Stability determinants in the chloroplast psbB/T/H mRNAs of Chlamydomonas reinhardtii

Chloroplast RNA processing and stability

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.

Chloroplast RNA-binding proteins

Chloroplast gene expression is regulated by nucleus-encoded factors, which mainly act at the post-transcriptional level. Plastid RNA-binding proteins (RBPs) represent good candidates for mediating these functions. The picture emerging from recent analyses is that of a great number of differentially regulated RBPs, which are organized in distinct, spatially separated supramolecular complexes. This reflects the complexity of the regulatory network that underlies the intracellular communication system between the nucleus and the chloroplast.

The stem-loop region of the tobacco psbA 5'UTR is an important determinant of mRNA stability and translation efficiency

Regulation of chloroplast gene expression involves networked and concerted interactions of nucleus-encoded factors with their target sites on untranslated regions (UTRs) of chloroplast transcripts. So far, only a few cis-acting elements within such 5'UTR sequences have been identified as functional determinants of mRNA stability and efficient translation in Chlamydomonas in vivo. In this study, we have used chloroplast transformation and site-directed mutagenesis to analyse the functions of the 5'UTRs of tobacco psbA and rbcL fused to the coding region of the reporter gene uidA. Various mutant versions of the psbA leader, as well as rbcL/psbA hybrid leader elements, were investigated. Our results showed a 1.5- to 3-fold decrease in uidA mRNA levels and a 1.5- to 6-fold reduction in uidA translation efficiency in all psbA 5'UTR stem-loop mutants generated by sequence deletions and base alterations. This indicates that the correct primary sequence and secondary structure of the psbA 5'UTR stem-loop are required for mRNA stabilisation and translation. The 5'-terminal segment of the rbcL 5'UTR did not enhance the stability or translational activity of chimeric uidA mRNA under the standard light-dark regime of 16 h light and 8 h dark. Stabilising effects were, however, observed when the cells were kept continuously in the dark. Possible reasons for the influence of the 5'UTR of the tobacco psbA on mRNA stability and translation efficiency are discussed.

From Genes to Photosynthesis in Arabidopsis thaliana

Although photosynthesis in higher plants is of cyanobacterial descent, it differs strikingly in organization and regulation from the prokaryotic process. Genomics, proteomics, and comparative genome analysis are now providing powerful new tools for the molecular dissection of photosynthesis in higher plants. Mutant screens and reverse genetics identify an increasing number of gene-function relationships that have a bearing on photosynthesis, revealing a marked interdependency between photosynthesis and other cellular processes. Photosynthesis-related functions are mostly located in the chloroplast, but can also be located in other compartments of the plant cell. The analysis by DNA-array hybridization of mRNA expression patterns both in the chloroplast and the nucleus, under various environmental conditions and/or in different genetic backgrounds that affect the function of the plastid, is rapidly improving our understanding of how photosynthesis is regulated, and it reveals that plastid-to-nucleus signaling plays a central role in its control.

A dominant nuclear mutation in Chlamydomonas identifies a factor controlling chloroplast mRNA stability by acting on the coding region of the atpA transcript

We have characterized a nuclear mutation, mda1-ncc1, that affects mRNA stability for the atpA gene cluster in the chloroplast of Chlamydomonas. Unlike all nuclear mutations altering chloroplast gene expression described to date, mda1-ncc1 is a dominant mutation that still allows accumulation of detectable amounts of atpA mRNAs. At variance with the subset of these mutations that affect mRNA stability through the 5' UTR of a single chloroplast transcript, the mutated version of MDA1 acts on the coding region of the atpA message. We discuss the action of MDA1 in relation to the unusual pattern of expression of atpA that associates particularly short lived-transcripts with a very high translational efficiency.

A chloroplast RNA binding protein from stromal thylakoid membranes specifically binds to the 5' untranslated region of the psbA mRNA

The intrachloroplastic localization of post-transcriptional gene expression steps represents one key determinant for the regulation of chloroplast development. We have characterized an RNA binding protein of 63 kDa (RBP63) from Chlamydomonas reinhardtii chloroplasts, which cofractionates with stromal thylakoid membranes. Solubility properties suggest that RBP63 is a peripheral membrane protein. Among RNA probes from different 5' untranslated regions of chloroplast transcripts, RBP63 preferentially binds to the psbA leader. This binding is dependent on a region comprising seven consecutive A residues, which is required for D1 protein synthesis. A possible role for this newly discovered RNA binding protein in membrane targeting of psbA gene expression is discussed.

Overexpression of the clpP 5'-untranslated region in a chimeric context causes a mutant phenotype, suggesting competition for a clpP-specific RNA maturation factor in tobacco chloroplasts

The plastid ribosomal RNA (rrn) operon promoter was fused with DNA segments encoding the leader sequence (5'-untranslated region [UTR]) of plastid mRNAs to compare their efficiency in mediating translation of a bacterial protein neomycin phosphotransferase (NPTII) in tobacco (Nicotiana tabacum) chloroplasts. In young leaves, NPTII accumulated at 0.26% and 0.8% of the total soluble leaf protein from genes with the clpP and atpB 5'-UTR, respectively. Interestingly, expression of NPTII from the promoter with the clpP 5'-UTR (0.26% NPTII) caused a mutant (chlorotic) phenotype, whereas plants accumulating approximately 0.8% NPTII from the atpB 5'-UTR were normal green, indicating that the mutant phenotype was independent of NPTII accumulation. Low levels of monocistronic clpP mRNA and accumulation of intron-containing clpP transcripts in the chlorotic leaves suggest competition between the clpP 5'-UTR in the chimeric transcript and the native clpP pre-mRNA (ratio 16:1) for an mRNA maturation factor. Because maturation of 11 other intron-containing mRNAs was unaffected in the chlorotic leaves, it appears that the factor is clpP specific. The mutant phenotype is correlated with reduced levels (approximately 2 times) of the ClpP1 protease subunit, supporting an important role for ClpP1 in chloroplast development.

The 3'-untranslated region of chloroplast psbA mRNA stabilizes binding of regulatory proteins to the leader of the message

The 5'-leader and 3'-tail of chloroplast mRNAs have been suggested to play a role in posttranscriptional regulation of expression of the message. The regulation is thought to be mediated, at least in part, by regulatory proteins that are encoded by the nuclear genome and targeted to the chloroplast where they interact with chloroplast mRNAs. Previous studies identified high affinity binding of the 5'-untranslated region (UTR) of the chloroplast psbA mRNA by Chlamydomonas reinhardtii proteins. Here we tested whether the 3'-UTR of psbA mRNA alone or linked in cis with the 5'-UTR of the mRNA affects the high affinity binding of the message in vitro. We did not detect high affinity binding that is unique to the 3'-UTR. However, we show that the cis-linked 3'-UTR increases the stability of the 5'-UTR binding complex. This effect could provide a means for translational discrimination against mRNAs that are incorrectly processed.

An mRNA 3' processing site targets downstream sequences for rapid degradation in Chlamydomonas chloroplasts

In Chlamydomonas chloroplasts, atpB pre-mRNA matures through a two-step process. Initially, endonuclease cleavage occurs 8-10 nt downstream of the mature 3' end, which itself lies at the end of a stem-loop-forming inverted repeat (IR) sequence. This intermediate product is then trimmed by a 3' -->5' exonuclease activity. Although the initial endonucleolytic cleavage by definition generates two products, the downstream product of atpB pre-mRNA endonucleolytic processing cannot be detected, even transiently. This product thus appears to be highly unstable, and it can be hypothesized that specific mechanisms exist to prevent its accumulation. In experiments described here, the atpB 3' maturation site was placed upstream of reporter genes in vivo. Constructs containing both the IR and endonuclease cleavage site (ECS) did not accumulate the reporter gene mRNA, whereas constructs containing only the IR did accumulate the reporter mRNA. The ECS alone gave an intermediate result, suggesting that the IR and ECS act synergistically. Additional secondary structures were used to test whether 5' -->3' and/or 3' -->5' exonuclease activities mediated degradation. Because these structures did not prevent degradation, rapid endonucleolytic cleavages most likely trigger RNA destruction after ECS cleavage. On the other hand, fragments resulting from cleavage within the endogenous atpB mRNA could occasionally be detected as antisense transcripts of the adjacent reporter genes. Because endonuclease cleavages are also involved in the 5' maturation of chloroplast mRNAs, where only the downstream cleavage product accumulates, it appears that chloroplast endoribonuclease activities have evolved mechanisms to selectively stabilize different ECS products.

Functional genomics of plant photosynthesis in the fast lane using Chlamydomonas reinhardtii

Oxygenic photosynthesis by algae and plants supports much of life on Earth. Several model organisms are used to study this vital process, but the unicellular green alga Chlamydomonas reinhardtii offers significant advantages for the genetic dissection of photosynthesis. Recent experiments with Chlamydomonas have substantially advanced our understanding of several aspects of photosynthesis, including chloroplast biogenesis, structure-function relationships in photosynthetic complexes, and environmental regulation. Chlamydomonas is therefore the organism of choice for elucidating detailed functions of the hundreds of genes involved in plant photosynthesis.

CHLAMYDOMONAS AS A MODEL ORGANISM

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.

The 5' untranslated region of the At-P5R gene is involved in both transcriptional and post-transcriptional regulation

The steady-state level of transcripts coding for the pyrroline-5-carboxylate reductase of Arabidopsis (At-P5R) increased under salt and heat stress, mainly because of an enhanced mRNA stability. However, the At-P5R protein level was not induced, and its translation was inhibited at initiation stage and probably also at later stages. Replacement of the 5' untranslated region (5'UTR) and beta-glucuronidase (gus) fusion analysis revealed that the first 92 bp region of the At-P5R 5'UTR was sufficient to mediate transcript stabilization and translation inhibition during salt and heat stresses. Furthermore, the first 92 bp region of the At-P5R 5'UTR was also involved in transcription efficiency in a promoter-dependent manner. The results demonstrated that the stress regulation of At-P5R is complex and involves the 5'UTR which acts at three levels, partly in opposing directions.

Characterization of Mbb1, a nucleus-encoded tetratricopeptide-like repeat protein required for expression of the chloroplast psbB/psbT/psbH gene cluster in Chlamydomonas reinhardtii

Genetic analysis has revealed that the accumulation of several chloroplast mRNAs of the green alga Chlamydomonas reinhardtii requires specific nucleus-encoded functions. To gain insight into this process, we have cloned the nuclear gene encoding the Mbb1 factor by genomic rescue of a mutant specifically deficient in the accumulation of the mRNAs of the psbB/psbT/psbH chloroplast transcription unit. Mbb1 is a soluble protein in the stromal phase of the chloroplast. It consists of 662 amino acids with a putative chloroplast-transit peptide at its N-terminal end. A striking feature is the presence of 10 tandemly arranged tetratricopeptide-like repeats that account for half of the protein sequence and are thought to be involved in protein-protein interactions. The Mbb1 protein seems to have a homologue in higher plants and is part of a 300-kDa complex that is associated with RNA. This complex is most likely involved in psbB mRNA processing, stability, and/or translation.

The Nac2 gene of Chlamydomonas encodes a chloroplast TPR-like protein involved in psbD mRNA stability

The psbD mRNA, which encodes the D2 reaction center polypeptide of photosystem II, is one of the most abundant chloroplast mRNAs. We have used genomic complementation to isolate the nuclear Nac2 gene, which is required for the stable accumulation of the psbD mRNA in Chlamydomonas reinhardtii. Nac2 encodes a hydrophilic polypeptide of 1385 amino acids with nine tetratricopeptide-like repeats (TPRs) in its C-terminal half. Cell fractionation studies indicate that the Nac2 protein is localized in the stromal compartment of the chloroplast. It is part of a high molecular weight complex that is associated with non-polysomal RNA. Change of a conserved alanine residue of the fourth TPR motif by site-directed mutagenesis leads to aggregation of Nac2 protein and completely abrogates its function, indicating that this TPR is important for proper folding of the protein and for psbD mRNA stability, processing and/or translation.

Processing and degradation of chloroplast mRNA

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).

Participation of nuclear genes in chloroplast gene expression

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.

Translation in chloroplasts

The discovery that chloroplasts have semi-autonomous genetic systems has led to many insights into the biogenesis of these organelles and their evolution from free-living photosynthetic bacteria. Recent developments of our understanding of the molecular mechanisms of translation in chloroplasts suggest selective pressures that have maintained the 100-200 genes of the ancestral endosymbiont in chloroplast genomes. The ability to introduce modified genes into chloroplast genomes by homologous recombination and the recent development of an in vitro chloroplast translation system have been exploited for analyses of the cis-acting requirements for chloroplast translation. Trans-acting translational factors have been identified by genetic and biochemical approaches. Several studies have suggested that chloroplast mRNAs are translated in association with membranes.