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Aboalroub AA, Al Azzam KM. Protein S-Nitrosylation: A Chemical Modification with Ubiquitous Biological Activities. Protein J 2024:10.1007/s10930-024-10223-y. [PMID: 39068633 DOI: 10.1007/s10930-024-10223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2024] [Indexed: 07/30/2024]
Abstract
Nitric oxide (NO) induces protein posttranslational modification (PTM), known as S-nitrosylation, which has started to gain attention as a critical regulator of thousands of substrate proteins. However, our understanding of the biological consequences of this emerging PTM is incomplete because of the limited number of identified S-nitrosylated proteins (S-NO proteins). Recent advances in detection methods have effectively contributed to broadening the spectrum of discovered S-NO proteins. This article briefly reviews the progress in S-NO protein detection methods and discusses how these methods are involved in characterizing the biological consequences of this PTM. Additionally, we provide insight into S-NO protein-related diseases, focusing on the role of these proteins in mitigating the severity of infectious diseases.
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Affiliation(s)
- Adam A Aboalroub
- Pharmacological and Diagnostic Research Center (PDRC), Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, 19328, Jordan.
| | - Khaldun M Al Azzam
- Department of Chemistry, School of Science, The University of Jordan, Amman, 11942, Jordan
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2
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Grünewald J, Miller BR, Szalay RN, Cabeceiras PK, Woodilla CJ, Holtz EJB, Petri K, Joung JK. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat Biotechnol 2023; 41:337-343. [PMID: 36163548 PMCID: PMC10023297 DOI: 10.1038/s41587-022-01473-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 08/15/2022] [Indexed: 12/16/2022]
Abstract
The CRISPR prime editor PE2 consists of a Streptococcus pyogenes Cas9 nickase (nSpCas9) fused at its C-terminus to a Moloney murine leukemia virus reverse transcriptase (MMLV-RT). Here we show that separated nSpCas9 and MMLV-RT proteins function as efficiently as intact PE2 in human cells. We use this Split-PE system to rapidly identify and engineer more compact prime editor architectures that also broaden the types of RTs used for prime editing.
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Affiliation(s)
- Julian Grünewald
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
- First Department of Medicine, Cardiology, Angiology, Pneumology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany.
- Center for Organoid Systems and Tissue Engineering (COS), Garching, Germany.
- TranslaTUM - Organoid Hub, Munich, Germany.
- DZHK (German Center of Cardiovascular Research), Munich Heart Alliance, Munich, Germany.
| | - Bret R Miller
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Regan N Szalay
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Peter K Cabeceiras
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Christopher J Woodilla
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Eliza Jane B Holtz
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Karl Petri
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.
- Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
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3
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Abstract
Reverse transcriptases (RTs) use their DNA polymerase and RNase H activities to catalyze the conversion of single-stranded RNA to double-stranded DNA (dsDNA), a crucial process for the replication of retroviruses. Foamy viruses (FVs) possess a unique RT, which is a fusion with the protease (PR) domain. The mechanism of substrate binding by this enzyme has been unknown. Here, we report a crystal structure of monomeric full-length marmoset FV (MFV) PR-RT in complex with an RNA/DNA hybrid substrate. We also describe a structure of MFV PR-RT with an RNase H deletion in complex with a dsDNA substrate in which the enzyme forms an asymmetric homodimer. Cryo-electron microscopy reconstruction of the full-length MFV PR-RT–dsDNA complex confirmed the dimeric architecture. These findings represent the first structural description of nucleic acid binding by a foamy viral RT and demonstrate its ability to change its oligomeric state depending on the type of bound nucleic acid. IMPORTANCE Reverse transcriptases (RTs) are intriguing enzymes converting single-stranded RNA to dsDNA. Their activity is essential for retroviruses, which are divided into two subfamilies differing significantly in their life cycles: Orthoretrovirinae and Spumaretrovirinae. The latter family is much more ancient and comprises five genera. A unique feature of foamy viral RTs is that they contain N-terminal protease (PR) domains, which are not present in orthoretroviral enzymes. So far, no structural information for full-length foamy viral PR-RT interacting with nucleic substrates has been reported. Here, we present crystal and cryo-electron microscopy structures of marmoset foamy virus (MFV) PR-RT. These structures revealed the mode of binding of RNA/DNA and dsDNA substrates. Moreover, unexpectedly, the structures and biochemical data showed that foamy viral PR-RT can adopt both a monomeric configuration, which is observed in our structures in the presence of an RNA/DNA hybrid, and an asymmetric dimer arrangement, which we observed in the presence of dsDNA.
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Harrison JJEK, Tuske S, Das K, Ruiz FX, Bauman JD, Boyer PL, DeStefano JJ, Hughes SH, Arnold E. Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT). Viruses 2021; 13:v13081495. [PMID: 34452360 PMCID: PMC8402755 DOI: 10.3390/v13081495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022] Open
Abstract
In most cases, proteolytic processing of the retroviral Pol portion of the Gag-Pol polyprotein precursor produces protease (PR), reverse transcriptase (RT), and integrase (IN). However, foamy viruses (FVs) express Pol separately from Gag and, when Pol is processed, only the IN domain is released. Here, we report a 2.9 Å resolution crystal structure of the mature PR-RT from prototype FV (PFV) that can carry out both proteolytic processing and reverse transcription but is in a configuration not competent for proteolytic or polymerase activity. PFV PR-RT is monomeric and the architecture of PFV PR is similar to one of the subunits of HIV-1 PR, which is a dimer. There is a C-terminal extension of PFV PR (101-145) that consists of two helices which are adjacent to the base of the RT palm subdomain, and anchors PR to RT. The polymerase domain of PFV RT consists of fingers, palm, thumb, and connection subdomains whose spatial arrangements are similar to the p51 subunit of HIV-1 RT. The RNase H and polymerase domains of PFV RT are connected by flexible linkers. Significant spatial and conformational (sub)domain rearrangements are therefore required for nucleic acid binding. The structure of PFV PR-RT provides insights into the conformational maturation of retroviral Pol polyproteins.
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Affiliation(s)
- Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry, University of Ghana, Legon P.O. Box LG 56, Ghana
| | - Steve Tuske
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Paul L. Boyer
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA; (P.L.B.); (S.H.H.)
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA;
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA; (P.L.B.); (S.H.H.)
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- Correspondence:
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Jaguva Vasudevan AA, Becker D, Luedde T, Gohlke H, Münk C. Foamy Viruses, Bet, and APOBEC3 Restriction. Viruses 2021; 13:504. [PMID: 33803830 PMCID: PMC8003144 DOI: 10.3390/v13030504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 01/24/2023] Open
Abstract
Non-human primates (NHP) are an important source of viruses that can spillover to humans and, after adaptation, spread through the host population. Whereas HIV-1 and HTLV-1 emerged as retroviral pathogens in humans, a unique class of retroviruses called foamy viruses (FV) with zoonotic potential are occasionally detected in bushmeat hunters or zookeepers. Various FVs are endemic in numerous mammalian natural hosts, such as primates, felines, bovines, and equines, and other animals, but not in humans. They are apathogenic, and significant differences exist between the viral life cycles of FV and other retroviruses. Importantly, FVs replicate in the presence of many well-defined retroviral restriction factors such as TRIM5α, BST2 (Tetherin), MX2, and APOBEC3 (A3). While the interaction of A3s with HIV-1 is well studied, the escape mechanisms of FVs from restriction by A3 is much less explored. Here we review the current knowledge of FV biology, host restriction factors, and FV-host interactions with an emphasis on the consequences of FV regulatory protein Bet binding to A3s and outline crucial open questions for future studies.
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Affiliation(s)
- Ananda Ayyappan Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Daniel Becker
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (D.B.); (H.G.)
| | - Tom Luedde
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (D.B.); (H.G.)
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre & Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
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