Structure of RNA 3′-phosphate cyclase bound to substrate RNA

Desai, Kevin K.; Bingman, C.A.; Cheng, Chin L.; Phillips, George N.; Raines, Ronald T.

doi:10.1261/rna.045823.114

Cited by 5 publications

(7 citation statements)

References 46 publications

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“…Predominant genome associations of RtcA with RtcB suggest that they might function together in 3′-end processing during RNA ligation (see discussion below). Additional roles for RtcA could include cyclic termini recognition/cyclic phosphate end maintenance, a possibility for eukaryotic RtcA acting on U6 snRNA ( 196 ).…”

Section: Major Classes Of Protein Domains Involved In Rna Repairmentioning

confidence: 99%

RNA damage in biological conflicts and the diversity of responding RNA repair systems

Burroughs

Aravind

2016

Nucleic Acids Res

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RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.

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Section: Major Classes Of Protein Domains Involved In Rna Repairmentioning

confidence: 99%

RNA damage in biological conflicts and the diversity of responding RNA repair systems

Burroughs

Aravind

2016

Nucleic Acids Res

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“…These findings were nicely complemented by structural analysis of the archaeon Pyrococcus horihoshi RtcA complexed with 3'-phosphate-terminated RNA, performed in Raines' laboratory [35] (Fig. 1D and Fig.…”

Section: Structural Studies and Refinement Of The Mechanistic Aspects Of The Enzymementioning

confidence: 54%

“…Moreover, comparison of the structures of complexes representing different steps of cyclisation with that of the apoenzyme indicated that the reaction progress is accompanied by conformational switches of the protein. The data led also to a detailed proposal of the mechanism of the cyclisation reaction [33][34][35].…”

Section: Structural Studies and Refinement Of The Mechanistic Aspects Of The Enzymementioning

confidence: 90%

“…2). Inspection of RtcA-ATP and RtcA-RNA complexes indicated a strong overlap between regions binding the ATP phosphates and the 3'-phosphorylated end of RNA substrate [34,35]. Moreover, comparison of the structures of complexes representing different steps of cyclisation with that of the apoenzyme indicated that the reaction progress is accompanied by conformational switches of the protein.…”

Section: Structural Studies and Refinement Of The Mechanistic Aspects Of The Enzymementioning

confidence: 99%

“…This modification optimally occurs at pH of 5.5-6.0, in contrast with the 3'-phosphate cyclisation reaction, which has optimum at pH 8.0-9.0 and very low activity at pH 5.5/6.0; [26]. In the view of the rather strict requirements for acceptance of the RNA phosphomonoester 3'end in the catalytic pocket of RtcA, including recognition of the 3'-phosphate and three terminal nucleotides with the ribose 2'-hydroxyls ( [35]; Fig. 2), the efficient use of the 5'-phosphorylated RNA or DNAs as substrate is rather surprising.…”

Section: Structural Studies and Refinement Of The Mechanistic Aspects Of The Enzymementioning

confidence: 99%

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RNA 3’-terminal phosphate cyclases and cyclase-like proteins

Filipowicz

2016

Postepy Biochem

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RNA molecules bearing terminal 2’,3’-cyclic phosphate are quite common in nature. For example, 2’,3’-cyclic phosphate termini are produced during RNA cleavage by many en-doribonucleases either as intermediates or final products. Many RNA-based nucleases (ribo-zymes) also generate cyclic phosphate termini. However, cleavage reactions are not the only way in which RNAs bearing cyclic phosphate ends are produced. They can also be generated by RNA 3’-terminal phosphate cyclases (RtcA), a family of enzymes conserved in eukaryotes, bacteria, and archaea. These enzymes catalyze the ATP-dependent conversion of the 3’-phos-phate to a 2’,3’-cyclic phosphodiester at the end of RNA. In this article, I review knowledge about the biochemistry and structure of RNA 3’-phosphate cyclases and also proteins of the RNA cyclase-like (Rcl1) family, and discuss their documented or possible roles in different RNA metabolic reactions.

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Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction

Shen,

Naveed,

Bao

2024

WIREs RNA

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Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post‐transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high‐throughput methods based on next‐generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA‐sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP‐seq and Ribo‐seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future.This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs

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Structure of RNA 3′-phosphate cyclase bound to substrate RNA

Cited by 5 publications

References 46 publications

RNA damage in biological conflicts and the diversity of responding RNA repair systems

RNA damage in biological conflicts and the diversity of responding RNA repair systems

RNA 3’-terminal phosphate cyclases and cyclase-like proteins

Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction

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