1
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Campbell SJ, Stern DB. Activation of an Endoribonuclease by Non-intein Protein Splicing. J Biol Chem 2016; 291:15911-15922. [PMID: 27311716 DOI: 10.1074/jbc.m116.727768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Indexed: 11/06/2022] Open
Abstract
The Chlamydomonas reinhardtii chloroplast-localized poly(A)-binding protein RB47 is predicted to contain a non-conserved linker (NCL) sequence flanked by highly conserved N- and C-terminal sequences, based on the corresponding cDNA. RB47 was purified from chloroplasts in association with an endoribonuclease activity; however, protein sequencing failed to detect the NCL. Furthermore, while recombinant RB47 including the NCL did not display endoribonuclease activity in vitro, versions lacking the NCL displayed strong activity. Both full-length and shorter forms of RB47 could be detected in chloroplasts, with conversion to the shorter form occurring in chloroplasts isolated from cells grown in the light. This conversion could be replicated in vitro in chloroplast extracts in a light-dependent manner, where epitope tags and protein sequencing showed that the NCL was excised from a full-length recombinant substrate, together with splicing of the flanking sequences. The requirement for endogenous factors and light differentiates this protein splicing from autocatalytic inteins, and may allow the chloroplast to regulate the activation of RB47 endoribonuclease activity. We speculate that this protein splicing activity arose to post-translationally repair proteins that had been inactivated by deleterious insertions or extensions.
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Affiliation(s)
- Stephen J Campbell
- From the Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
| | - David B Stern
- From the Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
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2
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Wang F, Johnson X, Cavaiuolo M, Bohne AV, Nickelsen J, Vallon O. Two Chlamydomonas OPR proteins stabilize chloroplast mRNAs encoding small subunits of photosystem II and cytochrome b6 f. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:861-73. [PMID: 25898982 DOI: 10.1111/tpj.12858] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/17/2015] [Accepted: 04/09/2015] [Indexed: 05/08/2023]
Abstract
In plants and algae, chloroplast gene expression is controlled by nucleus-encoded proteins that bind to mRNAs in a specific manner, stabilizing mRNAs or promoting their splicing, editing, or translation. Here, we present the characterization of two mRNA stabilization factors of the green alga Chlamydomonas reinhardtii, which both belong to the OctotricoPeptide Repeat (OPR) family. MCG1 is necessary to stabilize the petG mRNA, encoding a small subunit of the cytochrome b6 f complex, while MBI1 stabilizes the psbI mRNA, coding for a small subunit of photosystem II. In the mcg1 mutant, the small RNA footprint corresponding to the 5'-end of the petG transcript is reduced in abundance. In both cases, the absence of the small subunit perturbs assembly of the cognate complex. Whereas PetG is essential for formation of a functional cytochrome b6 f dimer, PsbI appears partly dispensable as a low level of PSII activity can still be measured in its absence. Thus, nuclear control of chloroplast gene expression is not only exerted on the major core subunits of the complexes, but also on small subunits with a single transmembrane helix. While OPR proteins have thus far been involved in translation or trans-splicing of plastid mRNAs, our results expand the potential roles of this repeat family to their stabilization.
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Affiliation(s)
- Fei Wang
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
- Biozentrum Ludwig-Maximilians-Universität München, D-82152, Planegg-Martinsried, Germany
| | - Xenie Johnson
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
| | - Marina Cavaiuolo
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
| | - Alexandra-Viola Bohne
- Biozentrum Ludwig-Maximilians-Universität München, D-82152, Planegg-Martinsried, Germany
| | - Joerg Nickelsen
- Biozentrum Ludwig-Maximilians-Universität München, D-82152, Planegg-Martinsried, Germany
| | - Olivier Vallon
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
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3
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Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, Harris EH, Stern DB. The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. THE PLANT CELL 2002; 14:2659-79. [PMID: 12417694 PMCID: PMC153795 DOI: 10.1105/tpc.006155] [Citation(s) in RCA: 296] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Accepted: 09/10/2002] [Indexed: 05/17/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular eukaryotic alga possessing a single chloroplast that is widely used as a model system for the study of photosynthetic processes. This report analyzes the surprising structural and evolutionary features of the completely sequenced 203,395-bp plastid chromosome. The genome is divided by 21.2-kb inverted repeats into two single-copy regions of approximately 80 kb and contains only 99 genes, including a full complement of tRNAs and atypical genes encoding the RNA polymerase. A remarkable feature is that >20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris appears to share this feature. The program MultiPipMaker was used to compare the genic complement of Chlamydomonas with those of other chloroplast genomes and to scan the genomes for sequence similarities and repetitive DNAs. Among the results was evidence that the SDRs were not derived from extant coding sequences, although some SDRs may have arisen from other genomic fragments. Phylogenetic reconstruction of changes in plastid genome content revealed that an accelerated rate of gene loss also characterized the Chlamydomonas/Chlorella lineage, a phenomenon that might be independent of the proliferation of SDRs. Together, our results reveal a dynamic and unusual plastid genome whose existence in a model organism will allow its features to be tested functionally.
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Affiliation(s)
- Jude E Maul
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
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4
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Hippler M, Redding K, Rochaix JD. Chlamydomonas genetics, a tool for the study of bioenergetic pathways. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1367:1-62. [PMID: 9784589 DOI: 10.1016/s0005-2728(98)00136-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- M Hippler
- Departments of Molecular Biology and Plant Biology, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva-4, Switzerland
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5
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Drapier D, Suzuki H, Levy H, Rimbault B, Kindle KL, Stern DB, Wollman FA. The chloroplast atpA gene cluster in Chlamydomonas reinhardtii. Functional analysis of a polycistronic transcription unit. PLANT PHYSIOLOGY 1998; 117:629-41. [PMID: 9625716 PMCID: PMC34983 DOI: 10.1104/pp.117.2.629] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/1997] [Accepted: 03/19/1998] [Indexed: 05/19/2023]
Abstract
Most chloroplast genes in vascular plants are organized into polycistronic transcription units, which generate a complex pattern of mono-, di-, and polycistronic transcripts. In contrast, most Chlamydomonas reinhardtii chloroplast transcripts characterized to date have been monocistronic. This paper describes the atpA gene cluster in the C. reinhardtii chloroplast genome, which includes the atpA, psbI, cemA, and atpH genes, encoding the alpha-subunit of the coupling-factor-1 (CF1) ATP synthase, a small photosystem II polypeptide, a chloroplast envelope membrane protein, and subunit III of the CF0 ATP synthase, respectively. We show that promoters precede the atpA, psbI, and atpH genes, but not the cemA gene, and that cemA mRNA is present only as part of di-, tri-, or tetracistronic transcripts. Deletions introduced into the gene cluster reveal, first, that CF1-alpha can be translated from di- or polycistronic transcripts, and, second, that substantial reductions in mRNA quantity have minimal effects on protein synthesis rates. We suggest that posttranscriptional mRNA processing is common in C. reinhardtii chloroplasts, permitting the expression of multiple genes from a single promoter.
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Affiliation(s)
- D Drapier
- Institut de Biologie Physico-Chimique, Paris, France
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6
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de Vitry C, Breyton C, Pierre Y, Popot JL. The 4-kDa nuclear-encoded PetM polypeptide of the chloroplast cytochrome b6f complex. Nucleic acid and protein sequences, targeting signals, transmembrane topology. J Biol Chem 1996; 271:10667-71. [PMID: 8631873 DOI: 10.1074/jbc.271.18.10667] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The 4-kDa subunit of cytochrome b6f complex encoded by the nuclear PetM gene in Chlamydomonas reinhardtii has been characterized. 38 of the 39 residues of the mature protein have been established by Edman degradation, a cDNA clone encoding the complete precursor has been isolated and sequenced, and a 0.6-kb transcript detected. The deduced amino acid sequence of the precursor includes an N-terminal transit peptide of 60 amino acids with stromal targeting features. Examination of the sequence suggests that PetM spans the membrane as a single transmembrane alpha-helix, which is supported by its non-extractability following dissociating treatments. When PetM and PetG, another small subunit of the b6f complex, are folded into alpha-helices, an array of identical residues becomes apparent. Proteolysis data, charge distribution, and homology with PetG are consistent with a lumenal localization of the N terminus of PetM.
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Affiliation(s)
- C de Vitry
- Service de Photosynthèse, CNRS/URA 1187, Institut de Biologie Physico-Chimique, Paris, France
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7
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Berthold DA, Schmidt CL, Malkin R. The deletion of petG in Chlamydomonas reinhardtii disrupts the cytochrome bf complex. J Biol Chem 1995; 270:29293-8. [PMID: 7493961 DOI: 10.1074/jbc.270.49.29293] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The 4-kDa protein encoded by chloroplast petG copurifies with the cytochrome bf complex of spinach and is found in a number of other photosynthetic organisms, including the eukaryotic alga Chlamydomonas reinhardtii. To determine whether petG is involved in the function or assembly of the cytochrome bf complex, the gene was cloned from C. reinhardtii, excised from the DNA fragment, and replaced with a spectinomycin resistance cassette. A petG deletion strain of C. reinhardtii was then obtained by biolistic transformation. The resulting homoplasmic petG deletion strains are unable to grow photosynthetically, and immunoblot analysis shows markedly decreased levels of cytochrome b6, cytochrome f, the Rieske iron-sulfur protein, and subunit IV. To verify that this phenotype was due to the removal of petG, we also constructed a strain with a deletion in the open reading frame (ORF56), which is found 25 base pairs downstream of petG. The ORF56 deletion strain grew photosynthetically and had wild-type levels of the four major cytochrome bf subunits. We conclude that the absence of the PetG protein affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii.
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Affiliation(s)
- D A Berthold
- Department of Plant Biology, University of California, Berkeley 94720-3102, USA
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8
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Gumpel NJ, Ralley L, Girard-Bascou J, Wollman FA, Nugent JH, Purton S. Nuclear mutants of Chlamydomonas reinhardtii defective in the biogenesis of the cytochrome b6f complex. PLANT MOLECULAR BIOLOGY 1995; 29:921-932. [PMID: 8555456 DOI: 10.1007/bf00014966] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The random integration of transforming DNA into the nuclear genome of Chlamydomonas has been employed as an insertional mutagen to generate a collection of photosynthetic mutants that display abnormal steady-state fluorescence levels and an acetate-requiring phenotype. Electron paramagnetic resonance spectroscopy was then used to identify those mutants that specifically lack a functional cytochrome b6f complex. Our analysis of RNA and protein synthesis in five of these mutants reveals four separate phenotypes. One mutant fails to accumulate transcript for cytochrome f, whilst a second displays a severely reduced accumulation of the cytochrome b6 transcript. Two other mutants appear to be affected in the insertion of the haem co-factor into cytochrome b6. The fifth mutant displays no detectable defect in the synthesis of any of the known subunits of the complex. Genetic analysis of the mutants demonstrates that in three cases, the mutant phenotype co-segregates with the introduced DNA. For the mutant affected in the accumulation of the cytochrome f transcript, we have used the introduced DNA as a tag to isolate the wild-type version of the affected gene.
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Affiliation(s)
- N J Gumpel
- Department of Biology, University College London, UK
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9
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Mor TS, Ohad I, Hirschberg J, Pakrasi HB. An unusual organization of the genes encoding cytochrome b559 in Chlamydomonas reinhardtii: psbE and psbF genes are separately transcribed from different regions of the plastid chromosome. MOLECULAR & GENERAL GENETICS : MGG 1995; 246:600-4. [PMID: 7700232 DOI: 10.1007/bf00298966] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The psbE and psbF genes encode the apoproteins of cytochrome b559, an essential component of the pigment protein complex photosystem II. Together with psbL and psbJ, these genes constitute a single operon in all photosynthetic organisms examined thus far. We have cloned and sequenced the psbE and psbF genes of the Chlamydomonas reinhardtii plastid genome. The predicted amino-terminal domains of both polypeptides are more basic than those of other organisms, and the sequence of the psbE gene product indicates a departure from the 'positive-inside' rule for the insertion of proteins in the thylakoid membrane. Northern blot analysis demonstrated that psbE is transcribed into a 0.3 kb mRNA, while transcription of psbF and psbL genes results in a 0.9 kb transcript. The splitting of the psbEFLJ operon into separate transcription units suggests a unique mechanism of regulation of expression of these genes in C. reinhardtii.
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Affiliation(s)
- T S Mor
- Department of Biological Chemistry, Hebrew University of Jerusalem, Israel
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10
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Boudreau E, Turmel M. Gene rearrangements in Chlamydomonas chloroplast DNAs are accounted for by inversions and by the expansion/contraction of the inverted repeat. PLANT MOLECULAR BIOLOGY 1995; 27:351-64. [PMID: 7888624 DOI: 10.1007/bf00020189] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
To gain insight into the mutational events responsible for the extensive variation of chloroplast DNA (cpDNA) within the green algal genus Chlamydomonas, we have investigated the chloroplast gene organization of Chlamydomonas pitschmannii, a close relative of the interfertile species C. eugametos and C. moewusii whose cpDNAs have been well characterized. At 187 kb, the circular cpDNA of C. pitschmannii is the smallest Chlamydomonas cpDNA yet reported; it is 56 and 105 kb smaller than those of its C. eugametos and C. moewusii counterparts, respectively. Despite this substantial size difference, the arrangement of 77 genes on the C. pitschmannii cpDNA displays only three noticeable differences from the organization of the corresponding genes on the collinear C. eugametos and C. moewusii cpDNAs. These changes in gene order are accounted for by the expansion/contraction of the inverted repeat and one or two inversions in a single-copy region. In land plant cpDNAs, these kinds of events are also responsible for gene rearrangements. The large size difference between the C. pitschmannii and C. eugametos/C. moewusii cpDNAs is mainly attributed to multiple events of deletions/additions as opposed to the usually observed expansion/contraction of the inverted repeat in land plant cpDNAs. We also found that the mitochondrial genome of C. pitschmannii is a circular DNA molecule of 16.5 kb which is 5.5 and 7.5 kb smaller than its C. moewusii and C. eugametos counterparts, respectively.
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Affiliation(s)
- E Boudreau
- Département de Biochimie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
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11
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Alizadeh S, Nechushtai R, Barber J, Nixon P. Nucleotide sequence of the psbE, psbF and trnM genes from the chloroplast genome of Chlamydomonas reinhardtii. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1188:439-42. [PMID: 7803458 DOI: 10.1016/0005-2728(94)90067-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have determined the nucleotide sequences of the psbE and psbF genes, which encode the alpha and beta subunits, respectively, of cytochrome b-559, from the chloroplast genome of the green alga Chlamydomonas reinhardtii. In contrast to other organisms psbE is not co-transcribed with psbF. The primary structures of the gene products are very similar to the equivalent proteins in cyanobacteria and plants. Each subunit contains a single histidine residue that is thought to ligate haem. Upstream of the psbE gene, a trnM gene is located which encodes an elongator tRNA(Met) molecule.
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Affiliation(s)
- S Alizadeh
- Wolfson Laboratories, Department of Biochemistry, Imperial College of Science, Technology and Medicine, London, UK
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12
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Abstract
Consistent with their postulated origin from endosymbiotic cyanobacteria, chloroplasts of plants and algae have ribosomes whose component RNAs and proteins are strikingly similar to those of eubacteria. Comparison of the secondary structures of 16S rRNAs of chloroplasts and bacteria has been particularly useful in identifying highly conserved regions likely to have essential functions. Comparative analysis of ribosomal protein sequences may likewise prove valuable in determining their roles in protein synthesis. This review is concerned primarily with the RNAs and proteins that constitute the chloroplast ribosome, the genes that encode these components, and their expression. It begins with an overview of chloroplast genome structure in land plants and algae and then presents a brief comparison of chloroplast and prokaryotic protein-synthesizing systems and a more detailed analysis of chloroplast rRNAs and ribosomal proteins. A description of the synthesis and assembly of chloroplast ribosomes follows. The review concludes with discussion of whether chloroplast protein synthesis is essential for cell survival.
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Affiliation(s)
- E H Harris
- DCMB Group, Department of Botany, Duke University, Durham, North Carolina 27708-1000
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13
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Turmel M, Otis C. The chloroplast gene cluster containing psbF, psbL, petG and rps3 is conserved in Chlamydomonas. Curr Genet 1994; 27:54-61. [PMID: 7750147 DOI: 10.1007/bf00326579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have sequenced a 6.8-kb segment of the Chlamydomonas eugametos chloroplast DNA which contains the psbF, psbL, petG and rps3 genes. As in the distantly related green alga Chlamydomonas reinhardtii, these genes reside in this order (5'-->3') on the same DNA strand, suggesting that such a chloroplast gene cluster was present in the most recent common ancestor of all Chlamydomonas species. For each of the four genes, with the exception of rps3, the C. eugametos and C. reinhardtii coding regions were found to be identical, or very similar, in length, whereas each of the intergenic spacers is substantially longer in C. eugametos than in C. reinhardtii. The central portion of both Chlamydomonas rps3 genes features a long extra coding region relative to other rps3 sequences. We have shown that the insertion sequence in the C. eugametos rps3 is not excised at the RNA level.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- Chlamydomonas/genetics
- Chlamydomonas reinhardtii/genetics
- Chloroplasts/genetics
- Cytochrome b Group
- DNA, Chloroplast/genetics
- DNA, Plant/genetics
- DNA, Protozoan/genetics
- Genes, Plant/genetics
- Genes, Protozoan/genetics
- Genome
- Molecular Sequence Data
- Multigene Family
- Operon
- Photosynthetic Reaction Center Complex Proteins/genetics
- Photosystem II Protein Complex
- Phylogeny
- Plant Proteins/genetics
- Proteins/genetics
- Protozoan Proteins/genetics
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Species Specificity
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Affiliation(s)
- M Turmel
- Département de biochimie, Faculté des sciences, Université Laval, Québec, Canada
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14
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The petD gene is transcribed by functionally redundant promoters in Chlamydomonas reinhardtii chloroplasts. Mol Cell Biol 1994. [PMID: 8065350 DOI: 10.1128/mcb.14.9.6171] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FUD6, a nonphotosynthetic mutant of Chlamydomonas reinhardtii, was previously found to be deficient in the synthesis of subunit IV of the cytochrome b6/f complex, the chloroplast petD gene product (C. Lemaire, J. Girard-Bascou, F.-A. Wollman, and P. Bennoun, Biochim. Biophys. Acta 851:229-238, 1986). The lesion in FUD6 is a 236-bp deletion between two 11-bp direct repeats in the chloroplast genome. It extends from 82 to 72 bp upstream of the 5' end of wild-type petD mRNA to 156 to 166 bp downstream of the 5' end. Thus, the deletion extends into the putative promoter and 5' untranslated region of petD. No petD mRNA of the normal size can be detected in FUD6 cells, but a low level of a dicistronic message accumulates, which contains the coding regions for subunit IV and cytochrome f, the product of the upstream petA gene. petD transcriptional activity in FUD6 is not significantly altered from the wild-type level. This transcriptional activity was eliminated by petA promoter disruptions, suggesting that it originates at the petA promoter. We conclude that the petD-coding portion of most cotranscripts is rapidly degraded in FUD6, possibly following processing events that generate the 3' end of petA mRNA. A chloroplast transformant was constructed in which only the sequence from -81 to -2 relative to the major 5' end of the petD transcript was deleted. Although this deletion eliminates all detectable petD promoter activity, the transformant grows phototrophically and accumulates high levels of monocistronic petD mRNA. We conclude that the petD gene can be transcribed by functionally redundant promoters. In the absence of a functional petD promoter, a lack of transcription termination allows the downstream petD gene to be cotranscribed with the petA coding region and thereby expressed efficiently.
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15
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Sturm NR, Kuras R, Büschlen S, Sakamoto W, Kindle KL, Stern DB, Wollman FA. The petD gene is transcribed by functionally redundant promoters in Chlamydomonas reinhardtii chloroplasts. Mol Cell Biol 1994; 14:6171-9. [PMID: 8065350 PMCID: PMC359144 DOI: 10.1128/mcb.14.9.6171-6179.1994] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
FUD6, a nonphotosynthetic mutant of Chlamydomonas reinhardtii, was previously found to be deficient in the synthesis of subunit IV of the cytochrome b6/f complex, the chloroplast petD gene product (C. Lemaire, J. Girard-Bascou, F.-A. Wollman, and P. Bennoun, Biochim. Biophys. Acta 851:229-238, 1986). The lesion in FUD6 is a 236-bp deletion between two 11-bp direct repeats in the chloroplast genome. It extends from 82 to 72 bp upstream of the 5' end of wild-type petD mRNA to 156 to 166 bp downstream of the 5' end. Thus, the deletion extends into the putative promoter and 5' untranslated region of petD. No petD mRNA of the normal size can be detected in FUD6 cells, but a low level of a dicistronic message accumulates, which contains the coding regions for subunit IV and cytochrome f, the product of the upstream petA gene. petD transcriptional activity in FUD6 is not significantly altered from the wild-type level. This transcriptional activity was eliminated by petA promoter disruptions, suggesting that it originates at the petA promoter. We conclude that the petD-coding portion of most cotranscripts is rapidly degraded in FUD6, possibly following processing events that generate the 3' end of petA mRNA. A chloroplast transformant was constructed in which only the sequence from -81 to -2 relative to the major 5' end of the petD transcript was deleted. Although this deletion eliminates all detectable petD promoter activity, the transformant grows phototrophically and accumulates high levels of monocistronic petD mRNA. We conclude that the petD gene can be transcribed by functionally redundant promoters. In the absence of a functional petD promoter, a lack of transcription termination allows the downstream petD gene to be cotranscribed with the petA coding region and thereby expressed efficiently.
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Affiliation(s)
- N R Sturm
- Boyce Thompson Institute for Plant Research at Cornell University, Ithaca, New York 14853
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16
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Huang C, Wang S, Chen L, Lemieux C, Otis C, Turmel M, Liu XQ. The Chlamydomonas chloroplast clpP gene contains translated large insertion sequences and is essential for cell growth. MOLECULAR & GENERAL GENETICS : MGG 1994; 244:151-9. [PMID: 8052234 DOI: 10.1007/bf00283516] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sequence determination of the chloroplast clpP gene from two distantly related Chlamydomonas species (C. reinhardtii and C. eugametos) revealed the presence of translated large insertion sequences (IS1 and IS2) that divide the clpP gene into two or three sequence domains (SDs) and are not found in homologous genes in other organisms. These insertion sequences do not resemble RNA introns, and are not spliced out at the mRNA level. Instead, each insertion sequence forms a continuous open reading frame with its upstream and downstream sequence domains. IS1 specifies a potential polypeptide sequence of 286 and 318 amino acid residues in C. reinhardtii and C. eugametos, respectively. IS2 encodes a 456 amino acid polypeptide and is present only in C. eugametos. The two Chlamydomonas IS1 sequences show substantial similarity; however, there is no significant sequence similarity either between IS1 and IS2 or between these insertion sequences and any other known protein coding sequences. The C. reinhardtii clpP gene was further shown to be essential for cell growth, as demonstrated through targeted gene disruption by particle gun-mediated chloroplast transformation. Only heteroplasmic transformants could be obtained, even under mixotrophic growth conditions. The heteroplasmic transformants were stable only under selection pressure for the disrupted clpP, rapidly segregated into wild-type cells when the selection pressure was removed, and grew significantly more slowly than wild-type cells under phototrophic conditions.
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Affiliation(s)
- C Huang
- Department of Biochemistry, Dalhouise University, Halifax, Nova Scotia, Canada
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17
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de Vitry C. Characterization of the gene of the chloroplast Rieske iron-sulfur protein in Chlamydomonas reinhardtii. Indications for an uncleaved lumen targeting sequence. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37330-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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18
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Boudreau E, Otis C, Turmel M. Conserved gene clusters in the highly rearranged chloroplast genomes of Chlamydomonas moewusii and Chlamydomonas reinhardtii. PLANT MOLECULAR BIOLOGY 1994; 24:585-602. [PMID: 8155879 DOI: 10.1007/bf00023556] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We have extended to about 75 the number of genes mapped on the Chlamydomonas moewusii and Chlamydomonas reinhardtii chloroplast DNAs (cpDNAs) by partial sequencing of the very closely related C. eugametos and C. moewusii cpDNAs and by hybridizations with Chlamydomonas chloroplast gene-specific sequences. Only four of these genes (tscA and three reading frames) have not been identified in any other algal cpDNAs and thus may be specific to Chlamydomonas. Although the C. moewusii and C. reinhardtii cpDNAs differ by complex sequence rearrangements, 38 genes scattered throughout the genome define 12 conserved clusters of closely linked loci. Aside from the rRNA operon, four of these gene clusters share similarity to evolutionarily primitive operons found in other cpDNAs, representing in fact remnants of these operons. Our results thus indicate that most of the ancestral bacterial operons that characterize the chloroplast genome organization of land plants and early-diverging photosynthetic eukaryotes have been disrupted before the emergence of the polyphyletic genus Chlamydomonas. All gene rearrangements between the C. moewusii and C. reinhardtii cpDNAs, with the exception of those accounting for the relocations of atpA, psbI and rbcL, occurred within corresponding regions of the genome. One of these rearrangements seems to have led to disruption of the ancestral region containing rpl23, rpl2, rps19, rpl16, rpl14, rpl5, rps8 and the psaA exon 1. This gene cluster, which bears striking similarity to the Escherichia coli S10 and spc operons, spans a continuous DNA segment in C. reinhardtii, while it maps to two separate fragments in C. moewusii.
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Affiliation(s)
- E Boudreau
- Département de biochimie, Faculté des sciences et de génie, Université Laval, Québec, Canada
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Liu XQ, Huang C, Xu H. The unusual rps3-like orf712 is functionally essential and structurally conserved in Chlamydomonas. FEBS Lett 1993; 336:225-30. [PMID: 8262234 DOI: 10.1016/0014-5793(93)80808-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Chlamydomonas reinhardtii chloroplast orf712 is a previously described open reading frame that lacks a detectable transcript but potentially encodes a polypeptide with sequence similarities to ribosomal protein Rps3 only at its N- and C-termini. Here we report that orf712 is an essential gene, as demonstrated through gene disruption by particle gun-mediated chloroplast transformation. We also show that an orf712 is present and structurally conserved in all of the two or three major Chlamydomonas lineages. Our results suggest that orf712 is an unusual rps3 gene that contains a large translated intervening sequence.
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Affiliation(s)
- X Q Liu
- Biochemistry Department, Dalhousie University, Halifax, Nova Scotia, Canada
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20
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Schmidt CL, Malkin R. Low molecular weight subunits associated with the cytochrome b 6 f complexes from spinach and Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 1993; 38:73-81. [PMID: 24317832 DOI: 10.1007/bf00015063] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/1993] [Accepted: 08/08/1993] [Indexed: 06/02/2023]
Abstract
Cytochrome b 6 f complexes, prepared from spinach and Chlamydomonas thylakoids, have been examined for their content of low molecular weight subunits. The spinach complex contains two prominent low molecular weight subunits of 3.7 and 4.1 kD while a single prominent component of 4.5 kD was present in the Chlamydomonas complex. An estimation of the relative stoichiometry of these subunits suggests several are present at levels approximating one copy per cytochrome complex. The low molecular weight subunits were purified by reversed phase HPLC and N-terminal sequences obtained. Both the spinach and Chlamydomonas cytochrome complexes contain a subunit that is identified as the previously characterized petG gene product (4.8 kD in spinach and 4.1 kD in Chlamydomonas). A second subunit (3.8 kD in spinach and 3.7 kD in Chlamydomonas) appears to be homologous in the two complexes and is likely to be a nuclear gene product. The possible presence of other low molecular weight subunits in these complexes is also considered.
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Affiliation(s)
- C L Schmidt
- Department of Plant Biology, University of California, 111 Koshland Hall, 94720, Berkeley, CA, USA
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21
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Lind L, Shukla V, Nyhus K, Pakrasi H. Genetic and immunological analyses of the cyanobacterium Synechocystis sp. PCC 6803 show that the protein encoded by the psbJ gene regulates the number of photosystem II centers in thylakoid membranes. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53891-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Fong SE, Surzycki SJ. Chloroplast RNA polymerase genes of Chlamydomonas reinhardtii exhibit an unusual structure and arrangement. Curr Genet 1992; 21:485-97. [PMID: 1617738 DOI: 10.1007/bf00351659] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nucleotide sequence analysis of a 17043 base-pair (bp) region of the Chlamydomonas reinhardtii plastome indicates the presence of three open reading frames (ORFs) similar to RNA polymerase subunit genes. Two, termed rpoB1 and rpoB2, are homologous to the 5'- and 3'-halves of the Escherichia coli beta subunit gene, respectively. A third, termed rpoC2, is similar to the 3'-half of the bacterial beta' subunit gene. These genes exhibit several unusual features: (1) all three represent chimeric structures in which RNA polymerase gene sequences are juxtaposed in-frame with long sequences of unknown identity; (2) unlike their counterparts in plants and eubacteria, rpoB1 and rpoB2 are separated from rpoC2 by a long (7 kilobase-pair, kbp) region containing genes unrelated to RNA polymerase; (3) DNA homologous to the 5' half of rpoC (termed rpoC1 in other species) is not present at the 5' end of rpoC2 and could not be detected in C. reinhardtii chloroplast DNA. RNA expression could not be detected for any of the RNA polymerase genes, suggesting that they are pseudogenes or genes expressed at stages of the C. reinhardtii life-cycle not investigated. The three genes are flanked by GC-rich repeat elements. We suggest that repeat DNA-mediated chloroplast recombination events may have contributed to their unusual arrangement.
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Affiliation(s)
- S E Fong
- Department of Biology, Indiana University, Bloomington 47505
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