mRNAs for two ribosomal proteins are preferentially translated in the chloroplast of Chlamydomonas reinhardtii under conditions of reduced protein synthesis

Conditional repression of essential chloroplast genes: Evidence for new plastid signaling pathways

The development of a repressible chloroplast gene expression system in Chlamydomonas reinhardtii has opened the door for studying the role of essential chloroplast genes. This approach has been used to analyze three chloroplast genes of this sort coding for the α subunit of RNA polymerase (rpoA), a ribosomal protein (rps12) and the catalytic subunit of the ATP-dependent ClpP protease (clpP1). Depletion of the three corresponding proteins leads to growth arrest and cell death. Shutdown of chloroplast transcription and translation increases the abundance of a set of plastid transcripts that includes mainly those involved in transcription, translation and proteolysis and reveals multiple regulatory feedback loops in the chloroplast gene circuitry. Depletion of ClpP profoundly affects plastid protein homeostasis and elicits an autophagy-like response with extensive cytoplasmic vacuolization of cells. It also triggers changes in chloroplast and nuclear gene expression resulting in increased abundance of chaperones, proteases, ubiquitin-related proteins and proteins involved in lipid trafficking and thylakoid biogenesis. These features are hallmarks of an unfolded protein response in the chloroplast and raise new questions on plastid protein homeostasis and plastid signaling. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

Repression of essential chloroplast genes reveals new signaling pathways and regulatory feedback loops in chlamydomonas

Although reverse genetics has been used to elucidate the function of numerous chloroplast proteins, the characterization of essential plastid genes and their role in chloroplast biogenesis and cell survival has not yet been achieved. Therefore, we developed a robust repressible chloroplast gene expression system in the unicellular alga Chlamydomonas reinhardtii based mainly on a vitamin-repressible riboswitch, and we used this system to study the role of two essential chloroplast genes: ribosomal protein S12 (rps12), encoding a plastid ribosomal protein, and rpoA, encoding the α-subunit of chloroplast bacterial-like RNA polymerase. Repression of either of these two genes leads to the arrest of cell growth, and it induces a response that involves changes in expression of nuclear genes implicated in chloroplast biogenesis, protein turnover, and stress. This response also leads to the overaccumulation of several plastid transcripts and reveals the existence of multiple negative regulatory feedback loops in the chloroplast gene circuitry.

Post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii

The biosynthesis of the photosynthetic apparatus depends on the concerted action of the nuclear and chloroplast genetic systems. Numerous nuclear and chloroplast mutants of Chlamydomonas deficient in photosynthetic activity have been isolated and characterized. While several of these mutations alter the genes of components of the photosynthetic complexes, a large number of the mutations affect the expression of chloroplast genes involved in photosynthesis. Most of these mutations are nuclear and only affect the expression of a single chloroplast gene. The mutations examined appear to act principally at post-transcriptional steps such as RNA stability, RNA processing, cis- and trans-splicing and translation. Directed chloroplast DNA surgery through biolistic transformation has provided a powerful tool for identifying important cis elements involved in chloroplast gene expression. Insertion of chimeric genes consisting of chloroplast regulatory regions fused to reporter genes into the chloroplast genome has led to the identification of target sites of the nuclear-encoded functions affected in some of the mutants. Biochemical studies have identified a set of RNA-binding proteins that interact with the 5'-untranslated regions of plastid mRNAs. The binding activity of some of these factors appears to be modulated by light and by the growth conditions.

Translational regulation of chloroplast genes. Proteins binding to the 5'-untranslated regions of chloroplast mRNAs in Chlamydomonas reinhardtii

We have examined the effects of illumination, carbon source, and levels of chloroplast protein synthesis on trans-acting proteins that bind to the leaders of five representative chloroplast mRNAs. The accumulation of these five chloroplast mRNAs and the proteins they encode were measured in cells grown under identical conditions. Extracts from all cell types examined contain a minimum set of six chloroplast 5'-untranslated region (UTR)-binding proteins (81, 62, 56, 47, 38, and 15 kDa). Fractionation results suggest that multiple forms of the 81-, 62-, and 47-kDa proteins may exist. A 36-kDa protein was found in all cells except those deficient in chloroplast protein synthesis. Binding of the 81-, 47-, and 38-kDa proteins to the rps12 leader is effectively competed by the atpB or rbcL 5'-UTRs, indicating that the same proteins bind to all three leaders. In contrast, these three proteins do not bind to the nuclear-encoded alpha-1 tubulin leader, which bound novel proteins of 110, 70, and 43 kDa. Cis-acting sequences within the 5'-UTRs of two chloroplast mRNAs (rps7 and atpB) have been identified which are protected from digestion by RNase T1 by extracts enriched for the 81-, 47-, and 38-kDa proteins.

Ribosome-binding sites on chloroplast rbcL and psbA mRNAs and light-induced initiation of D1 translation

Chloroplast ribosome-binding sites were identified on the plastid rbcL and psbA mRNAs using toeprint analysis. The rbcL translation initiation domain is highly conserved and contains a prokaryotic Shine-Dalgarno (SD) sequence (GGAGG) located 4 to 12 nucleotides upstream of the initiator AUG. Toeprint analysis of rbcL mRNA associated with plastid polysomes revealed strong toeprint signals 15 nucleotides downstream from the AUG indicating ribosome binding at the translation initiation site. Escherichia coli 30S ribosomes generated similar toeprint signals when mixed with rbcL mRNA in the presence of initiator tRNA. These results indicate that plastid SD sequences are functional in chloroplast translation initiation. The psbA initiator region lacks a SD sequence within 12 nucleotides of the initiator AUG. However, toeprint analysis of soluble and membrane polysome-associated psbA mRNA revealed ribosomes bound to the initiator region. E. coli 30S ribosomes did not associate with the psbA translation initiation region. E. coli and chloroplast ribosomes bind to an upstream region which contains a conserved SD-like sequence. Therefore, translation initiation on psbA mRNA may involve the transient binding of chloroplast ribosomes to this upstream SD-like sequence followed by scanning to localize the initiator AUG. Illumination 8-day-old dark-grown barley seedlings caused an increase in polysome-associated psbA mRNA and the abundance of initiation complexes bound to psbA mRNA. These results demonstrate that light modulates D1 translation initiation in plastids of older dark-grown barley seedlings.

The unusual rps3-like orf712 is functionally essential and structurally conserved in Chlamydomonas

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.

Differential expression of the partially duplicated chloroplast S10 ribosomal protein operon

The chloroplast S10 ribosomal protein operon is partially duplicated in many plants because it initiates within the inverted repeat of the circular chloroplast genome. In spinach, the complete S10 operon (S10B) spans the junction between inverted repeat B (IRB) and the large single-copy (LSC) region. The S10 operon is partially duplicated in the inverted repeat A (IRA), but the sequence of S10A completely diverges from S10B at the junction of S10A and the LSC region. The DNA sequence shared by S10A and S10B includes trnI1, the rpl23 pseudogene (rpl23 psi), the intron-containing rpl2 and rps19, which is truncated in S10A at the S10A/LSC junction (rps19'). Transcription of rps19' from the promoter region of S10A could result in the synthesis of a mutant S19 protein. Analysis of RNA accumulation and run-on transcription from S10A and S10B using unique probes from the S10A/LSC and S10B/LSC junctions reveals that expression of S10A is reduced. The difference in S10A and S10B expression appears to be the result of reduced transcription from S10A, rather than differences in RNA stability. Transcription of S10B can initiate at three distinct promoter regions, P1, P2 and P3, which map closely to transcripts detected by S1 nuclease analysis. P1 is located upstream of trnI1 and has the highest transcription initiation frequency in vitro of the three promoter regions. The DNA sequence of P1 is most similar to the chloroplast promoter consensus DNA sequence. Interference by the highly and convergently transcribed psbA-trnH1 operon is considered as a mechanism to explain the reduced activity of the S10A promoters.

Targeted disruption of chloroplast genes in Chlamydomonas reinhardtii

We have developed an efficient procedure for the disruption of Chlamydomonas chloroplast genes. Wild-type C. reinhardtii cells were bombarded with microprojectiles coated with a mixture of two plasmids, one encoding selectable, antibiotic-resistance mutations in the 16S ribosomal RNA gene and the other containing either the atpB or rbcL photosynthetic gene inactivated by an insertion of 0.48 kb of yeast DNA in the coding sequence. Antibiotic-resistant transformants were selected under conditions permissive for growth of non-photosynthetic mutants. Approximately half of these transformants were initially heteroplasmic for copies of the disrupted atpB or rbcL genes integrated into the recipient chloroplast genome but still retained photosynthetic competence. A small fraction of the transformants (1.1% for atpB; 4.3% for rbcL) were nonphotosynthetic and homoplasmic for the disrupted gene at the time they were isolated. Single cell cloning of the initially heteroplasmic transformants also yielded nonphotosynthetic segregants that were homoplasmic for the disrupted gene. Polypeptide products of the disrupted atpB and rbcL genes could not be detected using immunoblotting techniques. We believe that any nonessential Chlamydomonas chloroplast gene, such as those involved in photosynthesis, should be amenable to gene disruption by cotransformation. The method should prove useful for the introduction of site-specific mutations into chloroplast genes and flanking regulatory sequences with a view to elucidating their function.