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Ren J, Chen X, Li J, Zan Y, Wang S, Tan Y, Ding Y. TET1 inhibits the migration and invasion of cervical cancer cells by regulating autophagy. Epigenetics 2024; 19:2323751. [PMID: 38431880 PMCID: PMC10913696 DOI: 10.1080/15592294.2024.2323751] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Methylation modifications play pertinent roles in regulating gene expression and various biological processes. The silencing of the demethylase enzyme TET1 can affect the expressions of key oncogenes or tumour suppressor genes, thus contributing to tumour formation. Nonetheless, how TET1 affects the progression of cervical cancer is yet to be elucidated. In this study, we found that the expression of TET1 was significantly downregulated in cervical cancer tissues. Functionally, TET1 knockdown in cervical cancer cells can promote cell proliferation, migration, invasion, cervical xenograft tumour formation and EMT. On the contrary, its overexpression can reverse the aforementioned processes. Moreover, the autophagy level of cervical cancer cells can be enhanced after TET1 knockdown. Mechanistically, methylated DNA immunoprecipitation (MeDIP)-sequencing and MeDIP quantitative real-time PCR revealed that TET1 mediates the methylation of autophagy promoter regions. These findings suggest that TET1 affects the autophagy of cervical cancer cells by altering the methylation levels of NKRF or HIST1H2AK, but the specific mechanism needs to be investigated further.
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Affiliation(s)
- Ji Ren
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xiuying Chen
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Tongren city people’s hospital, Tongren, Guizhou, China
| | - Jing Li
- Gynecology, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxin Zan
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
| | - Shan Wang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yujie Tan
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Yan Ding
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
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2
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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 DOI: 10.1152/physrev.00026.2023] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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3
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Perillo B, Migliaccio A, Castoria G. Chromatin looping links gene expression to the assembly of transcription factories (Review). Mol Med Rep 2024; 29:97. [PMID: 38606508 DOI: 10.3892/mmr.2024.13221] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/20/2024] [Indexed: 04/13/2024] Open
Abstract
Genes are not randomly dispersed within the nuclear space, instead they occupy precise sites either with respect to the nuclear lamina as well as to each other. This observation stands at the basis of the today well accepted concept of nuclear territories where any chromosome shows reproducible spatial connections with a selection of others in a general picture that meets a functional criterion where genes that answer the same stimuli are grouped in the same sites. In fact, transcription is not visible widely dispersed throughout the nucleus but is gathered in several 'granules', called transcription factories that accommodates ~10 genes concurrently transcribed. This dynamic behavior of chromosomes is allowed by changes in chromatin plasticity that are governed by several classes of proteins that either modify its building or induce post‑translational modifications in the protein component of nucleosomes, triggering formation of chromosome loops that modify the location of specific sites along the DNA strand. For example, transcription associated to nuclear receptors benefits of the generation of nuclear ROS that induce nicks following activation of the DNA repair apparatus that enhance helix unfolding and chromosome bridging. In the present review, the role that protocols facing elucidation of chromosome architecture are playing and will play in the near future were highlighted in order to investigate composition of the transcription factories assembled in response of a specific trigger: The estrogen‑sensitive transcription was cited but the authors are convinced that the same portrait will be observed with a multitude of (if not all) other stimuli.
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Affiliation(s)
- Bruno Perillo
- Institute for Experimental Endocrinology and Oncology, C.N.R., I‑80131 Naples, Italy
| | - Antimo Migliaccio
- Department of Precision Medicine, Unicampania 'L. Vanvitelli', I‑80138 Naples, Italy
| | - Gabriella Castoria
- Department of Precision Medicine, Unicampania 'L. Vanvitelli', I‑80138 Naples, Italy
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4
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Ashour K, Sali S, Aldoukhi AH, Hall D, Mubaid S, Busque S, Lian XJ, Gagné JP, Khattak S, Di Marco S, Poirier GG, Gallouzi IE. pADP-ribosylation regulates the cytoplasmic localization, cleavage, and pro-apoptotic function of HuR. Life Sci Alliance 2024; 7:e202302316. [PMID: 38538092 PMCID: PMC10972696 DOI: 10.26508/lsa.202302316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
HuR (ElavL1) is one of the main post-transcriptional regulators that determines cell fate. Although the role of HuR in apoptosis is well established, the post-translational modifications that govern this function remain elusive. In this study, we show that PARP1/2-mediated poly(ADP)-ribosylation (PARylation) is instrumental in the pro-apoptotic function of HuR. During apoptosis, a substantial reduction in HuR PARylation is observed. This results in the cytoplasmic accumulation and the cleavage of HuR, both of which are essential events for apoptosis. These effects are mediated by a pADP-ribose-binding motif within the HuR-HNS region (HuR PAR-binding site). Under normal conditions, the association of the HuR PAR-binding site with pADP-ribose is responsible for the nuclear retention of HuR. Mutations within this motif prevent the binding of HuR to its import factor TRN2, leading to its cytoplasmic accumulation and cleavage. Collectively, our findings underscore the role of PARylation in controlling the pro-apoptotic function of HuR, offering insight into the mechanism by which PARP1/2 enzymes regulate cell fate and adaptation to various assaults.
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Affiliation(s)
- Kholoud Ashour
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
- Faculty of Applied Medical Sciences, Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Sujitha Sali
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Ali H Aldoukhi
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Derek Hall
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Souad Mubaid
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Sandrine Busque
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Xian Jin Lian
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Jean-Philippe Gagné
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Shahryar Khattak
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Sergio Di Marco
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Guy G Poirier
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Imed-Eddine Gallouzi
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
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5
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Zhao Y, Tang T, Zhao W, Fu W, Li T. Inhibition of PEDV viral entry upon blocking N-glycan elaboration. Virology 2024; 594:110039. [PMID: 38492520 DOI: 10.1016/j.virol.2024.110039] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/22/2024] [Accepted: 02/23/2024] [Indexed: 03/18/2024]
Abstract
Porcine Epidemic Diarrhea Virus (PEDV) poses a significant threat to the global swine industry, demanding a thorough understanding of its cellular invasion mechanism for effective interventions. This study meticulously investigates the impact of O- and N-linked glycans on PEDV proteins and host cell interaction, shedding light on their influence on the virus's invasion process. Utilizing CRISPR-Cas9 technology to inhibit cell surface O- and N-linked glycan synthesis demonstrated no discernible impact on virus infection. However, progeny PEDV strains lacking these glycans exhibited a minor effect of O-linked glycans on virus infection. Conversely, a notable 40% reduction in infectivity was observed when the virus surface lacked N-linked glycans, emphasizing their pivotal role in facilitating virus recognition and binding to host cells. Additionally, inhibition studies utilizing kifunensine, a natural glycosidase I inhibitor, reaffirmed the significant role of N-linked glycans in virus infection. Inhibiting N-linked glycan synthesis with kifunensine substantially decreased virus entry into cells and potentially influenced spike protein expression. Assessment of the stability and recovery potential of N-linked glycan-deficient strains underscored the critical importance of N-glycans at various stages of the virus lifecycle. In vivo experiments infecting piglets with N-glycan-deficient strains exhibited milder clinical symptoms, reduced virus excretion, and less severe pathological lesions compared to conventional strains. These findings offer promising translational applications, proposing N-glycosylation inhibitors as potential therapeutic interventions against PEDV. The utilization of these inhibitors might mitigate virus invasion and disease transmission, providing avenues for effective antiviral strategies and vaccine development. Nonetheless, further research is warranted to elucidate the precise mechanisms of N-linked glycans in PEDV infection for comprehensive clinical applications.
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Affiliation(s)
- Yong Zhao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China, No.1, Mingxian South Road, Taigu District, Shanxi Province, 030801.
| | - Tao Tang
- Cangzhou Hospital Of Integrated TCM-WM Hebei, No.31, Huanghe Road, Cangzhou City, Hebei Province, 061013, China.
| | - Wenchang Zhao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China, No.1, Mingxian South Road, Taigu District, Shanxi Province, 030801.
| | - Weiguang Fu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China, No.1, Mingxian South Road, Taigu District, Shanxi Province, 030801.
| | - Tao Li
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China, No.1, Mingxian South Road, Taigu District, Shanxi Province, 030801.
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6
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Akizuki Y, Kaypee S, Ohtake F, Ikeda F. The emerging roles of non-canonical ubiquitination in proteostasis and beyond. J Cell Biol 2024; 223:e202311171. [PMID: 38517379 PMCID: PMC10959754 DOI: 10.1083/jcb.202311171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance.
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Affiliation(s)
- Yoshino Akizuki
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Stephanie Kaypee
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Fumiyo Ikeda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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7
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Paluch KV, Platz KR, Rudisel EJ, Erdmann RR, Laurin TR, Dittenhafer-Reed KE. The role of lysine acetylation in the function of mitochondrial ribosomal protein L12. Proteins 2024; 92:583-592. [PMID: 38146092 DOI: 10.1002/prot.26654] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/27/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Mitochondria play a central role in energy production and cellular metabolism. Mitochondria contain their own small genome (mitochondrial DNA, mtDNA) that carries the genetic instructions for proteins required for ATP synthesis. The mitochondrial proteome, including the mitochondrial transcriptional machinery, is subject to post-translational modifications (PTMs), including acetylation and phosphorylation. We set out to determine whether PTMs of proteins associated with mtDNA may provide a potential mechanism for the regulation of mitochondrial gene expression. Here, we focus on mitochondrial ribosomal protein L12 (MRPL12), which is thought to stabilize mitochondrial RNA polymerase (POLRMT) and promote transcription. Numerous acetylation sites of MRPL12 were identified by mass spectrometry. We employed amino acid mimics of the acetylated (lysine to glutamine mutants) and deacetylated (lysine to arginine mutants) versions of MRPL12 to interrogate the role of lysine acetylation in transcription initiation in vitro and mitochondrial gene expression in HeLa cells. MRPL12 acetyl and deacetyl protein mimics were purified and assessed for their ability to impact mtDNA promoter binding of POLRMT. We analyzed mtDNA content and mitochondrial transcript levels in HeLa cells upon overexpression of acetyl and deacetyl mimics of MRPL12. Our results suggest that MRPL12 single-site acetyl mimics do not change the mtDNA promoter binding ability of POLRMT or mtDNA content in HeLa cells. Individual acetyl mimics may have modest effects on mitochondrial transcript levels. We found that the mitochondrial deacetylase, Sirtuin 3, is capable of deacetylating MRPL12 in vitro, suggesting a potential role for dynamic acetylation controlling MRPL12 function in a role outside of the regulation of gene expression.
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Affiliation(s)
- Katelynn V Paluch
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Karlie R Platz
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Emma J Rudisel
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Ryan R Erdmann
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Taylor R Laurin
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
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8
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Montserrat-Gomez M, Gogl G, Carrasco K, Betzi S, Durbesson F, Cousido-Siah A, Kostmann C, Essig DJ, Strømgaard K, Østergaard S, Morelli X, Trave G, Vincentelli R, Bailly E, Borg JP. PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2. Biochim Biophys Acta Proteins Proteom 2024; 1872:140989. [PMID: 38142947 DOI: 10.1016/j.bbapap.2023.140989] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
VANGL2 is a core component of the non-canonical Wnt/Planar Cell Polarity signaling pathway that uses its highly conserved carboxy-terminal type 1 PDZ-binding motif (PBM) to bind a variety of PDZ proteins. In this study, we characterize and quantitatively assess the largest VANGL2 PDZome-binding profile documented so far, using orthogonal methods. The results of our holdup approach support VANGL2 interactions with a large panel of both long-recognized and unprecedented PDZ domains. Truncation and point mutation analyses of the VANGL2 PBM establish that, beyond the strict requirement of the P-0 / V521 and P-2 / T519 amino acids, upstream residues, including E518, Q516 and R514 at, respectively, P-3, P-5 and P-7 further contribute to the robustness of VANGL2 interactions with two distinct PDZ domains, SNX27 and SCRIBBLE-PDZ3. In agreement with these data, incremental amino-terminal deletions of the VANGL2 PBM causes its overall affinity to progressively decline. Moreover, the holdup data establish that the PDZome binding repertoire of VANGL2 starts to diverge significantly with the truncation of E518. A structural analysis of the SYNJ2BP-PDZ/VANGL2 interaction with truncated PBMs identifies a major conformational change in the binding direction of the PBM peptide after the P-2 position. Finally, we report that the PDZome binding profile of VANGL2 is dramatically rearranged upon phosphorylation of S517, T519 and S520. Our crystallographic approach illustrates how SYNJ2BP accommodates a S520-phosphorylated PBM peptide through the ideal positioning of two basic residues, K48 and R86. Altogether our data provides a comprehensive view of the VANGL2 PDZ network and how this network specifically responds to the post-translation modification of distinct PBM residues. These findings should prove useful in guiding future functional and molecular studies of the key PCP component VANGL2.
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Affiliation(s)
- Marta Montserrat-Gomez
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France
| | - Gergo Gogl
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Kendall Carrasco
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Stephane Betzi
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Fabien Durbesson
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France
| | - Alexandra Cousido-Siah
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Camille Kostmann
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Dominic J Essig
- Center for Biopharmaceuticals, Jagtvej 162, 2100 Copenhagen, Denmark; Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | | | - Søren Østergaard
- Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | - Xavier Morelli
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Gilles Trave
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Renaud Vincentelli
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France.
| | - Eric Bailly
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France.
| | - Jean-Paul Borg
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France; Institut Universitaire de France (IUF), France.
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9
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Qiu K, Tian Y, Guo C, Liu O, Shi Y, Liu D, Luo T. Global proteomic analysis reveals lysine succinylation is involved in the pathogenesis of hypertrophic scar. J Proteomics 2024; 298:105155. [PMID: 38460743 DOI: 10.1016/j.jprot.2024.105155] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
Lysine succinylation (Ksucc) is a recently identified posttranslational modification that is involved in many diseases. This study examined the role of Ksucc in the pathogenesis of hypertrophic scar (HS). The presence of Ksucc in human skin was measured by immunoblotting. Ksucc occurs in many skin proteins ranging from 25 to 250 kDa, and higher levels of Ksucc are found in HS skin than in normal skin. An immunoaffinity approach coupled with LC-MS/MS was used to characterize the first succinylome of human skin, and 159 Ksucc sites in 79 proteins were identified. Among these, there were 38 increased succinylated sites in 29 proteins but no decreased succinylated sites in HS compared with normal skin. A parallel reaction monitoring assay was performed to validate the results of the succinylome and showed that the levels of Ksucc in decorin and collagens, which are involved in the pathogenesis of HS, were increased in HS than in normal skin. In addition, increasing the level of Ksucc enhanced cell proliferation and upregulated the expression of fibrosis markers (α-SMA, COL1, and COL3) in human skin fibroblasts. Our results provide global insights into the functional role of Ksucc in hypertrophic scarring.
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Affiliation(s)
- Keqing Qiu
- Department of Dermatology, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yan Tian
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Chunyan Guo
- Department of Dermatology, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Ougen Liu
- Department of Dermatology, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yan Shi
- Department of Plastic, Medical Center of Burn Plastic and Wound Repair, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Dewu Liu
- Department of Plastic, Medical Center of Burn Plastic and Wound Repair, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China.
| | - Tao Luo
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330031, China.
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10
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Chen L, Hu M, Chen L, Peng Y, Zhang C, Wang X, Li X, Yao Y, Song Q, Li J, Pei H. Targeting O-GlcNAcylation in cancer therapeutic resistance: The sugar Saga continues. Cancer Lett 2024; 588:216742. [PMID: 38401884 DOI: 10.1016/j.canlet.2024.216742] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
O-linked-N-acetylglucosaminylation (O-GlcNAcylation), a dynamic post-translational modification (PTM), holds profound implications in controlling various cellular processes such as cell signaling, metabolism, and epigenetic regulation that influence cancer progression and therapeutic resistance. From the therapeutic perspective, O-GlcNAc modulates drug efflux, targeting and metabolism. By integrating signals from glucose, lipid, amino acid, and nucleotide metabolic pathways, O-GlcNAc acts as a nutrient sensor and transmits signals to exerts its function on genome stability, epithelial-mesenchymal transition (EMT), cell stemness, cell apoptosis, autophagy, cell cycle. O-GlcNAc also attends to tumor microenvironment (TME) and the immune response. At present, several strategies aiming at targeting O-GlcNAcylation are under mostly preclinical evaluation, where the newly developed O-GlcNAcylation inhibitors markedly enhance therapeutic efficacy. Here we systematically outline the mechanisms through which O-GlcNAcylation influences therapy resistance and deliberate on the prospects and challenges associated with targeting O-GlcNAcylation in future cancer treatments.
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Affiliation(s)
- Lulu Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA.
| | - Mengxue Hu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Luojun Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yihan Peng
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Cai Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xin Wang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiangpan Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Huadong Pei
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA.
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11
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Wang J, Wang Y, Jiang X, Xu M, Wang M, Wang R, Zheng B, Chen M, Ke Q, Long J. Unleashing the power of immune checkpoints: Post-translational modification of novel molecules and clinical applications. Cancer Lett 2024; 588:216758. [PMID: 38401885 DOI: 10.1016/j.canlet.2024.216758] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
Immune checkpoint molecules play a pivotal role in the initiation, regulation, and termination of immune responses. Tumor cells exploit these checkpoints to dampen immune cell function, facilitating immune evasion. Clinical interventions target this mechanism by obstructing the binding of immune checkpoints to their ligands, thereby restoring the anti-tumor capabilities of immune cells. Notably, therapies centered on immune checkpoint inhibitors, particularly PD-1/PD-L1 and CTLA-4 blocking antibodies, have demonstrated significant clinical promise. However, a considerable portion of patients still encounter suboptimal efficacy and develop resistance. Recent years have witnessed an exponential surge in preclinical and clinical trials investigating novel immune checkpoint molecules such as TIM3, LAG3, TIGIT, NKG2D, and CD47, along with their respective ligands. The processes governing immune checkpoint molecules, from their synthesis to transmembrane deployment, interaction with ligands, and eventual degradation, are intricately tied to post-translational modifications. These modifications encompass glycosylation, phosphorylation, ubiquitination, neddylation, SUMOylation, palmitoylation, and ectodomain shedding. This discussion proceeds to provide a concise overview of the structural characteristics of several novel immune checkpoints and their ligands. Additionally, it outlines the regulatory mechanisms governed by post-translational modifications, offering insights into their potential clinical applications in immune checkpoint blockade.
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Affiliation(s)
- Jie Wang
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China.
| | - Yian Wang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Changsha, Hunan, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Meifang Xu
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Meifeng Wang
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Rong Wang
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Boshu Zheng
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Mingfen Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Fujian Medical University, Fujian Medical University, Quanzhou, Fujian, China
| | - Qi Ke
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Jun Long
- Shenzhen Geim Graphene Center, Tsinghua-Berkeley Shenzhen Institute & Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China.
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12
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Zhou W, Tang Q, Wang S, Ding L, Chen M, Liu H, Wu Y, Xiong X, Shen Z, Chen W. Local thiamet-G delivery by a thermosensitive hydrogel confers ischemic cardiac repair via myeloid M2-like activation in a STAT6 O-GlcNAcylation-dependent manner. Int Immunopharmacol 2024; 131:111883. [PMID: 38503016 DOI: 10.1016/j.intimp.2024.111883] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 03/21/2024]
Abstract
Infarct healing requires a dynamic and orchestrated inflammatory reaction following myocardial infarction (MI). While an uncontrolled excessive inflammatory response exaggerates ischemic injury post-MI, M2-like reparative macrophages may facilitate inflammation regression and promote myocardial healing. However, how protein post-translational modification regulates post-MI cardiac repair and dynamic myeloid activation remains unknown. Here we show that M2-like reparative, but not M1-like inflammatory activation, is enhanced by pharmacologically-induced hyper-O-GlcNAcylation. Mechanistically, myeloid knockdown of O-GlcNAc hydrolase O-GlcNAcase (Oga), which also results in hyper-O-GlcNAcylation, positively regulates M2-like activation in a STAT6-dependent fashion, which is controlled by O-GlcNAcylation of STAT6. Of note, both systemic and local supplementation of thiamet-G (TMG), an Oga inhibitor, effectively facilitates cardiac recovery in mice by elevating the accumulation of M2-like macrophages in infarcted hearts. Our study provides a novel clue for monocyte/macrophage modulating therapies aimed at reducing post-MI hyperinflammation in ischemic myocardium.
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Affiliation(s)
- Wenjing Zhou
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China; School of Life Science, Tianjin University, Tianjin, China
| | - Qingsong Tang
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China
| | - Shengnan Wang
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China
| | - Liang Ding
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China
| | - Ming Chen
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China
| | - Hongman Liu
- Department of Cardiology, the First Affiliated Hospital of Soochow University, Suzhou, China; Department of Cardiovascular Medicine, the Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Yong Wu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China
| | - Xiwen Xiong
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Zhenya Shen
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China.
| | - Weiqian Chen
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China.
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13
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Hilditch AT, Romanyuk A, Hodgson LR, Mantell J, Neal CR, Verkade P, Obexer R, Serpell LC, McManus JJ, Woolfson DN. Maturation and Conformational Switching of a De Novo Designed Phase-Separating Polypeptide. J Am Chem Soc 2024; 146:10240-10245. [PMID: 38578222 DOI: 10.1021/jacs.4c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Cellular compartments formed by biomolecular condensation are widespread features of cell biology. These organelle-like assemblies compartmentalize macromolecules dynamically within the crowded intracellular environment. However, the intermolecular interactions that produce condensed droplets may also create arrested states and potentially pathological assemblies such as fibers, aggregates, and gels through droplet maturation. Protein liquid-liquid phase separation is a metastable process, so maturation may be an intrinsic property of phase-separating proteins, where nucleation of different phases or states arises in supersaturated condensates. Here, we describe the formation of both phase-separated droplets and proteinaceous fibers driven by a de novo designed polypeptide. We characterize the formation of supramolecular fibers in vitro and in bacterial cells. We show that client proteins can be targeted to the fibers in cells using a droplet-forming construct. Finally, we explore the interplay between phase separation and fiber formation of the de novo polypeptide, showing that the droplets mature with a post-translational switch to largely β conformations, analogous to models of pathological phase separation.
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Affiliation(s)
- Alexander T Hilditch
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Andrey Romanyuk
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Lorna R Hodgson
- Wolfson Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
| | - Judith Mantell
- Wolfson Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
| | - Christopher R Neal
- Wolfson Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Richard Obexer
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
| | - Louise C Serpell
- School of Life Sciences, University of Sussex, Falmer, Brighton, JMS 3B17, U.K
| | - Jennifer J McManus
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- HH Wills Physics Laboratory, School of Physics, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
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14
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Emenike B, Czabala P, Farhi J, Swaminathan J, Anslyn EV, Spangle J, Raj M. Tertiary Amine Coupling by Oxidation for Selective Labeling of Dimethyl Lysine Post-Translational Modifications. J Am Chem Soc 2024; 146:10621-10631. [PMID: 38584362 DOI: 10.1021/jacs.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Lysine dimethylation (Kme2) is a crucial post-translational modification (PTM) that regulates biological processes and is implicated in diseases. There is significant interest in globally identifying these methylation marks. Unfortunately, this remains challenging due to the lack of robust technologies for selectively labeling Kme2. To address this, we present a chemical method named tertiary amine coupling by oxidation (TACO). This method selectively modifies Kme2 to aldehydes using Selectfluor and a base. The resulting aldehydes from Kme2 were then functionalized using reductive amination, thiolamine, and oxime chemistry. We successfully demonstrated the versatility of TACO in selectively labeling Kme2 peptides and proteins in complex cell lysate mixtures with varying payloads, including affinity tags and fluorophores. We further showed the application of TACO chemistry for the identification of Kme2 sites at a single-molecule level by fluorosequencing. We discovered novel 30 Kme2 sites, in addition to previously known 5 Kme2 sites, by proteomics analysis of TACO-modified nuclear extracts. Our work establishes a unique strategy for covalently modifying Kme2, facilitating the global identification of low-abundance Kme2-PTMs and their sites within complex cell lysate mixtures.
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Affiliation(s)
- Benjamin Emenike
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Patrick Czabala
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan Farhi
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Jagannath Swaminathan
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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15
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Amiri A, Abedanzadeh S, Davaeil B, Shaabani A, Moosavi-Movahedi AA. Protein click chemistry and its potential for medical applications. Q Rev Biophys 2024; 57:e6. [PMID: 38619322 DOI: 10.1017/s0033583524000027] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.
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Affiliation(s)
- Ahmad Amiri
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Bagher Davaeil
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Shaabani
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
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16
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Prabhu H, Bhosale H, Sane A, Dhadwal R, Ramakrishnan V, Valadi J. Protein feature engineering framework for AMPylation site prediction. Sci Rep 2024; 14:8695. [PMID: 38622194 DOI: 10.1038/s41598-024-58450-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
AMPylation is a biologically significant yet understudied post-translational modification where an adenosine monophosphate (AMP) group is added to Tyrosine and Threonine residues primarily. While recent work has illuminated the prevalence and functional impacts of AMPylation, experimental identification of AMPylation sites remains challenging. Computational prediction techniques provide a faster alternative approach. The predictive performance of machine learning models is highly dependent on the features used to represent the raw amino acid sequences. In this work, we introduce a novel feature extraction pipeline to encode the key properties relevant to AMPylation site prediction. We utilize a recently published dataset of curated AMPylation sites to develop our feature generation framework. We demonstrate the utility of our extracted features by training various machine learning classifiers, on various numerical representations of the raw sequences extracted with the help of our framework. Tenfold cross-validation is used to evaluate the model's capability to distinguish between AMPylated and non-AMPylated sites. The top-performing set of features extracted achieved MCC score of 0.58, Accuracy of 0.8, AUC-ROC of 0.85 and F1 score of 0.73. Further, we elucidate the behaviour of the model on the set of features consisting of monogram and bigram counts for various representations using SHapley Additive exPlanations.
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Affiliation(s)
- Hardik Prabhu
- Computing and Data Sciences, FLAME University, Pune, 412115, India
- Robert Bosch Centre for Cyber Physical Systems, Indian Institute of Science, Bengaluru, 560012, India
| | | | - Aamod Sane
- Computing and Data Sciences, FLAME University, Pune, 412115, India
| | - Renu Dhadwal
- Computing and Data Sciences, FLAME University, Pune, 412115, India
| | - Vigneshwar Ramakrishnan
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | - Jayaraman Valadi
- Computing and Data Sciences, FLAME University, Pune, 412115, India.
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17
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Yu H, Liu D, Zhang Y, Tang R, Fan X, Mao S, Lv L, Chen F, Qin H, Zhang Z, van Aalten DMF, Yang B, Yuan K. Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning. eLife 2024; 13:e91269. [PMID: 38619103 PMCID: PMC11018347 DOI: 10.7554/elife.91269] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 03/14/2024] [Indexed: 04/16/2024] Open
Abstract
O-GlcNAcylation is a dynamic post-translational modification that diversifies the proteome. Its dysregulation is associated with neurological disorders that impair cognitive function, and yet identification of phenotype-relevant candidate substrates in a brain-region specific manner remains unfeasible. By combining an O-GlcNAc binding activity derived from Clostridium perfringens OGA (CpOGA) with TurboID proximity labeling in Drosophila, we developed an O-GlcNAcylation profiling tool that translates O-GlcNAc modification into biotin conjugation for tissue-specific candidate substrates enrichment. We mapped the O-GlcNAc interactome in major brain regions of Drosophila and found that components of the translational machinery, particularly ribosomal subunits, were abundantly O-GlcNAcylated in the mushroom body of Drosophila brain. Hypo-O-GlcNAcylation induced by ectopic expression of active CpOGA in the mushroom body decreased local translational activity, leading to olfactory learning deficits that could be rescued by dMyc overexpression-induced increase of protein synthesis. Our study provides a useful tool for future dissection of tissue-specific functions of O-GlcNAcylation in Drosophila, and suggests a possibility that O-GlcNAcylation impacts cognitive function via regulating regional translational activity in the brain.
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Affiliation(s)
- Haibin Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Dandan Liu
- Life Sciences Institute, Zhejiang University, HangzhouZhejiangChina
| | - Yaowen Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Xunan Fan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Song Mao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Hongtao Qin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan UniversityChangshaChina
| | - Zhuohua Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
| | - Daan MF van Aalten
- Department of Molecular Biology and Genetics, University of AarhusAarhusDenmark
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, HangzhouZhejiangChina
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
- The Biobank of Xiangya Hospital, Central South UniversityChangshaChina
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18
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Liu X, Li J, Zhang Z, He Y, Wang M, Zhao Y, Lin S, Liu T, Liao Y, Zhang N, Yuan K, Ling Y, Liu Z, Chen X, Chen Z, Chen R, Wang X, Gu B. Acetylation of xenogeneic silencer H-NS regulates biofilm development through the nitrogen homeostasis regulator in Shewanella. Nucleic Acids Res 2024; 52:2886-2903. [PMID: 38142446 PMCID: PMC11014242 DOI: 10.1093/nar/gkad1219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023] Open
Abstract
Adjusting intracellular metabolic pathways and adopting suitable live state such as biofilms, are crucial for bacteria to survive environmental changes. Although substantial progress has been made in understanding how the histone-like nucleoid-structuring (H-NS) protein modulates the expression of the genes involved in biofilm formation, the precise modification that the H-NS protein undergoes to alter its DNA binding activity is still largely uncharacterized. This study revealed that acetylation of H-NS at Lys19 inhibits biofilm development in Shewanella oneidensis MR-1 by downregulating the expression of glutamine synthetase, a critical enzyme in glutamine synthesis. We further found that nitrogen starvation, a likely condition in biofilm development, induces deacetylation of H-NS and the trimerization of nitrogen assimilation regulator GlnB. The acetylated H-NS strain exhibits significantly lower cellular glutamine concentration, emphasizing the requirement of H-NS deacetylation in Shewanella biofilm development. Moreover, we discovered in vivo that the activation of glutamine biosynthesis pathway and the concurrent suppression of the arginine synthesis pathway during both pellicle and attached biofilms development, further suggesting the importance of fine tune nitrogen assimilation by H-NS acetylation in Shewanella. In summary, posttranslational modification of H-NS endows Shewanella with the ability to respond to environmental needs by adjusting the intracellular metabolism pathways.
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Affiliation(s)
- Xiaoxiao Liu
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Jun Li
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Zhixuan Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong 510080, China
| | - Yizhou He
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Mingfang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Yunhu Zhao
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Shituan Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiwen Liao
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Ni Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Kaixuan Yuan
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Yong Ling
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Ziyao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaozhong Chen
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Zhe Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
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19
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Ayuso-García P, Sánchez-Rueda A, Velasco-Avilés S, Tamayo-Caro M, Ferrer-Pinós A, Huarte-Sebastian C, Alvarez V, Riobello C, Jiménez-Vega S, Buendia I, Cañas-Martin J, Fernández-Susavila H, Aparicio-Rey A, Esquinas-Román EM, Ponte CR, Guhl R, Laville N, Pérez-Andrés E, Lavín JL, González-Lopez M, Cámara NM, Aransay AM, Lozano JJ, Sutherland JD, Barrio R, Martinez-Chantar ML, Azkargorta M, Elortza F, Soriano-Navarro M, Matute C, Sánchez-Gómez MV, Bayón-Cordero L, Pérez-Samartín A, Bravo SB, Kurz T, Lama-Díaz T, Blanco MG, Haddad S, Record CJ, van Hasselt PM, Reilly MM, Varela-Rey M, Woodhoo A. Neddylation orchestrates the complex transcriptional and posttranscriptional program that drives Schwann cell myelination. Sci Adv 2024; 10:eadm7600. [PMID: 38608019 PMCID: PMC11014456 DOI: 10.1126/sciadv.adm7600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Myelination is essential for neuronal function and health. In peripheral nerves, >100 causative mutations have been identified that cause Charcot-Marie-Tooth disease, a disorder that can affect myelin sheaths. Among these, a number of mutations are related to essential targets of the posttranslational modification neddylation, although how these lead to myelin defects is unclear. Here, we demonstrate that inhibiting neddylation leads to a notable absence of peripheral myelin and axonal loss both in developing and regenerating mouse nerves. Our data indicate that neddylation exerts a global influence on the complex transcriptional and posttranscriptional program by simultaneously regulating the expression and function of multiple essential myelination signals, including the master transcription factor EGR2 and the negative regulators c-Jun and Sox2, and inducing global secondary changes in downstream pathways, including the mTOR and YAP/TAZ signaling pathways. This places neddylation as a critical regulator of myelination and delineates the potential pathogenic mechanisms involved in CMT mutations related to neddylation.
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Affiliation(s)
- Paula Ayuso-García
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Alejandro Sánchez-Rueda
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Sergio Velasco-Avilés
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Miguel Tamayo-Caro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Aroa Ferrer-Pinós
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Cecilia Huarte-Sebastian
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Vanesa Alvarez
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Cristina Riobello
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Selene Jiménez-Vega
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Izaskun Buendia
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
| | - Jorge Cañas-Martin
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Héctor Fernández-Susavila
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Adrián Aparicio-Rey
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Eva M. Esquinas-Román
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Carlos Rodríguez Ponte
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Romane Guhl
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Université Paris Cité Magistère Européen de Génétique, 85 Boulevard Saint-Germain, 75006 Paris, France
| | - Nicolas Laville
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Université Paris Cité Magistère Européen de Génétique, 85 Boulevard Saint-Germain, 75006 Paris, France
| | - Encarni Pérez-Andrés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - José L. Lavín
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- NEIKER–Basque Institute for Agricultural Research and Development, Applied Mathematics Department, Bioinformatics Unit, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Monika González-Lopez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Nuria Macías Cámara
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Ana M. Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan José Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - James D. Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - María Luz Martinez-Chantar
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Félix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Mario Soriano-Navarro
- Electron Microscopy Core Facility, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
| | - Carlos Matute
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - María Victoria Sánchez-Gómez
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Laura Bayón-Cordero
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Alberto Pérez-Samartín
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Susana B. Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), 15705 Santiago de Compostela, A Coruña, Spain
| | - Thimo Kurz
- Evotec SE, Innovation Dr, Milton, Abingdon OX14 4RT, UK and School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Tomas Lama-Díaz
- DNA Repair and Genome Integrity Laboratory, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, 15706 Santiago de Compostela, A Coruña, Spain
| | - Miguel G. Blanco
- DNA Repair and Genome Integrity Laboratory, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, 15706 Santiago de Compostela, A Coruña, Spain
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
| | - Saif Haddad
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Christopher J. Record
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Peter M. van Hasselt
- Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, 3584 EA, Utrecht, Netherlands
| | - Mary M. Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Marta Varela-Rey
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Bizkaia, Spain
- Department of Functional Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
- Oportunius Research Professor at CIMUS/USC, Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, A Coruña, Spain
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20
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Rrustemi T, Meyer K, Roske Y, Uyar B, Akalin A, Imami K, Ishihama Y, Daumke O, Selbach M. Pathogenic mutations of human phosphorylation sites affect protein-protein interactions. Nat Commun 2024; 15:3146. [PMID: 38605029 PMCID: PMC11009412 DOI: 10.1038/s41467-024-46794-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.
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Affiliation(s)
| | - Katrina Meyer
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Bora Uyar
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Altuna Akalin
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Kanagawa, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Oliver Daumke
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany.
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21
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Nie H, Kong X, Song X, Guo X, Li Z, Fan C, Zhai B, Yang X, Wang Y. Roles of histone post-translational modifications in meiosis†. Biol Reprod 2024; 110:648-659. [PMID: 38224305 DOI: 10.1093/biolre/ioae011] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024] Open
Abstract
Histone post-translational modifications, such as phosphorylation, methylation, acetylation, and ubiquitination, play vital roles in various chromatin-based cellular processes. Meiosis is crucial for organisms that depend on sexual reproduction to produce haploid gametes, during which chromatin undergoes intricate conformational changes. An increasing body of evidence is clarifying the essential roles of histone post-translational modifications during meiotic divisions. In this review, we concentrate on the post-translational modifications of H2A, H2B, H3, and H4, as well as the linker histone H1, that are required for meiosis, and summarize recent progress in understanding how these modifications influence diverse meiotic events. Finally, challenges and exciting open questions for future research in this field are discussed. Summary Sentence Diverse histone post-translational modifications exert important effects on the meiotic cell cycle and these "histone codes" in meiosis might lead to the development of novel therapeutic strategies against reproductive diseases.
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Affiliation(s)
- Hui Nie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xueyu Kong
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Song
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Guo
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Zhanyu Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Cunxian Fan
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Binyuan Zhai
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiao Yang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Ying Wang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
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22
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Ma B, Khan KS, Xu T, Xeque Amada J, Guo Z, Huang Y, Yan Y, Lam H, Cheng ASL, Ng BWL. Targeted Protein O-GlcNAcylation Using Bifunctional Small Molecules. J Am Chem Soc 2024; 146:9779-9789. [PMID: 38561350 PMCID: PMC11009946 DOI: 10.1021/jacs.3c14380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Protein O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) plays a crucial role in regulating essential cellular processes. The disruption of the homeostasis of O-GlcNAcylation has been linked to various human diseases, including cancer, diabetes, and neurodegeneration. However, there are limited chemical tools for protein- and site-specific O-GlcNAc modification, rendering the precise study of the O-GlcNAcylation challenging. To address this, we have developed heterobifunctional small molecules, named O-GlcNAcylation TArgeting Chimeras (OGTACs), which enable protein-specific O-GlcNAcylation in living cells. OGTACs promote O-GlcNAcylation of proteins such as BRD4, CK2α, and EZH2 in cellulo by recruiting FKBP12F36V-fused O-GlcNAc transferase (OGT), with temporal, magnitude, and reversible control. Overall, the OGTACs represent a promising approach for inducing protein-specific O-GlcNAcylation, thus enabling functional dissection and offering new directions for O-GlcNAc-targeting therapeutic development.
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Affiliation(s)
- Bowen Ma
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Khadija Shahed Khan
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Tongyang Xu
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Josefina Xeque Amada
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Zhihao Guo
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Yunpeng Huang
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Yu Yan
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Henry Lam
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Sai Kung, Hong Kong
| | - Alfred Sze-Lok Cheng
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Billy Wai-Lung Ng
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
- Li Ka
Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong
Kong
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23
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Yang SK, Kubo S, Black CS, Peri K, Dai D, Legal T, Valente-Paterno M, Gaertig J, Bui KH. Effect of α-tubulin acetylation on the doublet microtubule structure. eLife 2024; 12:RP92219. [PMID: 38598282 PMCID: PMC11006419 DOI: 10.7554/elife.92219] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Acetylation of α-tubulin at the lysine 40 residue (αK40) by αTAT1/MEC-17 acetyltransferase modulates microtubule properties and occurs in most eukaryotic cells. Previous literatures suggest that acetylated microtubules are more stable and damage resistant. αK40 acetylation is the only known microtubule luminal post-translational modification site. The luminal location suggests that the modification tunes the lateral interaction of protofilaments inside the microtubule. In this study, we examined the effect of tubulin acetylation on the doublet microtubule (DMT) in the cilia of Tetrahymena thermophila using a combination of cryo-electron microscopy, molecular dynamics, and mass spectrometry. We found that αK40 acetylation exerts a small-scale effect on the DMT structure and stability by influencing the lateral rotational angle. In addition, comparative mass spectrometry revealed a link between αK40 acetylation and phosphorylation in cilia.
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Affiliation(s)
- Shun Kai Yang
- Department of Anatomy and Cell Biology, McGill UniversityMontréalCanada
| | - Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill UniversityMontréalCanada
| | | | - Katya Peri
- Department of Anatomy and Cell Biology, McGill UniversityMontréalCanada
| | - Daniel Dai
- Department of Anatomy and Cell Biology, McGill UniversityMontréalCanada
| | - Thibault Legal
- Department of Anatomy and Cell Biology, McGill UniversityMontréalCanada
| | | | - Jacek Gaertig
- Department of Cellular Biology, University of GeorgiaAthensUnited States
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill UniversityMontréalCanada
- Centre de Recherche en Biologie Structurale, McGill UniversityMontréalCanada
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24
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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25
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Rojsajjakul T, Selvan N, De B, Rosenberg JB, Kaminsky SM, Sondhi D, Janki P, Crystal RG, Mesaros C, Khanna R, Blair IA. Expression and processing of mature human frataxin after gene therapy in mice. Sci Rep 2024; 14:8391. [PMID: 38600238 PMCID: PMC11006666 DOI: 10.1038/s41598-024-59060-0] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/06/2024] [Indexed: 04/12/2024] Open
Abstract
Friedreich's ataxia is a degenerative and progressive multisystem disorder caused by mutations in the highly conserved frataxin (FXN) gene that results in FXN protein deficiency and mitochondrial dysfunction. While gene therapy approaches are promising, consistent induction of therapeutic FXN protein expression that is sub-toxic has proven challenging, and numerous therapeutic approaches are being tested in animal models. FXN (hFXN in humans, mFXN in mice) is proteolytically modified in mitochondria to produce mature FXN. However, unlike endogenous hFXN, endogenous mFXN is further processed into N-terminally truncated, extra-mitochondrial mFXN forms of unknown function. This study assessed mature exogenous hFXN expression levels in the heart and liver of C57Bl/6 mice 7-10 months after intravenous administration of a recombinant adeno-associated virus encoding hFXN (AAVrh.10hFXN) and examined the potential for hFXN truncation in mice. AAVrh.10hFXN induced dose-dependent expression of hFXN in the heart and liver. Interestingly, hFXN was processed into truncated forms, but found at lower levels than mature hFXN. However, the truncations were at different positions than mFXN. AAVrh.10hFXN induced mature hFXN expression in mouse heart and liver at levels that approximated endogenous mFXN levels. These results suggest that AAVrh.10hFXN can likely induce expression of therapeutic levels of mature hFXN in mice.
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Affiliation(s)
- Teerapat Rojsajjakul
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, Penn/CHOP Friedreich's Ataxia Center of Excellence, Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Bishnu De
- Department of Genetic Medicine, Weill Cornell College of Medicine, New York, NY, USA
| | - Jonathan B Rosenberg
- Department of Genetic Medicine, Weill Cornell College of Medicine, New York, NY, USA
| | - Stephen M Kaminsky
- Department of Genetic Medicine, Weill Cornell College of Medicine, New York, NY, USA
| | - Dolan Sondhi
- Department of Genetic Medicine, Weill Cornell College of Medicine, New York, NY, USA
| | | | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell College of Medicine, New York, NY, USA
| | - Clementina Mesaros
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, Penn/CHOP Friedreich's Ataxia Center of Excellence, Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, Penn/CHOP Friedreich's Ataxia Center of Excellence, Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, USA.
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26
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Luna S, Malard F, Pereckas M, Aoki M, Aoki K, Stichelen SOV. Studying the O-GlcNAcome of human placentas using banked tissue samples. Glycobiology 2024; 34:cwae005. [PMID: 38253038 PMCID: PMC11005170 DOI: 10.1093/glycob/cwae005] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
O-GlcNAcylation is a dynamic modulator of signaling pathways, equal in magnitude to the widely studied phosphorylation. With the rapid development of tools for its detection at the single protein level, the O-GlcNAc modification rapidly emerged as a novel diagnostic and therapeutic target in human diseases. Yet, mapping the human O-GlcNAcome in various tissues is essential for generating relevant biomarkers. In this study, we used human banked tissue as a sample source to identify O-GlcNAcylated protein targets relevant to human diseases. Using human term placentas, we propose (1) a method to clean frozen banked tissue of blood proteins; (2) an optimized protocol for the enrichment of O-GlcNAcylated proteins using immunoaffinity purification; and (3) a bioinformatic workflow to identify the most promising O-GlcNAc targets. As a proof-of-concept, we used 45 mg of banked placental samples from two pregnancies to generate intracellular protein extracts depleted of blood protein. Then, antibody-based O-GlcNAc enrichment on denatured samples yielded over 2000 unique HexNAc PSMs and 900 unique sites using 300 μg of protein lysate. Due to efficient sample cleanup, we also captured 82 HexNAc proteins with high placental expression. Finally, we provide a bioinformatic tool (CytOVS) to sort the HexNAc proteins based on their cellular localization and extract the most promising O-GlcNAc targets to explore further. To conclude, we provide a simple 3-step workflow to generate a manageable list of O-GlcNAc proteins from human tissue and improve our understanding of O-GlcNAcylation's role in health and diseases.
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Affiliation(s)
- Sarai Luna
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
| | - Florian Malard
- INSERM U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, 146 rue Léo Saignat, 33000 Bordeaux, France
| | - Michaela Pereckas
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
| | - Mayumi Aoki
- Cancer Research Center, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
| | - Kazuhiro Aoki
- Cancer Research Center, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
- Department of Cell Biology, Neurobiology and Anatomy (CBNA), Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
| | - Stephanie Olivier-Van Stichelen
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
- Cancer Research Center, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
- Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States
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27
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Rivera O, Sharma M, Dagar S, Shahani N, Ramĺrez-Jarquĺn UN, Crynen G, Karunadharma P, McManus F, Bonneil E, Pierre T, Subramaniam S. Rhes, a striatal enriched protein, regulates post-translational small-ubiquitin-like-modifier (SUMO) modification of nuclear proteins and alters gene expression. Cell Mol Life Sci 2024; 81:169. [PMID: 38589732 PMCID: PMC11001699 DOI: 10.1007/s00018-024-05181-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
Rhes (Ras homolog enriched in the striatum), a multifunctional protein that regulates striatal functions associated with motor behaviors and neurological diseases, can shuttle from cell to cell via the formation of tunneling-like nanotubes (TNTs). However, the mechanisms by which Rhes mediates diverse functions remain unclear. Rhes is a small GTPase family member which contains a unique C-terminal Small Ubiquitin-like Modifier (SUMO) E3-like domain that promotes SUMO post-translational modification of proteins (SUMOylation) by promoting "cross-SUMOylation" of the SUMO enzyme SUMO E1 (Aos1/Uba2) and SUMO E2 ligase (Ubc-9). Nevertheless, the identity of the SUMO substrates of Rhes remains largely unknown. Here, by combining high throughput interactome and SUMO proteomics, we report that Rhes regulates the SUMOylation of nuclear proteins that are involved in the regulation of gene expression. Rhes increased the SUMOylation of histone deacetylase 1 (HDAC1) and histone 2B, while decreasing SUMOylation of heterogeneous nuclear ribonucleoprotein M (HNRNPM), protein polybromo-1 (PBRM1) and E3 SUMO-protein ligase (PIASy). We also found that Rhes itself is SUMOylated at 6 different lysine residues (K32, K110, K114, K120, K124, and K245). Furthermore, Rhes regulated the expression of genes involved in cellular morphogenesis and differentiation in the striatum, in a SUMO-dependent manner. Our findings thus provide evidence for a previously undescribed role for Rhes in regulating the SUMOylation of nuclear targets and in orchestrating striatal gene expression via SUMOylation.
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Affiliation(s)
- Oscar Rivera
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Manish Sharma
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Sunayana Dagar
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Neelam Shahani
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Uri Nimrod Ramĺrez-Jarquĺn
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
- National Institute of Cardiology Ignacio Chávez, Department of Pharmacology, Mexico, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Pabalu Karunadharma
- Genomic Core, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Francis McManus
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Thibault Pierre
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
- Department of Chemistry, Université de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Srinivasa Subramaniam
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA.
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Norman Fixel Institute for Neurological Diseases, 3009 SW Williston Rd, Gainesville, FL, 32608, USA.
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28
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Zhang S, Yu Q, Li Z, Zhao Y, Sun Y. Protein neddylation and its role in health and diseases. Signal Transduct Target Ther 2024; 9:85. [PMID: 38575611 PMCID: PMC10995212 DOI: 10.1038/s41392-024-01800-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.
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Affiliation(s)
- Shizhen Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Qing Yu
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, China
| | - Zhijian Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
| | - Yi Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
- Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, Hangzhou, 310024, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.
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29
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Liu C, Xu M, Li W, Cao X, Wang Y, Chen H, Zhang T, Lu M, Xie H, Chen Y. Quantitative Pattern of hPTMs by Mass Spectrometry-Based Proteomics with Implications for Triple-Negative Breast Cancer. J Proteome Res 2024; 23:1495-1505. [PMID: 38576392 DOI: 10.1021/acs.jproteome.4c00034] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Triple-negative breast cancer (TNBC) is known for its aggressive nature, and TNBC management is currently challenging due to the lack of effective targets. Despite the importance of histone post-translational modifications (hPTMs) in breast cancer, their associations with molecular subtypes of breast cancer, especially TNBC, are poorly understood. In this study, a combination of untargeted and targeted proteomics approaches, supplemented by a derivatization method, was applied to breast cancer cells and tissue samples. Untargeted proteomics of eight breast cancer cell lines belonging to different molecular subtypes revealed 36 modified peptides with 12 lysine modification sites in histone H3, and the most frequently reported top 5 histone H3 methylation and acetylation sites were covered. Then, targeted proteomics was carried out to quantify the total 20 target hPTMs at the covered modification sites (i.e., mono-, di-, trimethylation, and acetylation for each site), indicating the difficulty in distinguishing TNBC cells from normal cells. Subsequently, the analysis in TNBC patients revealed significant expression differences in 4 specific hPTMs (H3K14ac, H3K27me1, H3K36me2, and H3K36me3) between TNBC and adjacent normal tissue samples. These unique hPTM patterns allowed for the differentiation of TNBC from normal cases. This finding provides promising implications for advancing targeted treatment strategies for TNBC in the future.
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Affiliation(s)
- Chunyan Liu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Mengying Xu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Wan Li
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Xiao Cao
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yan Wang
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Haoran Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Tianqi Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Meiyan Lu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Nanjing 211166, China
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30
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Fu S, Iqbal B, Li G, Alabbosh KF, Khan KA, Zhao X, Raheem A, Du D. The role of microbial partners in heavy metal metabolism in plants: a review. Plant Cell Rep 2024; 43:111. [PMID: 38568247 DOI: 10.1007/s00299-024-03194-y] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
Heavy metal pollution threatens plant growth and development as well as ecological stability. Here, we synthesize current research on the interplay between plants and their microbial symbionts under heavy metal stress, highlighting the mechanisms employed by microbes to enhance plant tolerance and resilience. Several key strategies such as bioavailability alteration, chelation, detoxification, induced systemic tolerance, horizontal gene transfer, and methylation and demethylation, are examined, alongside the genetic and molecular basis governing these plant-microbe interactions. However, the complexity of plant-microbe interactions, coupled with our limited understanding of the associated mechanisms, presents challenges in their practical application. Thus, this review underscores the necessity of a more detailed understanding of how plants and microbes interact and the importance of using a combined approach from different scientific fields to maximize the benefits of these microbial processes. By advancing our knowledge of plant-microbe synergies in the metabolism of heavy metals, we can develop more effective bioremediation strategies to combat the contamination of soil by heavy metals.
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Affiliation(s)
- Shilin Fu
- School of Environment and Safety Engineering, School of Emergency Management, Jiangsu Province Engineering Research Centre of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, 212013, Zhenjiang, People's Republic of China
| | - Babar Iqbal
- School of Environment and Safety Engineering, School of Emergency Management, Jiangsu Province Engineering Research Centre of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, 212013, Zhenjiang, People's Republic of China
| | - Guanlin Li
- School of Environment and Safety Engineering, School of Emergency Management, Jiangsu Province Engineering Research Centre of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, 212013, Zhenjiang, People's Republic of China.
- Jiangsu Collaborative Innovation Centre of Technology and Material of Water Treatment, Suzhou University of Science and Technology, 215009, Suzhou, People's Republic of China.
| | | | - Khalid Ali Khan
- Applied College, Center of Bee Research and its Products (CBRP), Unit of Bee Research and Honey Production, and Research Center for Advanced Materials Science (RCAMS), King Khalid University, 61413, Abha, Saudi Arabia
| | - Xin Zhao
- Department of Civil and Environmental Engineering, College of Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Abdulkareem Raheem
- School of Environment and Safety Engineering, School of Emergency Management, Jiangsu Province Engineering Research Centre of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, 212013, Zhenjiang, People's Republic of China.
| | - Daolin Du
- Jingjiang College, Institute of Environment and Ecology, School of Emergency Management, School of Environment and Safety Engineering, School of Agricultural Engineering, Jiangsu University, 212013, Zhenjiang, People's Republic of China.
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31
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Vargiu M, Xu Y, Kuipers OP, Roelfes G. Selective Aza-Michael Addition to Dehydrated Amino Acids in Natural Antimicrobial Peptides. Chembiochem 2024; 25:e202400043. [PMID: 38334959 DOI: 10.1002/cbic.202400043] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/10/2024]
Abstract
We report the efficient and site selective modification of non-canonical dehydroamino acids in ribosomally synthesized and post-transationally modified peptides (RiPPs) by β-amination. The singly modified thiopeptide Thiostrepton showed an up to 35-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity remained good, albeit lower than the unmodified peptide. Also the lanthipeptide nisin could be modified using this method.
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Affiliation(s)
- Michela Vargiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
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32
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Zhao T, Sachon E, Micouin L, Piccardi R. α-Silylated Diazoalkynes: New Tools for Bioconjugation of Proteins. Chemistry 2024; 30:e202302807. [PMID: 38305813 DOI: 10.1002/chem.202302807] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/03/2024]
Abstract
α-Silylated diazoalkynes are stabilized diazo compounds that can selectively react with carboxylic residues in buffered aqueous media. In-situ fluoride induced desilylation increases this reactivity, leading to a very fast reaction. Application to the selective functionalization of RNase A, followed by post-functionalization using click chemistry, is described. These new reagents expand the toolbox for native protein modification at carboxylic residues.
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Affiliation(s)
- Tuan Zhao
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006, Paris, France
| | - Emmanuelle Sachon
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Laurent Micouin
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006, Paris, France
| | - Riccardo Piccardi
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006, Paris, France
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33
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Yan Y, Shetty M, Harding HP, George G, Zyryanova A, Labbé K, Mafi A, Hao Q, Sidrauski C, Ron D. Substrate recruitment via eIF2γ enhances catalytic efficiency of a holophosphatase that terminates the integrated stress response. Proc Natl Acad Sci U S A 2024; 121:e2320013121. [PMID: 38547060 PMCID: PMC10998612 DOI: 10.1073/pnas.2320013121] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/16/2024] [Indexed: 04/02/2024] Open
Abstract
Dephosphorylation of pSer51 of the α subunit of translation initiation factor 2 (eIF2αP) terminates signaling in the integrated stress response (ISR). A trimeric mammalian holophosphatase comprised of a protein phosphatase 1 (PP1) catalytic subunit, the conserved C-terminally located ~70 amino acid core of a substrate-specific regulatory subunit (PPP1R15A/GADD34 or PPP1R15B/CReP) and G-actin (an essential cofactor) efficiently dephosphorylate eIF2αP in vitro. Unlike their viral or invertebrate counterparts, with whom they share the conserved 70 residue core, the mammalian PPP1R15s are large proteins of more than 600 residues. Genetic and cellular observations point to a functional role for regions outside the conserved core of mammalian PPP1R15A in dephosphorylating its natural substrate, the eIF2 trimer. We have combined deep learning technology, all-atom molecular dynamics simulations, X-ray crystallography, and biochemistry to uncover binding of the γ subunit of eIF2 to a short helical peptide repeated four times in the functionally important N terminus of human PPP1R15A that extends past its conserved core. Binding entails insertion of Phe and Trp residues that project from one face of an α-helix formed by the conserved repeats of PPP1R15A into a hydrophobic groove exposed on the surface of eIF2γ in the eIF2 trimer. Replacing these conserved Phe and Trp residues with Ala compromises PPP1R15A function in cells and in vitro. These findings suggest mechanisms by which contacts between a distant subunit of eIF2 and elements of PPP1R15A distant to the holophosphatase active site contribute to dephosphorylation of eIF2αP by the core PPP1R15 holophosphatase and to efficient termination of the ISR in mammals.
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Affiliation(s)
- Yahui Yan
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, CambridgeCB2 0XY, United Kingdom
| | - Maithili Shetty
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, CambridgeCB2 0XY, United Kingdom
| | - Heather P. Harding
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, CambridgeCB2 0XY, United Kingdom
| | - Ginto George
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, CambridgeCB2 0XY, United Kingdom
| | - Alisa Zyryanova
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, CambridgeCB2 0XY, United Kingdom
| | | | | | - Qi Hao
- Calico Life Sciences, South San Francisco, CA94080
| | | | - David Ron
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, CambridgeCB2 0XY, United Kingdom
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Wang J, Feng X, Liu X, Wang G, Xiong Y, Zhang L, Zhang Y, Lu H. In-Depth Profiling of 4-Hydroxy-2-nonenal Modification via Reversible Thiazolidine Chemistry. Anal Chem 2024; 96:5125-5133. [PMID: 38502245 DOI: 10.1021/acs.analchem.3c05060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Protein modification by lipid-derived electrophiles (LDEs) is associated with various signaling pathways. Among these LDEs, 4-hydroxy-2-nonenal (HNE) is the most toxic, and protein modified with HNE has been linked to various diseases, including Alzheimer's and Parkinson's. However, due to their low abundance, in-depth profiling of HNE modifications still presents challenges. This study introduces a novel strategy utilizing reversible thiazolidine chemistry to selectively capture HNE-modified proteins and a palladium-mediated cleavage reaction to release them. Thousands of HNE-modified sites in different cell lines were identified. Combined with ABPP, we discovered a set of HNE-sensitive sites that offer a new tool for studying LDE modifications in proteomes.
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Affiliation(s)
- Jun Wang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Xiaoxiao Feng
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Xuejiao Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Yingying Xiong
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Ying Zhang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Haojie Lu
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
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Harris LA, Saad H, Shelton KE, Zhu L, Guo X, Mitchell DA. Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications. Biochemistry 2024; 63:865-879. [PMID: 38498885 DOI: 10.1021/acs.biochem.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by a macrolactam linkage between the N-terminus and the side chain of an internal aspartic acid or glutamic acid residue. Instead of adopting a branched-cyclic conformation, lasso peptides are "threaded", with the C-terminal tail passing through the macrocycle to present a kinetically trapped rotaxane conformation. The availability of enhanced bioinformatics methods has led to a significant increase in the number of secondary modifications found on lasso peptides. To uncover new ancillary modifications in a targeted manner, a bioinformatic strategy was developed to discover lasso peptides with modifications to tryptophan. This effort identified numerous putative lasso peptide biosynthetic gene clusters with core regions of the precursor peptides enriched in tryptophan. Parsing of these tryptophan (Trp)-rich biosynthetic gene clusters uncovered several putative ancillary modifying enzymes, including halogenases and dimethylallyltransferases expected to act upon Trp. Characterization of two gene products yielded a lasso peptide with two 5-Cl-Trp modifications (chlorolassin) and another bearing 5-dimethylallyl-Trp and 2,3-didehydro-Tyr modifications (wygwalassin). Bioinformatic analysis of the requisite halogenase and dimethylallyltransferase revealed numerous other putative Trp-modified lasso peptides that remain uncharacterized. We anticipate that the Trp-centric strategy reported herein may be useful in discovering ancillary modifications for other RiPP classes and, more generally, guide the functional prediction of enzymes that act on specific amino acids.
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Affiliation(s)
- Lonnie A Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hamada Saad
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kyle E Shelton
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xiaorui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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36
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Zong Y, Weiss N, Wang K, Pagano AE, Heissel S, Perveen S, Huang J. Development of Complementary Photo-arginine/lysine to Promote Discovery of Arg/Lys hPTMs Interactomes. Adv Sci (Weinh) 2024; 11:e2307526. [PMID: 38298064 PMCID: PMC11005723 DOI: 10.1002/advs.202307526] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/03/2023] [Indexed: 02/02/2024]
Abstract
Arginine and lysine, frequently appearing as a pair on histones, have been proven to carry diverse modifications and execute various epigenetic regulatory functions. However, the most context-specific and transient effectors of these marks, while significant, have evaded study as detection methods have thus far not reached a standard to capture these ephemeral events. Herein, a pair of complementary photo-arginine/δ-photo-lysine (R-dz/K-dz) probes is developed and involve these into histone peptide, nucleosome, and chromatin substrates to capture and explore the interactomes of Arg and Lys hPTMs. By means of these developed tools, this study identifies that H3R2me2a can recruit MutS protein homolog 6 (MSH6), otherwise repelDouble PHD fingers 2 (DPF2), Retinoblastoma binding protein 4/7 (RBBP4/7). And it is disclosed that H3R2me2a inhibits the chromatin remodeling activity of the cBAF complex by blocking the interaction between DPF2 (one component of cBAF) and the nucleosome. In addition, the novel pairs of H4K5 PTMs and respective readers are highlighted, namely H4K5me-Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2), H4K5me2-L3MBTL2, and H4K5acK8ac-YEATS domain-containing protein 4 (YEATS4). These powerful tools pave the way for future investigation of related epigenetic mechanisms including but not limited to hPTMs.
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Affiliation(s)
- Yu Zong
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | - Nicole Weiss
- Program of PharmacologyWeill Cornell Medical College of Cornell UniversityNew York10065USA
| | - Ke Wang
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | | | - Søren Heissel
- Proteomics Resource CenterRockefeller UniversityNew York10065USA
| | - Sumera Perveen
- Structural Genomics ConsortiumUniversity of TorontoTorontoM5S3H2Canada
| | - Jian Huang
- Department of Molecular BiologyPrinceton UniversityPrinceton08544USA
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Zhu Z, Ren W, Li S, Gao L, Zhi K. Functional significance of O-linked N-acetylglucosamine protein modification in regulating autophagy. Pharmacol Res 2024; 202:107120. [PMID: 38417774 DOI: 10.1016/j.phrs.2024.107120] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Autophagy is a core molecular pathway that preserves cellular and organismal homeostasis. Being susceptible to nutrient availability and stress, eukaryotic cells recycle or degrade internal components via membrane transport pathways to provide sustainable biological molecules and energy sources. The dysregulation of this highly conserved physiological process has been strongly linked to human disease. Post-translational modification, a mechanism that regulates protein function, plays a crucial role in autophagy regulation. O-linked N-acetylglucosamine protein modification (O-GlcNAcylation), a monosaccharide post-translational modification of intracellular proteins, is essential in nutritional and stress regulatory mechanisms. O-GlcNAcylation has emerged as an essential regulatory mechanism of autophagy. It regulates autophagy throughout its lifetime by targeting the core components of the autophagy regulatory network. This review provides an overview of the O-GlcNAcylation of autophagy-associated proteins and their regulation and function in the autophagy pathway. Therefore, this article may contribute to further understanding of the role of O-GlcNAc-regulated autophagy and provide new perspectives for the treatment of human diseases.
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Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
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38
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Tang X, Zeng P, Liu K, Qing L, Sun Y, Liu X, Lu L, Wei C, Wang J, Jiang S, Sun J, Chang W, Yu H, Chen H, Zhou J, Xu C, Fan L, Miao YL, Ding J. The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation. Nat Commun 2024; 15:2813. [PMID: 38561336 PMCID: PMC10985093 DOI: 10.1038/s41467-024-47048-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
CCCTC-binding factor (CTCF), a ubiquitously expressed and highly conserved protein, is known to play a critical role in chromatin structure. Post-translational modifications (PTMs) diversify the functions of protein to regulate numerous cellular processes. However, the effects of PTMs on the genome-wide binding of CTCF and the organization of three-dimensional (3D) chromatin structure have not been fully understood. In this study, we uncovered the PTM profiling of CTCF and demonstrated that CTCF can be O-GlcNAcylated and arginine methylated. Functionally, we demonstrated that O-GlcNAcylation inhibits CTCF binding to chromatin. Meanwhile, deficiency of CTCF O-GlcNAcylation results in the disruption of loop domains and the alteration of chromatin loops associated with cellular development. Furthermore, the deficiency of CTCF O-GlcNAcylation increases the expression of developmental genes and negatively regulates maintenance and establishment of stem cell pluripotency. In conclusion, these results provide key insights into the role of PTMs for the 3D chromatin structure.
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Affiliation(s)
- Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Kezhi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yifei Sun
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Lizi Lu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jia Wang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jun Sun
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Wakam Chang
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Jiaguo Zhou
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chengfang Xu
- The obstetric and gynecology Department of The third affiliated hospital of Sun Yat-Sen University, Guangzhou, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Junjun Ding
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China.
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Tate EW, Soday L, de la Lastra AL, Wang M, Lin H. Protein lipidation in cancer: mechanisms, dysregulation and emerging drug targets. Nat Rev Cancer 2024; 24:240-260. [PMID: 38424304 DOI: 10.1038/s41568-024-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/02/2024] [Indexed: 03/02/2024]
Abstract
Protein lipidation describes a diverse class of post-translational modifications (PTMs) that is regulated by over 40 enzymes, targeting more than 1,000 substrates at over 3,000 sites. Lipidated proteins include more than 150 oncoproteins, including mediators of cancer initiation, progression and immunity, receptor kinases, transcription factors, G protein-coupled receptors and extracellular signalling proteins. Lipidation regulates the physical interactions of its protein substrates with cell membranes, regulating protein signalling and trafficking, and has a key role in metabolism and immunity. Targeting protein lipidation, therefore, offers a unique approach to modulate otherwise undruggable oncoproteins; however, the full spectrum of opportunities to target the dysregulation of these PTMs in cancer remains to be explored. This is attributable in part to the technological challenges of identifying the targets and the roles of protein lipidation. The early stage of drug discovery for many enzymes in the pathway contrasts with efforts for drugging similarly common PTMs such as phosphorylation and acetylation, which are routinely studied and targeted in relevant cancer contexts. Here, we review recent advances in identifying targetable protein lipidation pathways in cancer, the current state-of-the-art in drug discovery, and the status of ongoing clinical trials, which have the potential to deliver novel oncology therapeutics targeting protein lipidation.
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Affiliation(s)
- Edward W Tate
- Department of Chemistry, Imperial College London, London, UK.
- Francis Crick Institute, London, UK.
| | - Lior Soday
- Department of Chemistry, Imperial College London, London, UK
| | | | - Mei Wang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Hening Lin
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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40
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Li W, Yang F, Wang F, Rong Y, Liu L, Wu B, Zhang H, Yao J. scPROTEIN: a versatile deep graph contrastive learning framework for single-cell proteomics embedding. Nat Methods 2024; 21:623-634. [PMID: 38504113 DOI: 10.1038/s41592-024-02214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/16/2024] [Indexed: 03/21/2024]
Abstract
Single-cell proteomics sequencing technology sheds light on protein-protein interactions, posttranslational modifications and proteoform dynamics in the cell. However, the uncertainty estimation for peptide quantification, data missingness, batch effects and high noise hinder the analysis of single-cell proteomic data. It is important to solve this set of tangled problems together, but the existing methods tailored for single-cell transcriptomes cannot fully address this task. Here we propose a versatile framework designed for single-cell proteomics data analysis called scPROTEIN, which consists of peptide uncertainty estimation based on a multitask heteroscedastic regression model and cell embedding generation based on graph contrastive learning. scPROTEIN can estimate the uncertainty of peptide quantification, denoise protein data, remove batch effects and encode single-cell proteomic-specific embeddings in a unified framework. We demonstrate that scPROTEIN is efficient for cell clustering, batch correction, cell type annotation, clinical analysis and spatially resolved proteomic data exploration.
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Affiliation(s)
- Wei Li
- College of Artificial Intelligence, Nankai University, Tianjin, China
- AI Lab, Tencent, Shenzhen, China
| | - Fan Yang
- AI Lab, Tencent, Shenzhen, China
| | | | - Yu Rong
- AI Lab, Tencent, Shenzhen, China
| | | | | | - Han Zhang
- College of Artificial Intelligence, Nankai University, Tianjin, China.
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41
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Chen HS, Wang F, Chen JG. Epigenetic mechanisms in depression: Implications for pathogenesis and treatment. Curr Opin Neurobiol 2024; 85:102854. [PMID: 38401316 DOI: 10.1016/j.conb.2024.102854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
The risk of depression is influenced by both genetic and environmental factors. It has been suggested that epigenetic mechanisms may mediate the risk of depression following exposure to adverse life events. Epigenetics encompasses stable alterations in gene expression that are controlled through transcriptional, post-transcriptional, translational, or post-translational processes, including DNA modifications, chromatin remodeling, histone modifications, RNA modifications, and non-coding RNA (ncRNA) regulation, without any changes in the DNA sequence. In this review, we explore recent research advancements in the realm of epigenetics concerning depression. Furthermore, we evaluate the potential of epigenetic changes as diagnostic and therapeutic biomarkers for depression.
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Affiliation(s)
- Hong-Sheng Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China
| | - Fang Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China
| | - Jian-Guo Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China.
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42
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Zhang CC, Li Y, Jiang CY, Le QM, Liu X, Ma L, Wang FF. O-GlcNAcylation mediates H 2O 2-induced apoptosis through regulation of STAT3 and FOXO1. Acta Pharmacol Sin 2024; 45:714-727. [PMID: 38191912 PMCID: PMC10943090 DOI: 10.1038/s41401-023-01218-z] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
The O-linked-β-N-acetylglucosamine (O-GlcNAc) glycosylation (O-GlcNAcylation) is a critical post-translational modification that couples the external stimuli to intracellular signal transduction networks. However, the critical protein targets of O-GlcNAcylation in oxidative stress-induced apoptosis remain to be elucidated. Here, we show that treatment with H2O2 inhibited O-GlcNAcylation, impaired cell viability, increased the cleaved caspase 3 and accelerated apoptosis of neuroblastoma N2a cells. The O-GlcNAc transferase (OGT) inhibitor OSMI-1 or the O-GlcNAcase (OGA) inhibitor Thiamet-G enhanced or inhibited H2O2-induced apoptosis, respectively. The total and phosphorylated protein levels, as well as the promoter activities of signal transducer and activator of transcription factor 3 (STAT3) and Forkhead box protein O 1 (FOXO1) were suppressed by OSMI-1. In contrast, overexpressing OGT or treating with Thiamet-G increased the total protein levels of STAT3 and FOXO1. Overexpression of STAT3 or FOXO1 abolished OSMI-1-induced apoptosis. Whereas the anti-apoptotic effect of OGT and Thiamet-G in H2O2-treated cells was abolished by either downregulating the expression or activity of endogenous STAT3 or FOXO1. These results suggest that STAT3 or FOXO1 are the potential targets of O-GlcNAcylation involved in the H2O2-induced apoptosis of N2a cells.
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Affiliation(s)
- Chen-Chun Zhang
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Yuan Li
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Chang-You Jiang
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Qiu-Min Le
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Xing Liu
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Lan Ma
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Fei-Fei Wang
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China.
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China.
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43
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Li Z, Chen J, Huang H, Zhan Q, Wang F, Chen Z, Lu X, Sun G. Post-translational modifications in diabetic cardiomyopathy. J Cell Mol Med 2024; 28:e18158. [PMID: 38494853 PMCID: PMC10945092 DOI: 10.1111/jcmm.18158] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024] Open
Abstract
The increasing attention towards diabetic cardiomyopathy as a distinctive complication of diabetes mellitus has highlighted the need for standardized diagnostic criteria and targeted treatment approaches in clinical practice. Ongoing research is gradually unravelling the pathogenesis of diabetic cardiomyopathy, with a particular emphasis on investigating various post-translational modifications. These modifications dynamically regulate protein function in response to changes in the internal and external environment, and their disturbance of homeostasis holds significant relevance for the development of chronic ailments. This review provides a comprehensive overview of the common post-translational modifications involved in the initiation and progression of diabetic cardiomyopathy, including O-GlcNAcylation, phosphorylation, methylation, acetylation and ubiquitination. Additionally, the review discusses drug development strategies for targeting key post-translational modification targets, such as agonists, inhibitors and PROTAC (proteolysis targeting chimaera) technology that targets E3 ubiquitin ligases.
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Affiliation(s)
- Zhi Li
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Jie Chen
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Hailong Huang
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Qianru Zhan
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Fengzhi Wang
- Department of Neurology, People's Hospital of Liaoning ProvincePeople's Hospital of China Medical UniversityShenyangChina
| | - Zihan Chen
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Xinwei Lu
- Department of CardiologySiping Central People's HospitalSipingChina
| | - Guozhe Sun
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
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44
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Jurkovic CM, Boisvert FM. Evolution of techniques and tools for replication fork proteome and protein interaction studies. Biochem Cell Biol 2024; 102:135-144. [PMID: 38113480 DOI: 10.1139/bcb-2023-0215] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Understanding the complex network of protein-protein interactions (PPI) that govern cellular functions is essential for unraveling the molecular basis of biological processes and diseases. Mass spectrometry (MS) has emerged as a powerful tool for studying protein dynamics, enabling comprehensive analysis of protein function, structure, post-translational modifications, interactions, and localization. This article provides an overview of MS techniques and their applications in proteomics studies, with a focus on the replication fork proteome. The replication fork is a multi-protein assembly involved in DNA replication, and its proper functioning is crucial for maintaining genomic integrity. By combining quantitative MS labeling techniques with various data acquisition methods, researchers have made significant strides in elucidating the complex processes and molecular mechanisms at the replication fork. Overall, MS has revolutionized our understanding of protein dynamics, offering valuable insights into cellular processes and potential targets for therapeutic interventions.
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Affiliation(s)
- Carla-Marie Jurkovic
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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45
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Wang T, Li X, Ma R, Sun J, Huang S, Sun Z, Wang M. Advancements in colorectal cancer research: Unveiling the cellular and molecular mechanisms of neddylation (Review). Int J Oncol 2024; 64:39. [PMID: 38391033 PMCID: PMC10919758 DOI: 10.3892/ijo.2024.5627] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Neddylation, akin to ubiquitination, represents a post‑translational modification of proteins wherein neural precursor cell‑expressed developmentally downregulated protein 8 (NEDD8) is modified on the substrate protein through a series of reactions. Neddylation plays a pivotal role in the growth and proliferation of animal cells. In colorectal cancer (CRC), it predominantly contributes to the proliferation, metastasis and survival of tumor cells, decreasing overall patient survival. The strategic manipulation of the NEDD8‑mediated neddylation pathway holds immense therapeutic promise in terms of the potential to modulate the growth of tumors by regulating diverse biological responses within cancer cells, such as DNA damage response and apoptosis, among others. MLN4924 is an inhibitor of NEDD8, and its combined use with platinum drugs and irinotecan, as well as cycle inhibitors and NEDD activating enzyme inhibitors screened by drug repurposing, has been found to exert promising antitumor effects. The present review summarizes the recent progress made in the understanding of the role of NEDD8 in the advancement of CRC, suggesting that NEDD8 is a promising anti‑CRC target.
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Affiliation(s)
- Tianyu Wang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong 250117, P.R. China
| | - Xiaobing Li
- School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong 250117, P.R. China
| | - Ruijie Ma
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
| | - Jian Sun
- Department of General Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
| | - Shuhong Huang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong 250117, P.R. China
- Science and Technology Innovation Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250117, P.R. China
| | - Zhigang Sun
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Meng Wang
- Department of General Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
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46
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Su M, Hou S. Ethylene insensitive 2 (EIN2) destiny shaper: The post-translational modification. J Plant Physiol 2024; 295:154190. [PMID: 38460400 DOI: 10.1016/j.jplph.2024.154190] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/22/2024] [Accepted: 02/04/2024] [Indexed: 03/11/2024]
Abstract
PTMs (Post-Translational Modifications) of proteins facilitate rapid modulation of protein function in response to various environmental stimuli. The EIN2 (Ethylene Insensitive 2) protein is a core regulatory of the ethylene signaling pathway. Recent findings have demonstrated that PTMs, including protein phosphorylation, ubiquitination, and glycosylation, govern EIN2 trafficking, subcellular localization, stability, and physiological roles. The cognition of multiple PTMs in EIN2 underscores the stringent regulation of protein. Consequently, a thorough review of the regulatory role of PTMs in EIN2 functions will improve our profound comprehension of the regulation mechanism and various physiological processes of EIN2-mediated signaling pathways. This review discusses the evolution, functions, structure and characteristics of EIN2 protein in plants. Additionally, this review sheds light on the progress of protein ubiquitination, phosphorylation, O-Glycosylation in the regulation of EIN2 functions, and the unresolved questions and future perspectives.
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Affiliation(s)
- Meifei Su
- Key Laboratory of Gene Editing for Breeding, Gansu Province, China; Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Suiwen Hou
- Key Laboratory of Gene Editing for Breeding, Gansu Province, China; Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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47
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Carr AV, Bollis NE, Pavek JG, Shortreed MR, Smith LM. Spectral averaging with outlier rejection algorithms to increase identifications in top-down proteomics. Proteomics 2024; 24:e2300234. [PMID: 38487981 DOI: 10.1002/pmic.202300234] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/15/2024] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
The identification of proteoforms by top-down proteomics requires both high quality fragmentation spectra and the neutral mass of the proteoform from which the fragments derive. Intact proteoform spectra can be highly complex and may include multiple overlapping proteoforms, as well as many isotopic peaks and charge states. The resulting lower signal-to-noise ratios for intact proteins complicates downstream analyses such as deconvolution. Averaging multiple scans is a common way to improve signal-to-noise, but mass spectrometry data contains artifacts unique to it that can degrade the quality of an averaged spectra. To overcome these limitations and increase signal-to-noise, we have implemented outlier rejection algorithms to remove outlier measurements efficiently and robustly in a set of MS1 scans prior to averaging. We have implemented averaging with rejection algorithms in the open-source, freely available, proteomics search engine MetaMorpheus. Herein, we report the application of the averaging with rejection algorithms to direct injection and online liquid chromatography mass spectrometry data. Averaging with rejection algorithms demonstrated a 45% increase in the number of proteoforms detected in Jurkat T cell lysate. We show that the increase is due to improved spectral quality, particularly in regions surrounding isotopic envelopes.
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Affiliation(s)
- Austin V Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicholas E Bollis
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John G Pavek
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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48
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Gu L, Chen T, Li J, Huang YA, Du Z, Leung VCM, Chen J. Hybrid Bayesian Optimization-Based Graphical Discovery for Methylation Sites Prediction. IEEE J Biomed Health Inform 2024; 28:1917-1926. [PMID: 37801389 DOI: 10.1109/jbhi.2023.3322560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Protein methylation is one of the most important reversible post-translational modifications (PTMs), playing a vital role in the regulation of gene expression. Protein methylation sites serve as biomarkers in cardiovascular and pulmonary diseases, influencing various aspects of normal cell biology and pathogenesis. Nonetheless, the majority of existing computational methods for predicting protein methylation sites (PMSP) have been constructed based on protein sequences, with few methods leveraging the topological information of proteins. To address this issue, we propose an innovative framework for predicting Methylation Sites using Graphs (GraphMethySite) that employs graph convolution network in conjunction with Bayesian Optimization (BO) to automatically discover the graphical structure surrounding a candidate site and improve the predictive accuracy. In order to extract the most optimal subgraphs associated with methylation sites, we extend GraphMethySite by coupling it with a hybrid Bayesian optimization (together named GraphMethySite +) to determine and visualize the topological relevance among amino-acid residues. We evaluated our framework on two extended protein methylation datasets, and empirical results demonstrate that it outperforms existing state-of-the-art methylation prediction methods.
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49
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Gao J, Zhao Y, Chen C, Ning Q. MVNN-HNHC:A multi-view neural network for identification of human non-histone crotonylation sites. Anal Biochem 2024; 687:115426. [PMID: 38141798 DOI: 10.1016/j.ab.2023.115426] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Crotonylation on lysine sites in human non-histone proteins plays a crucial role in biology activities. However, because traditional experimental methods for crotonylation site identification are time-consuming and labor-intensive, computational prediction methods have become increasingly popular in recent years. Despite its significance, crotonylation site prediction has received less attention in non-histone proteins than in histones. In this study, we proposed a Multi-View Neural Network for identification of Human Non-Histone Crotonylation sites, named MVNN-HNHC. MVNN-HNHC integrated multi-view encoding features and adaptive encoding features through multi-channel neural network to deeply learn about attribute differences between crotonylation sites and non-crotonylation sites from various aspects. In MVNN-HNHC, convolutional neural networks can obtain local information from these features, and bidirectional long short term memory networks were utilized to extract sequence information. Then, we employ the attention mechanism to fuse the outputs of various feature extraction modules. Finally, the fully connection network acted as the classifier to predict whether a lysine site was crotonylation site or non-crotonylation site. Performance metrics on independent test set, including sensitivity, specificity, accuracy, Matthews correlation coefficient, and area under the curve (AUC) values reach 80.06 %, 75.77 %, 77.06 %, 0.5203, and 0.7792, respectively. To verify the effectiveness of this method, we carry out a series of experiments and the results show that MVNN-HNHC is an effective tool for predicting crotonylation sites in non-histone proteins. The data and code are available on https://github.com/xbbxhbc/junjun0612.git.
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Affiliation(s)
- Jun Gao
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yaomiao Zhao
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Chen Chen
- Naval Architecture and Ocean Engineering College, Dalian Maritime University, Dalian, 116026, China.
| | - Qiao Ning
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China.
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50
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Mydy LS, Hungerford J, Chigumba DN, Konwerski JR, Jantzi SC, Wang D, Smith JL, Kersten RD. An intramolecular macrocyclase in plant ribosomal peptide biosynthesis. Nat Chem Biol 2024; 20:530-540. [PMID: 38355722 DOI: 10.1038/s41589-024-01552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The biosynthetic dogma of ribosomally synthesized and posttranslationally modified peptides (RiPP) involves enzymatic intermolecular modification of core peptide motifs in precursor peptides. The plant-specific BURP-domain protein family, named after their four founding members, includes autocatalytic peptide cyclases involved in the biosynthesis of side-chain-macrocyclic plant RiPPs. Here we show that AhyBURP, a representative of the founding Unknown Seed Protein-type BURP-domain subfamily, catalyzes intramolecular macrocyclizations of its core peptide during the sequential biosynthesis of monocyclic lyciumin I via glycine-tryptophan crosslinking and bicyclic legumenin via glutamine-tyrosine crosslinking. X-ray crystallography of AhyBURP reveals the BURP-domain fold with two type II copper centers derived from a conserved stapled-disulfide and His motif. We show the macrocyclization of lyciumin-C(sp3)-N-bond formation followed by legumenin-C(sp3)-O-bond formation requires dioxygen and radical involvement based on enzyme assays in anoxic conditions and isotopic labeling. Our study expands enzymatic intramolecular modifications beyond catalytic moiety and chromophore biogenesis to RiPP biosynthesis.
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Affiliation(s)
- Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Jordan Hungerford
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Sarah C Jantzi
- Plasma Chemistry Laboratory, Center for Applied Isotope Studies, University of Georgia, Athens, GA, USA
| | - Di Wang
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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