Processing, degradation, and polyadenylation of chloroplast transcripts

Abstract

In this chapter, we describe the major enzymes and characteristics of transcript 5' and 3' end maturation, and polyadenylation-stimulated degradation. The picture which emerges is that maturation and degradation share many prokaryotic features, vestiges of the chloroplast endosymbiont ancestor. The major exoribonucleases are well-defined, being polynucleotide phosphorylase and RNase II/R. The endonucleases include CSP41, with largely informatic evidence for homologs of prokaryotic RNases E, J, and III. The polyadenylation-stimulated degradation pathway, which occurs in most living systems, is a major player in chloroplast RNA degradation. We discuss known or potential roles for polynucleotide phosphorylase and a prokaryotic-type poly(A) polymerase. Finally, we discuss nuclear mutations that affect RNA maturation and degradation, defining genes that are likely or known to encode regulatory factors. Major questions for future research include how the ribonucleases, which are inherently nonspecific, interact with these specificity factors, and whether newly-discovered noncoding RNAs in the chloroplast play any role in RNA metabolism.

A Phosphofructokinase B-Type Carbohydrate Kinase Family Protein, NARA5, for Massive Expressions of Plastid-Encoded Photosynthetic Genes in Arabidopsis

“…Stabilization of mRNA is an important factor in defining transcript levels in chloroplasts. It has been known that trans-acting factors bind to cis-sequences in the target mRNAs and protect them from degradation by endoribonucleases and exoribonucleases (Herrin and Nickelsen, 2004;Bollenbach et al, 2007), for example, in the pentatricopeptide repeat proteins in chloroplasts (Schmitz-Linneweber and Small, 2008;Pfalz et al, 2009). However, pfkB-type carbohydrate kinase family proteins have never been reported to have an mRNA stabilization function, and there is no possible RNA-binding domain in NARA5.…”

A Member of the Arabidopsis Mitochondrial Transcription Termination Factor Family Is Required for Maturation of Chloroplast Transfer RNAIle(GAU)

“…7). The 7.4-kb rRNA precursor is thought to be cleaved by unidentified endonuclease(s), releasing pre-tRNAs for Ile and Ala and pre-rRNAs for 16S rRNA, as well as the dicistronic intermediates rrn23-rrn4.5 and rrn5-tRNR.2 (Bollenbach et al, 2007). The pre-tRNAs and pre-rRNAs are subsequently processed at their 59 and 39 ends by chloroplast homologs of the bacterial RNases P, Z, and R1 and a polynucleotide phosphorylase, PNPase (Bollenbach et al, 2007).…”

“…The 7.4-kb rRNA precursor is thought to be cleaved by unidentified endonuclease(s), releasing pre-tRNAs for Ile and Ala and pre-rRNAs for 16S rRNA, as well as the dicistronic intermediates rrn23-rrn4.5 and rrn5-tRNR.2 (Bollenbach et al, 2007). The pre-tRNAs and pre-rRNAs are subsequently processed at their 59 and 39 ends by chloroplast homologs of the bacterial RNases P, Z, and R1 and a polynucleotide phosphorylase, PNPase (Bollenbach et al, 2007). In contrast to their bacterial counterparts, pre-rrn16 and pre-rrn5 rRNAs are not processed close to their mature termini; therefore, they accumulate long 39 tails, which require 39 to 59 exonucleolytic processing by RNR1 and/or PNPase (Yamamoto et al, 2000;Walter et al, 2002;Bollenbach et al, 2005).…”

An organellar maturase associates with multiple group II introns

“…Possibly, this area downstream of the matK ORF is a binding site for MatK. Speculatively, this binding could influence matK gene expression, as it is known that 3′-UTRs of plastid mRNAs are important determinants of RNA stability and often associate with regulatory RNA binding proteins (31).…”