1
|
Hanley RP, Nie DY, Tabor JR, Li F, Sobh A, Xu C, Barker NK, Dilworth D, Hajian T, Gibson E, Szewczyk MM, Brown PJ, Barsyte-Lovejoy D, Herring LE, Wang GG, Licht JD, Vedadi M, Arrowsmith CH, James LI. Discovery of a Potent and Selective Targeted NSD2 Degrader for the Reduction of H3K36me2. J Am Chem Soc 2023; 145:8176-8188. [PMID: 36976643 PMCID: PMC10116495 DOI: 10.1021/jacs.3c01421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Nuclear receptor-binding SET domain-containing 2 (NSD2) plays important roles in gene regulation, largely through its ability to dimethylate lysine 36 of histone 3 (H3K36me2). Despite aberrant activity of NSD2 reported in numerous cancers, efforts to selectively inhibit the catalytic activity of this protein with small molecules have been unsuccessful to date. Here, we report the development of UNC8153, a novel NSD2-targeted degrader that potently and selectively reduces the cellular levels of both NSD2 protein and the H3K36me2 chromatin mark. UNC8153 contains a simple warhead that confers proteasome-dependent degradation of NSD2 through a novel mechanism. Importantly, UNC8153-mediated reduction of H3K36me2 through the degradation of NSD2 results in the downregulation of pathological phenotypes in multiple myeloma cells including mild antiproliferative effects in MM1.S cells containing an activating point mutation and antiadhesive effects in KMS11 cells harboring the t(4;14) translocation that upregulates NSD2 expression.
Collapse
Affiliation(s)
- Ronan P Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - John R Tabor
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Amin Sobh
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida 32610, United States
| | - Chenxi Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Natalie K Barker
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Elisa Gibson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Jonathan D Licht
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida 32610, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
2
|
Douvaras P, Lepack A, Buenaventura D, Sun B, Sira E, Ibourk M, Kosmyna B, Pereira E, Ebel M, Srinivas M, Simpson L, LoSchiavo D, Dilworth D, Wilkinson D, Keightley A, Domian I, Soh C, Wang J, Fisher S, Tomishima M, Paladini C, Patsch C, Irion S. iPSC: Late Breaking Abstract: A UNIVERSAL APPROACH TO TREAT CNS MANIFESTATIONS IN LYSOSOMAL STORAGE DISEASES USING IPSC-DERIVED MICROGLIA. Cytotherapy 2022. [DOI: 10.1016/s1465-3249(22)00398-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
3
|
Szewczyk MM, Luciani GM, Vu V, Murison A, Dilworth D, Barghout SH, Lupien M, Arrowsmith CH, Minden MD, Barsyte-Lovejoy D. PRMT5 regulates ATF4 transcript splicing and oxidative stress response. Redox Biol 2022; 51:102282. [PMID: 35305370 PMCID: PMC8933703 DOI: 10.1016/j.redox.2022.102282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/18/2022] [Accepted: 03/08/2022] [Indexed: 02/07/2023] Open
Abstract
Protein methyltransferase 5 (PRMT5) symmetrically dimethylates arginine residues leading to regulation of transcription and splicing programs. Although PRMT5 has emerged as an attractive oncology target, the molecular determinants of PRMT5 dependency in cancer remain incompletely understood. Our transcriptomic analysis identified PRMT5 regulation of the activating transcription factor 4 (ATF4) pathway in acute myelogenous leukemia (AML). PRMT5 inhibition resulted in the expression of unstable, intron-retaining ATF4 mRNA that is detained in the nucleus. Concurrently, the decrease in the spliced cytoplasmic transcript of ATF4 led to lower levels of ATF4 protein and downregulation of ATF4 target genes. Upon loss of functional PRMT5, cells with low ATF4 displayed increased oxidative stress, growth arrest, and cellular senescence. Interestingly, leukemia cells with EVI1 oncogene overexpression demonstrated dependence on PRMT5 function. EVI1 and ATF4 regulated gene signatures were inversely correlated. We show that EVI1-high AML cells have reduced ATF4 levels, elevated baseline reactive oxygen species and increased sensitivity to PRMT5 inhibition. Thus, EVI1-high cells demonstrate dependence on PRMT5 function and regulation of oxidative stress response. Overall, our findings identify the PRMT5-ATF4 axis to be safeguarding the cellular redox balance that is especially important in high oxidative stress states, such as those that occur with EVI1 overexpression.
Collapse
Affiliation(s)
| | - Genna M Luciani
- Department of Medical Biophysics, University of Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Samir H Barghout
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mark D Minden
- Department of Medical Biophysics, University of Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
4
|
Dilworth D, Hanley RP, Ferreira de Freitas R, Allali-Hassani A, Zhou M, Mehta N, Marunde MR, Ackloo S, Carvalho Machado RA, Khalili Yazdi A, Owens DDG, Vu V, Nie DY, Alqazzaz M, Marcon E, Li F, Chau I, Bolotokova A, Qin S, Lei M, Liu Y, Szewczyk MM, Dong A, Kazemzadeh S, Abramyan T, Popova IK, Hall NW, Meiners MJ, Cheek MA, Gibson E, Kireev D, Greenblatt JF, Keogh MC, Min J, Brown PJ, Vedadi M, Arrowsmith CH, Barsyte-Lovejoy D, James LI, Schapira M. A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization. Nat Chem Biol 2022; 18:56-63. [PMID: 34782742 PMCID: PMC9189931 DOI: 10.1038/s41589-021-00898-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/09/2021] [Indexed: 01/03/2023]
Abstract
Nuclear receptor-binding SET domain-containing 2 (NSD2) is the primary enzyme responsible for the dimethylation of lysine 36 of histone 3 (H3K36), a mark associated with active gene transcription and intergenic DNA methylation. In addition to a methyltransferase domain, NSD2 harbors two proline-tryptophan-tryptophan-proline (PWWP) domains and five plant homeodomains (PHDs) believed to serve as chromatin reading modules. Here, we report a chemical probe targeting the N-terminal PWWP (PWWP1) domain of NSD2. UNC6934 occupies the canonical H3K36me2-binding pocket of PWWP1, antagonizes PWWP1 interaction with nucleosomal H3K36me2 and selectively engages endogenous NSD2 in cells. UNC6934 induces accumulation of endogenous NSD2 in the nucleolus, phenocopying the localization defects of NSD2 protein isoforms lacking PWWP1 that result from translocations prevalent in multiple myeloma (MM). Mutations of other NSD2 chromatin reader domains also increase NSD2 nucleolar localization and enhance the effect of UNC6934. This chemical probe and the accompanying negative control UNC7145 will be useful tools in defining NSD2 biology.
Collapse
Affiliation(s)
- David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- BlueRock Therapeutics, Toronto, Ontario, Canada.
| | - Ronan P Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- C4 Therapeutics, Watertown, MA, USA
| | - Renato Ferreira de Freitas
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, Brazil
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Incyte, Wilmington, DE, USA
| | - Mengqi Zhou
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Naimee Mehta
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nurix Therapeutics, San Francisco, CA, USA
| | | | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mona Alqazzaz
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Life Science Research Center, Southern University of Science and Technology, Shenzhen, China
| | - Ming Lei
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | | | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Sina Kazemzadeh
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tigran Abramyan
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Atomwise, San Francisco, CA, USA
| | | | | | | | | | - Elisa Gibson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
5
|
Calhoun S, Bell TAS, Dahlin LR, Kunde Y, LaButti K, Louie KB, Kuftin A, Treen D, Dilworth D, Mihaltcheva S, Daum C, Bowen BP, Northen TR, Guarnieri MT, Starkenburg SR, Grigoriev IV. A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. Commun Biol 2021; 4:333. [PMID: 33712730 PMCID: PMC7955037 DOI: 10.1038/s42003-021-01859-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalga Scenedesmus sp. NREL 46B-D3 demonstrating peak growth near 25 °C that reaches 30 g/m2/day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.
Collapse
Affiliation(s)
- Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tisza Ann Szeremy Bell
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Division of Biological Sciences, Genome Core, University of Montana, Missoula, MT, USA
| | - Lukas R Dahlin
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Yuliya Kunde
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine B Louie
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrea Kuftin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Treen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Dilworth
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sirma Mihaltcheva
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin P Bowen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Shawn R Starkenburg
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
6
|
Zhou M, Abdali SH, Dilworth D, Liu L, Cole B, Malhan N, Ahkami AH, Winkler TE, Hollingsworth J, Sievert J, Dahlberg J, Hutmacher R, Madera M, Owiti JA, Hixson KK, Lemaux PG, Jansson C, Paša-Tolić L. Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers. J Vis Exp 2021. [PMID: 33749685 DOI: 10.3791/61707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors, including histone PTMs, are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for innovative bioengineering solutions. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed in their intact forms by top-down mass spectrometry (MS) coupled with online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow, thus, yielding the global PTM profile of core histones (H4, H2A, H2B, H3). We have applied this protocol previously to profile histone PTMs from sorghum leaf tissue collected from a large-scale field study, aimed at identifying epigenetic markers of drought resistance. The protocol could potentially be adapted and optimized for chromatin immunoprecipitation-sequencing (ChIP-seq), or for studying histone PTMs in similar plants.
Collapse
Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Shadan H Abdali
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - David Dilworth
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory
| | - Lifeng Liu
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Tanya E Winkler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Joy Hollingsworth
- Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources
| | - Julie Sievert
- Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources
| | - Jeff Dahlberg
- Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources
| | - Robert Hutmacher
- West Side Research and Extension Center, University of California; Department of Plant Sciences, University of California, Davis
| | - Mary Madera
- Department of Plant and Microbial Biology, University of California, Berkeley
| | - Judith A Owiti
- Department of Plant and Microbial Biology, University of California, Berkeley
| | - Kim K Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Peggy G Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory;
| |
Collapse
|
7
|
Ferreira de Freitas R, Liu Y, Szewczyk MM, Mehta N, Li F, McLeod D, Zepeda-Velázquez C, Dilworth D, Hanley RP, Gibson E, Brown PJ, Al-Awar R, James LI, Arrowsmith CH, Barsyte-Lovejoy D, Min J, Vedadi M, Schapira M, Allali-Hassani A. Discovery of Small-Molecule Antagonists of the PWWP Domain of NSD2. J Med Chem 2021; 64:1584-1592. [PMID: 33522809 DOI: 10.1021/acs.jmedchem.0c01768] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Increased activity of the lysine methyltransferase NSD2 driven by translocation and activating mutations is associated with multiple myeloma and acute lymphoblastic leukemia, but no NSD2-targeting chemical probe has been reported to date. Here, we present the first antagonists that block the protein-protein interaction between the N-terminal PWWP domain of NSD2 and H3K36me2. Using virtual screening and experimental validation, we identified the small-molecule antagonist 3f, which binds to the NSD2-PWWP1 domain with a Kd of 3.4 μM and abrogates histone H3K36me2 binding to the PWWP1 domain in cells. This study establishes an alternative approach to targeting NSD2 and provides a small-molecule antagonist that can be further optimized into a chemical probe to better understand the cellular function of this protein.
Collapse
Affiliation(s)
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Naimee Mehta
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - David McLeod
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Carlos Zepeda-Velázquez
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ronan P Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Elisa Gibson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | |
Collapse
|
8
|
Szewczyk MM, Ishikawa Y, Organ S, Sakai N, Li F, Halabelian L, Ackloo S, Couzens AL, Eram M, Dilworth D, Fukushi H, Harding R, Dela Seña CC, Sugo T, Hayashi K, McLeod D, Zepeda C, Aman A, Sánchez-Osuna M, Bonneil E, Takagi S, Al-Awar R, Tyers M, Richard S, Takizawa M, Gingras AC, Arrowsmith CH, Vedadi M, Brown PJ, Nara H, Barsyte-Lovejoy D. Author Correction: Pharmacological inhibition of PRMT7 links arginine monomethylation to the cellular stress response. Nat Commun 2020; 11:2683. [PMID: 32457299 PMCID: PMC7250816 DOI: 10.1038/s41467-020-16613-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Yoshinori Ishikawa
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Shawna Organ
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nozomu Sakai
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Amber L Couzens
- Network Biology Collaborative Centre at the Lunenfeld-Tanenbaum Research Institute, 600 University Ave, Room 992, Toronto, ON, M5G 1X5, Canada
| | - Mohammad Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Hideto Fukushi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Rachel Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Carlo C Dela Seña
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Tsukasa Sugo
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Kozo Hayashi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - David McLeod
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Carlos Zepeda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Maria Sánchez-Osuna
- Institute for Research in Immunology and Cancer (IRIC) University of Montreal, 2950 Chemin de Polytechnique, Montreal, QC, H3T 1J4, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC) University of Montreal, 2950 Chemin de Polytechnique, Montreal, QC, H3T 1J4, Canada
| | - Shinji Takagi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer (IRIC) University of Montreal, 2950 Chemin de Polytechnique, Montreal, QC, H3T 1J4, Canada
| | - Stephane Richard
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Masayuki Takizawa
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Anne-Claude Gingras
- Network Biology Collaborative Centre at the Lunenfeld-Tanenbaum Research Institute, 600 University Ave, Room 992, Toronto, ON, M5G 1X5, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Hiroshi Nara
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Nature Research Center, Vilnius, Akademijos 2, Lithuania.
| |
Collapse
|
9
|
Allali-Hassani A, Szewczyk MM, Ivanochko D, Organ SL, Bok J, Ho JSY, Gay FPH, Li F, Blazer L, Eram MS, Halabelian L, Dilworth D, Luciani GM, Lima-Fernandes E, Wu Q, Loppnau P, Palmer N, Talib SZA, Brown PJ, Schapira M, Kaldis P, O'Hagan RC, Guccione E, Barsyte-Lovejoy D, Arrowsmith CH, Sanders JM, Kattar SD, Bennett DJ, Nicholson B, Vedadi M. Discovery of a chemical probe for PRDM9. Nat Commun 2019; 10:5759. [PMID: 31848333 PMCID: PMC6917776 DOI: 10.1038/s41467-019-13652-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC50: 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.
Collapse
Affiliation(s)
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Shawna L Organ
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Jabez Bok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florence P H Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levi Blazer
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Genna M Luciani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Qin Wu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - S Zakiah A Talib
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore (NUS), Department of Biochemistry, 117597, Singapore, Singapore
| | - Ronan C O'Hagan
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Nature Research Center, Vilnius, Akademijos, 2, Lithuania
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - John M Sanders
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Solomon D Kattar
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | | | - Benjamin Nicholson
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
10
|
Savic N, Shortill SP, Bilenky M, Dobbs JM, Dilworth D, Hirst M, Nelson CJ. Histone Chaperone Paralogs Have Redundant, Cooperative, and Divergent Functions in Yeast. Genetics 2019; 213:1301-1316. [PMID: 31604797 PMCID: PMC6893378 DOI: 10.1534/genetics.119.302235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/03/2019] [Indexed: 01/03/2023] Open
Abstract
Gene duplications increase organismal robustness by providing freedom for gene divergence or by increasing gene dosage. The yeast histone chaperones Fpr3 and Fpr4 are paralogs that can assemble nucleosomes in vitro; however, the genomic locations they target and their functional relationship is poorly understood. We refined the yeast synthetic genetic array approach to enable the functional dissection of gene paralogs. Applying this method to Fpr3 and Fpr4 uncovered redundant, cooperative, and divergent functions. While Fpr3 is uniquely involved in chromosome segregation, Fpr3 and Fpr4 cooperate to regulate genes involved in polyphosphate metabolism and ribosome biogenesis. We find that the TRAMP5 RNA exosome is critical for fitness in Δfpr3Δfpr4 yeast and leverage this information to identify an important role for Fpr4 at the 5' ends of protein coding genes. Additionally, Fpr4 and TRAMP5 negatively regulate RNAs from the nontranscribed spacers of ribosomal DNA. Yeast lacking Fpr3 and Fpr4 exhibit a genome instability phenotype at the ribosomal DNA, which implies that these histone chaperones regulate chromatin structure and DNA access at this location. Taken together. we provide genetic and transcriptomic evidence that Fpr3 and Fpr4 operate separately, cooperatively, and redundantly to regulate a variety of chromatin environments.
Collapse
Affiliation(s)
- Neda Savic
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - Shawn P Shortill
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - Misha Bilenky
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Joseph M Dobbs
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - David Dilworth
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - Martin Hirst
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Christopher J Nelson
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| |
Collapse
|
11
|
Lütkenhaus R, Traeger S, Breuer J, Carreté L, Kuo A, Lipzen A, Pangilinan J, Dilworth D, Sandor L, Pöggeler S, Gabaldón T, Barry K, Grigoriev IV, Nowrousian M. Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes. Genetics 2019; 213:1545-1563. [PMID: 31604798 PMCID: PMC6893386 DOI: 10.1534/genetics.119.302749] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/08/2019] [Indexed: 02/08/2023] Open
Abstract
Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.
Collapse
Affiliation(s)
- Ramona Lütkenhaus
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Stefanie Traeger
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jan Breuer
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Laia Carreté
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - David Dilworth
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, 37077 Göttingen, Germany
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08002 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Kerrie Barry
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- Department of Plant and Microbial Biology, University of California Berkeley, California 94720
| | - Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
| |
Collapse
|
12
|
Jain R, Jenkins J, Shu S, Chern M, Martin JA, Copetti D, Duong PQ, Pham NT, Kudrna DA, Talag J, Schackwitz WS, Lipzen AM, Dilworth D, Bauer D, Grimwood J, Nelson CR, Xing F, Xie W, Barry KW, Wing RA, Schmutz J, Li G, Ronald PC. Genome sequence of the model rice variety KitaakeX. BMC Genomics 2019; 20:905. [PMID: 31775618 PMCID: PMC6882167 DOI: 10.1186/s12864-019-6262-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/05/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. RESULTS Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. CONCLUSIONS The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.
Collapse
Affiliation(s)
- Rashmi Jain
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jerry Jenkins
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joel A Martin
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Phat Q Duong
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nikki T Pham
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wendy S Schackwitz
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna M Lipzen
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - David Dilworth
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Diane Bauer
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jane Grimwood
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Catherine R Nelson
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Feng Xing
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Kerrie W Barry
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines
| | - Jeremy Schmutz
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guotian Li
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. .,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,The Provincial Key Lab of Plant Pathology of Hubei Province and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. .,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
13
|
Xiong Y, Greschik H, Johansson C, Seifert L, Bacher J, Park KS, Babault N, Martini M, Fagan V, Li F, Chau I, Christott T, Dilworth D, Barsyte-Lovejoy D, Vedadi M, Arrowsmith CH, Brennan P, Fedorov O, Jung M, Farnie G, Liu J, Oppermann U, Schüle R, Jin J. Discovery of a Potent and Selective Fragment-like Inhibitor of Methyllysine Reader Protein Spindlin 1 (SPIN1). J Med Chem 2019; 62:8996-9007. [PMID: 31260300 DOI: 10.1021/acs.jmedchem.9b00522] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
By screening an epigenetic compound library, we identified that UNC0638, a highly potent inhibitor of the histone methyltransferases G9a and GLP, was a weak inhibitor of SPIN1 (spindlin 1), a methyllysine reader protein. Our optimization of this weak hit resulted in the discovery of a potent, selective, and cell-active SPIN1 inhibitor, compound 3 (MS31). Compound 3 potently inhibited binding of trimethyllysine-containing peptides to SPIN1, displayed high binding affinity, was highly selective for SPIN1 over other epigenetic readers and writers, directly engaged SPIN1 in cells, and was not toxic to nontumorigenic cells. The crystal structure of the SPIN1-compound 3 complex indicated that it selectively binds tudor domain II of SPIN1. We also designed a structurally similar but inactive compound 4 (MS31N) as a negative control. Our results have demonstrated for the first time that potent, selective, and cell-active fragment-like inhibitors can be generated by targeting a single tudor domain.
Collapse
Affiliation(s)
- Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Holger Greschik
- Department of Urology and Center for Clinical Research , University Freiburg Medical Center , Freiburg 79106 , Germany
| | - Catrine Johansson
- Structural Genomics Consortium, Botnar Research Center, NIHR Oxford BRU , University of Oxford , Oxford OX37LD , U.K
| | - Ludwig Seifert
- Institute of Pharmaceutical Sciences , University of Freiburg , Freiburg 79104 , Germany
| | - Johannes Bacher
- Institute of Pharmaceutical Sciences , University of Freiburg , Freiburg 79104 , Germany
| | - Kwang-Su Park
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Nicolas Babault
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Michael Martini
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Vincent Fagan
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | | | | | - Thomas Christott
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | | | | | - Masoud Vedadi
- Department of Pharmacology and Toxicology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada
| | | | - Paul Brennan
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | - Manfred Jung
- Institute of Pharmaceutical Sciences , University of Freiburg , Freiburg 79104 , Germany
- German Cancer Research Centre (DKFZ) , Heidelberg 69120 , Germany
- German Cancer Consortium (DKTK) , Freiburg 79106 , Germany
| | - Gillian Farnie
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Udo Oppermann
- Structural Genomics Consortium, Botnar Research Center, NIHR Oxford BRU , University of Oxford , Oxford OX37LD , U.K
| | - Roland Schüle
- Department of Urology and Center for Clinical Research , University Freiburg Medical Center , Freiburg 79106 , Germany
- BIOSS Centre of Biological Signalling Studies , University of Freiburg , Freiburg 79106 , Germany
- German Cancer Consortium (DKTK) , Freiburg 79106 , Germany
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| |
Collapse
|
14
|
Dilworth D, Arrowsmith CH. Guiding COMPASS: Dpy-30 Positions SET1/MLL Epigenetic Signaling. Structure 2019; 26:1567-1570. [PMID: 30517884 DOI: 10.1016/j.str.2018.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this issue of Structure, Haddad et al. (2018) solve the high-resolution trimeric crystal structure of human COMPASS-like components Dpy-30 and Ash2L (2:1) to unravel an uncharacterized interaction surface required for competent H3K4 methylation in cells and clarify Dpy-30's role in the allosteric regulation of KMT2 enzymes.
Collapse
Affiliation(s)
- David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
15
|
Dilworth D, Barsyte-Lovejoy D. Targeting protein methylation: from chemical tools to precision medicines. Cell Mol Life Sci 2019; 76:2967-2985. [PMID: 31104094 DOI: 10.1007/s00018-019-03147-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/15/2022]
Abstract
The methylation of proteins is integral to the execution of many important biological functions, including cell signalling and transcriptional regulation. Protein methyltransferases (PMTs) are a large class of enzymes that carry out the addition of methyl marks to a broad range of substrates. PMTs are critical for normal cellular physiology and their dysregulation is frequently observed in human disease. As such, PMTs have emerged as promising therapeutic targets with several inhibitors now in clinical trials for oncology indications. The discovery of chemical inhibitors and antagonists of protein methylation signalling has also profoundly impacted our general understanding of PMT biology and pharmacology. In this review, we present general principles for drugging protein methyltransferases or their downstream effectors containing methyl-binding modules, as well as best-in-class examples of the compounds discovered and their impact both at the bench and in the clinic.
Collapse
Affiliation(s)
- David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
| |
Collapse
|
16
|
Abstract
FK506-binding proteins (FKBPs) alter the conformation of proteins via cis-trans isomerization of prolyl-peptide bonds. While this activity can be demonstrated in vitro, the intractability of detecting prolyl isomerization events in cells has limited our understanding of the biological processes regulated by FKBPs. Here we report that FKBP25 is an active participant in the repair of DNA double-strand breaks (DSBs). FKBP25 influences DSB repair pathway choice by promoting homologous recombination (HR) and suppressing single-strand annealing (SSA). Consistent with this observation, cells depleted of FKBP25 form fewer Rad51 repair foci in response to etoposide and ionizing radiation, and they are reliant on the SSA repair factor Rad52 for viability. We find that FKBP25’s catalytic activity is required for promoting DNA repair, which is the first description of a biological function for this enzyme activity. Consistent with the importance of the FKBP catalytic site in HR, rapamycin treatment also impairs homologous recombination, and this effect is at least in part independent of mTor. Taken together these results identify FKBP25 as a component of the DNA DSB repair pathway.
Collapse
Affiliation(s)
- David Dilworth
- The Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Fade Gong
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712 USA
| | - Kyle Miller
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712 USA
| | - Christopher J Nelson
- The Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| |
Collapse
|
17
|
Luciani GM, Xie L, Dilworth D, Tierens A, Moskovitz Y, Murison A, Szewczyk MM, Mitchell A, Lupien M, Shlush L, Dick JE, Arrowsmith CH, Barsyte-Lovejoy D, Minden MD. Characterization of inv(3) cell line OCI-AML-20 with stroma-dependent CD34 expression. Exp Hematol 2018; 69:27-36. [PMID: 30352278 DOI: 10.1016/j.exphem.2018.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 11/26/2022]
Abstract
Acute myeloid leukemia (AML) is a complex, heterogeneous disease with variable outcomes following curative intent chemotherapy. AML with inv(3) is a genetic subgroup characterized by a very low response rate to current induction type chemotherapy and thus has among the worst long-term survivorship of the AMLs. Here, we describe OCI-AML-20, a new AML cell line with inv(3) and deletion of chromosome 7; the latter is a common co-occurrence in inv(3) AML. In OCI-AML-20, CD34 expression is maintained and required for repopulation in vitro and in vivo. CD34 expression in OCI-AML-20 shows dependence on the co-culture with stromal cells. Transcriptome analysis indicates that the OCI-AML-20 clusters with other AML patient data sets that have poor prognosis, as well as other AML cell lines, including another inv(3) line, MUTZ-3. OCI-AML-20 is a new cell line resource for studying the biology of inv(3) AML that can be used to identify potential therapies for this poor outcome disease.
Collapse
Affiliation(s)
- Genna M Luciani
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Lihua Xie
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Anne Tierens
- Toronto General Hospital, Laboratory Medicine Program, Toronto, Ontario, Canada
| | - Yoni Moskovitz
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Alex Murison
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Liran Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - John E Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | | | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada.
| |
Collapse
|
18
|
Daly P, López SC, Peng M, Lancefield CS, Purvine SO, Kim Y, Zink EM, Dohnalkova A, Singan VR, Lipzen A, Dilworth D, Wang M, Ng V, Robinson E, Orr G, Baker SE, Bruijnincx PCA, Hildén KS, Grigoriev IV, Mäkelä MR, de Vries RP. Dichomitus squalens
partially tailors its molecular responses to the composition of solid wood. Environ Microbiol 2018; 20:4141-4156. [DOI: 10.1111/1462-2920.14416] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Paul Daly
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
| | - Sara Casado López
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
| | - Mao Peng
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
| | - Christopher S. Lancefield
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science Utrecht University Utrecht The Netherlands
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Young‐Mo Kim
- Biological Sciences Division Pacific Northwest National Laboratory Richland WA USA
| | - Erika M. Zink
- Biological Sciences Division Pacific Northwest National Laboratory Richland WA USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - David Dilworth
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - Errol Robinson
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Scott E. Baker
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Pieter C. A. Bruijnincx
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science Utrecht University Utrecht The Netherlands
| | | | | | - Miia R. Mäkelä
- Department of Microbiology University of Helsinki Helsinki Finland
| | - Ronald P. de Vries
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
- Department of Microbiology University of Helsinki Helsinki Finland
| |
Collapse
|
19
|
Kalinin AA, Allyn-Feuer A, Ade A, Fon GV, Meixner W, Dilworth D, Husain SS, de Wet JR, Higgins GA, Zheng G, Creekmore A, Wiley JW, Verdone JE, Veltri RW, Pienta KJ, Coffey DS, Athey BD, Dinov ID. 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification. Sci Rep 2018; 8:13658. [PMID: 30209281 PMCID: PMC6135819 DOI: 10.1038/s41598-018-31924-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/29/2018] [Indexed: 02/08/2023] Open
Abstract
Quantitative analysis of morphological changes in a cell nucleus is important for the understanding of nuclear architecture and its relationship with pathological conditions such as cancer. However, dimensionality of imaging data, together with a great variability of nuclear shapes, presents challenges for 3D morphological analysis. Thus, there is a compelling need for robust 3D nuclear morphometric techniques to carry out population-wide analysis. We propose a new approach that combines modeling, analysis, and interpretation of morphometric characteristics of cell nuclei and nucleoli in 3D. We used robust surface reconstruction that allows accurate approximation of 3D object boundary. Then, we computed geometric morphological measures characterizing the form of cell nuclei and nucleoli. Using these features, we compared over 450 nuclei with about 1,000 nucleoli of epithelial and mesenchymal prostate cancer cells, as well as 1,000 nuclei with over 2,000 nucleoli from serum-starved and proliferating fibroblast cells. Classification of sets of 9 and 15 cells achieved accuracy of 95.4% and 98%, respectively, for prostate cancer cells, and 95% and 98% for fibroblast cells. To our knowledge, this is the first attempt to combine these methods for 3D nuclear shape modeling and morphometry into a highly parallel pipeline workflow for morphometric analysis of thousands of nuclei and nucleoli in 3D.
Collapse
Affiliation(s)
- Alexandr A Kalinin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.,Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan School of Nursing, Ann Arbor, MI, USA
| | - Ari Allyn-Feuer
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alex Ade
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gordon-Victor Fon
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Walter Meixner
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David Dilworth
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Syed S Husain
- Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan School of Nursing, Ann Arbor, MI, USA
| | - Jeffrey R de Wet
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gerald A Higgins
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gen Zheng
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Amy Creekmore
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John W Wiley
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James E Verdone
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert W Veltri
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth J Pienta
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donald S Coffey
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian D Athey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. .,Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, MI, USA.
| | - Ivo D Dinov
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. .,Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan School of Nursing, Ann Arbor, MI, USA. .,Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
20
|
Zuo C, Blow M, Sreedasyam A, Kuo RC, Ramamoorthy GK, Torres-Jerez I, Li G, Wang M, Dilworth D, Barry K, Udvardi M, Schmutz J, Tang Y, Xu Y. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnol Biofuels 2018; 11:170. [PMID: 29951114 PMCID: PMC6009963 DOI: 10.1186/s13068-018-1167-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/08/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. RESULTS We present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. CONCLUSIONS Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.
Collapse
Affiliation(s)
- Chunman Zuo
- College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA USA
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
| | - Matthew Blow
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Rita C. Kuo
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | | | - Guifen Li
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - David Dilworth
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Yuhong Tang
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Ying Xu
- College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA USA
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
| |
Collapse
|
21
|
Dilworth D, Gudavicius G, Xu X, Boyce AKJ, O’Sullivan C, Serpa JJ, Bilenky M, Petrochenko EV, Borchers CH, Hirst M, Swayne LA, Howard P, Nelson CJ. The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability. Nucleic Acids Res 2018; 46:2459-2478. [PMID: 29361176 PMCID: PMC5861405 DOI: 10.1093/nar/gky008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/14/2017] [Accepted: 01/12/2018] [Indexed: 12/25/2022] Open
Abstract
FK506 binding proteins (FKBPs) catalyze the interconversion of cis-trans proline conformers in proteins. Importantly, FK506 drugs have anti-cancer and neuroprotective properties, but the effectors and mechanisms underpinning these properties are not well understood because the cellular function(s) of most FKBP proteins are unclear. FKBP25 is a nuclear prolyl isomerase that interacts directly with nucleic acids and is associated with several DNA/RNA binding proteins. Here, we show the catalytic FKBP domain binds microtubules (MTs) directly to promote their polymerization and stabilize the MT network. Furthermore, FKBP25 associates with the mitotic spindle and regulates entry into mitosis. This interaction is important for mitotic spindle dynamics, as we observe increased chromosome instability in FKBP25 knockdown cells. Finally, we provide evidence that FKBP25 association with chromatin is cell-cycle regulated by Protein Kinase C phosphorylation. This disrupts FKBP25-DNA contacts during mitosis while maintaining its interaction with the spindle apparatus. Collectively, these data support a model where FKBP25 association with chromatin and MTs is carefully choreographed to ensure faithful genome duplication. Additionally, they highlight that FKBP25 is a MT-associated FK506 receptor and potential therapeutic target in MT-associated diseases.
Collapse
Affiliation(s)
- David Dilworth
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Geoff Gudavicius
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Xiaoxue Xu
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
| | - Andrew K J Boyce
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
| | - Connor O’Sullivan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Jason J Serpa
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Misha Bilenky
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Evgeniy V Petrochenko
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Martin Hirst
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Perry Howard
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| |
Collapse
|
22
|
Dilworth D, Upadhyay SK, Bonnafous P, Edoo AB, Bourbigot S, Pesek-Jardim F, Gudavicius G, Serpa JJ, Petrotchenko EV, Borchers CH, Nelson CJ, Mackereth CD. The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module. Nucleic Acids Res 2017; 45:11989-12004. [PMID: 29036638 PMCID: PMC5714180 DOI: 10.1093/nar/gkx852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/13/2017] [Indexed: 11/14/2022] Open
Abstract
Prolyl isomerases are defined by a catalytic domain that facilitates the cis–trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors. An independent mobility of the BTHB and FKBP catalytic domains supports a model by which the N-terminus of FKBP25 is anchored to regions of dsRNA, whereas the FKBP domain is free to interact with neighboring proteins. Apart from the identification of the BTHB as a new dsRNA-binding module, this domain adds to the growing list of auxiliary functions used by prolyl isomerases to define their primary cellular targets.
Collapse
Affiliation(s)
- David Dilworth
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Santosh K Upadhyay
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France.,CSIR-Institute of Genomics and Integrative Biology, New Delhi 110020, India
| | - Pierre Bonnafous
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Amiirah Bibi Edoo
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Sarah Bourbigot
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Francy Pesek-Jardim
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Geoff Gudavicius
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Jason J Serpa
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC V8Z 7X8, Canada
| | - Evgeniy V Petrotchenko
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC V8Z 7X8, Canada
| | - Christopher J Nelson
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Cameron D Mackereth
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| |
Collapse
|
23
|
Dilworth D, Nelson CJ. Rapid identification of chemical genetic interactions in Saccharomyces cerevisiae. J Vis Exp 2015:e52345. [PMID: 25867090 DOI: 10.3791/52345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described.
Collapse
Affiliation(s)
- David Dilworth
- Department of Biochemistry and Microbiology, University of Victoria
| | | |
Collapse
|
24
|
Gudavicius G, Dilworth D, Serpa JJ, Sessler N, Petrotchenko EV, Borchers CH, Nelson CJ. The prolyl isomerase, FKBP25, interacts with RNA-engaged nucleolin and the pre-60S ribosomal subunit. RNA 2014; 20:1014-22. [PMID: 24840943 PMCID: PMC4114681 DOI: 10.1261/rna.042648.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/27/2014] [Indexed: 05/26/2023]
Abstract
Peptidyl-proline isomerases of the FK506-binding protein (FKBP) family belong to a class of enzymes that catalyze the cis-trans isomerization of prolyl-peptide bonds in proteins. A handful of FKBPs are found in the nucleus, implying that the isomerization of proline in nuclear proteins is enzymatically controlled. FKBP25 is a nuclear protein that has been shown to associate with chromatin modifiers and transcription factors. In this study, we performed the first proteomic characterization of FKBP25 and found that it interacts with numerous ribosomal proteins, ribosomal processing factors, and a small selection of chromatin modifiers. In agreement with previous reports, we found that nucleolin is a major FKBP25-interacting protein and demonstrated that this interaction is dependent on rRNA. FKBP25 interacts with the immature large ribosomal subunit in nuclear extract but does not associate with mature ribosomes, implicating this FKBP's action in ribosome biogenesis. Despite engaging nascent 60S ribosomes, FKBP25 does not affect steady-state levels of rRNAs or its pre-rRNA intermediates. We conclude that FKBP25 is likely recruited to preribosomes to chaperone one of the protein components of the ribosome large subunit.
Collapse
Affiliation(s)
- Geoff Gudavicius
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P5C2, Canada
| | - David Dilworth
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P5C2, Canada
| | - Jason J. Serpa
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P5C2, Canada
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z7X8, Canada
| | - Nicole Sessler
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P5C2, Canada
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z7X8, Canada
| | - Evgeniy V. Petrotchenko
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P5C2, Canada
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z7X8, Canada
| | - Christoph H. Borchers
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P5C2, Canada
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z7X8, Canada
| | - Christopher J. Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P5C2, Canada
| |
Collapse
|
25
|
Abstract
The post-translational modification of proteins and enzymes provides a dynamic and reversible means to control protein function and transmit biological signals. While covalent modifications such as phosphorylation and acetylation have drawn much attention, in the past decade the involvement of peptidyl-proline isomerases (PPIs) in signaling and post-translational modification of protein function has become increasingly apparent. Three distinct families of PPI enzymes (parvulins, cyclophilins, and FK506-binding proteins (FKBPs)) each have the capacity to catalyze cis-trans proline isomerization in substrate proteins, and this modification can regulate both structure and function. In eukaryotic cells, a subset of these enzymes is localized to the nucleus, where they regulate gene expression at multiple control points. Here we summarize this body of work that together establishes a clear role of these enzymes as evolutionarily conserved players in the control of both transcription of mRNAs and the assembly of chromatin.
Collapse
Affiliation(s)
- David Dilworth
- The Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | | | | | | |
Collapse
|
26
|
Dilworth D, Liu L, Stewart AK, Berenson JR, Lassam N, Hogg D. Germline CDKN2A mutation implicated in predisposition to multiple myeloma. Blood 2000; 95:1869-71. [PMID: 10688850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Germline mutations of the CDKN2A (p16(INK4A)) tumor suppressor gene predispose patients to melanoma and pancreatic carcinoma. In contrast, mutations of the murine CDKN2A gene predispose BALB/c mice to pristane-induced plasmacytoma. We describe here a family in which a germline mutation of CDKN2A is present in 4 individuals who developed melanoma as well as in a fifth family member who is suffering from multiple myeloma. To determine whether the CDKN2A mutation predisposed the myeloma patient to her disease, we carried out loss of heterozygosity studies on sorted bone marrow from this individual and observed loss of the wild type CDKN2A allele in the malignant plasma cells. We suggest that germline mutations of CDKN2A may predispose individuals to a wider variety of malignancy than has been hitherto reported, but that the expression of these cancers may depend heavily on the genetic background of the patient. (Blood. 2000;95:1869-1871)
Collapse
Affiliation(s)
- D Dilworth
- Departments of Medical Biophysics, Clinical Science, and Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | |
Collapse
|
27
|
Liu L, Dilworth D, Gao L, Monzon J, Summers A, Lassam N, Hogg D. Mutation of the CDKN2A 5' UTR creates an aberrant initiation codon and predisposes to melanoma. Nat Genet 1999; 21:128-32. [PMID: 9916806 DOI: 10.1038/5082] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Approximately 8-12% of melanoma is inherited in an autosomal dominant fashion with variable penetrance. A chromosome 9p21 locus has been linked to this disease in 50-80% of affected families. CDKN2A (also known as P16, INK4, p16INK4A and MTS1) is allelic to this locus and encodes a cdk4/cdk6 kinase inhibitor that constrains cells from progressing through the G1 restriction point. Although germline CDKN2A coding mutations cosegregate with melanoma in 25-60% of families predisposed to the disease, there remains a number of mutation-negative families that demonstrate linkage of inherited melanoma to 9p21 markers. We show here that a subset of these kindreds possess a G-->T transversion at base -34 of CDKN2A, designated G-34T. This mutation gives rise to a novel AUG translation initiation codon that decreases translation from the wild-type AUG. The G-34T mutation is not seen in controls, segregates with melanoma in families and, on the basis of haplotyping studies, probably arose from a common founder in the United Kingdom. Characterization of this and other CDKN2A non-coding mutations should have an impact on current efforts to identify susceptible melanoma-prone families and individuals.
Collapse
Affiliation(s)
- L Liu
- Department of Clinical Science, University of Toronto, Ontario, Canada
| | | | | | | | | | | | | |
Collapse
|
28
|
Abstract
A method for imaging through highly scattering media is described that consists of forming a multiplicity of holograms and performing an extensive averaging process. This process produces an estimate of the phase distribution across the exiting surface of the medium. This information is combined with the available magnitude data to form an ensemble-averaged wave front that can be backprojected to form an image of absorbers within or behind the scattering medium.
Collapse
|
29
|
Naulleau P, Dilworth D. Motion-resolved imaging of moving objects embedded within scattering media by the use of time-gated speckle analysis. Appl Opt 1996; 35:5251-5257. [PMID: 21127516 DOI: 10.1364/ao.35.005251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Spectral analysis of a time-evolving speckle pattern is used to provide motion-resolved detection of moving objects embedded within scattering media. Results show that the ability to detect small nonstationary scattering objects and to discriminate between objects moving at different rates is greatly enhanced.
Collapse
|
30
|
Abstract
A noise analysis is performed on an electronic holography first-arriving-light system. Analytical expressions for the signal-to-noise ratio caused by the dominant noise terms are derived. The effect of various system parameters on the signal-to-noise ratio is explored; numerical and experimental examples are given.
Collapse
|
31
|
Arons E, Dilworth D. Improved imagery through scattering materials by quasi-Fourier-synthesis holography. Appl Opt 1996; 35:3104-3108. [PMID: 21102687 DOI: 10.1364/ao.35.003104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
An improvement on the technique of Fourier-synthesis holography is proposed and demonstrated. Artifacts produced during the process of sampling are eliminated when the laser is swept over a continuous bandwidth between samples. The advantages of Fourier-synthesis holography, such as the ability to select the gating time delay and to shape the autocorrelation function after data acquisition, are retained.
Collapse
|
32
|
Naulleau P, Dilworth D, Leith E, Lopez J. Resolution-enhanced detection of moving objects embedded within scattering media using time-gated speckle methods. Appl Opt 1996; 35:3065-3067. [PMID: 21085460 DOI: 10.1364/ao.35.003065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The holographic first-arriving-light method in combination with the speckle differencing method is used to provide resolution-enhanced detection of moving objects embedded in scattering media. Results show that the first-arriving-light technique provides significant resolution improvements over standard speckle differencing.
Collapse
|
33
|
Abstract
The technique of Fourier synthesis holography is extended to the spatial domain. A spatially extended source is decomposed into its Fourier components, and a hologram of an object distribution is formed at each spatial frequency and stored in a computer. Upon synthesis in the computer a clear image can be formed of the object without the use of lenses.
Collapse
|
34
|
Naulleau P, Dilworth D. Holographic first-arriving-light signal-to-noise ratio enhancement by differential holography. Opt Lett 1995; 20:2354. [PMID: 19865217 DOI: 10.1364/ol.20.002354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
35
|
Abstract
The technique of Fourier synthesis holography to image through scattering materials is analyzed in detail. A broad spectral source is decomposed into its Fourier components, and a hologram is formed at each wavelength and stored in the computer. Upon synthesis in the computer, a clear image can be formed of the obscured object. Post-data-acquisition processing such as selection of the gating time delay and autocorrelation shaping are also demonstrated.
Collapse
|
36
|
Naulleau P, Dilworth D, Leith E, Lopez J. Detection of moving objects embedded within scattering media by use of speckle methods. Opt Lett 1995; 20:498-500. [PMID: 19859233 DOI: 10.1364/ol.20.000498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Speckle-pattern subtraction methods are used for the detection of moving objects embedded in scattering media. Results show that the ability to detect small nonstationary objects is greatly enhanced.
Collapse
|
37
|
Chen H, Shih M, Arons E, Leith E, Lopez J, Dilworth D, Sun PC. Electronic holographic imaging through living human tissue. Appl Opt 1994; 33:3630-3632. [PMID: 20885752 DOI: 10.1364/ao.33.003630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electronic holography and a swept-frequency dye laser are used with the first-arriving-light method to image an absorbing object through the flesh of a human hand. Holography with living human tissue without the use of high-peak-power lasers is made possible by the high sensitivity of the CCD camera as well as its capability for making a large number of holograms in rapid succession, thus enabling the images to be combined to produce a resultant image with an improved signal-to-noise ratio.
Collapse
|
38
|
Abstract
A method for image formation through inhomogeneities is demonstrated. A broad spectral source is decomposed into its Fourier components, and a hologram is recorded at each wavelength through a diffusing medium. When the holograms are synthesized in a computer, a clear image can be formed of the obscured object.
Collapse
|
39
|
Chen Y, Chen H, Dilworth D, Leith E, Lopez J, Shih M, Sun PC, Vossler G. Evaluation of holographic methods for imaging through biological tissue. Appl Opt 1993; 32:4330-4336. [PMID: 20830089 DOI: 10.1364/ao.32.004330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Different holographic methods for imaging through biological tissue are evaluated and compared. The role of the source autocorrelation function is analyzed. A graphical plot for performance evaluation is introduced. Experimental results for the various methods are given, and possibilities for further development are indicated.
Collapse
|
40
|
Leith EN, Chen C, Chen H, Chen Y, Lopez J, Sun PC, Dilworth D. Imaging through scattering media using spatial incoherence techniques. Opt Lett 1991; 16:1820-2. [PMID: 19784149 DOI: 10.1364/ol.16.001820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Imaging of objects embedded in scattering media can be accomplished by sources with reduced spatial coherence instead of pulsed light or short temporal coherence light.
Collapse
|
41
|
Leith E, Chen H, Chen Y, Dilworth D, Lopez J, Masri R, Rudd J, Valdmanis J. Electronic holography and speckle methods for imaging through tissue using femtosecond gated pulses. Appl Opt 1991; 30:4204-4210. [PMID: 20706525 DOI: 10.1364/ao.30.004204] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electronic holography and speckle interferometry are combined with femtosecond gating techniques to form images of absorbing structures embedded in organic tissue. The method takes advantage of the inherent instability of living tissue.
Collapse
|
42
|
Chen H, Chen Y, Dilworth D, Leith E, Lopez J, Valdmanis J. Two-dimensional imaging through diffusing media using 150-fs gated electronic holography techniques. Opt Lett 1991; 16:487-489. [PMID: 19773975 DOI: 10.1364/ol.16.000487] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We combine 150-fs holographic gating with specifically adapted electronic holography techniques to produce transmission images of objects embedded in diffusing material. The technique captures, without the use of scanning procedures, complete two-dimensional images with 150-fs temporal resolution, thereby yielding submillimeter spatial resolution through diffusing objects several centimeters thick.
Collapse
|