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Abstract
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
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Affiliation(s)
- Jennifer Ortelt
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany
| | - Gerhard Link
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany.
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Abstract
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
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Affiliation(s)
- Jennifer Ortelt
- Plant Cell Physiology and Molecular Biology, University of Bochum, Bochum, Germany
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Redox Regulation of Chloroplast Gene Expression. PHOTOPROTECTION, PHOTOINHIBITION, GENE REGULATION, AND ENVIRONMENT 2008. [DOI: 10.1007/1-4020-3579-9_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Swiatecka-Hagenbruch M, Liere K, Börner T. High diversity of plastidial promoters in Arabidopsis thaliana. Mol Genet Genomics 2007; 277:725-34. [PMID: 17333279 DOI: 10.1007/s00438-007-0222-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 02/08/2007] [Indexed: 10/23/2022]
Abstract
Arabidopsis thaliana is well established as a model plant in modern plant biology. However, remarkably few details are known about plastidial promoters in Arabidopsis. Here, we report on the identification and analyses of sequences at transcription start sites of selected genes. The genes encoded by the plastome of higher plants are transcribed by a plastid-encoded (PEP) and a nuclear-encoded RNA plastid polymerase (NEP). To discriminate between NEP and PEP promoters we compared the 5'-ends of transcripts from chlorophyll-deficient Arabidopsis plants, which were grown on prokaryotic translation inhibitor spectinomycin to inhibit biosynthesis of PEP, with those of untreated plants. Using 5'-RACE combined with enzymatic treatment of RNAs to recognize primary and secondary 5'-ends, we unambiguously identified transcription initiation sites of the Arabidopsis accD, atpB, atpI, rpoB, rps4, rps15, and ycf1 genes. Comparison of plastidial promoters from tobacco and Arabidopsis revealed a high diversity, which may also apply to other plants. Furthermore, the diversity in individual promoter usage in different plants suggests that there are species-specific solutions for attaining control over gene expression in plastids.
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Transcription and transcriptional regulation in plastids. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0232] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Suzuki JY, Ytterberg AJ, Beardslee TA, Allison LA, Wijk KJ, Maliga P. Affinity purification of the tobacco plastid RNA polymerase and in vitro reconstitution of the holoenzyme. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 40:164-72. [PMID: 15361150 DOI: 10.1111/j.1365-313x.2004.02195.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We affinity-purified the tobacco plastid-encoded plastid RNA polymerase (PEP) complex by the alpha subunit containing a C-terminal 12 x histidine tag using heparin and Ni(2+) chromatography. The composition of the complex was determined by mass spectrometry after separating the proteins of the >900 kDa complex in blue native and SDS polyacrylamide gels. The purified PEP contained the core alpha, beta, beta', beta" subunits and five major associated proteins of unknown function, but lacked sigma factors required for promoter recognition. The holoenzyme efficiently recognized a plastid psbA promoter when it was reconstituted from the purified PEP and recombinant plastid sigma factors. Reconstitution of a plastid holoenzyme with individual sigma factors will facilitate identification of sigma factor-specific promoter elements.
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Affiliation(s)
- Jon Y Suzuki
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
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Homann A, Link G. DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1288-300. [PMID: 12631287 DOI: 10.1046/j.1432-1033.2003.03494.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have isolated and studied the cloned sigma factors SASIG1-3 from mustard (Sinapis alba). In functional analyses using both promoter and factor mutants, the three recombinant proteins all had similar basic properties but also revealed differences in promoter preference and requirements for single nucleotide positions. Directed muta- genesis of SASIG1 identified critical residues within the conserved regions 2.4 and 4.2 necessary for binding of the -10 and -35 promoter elements, respectively. SASIG1 and 2, but not SASIG3, each have a typical region 2.5 for binding of the extended -10 promoter element. SASIG3 has a pro-sequence reminiscent of sigma K from Bacillus subtilis, suggesting that proteolytic cleavage from an inactive precursor is involved in the regulation of plastid transcription. In addition, SASIG2 was found to be more abundant in light-grown as compared to dark-grown mustard seedlings, while the converse was true for SASIG3.
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Affiliation(s)
- Anke Homann
- Plant Cell Physiology and Molecular Biology, University of Bochum, Germany
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9
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Abstract
The nuclear genome of the model plant Arabidopsis thaliana contains a small gene family consisting of three genes encoding RNA polymerases of the single-subunit bacteriophage type. There is evidence that similar gene families also exist in other plants. Two of these RNA polymerases are putative mitochondrial enzymes, whereas the third one may represent the nuclear-encoded RNA polymerase (NEP) active in plastids. In addition, plastid genes are transcribed from another, entirely different multisubunit eubacterial-type RNA polymerase, the core subunits of which are encoded by plastid genes [plastid-encoded RNA polymerase (PEP)]. This core enzyme is complemented by one of several nuclear-encoded sigma-like factors. The development of photosynthetically active chloroplasts requires both PEP and NEP. Most NEP promoters show certain similarities to mitochondrial promoters in that they include the sequence motif 5'-YRTA-3' near the transcription initiation site. PEP promoters are similar to bacterial promoters of the -10/-35 sigma 70 type.
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Affiliation(s)
- W R Hess
- Institute of Biology, Humboldt University, Berlin, Germany
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Liere K, Maliga P. In vitro characterization of the tobacco rpoB promoter reveals a core sequence motif conserved between phage-type plastid and plant mitochondrial promoters. EMBO J 1999; 18:249-57. [PMID: 9878067 PMCID: PMC1171119 DOI: 10.1093/emboj/18.1.249] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report here the in vitro characterization of PrpoB-345, the tobacco rpoB promoter recognized by NEP, the phage-type plastid RNA polymerase. Transcription extracts were prepared from mutant tobacco plants lacking PEP, the Escherichia coli-like plastid-encoded RNA polymerase. Systematic dissection of a approximately 1 kb fragment determined that the rpoB promoter is contained in a 15-nucleotide segment (-14 to +1) upstream of the transcription initiation site (+1). Point mutations at every nucleotide reduced transcription, except at the -5 position which was neutral. Critical for rpoB promoter function was a CRT-motif (CAT or CGT) at -8 to -6 (transcription <30%), defining it as the promoter core. The core CAT sequence is also present in the maize rpoB promoter, which is faithfully recognized by tobacco extracts. Alignment of NEP promoters identified a CATA or TATA (=YATA) sequence at the rpoB core position, also present in plant mitochondrial promoters. Furthermore, NEP and the phage T7 RNA polymerase exhibit similar sensitivity to inhibitors of transcription. These data indicate that the nuclear RpoZ gene, identified by sequence conservation with mitochondrial RNA polymerases, encodes the NEP catalytic subunit.
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Affiliation(s)
- K Liere
- Waksman Institute, Rutgers, the State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
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Leon P, Arroyo A, Mackenzie S. NUCLEAR CONTROL OF PLASTID AND MITOCHONDRIAL DEVELOPMENT IN HIGHER PLANTS. ACTA ACUST UNITED AC 1998; 49:453-480. [PMID: 15012242 DOI: 10.1146/annurev.arplant.49.1.453] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nucleus must coordinate organelle biogenesis and function on a cell and tissue-specific basis throughout plant development. The vast majority of plastid and mitochondrial proteins and components involved in organelle biogenesis are encoded by nuclear genes. Molecular characterization of nuclear mutants has illuminated chloroplast development and function. Fewer mutants exist that affect mitochondria, but molecular and biochemical approaches have contributed to a greater understanding of this organelle. Similarities between organelles and prokaryotic regulatory molecules have been found, supporting the prokaryotic origin of chloroplasts and mitochondria. A striking characteristic for both mitochondria and chloroplast is that most regulation is posttranscriptional.
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Affiliation(s)
- P. Leon
- Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia UNAM, Cuernavaca, Morelos 62250 Mexico; e-mail: , Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana 47907
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Liere K, Kestermann M, Müller U, Link G. Identification and characterization of the Arabidopsis thaliana chloroplast DNA region containing the genes psbA, trnH and rps19'. Curr Genet 1995; 28:128-30. [PMID: 8590463 DOI: 10.1007/bf00315778] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A 1887-nucleotide chloroplast-DNA region from Arabidopsis thaliana was analyzed. It contains the conserved genes psbA for the precursor of the D1 reaction-centre protein of photosystem II, trnH for tRNAHis, and rps19' for the 6.8-kDa protein of the small ribosomal subunit. Northern hybridization and RNase protection experiments suggest co-transcription of a minor RNA fraction over the full lengths of psbA and the preceding trnK-UUU gene, but not including downstream trnH sequences. In front of the mapped 5' end of the major 1.2-kb psbA transcript is a DNA region that shows the typical architecture of a psbA promoter, consisting of the prokaryotic-type '-35' and '-10' elements as well as the eukaryotic-type 'TATA' motif. The common 3' end of psbA transcripts seems to be located immediately after a stem-loop structure downstream from the coding region.
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Affiliation(s)
- K Liere
- University of Bochum, Germany
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