The effect of N- or C-terminal alterations of the connector of bacteriophage phi29 DNA packaging motor on procapsid assembly, pRNA binding, and DNA packaging

Ying Cai1, Feng Xiao1, Peixuan Guo1
1Department of Biomedical Engineering, The Vontz Center for Molecular Studies, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA

Tài liệu tham khảo

Guo, 1986, A defined system for in vitro packaging of DNA-gp3 of the Bacillus subtilis bacteriophage ϕ29, Proc Natl Acad Sci U S A, 83, 3505, 10.1073/pnas.83.10.3505 Hohn, 1974, Phage lamda DNA packaging in vitro, J Supramol Struct, 2, 302, 10.1002/jss.400020220 Black, 1981, In vitro packaging of bacteriophage T4 DNA, Virology, 113, 336, 10.1016/0042-6822(81)90160-4 Strobel, 1984, In vitro packaging of mature phage DNA by Salmonella phage P22, Virology, 133, 158, 10.1016/0042-6822(84)90434-3 Guo, 1987, Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage ϕ29, J Mol Biol, 197, 229, 10.1016/0022-2836(87)90121-5 Rao, 1988, Cloning, overexpression and purification of the terminase proteins gp16 and gp17 of bacteriophage T4: construction of a defined in vitro DNA packaging system using purified terminase proteins, J Mol Biol, 200, 475, 10.1016/0022-2836(88)90537-2 Oliveira, 2005, A defined in vitro system for DNA packaging by the bacteriophage SPP1: insights into the headful packaging mechanism, J Mol Biol, 353, 529, 10.1016/j.jmb.2005.08.063 Becker, 1988, Prediction of an ATP reactive center in the small subunit, gpNul of phage λ terminase enzyme, J Mol Biol, 199, 219, 10.1016/0022-2836(88)90391-9 Catalano, 1995, Virus DNA packaging: the strategy used by phage λ, Mol Microbiol, 16, 1075, 10.1111/j.1365-2958.1995.tb02333.x Yamada, 1986, Cloning and sequencing of the genetic right end of bacteriophage T3 DNA, Virology, 151, 350, 10.1016/0042-6822(86)90055-3 Dunn, 1983, Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements, J Mol Biol, 166, 477, 10.1016/S0022-2836(83)80282-4 Casjens, 1987, Initiation of bacteriophage P22 DNA packaging series: analysis of a mutant which alters the DNA target specificity of the packaging apparatus, J Mol Biol, 194, 411, 10.1016/0022-2836(87)90671-1 Prasad, 1993, Three-dimensional transformation of capsids associated with genome packaging in a bacterial virus, J Mol Biol, 231, 65, 10.1006/jmbi.1993.1257 Galisteo, 1993, Conformational transformations in the protein lattice of phage P22 procapsids, Biophys J, 65, 227, 10.1016/S0006-3495(93)81073-7 Skorupski, 1992, Bacteriophage P1 genes involved in the recognition and cleavage of the phage packaging site (pac), J Mol Biol, 223, 977, 10.1016/0022-2836(92)90256-J Pfister, 1998, Molecular analysis of Methanobacterium phage ψM2, Mol Microbiol, 30, 233, 10.1046/j.1365-2958.1998.01073.x Desiere, 1998, Evolution of Streptococcus thermophilus bacteriophage genomes by modular exchanges followed by point mutations and small deletions and insertions, Virology, 241, 345, 10.1006/viro.1997.8959 Newcomb, 2001, The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid, J Virol, 75, 10923, 10.1128/JVI.75.22.10923-10932.2001 Yu, 1998, Generic analysis of the UL15 gene locus for the putative terminase of herpes simplex virus type 1, Virology, 243, 32, 10.1006/viro.1998.9041 Salmon, 1998, Herpes simplex virus DNA cleavage and packaging: association of multiple forms of U(L)15-encoded proteins with B capsids requires at least the U(L)6, U(L)17, and U(L)28 genes, J Virol, 72, 3045, 10.1128/JVI.72.4.3045-3050.1998 Deng, 2007, Direct visualization of the putative portal in the Kaposi's sarcoma-associated herpesvirus capsid by cryoelectron tomography, J Virol, 81, 3640, 10.1128/JVI.02254-06 Scheffczik, 2002, The terminase subunits pUL56 and pUL89 of human cytomegalovirus are DNA-metabolizing proteins with toroidal structure, Nucleic Acids Res, 30, 1695, 10.1093/nar/30.7.1695 Schmid, 1997, Bipartite structure and functional independence of adenovirus type 5 packaging elements, J Virol, 71, 3375, 10.1128/JVI.71.5.3375-3384.1997 Bett, 1993, Packaging capacity and stability of human adenovirus type 5 vectors, J Virol, 67, 5911, 10.1128/JVI.67.10.5911-5921.1993 Zhang, 2001, Role for the adenovirus IVa2 protein in packaging of viral DNA, J Virol, 75, 10446, 10.1128/JVI.75.21.10446-10454.2001 Koonin, 1993, Gene A32 product of vaccinia virus may be an ATPase involved in viral DNA packaging as indicated by sequence comparisons with other putative viral ATPases, Virus Genes, 7, 89, 10.1007/BF01702351 Cassetti, 1998, DNA package mutant: repression of the vaccinia virus A32 gene results in noninfectious, DNA-deficient, spherical, enveloped particles, J Virol, 72, 5769, 10.1128/JVI.72.7.5769-5780.1998 Graeble, 1992, Cis and trans requirements for the selective packaging of adenovirus type 5 DNA, J Virol, 66, 723, 10.1128/JVI.66.2.723-731.1992 Higgins, 1995, Interaction of terminase, the DNA packaging enzyme of phage λ, with its cos DNA substrate, J Mol Biol, 252, 31, 10.1006/jmbi.1995.0473 Hang, 2001, The functional asymmetry of cosN, the nicking site for bacteriophage λDNA packaging, is dependent on the terminase binding site, cosB, Biochemistry, 40, 13370, 10.1021/bi011126r Guo, 2005, Bacterial virus phi29 DNA-packaging motor and its potential applications in gene therapy and nanotechnology, Methods Mol Biol, 300, 285 Hwang, 1997, A defined system for in vitro λ-DNA packaging, Virology, 211, 367, 10.1006/viro.1995.1419 Zhang, 1995, Inhibition of phage ϕ29 assembly by antisense oligonucleotides targeting viral pRNA essential for DNA packaging, Virology, 211, 568, 10.1006/viro.1995.1439 Trottier, 1996, Complete inhibition of virion assembly in vivo with mutant pRNA essential for phage ϕ29 DNA packaging, J Virol, 70, 55, 10.1128/JVI.70.1.55-61.1996 Bogner, 2002, Human cytomegalovirus terminase as a target for antiviral chemotherapy, Rev Med Virol, 12, 115, 10.1002/rmv.344 Visalli, 2003, DNA encapsidation as a target for anti-herpesvirus drug therapy, Antiviral Res, 59, 73, 10.1016/S0166-3542(03)00108-6 Shu, 2003, Construction of phi29 DNA-packaging RNA (pRNA) monomers, dimers and trimers with variable sizes and shapes as potential parts for nano-devices, J Nanosci Nanotechnol, 3, 295, 10.1166/jnn.2003.160 Hess, 2004, Powering nanodevices with biomolecular motors, Chemistry, 10, 2110, 10.1002/chem.200305712 Schmidt, 2004, Bionanomechanical systems, Annu Rev Mater Res, 34, 315, 10.1146/annurev.matsci.34.040203.115827 Shu, 2004, Bottom-up assembly of RNA arrays and superstructures as potential parts in nanotechnology, Nano Lett, 4, 1717, 10.1021/nl0494497 Guo, 2005, RNA nanotechnology: engineering, assembly and applications in detection, gene delivery and therapy, J Nanosci Nanotechnol, 5, 1964, 10.1166/jnn.2005.446 Meifer, 2001, Phi29 family of phages, Microbiol Mol Biol Rev, 65, 261, 10.1128/MMBR.65.2.261-287.2001 Lee, 1995, In vitro assembly of infectious virions of ds-DNA phage ϕ29 from cloned gene products and synthetic nucleic acids, J Virol, 69, 5018, 10.1128/JVI.69.8.5018-5023.1995 Guo, 1987, A small viral RNA is required for in vitro packaging of bacteriophage ϕ29 DNA, Science, 236, 690, 10.1126/science.3107124 Shu, 2007, Counting of six pRNAs of phi29 DNA-packaging motor with customized single molecule dual-view system, EMBO J, 26, 527, 10.1038/sj.emboj.7601506 Guasch, 2002, Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle, J Mol Biol, 315, 663, 10.1006/jmbi.2001.5278 Orlova, 2003, Structure of a viral DNA gatekeeper at 10 Å resolution by cryo-electron microscopy, EMBO J, 22, 1255, 10.1093/emboj/cdg123 Badasso, 2000, Purification, crystallization and initial X-ray analysis of the head-tail connector of bacteriophage phi29, Acta Crystallogr D, 56, 1187, 10.1107/S0907444900009239 Doan, 2007, The gpQ portal protein of bacteriophage P2 forms dodecameric connectors in crystals, J Struct Biol, 157, 432, 10.1016/j.jsb.2006.08.009 Carazo, 1986, Bacteriophage T3 gene 8 product oligomer structure, J Ultrastruct Mol Struct Res, 94, 105, 10.1016/0889-1605(86)90056-X Trus, 2004, Structure and polymorphism of the UL6 portal protein of herpes simplex virus type 1, J Virol, 78, 12668, 10.1128/JVI.78.22.12668-12671.2004 Cerritelli, 1996, Purification and characterization of T7 head-tail connectors expressed from the cloned gene, J Mol Biol, 285, 299, 10.1006/jmbi.1996.0251 Kochan, 1984, Bacteriophage λ preconnectors: purification and structure, J Mol Biol, 174, 433, 10.1016/0022-2836(84)90330-9 Agirrezabala, 2005, Structure of the connector of bacteriophage T7 at 8 Å resolution: structural homologies of a basic component of a DNA translocating machinery, J Mol Biol, 347, 895, 10.1016/j.jmb.2005.02.005 Cingolani, 2002, Preliminary crystallographic analysis of the bacteriophage P22 portal protein, J Struct Biol, 139, 46, 10.1016/S1047-8477(02)00512-9 Kato, 1997, Isolation of a gp20-complex and its role in in vitro assembly of both prohead and core of bacteriophage T4, Virology, 227, 400, 10.1006/viro.1996.8322 Cerritelli, 1996, Assembly of T7 capsids from independently expressed and purified head protein and scaffolding protein, J Mol Biol, 258, 286, 10.1006/jmbi.1996.0250 Guo, 1991, Regulation of the phage ϕ29 prohead shape and size by the portal vertex, Virology, 183, 366, 10.1016/0042-6822(91)90149-6 Fu, 2007, Molecular dissection of ϕ29 scaffolding protein function in an in vitro assembly system, J Mol Biol, 366, 1161, 10.1016/j.jmb.2006.11.091 Simpson, 2001, Structure determination of the head-tail connector of bacteriophage phi29, Acta Crystallogr D Biol Crystallogr, 57, 1260, 10.1107/S0907444901010435 Xiao, 2005, Binding of pRNA to the N-terminal 14 amino acids of connector protein of bacterial phage ϕ29, Nucleic Acids Res, 33, 2640, 10.1093/nar/gki554 Sun, 2006, Controlling bacteriophage phi29 DNA-packaging motor by addition or discharge of a peptide at N-terminus of connector protein that interacts with pRNA, Nucleic Acids Res, 34, 5482, 10.1093/nar/gkl701 Vives, 1997, A truncated HIV-1 Tat protein basic domain rapidly translocates through the plasma membrane and accumulates in the cell nucleus, J Biol Chem, 20, 16010, 10.1074/jbc.272.25.16010 Wang, 1996, Protein orientation in the Tat-TAR complex determined by psoralen photocross-linking, J Biol Chem, 19, 16995, 10.1074/jbc.271.29.16995 Wender, 2000, The design, synthesis, and evaluation of molecules that enable or enhance cellular uptake: peptoid molecular transporters, Proc Natl Acad Sci U S A, 97, 13003, 10.1073/pnas.97.24.13003 Atz, 2007, Alanine scanning and Fe-BABE probing of the bacteriophage ϕ29 prohead RNA-connector interaction, J Mol Biol, 369, 239, 10.1016/j.jmb.2007.03.033 Robinson, 2006, Affinity of molecular interactions in the bacteriophage ϕ29 DNA packaging motor, Nucleic Acids Res, 34, 2698, 10.1093/nar/gkl318 Chen, 2000, A dimer as a building block in assembling RNA. A hexamer that gears bacterial virus ϕ29 DNA-translocating machinery, J Biol Chem, 275, 17510, 10.1074/jbc.M909662199 Chen, 1999, Sequence requirement for hand-in-hand interaction in formation of pRNA dimers and hexamers to gear ϕ29 DNA translocation motor, RNA, 5, 805, 10.1017/S1355838299990350 Ha, 2002, Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase, Nature, 419, 638, 10.1038/nature01083