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Daniell H, Wurdack KJ, Kanagaraj A, Lee SB, Saski C, Jansen RK. The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:723-37. [PMID: 18214421 PMCID: PMC2587239 DOI: 10.1007/s00122-007-0706-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Accepted: 12/20/2007] [Indexed: 05/07/2023]
Abstract
The complete sequence of the chloroplast genome of cassava (Manihot esculenta, Euphorbiaceae) has been determined. The genome is 161,453 bp in length and includes a pair of inverted repeats (IR) of 26,954 bp. The genome includes 128 genes; 96 are single copy and 16 are duplicated in the IR. There are four rRNA genes and 30 distinct tRNAs, seven of which are duplicated in the IR. The infA gene is absent; expansion of IRb has duplicated 62 amino acids at the 3' end of rps19 and a number of coding regions have large insertions or deletions, including insertions within the 23S rRNA gene. There are 17 intron-containing genes in cassava, 15 of which have a single intron while two (clpP, ycf3) have two introns. The usually conserved atpF group II intron is absent and this is the first report of its loss from land plant chloroplast genomes. The phylogenetic distribution of the atpF intron loss was determined by a PCR survey of 251 taxa representing 34 families of Malpighiales and 16 taxa from closely related rosids. The atpF intron is not only missing in cassava but also from closely related Euphorbiaceae and other Malpighiales, suggesting that there have been at least seven independent losses. In cassava and all other sequenced Malphigiales, atpF gene sequences showed a strong association between C-to-T substitutions at nucleotide position 92 and the loss of the intron, suggesting that recombination between an edited mRNA and the atpF gene may be a possible mechanism for the intron loss.
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Affiliation(s)
- Henry Daniell
- Department Molecular Biology and Microbiology, College of Medicine, University of Central Florida, 4000 Central Florida Blvd, Biomolecular Science Bldg # 20, Room 336, Orlando, FL 32816-2364, USA, e-mail:
| | - Kenneth J. Wurdack
- Department of Botany, Smithsonian Institution, NMNH MRC 166, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Anderson Kanagaraj
- Department Molecular Biology and Microbiology, College of Medicine, University of Central Florida, 4000 Central Florida Blvd, Biomolecular Science Bldg # 20, Room 336, Orlando, FL 32816-2364, USA, e-mail:
| | - Seung-Bum Lee
- Department Molecular Biology and Microbiology, College of Medicine, University of Central Florida, 4000 Central Florida Blvd, Biomolecular Science Bldg # 20, Room 336, Orlando, FL 32816-2364, USA, e-mail:
| | - Christopher Saski
- Clemson University Genomics Institute, Biosystems Research Complex, Clemson University, 51 New Cherry Street, Clemson, SC 29634, USA
| | - Robert K. Jansen
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
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Ahlert D, Piepenburg K, Kudla J, Bock R. Evolutionary origin of a plant mitochondrial group II intron from a reverse transcriptase/maturase-encoding ancestor. JOURNAL OF PLANT RESEARCH 2006; 119:363-71. [PMID: 16763758 DOI: 10.1007/s10265-006-0284-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 03/23/2006] [Indexed: 05/10/2023]
Abstract
Group II introns are widespread in plant cell organelles. In vivo, most if not all plant group II introns do not self-splice but require the assistance of proteinaceous splicing factors. In some cases, a splicing factor (also referred to as maturase) is encoded within the intronic sequence and produced by translation of the (excised) intron RNA. However, most present-day group II introns in plant organellar genomes do not contain open reading frames (ORFs) for splicing factors, and their excision may depend on proteins encoded by other organellar introns or splicing factors encoded in the nuclear genome. Whether or not the ancestors of all of these noncoding organellar introns originally contained ORFs for maturases is currently unknown. Here we show that a noncoding intron in the mitochondrial cox2 gene of seed plants is likely to be derived from an ancestral reverse transcriptase/maturase-encoding form. We detected remnants of maturase and reverse transcriptase sequences in the 2.7 kb cox2 intron of Ginkgo biloba, the only living species of an ancient gymnosperm lineage, suggesting that the intron originally harbored a splicing factor. This finding supports the earlier proposed hypothesis that the ancient group II introns that invaded organellar genomes were autonomous genetic entities in that they encoded the factor(s) required for their own excision and mobility.
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Affiliation(s)
- Daniela Ahlert
- Westfälische Wilhelms-Universität Münster, Institut für Biochemie und Biotechnologie der Pflanzen, Hindenburgplatz 55, 48143, Münster, Germany
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Schock I, Gregan J, Steinhauser S, Schweyen R, Brennicke A, Knoop V. A member of a novel Arabidopsis thaliana gene family of candidate Mg2+ ion transporters complements a yeast mitochondrial group II intron-splicing mutant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000. [PMID: 11115130 DOI: 10.1111/j.1365-313x.2000.00895.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Autocatalytic activity of some group II introns has been demonstrated in vitro, but helper functions such as the yeast MRS2 protein are essential for splicing in vivo. In our search for such helper factors in plants, we pursued the cloning of two Arabidopsis thaliana homologues, atmrs2-1 and atmrs2-2. Atmrs2-1, but not atmrs2-2, complements the yeast deletion mutant of mrs2, and this is congruent with the prediction of two adjacent transmembrane stretches in AtMRS2-1 and yeast MRS2 but not in AtMRS2-2. This complementation depends on fusion of the native yeast mitochondrial import sequence to atmrs2-1. A differing, non-mitochondrial, cellular targeting in Arabidopsis is supported by the analysis of green fluorescent protein fusion constructs after transient transformation into plant protoplasts. Further members of what now appears to be a family of 10 mrs2 homologues are identified in the Arabidopsis genome. Similarity searches with the PSI-BLAST algorithm in the protein database fail to identify homologues of this novel gene family in any eukaryotes other than yeasts, but do identify its distant relatedness to the corA group of bacterial magnesium transporters. In line with this observation, intramitochondrial magnesium concentrations are indeed restored to wild-type levels in the yeast mutant on complementation with atmrs2-1.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Biological Transport
- Carrier Proteins/genetics
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Exons
- Genes, Plant/genetics
- Genetic Complementation Test
- Green Fluorescent Proteins
- Introns
- Ion Channels
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Magnesium/metabolism
- Microscopy, Fluorescence
- Mitochondrial Proteins
- Molecular Sequence Data
- Multigene Family
- Mutation
- Nuclear Proteins/genetics
- Phylogeny
- Plants, Toxic
- Protoplasts/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tobacco
- Transcription, Genetic
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Affiliation(s)
- I Schock
- Department of Molecular Botany, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
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Holländer V, Kück U. Group II intron splicing in Escherichia coli: phenotypes of cis-acting mutations resemble splicing defects observed in organelle RNA processing. Nucleic Acids Res 1999; 27:2339-44. [PMID: 10325423 PMCID: PMC148800 DOI: 10.1093/nar/27.11.2339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mitochondrial group IIB intron rI1, from the green algae Scenedesmus obliquus ' LSUrRNA gene, has been introduced into the lacZ gene encoding beta-galacto-sidase. After DNA-mediated transformation of the recombinant lacZ gene into Escherichia coli, we observed correct splicing of the chimeric precursor RNA in vivo. In contrast to autocatalytic in vitro self-splicing, intron processing in vivo is independent of the growth temperature, suggesting that in E.coli, trans -acting factors are involved in group II intron splicing. Such a system would seem suitable as a model for analyzing intron processing in a prokaryotic host. In order to study further the effect of cis -mutations on intron splicing, different rI1 mutants were analyzed (with respect to their splicing activity) in E.coli. Although the phenotypes of these E. coli intron splicing mutants were identical to those which can be observed during organellar splicing of rI1, they are different to those observed in in vitro self-splicing experiments. Therefore, in both organelles and prokaryotes, it is likely that either similar splicing factors or trans -acting factors exhibiting similar functions are involved in splicing. We speculate that ubiquitous trans -acting factors, via recent horizontal transfer, have contributed to the spread of group II introns.
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Affiliation(s)
- V Holländer
- Lehrstuhl für Allgemeine Botanik, Fakultät für Biologie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Sugita M, Sugiura M. Regulation of gene expression in chloroplasts of higher plants. PLANT MOLECULAR BIOLOGY 1996; 32:315-26. [PMID: 8980485 DOI: 10.1007/bf00039388] [Citation(s) in RCA: 153] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chloroplasts contain their own genetic system which has a number of prokaryotic as well as some eukaryotic features. Most chloroplast genes of higher plants are organized in clusters and are cotranscribed as polycistronic pre-RNAs which are generally processes into many shorter overlapping RNA species, each of which accumulates of steady-state RNA levels. This indicates that posttranscriptional RNA processing of primary transcripts is an important step in the control of chloroplast gene expression. Chloroplast RNA processing steps include RNA cleavage/trimming, RNA splicing, ENA editing and RNA stabilization. Several chloroplast genes are interrupted by introns and therefore require processing for gene function. In tobacco chloroplasts, 18 genes contain introns, six for tRNA genes and 12 for protein-encoding genes. A number of specific proteins and RNA factors are believed to be involved in splicing and maturation of pre-RNAs in chloroplasts. Processing enzymes and RNA-binding proteins which could be involved in posttranscriptional steps have been identified in the last several years. Our current knowledge of the regulation of gene expression in chloroplasts of higher plants is overviewed and further studies on this matter are also considered.
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Affiliation(s)
- M Sugita
- Center for Gene Research, Nagoya University, Japan
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Rochaix JD. Post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii. PLANT MOLECULAR BIOLOGY 1996; 32:327-341. [PMID: 8980486 DOI: 10.1007/bf00039389] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The biosynthesis of the photosynthetic apparatus depends on the concerted action of the nuclear and chloroplast genetic systems. Numerous nuclear and chloroplast mutants of Chlamydomonas deficient in photosynthetic activity have been isolated and characterized. While several of these mutations alter the genes of components of the photosynthetic complexes, a large number of the mutations affect the expression of chloroplast genes involved in photosynthesis. Most of these mutations are nuclear and only affect the expression of a single chloroplast gene. The mutations examined appear to act principally at post-transcriptional steps such as RNA stability, RNA processing, cis- and trans-splicing and translation. Directed chloroplast DNA surgery through biolistic transformation has provided a powerful tool for identifying important cis elements involved in chloroplast gene expression. Insertion of chimeric genes consisting of chloroplast regulatory regions fused to reporter genes into the chloroplast genome has led to the identification of target sites of the nuclear-encoded functions affected in some of the mutants. Biochemical studies have identified a set of RNA-binding proteins that interact with the 5'-untranslated regions of plastid mRNAs. The binding activity of some of these factors appears to be modulated by light and by the growth conditions.
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Affiliation(s)
- J D Rochaix
- Department of Molecular Biology, University of Geneva, Switzerland
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