chloroplast genomes from chromophyte (chlorophyll a/c-containing) and rhodophyte/glaucophyte (c...

show abstract

“…This gene has also been lost in the genus Adonis in the Ranunculaceae based on filter hybridization data (Johansson, 1999). The loss of ycf4 (formerly called ORF184) has been documented in Pisum (Nagano et al, 1991;Smith et al, 1991) and it is lacking in three (Cicer, Glycine, and Medicago) of the five completely sequenced legume plastid genomes. An earlier survey of the phylogenetic distribution of this loss among 392 legume genera based on filter hybridization screens with ycf4 gene-specific probes indicated at least 15 independent losses within tribe Phaseoleae alone .…”

Section: Phylogenetic Distribution Of Chloroplast Genomic Rearrangemementioning

confidence: 99%

Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)

Jansen

Wojciechowski

Elumalai

et al. 2008

Molecular Phylogenetics and Evolution

187

200

View full text Add to dashboard Cite

Chickpea (Cicer arietinum, Leguminosae), an important grain legume, is widely used for food and fodder throughout the world. We sequenced the complete plastid genome of chickpea, which is 125,319 bp in size, and contains only one copy of the inverted repeat (IR). The genome encodes 108 genes, including 4 rRNAs, 29 tRNAs, and 75 proteins. The genes rps16, infA, and ycf4 are absent in the chickpea plastid genome, and ndhB has an internal stop codon in the 5′exon, similar to other legumes. Two genes have lost their introns, one in the 3′exon of the transpliced gene rps12, and the one between exons 1 and 2 of clpP; this represents the first documented case of the loss of introns from both of these genes in the same plastid genome. An extensive phylogenetic survey of these intron losses was performed on 302 taxa across legumes and the related family Polygalaceae. The clpP intron has been lost exclusively in taxa from the temperate "IR-lacking clade" (IRLC), whereas the rps12 intron has been lost in most members of the IRLC (with the exception of Wisteria, Callerya, Afgekia, and certain species of Millettia, which represent the earliest diverging lineages of this clade), and in the tribe Desmodieae, which is closely related to the tribes Phaseoleae and Psoraleeae. Data provided here suggest that the loss of the rps12 intron occurred after the loss of the IR. The two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade. The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering.

show abstract

Pea chloroplast genes encoding a 4kDa polypeptide of photosystem I and a putative enzyme of C1 metabolism

Cited by 24 publications

References 54 publications

Localized hypermutation and associated gene losses in legume chloroplast genomes

Localized hypermutation and associated gene losses in legume chloroplast genomes

A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea.

Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)

Contact Info

Product

Resources

About