The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities

Halpert, Michal; Liveanu, Varda; Glaser, Fabian; Schuster, Gadi

doi:10.1007/s11103-018-0799-5

Cited by 20 publications

(26 citation statements)

References 40 publications

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“…In order to examine the conservation degree of the GT-1 domain in plant RNase J, its predicted structure was superimposed on that of the known GT-1 transcription factor PDB 2EBI ( Figure 2). The DNA-GT-1 interface was located exactly as predicted by the conserved, electropositive, tryptophan-rich interface [52,62]. The predicted structure also displayed similar physicochemical characteristics and a conserved DNA binding site.…”

Section: The Plant Rnase J Gt-1 Domainmentioning

confidence: 66%

“…The function of the GT-1 domain in plant RNase J remains enigmatic. While deletion of the GT-1 domain did not interfere with RNase J degradation activity in vitro when incubated with synthetic RNAs [52], it is more likely in vivo function would be related to sequence specificity, interaction with a PPR protein, and/or dimerization, which have not yet been rigorously tested. These possibilities are illustrated in Figure 3.…”

Section: The Plant Rnase J Gt-1 Domainmentioning

confidence: 95%

“…Chlamydomonas reinhardtii RNase J (CrRNase J) is one of only three family members reported to exhibit exclusively endonucleolytic activity in vitro [37,49,50]. On the other hand, Bacillus subtilis RNase J1 is mainly exonucleolytic in vitro [51], whereas Arabidopsis RNase J (AtRNase J) displays robust endonucleolytic and relatively minor exonucleolytic activities in vitro [52]. The biological significance and structural basis of the variable exo-and endonucleolytic activities are unknown, but one can predict substrate preferences.…”

Section: Ribonuclease J and β-Casp Proteinsmentioning

confidence: 99%

“…In spite of their overall conservation with bacterial, archaeal, and animal RNase J-CPSF members, plant RNase Js are distinguished by a C-terminal extension with high homology to the GT-1 DNA-binding domain (Figure 1) [9,52]. The GT-1 domain was defined initially in pea and subsequently in about 30-member families of Arabidopsis, wheat, and rice transcription factors that regulate various developmental processes and are stress-responsive [58][59][60][61].…”

Section: The Plant Rnase J Gt-1 Domainmentioning

confidence: 99%

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Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression

Hotto

Stern

Schuster

2020

Plants

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RNA quality control is an indispensable but poorly understood process that enables organisms to distinguish functional RNAs from nonfunctional or inhibitory ones. In chloroplasts, whose gene expression activities are required for photosynthesis, retrograde signaling, and plant development, RNA quality control is of paramount importance, as transcription is relatively unregulated. The functional RNA population is distilled from this initial transcriptome by a combination of RNA-binding proteins and ribonucleases. One of the key enzymes is RNase J, a 5′→3′ exoribonuclease and an endoribonuclease that has been shown to trim 5′ RNA termini and eliminate deleterious antisense RNA. In the absence of RNase J, embryo development cannot be completed. Land plant RNase J contains a highly conserved C-terminal domain that is found in GT-1 DNA-binding transcription factors and is not present in its bacterial, archaeal, and algal counterparts. The GT-1 domain may confer specificity through DNA and/or RNA binding and/or protein–protein interactions and thus be an element in the mechanisms that identify target transcripts among diverse RNA populations. Further understanding of chloroplast RNA quality control relies on discovering how RNase J is regulated and how its specificity is imparted.

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Section: The Plant Rnase J Gt-1 Domainmentioning

confidence: 66%

Section: The Plant Rnase J Gt-1 Domainmentioning

confidence: 95%

Section: Ribonuclease J and β-Casp Proteinsmentioning

confidence: 99%

Section: The Plant Rnase J Gt-1 Domainmentioning

confidence: 99%

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Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression

Hotto

Stern

Schuster

2020

Plants

Self Cite

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“…Nevertheless, chloroplast RNase J exhibits a DNA binding domain found in transcription factors of plants that is not present in archaeal RNase J and that could be essential to fulfil this function (58).…”

Section: Discussionmentioning

confidence: 99%

RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

Phung

Etienne

Batista

et al. 2019

Preprint

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A network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.

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“Life is short, and art is long”: RNA degradation in cyanobacteria and model bacteria

Zhang

Hess

Zhang

2022

mLife

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RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes. In bacteria, the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis, but not much is known in other bacteria. Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO2 and solar energy. A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria. Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E. coli and B. subtilis, and only a limited number of them have been experimentally investigated. In this review, we summarize the current knowledge about these RNA‐turnover‐related proteins in cyanobacteria. Although many of them are biochemically similar to their counterparts in E. coli and B. subtilis, they appear to have distinct cellular functions, suggesting a different mechanism of RNA turnover regulation in cyanobacteria. The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field.

show abstract

The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities

Cited by 20 publications

References 40 publications

Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression

Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression

RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

“Life is short, and art is long”: RNA degradation in cyanobacteria and model bacteria

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