1
|
Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB. Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A. Nat Commun 2023; 14:6382. [PMID: 37821454 PMCID: PMC10567711 DOI: 10.1038/s41467-023-42174-w] [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: 03/07/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
The normally antiviral enzyme APOBEC3A is an endogenous mutagen in human cancer. Its single-stranded DNA C-to-U editing activity results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations. APOBEC3A inhibitors may therefore comprise a unique class of anti-cancer agents that work by blocking mutagenesis, slowing tumor evolvability, and preventing detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC substrate motif that is part of a 3-nucleotide loop. In addition, the structural basis of APOBEC3A's preference for YTCD motifs (Y = T, C; D = A, G, T) is explained. The nuclease-resistant phosphorothioated derivatives of these inhibitors have nanomolar potency in vitro and block APOBEC3A activity in human cells. These inhibitors may be useful probes for studying APOBEC3A activity in cellular systems and leading toward, potentially as conjuvants, next-generation, combinatorial anti-mutator and anti-cancer therapies.
Collapse
Affiliation(s)
- Stefan Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Amanda E Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maitsetseg Bayarjargal
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jana Filitcheva
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yongdong Su
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Department of Pediatrics, Emory University School of Medicine, and the Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tracy K Hale
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Elena Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| |
Collapse
|
2
|
Harjes E, Edwards PJB, Bisset SW, Patchett ML, Jameson GB, Yang SH, Navo CD, Harris PWR, Brimble MA, Norris GE. NMR Shows Why a Small Chemical Change Almost Abolishes the Antimicrobial Activity of Glycocin F. Biochemistry 2023; 62:2669-2676. [PMID: 37531216 DOI: 10.1021/acs.biochem.3c00197] [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: 08/03/2023]
Abstract
Glycocin F (GccF), a ribosomally synthesized, post-translationally modified peptide secreted by Lactobacillus plantarum KW30, rapidly inhibits the growth of susceptible bacteria at nanomolar concentrations. Previous studies have highlighted structural features important for its activity and have shown the absolute requirement for the Ser18 O-linked GlcNAc on the eight-residue loop linking the two short helices of the (C-X6-C)2 structure. Here, we show that an ostensibly very small chemical modification to Ser18, the substitution of the Cα proton with a methyl group, reduces the antimicrobial activity of GccF 1000-fold (IC50 1.5 μM cf. 1.5 nM). A comparison of the GccFα-methylSer18 NMR structure (PDB 8DFZ) with that of the native protein (PDB 2KUY) showed a marked difference in the orientation and mobility of the loop, as well as a markedly different positioning of the GlcNAc, suggesting that loop conformation, dynamics, and glycan presentation play an important role in the interaction of GccF with as yet unknown but essential physiological target molecules.
Collapse
Affiliation(s)
- Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Patrick J B Edwards
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Sean W Bisset
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Mark L Patchett
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Sung-Hyun Yang
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Claudio D Navo
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Paul W R Harris
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Margaret A Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Gillian E Norris
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| |
Collapse
|
3
|
Kurup HM, Kvach MV, Harjes S, Jameson GB, Harjes E, Filichev VV. Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A. Org Biomol Chem 2023; 21:5117-5128. [PMID: 37282621 PMCID: PMC10282898 DOI: 10.1039/d3ob00392b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/12/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2'-deoxyzebularine (dZ) and 5-fluoro-2'-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2'-deoxycytidine providing a Ki of 290 ± 40 nM, which is only slightly weaker than the Ki of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2'-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors.
Collapse
Affiliation(s)
- Harikrishnan M Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| |
Collapse
|
4
|
Harjes S, Kurup HM, Rieffer AE, Bayaijargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB. Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A. bioRxiv 2023:2023.02.17.528918. [PMID: 36824964 PMCID: PMC9949147 DOI: 10.1101/2023.02.17.528918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The normally antiviral enzyme APOBEC3A1-4 is an endogenous mutagen in many different human cancers5-7, where it becomes hijacked to fuel tumor evolvability. APOBEC3A's single-stranded DNA C-to-U editing activity1,8 results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations5-7. Transgenic expression in mice demonstrates its tumorigenic potential9. APOBEC3A inhibitors may therefore comprise a novel class of anti-cancer agents that work by blocking mutagenesis, preventing tumor evolvability, and lessening detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC recognition motif that is part of a three-nucleotide loop. The nuclease-resistant phosphorothioated derivatives of these inhibitors maintain nanomolar in vitro potency against APOBEC3A, localize to the cell nucleus, and block APOBEC3A activity in human cells. These results combine to suggest roles for these inhibitors to study A3A activity in living cells, potentially as conjuvants, leading toward next-generation, combinatorial anti-mutator and anti-cancer therapies.
Collapse
Affiliation(s)
- Stefan Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Amanda E. Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota–Twin Cities, Minneapolis, MN, USA
| | - Maitsetseg Bayaijargal
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Current address: Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jana Filitcheva
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yongdong Su
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Current address: Department of Pediatrics, Emory University School of Medicine, and the Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Tracy K. Hale
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| |
Collapse
|
5
|
Kurup HM, Kvach MV, Harjes S, Barzak FM, Jameson GB, Harjes E, Filichev VV. Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A. Biochemistry 2022; 61:2568-2578. [DOI: 10.1021/acs.biochem.2c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harikrishnan M. Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V. Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Fareeda M. Barzak
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| |
Collapse
|
6
|
Barzak FM, Ryan TM, Kvach MV, Kurup HM, Aihara H, Harris RS, Filichev VV, Harjes E, Jameson GB. Small-Angle X-ray Scattering Models of APOBEC3B Catalytic Domain in a Complex with a Single-Stranded DNA Inhibitor. Viruses 2021; 13:290. [PMID: 33673243 PMCID: PMC7918907 DOI: 10.3390/v13020290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
In normal cells APOBEC3 (A3A-A3H) enzymes as part of the innate immune system deaminate cytosine to uracil on single-stranded DNA (ssDNA) to scramble DNA in order to give protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroelements. However, some viruses and cancer cells use these enzymes, especially A3A and A3B, to escape the adaptive immune response and thereby lead to the evolution of drug resistance. We have synthesized first-in-class inhibitors featuring modified ssDNA. We present models based on small-angle X-ray scattering (SAXS) data that (1) confirm that the mode of binding of inhibitor to an active A3B C-terminal domain construct in the solution state is the same as the mode of binding substrate to inactive mutants of A3A and A3B revealed in X-ray crystal structures and (2) give insight into the disulfide-linked inactive dimer formed under the oxidizing conditions of purification.
Collapse
Affiliation(s)
- Fareeda M. Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Timothy M. Ryan
- SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia;
| | - Maksim V. Kvach
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Harikrishnan M. Kurup
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.); (R.S.H.)
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.); (R.S.H.)
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vyacheslav V. Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Geoffrey B. Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| |
Collapse
|
7
|
Varnava KG, Edwards PJB, Cameron AJ, Harjes E, Sarojini V. Cyclic peptides bearing the d-Phe-2-Abz turn motif: Structural characterization and antimicrobial potential. J Pept Sci 2020; 27:e3291. [PMID: 33283398 DOI: 10.1002/psc.3291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/07/2020] [Accepted: 10/14/2020] [Indexed: 11/10/2022]
Abstract
The effect on secondary structure and antimicrobial activity of introducing different cyclic constraints in linear β-hairpin antimicrobial peptides has been investigated with the intention of generating cyclic β sheets as promising antimicrobials with improved therapeutic potential. The linear peptides were cyclized head to tail either directly or after the addition of either a second turn motif or a disulfide bridge. The propensity of these peptides to adopt a cyclic β-sheet structure has been correlated to their antibacterial activity. All cyclic peptides showed enhanced activity, compared with their linear counterparts against methicillin-resistant Staphylococcus aureus. Scanning electron microscopy and transmission electron microscopy studies showed that this family kills bacteria through membrane lysis. The peptide that showed the best efficacy against all strains (exhibiting nanomolar activity), while retaining low haemolysis, bears two symmetrical, homochiral d-phe-2-Abz-d-ala turns and adopted a flexible structure. Its twin peptide that bears heterochiral turns (one with d-ala and one with L-Ala) showed reduced antibacterial activity and higher percentage of haemolysis. Circular dichroism and nuclear magnetic resonance spectroscopy indicate that heterochirality in the two turns leads to oligomerization of the peptide at higher concentrations, stabilizing the β-sheet secondary structure. More rigid secondary structure is associated with lower activity against bacteria and loss of selectivity.
Collapse
Affiliation(s)
- Kyriakos G Varnava
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140, New Zealand
| |
Collapse
|
8
|
Harjes E, Jameson GB, Tu YH, Burr N, Loo TS, Goroncy AK, Edwards PJB, Harjes S, Munro B, Göbl C, Sattlegger E, Norris GE. Experimentally based structural model of Yih1 provides insight into its function in controlling the key translational regulator Gcn2. FEBS Lett 2020; 595:324-340. [PMID: 33156522 DOI: 10.1002/1873-3468.13990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Yeast impact homolog 1 (Yih1), or IMPACT in mammals, is part of a conserved regulatory module controlling the activity of General Control Nonderepressible 2 (Gcn2), a protein kinase that regulates protein synthesis. Yih1/IMPACT is implicated not only in many essential cellular processes, such as neuronal development, immune system regulation and the cell cycle, but also in cancer. Gcn2 must bind to Gcn1 in order to impair the initiation of protein translation. Yih1 hinders this key Gcn1-Gcn2 interaction by binding to Gcn1, thus preventing Gcn2-mediated inhibition of protein synthesis. Here, we solved the structures of the two domains of Saccharomyces cerevisiae Yih1 separately using Nuclear Magnetic Resonance and determined the relative positions of the two domains using a range of biophysical methods. Our findings support a compact structural model of Yih1 in which the residues required for Gcn1 binding are buried in the interface. This model strongly implies that Yih1 undergoes a large conformational rearrangement from a latent closed state to a primed open state to bind Gcn1. Our study provides structural insight into the interactions of Yih1 with partner molecules.
Collapse
Affiliation(s)
- Elena Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
| | - Yi-Hsuan Tu
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Natalie Burr
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Trevor S Loo
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alexander K Goroncy
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Stefan Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Ben Munro
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Christoph Göbl
- Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Evelyn Sattlegger
- Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand.,School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Gillian E Norris
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
| |
Collapse
|
9
|
Kvach MV, Barzak FM, Harjes S, Schares HAM, Kurup HM, Jones KF, Sutton L, Donahue J, D'Aquila RT, Jameson GB, Harki DA, Krause KL, Harjes E, Filichev VV. Differential Inhibition of APOBEC3 DNA-Mutator Isozymes by Fluoro- and Non-Fluoro-Substituted 2'-Deoxyzebularine Embedded in Single-Stranded DNA. Chembiochem 2019; 21:1028-1035. [PMID: 31633265 PMCID: PMC7142307 DOI: 10.1002/cbic.201900505] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/20/2019] [Indexed: 12/17/2022]
Abstract
The APOBEC3 (APOBEC3A‐H) enzyme family is part of the human innate immune system that restricts pathogens by scrambling pathogenic single‐stranded (ss) DNA by deamination of cytosines to produce uracil residues. However, APOBEC3‐mediated mutagenesis of viral and cancer DNA promotes its evolution, thus enabling disease progression and the development of drug resistance. Therefore, APOBEC3 inhibition offers a new strategy to complement existing antiviral and anticancer therapies by making such therapies effective for longer periods of time, thereby preventing the emergence of drug resistance. Here, we have synthesised 2′‐deoxynucleoside forms of several known inhibitors of cytidine deaminase (CDA), incorporated them into oligodeoxynucleotides (oligos) in place of 2′‐deoxycytidine in the preferred substrates of APOBEC3A, APOBEC3B, and APOBEC3G, and evaluated their inhibitory potential against these enzymes. An oligo containing a 5‐fluoro‐2′‐deoxyzebularine (5FdZ) motif exhibited an inhibition constant against APOBEC3B 3.5 times better than that of the comparable 2′‐deoxyzebularine‐containing (dZ‐containing) oligo. A similar inhibition trend was observed for wild‐type APOBEC3A. In contrast, use of the 5FdZ motif in an oligo designed for APOBEC3G inhibition resulted in an inhibitor that was less potent than the dZ‐containing oligo both in the case of APOBEC3GCTD and in that of full‐length wild‐type APOBEC3G.
Collapse
Affiliation(s)
- Maksim V Kvach
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Fareeda M Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Stefan Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Henry A M Schares
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Harikrishnan M Kurup
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Katherine F Jones
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN, 55455, USA
| | - Lorraine Sutton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, 21st Ave S, Nashville, TN, 37232, USA
| | - John Donahue
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, 21st Ave S, Nashville, TN, 37232, USA
| | - Richard T D'Aquila
- Division of Infectious Diseases and, Northwestern HIV Translational Research Center, Department of Medicine, Northwestern University Feinberg School of Medicine, 676 N. St. Clair Street, Suite 2330, Chicago, IL, 60611, USA
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN, 55455, USA
| | - Kurt L Krause
- Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand.,Department of Biochemistry, University of Otago, P. O. Box 56, Dunedin, 9054, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| |
Collapse
|
10
|
Barzak FM, Harjes S, Kvach MV, Kurup HM, Jameson GB, Filichev VV, Harjes E. Selective inhibition of APOBEC3 enzymes by single-stranded DNAs containing 2'-deoxyzebularine. Org Biomol Chem 2019; 17:9435-9441. [PMID: 31603457 DOI: 10.1039/c9ob01781j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
To restrict pathogens, in a normal human cell, APOBEC3 enzymes mutate cytosine to uracil in foreign single-stranded DNAs. However, in cancer cells, APOBEC3B (one of seven APOBEC3 enzymes) has been identified as the primary source of genetic mutations. As such, APOBEC3B promotes evolution and progression of cancers and leads to development of drug resistance in multiple cancers. As APOBEC3B is a non-essential protein, its inhibition can be used to suppress emergence of drug resistance in existing anti-cancer therapies. Because of the vital role of APOBEC3 enzymes in innate immunity, selective inhibitors targeting only APOBEC3B are required. Here, we use the discriminative properties of wild-type APOBEC3A, APOBEC3B and APOBEC3G to deaminate different cytosines in the CCC-recognition motif in order to best place the cytidine analogue 2'-deoxyzebularine (dZ) in the CCC-motif. Using several APOBEC3 variants that mimic deamination patterns of wild-type enzymes, we demonstrate that selective inhibition of APOBEC3B in preference to other APOBEC3 constructs is feasible for the dZCC motif. This work is an important step towards development of in vivo tools to inhibit APOBEC3 enzymes in living cells by using short, chemically modified oligonucleotides.
Collapse
Affiliation(s)
- Fareeda M Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | | | | | | | | | | | | |
Collapse
|
11
|
Kvach MV, Barzak FM, Harjes S, Schares HAM, Jameson GB, Ayoub AM, Moorthy R, Aihara H, Harris RS, Filichev VV, Harki DA, Harjes E. Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2'-Deoxyzebularine Analogues. Biochemistry 2018; 58:391-400. [PMID: 30418757 PMCID: PMC6365909 DOI: 10.1021/acs.biochem.8b00858] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
APOBEC3 enzymes form part of the innate immune system by deaminating cytosine to uracil in single-stranded DNA (ssDNA) and thereby preventing the spread of pathogenic genetic information. However, APOBEC mutagenesis is also exploited by viruses and cancer cells to increase rates of evolution, escape adaptive immune responses, and resist drugs. This raises the possibility of APOBEC3 inhibition as a strategy for augmenting existing antiviral and anticancer therapies. Here we show that, upon incorporation into short ssDNAs, the cytidine nucleoside analogue 2'-deoxyzebularine (dZ) becomes capable of inhibiting the catalytic activity of selected APOBEC variants derived from APOBEC3A, APOBEC3B, and APOBEC3G, supporting a mechanism in which ssDNA delivers dZ to the active site. Multiple experimental approaches, including isothermal titration calorimetry, fluorescence polarization, protein thermal shift, and nuclear magnetic resonance spectroscopy assays, demonstrate nanomolar dissociation constants and low micromolar inhibition constants. These dZ-containing ssDNAs constitute the first substrate-like APOBEC3 inhibitors and, together, comprise a platform for developing nucleic acid-based inhibitors with cellular activity.
Collapse
Affiliation(s)
- Maksim V Kvach
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | - Fareeda M Barzak
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | - Stefan Harjes
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | | | - Geoffrey B Jameson
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
| | | | | | | | - Reuben S Harris
- Howard Hughes Medical Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
| | | | - Elena Harjes
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
| |
Collapse
|
12
|
Cameron AJ, Varnava KG, Edwards PJB, Harjes E, Sarojini V. Acyclic peptides incorporating the d-Phe-2-Abz turn motif: Investigations on antimicrobial activity and propensity to adopt β-hairpin conformations. J Pept Sci 2018; 24:e3094. [PMID: 29900628 DOI: 10.1002/psc.3094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/08/2018] [Accepted: 05/16/2018] [Indexed: 02/01/2023]
Abstract
Three linear peptides incorporating d-Phe-2-Abz as the turn motif are reported. Peptide 1, a hydrophobic β-hairpin, served as a proof of principle for the design strategy with both NMR and CD spectra strongly suggesting a β-hairpin conformation. Peptides 2 and 3, designed as amphipathic antimicrobials, exhibited broad spectrum antimicrobial activity, with potency in the nanomolar range against Staphylococcus aureus. Both compounds possess a high degree of selectivity, proving non-haemolytic at concentrations 500 to 800 times higher than their respective minimal inhibitory concentrations (MICs) against S. aureus. Peptide 2 induced cell membrane and cell wall disintegration in both S. aureus and Pseudomonas aeruginosa as observed by transmission electron microscopy. Peptide 2 also demonstrated moderate antifungal activity against Candida albicans with an MIC of 50 μM. Synergism was observed with sub-MIC levels of amphotericin B (AmB), leading to nanomolar MICs against C. albicans for peptide 2. Based on circular dichroism spectra, both peptides 2 and 3 appear to exist as a mixture of conformers with the β-hairpin as a minor conformer in aqueous solution, and a slight increase in hairpin population in 50% trifluoroethanol, which was more pronounced for peptide 3. NMR spectra of peptide 2 in a 1:1 CD3 CN/H2 O mixture and 30 mM deuterated sodium dodecyl sulfate showed evidence of an extended backbone conformation of the β-strand residues. However, inter-strand rotating frame Overhauser effects (ROE) could not be detected and a loosely defined divergent hairpin structure resulted from ROE structure calculation in CD3 CN/H2 O. The loosely defined hairpin conformation is most likely a result of the electrostatic repulsions between cationic strand residues which also probably contribute towards maintaining low haemolytic activity.
Collapse
Affiliation(s)
- Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Kyriakos G Varnava
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | | |
Collapse
|
13
|
Cameron AJ, Edwards PJB, Harjes E, Sarojini V. Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity. J Med Chem 2017; 60:9565-9574. [DOI: 10.1021/acs.jmedchem.7b00953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alan J. Cameron
- School
of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Patrick J. B. Edwards
- Institute
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Elena Harjes
- Institute
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | | |
Collapse
|
14
|
Cameron AJ, Squire CJ, Edwards PJB, Harjes E, Sarojini V. Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides. Chem Asian J 2017; 12:3195-3202. [PMID: 29098772 DOI: 10.1002/asia.201701422] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/30/2017] [Indexed: 12/31/2022]
Abstract
Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H2 N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution.
Collapse
Affiliation(s)
- Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Christopher J Squire
- School of Biological Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | | |
Collapse
|
15
|
Harjes S, Jameson GB, Filichev VV, Edwards P, Harjes E. NMR-based method of small changes reveals how DNA mutator APOBEC3A interacts with its single-stranded DNA substrate. Nucleic Acids Res 2017; 45:5602-5613. [PMID: 28369637 PMCID: PMC5435981 DOI: 10.1093/nar/gkx196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/21/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
Abstract
APOBEC3 proteins are double-edged swords. They deaminate cytosine to uracil in single-stranded DNA and provide protection, as part of our innate immune system, against viruses and retrotransposons, but they are also involved in cancer evolution and development of drug resistance. We report a solution-state model of APOBEC3A interaction with its single-stranded DNA substrate obtained with the 'method of small changes'. This method compares pairwise the 2D 15N-1H NMR spectra of APOBEC3A bearing a deactivating mutation E72A in the presence of 36 slightly different DNA substrates. From changes in chemical shifts of peptide N-H moieties, the positions of each nucleotide relative to the protein can be identified. This provided distance restraints for molecular-dynamic simulations to derive a 3-D molecular model of the APOBEC3A-ssDNA complex. The model reveals that loops 1 and 7 of APOBEC3A move to accommodate substrate binding, indicating an important role for protein-DNA dynamics. Overall, our method may prove useful to study other DNA-protein complexes where crystallographic techniques or full NMR structure calculations are hindered by weak binding or other problems. Subsequent to submission, an APOBEC3A structure with a bound DNA oligomer was published and coordinates released, which has provided an unbiased validation of the 'method of small changes'.
Collapse
Affiliation(s)
- Stefan Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Vyacheslav V. Filichev
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Patrick J. B. Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| |
Collapse
|
16
|
Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS. Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F. J Mol Biol 2013; 425:1172-82. [PMID: 23318957 PMCID: PMC3602375 DOI: 10.1016/j.jmb.2013.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/20/2022]
Abstract
APOBEC3F (A3F) and APOBEC3G (A3G) are DNA cytosine deaminases that potently restrict human immunodeficiency virus type 1 replication when the virus is deprived of its accessory protein Vif (virion infectivity factor). Vif counteracts these restriction factors by recruiting A3F and A3G to an E3 ubiquitin (Ub) ligase complex that mediates their polyubiquitination (polyUb) and proteasomal degradation. While previous efforts have identified single amino acid residues in APOBEC3 proteins required for Vif recognition, less is known about the downstream Ub acceptor sites that are targeted. One prior report identified a cluster of polyubiquitinated residues in A3G and proposed an antiparallel model of A3G interaction with the Vif-E3 Ub ligase complex wherein Vif binding at one terminus of A3G orients the opposite terminus for polyUb [Iwatani et al. (2009). Proc. Natl. Acad. Sci. USA, 106, 19539-19544]. To test the generalizability of this model, we carried out a complete mutagenesis of the lysine residues in A3F and used a complementary, unbiased proteomic approach to identify Ub acceptor sites targeted by Vif. Our data indicate that internal lysines are the dominant Ub acceptor sites in both A3F and A3G. In contrast with the proposed antiparallel model, however, we find that the Vif-dependent polyUb of A3F and A3G can occur at multiple acceptor sites dispersed along predicted lysine-enriched surfaces of both the N- and C-terminal deaminase domains. These data suggest an alternative model for binding of APOBEC3 proteins to the Vif-E3 Ub ligase complex and diminish enthusiasm for the amenability of APOBEC3 Ub acceptor sites to therapeutic intervention.
Collapse
Affiliation(s)
- John S. Albin
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455
| | - John S. Anderson
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Jeffrey R. Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- J. David Gladstone Institutes, San Francisco, CA 94158
| | - Elena Harjes
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
| | - Hiroshi Matsuo
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- J. David Gladstone Institutes, San Francisco, CA 94158
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
17
|
Harjes E, Kitamura A, Zhao W, Morais MC, Jardine PJ, Grimes S, Matsuo H. Structure of the RNA claw of the DNA packaging motor of bacteriophage Φ29. Nucleic Acids Res 2012; 40:9953-63. [PMID: 22879380 PMCID: PMC3479190 DOI: 10.1093/nar/gks724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage ϕ29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base bulge (18-CCA-20) in the pRNA A-helix was shown to abolish packaging activity. Here, we solved the structure of this crucial bulge by nuclear magnetic resonance (NMR) using a 27mer RNA fragment containing the bulge (27b). The bulge actually involves five nucleotides (17-UCCA-20 and A100), as U17 and A100 are not base paired as predicted. Mutational analysis showed these newly identified bulge residues are important for DNA packaging. The bulge introduces a 33–35° bend in the helical axis, and inter-helical motion around this bend appears to be restricted. A model of the functional 120b pRNA was generated using a 27b NMR structure and the crystal structure of the 66b prohead-binding domain. Fitting this model into a cryo-EM map generated a pentameric pRNA structure; five helices projecting from the pRNA ring resemble an RNA claw. Biochemical analysis suggested that this shape is important for coordinated motor action required for DNA translocation.
Collapse
Affiliation(s)
- Elena Harjes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | | | | | | |
Collapse
|
18
|
Shindo K, Li M, Gross PJ, Brown WL, Harjes E, Lu Y, Matsuo H, Harris RS. A Comparison of Two Single-Stranded DNA Binding Models by Mutational Analysis of APOBEC3G. Biology (Basel) 2012; 1:260-76. [PMID: 24832226 PMCID: PMC4009770 DOI: 10.3390/biology1020260] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/01/2012] [Accepted: 07/14/2012] [Indexed: 12/21/2022]
Abstract
APOBEC3G is the best known of several DNA cytosine deaminases that function to inhibit the replication of parasitic genetic elements including the lentivirus HIV. Several high-resolution structures of the APOBEC3G catalytic domain have been generated, but none reveal how this enzyme binds to substrate single-stranded DNA. Here, we constructed a panel of APOBEC3G amino acid substitution mutants and performed a series of biochemical, genetic, and structural assays to distinguish between “Brim” and “Kink” models for single-strand DNA binding. Each model predicts distinct sets of interactions between surface arginines and negatively charged phosphates in the DNA backbone. Concordant with both models, changing the conserved arginine at position 313 to glutamate abolished both catalytic and restriction activities. In support of the Brim model, arginine to glutamate substitutions at positions 213, 215, and 320 also compromised these APOBEC3G activities. Arginine to glutamate substitutions at Kink model residues 374 and 376 had smaller effects. These observations were supported by A3G catalytic domain-ssDNA chemical shift perturbation experiments. The overall data set is most consistent with the Brim model for single-stranded DNA binding by APOBEC3G.
Collapse
Affiliation(s)
- Keisuke Shindo
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Ming Li
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Phillip J Gross
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Elena Harjes
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Yongjian Lu
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Hiroshi Matsuo
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
19
|
Dang Y, Abudu A, Son S, Harjes E, Spearman P, Matsuo H, Zheng YH. Identification of a single amino acid required for APOBEC3 antiretroviral cytidine deaminase activity. J Virol 2011; 85:5691-5. [PMID: 21430060 PMCID: PMC3094948 DOI: 10.1128/jvi.00243-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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: 02/02/2011] [Accepted: 03/10/2011] [Indexed: 11/20/2022] Open
Abstract
During studies of APOBEC3 (A3) anti-human immunodeficiency virus type 1 (anti-HIV-1) mechanisms, we identified a single cysteine at position 320 (C320) that disrupts A3DE activity. This residue is located in the recently identified DNA binding domain in A3G. Replacing C320 with a corresponding tyrosine from A3F (Y307) increased A3DE antiviral activity more than 20-fold. Conversely, replacing A3F Y307 with a cysteine or inserting a similar cysteine into A3B or A3G disrupted the anti-HIV activity of A3. Further investigation uncovered that C320 significantly reduces A3DE catalytic activity.
Collapse
Affiliation(s)
- Ying Dang
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Aierken Abudu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - SungMo Son
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Elena Harjes
- Department of Biochemistry, Molecular Biology & Biophysics, and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota
| | - Paul Spearman
- Departments of Pediatrics & Microbiology & Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Hiroshi Matsuo
- Department of Biochemistry, Molecular Biology & Biophysics, and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota
| | - Yong-Hui Zheng
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| |
Collapse
|
20
|
Albin JS, LaRue RS, Weaver JA, Brown WL, Shindo K, Harjes E, Matsuo H, Harris RS. A single amino acid in human APOBEC3F alters susceptibility to HIV-1 Vif. J Biol Chem 2010; 285:40785-92. [PMID: 20971849 PMCID: PMC3003379 DOI: 10.1074/jbc.m110.173161] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [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: 08/06/2010] [Revised: 10/21/2010] [Indexed: 11/06/2022] Open
Abstract
Human APOBEC3F (huA3F) potently restricts the infectivity of HIV-1 in the absence of the viral accessory protein virion infectivity factor (Vif). Vif functions to preserve viral infectivity by triggering the degradation of huA3F but not rhesus macaque A3F (rhA3F). Here, we use a combination of deletions, chimeras, and systematic mutagenesis between huA3F and rhA3F to identify Glu(324) as a critical determinant of huA3F susceptibility to HIV-1 Vif-mediated degradation. A structural model of the C-terminal deaminase domain of huA3F indicates that Glu(324) is a surface residue within the α4 helix adjacent to residues corresponding to other known Vif susceptibility determinants in APOBEC3G and APOBEC3H. This structural clustering suggests that Vif may bind a conserved surface present in multiple APOBEC3 proteins.
Collapse
Affiliation(s)
- John S. Albin
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Rebecca S. LaRue
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jessalyn A. Weaver
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - William L. Brown
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Keisuke Shindo
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Elena Harjes
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
| | - Hiroshi Matsuo
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
| | - Reuben S. Harris
- From the Department of Biochemistry, Molecular Biology, and Biophysics
- Institute for Molecular Virology, and
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| |
Collapse
|
21
|
Shandilya SMD, Nalam MNL, Nalivaika EA, Gross PJ, Valesano JC, Shindo K, Li M, Munson M, Royer WE, Harjes E, Kono T, Matsuo H, Harris RS, Somasundaran M, Schiffer CA. Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. Structure 2010; 18:28-38. [PMID: 20152150 DOI: 10.1016/j.str.2009.10.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Revised: 10/01/2009] [Accepted: 10/21/2009] [Indexed: 01/09/2023]
Abstract
APOBEC3G is a DNA cytidine deaminase that has antiviral activity against HIV-1 and other pathogenic viruses. In this study the crystal structure of the catalytically active C-terminal domain was determined to 2.25 A. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second beta strand and a lengthening of the second alpha helix. Oligomerization is postulated to be critical for the function of APOBEC3G. In this structure, four extensive intermolecular interfaces are observed, suggesting potential models for APOBEC3G oligomerization. The structural and functional significance of these interfaces was probed by solution NMR and disruptive variants were designed and tested for DNA deaminase and anti-HIV activities. The variant designed to disrupt the most extensive interface lost both activities. NMR solution data provides evidence that another interface, which coordinates a novel zinc site, also exists. Thus, the observed crystallographic interfaces of APOBEC3G may be important for both oligomerization and function.
Collapse
Affiliation(s)
- Shivender M D Shandilya
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Harjes E, Gross PJ, Chen KM, Lu Y, Shindo K, Nowarski R, Gross JD, Kotler M, Harris RS, Matsuo H. An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model. J Mol Biol 2009; 389:819-32. [PMID: 19389408 DOI: 10.1016/j.jmb.2009.04.031] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 04/15/2009] [Accepted: 04/16/2009] [Indexed: 01/27/2023]
Abstract
Human APOBEC3G (A3G) belongs to a family of polynucleotide cytidine deaminases. This family includes APOBEC1 and AID, which edit APOB mRNA and antibody gene DNA, respectively. A3G deaminates cytidines to uridines in single-strand DNA and inhibits the replication of human immunodeficiency virus-1, other retroviruses, and retrotransposons. Although the mechanism of A3G-catalyzed DNA deamination has been investigated genetically and biochemically, atomic details are just starting to emerge. Here, we compare the DNA cytidine deaminase activities and NMR structures of two A3G catalytic domain constructs. The longer A3G191-384 protein is considerably more active than the shorter A3G198-384 variant. The longer structure has an alpha1-helix (residues 201-206) that was not apparent in the shorter protein, and it contributes to catalytic activity through interactions with hydrophobic core structures (beta1, beta3, alpha5, and alpha6). Both A3G catalytic domain solution structures have a discontinuous beta2 region that is clearly different from the continuous beta2 strand of another family member, APOBEC2. In addition, the longer A3G191-384 structure revealed part of the N-terminal pseudo-catalytic domain, including the interdomain linker and some of the last alpha-helix. These structured residues (residues 191-196) enabled a novel full-length A3G model by providing physical overlap between the N-terminal pseudo-catalytic domain and the new C-terminal catalytic domain structure. Contrary to predictions, this structurally constrained model suggested that the two domains are tethered by structured residues and that the N- and C-terminal beta2 regions are too distant from each other to participate in this interaction.
Collapse
Affiliation(s)
- Elena Harjes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Harjes E, Harjes S, Wohlgemuth S, Müller KH, Krieger E, Herrmann C, Bayer P. GTP-Ras disrupts the intramolecular complex of C1 and RA domains of Nore1. Structure 2006; 14:881-8. [PMID: 16698549 DOI: 10.1016/j.str.2006.03.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [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: 03/01/2005] [Revised: 02/27/2006] [Accepted: 03/03/2006] [Indexed: 11/21/2022]
Abstract
The novel Ras effector mNore1, capable of inducing apoptosis, is a multidomain protein. It comprises a C1 domain homologous to PKC and an RA domain similar to the Ras effectors AF-6 and RalGDS. Here, we determine the affinity of these two domains to the active forms of Ras and Rap1 using isothermal calorimetric titration. The interaction of Ras/Rap1-GTP with the RA domain of mNore1 is weakened significantly by direct binding of the C1 domain to the RA domain. In order to analyze this observation in atomic detail, we solved the C1 solution structure by NMR. By determining chemical shifts and relaxation rates, we can show an intramolecular complex of C1-RA. GTP-Ras titration and binding to RA disrupts this complex and displaces the C1 domain. Once the C1 domain tumbles freely in solution, a lipid binding interface becomes accessible. Furthermore, we provide evidence of phosphatidylinositol 3-phosphate binding of the free C1 domain.
Collapse
Affiliation(s)
- Elena Harjes
- Molecular and Structural Biophysics, Max-Planck Institute of Molecular Physiology, Otto-Hahn Strasse 11, D-44227 Dortmund, Germany
| | | | | | | | | | | | | |
Collapse
|