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Zicola J. From the archives: Regulation of mRNA translation, epigenetic machinery components, and processing of a composite large subunit rRNA. THE PLANT CELL 2023:koad102. [PMID: 37032430 DOI: 10.1093/plcell/koad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Affiliation(s)
- Johan Zicola
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA
- Center for Integrated Breeding Research, Department of Crop Sciences, The University of Göttingen, 37073 Göttingen, Germany
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2
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Jalal A, Schwarz C, Schmitz-Linneweber C, Vallon O, Nickelsen J, Bohne AV. A small multifunctional pentatricopeptide repeat protein in the chloroplast of Chlamydomonas reinhardtii. MOLECULAR PLANT 2015; 8:412-26. [PMID: 25702521 DOI: 10.1016/j.molp.2014.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 11/10/2014] [Accepted: 11/24/2014] [Indexed: 05/21/2023]
Abstract
Organellar biogenesis is mainly regulated by nucleus-encoded factors, which act on various steps of gene expression including RNA editing, processing, splicing, stabilization, and translation initiation. Among these regulatory factors, pentatricopeptide repeat (PPR) proteins form the largest family of RNA binding proteins, with hundreds of members in flowering plants. In striking contrast, the genome of the unicellular green alga Chlamydomonas reinhardtii encodes only 14 such proteins. In this study, we analyzed PPR7, the smallest and most highly expressed PPR protein in C. reinhardtii. Green fluorescent protein-based localization and gel-filtration analysis revealed that PPR7 forms a part of a high-molecular-weight ribonucleoprotein complex in the chloroplast stroma. RIP-chip analysis of PPR7-bound RNAs demonstrated that the protein associates with a diverse set of chloroplast transcripts in vivo, i.e. rrnS, psbH, rpoC2, rbcL, atpA, cemA-atpH, tscA, and atpI-psaJ. Furthermore, the investigation of PPR7 RNAi strains revealed that depletion of PPR7 results in a light-sensitive phenotype, accompanied by altered levels of its target RNAs that are compatible with the defects in their maturation or stabilization. PPR7 is thus an unusual type of small multifunctional PPR protein, which interacts, probably in conjunction with other RNA binding proteins, with numerous target RNAs to promote a variety of post-transcriptional events.
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Affiliation(s)
- Abdullah Jalal
- Molecular Plant Sciences, Ludwig-Maximillians-University, Grosshaderner Straße 2-4, 82152 Planegg-Martinsried, Germany
| | - Christian Schwarz
- Molecular Plant Sciences, Ludwig-Maximillians-University, Grosshaderner Straße 2-4, 82152 Planegg-Martinsried, Germany
| | | | - Olivier Vallon
- UMR7141 CNRS/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Jörg Nickelsen
- Molecular Plant Sciences, Ludwig-Maximillians-University, Grosshaderner Straße 2-4, 82152 Planegg-Martinsried, Germany
| | - Alexandra-Viola Bohne
- Molecular Plant Sciences, Ludwig-Maximillians-University, Grosshaderner Straße 2-4, 82152 Planegg-Martinsried, Germany.
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3
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Luo L, Herrin DL. A novel rhodanese is required to maintain chloroplast translation in Chlamydomonas. PLANT MOLECULAR BIOLOGY 2012; 79:495-508. [PMID: 22644440 DOI: 10.1007/s11103-012-9926-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
Rhodanese-domain proteins (RDPs) are widespread in plants and other organisms, but their biological roles are mostly unknown. Here we report on a novel RDP from Chlamydomonas that has a single rhodanese domain, and a predicted chloroplast transit peptide. The protein was produced in Escherichia coli with a His-tag, but lacking most of the N-terminal transit peptide, and after purification was found to have rhodanese activity in vitro. It was also used to elicit antibodies for western blot analysis, which showed that the native Chlamydomonas protein migrated slower on SDS gels (apparent M(r) =34 kDa) than its predicted size (27 kDa), and co-fractionated with chloroplasts. To assess function in vivo, the tandem-RNAi approach was used to generate Chlamydomonas strains that had reductions of 30-70% for the mRNA and ~20-40% for the 34-kDa protein. These strains showed reduced growth under all trophic conditions, and were sensitive to even moderate light; properties reminiscent of chloroplast translation mutants. Pulse-labeling in the presence of cycloheximide indicated that chloroplast protein synthesis was broadly reduced in the RNAi strains, and transcript analysis (by RT-PCR and northern blotting) indicated the effect was mainly translational. These results identify a novel rhodanese-like protein that we have named CRLT, because it is required to maintain chloroplast translation.
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Affiliation(s)
- Liming Luo
- Section of Molecular Cell and Developmental Biology, School of Biological Sciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
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4
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Luo L, Lee J, Herrin DL. Mapping of the css (chloroplast splicing suppressor) gene(s) to a recombinationally suppressed region of chromosome III in Chlamydomonas reinhardtii. Genome 2012; 55:483-91. [PMID: 22708527 DOI: 10.1139/g2012-035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In previous work, three suppressors of defective group I introns (7151, 71N1, 7120) were isolated from a mutant of Chlamydomonas reinhardtii that had a splicing-deficient chloroplast large subunit (LSU) rRNA intron. Genetic analysis indicated that the 7151 and 71N1 suppressor mutations each involved single nuclear loci, and that the 7151 mutation was dominant. Here we present genetic evidence that the 7120 suppressor also involves a single nuclear locus and that the mutation is dominant in vegetative diploids. Moreover, we have employed crosses with the S1D2 strain and molecular markers to map the 7120 and 71N1 suppressors. Based on an analysis of 800 progeny from 7120 × S1D2, the 7120 suppressor is located in a region of ~400 kb on chromosome III that is devoid of recombination. The ~400-kb region contains at least 72 genes, about one-third of which (i.e., 22) are predicted to be organelle targeted. Similar analysis of 71N1 × S1D2 using 400 progeny also pointed to the recombination-deficient region of chromosome III, raising the possibility that these mutations could affect the same gene. These efforts lay the foundation for identifying the css (chloroplast splicing suppressor) gene(s), which promotes splicing of multiple chloroplast group I introns.
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Affiliation(s)
- Liming Luo
- Section of Molecular Cell and Developmental Biology, and the Institute for Cellular and Molecular Biology, 1 University Station A6700, University of Texas at Austin, Austin, TX 78712, USA
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5
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Park YJ, Cho HK, Jung HJ, Ahn CS, Kang H, Pai HS. PRBP plays a role in plastid ribosomal RNA maturation and chloroplast biogenesis in Nicotiana benthamiana. PLANTA 2011; 233:1073-85. [PMID: 21290146 DOI: 10.1007/s00425-011-1362-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 01/12/2011] [Indexed: 05/08/2023]
Abstract
In the present study, we investigated protein characteristics and physiological functions of PRBP (plastid RNA-binding protein) in Nicotiana benthamiana. PRBP fused to green fluorescent protein (GFP) localized to the chloroplasts. Recombinant PRBP proteins bind to single-stranded RNA in vitro, but not to DNA in a double- or a single-stranded form. Virus-induced gene silencing (VIGS) of PRBP resulted in leaf yellowing in N. benthamiana. At the cellular level, PRBP depletion disrupted chloroplast biogenesis: chloroplast number and size were reduced, and the thylakoid membrane was poorly developed. In PRBP-silenced leaves, protein levels of plastid-encoded genes were significantly reduced, whereas their mRNA levels were normal regardless of their promoter types indicating that PRBP deficiency primarily affects translational or post-translational processes. Depletion of PRBP impaired processing of the plastid-encoded 4.5S ribosomal RNA, resulting in accumulation of the larger precursor rRNAs in the chloroplasts. In addition, PRBP-deficient chloroplasts contained significantly reduced levels of mature 4.5S and 5S rRNAs in the polysomal fractions, indicating decreased chloroplast translation. These results suggest that PRBP plays a role in chloroplast rRNA processing and chloroplast development in higher plants.
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Affiliation(s)
- Yong-Joon Park
- Department of Biology, Yonsei University, Seoul 120-749, Korea
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6
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Abstract
The chloroplast genome encodes proteins required for photosynthesis, gene expression, and other essential organellar functions. Derived from a cyanobacterial ancestor, the chloroplast combines prokaryotic and eukaryotic features of gene expression and is regulated by many nucleus-encoded proteins. This review covers four major chloroplast posttranscriptional processes: RNA processing, editing, splicing, and turnover. RNA processing includes the generation of transcript 5' and 3' termini, as well as the cleavage of polycistronic transcripts. Editing converts specific C residues to U and often changes the amino acid that is specified by the edited codon. Chloroplasts feature introns of groups I and II, which undergo protein-facilitated cis- or trans-splicing in vivo. Each of these RNA-based processes involves proteins of the pentatricopeptide motif-containing family, which does not occur in prokaryotes. Plant-specific RNA-binding proteins may underpin the adaptation of the chloroplast to the eukaryotic context.
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Affiliation(s)
- David B Stern
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA.
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Yu F, Liu X, Alsheikh M, Park S, Rodermel S. Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal chloroplast translation, suppress var2-mediated leaf variegation in Arabidopsis. THE PLANT CELL 2008; 20:1786-804. [PMID: 18599582 PMCID: PMC2518225 DOI: 10.1105/tpc.107.054965] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 05/13/2008] [Accepted: 05/28/2008] [Indexed: 05/18/2023]
Abstract
The Arabidopsis thaliana yellow variegated2 (var2) mutant is variegated due to lack of a chloroplast FtsH-like metalloprotease (FtsH2/VAR2). We have generated suppressors of var2 variegation to gain insight into factors and pathways that interact with VAR2 during chloroplast biogenesis. Here, we describe two such suppressors. Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (Psi) synthase, which isomerizes uridine to Psi in noncoding RNAs. svr1 single mutants were epistatic to var2, and they displayed a phenotypic syndrome that included defects in chloroplast rRNA processing, reduced chloroplast translation, reduced chloroplast protein accumulation, and elevated chloroplast mRNA levels. In the second line (TAG-IE), suppression of variegation was caused by a lesion in SVR2, the gene for the ClpR1 subunit of the chloroplast ClpP/R protease. Like svr1, svr2 was epistatic to var2, and clpR1 mutants had a phenotype that resembled svr1. We propose that an impairment of chloroplast translation in TAG-FN and TAG-IE decreased the demand for VAR2 activity during chloroplast biogenesis and that this resulted in the suppression of var2 variegation. Consistent with this hypothesis, var2 variegation was repressed by chemical inhibitors of chloroplast translation. In planta mutagenesis revealed that SVR1 not only played a role in uridine isomerization but that its physical presence was necessary for proper chloroplast rRNA processing. Our data indicate that defects in chloroplast rRNA processing are a common, but not universal, molecular phenotype associated with suppression of var2 variegation.
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Affiliation(s)
- Fei Yu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
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8
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Beligni MV, Mayfield SP. Arabidopsis thaliana mutants reveal a role for CSP41a and CSP41b, two ribosome-associated endonucleases, in chloroplast ribosomal RNA metabolism. PLANT MOLECULAR BIOLOGY 2008; 67:389-401. [PMID: 18398686 DOI: 10.1007/s11103-008-9328-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 03/19/2008] [Indexed: 05/04/2023]
Abstract
A proteomic analysis of Chlamydomonas reinhardtii 70S ribosomes identified two proteins, RAP38 and RAP41, which associate in stoichiometric amounts with intact ribosomes. In this work we show results that suggest the Arabidopsis thaliana homologs, CSP41b and CSP41a, participate in ribosomal RNA metabolism. Csp41a-1 and csp41b-1 single mutants show little phenotype, while the loss of both proteins is lethal. Plants homozygous for the csp41b-1 mutation and heterozygous for the csp41a-1 mutation (csp41b-1/csp41a-1*) fail to accumulate CSP41b and show a marked reduction in the levels of CSP41a. These mutants have reduced chlorophyll content, grow slower and over-accumulate 23S precursor rRNAs compared to their wild-type (WT) siblings, whereas other rRNAs or mRNAs are unaffected. Chloroplast polysome assembly is reduced in csp41b-1/csp41a-1* mutants, which also contain increased amounts of pre-ribosomal particles compared to mature 70S ribosomes. Our results also indicate that CSP41b associates with pre-ribosomal particles in vivo. In vitro, the pattern of 23S precursors and mature rRNAs is altered upon incubation with recombinant CSP41a and CSP41b. Taken together, these results suggest that CSP41a and CSP41b have a role in chloroplast ribosomal RNA metabolism, most likely acting in the final steps of 23S rRNA maturation.
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Affiliation(s)
- María Verónica Beligni
- Department of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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9
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Zicker AA, Kadakia CS, Herrin DL. Distinct roles for the 5' and 3' untranslated regions in the degradation and accumulation of chloroplast tufA mRNA: identification of an early intermediate in the in vivo degradation pathway. PLANT MOLECULAR BIOLOGY 2007; 63:689-702. [PMID: 17180456 DOI: 10.1007/s11103-006-9117-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 11/13/2006] [Indexed: 05/13/2023]
Abstract
Elongation factor Tu in Chlamydomonas reinhardtii is a chloroplast-encoded gene (tufA) whose 1.7-kb mRNA has a relatively short half-life. In the presence of chloramphenicol (CAP), which freezes translating chloroplast ribosomes, a 1.5-kb tufA RNA becomes prominent. Rifampicin-chase analysis indicates that the 1.5-kb RNA is a degradation intermediate, and mapping studies show that it is missing 176-180 nucleotides from the 5' end of tufA. The 5' terminus of the intermediate maps to a section of the untranslated region (UTR) predicted to be highly structured and to encode a small ORF. The intermediate could be detected in older cultures in the absence of CAP, indicating that it is not an artifact of drug treatment. Also, it did not overaccumulate in the chloroplast ribosome-deficient mutant, ac20 cr1, indicating its stabilization is specific to elongation-arrested ribosomes. To determine if the 5' UTR of tufA is destabilizing, the corresponding region of the atpA-aadA-rbcL gene was replaced with the tufA sequence, and introduced into the chloroplast genome; the 3' UTR was also substituted for comparison. Analysis of these transformants showed that the transcripts containing the tufA 3'-UTR accumulate to significantly lower levels. Data from constructs based on the vital reporter, Renilla luciferase, confirmed the importance of the tufA 3'-UTR in determining RNA levels, and suggested that the 5' UTR of tufA affects translation efficiency. These data indicate that the in vivo degradation of tufA mRNA begins in the 5' UTR, and is promoted by translation. The data also suggest, however, that the level of the mature RNA is determined more by the 3' UTR than the 5' UTR.
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Affiliation(s)
- Alicia A Zicker
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, School of Biological Sciences, University of Texas at Austin, 1 University Station A6700, Austin, TX 78712, USA
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10
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Processing, degradation, and polyadenylation of chloroplast transcripts. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0235] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Kuo TC, Odom OW, Herrin DL. Unusual metal specificity and structure of the group I ribozyme from Chlamydomonas reinhardtii 23S rRNA. FEBS J 2006; 273:2631-44. [PMID: 16817892 DOI: 10.1111/j.1742-4658.2006.05280.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Group I intron ribozymes require cations for folding and catalysis, and the current literature indicates that a number of cations can promote folding, but only Mg2+ and Mn2+ support both processes. However, some group I introns are active only with Mg2+, e.g. three of the five group I introns in Chlamydomonas reinhardtii. We have investigated one of these ribozymes, an intron from the 23S LSU rRNA gene of Chlamydomonas reinhardtii (Cr.LSU), by determining if the inhibition by Mn2+ involves catalysis, folding, or both. Kinetic analysis of guanosine-dependent cleavage by a Cr.LSU ribozyme, 23S.5 Delta Gb, that lacks the 3' exon and intron-terminal G shows that Mn2+ does not affect guanosine binding or catalysis, but instead promotes misfolding of the ribozyme. Surprisingly, ribozyme misfolding induced by Mn2+ is highly cooperative, with a Hill coefficient larger than that of native folding induced by Mg2+. At lower Mn2+ concentrations, metal inhibition is largely alleviated by the guanosine cosubstrate (GMP). The concentration dependence of guanosine cosubstrate-induced folding suggests that it functions by interacting with the G binding site, perhaps by displacing an inhibitory Mn2+. Because of these and other properties of Cr.LSU, the tertiary structure of the intron from 23S.5 Delta Gb was examined using Fe2+-EDTA cleavage. The ground-state structure shows evidence of an unusually open ribozyme core: the catalytic P3-P7 domain and the nucleotides that connect it to the P4-P5-P6 domain are exposed to solvent. The implications of this structure for the in vitro and in vivo properties of this intron ribozyme are discussed.
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Affiliation(s)
- Tai-Chih Kuo
- Department of Biochemistry, Tapei Medical University, Taiwan
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12
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Mizrahi-Aviv E, Mills D, Benzioni A, Bar-Zvi D. Salinity inhibits post transcriptional processing of chloroplast 16S rRNA in shoot cultures of jojoba (Simmondsia chinesis). PLANT CELL REPORTS 2005; 23:770-774. [PMID: 15645309 DOI: 10.1007/s00299-004-0897-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2004] [Revised: 09/29/2004] [Accepted: 09/29/2004] [Indexed: 05/24/2023]
Abstract
Chloroplast metabolism is rapidly affected by salt stress. Photosynthesis is one of the first processes known to be affected by salinity. Here, we report that salinity inhibits chloroplast post-transcriptional RNA processing. A differentially expressed 680-bp cDNA, containing the 3' sequence of 16S rRNA, transcribed intergenic spacer, exon 1 and intron of tRNA(Ile), was isolated by differential display reverse transcriptase PCR from salt-grown jojoba (Simmondsia chinesis) shoot cultures. Northern blot analysis indicated that although most rRNA appears to be fully processed, partially processed chloroplast 16S rRNA accumulates in salt-grown cultures. Thus, salinity appears to decrease the processing of the rrn transcript. The possible effect of this decreased processing on physiological processes is, as yet, unknown.
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Affiliation(s)
- Ela Mizrahi-Aviv
- Department of Life Sciences and Doris and Bertie Center for Bioenergetics in Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel
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13
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Bellaoui M, Gruissem W. Altered expression of the Arabidopsis ortholog of DCL affects normal plant development. PLANTA 2004; 219:819-26. [PMID: 15197595 DOI: 10.1007/s00425-004-1295-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Accepted: 04/17/2004] [Indexed: 05/10/2023]
Abstract
The DCL ( defective chloroplasts and leaves) gene of tomato ( Lycopersicon esculentum Mill.) is required for chloroplast development, palisade cell morphogenesis, and embryogenesis. Previous work suggested that DCL protein is involved in 4.5S rRNA processing. The Arabidopsis thaliana (L.) Heynh. genome contains five sequences encoding for DCL-related proteins. In this paper, we investigate the function of AtDCL protein, which shows the highest amino acid sequence similarity with tomato DCL. AtDCL mRNA was expressed in all tissues examined and a fusion between AtDCL and green fluorescent protein (GFP) was sufficient to target GFP to plastids in vivo, consistent with the localization of AtDCL to chloroplasts. In an effort to clarify the function of AtDCL, transgenic plants with altered expression of this gene were constructed. Deregulation of AtDCL gene expression caused multiple phenotypes such as chlorosis, sterile flowers and abnormal cotyledon development, suggesting that this gene is required in different organs. The processing of the 4.5S rRNA was significantly altered in these transgenic plants, indicating that AtDCL is involved in plastid rRNA maturation. These results suggest that AtDCL is the Arabidopsis ortholog of tomato DCL, and indicate that plastid function is required for normal plant development.
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Affiliation(s)
- Mohammed Bellaoui
- Institute of Plant Sciences, Swiss Federal Institute of Technology, 8092, Zurich, Switzerland.
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Kishine M, Takabayashi A, Munekage Y, Shikanai T, Endo T, Sato F. Ribosomal RNA processing and an RNase R family member in chloroplasts of Arabidopsis. PLANT MOLECULAR BIOLOGY 2004; 55:595-606. [PMID: 15604703 DOI: 10.1007/s11103-004-1507-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An Arabidopsis mutant rnr1 , which has a defect in the basic genetic system in chloroplasts, was isolated using the screening of the high chlorophyll fluorescence phenotype. Whereas chlorophyll fluorescence and immunoblot studies showed the mutant had reduced activities of photosystems I and II, molecular characterization of the mutant suggested that a T-DNA insertion impaired the expression of a gene encoding a RNase R family member with a targeting signal to chloroplasts. Since RNase R family members have a 3'-5' exoribonuclease activity, we examined the RNA profile in chloroplasts. In rnr1 the intercistronic cleavage between 23S and 4.5S rRNA was impaired, and a significant reduction in rRNA in chloroplasts was found, suggesting that RNR1 functions in the maturation of chloroplast rRNA. The present results suggest that defects in the genetic system in chloroplasts cause high chlorophyll fluorescence, pale green leaf, and marked reduction in the growth rate, whereas the levels of some chloroplast RNA were higher in rnr1 than in the wild-type.
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15
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Herrin DL, Nickelsen J. Chloroplast RNA processing and stability. PHOTOSYNTHESIS RESEARCH 2004; 82:301-14. [PMID: 16143842 DOI: 10.1007/s11120-004-2741-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Accepted: 03/18/2004] [Indexed: 05/04/2023]
Abstract
Primary chloroplast transcripts are processed in a number of ways, including intron splicing, internal cleavage of polycistronic RNAs, and endonucleolytic or exonucleolytic cleavages at the transcript termini. All chloroplast RNAs are also subject to degradation, although a curious feature of many chloroplast mRNAs is their relative longevity. Some of these processes, e.g., psbA splicing and stability of a number of chloroplast mRNAs, are regulated in response to light-dark cycles or nutrient availability. This review highlights recent advances in our understanding of these processes in the model organism Chlamydomonas reinhardtii, focusing on results since the extensive reviews published in 1998 [Herrin DL et al. 1998 (pp. 183-195), Nickelsen Y 1998 (pp. 151-163), Stern DB and Drager RG 1998 (pp. 164-182), in Rochaix JD et al. (eds) The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas. Kluwer Academic Publishers, Dordrecht, The Netherlands]. We also allude to studies with other organisms, and to the potential impact of the Chlamydomonas genome project where appropriate.
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Affiliation(s)
- David L Herrin
- Section of Molecular Cell and Developmental Biology, University of Texas at Austin, 1 University Station A6700, Austin, TX, 78712, USA,
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16
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Li F, Holloway SP, Lee J, Herrin DL. Nuclear genes that promote splicing of group I introns in the chloroplast 23S rRNA and psbA genes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 32:467-480. [PMID: 12445119 DOI: 10.1046/j.1365-313x.2002.01437.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Single nucleotide substitutions were made in the core helices P4, P6, and P7, and in the metal-binding GAAA motif in the J4/5 region of the chloroplast group I rRNA intron of Chlamydomonas reinhardtii, Cr.LSU. In vitro assays showed that these substitutions had surprisingly strong effects on Cr.LSU self-splicing; however, splicing of all but the P6 mutations could be at least partially recovered by increasing the Mg2+ concentration. The mutant constructs were transformed into chloroplasts to replace the wild-type intron; however, only the P4 mutants became homoplasmic, indicating that the other mutations were lethal. The splicing-deficient P4125A mutant, which exhibited slow growth and light sensitivity, was used to isolate suppressor strains that showed a substantial restoration of Cr.LSU splicing. Genetic analysis of the 7151, 7120 and 71N1 suppressors indicated that these mutations are in at least two nuclear genes. The 7151 suppressor mutation, which defines the chloroplast-splicing suppressor (css1) gene, had no obviously altered growth phenotype with the wild-type intron, and was dominant in vegetative diploids containing the mutant intron. All three of the suppressor strains also suppressed a mutation in the P4 region of the fourth psbA intron, Cr.psbA4, indicating that these genes play a role in splicing of multiple group I introns in the chloroplast.
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MESH Headings
- Animals
- Base Sequence
- Cell Nucleus/genetics
- Chlamydomonas reinhardtii/cytology
- Chlamydomonas reinhardtii/genetics
- Genes, Dominant/genetics
- Genes, Plant/genetics
- Introns/genetics
- Mutation
- Nucleic Acid Conformation
- Photosynthetic Reaction Center Complex Proteins/genetics
- Photosystem II Protein Complex
- RNA Splicing
- RNA, Chloroplast/chemistry
- RNA, Chloroplast/genetics
- RNA, Chloroplast/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Suppression, Genetic
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Affiliation(s)
- Fei Li
- Molecular Cell and Developmental Biology Section and Institute for Cellular and Molecular Biology, Bio 311, University of Texas at Austin, Austin, TX 78712, USA
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17
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Simpson C, Stern D. Chlamydomonas reinhardtii as a model system for dissecting chloroplast RNA processing and decay mechanisms. Methods Enzymol 2002; 342:384-407. [PMID: 11586911 DOI: 10.1016/s0076-6879(01)42561-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- C Simpson
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
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Harris EH. CHLAMYDOMONAS AS A MODEL ORGANISM. ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY 2001; 52:363-406. [PMID: 11337403 DOI: 10.1146/annurev.arplant.52.1.363] [Citation(s) in RCA: 429] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The unicellular green alga Chlamydomonas offers a simple life cycle, easy isolation of mutants, and a growing array of tools and techniques for molecular genetic studies. Among the principal areas of current investigation using this model system are flagellar structure and function, genetics of basal bodies (centrioles), chloroplast biogenesis, photosynthesis, light perception, cell-cell recognition, and cell cycle control. A genome project has begun with compilation of expressed sequence tag data and gene expression studies and will lead to a complete genome sequence. Resources available to the research community include wild-type and mutant strains, plasmid constructs for transformation studies, and a comprehensive on-line database.
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Affiliation(s)
- Elizabeth H Harris
- Developmental, Cell and Molecular Biology Group, Biology Department, Duke University, Durham, North Carolina 27708-1000; e-mail:
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Odom OW, Holloway SP, Deshpande NN, Lee J, Herrin DL. Mobile self-splicing group I introns from the psbA gene of Chlamydomonas reinhardtii: highly efficient homing of an exogenous intron containing its own promoter. Mol Cell Biol 2001; 21:3472-81. [PMID: 11313473 PMCID: PMC100269 DOI: 10.1128/mcb.21.10.3472-3481.2001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 and Cr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16S rrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. The Cr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/microgram of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp -88 and -194 (relative to the ORF) that stimulated homing and contained a possible bacterial (-10, -35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.
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Affiliation(s)
- O W Odom
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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Kuo TC, Herrin DL. A kinetically efficient form of the Chlamydomonas self-splicing ribosomal RNA precursor. Biochem Biophys Res Commun 2000; 273:967-71. [PMID: 10891356 DOI: 10.1006/bbrc.2000.3047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 23S rRNA gene of Chlamydomonas reinhardtii contains a group IA3 intron, Cr.LSU, whose splicing is essential for cell growth. To better understand Cr.LSU splicing, kinetic analyses were undertaken with 23S.3, a preRNA previously shown to self-splice. Self-splicing of 23S.3 showed biphasic kinetics, with only approximately 33% reacting efficiently. Removal of a region of the 5' exon that could potentially interfere with the intron core (i.e., P3) increased the size (53%) of the active fraction. Replacement of the large P6a-extension by a 20-nt stem-loop further increased the active fraction to approximately 80%. The k(cat) and K(G)(M) for self-splicing (first step) by these latter RNAs were approximately 1 min(-1) and approximately 20 microM, respectively. These results indicate that Cr.LSU is a highly efficient ribozyme whose folding in vitro is impeded by exonic and/or intronic sequences. The implications for in vivo splicing of Cr.LSU are discussed.
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Affiliation(s)
- T C Kuo
- Molecular Cell and Developmental Biology Section, Institute for Cellular and Molecular Biology, Austin, Texas 78712, USA
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Abstract
The conversion of genetic information stored in DNA into a protein product proceeds through the obligatory intermediate of messenger RNA. The steady-state level of an mRNA is determined by its relative synthesis and degradation rates, i.e., an interplay between transcriptional regulation and control of RNA stability. When the biological status of an organism requires that a gene product's abundance varies as a function of developmental stage, environmental factors or intracellular signals, increased or decreased RNA stability can be the determining factor. RNA stability and processing have long been known as important regulatory points in chloroplast gene expression. Here we summarize current knowledge and prospects relevant to these processes, emphasizing biochemical data. The extensive literature on nuclear mutations affecting chloroplast RNA metabolism is reviewed in another article in this volume (Barkan and Goldschmidt-Clermont, this issue).
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Affiliation(s)
- R A Monde
- Boyce Thompson Institute for Plant Research, Tower Rd., Cornell University, Ithaca, NY 14853, USA
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Abstract
The expression of the plastid genome is dependent on a large number of nucleus-encoded factors. Some of these factors have been identified through biochemical assays, and many others by genetic screens in Arabidopsis, Chlamydomonas and maize. Nucleus-encoded factors function in each step in plastid gene expression, including transcription, RNA editing, RNA splicing, RNA processing, RNA degradation, and translation. Many of the factors discovered via biochemical approaches play general roles as components of the basic gene expression machinery, whereas the majority of those identified by genetic approaches are specifically required for the expression of small subsets of chloroplast genes and are involved in post-transcriptional steps. Some of the nucleus-encoded factors may play regulatory roles and modulate chloroplast gene expression in response to developmental or environmental cues. They may also serve to couple chloroplast gene expression with the assembly of the protein products into the large complexes of the photosynthetic apparatus. The convergence of biochemical approaches with those of classical and reverse genetics, and the contributions from large scale genomic sequencing should result in rapid advances in our understanding of the regulatory interactions that govern plastid gene expression.
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Affiliation(s)
- A Barkan
- Institute of Molecular Biology, University of Oregon, OR 97403, Eugene, USA
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