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1.
L. D. Gottlieb R. C. Higgins 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1984,68(4):369-373
Summary The apparent molecular weight of cytosolic phosphoglucose isomerase (PGI) subunits was evaluated in 18 species of Clarkia which have or do not have duplicated genes specifying this glycolytic enzyme. Species that lack the duplication had subunits of 59,000 or 60,400 whereas species with the duplication generally possessed two types of PGI subunits with these or closely similar molecular weights. The additive pattern in the species with the duplication suggests that the molecular weight divergence preceded the origin of the duplication, and that the duplication arose following hybridization between taxa that represented different lineages within Clarkia. 相似文献
2.
We recently reported an 868-bp plastid DNA minicircle, NICE1, that formed during transformation in a transplastomic Nicotiana tabacum line. Shuttle plasmids containing NICEI sequences were maintained extrachromosomally in plastids and shown to undergo recombination with NICE1 sequences on the plastid genome. To prove the general utility of the shuttle plasmids, we tested whether plastid genes outside the NICE1 region could be rescued in Escherichia coli. The NICE1-based rescue plasmid, pNICER1, carries NICE1 sequences for maintenance in plastids, the CoIE1 ori for maintenance in E. coli and a spectinomcyin resistance gene (aadA) for selection in both systems. In addition, pNICERl carries a defective kanamycin resistance gene, kan*, to target the rescue of a functional kanamycin resistance gene, kan, from the recipient plastid genome. pNICERl was introduced into plastids where recombination could occur between the homologous kan/kan* sequences, and subsequently rescued in E. coli to recover the products of recombination. Based on the expression of kanamycin resistance in E. coli and the analysis of three restriction fragment polymorphisms, recombinant kan genes were recovered at a high frequency. Efficient rescue of kan from the plastid genome in E. coli indicates that NICE 1-based plasmids are suitable for rescuing mutations from any part of the plastid genome, expanding the repertoire of genetic tools available for plastid biology. 相似文献
3.
Goldring A. Zamir D. Degani Ch. 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1985,71(3):491-494
Summary Avocado (Persea americana) cultivars were assayed for phosphoglucose isomerase (PGI) isozymes using starch gel electrophoresis. Three PGI genes were identified: one monomorphic locus, Pgi-I, coding for the plastid isozyme and two independently assorting loci, Pgi-2 and Pgi-3, coding for the cytosolic isozymes. The genetic analysis was based on comparisons of PGI zymograms from somatic and pollen tissue and on Mendelian analysis of progeny from selfed trees. The isozymic variability for PGI can be used for cultivar identification and for differentiating between hybrid and selfed progeny in avocado breeding. 相似文献
4.
Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses 总被引:11,自引:0,他引:11
Huang S Sirikhachornkit A Faris JD Su X Gill BS Haselkorn R Gornicki P 《Plant molecular biology》2002,48(5-6):805-820
We have applied a two-gene system based on the sequences of nuclear genes encoding multi-domain plastid acetyl-CoA carboxylase (ACCase) and plastid 3-phosphoglycerate kinase (PGK) to study grass evolution. Our analysis revealed that these genes are single-copy in most of the grass species studied, allowing the establishment of orthologous relationships between them. These relationships are consistent with the known facts of their evolution: the eukaryotic origin of the plastid ACCase, created by duplication of a gene encoding the cytosolic multi-domain ACCase gene early in grass evolution, and the prokaryotic (endosymbiont) origin of the plastid PGK. The major phylogenetic relationships among grasses deduced from the nucleotide sequence comparisons of ACCase and PGK genes are consistent with each other and with the milestones of grass evolution revealed by other methods. Nucleotide substitution rates were calculated based on multiple pairwise sequence comparisons. On a relative basis, with the divergence of the Pooideae and Panicoideae subfamilies set at 60 million years ago (MYA), events leading to the Triticum/Aegilops complex occurred at the following intervals: divergence of Lolium (Lolium rigidum) at 35 MYA, divergence of Hordeum (Hordeum vulgare) at 11 MYA and divergence of Secale (Secale cereale) at 7 MYA. On the same scale, gene duplication leading to the multi-domain plastid ACCase in grasses occurred at 129 MYA, divergence of grass and dicot plastid PGK genes at 137 MYA, and divergence of grass and dicot cytosolic PGK genes at 155 MYA. The ACCase and PGK genes provide a well-understood two-locus system to study grass phylogeny, evolution and systematics. 相似文献
5.
We have cloned and sequenced an area of about 9.0 kb of the plastid DNA (ptDNA) from the holoparasitic flowering plant Cuscuta reflexa to investigate the evolutionary response of plastid genes to a reduced selective pressure. The region contains genes for the 16S rRNA, a subunit of a plastid NAD(P)H dehydrogenase (ndhB), three transfer RNAs (trnA, trnI, trnV) as well as the gene coding for the ribosomal protein S7 (rps7). While the other genes are strongly conserved in C. reflexa, the ndhB gene is a pseudogene due to many frameshift mutations. In addition we used heterologous gene probes to identify the other ndh genes encoded by the plastid genome in higher plants. No hybridization signals could be obtained, suggesting that these genes are either lost or strongly altered in the ptDNA of C. reflexa. Together with evidence of deleted genes in the ptDNA of C. reflexa, the plastid genome can be grouped into four classes reflecting a different evolutionary rate in each case. The phylogenetic position of Cuscuta and the significance of ndh genes in the plastid genome of higher plants are discussed. 相似文献
6.
Daniel J. Crawford Edwin B. Smith Marvin L. Roberts Maryan Benkowski Melinda Hoffman 《American journal of botany》1990,77(1):54-63
Enzyme electrophoresis was employed to ascertain the number of loci encoding plastid phosphoglucose isomerase (PGI) in species representing all sections of North American Coreopsis. Several species from each of the closely related genera Bidens, Coreocarpus, Cosmos, and Thelesperma were also examined. Species in nine of the 11 sections of North American Coreopsis have two isozymes for plastid PGI, and nearly all species examined in the four other genera also have two (one species has three) isozymes. Since most diploid vascular plants have one plastid PGI isozyme, a gene duplication probably occurred in an ancestor that is common to Coreopsis and the other four genera. That is, two isozymes represent the ancestral number for Coreopsis. The two sections (Electra and Anathysana) apparently lacking the duplication are closely related woody plants restricted largely to Mexico. One gene encoding plastid PGI ostensibly was silenced in a common ancestor of these two sections. This is concordant with other data suggesting a close relationship between the two sections, i.e., they appear to represent a monophyletic group. The electrophoretic data also indicate that 1) the enigmatic monotypic section Silphidium is more closely related to eastern North American sections and not derived from section Electra; and 2) section Anathysana is not ancestral to the three California sections Leptosyne, Pugiopappus, and Tuckermannia; rather, it represents a terminal element closely related to and possibly derived from section Electra. 相似文献
7.
Sugey Ramona Sinagawa-García Tarinee Tungsuchat-Huang Octavio Paredes-López Pal Maliga 《Plant molecular biology》2009,70(5):487-498
Plastid transformation vectors are E. coli plasmids carrying a plastid marker gene for selection, adjacent cloning sites and flanking plastid DNA to target insertions
in the plastid genome by homologous recombination. We report here on a family of next generation plastid vectors carrying
synthetic DNA vector arms targeting insertions in the rbcL-accD intergenic region of the tobacco (Nicotiana tabacum) plastid genome. The pSS22 plasmid carries only synthetic vector arms from which the undesirable restriction sites have been
removed by point mutations. The pSS24 vector carries a c-Myc tagged spectinomycin resistance (aadA) marker gene whereas in vector pSS30 aadA is flanked with loxP sequences for post-transformation marker excision. The synthetic vectors will enable direct manipulation of passenger genes
in the transformation vector targeting insertions in the rbcL-accD intergenic region that contains many commonly used restriction sites.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
8.
Codon Usage in Plastid Genes Is Correlated with Context, Position Within the Gene, and Amino Acid Content 总被引:5,自引:0,他引:5
Highly expressed plastid genes display codon adaptation, which is defined as a bias toward a set of codons which are complementary
to abundant tRNAs. This type of adaptation is similar to what is observed in highly expressed Escherichia coli genes and is probably the result of selection to increase translation efficiency. In the current work, the codon adaptation
of plastid genes is studied with regard to three specific features that have been observed in E. coli and which may influence translation efficiency. These features are (1) a relatively low codon adaptation at the 5′ end of
highly expressed genes, (2) an influence of neighboring codons on codon usage at a particular site (codon context), and (3)
a correlation between the level of codon adaptation of a gene and its amino acid content. All three features are found in
plastid genes. First, highly expressed plastid genes have a noticeable decrease in codon adaptation over the first 10–20 codons.
Second, for the twofold degenerate NNY codon groups, highly expressed genes have an overall bias toward the NNC codon, but
this is not observed when the 3′ neighboring base is a G. At these sites highly expressed genes are biased toward NNT instead
of NNC. Third, plastid genes that have higher codon adaptations also tend to have an increased usage of amino acids with a
high G + C content at the first two codon positions and GNN codons in particular. The correlation between codon adaptation
and amino acid content exists separately for both cytosolic and membrane proteins and is not related to any obvious functional
property. It is suggested that at certain sites selection discriminates between nonsynonymous codons based on translational,
not functional, differences, with the result that the amino acid sequence of highly expressed proteins is partially influenced
by selection for increased translation efficiency.
Received: 21 July 1999 / Accepted: 5 November 1999 相似文献
9.
The plastid genomes of higher plants contain eleven reading frames (ndhA-K) that are homologous to genes encoding subunits of the mitochondrial NADH-ubiquinone-oxidoreductase (complex I). The carboxyterminal end of the NDH-H subunit from rice (Oryza sativa L.) was expressed as a fusion protein in Escherichia coli and antibodies against the fusion protein were generated in rabbits. The antibody was used to study the expression of NDH-H, and the following results were obtained: (i) NDH-H is expressed in mono- and dicotyledonous plants, (ii) NDH-H is localized on the stroma lamellae of the thylakoid membrane and (iii) NDH-H is expressed in etioplasts. Together with the finding that two other ndh genes (ndhI and ndhK) are expressed in plastids, these results point to the existence of an NAD(P)H-plastoquinone-oxidoreductase on the thylakoid membrane. The possible function of the enzyme in plastids is discussed and it is suggested that it works in balancing the ATP/ADP and the NADPH/NADP ratios during changing external (i.e. light) or internal (i.e. ATP and NADPH demands of biosynthetic pathways of the plastid) conditions.Abbreviations PVDF
polyvinylidene difluoride
- SDS
sodium dodecyl sulfate
We thank Professor M. Sugiura for the rice plastid DNA clone bank, Oliver Buchholz for Sorghum plastid membranes, Pioneer Hi-Bred Inc. for maize and Sorghum seeds and the Deutsche Forschungsgemeinschaft for financial support (SFB189). 相似文献
10.
We recently reported an 868-bp plastid DNA minicircle, NICE1, that formed during transformation in a transplastomic Nicotiana tabacum line. Shuttle plasmids containing NICEI sequences were maintained extrachromosomally in plastids and shown to undergo recombination with NICE1 sequences on the plastid genome. To prove the general utility of the shuttle plasmids, we tested whether plastid genes outside the NICE1 region could be rescued in Escherichia coli. The NICE1-based rescue plasmid, pNICER1, carries NICE1 sequences for maintenance in plastids, the CoIE1 ori for maintenance in E. coli and a spectinomcyin resistance gene (aadA) for selection in both systems. In addition, pNICERl carries a defective kanamycin resistance gene, kan*, to target the rescue of a functional kanamycin resistance gene, kan, from the recipient plastid genome. pNICERl was introduced into plastids where recombination could occur between the homologous kan/kan* sequences, and subsequently rescued in E. coli to recover the products of recombination. Based on the expression of kanamycin resistance in E. coli and the analysis of three restriction fragment polymorphisms, recombinant kan genes were recovered at a high frequency. Efficient rescue of kan from the plastid genome in E. coli indicates that NICE 1-based plasmids are suitable for rescuing mutations from any part of the plastid genome, expanding the repertoire of genetic tools available for plastid biology. 相似文献
11.
The structural gene locus specifying subunits of the cytoplasmic isozymes of phosphoglucose isomerase (PGI) is present in duplicate in many diploid species of Clarkia (Onagraceae), a genus of annual plants native to California. We studied the kinetic properties and molecular weights of a large number of genetically defined and highly purified PGIs in C. xantiana, a species with the duplication, as a means of examining the biochemical consequences of the evolution of a new gene locus. This species is primarily outcrossing, but also includes several previously described predominantly self-pollinating populations. Both cytoplasmic PGI loci in the outcrossing populations are polymorphic and their enzyme products are readily separated by electrophoresis. The PGIs from the outcrossing populations were generally closely similar in molecular weight, pH optimum, heat sensitivity, energy of activation, and apparent K
m
(fructose-6-phosphate). The PGI loci in the selfing populations are monomorphic and specify enzymes having identical electrophoretic mobilities to those coded by the most frequent alleles of the outcrosser. The PGI isozymes in the selfers differed fivefold in K
m
, suggesting that they have a very different catalytic effectiveness. The high K
m
of the PGI-3A isozyme (1.1mm) was anomalous among the examined and would likely be disadvantageous in a species which lacked other more normally functioning PGIs. But in the cytoplasm of the selfing plants, it is present with other PGIs that have low K
m
values. The PGI-3A enzyme is a good candidate for a gene product coded by a forbidden mutation that could not have been established in the absence of the duplication. The rationale for this suggestion is described and it is also pointed out that the divergence of duplicated genes is influenced by many factors such as the breeding system and other population factors as well as the effect of particular mutations.This research was supported by NSF Grant DEB77-08448. 相似文献
12.
Hagopian JC Reis M Kitajima JP Bhattacharya D de Oliveira MC 《Journal of molecular evolution》2004,59(4):464-477
We sequenced to completion the circular plastid genome of the red alga Gracilaria tenuistipitata var. liui. This is the first plastid genome sequence from the subclass Florideophycidae (Rhodophyta). The genome is composed of 183,883 bp and contains 238 predicted genes, including a single copy of the ribosomal RNA operon. Comparisons with the plastid genome of Porphyra pupurea reveal strong conservation of gene content and order, but we found major genomic rearrangements and the presence of coding regions that are specific to Gracilaria. Phylogenetic analysis of a data set of 41 concatenated proteins from 23 plastid and two cyanobacterial genomes support red algal plastid monophyly and a specific evolutionary relationship between the Florideophycidae and the Bangiales. Gracilaria maintains a surprisingly ancient gene content in its plastid genome and, together with other Rhodophyta, contains the most complete repertoire of plastid genes known in photosynthetic eukaryotes.Supplementary material () is available for this article.[Reviewing Editor: Dr. W. Ford Doolittle] 相似文献
13.
14.
Pairwise comparison of whole plastid and draft nuclear genomic sequences of Arabidopsis thaliana and Oryza sativa L. ssp. indica shows that rice nuclear genomic sequences contain homologs of plastid DNA covering about 94 kb (83%) of plastid genome and including one or more full-length intact (without mutations resulting in premature stop codons) homologues of 26 known protein-coding (KPC) plastid genes. By contrast, only about 20 kb (16%) of chloroplast DNA, including a single intact plastid-derived KPC gene, is presented in the nucleus of A. thaliana. Sixteen rice plastid genes have at least one nuclear copy without any mutation or with only synonymous substitutions. Nuclear copies for other ten plastid genes contain both synonymous and non-synonymous substitutions. Multiple ESTs for 25 out of 26 KPC genes were also found, as well as putative promoters for some of them. The study of substitutions pattern shows that some of nuclear homologues of plastid genes may be functional and/or are under the pressure of the positive natural selection. The similar comparative analysis performed on rice chromosome 1 revealed 27 contigs containing plastid-derived sequences, totalling about 84 kb and covering two thirds of chloroplast DNA, with the intact nuclear copies of 26 different KPC genes. One of these contigs, AP003280, includes almost 57 kb (45%) of chloroplast genome with the intact copies of 22 KPC genes. At the same time, we observed that relative locations of homologues in plastid DNA and the nuclear genome are significantly different. 相似文献
15.
Aurora M. Nedelcu 《Journal of molecular evolution》2001,53(6):670-679
This study provides a phylogenetic/comparative approach to deciphering the processes underlying the evolution of plastid
rRNA genes in genomes under relaxed functional constraints. Nonphotosynthetic green algal taxa that belong to two distinct
classes, Chlorophyceae (Polytoma) and Trebouxiophyceae (Prototheca), were investigated. Similar to the situation described previously for plastid 16S rRNA genes in nonphotosynthetic land plants,
nucleotide substitution levels, extent of structural variations, and percentage AT values are increased in nonphotosynthetic
green algae compared to their closest photosynthetic relatives. However, the mutational processes appear to be different in
many respects. First, with the increase in AT content, more transversions are noted in Polytoma and holoparasite angiosperms, while more transitions characterize the evolution of the 16S rDNA sequences in Prototheca. Second, although structural variations do accumulate in both Polytoma and Prototheca (as well as holoparasitic plastid 16S rRNAs), insertions as large as 1.6 kb characterize the plastid 16S rRNA genes in the
former, whereas significantly smaller indels (not exceeding 24 bp) seem to be more prevalent in the latter group. The differences
in evolutionary rates and patterns within and between lineages might be due to mutations in replication/repair-related genes;
slipped-strand mispairing is likely the mechanism responsible for the expansion of insertions in Polytoma plastid 16S rRNA genes.
Received: 29 December 2000 / Accepted: 18 May 2001 相似文献
16.
Marker genes are essential for selective amplification of rare transformed plastid genome copies to obtain genetically stable
transplastomic plants. However, the marker gene becomes dispensable when homoplastomic plants are obtained. Here we report
excision of plastid marker genes by the phiC31 phage site-specific integrase (Int) that mediates recombination between bacterial
(attB) and phage (attP) attachment sites. We tested marker gene excision in a two-step process. First we transformed the tobacco plastid genome
with the pCK2 vector in which the spectinomycin resistance (aadA) marker gene is flanked with suitably oriented attB and attP sites. The transformed plastid genomes were stable in the absence of Int. We then transformed the nucleus with a gene encoding
a plastid-targeted Int that led to efficient marker gene excision. The aadA marker free Nt-pCK2-Int plants were resistant to phosphinothricin herbicides since the pCK2 plastid vector also carried a
bar herbicide resistance gene that, due to the choice of its promoter, causes a yellowish-golden (aurea) phenotype. Int-mediated
marker excision reported here is an alternative to the currently used CRE/loxP plastid marker excision system and expands the repertoire of the tools available for the manipulation of the plastid genome. 相似文献
17.
Fates of Evolutionarily Distinct,Plastid‐type Glyceraldehyde 3‐phosphate Dehydrogenase Genes in Kareniacean Dinoflagellates
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Ryoma Kamikawa Euki Yazaki Michiru Tahara Takaya Sakura Eriko Matsuo Kisaburo Nagamune Tetsuo Hashimoto Yuji Inagaki 《The Journal of eukaryotic microbiology》2018,65(5):669-678
The ancestral kareniacean dinoflagellate has undergone tertiary endosymbiosis, in which the original plastid is replaced by a haptophyte endosymbiont. During this plastid replacement, the endosymbiont genes were most likely flowed into the host dinoflagellate genome (endosymbiotic gene transfer or EGT). Such EGT may have generated the redundancy of functionally homologous genes in the host genome—one has resided in the host genome prior to the haptophyte endosymbiosis, while the other transferred from the endosymbiont genome. However, it remains to be well understood how evolutionarily distinct but functionally homologous genes were dealt in the dinoflagellate genomes bearing haptophyte‐derived plastids. To model the gene evolution after EGT in plastid replacement, we here compared the characteristics of the two evolutionally distinct genes encoding plastid‐type glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) in Karenia brevis and K. mikimotoi bearing haptophyte‐derived tertiary plastids: “gapC1h” acquired from the haptophyte endosymbiont and “gapC1p” inherited from the ancestral dinoflagellate. Our experiments consistently and clearly demonstrated that, in the two species examined, the principal plastid‐type GAPDH is encoded by gapC1h rather than gapC1p. We here propose an evolutionary scheme resolving the EGT‐derived redundancy of genes involved in plastid function and maintenance in the nuclear genomes of dinoflagellates that have undergone plastid replacements. Although K. brevis and K. mikimotoi are closely related to each other, the statuses of the two evolutionarily distinct gapC1 genes in the two Karenia species correspond to different steps in the proposed scheme. 相似文献
18.
Stable transformation of petunia plastids 总被引:11,自引:0,他引:11
Plastid transformation results in stably expressed foreign genes, which for most Angiosperms are largely excluded from sperm cells, thereby greatly reducing the risk of foreign gene spread through pollen. Prior to this work, fertile plastid transformants were restricted to tobacco, tomato and Lesquerella . Application of plastid engineering in the important floriculture industry requires the development of stable plastid transformation in a major ornamental plant species such as Petunia hybrida. Here we describe the successful isolation of fertile and stable plastid transformants in a commercial cultivar of P. hybrida (var. Pink Wave). Plastid targeting regions from tobacco were used to integrate aad A and gusA between the acc D and rbc L genes of P. hybrida plastid DNA following particle bombardment of leaves. For three spectinomycin and streptomycin resistant lines, DNA blot analysis confirmed transgene integration into plastid DNA and homoplasmy. Maternal inheritance and homoplasmy resulted in 100 transmission of spectinomycin resistance to progeny after selfing. Plastid transformants expressed the gusA gene uniformly within leaves and to comparable levels in all three lines. Insertion of trait genes in place of gusA coding sequences enables immediate applications of our plastid transformation vector. Establishment of plastid transformation in P. hybrida facilitates a safe and reliable use of this important ornamental plant for research and plant biotechnology.These two authors contributed equally to this work. 相似文献
19.