The nucleus-encoded factor MCD4 participates in degradation of nonfunctional 3' UTR sequences generated by cleavage of pre-mRNA in Chlamydomonas chloroplasts

Small RNA profiling in Chlamydomonas: insights into chloroplast RNA metabolism

In Chlamydomonas reinhardtii, regulation of chloroplast gene expression is mainly post-transcriptional. It requires nucleus-encoded trans-acting protein factors for maturation/stabilization (M factors) or translation (T factors) of specific target mRNAs. We used long- and small-RNA sequencing to generate a detailed map of the transcriptome. Clusters of sRNAs marked the 5' end of all mature mRNAs. Their absence in M-factor mutants reflects the protection of transcript 5' end by the cognate factor. Enzymatic removal of 5'-triphosphates allowed identifying those cosRNA that mark a transcription start site. We detected another class of sRNAs derived from low abundance transcripts, antisense to mRNAs. The formation of antisense sRNAs required the presence of the complementary mRNA and was stimulated when translation was inhibited by chloramphenicol or lincomycin. We propose that they derive from degradation of double-stranded RNAs generated by pairing of antisense and sense transcripts, a process normally hindered by the traveling of the ribosomes. In addition, chloramphenicol treatment, by freezing ribosomes on the mRNA, caused the accumulation of 32-34 nt ribosome-protected fragments. Using this 'in vivo ribosome footprinting', we identified the function and molecular target of two candidate trans-acting factors.

The effect of different 3' untranslated regions on the accumulation and stability of transcripts of a gfp transgene in chloroplasts of transplastomic tobacco

The 3' untranslated region (3' UTR) of transcripts is a major determinant of transcript stability in plastids and plays an important role in regulating gene expression. In order to compare the effect of different 3' UTRs on transgene expression in tobacco chloroplasts, the 3' UTRs from the tobacco chloroplast rbcL, psbA, petD and rpoA genes and the terminator region of the Escherichia coli rrnB operon were inserted downstream of the gfp reporter gene under the control of the psbA promoter, and the constructs were introduced into the plastid genome by particle bombardment. RNA-gel blot analysis of homoplasmic transplastomic plants identified gfp transcripts of ~1.0 and ~1.4 kb from all constructs and showed that plants expressing gfp with the rrnB terminator contained 4 times more gfp transcripts than plants expressing gfp with the rbcL and rpoA 3' UTRs. The amounts of transcripts accumulated roughly correlated with the half-life of the transcripts, determined by RNA-gel blot analysis of transcripts present in leaves treated with actinomycin D to prevent continued transcription of the chimeric gfp genes. Transcripts containing the 3' region of rrnB were most stable, with half-lives of ~43 h, considerably longer than the half-lives of the other ~1.0 kb gfp transcripts (13-26 h). Immunoblot analysis with antibodies to GFP indicated that all plants contained about the same amount of GFP (~0.2% total soluble protein), suggesting either that translation was limited by something other than the amount of transcript or that the 3' UTR was affecting translation.

Redundant cis-acting determinants of 3' processing and RNA stability in the chloroplast rbcL mRNA of Chlamydomonas

We have designed a screen for mutants affected in 3' maturation of the chloroplast rbcL mRNA in Chlamydomonas reinhardtii. We inserted a spectinomycin resistance cassette, 5'atpA::aadA::3'rbcL, in a peripheral domain of tscA, the gene for a small non-coding RNA involved in trans-splicing of psaA. Depending on the orientation of the cassette, a polar effect was observed which was due to processing at the 3'rbcL element: the chimeric tscA RNA was truncated and splicing of psaA was blocked. We selected phenotypic revertants of this insertion mutant that restored psaA splicing, which correlated with the presence of chimeric transcripts that regained the 3' part of tscA. We analyzed two nuclear and six chloroplast suppressors. Five chloroplast mutations altered a short element in the center of the second inverted repeat in the 3'rbcL (IR2), and one deleted a larger region including this element. These mutations revealed a cis-acting element in IR2 which is required for 3' processing. When the same mutations were inserted in the 3' untranslated region (UTR) of the native rbcL gene, the rbcL mRNA accumulated to normal levels, but in strong alleles its 3' end was located upstream, near the end of the first inverted repeat (IR1). Deletion of either IR1 or IR2 allowed stable accumulation of rbcL mRNA, but deletion of both resulted in its complete absence. This indicated that the two inverted repeats function as redundant mRNA stability determinants in the 3' UTR of rbcL.