1
|
Musaev D, Abdelmessih M, Vejnar CE, Yartseva V, Weiss LA, Strayer EC, Takacs CM, Giraldez AJ. UPF1 regulates mRNA stability by sensing poorly translated coding sequences. Cell Rep 2024; 43:114074. [PMID: 38625794 PMCID: PMC11259039 DOI: 10.1016/j.celrep.2024.114074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 04/18/2024] Open
Abstract
Post-transcriptional mRNA regulation shapes gene expression, yet how cis-elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that the strength of translation initiation, upstream open reading frame (uORF) content, codon optimality, AU-rich elements, microRNA binding sites, and open reading frame (ORF) length function combinatorially to regulate mRNA stability. Machine-learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs, which are associated with a higher decay rate, including mRNAs with uORFs and those with exposed ORFs after stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated, such as mRNAs with long ORFs, ORF-like 3' UTRs, and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an exon-junction complex (EJC)-independent nonsense-mediated decay (NMD) pathway that we term ORF-mediated decay (OMD).
Collapse
Affiliation(s)
- Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mario Abdelmessih
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; AstraZeneca, Waltham, MA 02451, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kenai Therapeutics, San Diego, CA, USA
| | - Linnea A Weiss
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ethan C Strayer
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; University of New Haven, West Haven, CT 06516, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
2
|
Mohsen JJ, Martel AA, Slavoff SA. Microproteins-Discovery, structure, and function. Proteomics 2023; 23:e2100211. [PMID: 37603371 PMCID: PMC10841188 DOI: 10.1002/pmic.202100211] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.
Collapse
Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alina A. Martel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| |
Collapse
|
3
|
Vock IW, Simon MD. bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA (NEW YORK, N.Y.) 2023; 29:958-976. [PMID: 37028916 DOI: 10.1261/rna.079451.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in cellular RNA levels, but provides limited information about the kinetic mechanisms underlying such changes. Nucleotide recoding RNA-seq methods (NR-seq; e.g., TimeLapse-seq, SLAM-seq, etc.) address this shortcoming and are widely used approaches to identify changes in RNA synthesis and degradation kinetics. While advanced statistical models implemented in user-friendly software (e.g., DESeq2) have ensured the statistical rigor of differential expression analyses, no such tools that facilitate differential kinetic analysis with NR-seq exist. Here, we report the development of Bayesian analysis of the kinetics of RNA (bakR; https:// github.com/simonlabcode/bakR), an R package to address this need. bakR relies on Bayesian hierarchical modeling of NR-seq data to increase statistical power by sharing information across transcripts. Analyses of simulated data confirmed that bakR implementations of the hierarchical model outperform attempts to analyze differential kinetics with existing models. bakR also uncovers biological signals in real NR-seq data sets and provides improved analyses of existing data sets. This work establishes bakR as an important tool for identifying differential RNA synthesis and degradation kinetics.
Collapse
Affiliation(s)
- Isaac W Vock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
| |
Collapse
|
4
|
Borbolis F, Ranti D, Papadopoulou MD, Dimopoulou S, Malatras A, Michalopoulos I, Syntichaki P. Selective Destabilization of Transcripts by mRNA Decapping Regulates Oocyte Maturation and Innate Immunity Gene Expression during Ageing in C. elegans. BIOLOGY 2023; 12:biology12020171. [PMID: 36829450 PMCID: PMC9952881 DOI: 10.3390/biology12020171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023]
Abstract
Removal of the 5' cap structure of RNAs (termed decapping) is a pivotal event in the life of cytoplasmic mRNAs mainly catalyzed by a conserved holoenzyme, composed of the catalytic subunit DCP2 and its essential cofactor DCP1. While decapping was initially considered merely a step in the general 5'-3' mRNA decay, recent data suggest a great degree of selectivity that plays an active role in the post-transcriptional control of gene expression, and regulates multiple biological functions. Studies in Caenorhabditis elegans have shown that old age is accompanied by the accumulation of decapping factors in cytoplasmic RNA granules, and loss of decapping activity shortens the lifespan. However, the link between decapping and ageing remains elusive. Here, we present a comparative microarray study that was aimed to uncover the differences in the transcriptome of mid-aged dcap-1/DCP1 mutant and wild-type nematodes. Our data indicate that DCAP-1 mediates the silencing of spermatogenic genes during late oogenesis, and suppresses the aberrant uprise of immunity gene expression during ageing. The latter is achieved by destabilizing the mRNA that encodes the transcription factor PQM-1 and impairing its nuclear translocation. Failure to exert decapping-mediated control on PQM-1 has a negative impact on the lifespan, but mitigates the toxic effects of polyglutamine expression that are involved in human disease.
Collapse
Affiliation(s)
- Fivos Borbolis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Dimitra Ranti
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | | | - Sofia Dimopoulou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Apostolos Malatras
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Ioannis Michalopoulos
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Correspondence: (I.M.); (P.S.); Tel.: +30-21-0659-7127 (I.M.); +30-21-0659-7474 (P.S.)
| | - Popi Syntichaki
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Correspondence: (I.M.); (P.S.); Tel.: +30-21-0659-7127 (I.M.); +30-21-0659-7474 (P.S.)
| |
Collapse
|
5
|
Feng D, Liu L, Shi Y, Du P, Xu S, Zhu Z, Xu J, Yao H. Current development of bicyclic peptides. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
6
|
Nahalka J. 1-L Transcription in Alzheimer's Disease. Curr Issues Mol Biol 2022; 44:3533-3551. [PMID: 36005139 PMCID: PMC9406503 DOI: 10.3390/cimb44080243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022] Open
Abstract
Alzheimer's disease is a very complex disease and better explanations and models are needed to understand how neurons are affected and microglia are activated. A new model of Alzheimer's disease is presented here, the β-amyloid peptide is considered an important RNA recognition/binding peptide. 1-L transcription revealed compatible sequences with AAUAAA (PAS signal) and UUUC (class III ARE rich in U) in the Aβ peptide, supporting the peptide-RNA regulatory model. When a hypothetical model of fibril selection with the prionic character of amyloid assemblies is added to the peptide-RNA regulatory model, the downregulation of the PI3K-Akt pathway and the upregulation of the PLC-IP3 pathway are well explained. The model explains why neurons are less protected from inflammation and why microglia are activated; why mitochondria are destabilized; why the autophagic flux is destabilized; and why the post-transcriptional attenuation of the axonal signal "noise" is interrupted. For example, the model suggests that Aβ peptide may post-transcriptionally control ELAVL2 (ELAV-like RNA binding protein 2) and DCP2 (decapping mRNA protein 2), which are known to regulate RNA processing, transport, and stability.
Collapse
Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia;
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
| |
Collapse
|
7
|
Xiao Y, Yang J, Yang M, Len J, Yu Y. Comprehensive analysis of 7-methylguanosine and immune microenvironment characteristics in clear cell renal cell carcinomas. Front Genet 2022; 13:866819. [PMID: 36003341 PMCID: PMC9393245 DOI: 10.3389/fgene.2022.866819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common tumors in the urinary system. ccRCC has obvious immunological characteristics, and the infiltration of immune cells is related to the prognosis of ccRCC. The effect of immune checkpoint therapy is related to the dynamic changes of the tumor immune microenvironment (TIM). The 7-methylguanosine (m7G) is an additional mRNA modification ability besides m6A, which is closely related to the TIM and affects the occurrence and development of tumors. At present, the correlations between m7G and the immune microenvironment, treatment, and prognosis of ccRCC are not clear. As far as we know, there was no study on the relationship between m7G and the immune microenvironment and survival of clear cell renal cell carcinomas. A comprehensive analysis of the correlations between them and the construction of a prognosis model are helpful to improve the treatment strategy. Two different molecular subtypes were identified in 539 ccRCC samples by describing the differences of 29 m7G-related genes. It was found that the clinical features, TIM, and prognosis of ccRCC patients were correlated with the m7G-related genes. We found that there were significant differences in the expression of PD-1, CTLA4, and PD-L1 between high- and low-risk groups. To sum up, m7G-related genes play a potential role in the TIM, treatment, and prognosis of ccRCC. Our results provide new findings for ccRCC and help to improve the immunotherapy strategies and prognosis of patients.
Collapse
Affiliation(s)
- Yu Xiao
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China
- Department of Urology, The First People’s Hospital of Yunnan Province, Kunming, YN, China
| | - Junfeng Yang
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China
- Department of Urology, The First People’s Hospital of Yunnan Province, Kunming, YN, China
| | - Maolin Yang
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China
- Department of Urology, The First People’s Hospital of Yunnan Province, Kunming, YN, China
| | - Jinjun Len
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China
- Department of Urology, The First People’s Hospital of Yunnan Province, Kunming, YN, China
| | - Yanhong Yu
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China
- Department of Urology, The First People’s Hospital of Yunnan Province, Kunming, YN, China
- *Correspondence: Yanhong Yu,
| |
Collapse
|
8
|
Swartzel JC, Bond MJ, Pintado-Urbanc AP, Daftary M, Krone MW, Douglas T, Carder EJ, Zimmer JT, Maeda T, Simon MD, Crews CM. Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS Chem Biol 2022; 17:1789-1798. [PMID: 35749470 PMCID: PMC10367122 DOI: 10.1021/acschembio.2c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The RNA decapping scavenger protein, DcpS, has recently been identified as a dependency in acute myeloid leukemia (AML). The potent DcpS inhibitor RG3039 attenuates AML cell viability, and shRNA knockdown of DcpS is also antiproliferative. Importantly, DcpS was found to be non-essential in normal human hematopoietic cells, which opens a therapeutic window for AML treatment by DcpS modulation. Considering this strong DcpS dependence in AML cell lines, we explored PROTAC-mediated degradation as an alternative strategy to modulate DcpS activity. Herein, we report the development of JCS-1, a PROTAC exhibiting effective degradation of DcpS at nanomolar concentrations. JCS-1 non-covalently binds DcpS with a RG3039-based warhead and recruits the E3 ligase VHL, which induces potent, rapid, and sustained DcpS degradation in several AML cell lines. JCS-1 serves as a chemical biology tool to interrogate DcpS degradation and associated changes in RNA processes in different cellular contexts, which may be an attractive strategy for the treatment of AML and other DcpS-dependent genetic disorders.
Collapse
Affiliation(s)
- Jake C Swartzel
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Michael J Bond
- Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Andreas P Pintado-Urbanc
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Mehana Daftary
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Mackenzie W Krone
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Todd Douglas
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Evan J Carder
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Joshua T Zimmer
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Matthew D Simon
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M Crews
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States.,Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| |
Collapse
|
9
|
Bednarczyk M, Peters JK, Kasprzyk R, Starek J, Warminski M, Spiewla T, Mugridge JS, Gross JD, Jemielity J, Kowalska J. Fluorescence-Based Activity Screening Assay Reveals Small Molecule Inhibitors of Vaccinia Virus mRNA Decapping Enzyme D9. ACS Chem Biol 2022; 17:1460-1471. [PMID: 35576528 PMCID: PMC9207806 DOI: 10.1021/acschembio.2c00049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vaccinia virus (VACV) represents a family of poxviruses, which possess their own decapping machinery as a part of their strategy to eliminate host mRNAs and evade the innate immune response. D9 is one of the two encoded VACV decapping enzymes that is responsible for cap removal from the 5' end of both host mRNA transcripts and viral double-stranded RNAs. Little is known about the structural requirements for D9 inhibition by small molecules. Here, we identified a minimal D9 substrate and used it to develop a real-time fluorescence assay for inhibitor discovery and characterization. We screened a panel of nucleotide-derived substrate analogues and pharmacologically active candidates to identify several compounds with nano- and low micromolar IC50 values. m7GpppCH2p was the most potent nucleotide inhibitor (IC50 ∼ 0.08 μM), and seliciclib and CP-100356 were the most potent drug-like compounds (IC50 0.57 and 2.7 μM, respectively). The hits identified through screening inhibited D9-catalyzed decapping of 26 nt RNA substrates but were not active toward VACV D10 or human decapping enzyme, Dcp1/2. The inhibition mode for one of the compounds (CP-100356) was elucidated based on the X-ray cocrystal structure, opening the possibility for structure-based design of novel D9 inhibitors and binding probes.
Collapse
Affiliation(s)
- Marcelina Bednarczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Jessica K. Peters
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Jagoda Starek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Tomasz Spiewla
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Jeffrey S. Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - John D. Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| |
Collapse
|
10
|
Wong JYK, Mukherjee R, Miao J, Bilyk O, Triana V, Miskolzie M, Henninot A, Dwyer JJ, Kharchenko S, Iampolska A, Volochnyuk DM, Lin YS, Postovit LM, Derda R. Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL. Chem Sci 2021; 12:9694-9703. [PMID: 34349940 PMCID: PMC8294009 DOI: 10.1039/d1sc01916c] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
In this manuscript, we developed a two-fold symmetric linchpin (TSL) that converts readily available phage-displayed peptides libraries made of 20 common amino acids to genetically-encoded libraries of bicyclic peptides displayed on phage. TSL combines an aldehyde-reactive group and two thiol-reactive groups; it bridges two side chains of cysteine [C] with an N-terminal aldehyde group derived from the N-terminal serine [S], yielding a novel bicyclic topology that lacks a free N-terminus. Phage display libraries of SX1CX2X3X4X5X6X7C sequences, where X is any amino acid but Cys, were converted to a library of bicyclic TSL-[S]X1[C]X2X3X4X5X6X7[C] peptides in 45 ± 15% yield. Using this library and protein morphogen NODAL as a target, we discovered bicyclic macrocycles that specifically antagonize NODAL-induced signaling in cancer cells. At a 10 μM concentration, two discovered bicyclic peptides completely suppressed NODAL-induced phosphorylation of SMAD2 in P19 embryonic carcinoma cells. The TSL-[S]Y[C]KRAHKN[C] bicycle inhibited NODAL-induced proliferation of NODAL-TYK-nu ovarian carcinoma cells with apparent IC50 of 1 μM. The same bicycle at 10 μM concentration did not affect the growth of the control TYK-nu cells. TSL-bicycles remained stable over the course of the 72 hour-long assays in a serum-rich cell-culture medium. We further observed general stability in mouse serum and in a mixture of proteases (Pronase™) for 21 diverse bicyclic macrocycles of different ring sizes, amino acid sequences, and cross-linker geometries. TSL-constrained peptides to expand the previously reported repertoire of phage-displayed bicyclic architectures formed by cross-linking Cys side chains. We anticipate that it will aid the discovery of proteolytically stable bicyclic inhibitors for a variety of protein targets.
Collapse
Affiliation(s)
- Jeffrey Y-K Wong
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Olena Bilyk
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Vivian Triana
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Mark Miskolzie
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | | | - John J Dwyer
- Ferring Research Institute San Diego California 92121 USA
| | | | - Anna Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Lynne-Marie Postovit
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| |
Collapse
|
11
|
Borbolis F, Syntichaki P. Biological implications of decapping: beyond bulk mRNA decay. FEBS J 2021; 289:1457-1475. [PMID: 33660392 DOI: 10.1111/febs.15798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022]
Abstract
It is well established that mRNA steady-state levels do not directly correlate with transcription rate. This is attributed to the multiple post-transcriptional mechanisms, which control both mRNA turnover and translation within eukaryotic cells. One such mechanism is the removal of the 5' end cap structure of RNAs (decapping). This 5' cap plays a fundamental role in cellular functions related to mRNA processing, transport, translation, quality control, and decay, while its chemical modifications influence the fate of cytoplasmic mRNAs. Decapping is a highly controlled process, performed by multiple decapping enzymes, and regulated by complex cellular networks. In this review, we provide an updated synopsis of 5' end modifications and functions, and give an overview of mRNA decapping enzymes, presenting their enzymatic properties. Focusing on DCP2 decapping enzyme, a major component on the 5'-3' mRNA decay pathway, we describe cis-elements and trans-acting factors that affect its activity, substrate specificity, and cellular localization. Finally, we discuss current knowledge on the biological functions of mRNA decapping and decay factors, highlighting the major questions that remain to be addressed.
Collapse
Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
| | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
| |
Collapse
|