1
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Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 DOI: 10.1016/j.devcel.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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2
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Ferdous AS, Costa Dos Santos SJ, Kanzler CR, Shin H, Carrick BH, Crittenden SL, Wickens M, Kimble J. The in vivo functional significance of PUF hub partnerships in C. elegans germline stem cells. Development 2023; 150:308904. [PMID: 37070766 DOI: 10.1242/dev.201705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/29/2023] [Indexed: 04/19/2023]
Abstract
PUF RNA-binding proteins are conserved stem cell regulators. Four PUF proteins govern self-renewal of C. elegans germline stem cells together with two intrinsically disordered proteins, LST-1 and SYGL-1. Based on yeast two-hybrid results, we proposed a composite self-renewal hub in the stem cell regulatory network, with eight PUF partnerships and extensive redundancy. Here, we investigate LST-1-PUF and SYGL-1-PUF partnerships and their molecular activities in their natural context - nematode stem cells. We confirm LST-1-PUF partnerships and their specificity to self-renewal PUFs by co-immunoprecipitation and show that an LST-1(AmBm) mutant defective for PUF-interacting motifs does not complex with PUFs in nematodes. LST-1(AmBm) is used to explore the in vivo functional significance of the LST-1-PUF partnership. Tethered LST-1 requires the partnership to repress expression of a reporter RNA, and LST-1 requires the partnership to co-immunoprecipitate with NTL-1/Not1 of the CCR4-NOT complex. We suggest that the partnership provides multiple molecular interactions that work together to form an effector complex on PUF target RNAs in vivo. Comparison of PUF-LST-1 and Pumilio-Nanos reveals fundamental molecular differences, making PUF-LST-1 a distinct paradigm for PUF partnerships.
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Affiliation(s)
- Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Charlotte R Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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Ferdous AS, Costa Dos Santos SJ, Kanzler CR, Shin H, Carrick BH, Crittenden SL, Wickens M, Kimble J. Functional significance of PUF partnerships in C. elegans germline stem cells. bioRxiv 2023:2023.02.15.528708. [PMID: 36824876 PMCID: PMC9949348 DOI: 10.1101/2023.02.15.528708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
PUF RNA-binding proteins are conserved stem cell regulators. Four PUF proteins govern self-renewal of C. elegans germline stem cells together with two intrinsically disordered proteins, LST-1 and SYGL-1. Based on yeast two-hybrid results, we proposed a composite self-renewal hub in the stem cell regulatory network, with eight PUF partnerships and extensive redundancy. Here, we investigate LST-1-PUF and SYGL-1-PUF partnerships and their molecular activities in their natural context - nematode stem cells. We confirm LST-1-PUF partnerships and their specificity to self-renewal PUFs by co-immunoprecipitation and show that an LST-1(A m B m ) mutant defective for PUF-interacting motifs does not complex with PUFs in nematodes. LST-1(A m B m ) is used to explore the functional significance of the LST-1-PUF partnership. Tethered LST-1 requires the partnership to repress expression of a reporter RNA, and LST-1 requires the partnership to co-immunoprecipitate with NTL-1/Not1 of the CCR4-NOT complex. We suggest that the partnership provides multiple molecular interactions that work together to form an effector complex on PUF target RNAs. Comparison of PUF-LST-1 and Pumilio-Nanos reveals fundamental molecular differences, making PUF-LST-1 a distinct paradigm for PUF partnerships. Summary statement Partnerships between PUF RNA-binding proteins and intrinsically disordered proteins are essential for stem cell maintenance and RNA repression.
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Affiliation(s)
- Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Charlotte R Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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4
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Zhou W, Melamed D, Banyai G, Meyer C, Tuschl T, Wickens M, Cao J, Fields S. Publisher Correction: Expanding the binding specificity for RNA recognition by a PUF domain. Nat Commun 2022; 13:3693. [PMID: 35760818 PMCID: PMC9237016 DOI: 10.1038/s41467-022-31463-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Wei Zhou
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA.,The Rockefeller University, New York, NY, USA
| | - Daniel Melamed
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.,Institute of Evolution, University of Haifa, Haifa, Israel
| | | | - Cindy Meyer
- The Rockefeller University, New York, NY, USA
| | | | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Junyue Cao
- The Rockefeller University, New York, NY, USA.
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA. .,Department of Medicine, University of Washington, Seattle, Washington, USA.
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5
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Zhou W, Melamed D, Banyai G, Meyer C, Tuschl T, Wickens M, Cao J, Fields S. Expanding the binding specificity for RNA recognition by a PUF domain. Nat Commun 2021; 12:5107. [PMID: 34429425 PMCID: PMC8384837 DOI: 10.1038/s41467-021-25433-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/29/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
The ability to design a protein to bind specifically to a target RNA enables numerous applications, with the modular architecture of the PUF domain lending itself to new RNA-binding specificities. For each repeat of the Pumilio-1 PUF domain, we generate a library that contains the 8,000 possible combinations of amino acid substitutions at residues critical for RNA contact. We carry out yeast three-hybrid selections with each library against the RNA recognition sequence for Pumilio-1, with any possible base present at the position recognized by the randomized repeat. We use sequencing to score the binding of each variant, identifying many variants with highly repeat-specific interactions. From these data, we generate an RNA binding code specific to each repeat and base. We use this code to design PUF domains against 16 RNAs, and find that some of these domains recognize RNAs with two, three or four changes from the wild type sequence.
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Affiliation(s)
- Wei Zhou
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.34477.330000000122986657Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA ,grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Daniel Melamed
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.18098.380000 0004 1937 0562Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel ,grid.18098.380000 0004 1937 0562Institute of Evolution, University of Haifa, Haifa, Israel
| | - Gabor Banyai
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Cindy Meyer
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Thomas Tuschl
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Marvin Wickens
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Junyue Cao
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Stanley Fields
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.34477.330000000122986657Department of Medicine, University of Washington, Seattle, Washington, USA
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6
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Aoki ST, Lynch TR, Crittenden SL, Bingman CA, Wickens M, Kimble J. C. elegans germ granules require both assembly and localized regulators for mRNA repression. Nat Commun 2021; 12:996. [PMID: 33579952 PMCID: PMC7881195 DOI: 10.1038/s41467-021-21278-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 07/05/2019] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
Cytoplasmic RNA-protein (RNP) granules have diverse biophysical properties, from liquid to solid, and play enigmatic roles in RNA metabolism. Nematode P granules are paradigmatic liquid droplet granules and central to germ cell development. Here we analyze a key P granule scaffolding protein, PGL-1, to investigate the functional relationship between P granule assembly and function. Using a protein-RNA tethering assay, we find that reporter mRNA expression is repressed when recruited to PGL-1. We determine the crystal structure of the PGL-1 N-terminal region to 1.5 Å, discover its dimerization, and identify key residues at the dimer interface. Mutations of those interface residues prevent P granule assembly in vivo, de-repress PGL-1 tethered mRNA, and reduce fertility. Therefore, PGL-1 dimerization lies at the heart of both P granule assembly and function. Finally, we identify the P granule-associated Argonaute WAGO-1 as crucial for repression of PGL-1 tethered mRNA. We conclude that P granule function requires both assembly and localized regulators.
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Affiliation(s)
- Scott Takeo Aoki
- grid.257413.60000 0001 2287 3919Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN USA ,grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Tina R. Lynch
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sarah L. Crittenden
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA ,grid.14003.360000 0001 2167 3675Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI USA
| | - Craig A. Bingman
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Marvin Wickens
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Judith Kimble
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA ,grid.14003.360000 0001 2167 3675Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI USA
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7
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Alexander KE, Wickens M, Fletcher-Lartey SM. Measles elimination in Australia: Hard won, easily lost. Aust J Gen Pract 2020; 49:112-114. [PMID: 32113204 DOI: 10.31128/ajgp-11-19-5147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- K E Alexander
- BHB, MBChB, MPH, FAFPHM, Public Health Physician, Public Health Unit, South Western Sydney Local Health District, NSW
| | - M Wickens
- BMedSc, GradCertPubHlth, MIPH, Epidemiologist, Vaccine Preventable Diseases, Communicable Diseases Branch, Health Protection NSW, NSW
| | - S M Fletcher-Lartey
- Dip PHI, MPH, PhD, Epidemiologist, Public Health Unit, South Western Sydney Local Health District, NSW
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8
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Haupt KA, Law KT, Enright AL, Kanzler CR, Shin H, Wickens M, Kimble J. A PUF Hub Drives Self-Renewal in Caenorhabditis elegans Germline Stem Cells. Genetics 2020; 214:147-161. [PMID: 31740451 PMCID: PMC6944405 DOI: 10.1534/genetics.119.302772] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/05/2019] [Indexed: 01/12/2023] Open
Abstract
Stem cell regulation relies on extrinsic signaling from a niche plus intrinsic factors that respond and drive self-renewal within stem cells. A priori, loss of niche signaling and loss of the intrinsic self-renewal factors might be expected to have equivalent stem cell defects. Yet this simple prediction has not been borne out for most stem cells, including Caenorhabditis elegans germline stem cells (GSCs). The central regulators of C. elegans GSCs include extrinsically acting GLP-1/Notch signaling from the niche; intrinsically acting RNA-binding proteins in the PUF family, termed FBF-1 and FBF-2 (collectively FBF); and intrinsically acting PUF partner proteins that are direct Notch targets. Abrogation of either GLP-1/Notch signaling or its targets yields an earlier and more severe GSC defect than loss of FBF-1 and FBF-2, suggesting that additional intrinsic regulators must exist. Here, we report that those missing regulators are two additional PUF proteins, PUF-3 and PUF-11 Remarkably, an fbf-1fbf-2 ; puf-3puf-11 quadruple null mutant has a GSC defect virtually identical to that of a glp-1/Notch null mutant. PUF-3 and PUF-11 both affect GSC maintenance, both are expressed in GSCs, and epistasis experiments place them at the same position as FBF within the network. Therefore, action of PUF-3 and PUF-11 explains the milder GSC defect in fbf-1fbf-2 mutants. We conclude that a "PUF hub," comprising four PUF proteins and two PUF partners, constitutes the intrinsic self-renewal node of the C. elegans GSC RNA regulatory network. Discovery of this hub underscores the significance of PUF RNA-binding proteins as key regulators of stem cell maintenance.
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Affiliation(s)
- Kimberly A Haupt
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Kimberley T Law
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Amy L Enright
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Charlotte R Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
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9
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Aoki ST, Porter DF, Prasad A, Wickens M, Bingman CA, Kimble J. An RNA-Binding Multimer Specifies Nematode Sperm Fate. Cell Rep 2019; 23:3769-3775. [PMID: 29949762 PMCID: PMC6066285 DOI: 10.1016/j.celrep.2018.05.095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 03/06/2018] [Revised: 04/26/2018] [Accepted: 05/30/2018] [Indexed: 11/27/2022] Open
Abstract
FOG-3 is a master regulator of sperm fate in Caenorhabditis elegans and homologous to Tob/BTG proteins, which in mammals are monomeric adaptors that recruit enzymes to RNA binding proteins. Here, we determine the FOG-3 crystal structure and in vitro demonstrate that FOG-3 forms dimers that can multi-merize. The FOG-3 multimeric structure has a basic surface potential, suggestive of binding nucleic acid. Consistent with that prediction, FOG-3 binds directly to nearly 1,000 RNAs in nematode spermatogenic germ cells. Most binding is to the 3′ UTR, and most targets (94%) are oogenic mRNAs, even though assayed in spermatogenic cells. When tethered to a reporter mRNA, FOG-3 represses its expression. Together these findings elucidate the molecular mechanism of sperm fate specification and reveal the evolution of a protein from monomeric to multimeric form with acquisition of a distinct mode of mRNA repression. The mechanism of the sperm or oocyte fate decision has been elusive. Aoki et al. report that nematode FOG-3, a Tob/BTG protein driving sperm fate, has evolved from monomeric to multimeric form with acquisition of a divergent Tob/BTG mechanism for mRNA repression.
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Affiliation(s)
- Scott T Aoki
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.
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10
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Haupt KA, Enright AL, Ferdous AS, Kershner AM, Shin H, Wickens M, Kimble J. The molecular basis of LST-1 self-renewal activity and its control of stem cell pool size. Development 2019; 146:dev.181644. [PMID: 31515205 DOI: 10.1242/dev.181644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023]
Abstract
PUF RNA-binding proteins have diverse roles in animal development, with a broadly conserved role in stem cells. Two paradigmatic PUF proteins, FBF-1 and FBF-2, promote both self-renewal and differentiation in the C. elegans germline. The LST-1 protein is a pivotal regulator of self-renewal and is oncogenic when mis-expressed. Here, we demonstrate that LST-1 self-renewal activity resides within a predicted disordered region that harbors two KXXL motifs. We find that the KXXL motifs mediate the binding of LST-1 to FBF, and that point mutations of these motifs abrogate LST-1 self-renewal activity. The LST-1-FBF partnership is therefore crucial to stem cell maintenance and is a key element in the FBF regulatory network. A distinct region within LST-1 determines its spatial expression and size of the GSC pool. Most importantly, the molecular understanding of how an IDR-rich protein works in an essential partnership with a conserved stem cell regulator and RNA-binding protein suggests broad new avenues for combinatorial control.
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Affiliation(s)
- Kimberly A Haupt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy L Enright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron M Kershner
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA .,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
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11
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Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TM. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Nucleic Acids Res 2019; 47:8770-8784. [PMID: 31294800 PMCID: PMC7145691 DOI: 10.1093/nar/gkz583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023] Open
Abstract
PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct architecture and comprise a highly conserved subfamily among fungal species. Puf1/Puf2 proteins contain two types of RNA-binding domain: a divergent PUM-HD and an RNA recognition motif (RRM). They recognize RNAs containing UAAU motifs, often in clusters. Here, we report a crystal structure of the PUM-HD of a fungal Puf1 in complex with a dual UAAU motif RNA. Each of the two UAAU tetranucleotides are bound by a Puf1 PUM-HD forming a 2:1 protein-to-RNA complex. We also determined crystal structures of the Puf1 RRM domain that identified a dimerization interface. The PUM-HD and RRM domains act in concert to determine RNA-binding specificity: the PUM-HD dictates binding to UAAU, and dimerization of the RRM domain favors binding to dual UAAU motifs rather than a single UAAU. Cooperative action of the RRM and PUM-HD identifies a new mechanism by which multiple RNA-binding modules in a single protein collaborate to create a unique RNA-binding specificity.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert C Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yoav Arava
- Department of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Correspondence may also be addressed to Marvin Wickens. Tel: +1 608 263 0858; Fax: +1 608 262 9108;
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA,To whom correspondence should be addressed. Tel: +1 984 287 3556; Fax: +1 310 480 3055;
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12
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Preston MA, Porter DF, Chen F, Buter N, Lapointe CP, Keles S, Kimble J, Wickens M. Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase. Nat Methods 2019; 16:437-445. [PMID: 30988468 PMCID: PMC6613791 DOI: 10.1038/s41592-019-0370-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
Ribonucleotidyl transferases (rNTases) add untemplated ribonucleotides to diverse RNAs. We have developed TRAID-seq, a screening strategy in Saccharomyces cerevisiae to identify sequences added to a reporter RNA at single-nucleotide resolution by overexpressed candidate enzymes from different organisms. The rNTase activities of 22 previously unexplored enzymes were determined. In addition to poly(A)- and poly(U)-adding enzymes, we identified a cytidine-adding enzyme that is likely to be part of a two-enzyme system that adds CCA to tRNAs in a eukaryote; a nucleotidyl transferase that adds nucleotides to RNA without apparent nucleotide preference; and a poly(UG) polymerase, Caenorhabditis elegans MUT-2, that adds alternating uridine and guanosine nucleotides to form poly(UG) tails. MUT-2 is known to be required for certain forms of RNA silencing, and mutants of the enzyme that result in defective silencing did not add poly(UG) tails in our assay. We propose that MUT-2 poly(UG) polymerase activity is required to promote genome integrity and RNA silencing.
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Affiliation(s)
- Melanie A Preston
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Program in Epithelial Biology, Stanford University Medical School, Stanford, CA, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Natascha Buter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Sunduz Keles
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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13
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Porter DF, Prasad A, Carrick BH, Kroll-Connor P, Wickens M, Kimble J. Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines. G3 (Bethesda) 2019; 9:153-165. [PMID: 30459181 PMCID: PMC6325917 DOI: 10.1534/g3.118.200300] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022]
Abstract
Metazoan PUF (Pumilio and FBF) RNA-binding proteins regulate various biological processes, but a common theme across phylogeny is stem cell regulation. In Caenorhabditis elegans, FBF (fem-3 Binding Factor) maintains germline stem cells regardless of which gamete is made, but FBF also functions in the process of spermatogenesis. We have begun to "disentangle" these biological roles by asking which FBF targets are gamete-independent, as expected for stem cells, and which are gamete-specific. Specifically, we compared FBF iCLIP binding profiles in adults making sperm to those making oocytes. Normally, XX adults make oocytes. To generate XX adults making sperm, we used a fem-3(gf) mutant requiring growth at 25°; for comparison, wild-type oogenic hermaphrodites were also raised at 25°. Our FBF iCLIP data revealed FBF binding sites in 1522 RNAs from oogenic adults and 1704 RNAs from spermatogenic adults. More than half of these FBF targets were independent of germline gender. We next clustered RNAs by FBF-RNA complex frequencies and found four distinct blocks. Block I RNAs were enriched in spermatogenic germlines, and included validated target fog-3, while Block II and III RNAs were common to both genders, and Block IV RNAs were enriched in oogenic germlines. Block II (510 RNAs) included almost all validated FBF targets and was enriched for cell cycle regulators. Block III (21 RNAs) was enriched for RNA-binding proteins, including previously validated FBF targets gld-1 and htp-1 We suggest that Block I RNAs belong to the FBF network for spermatogenesis, and that Blocks II and III are associated with stem cell functions.
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Affiliation(s)
- Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Peggy Kroll-Connor
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
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14
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Abstract
Protein-RNA networks, in which a single protein binds and controls multiple mRNAs, are central in biological control. As a result, methods to identify protein-RNA interactions that occur in vivo are valuable. The "RNA Tagging" approach enables the investigator to unambiguously identify global protein-RNA interactions in vivo and is independent of protein purification, cross-linking, and radioactive labeling steps. Here, we provide a protocol to prepare high-throughput sequencing libraries for RNA Tagging experiments.
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Affiliation(s)
- Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
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15
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Lapointe CP, Stefely JA, Jochem A, Hutchins PD, Wilson GM, Kwiecien NW, Coon JJ, Wickens M, Pagliarini DJ. Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis. Cell Syst 2017; 6:125-135.e6. [PMID: 29248374 DOI: 10.1016/j.cels.2017.11.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/14/2017] [Accepted: 11/19/2017] [Indexed: 12/31/2022]
Abstract
Coenzyme Q (CoQ) is a redox-active lipid required for mitochondrial oxidative phosphorylation (OxPhos). How CoQ biosynthesis is coordinated with the biogenesis of OxPhos protein complexes is unclear. Here, we show that the Saccharomyces cerevisiae RNA-binding protein (RBP) Puf3p regulates CoQ biosynthesis. To establish the mechanism for this regulation, we employed a multi-omic strategy to identify mRNAs that not only bind Puf3p but also are regulated by Puf3p in vivo. The CoQ biosynthesis enzyme Coq5p is a critical Puf3p target: Puf3p regulates the abundance of Coq5p and prevents its detrimental hyperaccumulation, thereby enabling efficient CoQ production. More broadly, Puf3p represses a specific set of proteins involved in mitochondrial protein import, translation, and OxPhos complex assembly (pathways essential to prime mitochondrial biogenesis). Our data reveal a mechanism for post-transcriptionally coordinating CoQ production with OxPhos biogenesis, and they demonstrate the power of multi-omics for defining genuine targets of RBPs.
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Affiliation(s)
| | | | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Paul D Hutchins
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gary M Wilson
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicholas W Kwiecien
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA.
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16
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Lapointe CP, Preston MA, Wilinski D, Saunders HAJ, Campbell ZT, Wickens M. Architecture and dynamics of overlapped RNA regulatory networks. RNA 2017; 23:1636-1647. [PMID: 28768715 PMCID: PMC5648032 DOI: 10.1261/rna.062687.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/28/2017] [Indexed: 06/07/2023]
Abstract
A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is known about the architecture or dynamics of overlapped networks. We focused on three proteins with similar structures and related RNA-binding specificities-Puf3p, Puf4p, and Puf5p of S. cerevisiae Using RNA Tagging, we identified a "super-network" comprised of four subnetworks: Puf3p, Puf4p, and Puf5p subnetworks, and one controlled by both Puf4p and Puf5p. The architecture of individual subnetworks, and thus the super-network, is determined by competition among particular PUF proteins to bind mRNAs, their affinities for binding elements, and the abundances of the proteins. The super-network responds dramatically: The remaining network can either expand or contract. These strikingly opposite outcomes are determined by an interplay between the relative abundance of the RNAs and proteins, and their affinities for one another. The diverse interplay between overlapping RNA-protein networks provides versatile opportunities for regulation and evolution.
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Affiliation(s)
- Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Melanie A Preston
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Daniel Wilinski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Harriet A J Saunders
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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17
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Prasad A, Porter DF, Kroll-Conner PL, Mohanty I, Ryan AR, Crittenden SL, Wickens M, Kimble J. The PUF binding landscape in metazoan germ cells. RNA 2016; 22:1026-43. [PMID: 27165521 PMCID: PMC4911911 DOI: 10.1261/rna.055871.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/14/2016] [Indexed: 05/09/2023]
Abstract
PUF (Pumilio/FBF) proteins are RNA-binding proteins and conserved stem cell regulators. The Caenorhabditis elegans PUF proteins FBF-1 and FBF-2 (collectively FBF) regulate mRNAs in germ cells. Without FBF, adult germlines lose all stem cells. A major gap in our understanding of PUF proteins, including FBF, is a global view of their binding sites in their native context (i.e., their "binding landscape"). To understand the interactions underlying FBF function, we used iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) to determine binding landscapes of C. elegans FBF-1 and FBF-2 in the germline tissue of intact animals. Multiple iCLIP peak-calling methods were compared to maximize identification of both established FBF binding sites and positive control target mRNAs in our iCLIP data. We discovered that FBF-1 and FBF-2 bind to RNAs through canonical as well as alternate motifs. We also analyzed crosslinking-induced mutations to map binding sites precisely and to identify key nucleotides that may be critical for FBF-RNA interactions. FBF-1 and FBF-2 can bind sites in the 5'UTR, coding region, or 3'UTR, but have a strong bias for the 3' end of transcripts. FBF-1 and FBF-2 have strongly overlapping target profiles, including mRNAs and noncoding RNAs. From a statistically robust list of 1404 common FBF targets, 847 were previously unknown, 154 were related to cell cycle regulation, three were lincRNAs, and 335 were shared with the human PUF protein PUM2.
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Affiliation(s)
- Aman Prasad
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Douglas F Porter
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Peggy L Kroll-Conner
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Ipsita Mohanty
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Anne R Ryan
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sarah L Crittenden
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Judith Kimble
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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18
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Waghray S, Williams C, Coon JJ, Wickens M. Xenopus CAF1 requires NOT1-mediated interaction with 4E-T to repress translation in vivo. RNA 2015; 21:1335-45. [PMID: 26015597 PMCID: PMC4478352 DOI: 10.1261/rna.051565.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/22/2015] [Indexed: 05/25/2023]
Abstract
RNA-regulatory factors bound to 3' UTRs control translation and stability. Repression often is associated with poly(A) removal. The deadenylase CAF1 is a core component of the CCR4-NOT complex. Our prior studies established that CAF1 represses translation independent of deadenylation. We sought the mechanism of its deadenylation-independent repression in Xenopus oocytes. Our data reveal a chain of interacting proteins that links CAF1 to CCR4-NOT and to Xp54 and 4E-T. Association of CAF1 with NOT1, the major subunit of CCR4-NOT, is required for repression by CAF1 tethered to a reporter mRNA. Affinity purification-mass spectrometry and coimmunoprecipitation revealed that at least five members of the CCR4-NOT complex were recruited by CAF1. The recruitment of these proteins required NOT1, as did the ability of tethered CAF1 to repress translation. In turn, NOT1 was needed to recruit Xp54 and 4E-T. We examined the role of 4E-T in repression using mutations that disrupted either eIF4E-dependent or -independent mechanisms. Expression of a 4E-T truncation that still bound eIF4E alleviated repression by tethered CAF1, NOT1, and Xp54. In contrast, a mutant 4E-T that failed to bind eIF4E did not. Repression of global translation was affected only by the eIF4E-dependent mechanism. Reporters bearing IRES elements revealed that repression via tethered CAF1 and Xp54 is cap- and eIF4E-independent, but requires one or more of eIF4A, eIF4B, and eIF4G. We propose that RNA-binding proteins, and perhaps miRNAs, repress translation through an analogous chain of interactions that begin with the 3' UTR-bound repressor and end with the noncanonical activity of 4E-T.
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Affiliation(s)
- Shruti Waghray
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Clay Williams
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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19
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Wickens M. Lessons from the RNA World: humility and hubris. RNA 2015; 21:482. [PMID: 25780104 PMCID: PMC4371246 DOI: 10.1261/rna.050963.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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20
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Campbell ZT, Wickens M. Probing RNA-protein networks: biochemistry meets genomics. Trends Biochem Sci 2015; 40:157-64. [PMID: 25636997 DOI: 10.1016/j.tibs.2015.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/05/2015] [Accepted: 01/06/2015] [Indexed: 12/26/2022]
Abstract
RNA-protein interactions are pervasive. The specificity of these interactions dictates which RNAs are controlled by what protein. Here we describe a class of revolutionary new methods that enable global views of RNA-binding specificity in vitro, for both single proteins and multiprotein complexes. These methods provide insight into central issues in RNA regulation in living cells, including understanding the balance between free and bound components, the basis for exclusion of binding sites, detection of binding events in the absence of discernible regulatory elements, and new approaches to targeting endogenous transcripts by design. Comparisons of in vitro and in vivo binding provide a foundation for comprehensive understanding of the biochemistry of protein-mediated RNA regulatory networks.
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Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
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21
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Campbell ZT, Valley CT, Wickens M. A protein-RNA specificity code enables targeted activation of an endogenous human transcript. Nat Struct Mol Biol 2014; 21:732-8. [PMID: 24997599 PMCID: PMC4125476 DOI: 10.1038/nsmb.2847] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [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: 01/24/2014] [Accepted: 05/30/2014] [Indexed: 12/27/2022]
Abstract
Programmable protein scaffolds that target DNA are invaluable tools for genome engineering and designer control of transcription. RNA manipulation provides broad new opportunities for control, including changes in translation. PUF proteins are an attractive platform for that purpose because they bind specific single-stranded RNA sequences by using short repeated modules, each contributing three amino acids that contact an RNA base. Here, we identified the specificities of natural and designed combinations of those three amino acids, using a large randomized RNA library. The resulting specificity code reveals the RNA binding preferences of natural proteins and enables the design of new specificities. Using the code and a translational activation domain, we designed a protein that targets endogenous cyclin B1 mRNA in human cells, increasing sensitivity to chemotherapeutic drugs. Our study provides a guide for rational design of engineered mRNA control, including translational stimulation.
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Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cary T Valley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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22
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Abstract
The Xenopus Cripto-1 protein is confined to the cells of the animal hemisphere during early embryogenesis where it regulates the formation of anterior structures. Cripto-1 protein accumulates only in animal cells because cripto-1 mRNA in cells of the vegetal hemisphere is translationally repressed. Here, we show that the RNA binding protein, Bicaudal-C (Bic-C), functioned directly in this vegetal cell-specific repression. While Bic-C protein is normally confined to vegetal cells, ectopic expression of Bic-C in animal cells repressed a cripto-1 mRNA reporter and associated with endogenous cripto-1 mRNA. Repression by Bic-C required its N-terminal domain, comprised of multiple KH motifs, for specific binding to relevant control elements within the cripto-1 mRNA and a functionally separable C-terminal translation repression domain. Bic-C-mediated repression required the 5' CAP and translation initiation factors, but not a poly(A) tail or the conserved SAM domain within Bic-C. Bic-C-directed immunoprecipitation followed by deep sequencing of associated mRNAs identified multiple Bic-C-regulated mRNA targets, including cripto-1 mRNA, providing new insights and tools for understanding the role of Bic-C in vertebrate development.
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Affiliation(s)
- Yan Zhang
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Amy Cooke
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sookhee Park
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Colin N. Dewey
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael D. Sheets
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Corresponding authorE-mail
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23
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Lapointe CP, Wickens M. The nucleic acid-binding domain and translational repression activity of a Xenopus terminal uridylyl transferase. J Biol Chem 2013; 288:20723-33. [PMID: 23709223 DOI: 10.1074/jbc.m113.455451] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Terminal uridylyl transferases (TUTs) catalyze the addition of uridines to the 3' ends of RNAs and are implicated in the regulation of both messenger RNAs and microRNAs. To better understand how TUTs add uridines to RNAs, we focused on a putative TUT from Xenopus laevis, XTUT7. We determined that XTUT7 catalyzed the addition of uridines to RNAs. Mutational analysis revealed that a truncated XTUT7 enzyme, which contained solely the nucleotidyl transferase and poly(A) polymerase-associated domains, was sufficient for catalytic activity. XTUT7 activity decreased upon removal of the CCHC zinc finger domains and a short segment of basic amino acids (the basic region). This basic region bound nucleic acids in vitro. We also demonstrated that XTUT7 repressed translation of a polyadenylated RNA, to which it added a distinct number of uridines. We generated a predicted structure of the XTUT7 catalytic core that indicated histidine 1269 was likely important for uridine specificity. Indeed, mutation of histidine 1269 broadened the nucleotide specificity of XTUT7 and abolished XTUT7-dependent translational repression. Our data reveal key aspects of how XTUT7 adds uridines to RNAs, highlight the role of the basic region, illustrate that XTUT7 can repress translation, and identify an amino acid important for uridine specificity.
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Affiliation(s)
- Christopher P Lapointe
- Integrated Program in Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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24
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Campbell ZT, Bhimsaria D, Valley CT, Rodriguez-Martinez JA, Menichelli E, Williamson JR, Ansari AZ, Wickens M. Cooperativity in RNA-protein interactions: global analysis of RNA binding specificity. Cell Rep 2013; 1:570-81. [PMID: 22708079 DOI: 10.1016/j.celrep.2012.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [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: 12/23/2022] Open
Abstract
The control and function of RNA are governed by the specificity of RNA binding proteins. Here, we describe a method for global unbiased analysis of RNA-protein interactions that uses in vitro selection, high-throughput sequencing, and sequence-specificity landscapes. The method yields affinities for a vast array of RNAs in a single experiment, including both low- and high-affinity sites. It is reproducible and accurate. Using this approach,we analyzed members of the PUF (Pumilio and FBF) family of eukaryotic mRNA regulators. Our data identify effects of a specific protein partner on PUF-RNA interactions, reveal subsets of target sites not previously detected, and demonstrate that designer PUF proteins can precisely alter specificity. The approach described here is, in principle, broadly applicable for analysis of any molecule that binds RNA, including proteins, nucleic acids, and small molecules.
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Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1554, USA
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25
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LeGendre JB, Campbell ZT, Kroll-Conner P, Anderson P, Kimble J, Wickens M. RNA targets and specificity of Staufen, a double-stranded RNA-binding protein in Caenorhabditis elegans. J Biol Chem 2012. [PMID: 23195953 DOI: 10.1074/jbc.m112.397349] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Staufen family consists of proteins that possess double-stranded RNA-binding domains (dsRBDs). Staufen proteins of Drosophila and mammals regulate mRNA localization, translation, and decay. We report analysis of Staufen in Caenorhabditis elegans, which we have designated STAU-1. We focus on its biochemical properties, mRNA targets, and possible role in RNAi. We show that STAU-1 is expressed as mRNA and protein at all stages of C. elegans development. The wild-type, full-length protein, purified from bacteria, binds duplex RNA with high affinity in vitro. Purified, mutant proteins lacking single dsRBDs still bind RNA efficiently, demonstrating that no single domain is required for binding to duplex RNA (although dsRBD2 could not be tested). STAU-1 mRNA targets were identified via immunoprecipitation with specific anti-STAU-1 antibodies, followed by microarray analysis (RIP-Chip). These studies define a set of 418 likely STAU-1 mRNA targets. Finally, we demonstrate that stau-1 mutants enhance exogenous RNAi and that stau-1;eri-1 double mutants exhibit sterility and synthetic germ line defects.
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Affiliation(s)
- Jacqueline Baca LeGendre
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706, USA
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26
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Wu J, Campbell ZT, Menichelli E, Wickens M, Williamson JR. A protein.protein interaction platform involved in recruitment of GLD-3 to the FBF.fem-3 mRNA complex. J Mol Biol 2012; 425:738-54. [PMID: 23159559 DOI: 10.1016/j.jmb.2012.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/01/2012] [Accepted: 11/07/2012] [Indexed: 02/03/2023]
Abstract
The Pumilio and FBF (PUF) family of RNA-binding proteins interacts with protein partners to post-transcriptionally regulate mRNAs in eukaryotes. The interaction between PUF family member fem-3 binding factor (FBF) and germline development defective-3 (GLD-3) protein promotes spermatogenesis in Caenorhabditis elegans by increasing expression of the fem-3 mRNA. Defined here in these studies is the molecular basis for this critical interaction. A 10-amino-acid region within GLD-3 is required for FBF binding, while a 7-amino-acid loop in FBF between PUF repeats 7 and 8 is necessary for GLD-3 binding. These short sequences are conserved, as other FBF-binding proteins bear sequences similar to those in GLD-3 and other C. elegans PUF proteins contain sequences similar to those in FBF. The FBF-binding region of GLD-3 forms a ternary complex with FBF on the point mutation element (PME) in the fem-3 3' untranslated region, and formation of this GLD-3⋅FBF complex does not impact the RNA-binding activity of FBF. These data raise the possibility of alternative models involving the formation of a GLD-3⋅FBF⋅RNA complex in the regulation of germline mRNAs.
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Affiliation(s)
- Joann Wu
- Department of Molecular Biology, Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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27
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Menichelli E, Wu J, Campbell ZT, Wickens M, Williamson JR. Biochemical characterization of the Caenorhabditis elegans FBF.CPB-1 translational regulation complex identifies conserved protein interaction hotspots. J Mol Biol 2012; 425:725-37. [PMID: 23159558 DOI: 10.1016/j.jmb.2012.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/01/2012] [Accepted: 11/07/2012] [Indexed: 10/27/2022]
Abstract
Caenorhabditis elegans CPB-1 (cytoplasmic polyadenylation element binding protein homolog-1) and FBF (fem-3 mRNA binding factor) are evolutionary conserved regulators of mRNA translation that belong to the CPEB (cytoplasmic polyadenylation element binding) and PUF (Pumilio and FBF) protein families, respectively. In hermaphrodite worms, CPB-1 and FBF control key steps during germline development, including stem cell maintenance and sex determination. While CPB-1 and FBF are known to interact, the molecular basis and function of the CPB-1⋅FBF complex are not known. The surface of CPB-1 that interacts with FBF was localized using in vivo and in vitro methods to a 10-residue region at the N-terminus of the protein and these residues are present in the FBF-binding protein GLD-3 (germline development defective-3). PUF proteins are characterized by the presence of eight α-helical repeats (PUF repeats) arranged side by side in an elongated structure. Critical residues for CPB-1 binding are found in the extended loop that connects PUF repeats 7 and 8. The same FBF residues also mediate binding to GLD-3, indicating a conserved binding mode between different protein partners. CPB-1 binding was competitive with GLD-3, suggestive of mutual exclusivity in vivo. RNA binding measurements demonstrated that CPB-1 alters the affinity of FBF for specific RNA sequences, implying a functional model where the coregulatory protein CPB-1 modulates FBF target selection.
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Affiliation(s)
- Elena Menichelli
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Campbell ZT, Menichelli E, Friend K, Wu J, Kimble J, Williamson JR, Wickens M. Identification of a conserved interface between PUF and CPEB proteins. J Biol Chem 2012; 287:18854-62. [PMID: 22496444 DOI: 10.1074/jbc.m112.352815] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Members of the PUF (Pumilio and FBF) and CPEB (cytoplasmic polyadenylation element-binding) protein families collaborate to regulate mRNA expression throughout eukaryotes. Here, we focus on the physical interactions between members of these two families, concentrating on Caenorhabditis elegans FBF-2 and CPB-1. To localize the site of interaction on FBF-2, we identified conserved amino acids within C. elegans PUF proteins. Deletion of an extended loop containing several conserved residues abolished binding to CPB-1. We analyzed alanine substitutions at 13 individual amino acids in FBF-2, each identified via its conservation. Multiple single point mutations disrupted binding to CPB-1 but not to RNA. Position Tyr-479 was particularly critical as multiple substitutions to other amino acids at this position did not restore binding. The complex of FBF-2 and CPB-1 repressed translation of an mRNA containing an FBF binding element. Repression required both proteins and was disrupted by FBF-2 alleles that failed to bind CPB-1 or RNA. The equivalent loop in human PUM2 is required for binding to human CPEB3 in vitro, although the primary sequences of the human and C. elegans PUF proteins have diverged in that region. Our findings define a key region in PUF/CPEB interactions and imply a conserved platform through which PUF proteins interact with their protein partners.
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Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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29
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Abstract
The modification of transcriptional regulation is a well-documented evolutionary mechanism in both plants and animals, but post-transcriptional controls have received less attention. The derived hermaphrodite of C. elegans has regulated spermatogenesis in an otherwise female body. The PUF family RNA-binding proteins FBF-1 and FBF-2 limit XX spermatogenesis by repressing the male-promoting proteins FEM-3 and GLD-1. Here, we examine the function of PUF homologs from other Caenorhabditis species, with emphasis on C. briggsae, which evolved selfing convergently. C. briggsae lacks a bona fide fbf-1/2 ortholog, but two members of the related PUF-2 subfamily, Cbr-puf-2 and Cbr-puf-1.2, do have a redundant germline sex determination role. Surprisingly, this is to promote, rather than limit, hermaphrodite spermatogenesis. We provide genetic, molecular and biochemical evidence that Cbr-puf-2 and Cbr-puf-1.2 repress Cbr-gld-1 by a conserved mechanism. However, Cbr-gld-1 acts to limit, rather than promote, XX spermatogenesis. As with gld-1, no sex determination function for fbf or puf-2 orthologs is observed in gonochoristic Caenorhabditis. These results indicate that PUF family genes were co-opted for sex determination in each hermaphrodite via their long-standing association with gld-1, and that their precise sex-determining roles depend on the species-specific context in which they act. Finally, we document non-redundant roles for Cbr-puf-2 in embryonic and early larval development, the latter role being essential. Thus, recently duplicated PUF paralogs have already acquired distinct functions.
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Affiliation(s)
- Qinwen Liu
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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Qiu C, Kershner A, Wang Y, Holley CP, Wilinski D, Keles S, Kimble J, Wickens M, Hall TMT. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket. J Biol Chem 2011; 287:6949-57. [PMID: 22205700 DOI: 10.1074/jbc.m111.326264] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
mRNA control networks depend on recognition of specific RNA sequences. Pumilio-fem-3 mRNA binding factor (PUF) RNA-binding proteins achieve that specificity through variations on a conserved scaffold. Saccharomyces cerevisiae Puf3p achieves specificity through an additional binding pocket for a cytosine base upstream of the core RNA recognition site. Here we demonstrate that this chemically simple adaptation is prevalent and contributes to the diversity of RNA specificities among PUF proteins. Bioinformatics analysis shows that mRNAs associated with Caenorhabditis elegans fem-3 mRNA binding factor (FBF)-2 in vivo contain an upstream cytosine required for biological regulation. Crystal structures of FBF-2 and C. elegans PUF-6 reveal binding pockets structurally similar to that of Puf3p, whereas sequence alignments predict a pocket in PUF-11. For Puf3p, FBF-2, PUF-6, and PUF-11, the upstream pockets and a cytosine are required for maximal binding to RNA, but the quantitative impact on binding affinity varies. Furthermore, the position of the upstream cytosine relative to the core PUF recognition site can differ, which in the case of FBF-2 originally masked the identification of this consensus sequence feature. Importantly, other PUF proteins lack the pocket and so do not discriminate upstream bases. A structure-based alignment reveals that these proteins lack key residues that would contact the cytosine, and in some instances, they also present amino acid side chains that interfere with binding. Loss of the pocket requires only substitution of one serine, as appears to have occurred during the evolution of certain fungal species.
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Affiliation(s)
- Chen Qiu
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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31
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Yosefzon Y, Koh YY, Chritton JJ, Lande A, Leibovich L, Barziv L, Petzold C, Yakhini Z, Mandel-Gutfreund Y, Wickens M, Arava Y. Divergent RNA binding specificity of yeast Puf2p. RNA 2011; 17:1479-88. [PMID: 21685478 PMCID: PMC3153972 DOI: 10.1261/rna.2700311] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PUF proteins bind mRNAs and regulate their translation, stability, and localization. Each PUF protein binds a selective group of mRNAs, enabling their coordinate control. We focus here on the specificity of Puf2p and Puf1p of Saccharomyces cerevisiae, which copurify with overlapping groups of mRNAs. We applied an RNA-adapted version of the DRIM algorithm to identify putative binding sequences for both proteins. We first identified a novel motif in the 3' UTRs of mRNAs previously shown to associate with Puf2p. This motif consisted of two UAAU tetranucleotides separated by a 3-nt linker sequence, which we refer to as the dual UAAU motif. The dual UAAU motif was necessary for binding to Puf2p, as judged by gel shift, yeast three-hybrid, and coimmunoprecipitation from yeast lysates. The UAAU tetranucleotides are required for optimal binding, while the identity and length of the linker sequences are less critical. Puf1p also binds the dual UAAU sequence, consistent with the prior observation that it associates with similar populations of mRNAs. In contrast, three other canonical yeast PUF proteins fail to bind the Puf2p recognition site. The dual UAAU motif is distinct from previously known PUF protein binding sites, which invariably possess a UGU trinucleotide. This study expands the repertoire of cis elements bound by PUF proteins and suggests new modes by which PUF proteins recognize their mRNA targets.
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Affiliation(s)
- Yahav Yosefzon
- Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Yvonne Y. Koh
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Jacqueline J. Chritton
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Avigail Lande
- Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Limor Leibovich
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Lavi Barziv
- Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Christine Petzold
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Zohar Yakhini
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa 32000, Israel
- Agilent Laboratories Israel, Petach-Tikva 49527, Israel
| | | | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
- Corresponding authors.E-mail .E-mail .
| | - Yoav Arava
- Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
- Corresponding authors.E-mail .E-mail .
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32
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Abstract
PUF proteins regulate translation and mRNA stability throughout eukaryotes. Using a cell-free translation assay, we examined the mechanisms of translational repression of PUF proteins in the budding yeast Saccharomyces cerevisiae. We demonstrate that the poly(A)-binding protein Pab1p is required for PUF-mediated translational repression for two distantly related PUF proteins: S. cerevisiae Puf5p and Caenorhabditis elegans FBF-2. Pab1p interacts with oligo(A) tracts in the HO 3'-UTR, a target of Puf5p, to dramatically enhance the efficiency of Puf5p repression. Both the Pab1p ability to activate translation and interact with eukaryotic initiation factor 4G (eIF4G) were required to observe maximal repression by Puf5p. Repression was also more efficient when Pab1p was bound in close proximity to Puf5p. Puf5p may disrupt translation initiation by interfering with the interaction between Pab1p and eIF4G. Finally, we demonstrate two separable mechanisms of translational repression employed by Puf5p: a Pab1p-dependent mechanism and a Pab1p-independent mechanism.
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Affiliation(s)
- Jacqueline J Chritton
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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33
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Abstract
Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stacking amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to "target" versus "off-target" interactions, and thus be an important consideration in the design of proteins with new specificities.
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Affiliation(s)
- Yvonne Yiling Koh
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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34
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Lawson MH, Cummings NM, Rassl DM, Vowler SL, Wickens M, Howat WJ, Brenton JD, Murphy G, Rintoul RC. Bcl-2 and β1-integrin predict survival in a tissue microarray of small cell lung cancer. Br J Cancer 2010; 103:1710-5. [PMID: 21063403 PMCID: PMC2994222 DOI: 10.1038/sj.bjc.6605950] [Citation(s) in RCA: 27] [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] [Indexed: 01/01/2023] Open
Abstract
INTRODUCTION Survival in small cell lung cancer (SCLC) is limited by the development of chemoresistance. Factors associated with chemoresistance in vitro have been difficult to validate in vivo. Both Bcl-2 and β(1)-integrin have been identified as in vitro chemoresistance factors in SCLC but their importance in patients remains uncertain. Tissue microarrays (TMAs) are useful to validate biomarkers but no large TMA exists for SCLC. We designed an SCLC TMA to study potential biomarkers of prognosis and then used it to clarify the role of both Bcl-2 and β(1)-integrin in SCLC. METHODS A TMA was constructed consisting of 184 cases of SCLC and stained for expression of Bcl-2 and β(1)-integrin. The slides were scored and the role of the proteins in survival was determined using Cox regression analysis. A meta-analysis of the role of Bcl-2 expression in SCLC prognosis was performed based on published results. RESULTS Both proteins were expressed at high levels in the SCLC cases. For Bcl-2 (n=140), the hazard ratio for death if the staining was weak in intensity was 0.55 (0.33-0.94, P=0.03) and for β(1)-integrin (n=151) was 0.60 (0.39-0.92, P=0.02). The meta-analysis showed an overall hazard ratio for low expression of Bcl-2 of 0.91(0.74-1.09). CONCLUSIONS Both Bcl-2 and β(1)-integrin are independent prognostic factors in SCLC in this cohort although further validation is required to confirm their importance. A TMA of SCLC cases is feasible but challenging and an important tool for biomarker validation.
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Affiliation(s)
- M H Lawson
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
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35
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Abstract
The CCR4-CAF1-NOT complex is a major cytoplasmic deadenylation complex in yeast and mammals. This complex associates with RNA-binding proteins and microRNAs to repress translation of target mRNAs. We sought to determine how CCR4 and CAF1 participate in repression and control of maternal mRNAs using Xenopus laevis oocytes. We show that Xenopus CCR4 and CAF1 enzymes are active deadenylases and repress translation of an adenylated mRNA. CAF1 also represses translation independent of deadenylation. The deadenylation-independent repression requires a 5' cap structure on the mRNA; however, deadenylation does not. We suggest that mere recruitment of CAF1 is sufficient for repression, independent of deadenylation.
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Affiliation(s)
- Amy Cooke
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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36
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Abstract
PUF (Pumilio and FBF) proteins provide a paradigm for mRNA regulatory proteins. They interact with specific sequences in the 3' untranslated regions (UTRs) of target mRNAs and cause changes in RNA stability or translational activity. Here we describe an in vitro translation assay that reconstitutes the translational repression activity of canonical PUF proteins. In this system, recombinant PUF proteins were added to yeast cell lysates to repress reporter mRNAs bearing the 3'UTRs of specific target mRNAs. PUF proteins from Saccharomyces cerevisiae and Caenorhabditis elegans were active in the assay and were specific by multiple criteria. Puf5p, a yeast PUF protein, repressed translation of four target RNAs. Repression mediated by the HO 3'UTR was particularly efficient, due to a specific sequence in that 3'UTR. The sequence lies downstream from the PUF binding site and does not affect PUF protein binding. PUF-mediated repression was sensitive to the distance between the ORF and the regulatory elements in the 3'UTR: excessive distance decreased repression activity. Our data demonstrate that PUF proteins function in vitro across species, that different mRNA targets are regulated differentially, and that specific ancillary sequences distinguish one yeast mRNA target from another. We suggest a model in which PUF proteins can control translation termination or elongation.
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Affiliation(s)
- Jacqueline J Chritton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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37
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Abstract
PUF proteins specifically bind mRNAs to regulate their stability and translation. Here we focus on the RNA-binding specificity of a C. elegans PUF protein, PUF-11. Our findings reveal that PUF-11 binds RNA in multiple modes, in which the protein can accommodate variable spacings between two distinct recognition elements. We propose a structural model in which flexibility in the central region of the protein enables the protein to adopt at least two distinct structures, one of which results in base flipping.
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Affiliation(s)
- Yvonne Yiling Koh
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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38
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Hall T, Miller M, Wang Y, Zhu D, Opperman L, Stumpf C, Wickens M. Probing RNA sequence specificity and function of PUF proteins. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.326.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Traci Hall
- Laboratory of Structural BiologyNIEHS, NIHResearch Triangle ParkNC
| | - Matthew Miller
- Laboratory of Structural BiologyNIEHS, NIHResearch Triangle ParkNC
| | - Yeming Wang
- Laboratory of Structural BiologyNIEHS, NIHResearch Triangle ParkNC
| | - Deyu Zhu
- Laboratory of Structural BiologyNIEHS, NIHResearch Triangle ParkNC
| | - Laura Opperman
- Department of BiochemistryUniversity of WisconsinMadisonWI
| | - Craig Stumpf
- Department of BiochemistryUniversity of WisconsinMadisonWI
| | - Marvin Wickens
- Department of BiochemistryUniversity of WisconsinMadisonWI
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39
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40
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Kwak JE, Drier E, Barbee SA, Ramaswami M, Yin JCP, Wickens M. GLD2 poly(A) polymerase is required for long-term memory. Proc Natl Acad Sci U S A 2008; 105:14644-9. [PMID: 18780789 PMCID: PMC2567210 DOI: 10.1073/pnas.0803185105] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [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: 04/01/2008] [Indexed: 01/17/2023] Open
Abstract
The formation of long-term memory is believed to require translational control of localized mRNAs. In mammals, dendritic mRNAs are maintained in a repressed state and are activated upon repetitive stimulation. Several regulatory proteins required for translational control in early development are thought to be required for memory formation, suggesting similar molecular mechanisms. Here, using Drosophila, we identify the enzyme responsible for poly(A) elongation in the brain and demonstrate that its activity is required specifically for long-term memory. These findings provide strong evidence that cytoplasmic polyadenylation is critical for memory formation, and that GLD2 is the enzyme responsible.
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Affiliation(s)
| | - Eric Drier
- Genetics, and Psychiatry, Waisman Center, University of Wisconsin, Madison, WI 53706
| | - Scott A. Barbee
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721; and
| | - Mani Ramaswami
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721; and
- Smurfit Institute of Genetics and Trinity College Institute for Neuroscience,Trinity College, Dublin 2, Ireland
| | - Jerry C. P. Yin
- Genetics, and Psychiatry, Waisman Center, University of Wisconsin, Madison, WI 53706
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41
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Abstract
PUF proteins comprise a highly conserved family of sequence-specific RNA binding proteins that regulate target mRNAs via binding directly to their 3'UTRs. The Caenorhabditis elegans genome encodes several PUF proteins, which cluster into four groups based on sequence similarity; all share amino acids that interact with the RNA in the cocrystal of human Pumilio with RNA. Members of the FBF and the PUF-8/9 groups bind different but related RNA sequences. We focus here on the binding specificity of representatives of a third cluster, comprising PUF-5, -6, and -7. We performed in vivo selection experiments using the yeast three-hybrid system to identify RNA sequences that bind PUF-5 and PUF-6, and we confirmed binding to optimal sites in vitro. The consensus sequences derived from the screens are similar for PUF-5 and PUF-6 but differ from those of the FBF or PUF-8/-9 groups. Similarly, neither PUF-5 nor PUF-6 bind the recognition sites preferred by the other clusters. Mutagenesis studies confirmed the unique RNA specificity of PUF-5/-6. Using the PUF-5 consensus derived from our experiments, we searched a database of C. elegans 3'UTRs to identify potential targets of PUF-5, several of which indeed bind PUF-5. Therefore the consensus has predictive value and provides a route to finding genuine targets of these proteins.
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Affiliation(s)
- Craig R Stumpf
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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42
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Affiliation(s)
- Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
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43
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Wickens M. mRNA control: PUF repressors and GLD2 activators. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.247.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marvin Wickens
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWI
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44
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Lee MH, Hook B, Pan G, Kershner AM, Merritt C, Seydoux G, Thomson JA, Wickens M, Kimble J. Conserved regulation of MAP kinase expression by PUF RNA-binding proteins. PLoS Genet 2008; 3:e233. [PMID: 18166083 PMCID: PMC2323325 DOI: 10.1371/journal.pgen.0030233] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Accepted: 11/14/2007] [Indexed: 01/06/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) and PUF (for Pumilio and FBF [fem-3 binding factor]) RNA-binding proteins control many cellular processes critical for animal development and tissue homeostasis. In the present work, we report that PUF proteins act directly on MAPK/ERK-encoding mRNAs to downregulate their expression in both the Caenorhabditis elegans germline and human embryonic stem cells. In C. elegans, FBF/PUF binds regulatory elements in the mpk-1 3′ untranslated region (3′ UTR) and coprecipitates with mpk-1 mRNA; moreover, mpk-1 expression increases dramatically in FBF mutants. In human embryonic stem cells, PUM2/PUF binds 3′UTR elements in both Erk2 and p38α mRNAs, and PUM2 represses reporter constructs carrying either Erk2 or p38α 3′ UTRs. Therefore, the PUF control of MAPK expression is conserved. Its biological function was explored in nematodes, where FBF promotes the self-renewal of germline stem cells, and MPK-1 promotes oocyte maturation and germ cell apoptosis. We found that FBF acts redundantly with LIP-1, the C. elegans homolog of MAPK phosphatase (MKP), to restrict MAPK activity and prevent apoptosis. In mammals, activated MAPK can promote apoptosis of cancer cells and restrict stem cell self-renewal, and MKP is upregulated in cancer cells. We propose that the dual negative regulation of MAPK by both PUF repression and MKP inhibition may be a conserved mechanism that influences both stem cell maintenance and tumor progression. The mitogen-activated protein (MAP) kinase (MAPK) enzyme is crucial for regulation of both stem cell maintenance and tumorigenesis. Two conserved controls of MAPK include its activation by RAS signaling and a kinase cascade as well as its inactivation by MAPK phosphatases (MKPs). We identify a third mode of conserved MAPK regulation. We demonstrate that PUF (for Pumilio and FBF [fem-3 binding factor]) RNA-binding proteins repress mRNAs encoding MAPK enzymes in both the Caenorhabditis elegans germline and human embryonic stem cells. PUF proteins have emerged as conserved regulators of germline stem cells in C. elegans, Drosophila, and probably vertebrates. Their molecular mode of action relies on binding to sequence elements in the 3′ untranslated region of target mRNAs. We report that PUF proteins bind and repress mRNAs encoding C. elegans MPK-1 as well as human ERK2 and p38α. We also report that PUF repression and MKP inactivation function redundantly in the C. elegans germline to restrict MPK-1/MAPK activity and prevent germ cell apoptosis. We suggest that this dual regulation of MAPK activity by PUF and MKP proteins may be a conserved mechanism for the control of growth and differentiation during animal development and tissue homeostasis.
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Affiliation(s)
- Myon-Hee Lee
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brad Hook
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Guangjin Pan
- Genome Centre of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Aaron M Kershner
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christopher Merritt
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - James A Thomson
- Genome Centre of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Judith Kimble
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * To whom correspondence should be addressed. E-mail:
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45
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Abstract
RNA-protein interactions play an essential role in the maturation and regulation of RNAs within eukaryotic organisms. The three-hybrid system provides a simple, yet powerful means to study RNA-protein interactions within the eukaryote Saccharomyces cerevisiae. This chapter describes the basis of the system and applications in both examining specific RNA-protein interactions and screening libraries for novel interactions. We provide a detailed discussion on affinity versus reporter output, variations on library screening (e.g., randomization studies), some adaptations of the system, and updated reagents and protocols.
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Affiliation(s)
- Craig R Stumpf
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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46
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Abstract
The 3'-poly(A) tail, found on virtually all mRNAs, is enzymatically shortened by a process referred to as "deadenylation." Deadenylation is a widespread means of controlling mRNA stability and translation. The enzymes involved-so-called deadenylases-are surprisingly diverse. They are controlled by RNA sequences commonly found in 3'-untranslated regions (UTRs), which bind regulatory factors. Both RNA-binding proteins and microRNAs accelerate deadenylation of specific mRNAs. In some cases, regulators enhance deadenylation by binding to and recruiting specific deadenylases to the target mRNA. The many hundreds of potential regulators encoded in mammalian genomes (both RNA-binding proteins and microRNAs) and the numerous deadenylases, coupled with the many potential regulatory sites represented in 3' UTRs of mRNAs, provide fertile ground for regulated deadenylation. Recent global studies of poly(A) regulation support this conclusion. Biochemical and genetic approaches will be essential for exploring regulated deadenylation. The methods we describe focus on the reconstruction in vitro of regulated deadenylation with purified components from yeast. We discuss broadly the strategies, problems, and history of in vitro deadenylation systems. We combine this with a more detailed discussion of the purification, activity, and regulation of the Saccharomyces cerevisiae Ccr4p-Pop2p deadenylase complex and its regulation by PUF (Pumilio and Fem-3 binding factor) RNA-binding proteins.
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Affiliation(s)
- Aaron C Goldstrohm
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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47
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Abstract
The GLD-2 family of poly(A) polymerases add successive AMP monomers to the 3' end of specific RNAs, forming a poly(A) tail. Here, we identify a new group of GLD-2-related nucleotidyl transferases from Arabidopsis, Schizosaccharomyces pombe, Caenorhabditis elegans, and humans. Like GLD-2, these enzymes are template independent and add nucleotides to the 3' end of an RNA substrate. However, these new enzymes, which we refer to as poly(U) polymerases, add poly(U) rather than poly(A) to their RNA substrates.
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Affiliation(s)
- Jae Eun Kwak
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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48
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Abstract
mRNA stability and translation are regulated by protein repressors that bind 3'-untranslated regions. PUF proteins provide a paradigm for these regulatory molecules: like other repressors, they inhibit translation, enhance mRNA decay, and promote poly(A) removal. Here we show that a single mRNA in Saccharomyces cerevisiae, encoding the HO endonuclease, is regulated by two distinct PUF proteins, Puf4p and Mpt5p. These proteins bind to adjacent sites and can co-occupy the mRNA. Both proteins are required for full repression and deadenylation in vivo; their removal dramatically stabilizes the mRNA. The two proteins act through overlapping but non-identical mechanisms: repression by Puf4p is dependent on deadenylation, whereas repression by Mpt5p can occur through additional mechanisms. Combinatorial action of the two regulatory proteins may allow responses to specific environmental cues and be common in 3'-untranslated region-mediated control.
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Affiliation(s)
- Brad A Hook
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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49
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Abstract
Cytoplasmic polyadenylation regulates mRNA stability and translation and is required for early development and synaptic plasticity. The GLD-2 poly(A) polymerase catalyzes cytoplasmic polyadenylation in the germline of metazoa. Among vertebrates, the enzyme is encoded by two isoforms of mRNA that differ only in the length of their 3'-UTRs. Here we focus on regulation of vertebrate GLD-2 mRNA. We show that the 3'-UTR of GLD-2 mRNA elicits its own polyadenylation and translational activation during frog oocyte maturation. We identify the sequence elements responsible for repression and activation, and demonstrate that CPEB and PUF proteins likely mediate repression in the resting oocyte. Regulated polyadenylation of GLD-2 mRNA is conserved, as are the key regulatory elements. Poly(A) tails of GLD-2 mRNA increase in length in the brain in response to neuronal stimulation, suggesting that a comparable system exists in that tissue. We propose a positive feedback circuit in which translation of GLD-2 mRNA is stimulated by its polyadenylation, thereby reinforcing the switch to polyadenylate and activate batteries of mRNAs.
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Affiliation(s)
- Labib Rouhana
- Department of Biochemistry, Laboratory of Genetics, University of Wisconsin-Madison 53706, USA
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50
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Abstract
PUF proteins control gene expression by binding to the 3'-untranslated regions of specific mRNAs and triggering mRNA decay or translational repression. Here we focus on the mechanism of PUF-mediated regulation. The yeast PUF protein, Mpt5p, regulates HO mRNA and stimulates removal of its poly(A) tail (i.e. deadenylation). Mpt5p repression in vivo is dependent on POP2, a component of the cytoplasmic Ccr4p-Pop2p-Not complex that deadenylates mRNAs. In this study, we elucidate the individual roles of the Ccr4p and Pop2p deadenylases in Mpt5p-regulated deadenylation. Both in vivo and in vitro, Pop2p and Ccr4p proteins are required for Mpt5p-regulated deadenylation of HO. However, the requirements for the two proteins differ dramatically: the enzymatic activity of Ccr4p is essential, whereas that of Pop2p is dispensable. We conclude that Pop2p is a bridge through which the PUF protein recruits the Ccr4p enzyme to the target mRNA, thereby stimulating deadenylation. Our data suggest that PUF proteins may enhance mRNA degradation and repress expression by both deadenylation-dependent and -independent mechanisms, using the same Pop2p bridge to recruit a multifunctional Pop2p complex to the mRNA.
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Affiliation(s)
- Aaron C Goldstrohm
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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