Mammalian 2′,3′ cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo

Schwer, Beate; Aronova, Anna; Ramı́rez, Alejandro F.; Braun, Peter E.; Shuman, Stewart

doi:10.1261/rna.858108

Cited by 47 publications

(52 citation statements)

References 43 publications

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“…These data are in line with the finding that hClp1 expression in Saccharomyces cerevisiae complements mutations in the essential PNK module of yeast tRNA ligase (15). It is also known that mammalian 2′,3′-cyclic nucleotide phosphodiesterase (CNP) is able to complement mutations in the CPDase domain of the yeast tRNA ligase (16). Thus, if CNP and hClp1 were genuine components of the animal 5′-P ligation pathway, then all enzymatic activities including the RNA ligase would be encoded by separate genes, and all would act in concert.…”

supporting

confidence: 85%

“…1) in a single protein like class I and II enzymes or in separate polypeptides like B. floridae. The latter scenario is supported by the finding that human RNA 5′-kinase (hClp1) and mammalian CNP can complement the corresponding yeast tRNA ligase activities in vivo (15,16). The single polypeptide hypothesis is consistent with the observation that HeLa cell nuclear extracts contain a protein that cross-reacts with antibodies against purified yeast tRNA ligase upon immunoblot analysis and that this protein has approximately the same molecular weight (∼95 kDa) as yeast tRNA ligase (13).…”

Section: Discussionsupporting

confidence: 54%

See 1 more Smart Citation

Branchiostoma floridae has separate healing and sealing enzymes for 5′-phosphate RNA ligation

Englert

Sheppard

Gundllapalli

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Animal cells have two tRNA splicing pathways: (i) a 5′-P ligation mechanism, where the 5′-phosphate of the 3′ tRNA half becomes the junction phosphate of the new phosphodiester linkage, and (ii) a 3′-P ligation process, in which the 3′-phosphate of the 5′ tRNA half turns into the junction phosphate. Although both activities are known to exist in animals, in almost three decades of investigation, neither of the two RNA ligases has been identified. Here we describe a gene from the chordate Branchiostoma floridae that encodes an RNA ligase (Bf RNL) with a strict requirement for RNA substrates with a 2′-phosphate terminus for the ligation of RNAs with 5′-phosphate and 3′-hydroxyl ends. Unlike the yeast and plant tRNA ligases involved in tRNA splicing, Bf RNL lacks healing activities and requires the action of a polynucleotide kinase (PNK) and a cyclic phosphodiesterase (CDPase) in trans. The activities of these two enzymes were identified in a single B. floridae protein (Bf PNK/ CPDase). The combined activities of Bf RNL and Bf PNK/CPDase are sufficient for the joining of tRNA splicing intermediates in vitro, and for the functional complementation of a tRNA ligase-deficient Saccharomyces cerevisiae strain in vivo. Hence, these two proteins constitute the 5′-P RNA ligation pathway in an animal organism.A rchaeal and eukaryal cells have ubiquitous intron-containing tRNA precursors, and their correct processing to mature tRNA is essential for viability. The first step in tRNA maturation is the removal of introns by the tRNA splicing endonuclease (1) generating the linear intron and two tRNA halves with 2′,3′-cyclic phosphate and 5′-hydroxyl termini (Fig. 1A, Top). Different strategies are used to subsequently join the tRNA halves together. A 3′-P ligation pathway exists in archaea and in animals (2, 3). Fungi, plants, and-as a second pathway-animals employ a more complex reaction that requires GTP and ATP to generate the crucial 5′-phosphate involved in a 5′-P ligation process (Fig. 1). The multifunctional yeast (class I) and plant (class II) tRNA ligases combine three enzymatic activities in a single polypeptide (Fig. 1B): an adenylyltransferase, a polynucleotide kinase (PNK), and a cyclic phosphodiesterase (CPDase) (4). These RNA ligases perform both "healing" and "sealing" steps (5) during ligation (Fig. 1A). The 2′,3′-cyclic phosphate at the 3′-end of the 5′ tRNA half is hydrolyzed by the CPDase to generate a 2′-phosphate and 3′-OH (gray box). Then the 5′-OH group of the 3′ tRNA half is phosphorylated by the GTP-dependent PNK (yellow box). In a third step, the ligase protein is adenylylated and the AMP is transferred to the 5′-phosphate of the 3′ tRNA half followed by the formation of the 2′-phosphomonoester-3′,5′-phosphodiester bond and the release of AMP. Finally, the 2′-phosphate at the splice junction is removed by a nicotinamide-adenine dinucleotide-dependent phosphotransferase (4, 6-11). This enzyme cascade is called the 5′-P (yeast-type) RNA ligation pathway.A PNK and an RNA ligase activity involved in the m...

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supporting

confidence: 85%

Section: Discussionsupporting

confidence: 54%

Branchiostoma floridae has separate healing and sealing enzymes for 5′-phosphate RNA ligation

Englert

Sheppard

Gundllapalli

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…CNPase is capable of rescuing yeast with the cyclic phosphodiesterase (CPDase) domain inactivated from the multifunctional tRNA ligase Trl1p, an essential protein for tRNA maturation [64] .…”

Section: Activitymentioning

confidence: 99%

“…This was supported by CNPase being able to bind RNA molecules and having phosphodiesterase activity towards oligonucleotides with terminal 2′,3′-cyclic monophosphates, which, prior to the discovery of the 2′,3′-cAMP pathway, were the only known endogenous molecules containing such a cyclic phosphodiester linkage [61][62][63] . Indicating enzymatic functionality in vivo,CNPase is capable of rescuing yeast with the cyclic phosphodiesterase (CPDase) domain inactivated from the multifunctional tRNA ligase Trl1p, an essential protein for tRNA maturation [64] .The enzymatic phosphodiesterase activity of CNPase is one of the best characterized features of the protein. The reaction itself was discovered together with the enzyme in the early 1960s, but the catalytically essential residues were identified 40 years later via mutagenesis [12,28] .…”

mentioning

confidence: 99%

The myelin membrane-associated enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase: on a highway to structure and function

Raasakka

Kursula

2014

Neurosci. Bull.

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The membrane-anchored myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase) was discovered in the early 1960s and has since then troubled scientists with its peculiar catalytic activity and high expression levels in the central nervous system. Despite decades of research, the actual physiological relevance of CNPase has only recently begun to unravel. In addition to a role in myelination, CNPase is also involved in local adenosine production in traumatic brain injury and possibly has a regulatory function in mitochondrial membrane permeabilization. Although research focusing on the CNPase phosphodiesterase activity has been helpful, several open questions concerning the protein function in vivo remain unanswered. This review is focused on past research on CNPase, especially in the fields of structural biology and enzymology, and outlines the current understanding regarding the biochemical and physiological signifi cance of CNPase, providing ideas and directions for future research.Keywords: 2′,3′-cyclic nucleotide 3′-phosphodiesterase; calmodulin; central nervous system; cytoskeleton; myelin proteins; RNA ·Review· IntroductionMyelin is a specialized multilamellar structure, which is wrapped around neuronal axons by oligodendrocytes in the central nervous system (CNS) and by Schwann cells in the peripheral nervous system (PNS). The membrane sheets of myelin are densely packed, resulting in the extrusion of cytosolic elements and in the formation of a lipid-rich, insulating sheath that enables the acceleration of nerve impulses. A mature myelin sheath can be morphologically divided into compact and non-compact myelin, of which the latter has a higher cytosolic content and further contains several subcompartments, such as the abaxonal and adaxonal layers, as well as the paranodal loops [1,2] .Myelin contains a set of unique proteins that generally display strict localization to either compact or non-compact myelin, which is thought to be at least partially driven by size exclusion [3,4] . The myelin environment being low in aqueous content and harboring negatively charged, tightly packed membrane interfaces, myelin proteins typically exhibit attributes such as strong hydrophobicity, peripheral membrane association, transmembrane domains, and a high positive net charge, as well as intrinsic disorder [5] .Several myelin proteins have delicately regulated expression levels and functions. Past research using cell culture and animal models have outlined the importance of various proteins in demyelination -a situation where myelin undergoes morphological changes and loss [6] .Demyelination causes neurological disorders, including multiple sclerosis (MS), Charcot-Marie-Tooth disease, and leukodystrophies, such as Pelizaeus-Merzbacher disease [7][8][9][10] .2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase)is one of the most abundant proteins in CNS myelin and a possible auto-antigen in MS [4,11] . The high expression levels of CNPase, together with its rather unusual enzymatic after the initial di...

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“…Rat CNPase can rescue yeast with an inactive tRNA ligase 2H domain, but not yeast with an inactive PNK domain 21 . On the other hand, lancelet CNPase can rescue the PNK-inactive mutants 44 .…”

Section: -13 -mentioning

confidence: 97%

Self-Assembly Characteristics of a Crystalline–Amorphous Diblock Copolymer in Nanoscale Thin Films

Kim

Ahn

et al. 2013

Macromolecules

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Abstract2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), a membrane-associated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the β5-α7 loop is observed. The role of the N terminus of helix α7 -unique for CNPase in the 2H family -during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms, despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms.

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Mammalian 2′,3′ cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo

Cited by 47 publications

References 43 publications

Branchiostoma floridae has separate healing and sealing enzymes for 5′-phosphate RNA ligation

Branchiostoma floridae has separate healing and sealing enzymes for 5′-phosphate RNA ligation

The myelin membrane-associated enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase: on a highway to structure and function

Self-Assembly Characteristics of a Crystalline–Amorphous Diblock Copolymer in Nanoscale Thin Films

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