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Yu H, Li Q, Shen X, Zhang L, Liu J, Tan Q, Li Y, Lv B, Shang X. Transcriptomic Analysis of Two Lentinula edodes Genotypes With Different Cadmium Accumulation Ability. Front Microbiol 2020; 11:558104. [PMID: 33042065 PMCID: PMC7526509 DOI: 10.3389/fmicb.2020.558104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/24/2020] [Indexed: 01/26/2023] Open
Abstract
Lentinula edodes, also known as Xiang'gu, is commonly eaten in cultures around the world. However, L. edodes is particularly susceptible to enrichment with heavy metals, particularly cadmium (Cd), which is toxic to human health. Understanding the molecular mechanism and mining key genes involved in Cd enrichment will facilitate genetic modification of L. edodes strains. Two L. edodes genotypes, Le4625 (with higher Cd enrichment capability) and Le4606 (with lower Cd enrichment capability) were used in this study. The Cd concentrations in the mycelia of the tested genotypes differed significantly after Cd (0.1 mg/L) exposure; and the Cd content in Le4625 (1.390 ± 0.098 mg/kg) was approximately three-fold that in Le4606 (0.440 ± 0.038 mg/kg) after 7 h of Cd exposure. A total of 24,592 transcripts were assessed by RNA-Seq to explore variance in Cd accumulation. Firstly, differentially expressed genes (DEGs) were analyzed separately following Cd exposure. In comparison with Ld4625, Ld4606 showed a greater number of Cd-induced changes in transcription. In Ld4606, DEGs following Cd exposure were associated with transmembrane transport, glutathione transfer and cytochrome P450, indicating that these genes could be involved in Cd resistance in L. edodes. Next, Le4606 and Le4625 were exposed to Cd, after which DEGs were identified to explore genetic factors affecting Cd accumulation. After Cd exposure, DEGs between Le4606 and Le4625 encoded proteins involved in multiple biological pathways, including transporters on the membrane, cell wall modification, oxidative stress response, translation, degradation, and signaling pathways. Cadmium enrichment in cells may activate MAPK signaling and the anti-oxidative stress response, which can subsequently alter signal transduction and the intracellular oxidation/reduction balance. Furthermore, several possible candidate genes involved in the Cd accumulation were identified, including the major facilitator superfamily genes, heat shock proteins, and laccase 11, a multicopper oxidase. This comparison of the transcriptomes of two L. edodes strains with different capacities for Cd accumulation provides valuable insight into the cultivation of mushrooms with less Cd enrichment and also serves as a reference for the construction of engineered strains for environmental pollution control.
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Affiliation(s)
- Hailong Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Qiaozhen Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Xiufen Shen
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Lujun Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Jianyu Liu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Yu Li
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Beibei Lv
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiaodong Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China
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2
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Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA. Nat Commun 2018; 9:1749. [PMID: 29717126 PMCID: PMC5931518 DOI: 10.1038/s41467-018-04145-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/06/2018] [Indexed: 01/09/2023] Open
Abstract
The spliceosome removes introns from precursor messenger RNA (pre-mRNA) to produce mature mRNA. Prior to catalysis, spliceosomes are assembled de novo onto pre-mRNA substrates. During this assembly process, U6 small nuclear RNA (snRNA) undergoes extensive structural remodeling. The early stages of this remodeling process are chaperoned by U6 snRNP proteins Prp24 and the Lsm2-8 heteroheptameric ring. We now report a structure of the U6 snRNP from Saccharomyces cerevisiae. The structure reveals protein-protein contacts that position Lsm2-8 in close proximity to the chaperone "active site" of Prp24. The structure also shows how the Lsm2-8 ring specifically recognizes U6 snRNA that has been post-transcriptionally modified at its 3' end, thereby elucidating the mechanism by which U6 snRNPs selectively recruit 3' end-processed U6 snRNA into spliceosomes. Additionally, the structure reveals unanticipated homology between the C-terminal regions of Lsm8 and the cytoplasmic Lsm1 protein involved in mRNA decay.
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3
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Didychuk AL, Butcher SE, Brow DA. The life of U6 small nuclear RNA, from cradle to grave. RNA (NEW YORK, N.Y.) 2018; 24:437-460. [PMID: 29367453 PMCID: PMC5855946 DOI: 10.1261/rna.065136.117] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Removal of introns from precursor messenger RNA (pre-mRNA) and some noncoding transcripts is an essential step in eukaryotic gene expression. In the nucleus, this process of RNA splicing is carried out by the spliceosome, a multi-megaDalton macromolecular machine whose core components are conserved from yeast to humans. In addition to many proteins, the spliceosome contains five uridine-rich small nuclear RNAs (snRNAs) that undergo an elaborate series of conformational changes to correctly recognize the splice sites and catalyze intron removal. Decades of biochemical and genetic data, along with recent cryo-EM structures, unequivocally demonstrate that U6 snRNA forms much of the catalytic core of the spliceosome and is highly dynamic, interacting with three snRNAs, the pre-mRNA substrate, and >25 protein partners throughout the splicing cycle. This review summarizes the current state of knowledge on how U6 snRNA is synthesized, modified, incorporated into snRNPs and spliceosomes, recycled, and degraded.
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Affiliation(s)
- Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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4
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Didychuk AL, Montemayor EJ, Brow DA, Butcher SE. Structural requirements for protein-catalyzed annealing of U4 and U6 RNAs during di-snRNP assembly. Nucleic Acids Res 2015; 44:1398-410. [PMID: 26673715 PMCID: PMC4756825 DOI: 10.1093/nar/gkv1374] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/26/2015] [Indexed: 01/01/2023] Open
Abstract
Base-pairing of U4 and U6 snRNAs during di-snRNP assembly requires large-scale remodeling of RNA structure that is chaperoned by the U6 snRNP protein Prp24. We investigated the mechanism of U4/U6 annealing in vitro using an assay that enables visualization of ribonucleoprotein complexes and faithfully recapitulates known in vivo determinants for the process. We find that annealing, but not U6 RNA binding, is highly dependent on the electropositive character of a 20 Å-wide groove on the surface of Prp24. During annealing, we observe the formation of a stable ternary complex between U4 and U6 RNAs and Prp24, indicating that displacement of Prp24 in vivo requires additional factors. Mutations that stabilize the U6 ‘telestem’ helix increase annealing rates by up to 15-fold, suggesting that telestem formation is rate-limiting for U4/U6 pairing. The Lsm2–8 complex, which binds adjacent to the telestem at the 3′ end of U6, provides a comparable rate enhancement. Collectively, these data identify domains of the U6 snRNP that are critical for one of the first steps in assembly of the megaDalton U4/U6.U5 tri-snRNP complex, and lead to a dynamic model for U4/U6 pairing that involves a striking degree of evolved cooperativity between protein and RNA.
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Affiliation(s)
- Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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5
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Rodgers ML, Paulson J, Hoskins AA. Rapid isolation and single-molecule analysis of ribonucleoproteins from cell lysate by SNAP-SiMPull. RNA (NEW YORK, N.Y.) 2015; 21:1031-41. [PMID: 25805862 PMCID: PMC4408783 DOI: 10.1261/rna.047845.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/03/2015] [Indexed: 05/08/2023]
Abstract
Large macromolecular complexes such as the spliceosomal small nuclear ribonucleoproteins (snRNPs) play a variety of roles within the cell. Despite their biological importance, biochemical studies of snRNPs and other machines are often thwarted by practical difficulties in the isolation of sufficient amounts of material. Studies of the snRNPs as well as other macromolecular machines would be greatly facilitated by new approaches that enable their isolation and biochemical characterization. One such approach is single-molecule pull-down (SiMPull) that combines in situ immunopurification of complexes from cell lysates with subsequent single-molecule fluorescence microscopy experiments. We report the development of a new method, called SNAP-SiMPull, that can readily be applied to studies of splicing factors and snRNPs isolated from whole-cell lysates. SNAP-SiMPull overcomes many of the limitations imposed by conventional SiMPull strategies that rely on fluorescent proteins. We have used SNAP-SiMPull to study the yeast branchpoint bridging protein (BBP) as well as the U1 and U6 snRNPs. SNAP-SiMPull will likely find broad use for rapidly isolating complex cellular machines for single-molecule fluorescence colocalization experiments.
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Affiliation(s)
- Margaret L Rodgers
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Joshua Paulson
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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6
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Montemayor EJ, Curran EC, Liao HH, Andrews KL, Treba CN, Butcher SE, Brow DA. Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution. Nat Struct Mol Biol 2014; 21:544-51. [PMID: 24837192 PMCID: PMC4141773 DOI: 10.1038/nsmb.2832] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/28/2014] [Indexed: 12/11/2022]
Abstract
The spliceosome is a dynamic assembly of five small nuclear ribonucleoproteins
(snRNPs) that removes introns from eukaryotic pre-mRNA. U6 is the most conserved of the
spliceosomal snRNAs and participates directly in catalysis. Here, we report the crystal
structure of the Saccharomyces cerevisiae U6 snRNP core, containing most
of U6 snRNA and all four RRM domains of the Prp24 protein. It reveals a unique interlocked
RNP architecture that sequesters the 5′ splice site-binding bases of U6 snRNA.
RRMs 1, 2 and 4 of Prp24 form an electropositive groove that binds double-stranded RNA and
may nucleate annealing of U4 and U6 snRNAs. Substitutions in Prp24 that suppress a
mutation in U6 localize to direct RNA-protein contacts. Our results provide the most
complete view to date of a multi-RRM protein bound to RNA, and reveal striking
co-evolution of protein and RNA structure.
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Affiliation(s)
- Eric J Montemayor
- 1] Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2] Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth C Curran
- 1] Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2]
| | - Hong Hong Liao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kristie L Andrews
- 1] Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2]
| | - Christine N Treba
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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7
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Melamed D, Young DL, Gamble CE, Miller CR, Fields S. Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein. RNA (NEW YORK, N.Y.) 2013; 19:1537-51. [PMID: 24064791 PMCID: PMC3851721 DOI: 10.1261/rna.040709.113] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The RNA recognition motif (RRM) is the most common RNA-binding domain in eukaryotes. Differences in RRM sequences dictate, in part, both RNA and protein-binding specificities and affinities. We used a deep mutational scanning approach to study the sequence-function relationship of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein (Pab1). By scoring the activity of more than 100,000 unique Pab1 variants, including 1246 with single amino acid substitutions, we delineated the mutational constraints on each residue. Clustering of residues with similar mutational patterns reveals three major classes, composed principally of RNA-binding residues, of hydrophobic core residues, and of the remaining residues. The first class also includes a highly conserved residue not involved in RNA binding, G150, which can be mutated to destabilize Pab1. A comparison of the mutational sensitivity of yeast Pab1 residues to their evolutionary conservation reveals that most residues tolerate more substitutions than are present in the natural sequences, although other residues that tolerate fewer substitutions may point to specialized functions in yeast. An analysis of ∼40,000 double mutants indicates a preference for a short distance between two mutations that display an epistatic interaction. As examples of interactions, the mutations N139T, N139S, and I157L suppress other mutations that interfere with RNA binding and protein stability. Overall, this study demonstrates that living cells can be subjected to a single assay to analyze hundreds of thousands of protein variants in parallel.
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Affiliation(s)
- Daniel Melamed
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - David L. Young
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Caitlin E. Gamble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Christina R. Miller
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Stanley Fields
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
- Corresponding authorE-mail
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8
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Abstract
RNA splicing is one of the fundamental processes in gene expression in eukaryotes. Splicing of pre-mRNA is catalysed by a large ribonucleoprotein complex called the spliceosome, which consists of five small nuclear RNAs and numerous protein factors. The spliceosome is a highly dynamic structure, assembled by sequential binding and release of the small nuclear RNAs and protein factors. DExD/H-box RNA helicases are required to mediate structural changes in the spliceosome at various steps in the assembly pathway and have also been implicated in the fidelity control of the splicing reaction. Other proteins also play key roles in mediating the progression of the spliceosome pathway. In this review, we discuss the functional roles of the protein factors involved in the spliceosome pathway primarily from studies in the yeast system.
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9
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Martin-Tumasz S, Richie AC, Clos LJ, Brow DA, Butcher SE. A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop. Nucleic Acids Res 2011; 39:7837-47. [PMID: 21653550 PMCID: PMC3177201 DOI: 10.1093/nar/gkr455] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The essential splicing factor Prp24 contains four RNA Recognition Motif (RRM) domains, and functions to anneal U6 and U4 RNAs during spliceosome assembly. Here, we report the structure and characterization of the C-terminal RRM4. This domain adopts a novel non-canonical RRM fold with two additional flanking α-helices that occlude its β-sheet face, forming an occluded RRM (oRRM) domain. The flanking helices form a large electropositive surface. oRRM4 binds to and unwinds the U6 internal stem loop (U6 ISL), a stable helix that must be unwound during U4/U6 assembly. NMR data indicate that the process starts with the terminal base pairs of the helix and proceeds toward the loop. We propose a mechanistic and structural model of Prp24′s annealing activity in which oRRM4 functions to destabilize the U6 ISL during U4/U6 assembly.
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10
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Martin-Tumasz S, Reiter NJ, Brow DA, Butcher SE. Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24. RNA (NEW YORK, N.Y.) 2010; 16:792-804. [PMID: 20181740 PMCID: PMC2844626 DOI: 10.1261/rna.1913310] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
U6 RNA plays a critical role in pre-mRNA splicing. Assembly of U6 into the spliceosome requires a significant structural rearrangement and base-pairing with U4 RNA. In the yeast Saccharomyces cerevisiae, this process requires the essential splicing factor Prp24. We present the characterization and structure of a complex containing one of Prp24's four RNA recognition motif (RRM) domains, RRM2, and a fragment of U6 RNA. NMR methods were used to identify the preferred U6 binding sequence of RRM2 (5'-GAGA-3'), measure the affinity of the interaction, and solve the structure of RRM2 bound to the hexaribonucleotide AGAGAU. Interdomain contacts observed between RRM2 and RRM3 in a crystal structure of the free protein are not detectable in solution. A structural model of RRM1 and RRM2 bound to a longer segment of U6 RNA is presented, and a partial mechanism for Prp24's annealing activity is proposed.
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Affiliation(s)
- Stephen Martin-Tumasz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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11
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Martin-Tumasz S, Butcher SE. (1)H, (13)C and (15)N resonance assignments of a ribonucleoprotein complex consisting of Prp24-RRM2 bound to a fragment of U6 RNA. BIOMOLECULAR NMR ASSIGNMENTS 2009; 3:227-30. [PMID: 19693704 PMCID: PMC2972308 DOI: 10.1007/s12104-009-9181-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 08/09/2009] [Indexed: 05/19/2023]
Abstract
Saccharomyces cerevisiae Prp24 is an essential RNA binding protein involved in pre-mRNA splicing. Nearly complete backbone and side chain resonance assignments have been obtained for the second RNA recognition motif (RRM) of Prp24 (RRM2, residues M114-E197) both in isolation and bound to a six nucleotide fragment of U6 RNA (AGAGAU). In addition, nearly complete backbone assignments have been made for a Prp24 construct spanning the second and third RRMs (RRM23, residues M114-K290), both free and bound to AGAGAU.
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12
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Venditti V, Clos L, Niccolai N, Butcher SE. Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping. J Mol Biol 2009; 391:894-905. [PMID: 19591840 DOI: 10.1016/j.jmb.2009.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 06/29/2009] [Accepted: 07/01/2009] [Indexed: 11/28/2022]
Abstract
The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a)=6.5). Lower pH favors formation of a protonated C-A(+) wobble pair and base flipping of the adjacent uracil. Higher pH favors stacking of the uracil and allows an essential metal ion to bind at this position. Here, we define the minimal-energy path for this conformational transition. To do this, we solved the U6 ISL structure at higher pH (8.0) in order to eliminate interference from the low-pH conformer. This structure reveals disruption of the protonated C-A(+) pair and formation of a new C-U pair, which explains the preference for a stacked uracil at higher pH. Next, we used nudged elastic band molecular dynamics simulations to calculate the minimum-energy path between the two conformations. Our results indicate that the C-U pair is dynamic, which allows formation of the more stable C-A(+) pair upon adenine protonation. After formation of the C-A(+) pair, the unpaired uracil follows a minor-groove base-flipping pathway. Molecular dynamics simulations suggest that the extrahelical uracil is stabilized by contacts with the adjacent helix.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, Italy
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13
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Karaduman R, Dube P, Stark H, Fabrizio P, Kastner B, Lührmann R. Structure of yeast U6 snRNPs: arrangement of Prp24p and the LSm complex as revealed by electron microscopy. RNA (NEW YORK, N.Y.) 2008; 14:2528-37. [PMID: 18971323 PMCID: PMC2590955 DOI: 10.1261/rna.1369808] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Protein components of the U6 snRNP (Prp24p and LSm2-8) are thought to act cooperatively in facilitating the annealing of U6 and U4 snRNAs during U4/U6 di-snRNP formation. To learn more about the spatial arrangement of these proteins in S. cerevisiae U6 snRNPs, we investigated the structure of this particle by electron microscopy. U6 snRNPs, purified by affinity chromatography and gradient centrifugation, and then immediately adsorbed to the carbon film support, revealed an open form in which the Prp24 protein and the ring formed by the LSm proteins were visible as two separate morphological domains, while particles stabilized by chemical cross-linking in solution under mild conditions before binding to the carbon film exhibited a compact form, with the two domains in close proximity to one another. In the open form, individual LSm proteins were located by a novel approach employing C-terminal genetic tagging of the LSm proteins with yECitrine. These studies show the Prp24 protein at defined distances from each subunit of the LSm ring, which in turn suggests that the LSm ring is positioned in a consistent manner on the U6 RNA. Furthermore, in agreement with the EM observations, UV cross-linking revealed U6 RNA in contact with the LSm2 protein at the interface between Prp24p and the LSm ring. Further, LSmp-Prp24p interactions may be restricted to the closed form, which appears to represent the solution structure of the U6 snRNP particle.
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Affiliation(s)
- Ramazan Karaduman
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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14
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Cléry A, Blatter M, Allain FHT. RNA recognition motifs: boring? Not quite. Curr Opin Struct Biol 2008; 18:290-8. [PMID: 18515081 DOI: 10.1016/j.sbi.2008.04.002] [Citation(s) in RCA: 455] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 04/09/2008] [Indexed: 01/10/2023]
Abstract
The RNA recognition motif (RRM) is one of the most abundant protein domains in eukaryotes. While the structure of this domain is well characterized by the packing of two alpha-helices on a four-stranded beta-sheet, the mode of protein and RNA recognition by RRMs is not clear owing to the high variability of these interactions. Here we report recent structural data on RRM-RNA and RRM-protein interactions showing the ability of this domain to modulate its binding affinity and specificity using each of its constitutive elements (beta-strands, loops, alpha-helices). The extreme structural versatility of the RRM interactions explains why RRM-containing proteins have so diverse biological functions.
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Affiliation(s)
- Antoine Cléry
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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15
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McManus CJ, Schwartz ML, Butcher SE, Brow DA. A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. RNA (NEW YORK, N.Y.) 2007; 13:2252-65. [PMID: 17925343 PMCID: PMC2080595 DOI: 10.1261/rna.699907] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 08/15/2007] [Indexed: 05/20/2023]
Abstract
The highly conserved internal stem-loop (ISL) of U6 spliceosomal RNA is unwound for U4/U6 complex formation during spliceosome assembly and reformed upon U4 release during spliceosome activation. The U6 ISL is structurally similar to Domain 5 of group II self-splicing introns, and contains a dynamic bulge that coordinates a Mg++ ion essential for the first catalytic step of splicing. We have analyzed the causes of growth defects resulting from mutations in the Saccharomyces cerevisiae U6 ISL-bulged nucleotide U80 and the adjacent C67-A79 base pair. Intragenic suppressors and enhancers of the cold-sensitive A79G mutation, which replaces the C-A pair with a C-G pair, suggest that it stabilizes the ISL, inhibits U4/U6 assembly, and may also disrupt spliceosome activation. The lethality of mutations C67A and C67G results from disruption of base-pairing potential between U4 and U6, as these mutations are fully suppressed by compensatory mutations in U4 RNA. Strikingly, suppressor analysis shows that the lethality of the U80G mutation is due not only to formation of a stable base pair with C67, as previously proposed, but also another defect. A U6-U80G strain in which mispairing with position 67 is prevented grows poorly and assembles aberrant spliceosomes that retain U1 snRNP and fail to fully unwind the U4/U6 complex at elevated temperatures. Our data suggest that the U6 ISL bulge is important for coupling U1 snRNP release with U4/U6 unwinding during spliceosome activation.
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Affiliation(s)
- C Joel McManus
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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16
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Trede NS, Medenbach J, Damianov A, Hung LH, Weber GJ, Paw BH, Zhou Y, Hersey C, Zapata A, Keefe M, Barut BA, Stuart AB, Katz T, Amemiya CT, Zon LI, Bindereif A. Network of coregulated spliceosome components revealed by zebrafish mutant in recycling factor p110. Proc Natl Acad Sci U S A 2007; 104:6608-13. [PMID: 17416673 PMCID: PMC1871833 DOI: 10.1073/pnas.0701919104] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spliceosome cycle consists of assembly, catalysis, and recycling phases. Recycling of postspliceosomal U4 and U6 small nuclear ribonucleoproteins (snRNPs) requires p110/SART3, a general splicing factor. In this article, we report that the zebrafish earl grey (egy) mutation maps in the p110 gene and results in a phenotype characterized by thymus hypoplasia, other organ-specific defects, and death by 7 to 8 days postfertilization. U4/U6 snRNPs were disrupted in egy mutant embryos, demonstrating the importance of p110 for U4/U6 snRNP recycling in vivo. Surprisingly, expression profiling of the egy mutant revealed an extensive network of coordinately up-regulated components of the spliceosome cycle, providing a mechanism compensating for the recycling defect. Together, our data demonstrate that a mutation in a general splicing factor can lead to distinct defects in organ development and cause disease.
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Affiliation(s)
- Nikolaus S. Trede
- *Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Jan Medenbach
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
| | - Andrey Damianov
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
| | - Gerhard J. Weber
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Barry H. Paw
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Yi Zhou
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Candace Hersey
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Agustin Zapata
- Department of Cell Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain; and
| | - Matthew Keefe
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Bruce A. Barut
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Andrew B. Stuart
- Benaroya Research Institute at Virginia Mason, Department of Biology, University of Washington, Seattle, WA 98101
| | - Tammisty Katz
- *Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Chris T. Amemiya
- Benaroya Research Institute at Virginia Mason, Department of Biology, University of Washington, Seattle, WA 98101
| | - Leonard I. Zon
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
- **To whom correspondence may be addressed at:
Howard Hughes Medical Institute, Department of Hematology/Oncology, Children's Hospital, Harvard Medical School, Karp Family Research Laboratories, 300 Longwood Avenue, Boston, MA 02115. E-mail:
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
- To whom correspondence may be addressed at:
Institute of Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany. E-mail:
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17
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Bae E, Reiter NJ, Bingman CA, Kwan SS, Lee D, Phillips GN, Butcher SE, Brow DA. Structure and interactions of the first three RNA recognition motifs of splicing factor prp24. J Mol Biol 2007; 367:1447-58. [PMID: 17320109 PMCID: PMC1939982 DOI: 10.1016/j.jmb.2007.01.078] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 01/24/2007] [Accepted: 01/31/2007] [Indexed: 11/21/2022]
Abstract
The essential Saccharomyces cerevisiae pre-messenger RNA splicing protein 24 (Prp24) has four RNA recognition motifs (RRMs) and facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 is a component of the free U6 small nuclear ribonucleoprotein particle (snRNP) but not the U4/U6 bi-snRNP, and so is thought to be displaced from U6 by U4/U6 base-pairing. The interaction partners of each of the four RRMs of Prp24 and how these interactions direct U4/U6 pairing are not known. Here we report the crystal structure of the first three RRMs and the solution structure of the first two RRMs of Prp24. Strikingly, RRM 2 forms extensive inter-domain contacts with RRMs 1 and 3. These contacts occupy much of the canonical RNA-binding faces (beta-sheets) of RRMs 1 and 2, but leave the beta-sheet of RRM 3 exposed. Previously identified substitutions in Prp24 that suppress mutations in U4 and U6 spliceosomal RNAs cluster primarily in the beta-sheet of RRM 3, but also in a conserved loop of RRM 2. RNA binding assays and chemical shift mapping indicate that a large basic patch evident on the surface of RRMs 1 and 2 is part of a high affinity U6 RNA binding site. Our results suggest that Prp24 binds free U6 RNA primarily with RRMs 1 and 2, which may remodel the U6 secondary structure. The beta-sheet of RRM 3 then influences U4/U6 pairing through interaction with an unidentified ligand.
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Affiliation(s)
- Euiyoung Bae
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - Nicholas J. Reiter
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - Sharon S. Kwan
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Donghan Lee
- National Cancer Institute, Frederick, MD 21702, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - David A. Brow
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
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18
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Reiter NJ, Lee D, Wang YX, Tonelli M, Bahrami A, Cornilescu CC, Butcher SE. Resonance assignments for the two N-terminal RNA recognition motifs (RRM) of the S. cerevisiae pre-mRNA processing protein Prp24. JOURNAL OF BIOMOLECULAR NMR 2006; 36 Suppl 1:58. [PMID: 17131032 DOI: 10.1007/s10858-006-9039-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 06/02/2006] [Indexed: 05/12/2023]
Affiliation(s)
- Nicholas J Reiter
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
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19
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Karaduman R, Fabrizio P, Hartmuth K, Urlaub H, Lührmann R. RNA structure and RNA-protein interactions in purified yeast U6 snRNPs. J Mol Biol 2005; 356:1248-62. [PMID: 16410014 DOI: 10.1016/j.jmb.2005.12.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 12/01/2005] [Accepted: 12/03/2005] [Indexed: 11/21/2022]
Abstract
The U6 small nuclear RNA (snRNA) undergoes major conformational changes during the assembly of the spliceosome and catalysis of splicing. It associates with the specific protein Prp24p, and a set of seven LSm2p-8p proteins, to form the U6 small nuclear ribonucleoprotein (snRNP). These proteins have been proposed to act as RNA chaperones that stimulate pairing of U6 with U4 snRNA to form the intermolecular stem I and stem II of the U4/U6 duplex, whose formation is essential for spliceosomal function. However, the mechanism whereby Prp24p and the LSm complex facilitate U4/U6 base-pairing, as well as the exact binding site(s) of Prp24p in the native U6 snRNP, are not well understood. Here, we have investigated the secondary structure of the U6 snRNA in purified U6 snRNPs and compared it with its naked form. Using RNA structure-probing techniques, we demonstrate that within the U6 snRNP a large internal region of the U6 snRNA is unpaired and protected from chemical modification by bound Prp24p. Several of these U6 nucleotides are available for base-pairing interaction, as only their sugar backbone is contacted by Prp24p. Thus, Prp24p can present them to the U4 snRNA and facilitate formation of U4/U6 stem I. We show that the 3' stem-loop is not bound strongly by U6 proteins in native particles. However, when compared to the 3' stem-loop in the naked U6 snRNA, it has a more open conformation, which would facilitate formation of stem II with the U4 snRNA. Our data suggest that the combined association of Prp24p and the LSm complex confers upon U6 nucleotides a conformation favourable for U4/U6 base-pairing. Interestingly, we find that the open structure of the yeast U6 snRNA in native snRNPs can also be adopted by human U6 and U6atac snRNAs.
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Affiliation(s)
- Ramazan Karaduman
- Max-Planck-Institute of Biophysical Chemistry, Department of Cellular Biochemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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