Translation of psbC mRNAs Starts from the Downstream GUG, not the Upstream AUG, and Requires the Extended Shine–Dalgarno Sequence in Tobacco Chloroplasts

Kuroda, Hiroshi; Suzuki, Haruka; Kusumegi, Takahiro; Hirose, Tetsuro; Yukawa, Yasushi; Sugiura, Masahiro

doi:10.1093/pcp/pcm097

Cited by 49 publications

(35 citation statements)

References 29 publications

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“…The spread of 39 ends is most easily interpreted as nibbling by an exoribonuclease(s) in rnc3/4. The importance of chloroplast SD sequences, and by implication the anti-SD motif, varies among genes and species (Lim et al 2014), but the necessity of an SD sequence for effective translation of at least some chloroplast transcripts is indisputable (Hirose et al, 1998;Kuroda et al, 2007;Drechsel and Bock, 2011). Therefore, it was possible that SD-dependent transcripts would bind to ribosomes less efficiently than their SD-independent counterparts in rnc3/4.…”

Section: Aberrant Maturation Of the 16s Rrna Does Not Affect Ribosomementioning

confidence: 99%

Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling

et al. 2015

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RNase III proteins recognize double-stranded RNA structures and catalyze endoribonucleolytic cleavages that often regulate gene expression. Here, we characterize the functions of RNC3 and RNC4, two Arabidopsis thaliana chloroplast Mini-RNase III-like enzymes sharing 75% amino acid sequence identity. Whereas rnc3 and rnc4 null mutants have no visible phenotype, rnc3/rnc4 (rnc3/4) double mutants are slightly smaller and chlorotic compared with the wild type. In Bacillus subtilis, the RNase Mini-III is integral to 23S rRNA maturation. In Arabidopsis, we observed imprecise maturation of 23S rRNA in the rnc3/4 double mutant, suggesting that exoribonucleases generated staggered ends in the absence of specific Mini-III-catalyzed cleavages. A similar phenotype was found at the 39 end of the 16S rRNA, and the primary 4.5S rRNA transcript contained 39 extensions, suggesting that Mini-III catalyzes several processing events of the polycistronic rRNA precursor. The rnc3/4 mutant showed overaccumulation of a noncoding RNA complementary to the 4.5S-5S rRNA intergenic region, and its presence correlated with that of the extended 4.5S rRNA precursor. Finally, we found rnc3/4-specific intron degradation intermediates that are probable substrates for Mini-III and show that B. subtilis Mini-III is also involved in intron regulation. Overall, this study extends our knowledge of the key role of Mini-III in intron and noncoding RNA regulation and provides important insight into plastid rRNA maturation.

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Section: Aberrant Maturation Of the 16s Rrna Does Not Affect Ribosomementioning

confidence: 99%

Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling

et al. 2015

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“…There are often multiple possible initiation codons in chloroplast mRNAs (17,18). A striking case is the ndhK mRNA from tobacco and many other dicot plants, and the mRNA contains 4 possible AUG codons (15).…”

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confidence: 99%

“…We used the modified (m)GFP, in which 3 amino acids were replaced to enhance fluorescence (23), so that one can detect minor translation products that are undetectable by using 35 S-Met. This system has allowed us to analyze the effect of mRNA processing on translation (23), the translation efficiency of several synonymous codons (24), and the translation initiation site of psbC mRNAs (18).…”

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confidence: 99%

Termination codon-dependent translation of partially overlapping ndhC-ndhK transcripts in chloroplasts

Yukawa

Sugiura

2008

Proc. Natl. Acad. Sci. U.S.A.

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The chloroplast NAD(P)H dehydrogenase complex, a homologue of mitochondrial complex I, consists of >15 subunits, of which 11 are encoded by the chloroplast genome (ndhA-K). The ndhC and ndhK genes are partially overlapped and cotranscribed in many land plants. The downstream ndhK mRNA possesses 4 possible AUG initiation codons in many dicot plants. By using an efficient in vitro translation system from tobacco chloroplasts, we defined that the major initiation site of tobacco ndhK mRNAs is the third AUG that is located 4 nt upstream from the ndhC stop codon. Mutation of the ndhC stop codon (UAG) arrested translation of the ndhK cistron. Frameshift of the ndhC coding strand inhibited also translation of the distal cistron. The results indicated that ndhK translation depends on termination of the preceding cistron, namely translational coupling. Surprisingly, removal of the ndhC 5-UTR and its AUG still supported substantial translation of the ndhK cistron. This translation was abolished again by removing the ndhC stop codon. Although translation of the downstream cistron of an overlapping mRNA is generally very low, we found that the ndhC/K mRNA produces NdhK and NdhC in similar amounts. Based on subunit compositions of the bacterial complex I, the stoichiometry of NdhK and NdhC is suggested to be 1:1 in chloroplasts. To meet this stoichiometry, the ndhC/K mRNA is translated not only by a translational coupling event but also by a termination codondependent pathway.mRNA ͉ cistron ͉ initiation codon ͉ translational coupling

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“…These downstream cistrons are fully or mostly independently translated. In addition, they have additional promoters within the upstream genes and produce monocistronic atpE and psbC mRNAs, which are actively translated in vitro (42,44).…”

Section: Discussionmentioning

confidence: 99%

Additional pathway to translate the downstream ndhK cistron in partially overlapping ndhC-ndhK mRNAs in chloroplasts

Yukawa

Sugiura

2013

Proc. Natl. Acad. Sci. U.S.A.

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The chloroplast NAD(P)H dehydrogenase ( NDH ) C ( ndhC ) and ndhK genes partially overlap and are cotranscribed in many plants. We previously reported that the tobacco ndhC/K genes are translationally coupled but produce NdhC and NdhK, subunits of the NDH complex, in similar amounts. Generally, translation of the downstream cistron in overlapping mRNAs is very low. Hence, these findings suggested that the ndhK cistron is translated not only from the ndhC 5′UTR but also by an additional pathway. Using an in vitro translation system from tobacco chloroplasts, we report here that free ribosomes enter, with formylmethionyl-tRNA fMet , at an internal AUG start codon that is located in frame in the middle of the upstream ndhC cistron, translate the 3′ half of the ndhC cistron, reach the ndhK start codon, and that, at that point, some ribosomes resume ndhK translation. We detected a peptide corresponding to a 57-amino-acid product encoded by the sequence from the internal AUG to the ndhC stop codon. We propose a model in which the internal initiation site AUG is not designed for synthesizing a functional isoform but for delivering additional ribosomes to the ndhK cistron to produce NdhK in the amount required for the assembly of the NDH complex. This pathway is a unique type of translation to produce protein in the needed amount with the cost of peptide synthesis.

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Translation of psbC mRNAs Starts from the Downstream GUG, not the Upstream AUG, and Requires the Extended Shine–Dalgarno Sequence in Tobacco Chloroplasts

Cited by 49 publications

References 29 publications

Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling

Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling

Termination codon-dependent translation of partially overlapping ndhC-ndhK transcripts in chloroplasts

Additional pathway to translate the downstream ndhK cistron in partially overlapping ndhC-ndhK mRNAs in chloroplasts

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