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PARN – The Tail End: Function and mechanisms of specificity and processivity
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology. (Anders virtanen)
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Poly(A)-specific ribonuclease (PARN) is an exoribonuclease that is processive, poly(A) specific and cap-binding. PARN deadenylates the poly(A) tails present on a subset of mRNAs and non-coding RNAs, including among others certain snoRNAs, miRNAs and precursor rRNAs. 

Here, we have investigated molecular mechanisms behind PARN’s specificity for adenine and ribose, essential properties for PARN’s ability to degrade poly(A) on RNAs. We have applied enzyme kinetics and used divalent metal ions as mechanistic probes to show that PARN’s poly(A) specificity is tightly linked to a translocation event during the hydrolytic cycle of PARN action. 

To further understand the mechanism of PARN’s processive mode of action we are developing a kinetic model that allow us to measure the probability of processive action for each round of the hydrolytic cycle. Our kinetic model will be general and applicable to the processive action of any processive enzymatic activity. In conclusion, our study has so far established a mechanistic link between PARN’s processive mode of action, hydrolytic activity and preference for degrading poly(A). 

Human patients with genetic lesions in PARN suffer from a spectrum of syndromes called telomere biology disorders (TBD), which are associated with short telomeres. PARN is involved in the maturation of the snoRNA telomerase RNA component (TERC) that is used as template during the elongation of the telomer by the telomerase. Point mutations in the gene for PARN have been identified in patients. We show that point mutations in PARN that perturb its deadenylation activity correlated with TBDs and developmental disorders.

Our mechanistic studies of PARN action will provide a framework for our understanding of PARN’s physiological role and in extension the molecular basis for human diseases caused by perturbed PARN action. Our studies will also be of general interest for our detailed and mechanistic understanding of basic and essential mechanisms of gene expression and RNA biology.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. , p. 46
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1854
Keywords [en]
Poly(A) specific ribonuclease, Adenosine, Specificity, Processivty, Telomere biology disorders
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Cellbiology
Identifiers
URN: urn:nbn:se:uu:diva-392998ISBN: 978-91-513-0752-7 (print)OAI: oai:DiVA.org:uu-392998DiVA, id: diva2:1350890
Public defence
2019-10-31, B:21, Biomedicinskt centrum (BMC), Husargatan 3, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2019-10-08 Created: 2019-09-12 Last updated: 2019-10-15
List of papers
1. Specificity for adenine is established during the hydrolytic cycle of poly(A)-specific ribonuclease (PARN): Mechanism for poly(A) selectivity by PARN
Open this publication in new window or tab >>Specificity for adenine is established during the hydrolytic cycle of poly(A)-specific ribonuclease (PARN): Mechanism for poly(A) selectivity by PARN
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(English)In: Article in journal, Editorial material (Refereed) Submitted
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-392781 (URN)
Available from: 2019-09-09 Created: 2019-09-09 Last updated: 2019-09-12
2. Mechanisms of PARN action: Specificity and requirement for the 2’OH groups of the substrate
Open this publication in new window or tab >>Mechanisms of PARN action: Specificity and requirement for the 2’OH groups of the substrate
(English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-392970 (URN)
Available from: 2019-09-11 Created: 2019-09-11 Last updated: 2019-09-12
3. Mechanisms of PARN action: Kinetic analysis of processive mode of degradation
Open this publication in new window or tab >>Mechanisms of PARN action: Kinetic analysis of processive mode of degradation
(English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology
Research subject
Microbiology
Identifiers
urn:nbn:se:uu:diva-392971 (URN)
Available from: 2019-09-11 Created: 2019-09-11 Last updated: 2019-09-12
4. Bone marrow failure and developmental delay caused by mutations in poly(A)-specific ribonuclease (PARN)
Open this publication in new window or tab >>Bone marrow failure and developmental delay caused by mutations in poly(A)-specific ribonuclease (PARN)
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2015 (English)In: Journal of Medical Genetics, ISSN 0022-2593, E-ISSN 1468-6244, Vol. 52, no 11, p. 738-748Article in journal (Refereed) Published
Abstract [en]

Background Deadenylation regulates RNA function and fate. Poly(A)-specific ribonuclease (PARN) is a deadenylase that processes mRNAs and non-coding RNA. Little is known about the biological significance of germline mutations in PARN. Methods We identified mutations in PARN in patients with haematological and neurological manifestations. Genomic, biochemical and knockdown experiments in human marrow cells and in zebrafish have been performed to clarify the role of PARN in the human disease. Results We identified large monoallelic deletions in PARN in four patients with developmental delay or mental illness. One patient in particular had a severe neurological phenotype, central hypomyelination and bone marrow failure. This patient had an additional missense mutation on the non-deleted allele and severely reduced PARN protein and deadenylation activity. Cells from this patient had impaired oligoadenylation of specific H/ACA box small nucleolar RNAs. Importantly, PARN-deficient patient cells manifested short telomeres and an aberrant ribosome profile similar to those described in some variants of dyskeratosis congenita. Knocking down PARN in human marrow cells and zebrafish impaired haematopoiesis, providing further evidence for a causal link with the human disease. Conclusions Large monoallelic mutations of PARN can cause developmental/mental illness. Biallelic PARN mutations cause severe bone marrow failure and central hypomyelination.

Keywords
Genetics, Haematology (incl Blood transfusion), Copy-number, Molecular genetics, Neurology
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-269251 (URN)10.1136/jmedgenet-2015-103292 (DOI)000364633100003 ()26342108 (PubMedID)
Funder
Swedish Research Council
Available from: 2015-12-17 Created: 2015-12-15 Last updated: 2019-09-12Bibliographically approved
5. From incomplete penetrance with normal telomere length to severe disease and telomere shortening in a family with monoallelic and biallelic PARN pathogenic variants
Open this publication in new window or tab >>From incomplete penetrance with normal telomere length to severe disease and telomere shortening in a family with monoallelic and biallelic PARN pathogenic variants
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2019 (English)In: Human Mutation, ISSN 1059-7794, E-ISSN 1098-1004Article in journal (Refereed) Published
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-392969 (URN)10.1002/humu.23898 (DOI)
Available from: 2019-09-11 Created: 2019-09-11 Last updated: 2019-09-12

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