Characterization of the 5′- and 3′-ends of mRNAs of ndhH, ndhA and ndhI genes of the plastid ndhH-D operon

Abstract

The monocistronic mRNAs of ndhH and ndhA genes of the plastid ndhH-D operon accumulate during senescence. In a step forward to discover the mechanisms involved in the production of mature transcripts of the ndhH-D operon, we determined the 5´- and 3´-ends of low-molecular-weight ndhH, ndhA and ndhI transcripts of barley. The 3′-end of the only ndhH mRNA detected (1622 b) extends 421 b into exon1 of ndhA. Several monocistronic ndhA mRNAs were identified and most of them extend their 3′-ends through the adjacent intergenic 101 b region to around 105 b into ndhI, the neighboring gene in the operon. Unspliced ndhA transcripts (around 2.4 kb and intron-containing) were also identified with different 3′-ends extending almost 200 b into ndhI. In contrast, all ndhA transcripts showed the same 5′-end 65 b upstream of the ndhH stop codon. 5′-ends of all ndhA and ndhH transcripts seem produced by nuclease cleavages between the last AA of the consensus sequence AAUGAA present 66 and 16 b upstream of the respective start codon. Secondary structure predictions suggest that 3′-end extensions provide 3′-UTR stabilizing elements to ndhH-D transcripts. Therefore, the processing of the 7.8 kb primary transcript frequently involves intra-genic cleavages sacrificing downstream gene messages and decreasing the efficiency of the conversion to mature ndh mRNAs. Significantly, the maturation of ndhE mRNA would not sacrifice the downstream psaC message, contributing to higher levels of psaC mRNA than of ndh mRNAs.