Protein phosphorylation regulates in vitro spinach chloroplast petD mRNA 3′-untranslated region stability, processing, and degradation

Vargas-Suárez, Martín; Castro-Sánchez, Alina; Toledo‐Ortiz, Gabriela; Vara, Luis E. González de la; García, Elpidio; Loza-Tavera, Herminia

doi:10.1016/j.biochi.2012.10.012

Cited by 13 publications

(11 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One explanation would be a direct influence of PNPase, which forms trimers but has not been detected in other stable macromolecular complexes [25]. This does not exclude, however, that PNPase has transient interactions with RNA-binding proteins, as has been suggested in a recent study of chloroplast 3 0 end processing [30]. An alternative possibility is that editing efficiency is affected by impaired RNA processing, perhaps through alteration of RNA secondary structure.…”

Section: The Absence Of Pnpase Affects Rna Editingmentioning

confidence: 95%

Arabidopsis chloroplast quantitative editotype

et al. 2013

View full text Add to dashboard Cite

Edited by Ulf-Ingo FlüggeKeywords: RNA editing Chloroplast RNA-seq PNPase Pentatricopeptide repeat RNA processing a b s t r a c t Chloroplast C-to-U RNA editing is an essential post-transcriptional process. Here we analyzed RNA editing in Arabidopsis thaliana using strand-specific deep sequencing datasets from the wild-type and a mutant defective in RNA 3 0 end maturation. We demonstrate that editing at all sites is partial, with an average of 5-6% of RNAs remaining unedited. Furthermore, we identified nine novel sites with a low extent of editing. Of these, three sites are absent from the WT transcriptome because they are removed by 3 0 end RNA processing, but these regions accumulate, and are edited, in a mutant lacking polynucleotide phosphorylase.

show abstract

Section: The Absence Of Pnpase Affects Rna Editingmentioning

confidence: 95%

Arabidopsis chloroplast quantitative editotype

et al. 2013

View full text Add to dashboard Cite

show abstract

“…In addition, plastid ncRNAs (pncRNAs) could modulate stability or processing of some transcripts. Finally, RBPs themselves can be developmentally regulated and posttranslationally modified,71,72 offering another modality to achieve their regulatory targets.…”

Section: Processing Of Primary Transcriptsmentioning

confidence: 99%

RNA processing and decay in plastids

et al. 2013

View full text Add to dashboard Cite

Plastids were derived through endosymbiosis from a cyanobacterial ancestor, whose uptake was followed by massive gene transfer to the nucleus, resulting in the compact size and modest coding capacity of the extant plastid genome. Plastid gene expression is essential for plant development, but depends on nucleus-encoded proteins recruited from cyanobacterial or host-cell origins. The plastid genome is heavily transcribed from numerous promoters, giving posttranscriptional events a critical role in determining the quantity and sizes of accumulating RNA species. The major events reviewed here are RNA editing, which restores protein conservation or creates correct open reading frames by converting C residues to U, RNA splicing, which occurs both in cis and trans, and RNA cleavage, which relies on a variety of exoribonucleases and endoribonucleases. Because the RNases have little sequence specificity, they are collectively able to remove extraneous RNAs whose ends are not protected by RNA secondary structures or sequence-specific RNA-binding proteins (RBPs). Other plastid RBPs, largely members of the helical-repeat superfamily, confer specificity to editing and splicing reactions. The enzymes that catalyze RNA processing are also the main actors in RNA decay, implying that these antagonistic roles are optimally balanced. We place the actions of RBPs and RNases in the context of a recent proteomic analysis that identifies components of the plastid nucleoid, a protein-DNA complex with multiple roles in gene expression. These results suggest that sublocalization and/or concentration gradients of plastid proteins could underpin the regulation of RNA maturation and degradation.

show abstract

“…In general, cpRNPs are involved in a variety of posttranscriptional processes, including 3'-end processing of RNAs [15], RNA editing [16,17], RNA splicing [7], and RNA stabilization [7,8,10]. Some of these processes are modulated by cpRNPs in response to environmental cues and several cpRNPs have been implicated in different acclimation and stress responses [2,7,13,18]. Such a multi-level and far-reaching regulation by multiple external and internal stimuli is unknown for most other chloroplast RBPs, including PPR proteins.…”

mentioning

confidence: 99%

The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA

Teubner

Lenzen

Espenberger

et al. 2020

Plants

View full text Add to dashboard Cite

Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the psbA mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the psbA mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers psbA over all other chloroplast RNAs and associates with the vast majority of the psbA transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B's preference for psbA, suggesting that there are other determinants of specificity in vivo.Plants 2020, 9, 367 2 of 15 of target mRNAs for various cpRNPs [7][8][9]. rRNAs and intron-less tRNAs are not or only weakly bound [6,7,10]. Since the cpRNPs do not co-fractionate with polysomal RNAs [6,8,11], they are mainly attributed a function prior to translation within posttranscriptional processes.Prediction algorithms for subcellular localization and shotgun proteome analysis identified all ten cpRNPs of Arabidopsis in the chloroplast [summarized in 2]. Fluorescence microscopy of GFP fusion proteins confirmed the chloroplast localization [8,[12][13][14]. Within the chloroplasts, the stroma is the main destination of cpRNPs, with small amounts also being associated with thylakoids. This was proven by immunological analyses for the five cpRNPs from tobacco [6].The expression of cpRNPs is regulated by various external and internal signals. Light especially leads to an accumulation of cpRNPs [summarized in 2]. In general, cpRNPs are involved in a variety of posttranscriptional processes, including 3'-end processing of RNAs [15], RNA editing [16,17], RNA splicing [7], and RNA stabilization [7,8,10]. Some of these processes are modulated by cpRNPs in response to environmental cues and several cpRNPs have been implicated in different acclimation and stress responses [2,7,13,18]. Such a multi-level and far-reaching regulation by multiple external and internal stimuli is unknown for most other chloroplast RBPs, including PPR proteins. cpRNPs are thus considered as prime candidates for post-transcriptional regulators of plastid gene expression [19].A particularly interesting case of chloroplast gene regulation is the light-induced translation of psbA, which codes for the D1 protein, the core subunit of photosytem II [20][21][22][23]. D1 is constantly damaged, most pronouncedly by excess light and other unfavourable conditions, i.e., cold. As a consequence, D1 is constantly synthesized for the repair of PSII [24][25][26]. Moreover, regulated D1 synthesis for de novo biogenesis of PSII during cell growth requires additional regulatory levels of psbA mRNA translation. Consistently, a number of proteins have been co-purified with the psbA mRNA in Chlamydomonas, spinach, A...

show abstract

Protein phosphorylation regulates in vitro spinach chloroplast petD mRNA 3′-untranslated region stability, processing, and degradation

Cited by 13 publications

References 37 publications

Arabidopsis chloroplast quantitative editotype

Arabidopsis chloroplast quantitative editotype

RNA processing and decay in plastids

The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA

Contact Info

Product

Resources

About