Our laboratory uses structural biology techniques such as X-ray crystallography and cryo-electron microscopy to understand various important biological processes, especially protein-DNA and protein-RNA interactions relevant to virology and cancer. Topics of interest include how retroviruses (such as HIV and HTLV) integrate the viral genome into host chromosomes, how the unique proofreading machinery of coronaviruses (SARS-CoV-2 in particular) can be inhibited to block virus replication, and how the antiviral human APOBEC DNA cytosine deaminase enzymes introduce mutations in cancer genomes. We are also interested in understanding and engineering cytosine deaminases and other DNA-modifying enzymes for genome-editing applications.
DNA is the genetic material for all organisms, and thus its integrity is maintained by extensive damage surveillance and repair mechanisms. On the other hand, DNA strands are constantly cut and rearranged in programmed fashions during numerous biological processes, including the generation of genetic and immunological diversities, resolution of topological problems in chromosomes, and the genome maintenance/repair pathways themselves. In addition, some viruses, such as HIV that causes AIDS, achieve infection by inserting viral DNA into the host's genomic DNA.
We are studying various DNA rearrangement systems relevant to human health including:
(1) Resolution of a concatenated DNA-replication intermediate into linear chromosomes in Borrelia burgdorferi , the Lyme disease spirochete
(2) Retroviral integration reaction in which the integrase protein encoded by HIV-1 and related retroviruses inserts viral DNA into the host's genome
We use x-ray crystallography as our primary tool to determine three-dimensional structures of the protein machineries that catalyze DNA strand cutting and rejoining reactions. The structural information helps us address mechanistic questions, namely how particular DNA sequences are recognized to initiate a DNA rearrangement reaction, how separate pieces of DNA are brought together and arranged for coordinated chemical reactions, and how reaction directionality is regulated. Better understanding of these aspects of the DNA rearrangement processes may ultimately aid in the design of new antibiotics and anti-viral drugs as well as the development of a sequence-specific gene delivery tool for safer gene therapy.
- Bohl, T.E., Shi, K., Lee, J.K., Aihara, H. (2018) Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Nat. Commun. 9:377 [PubMed]
- Shaban, N.M., Shi, K., Lauer, K.V., Carpenter, M.A., Richards, C.M., Salamango, D., Wang, J., Lopresti, M.W., Banerjee, S., Levin-Klein, R., Brown, W.L., Aihara, H., Harris, R.S. (2018) The antiviral and cancer genomic DNA deaminase APOBEC3H is regulated by an RNA-mediated dimerization mechanism. Mol. Cell 69, 75–86.e9 [PubMed]
- Shi, K., Demir, Ö., Carpenter, M.A., Wagner, J., Kurahashi, K., Harris, R.S., Amaro, R.E., Aihara, H. (2017) Conformational switch regulates the DNA cytosine deaminase activity of human APOBEC3B. Sci Rep. 7:17415 [PubMed]
- Bertram, J.H., Mulliner, K.M., Shi, K., Plunkett, M.H., Nixon, P., Serratore, N.A., Douglas, C.J., Aihara, H., Barney, B.M. (2017) Five fatty aldehyde dehydrogenase enzymes from Marinobacter and Acinetobacter spp. and structural insights into the aldehyde binding pocket. Appl. Environ. Microbiol. 83:e00018-17 [PubMed]
- Pandey, K.K., Bera, S., Shi, K., Aihara, H., Grandgenett, D.P. (2017) A C-terminal "tail" region in the Rous sarcoma virus integrase provides high plasticity of functional integrase oligomerization during intasome assembly. J. Biol. Chem. 292, 5018-5030. [PubMed]
- Shi, K.†, Carpenter, M.A.†, Banerjee, S. Shaban, N.M., Kurahashi, K., Salamango, D.J., McCann, J.L., Starrett, G.J., Duffy, J.V., Demir, Ö., Amaro, R.E., Harki, D.A., Harris, R.S.*, Aihara, H.* (2017) Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. 24,131–139 (†co-first authors, *co-corresponding authors) [PubMed]
- Rao, T., Gao, R., Takada, S., Al Abo, M., Chen, X., Walters, K.J., Pommier, Y., Aihara, H. (2016) Novel TDP2-ubiquitin interactions and their importance for the repair of topoisomerase II-mediated DNA damage. Nucleic Acids Res. 44, 10201-10215. [PubMed]
- Chen, X., Randles, L., Shi, K., Tarasov, S.G., Aihara, H., Walters, K.J. (2016) Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 reveal distinct binding mechanisms between substrate receptors and shuttle factors of the proteasome. Structure 24, 1257–1270. [PubMed]
- Marchand, C., Abdelmalak, M., Kankanala, J., Huang, S.Y., Kiselev, E., Fesen, K., Kurahashi, K., Sasanuma, H., Takeda, S., Aihara, H., Wang, Z., Pommier, Y. (2016) Deazaflavin inhibitors of Tyrosyl-DNA Phosphodiesterase 2 (TDP2) specific for the human enzyme and active against cellular TDP2. ACS Chem Biol. 11, 1925-1933. [PubMed]
- Shaban, N.M., Shi, K., Li, M., Aihara, H., Harris, R.S. (2016) 1.92 angstrom zinc-free APOBEC3F catalytic domain crystal structure. J Mol Biol.428, 2307-2316. [PubMed]
- Kankanala, J., Marchand, C., Abdelmalak, M., Aihara, H., Pommier, Y., Wang, Z. (2016) Isoquinoline-1,3-diones as selective inhibitors of Tyrosyl DNA Phosphodiesterase II (TDP2). J Med. Chem. 59, 2734-2746. [PubMed]
- Yin, Z.*, Shi, K.*, Banerjee, S., Pandey, K.K., Bera, S., Grandgenett, D.P., Aihara, H. (2016) Crystal structure of the Rous sarcoma virus intasome. Nature 530, 362-366 (*co-first authors) [PubMed]
- Zhang, Y., Lee, J.K., Toso, E.A., Lee, J.S., Choi, S.H., Slattery, M., Aihara, H., Kyba, M. (2016) DNA-binding sequence specificity of DUX4. Skelet Muscle 6:8 [PubMed]
- Shi K., Carpenter M.A., Kurahashi K., Harris R.S. *, Aihara H. * (2015) Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. J. Biol. Chem. 290, 28120-28130. ( *co-corresponding authors) [PubMed]
- Grandgenett D.P., Pandey K.K., Bera S., Aihara H. (2015) Multifunctional facets of retrovirus integrase. World J. Biol. Chem. 6, 83-94. [PubMed]
- Murphy, M.W.†, Lee, J.K.†, Rojo, S.†, Gearhart, M.D.†, Kurahashi, K., Banerjee, S., Loeuille G.A., Bashamboo, A., McElreavey, K., Zarkower, D., Aihara, H.*, Bardwell, V.J.* (2015) An ancient protein-DNA interaction underlying metazoan sex determination. Nat. Struct. Mol. Biol. 22, 442-451 (†co-first authors, *co-corresponding authors) [PubMed]
- Pandey, KK, Bera, S, Korolev, S, Campbell, M, Yin, Z, Aihara, H, Grandgenett, DP(2014) Rous sarcoma virus synaptic complex capable of concerted integration is kinetically trapped by human immunodeficiency virus integrase strand transfer inhibitors. J. Biol. Chem. 289, 19648-19658. [PubMed]
- Cho, S, Shi, K, Seffernick, JL, Dodge, AG, Wackett, LP, Aihara H (2014) Cyanuric Acid Hydrolase from Azorhizobium caulinodans ORS 571: Crystal Structure and Insights into a New Class of Ser-Lys Dyad Proteins. PLoS One 9(6): e99349. [PubMed]
- Cho S., Shi K., Wackett L.P., Aihara H. (2013) Crystallization and preliminary X-ray diffraction studies of cyanuric acid hydrolase from Azorhizobium caulinodans. Acta Cryst. F69, 880-883 [PubMed]
- Shi K, Pandey KK, Bera S, Vora AC, Grandgenett DP, Aihara H (2013) A Possible Role for the Asymmetric C-terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding. PLoS One 8(2): e56892.[PubMed]
- Shi K, Huang WM, Aihara H (2013) An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation. PLoS Biol 11(1): e1001472. [PubMed]
- Chen L, Shi K, Yin Z, Aihara H (2013) Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution. Nucleic Acids Res. 41: 648-656. [PubMed]
- Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H (2012) Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nat Struct Mol Biol. 19: 1372-1377. [PubMed]
- Huang WM, DaGloria J, Fox H, Ruan Q, Tillou J, Shi K, Aihara H, Aron J, Casjens S (2012) Linear chromosome-generating system of Agrobacterium tumefaciens C58: protelomerase generates and protects hairpin ends. J Biol Chem. 287:25551-25563. [PubMed]
- Aihara, H., Huang, W.M. and Ellenberger, T. (2007) An interlocked dimer of the Protelomerase TelK Distorts DNA Structure for the Formation of Hairpin Telemeres. Mol Cell. 27:901-913 [PubMed].
- Biswas, T., Aihara, H., Radman-Livaja, M., Filman, D., Landy, A., and Ellenberger, T. (2005). A structural basis for allosteric control of DNA recombination by lambda integrase. Nature 435, 1059-1066. [PubMed]
- Aihara, H., Kwon, H.J., Nunes-Düby, S.E., Landy, A., and Ellenberger, T. (2003). A Conformational Switch Controls the DNA Cleavage Activity of Integrase. Mol. Cell 12, 187-198. [PubMed]