The DNA-packaging nanomotor of tailed bacteriophages (original) (raw)
Bergh, O., Borsheim, K. Y., Bratbak, G. & Heldal, M. High abundance of viruses found in aquatic environments. Nature340, 467–468 (1989). CASPubMed Google Scholar
Boyd, E. F., Davis, B. M. & Hochhut, B. Bacteriophage–bacteriophage interactions in the evolution of pathogenic bacteria. Trends Microbiol.9, 137–144 (2001). ArticleCASPubMed Google Scholar
Casjens, S. & Hendrix, R. in The Bacterial Chromosome (ed. Higgins, N. P.) 39–52 (American Society for Microbiology Press, Washingtion DC, 2005). Book Google Scholar
Cheetham, B. F. & Katz, M. E. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol. Microbiol.18, 201–208 (1995). ArticleCASPubMed Google Scholar
Denou, E. et al. T4 phages against Escherichia coli diarrhea: potential and problems. Virology388, 21–30 (2009). ArticleCASPubMed Google Scholar
Luftig, R. B., Wood, W. B. & Okinaka, R. Bacteriophage T4 head morphogenesis. On the nature of gene 49-defective heads and their role as intermediates. J. Mol. Biol.57, 555–573 (1971). ArticleCASPubMed Google Scholar
Kaiser, D., Syvanen, M. & Masuda, T. DNA packaging steps in bacteriophage lambda head assembly. J. Mol. Biol.91, 175–186 (1975). ArticleCASPubMed Google Scholar
Catalano, C. (ed.) Viral Genome Packaging Machines: Genetics, Structure, and Mechanism (Landes Bioscience, Georgetown, Texas, 2005). Book Google Scholar
Casjens, S. & Hendrix, R. in The Bacteriophages (ed. Calendar, R.) 15–91 (Plenum, New York, 1988). Book Google Scholar
Earnshaw, W. & Casjens, S. DNA packaging by the double-stranded DNA bacteriophages. Cell21, 319–331 (1980). ArticleCASPubMed Google Scholar
Black, L. W. DNA packaging in dsDNA bacteriophages. Annu. Rev. Microbiol.43, 267–292 (1989). ArticleCASPubMed Google Scholar
Maluf, N. K. & Feiss, M. Virus DNA translocation: progress towards a first ascent of Mount Pretty Difficult. Mol. Microbiol.61, 1–4 (2006). ArticleCASPubMed Google Scholar
Rao, V. B. & Feiss, M. The bacteriophage DNA packaging motor. Annu. Rev. Genet.42, 647–681 (2008). ArticleCASPubMed Google Scholar
Jeembaeva, M., Jonsson, B., Castelnovo, M. & Evilevitch, A. DNA heats up: energetics of genome ejection from phage revealed by isothermal titration calorimetry. J. Mol. Biol.395, 1079–1087 (2010). ArticleCASPubMed Google Scholar
Panja, D. & Molineux, I. J. Dynamics of bacteriophage genome ejection in vitro and in vivo. Phys. Biol.7, 045006 (2010). ArticlePubMed Google Scholar
Kindt, J., Tzlil, S., Ben-Shaul, A. & Gelbart, W. M. DNA packaging and ejection forces in bacteriophage. Proc. Natl Acad. Sci. USA98, 13671–13674 (2001). ArticleCASPubMedPubMed Central Google Scholar
Riemer, S. C. & Bloomfield, V. A. Packaging of DNA in bacteriophage heads: some considerations on energetics. Biopolymers17, 785–794 (1978). ArticleCASPubMed Google Scholar
Agirrezabala, X. et al. Maturation of phage T7 involves structural modification of both shell and inner core components. EMBO J.24, 3820–3829 (2005). ArticleCASPubMedPubMed Central Google Scholar
Choi, K. H. et al. Insight into DNA and protein transport in double-stranded DNA viruses: the structure of bacteriophage N4. J. Mol. Biol.378, 726–736 (2008). ArticleCASPubMedPubMed Central Google Scholar
Jiang, W. et al. Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature439, 612–616 (2006). ArticleCASPubMedPubMed Central Google Scholar
Lander, G. C. et al. The structure of an infectious P22 virion shows the signal for headful DNA packaging. Science312, 1791–1795 (2006). ArticleCASPubMed Google Scholar
Lander, G. C. et al. Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM. Structure16, 1399–1406 (2008). This report describes the subnanometre, cryo-electron microscopy-derived three-dimensional reconstruction of phage λ capsids, with a focus on the bacteriophage shell-strengthening protein. ArticleCASPubMedPubMed Central Google Scholar
Leiman, P. G. et al. The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. J. Mol. Biol.371, 836–849 (2007). ArticleCASPubMed Google Scholar
Chang, J., Weigele, P., King, J., Chiu, W. & Jiang, W. Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure14, 1073–1082 (2006). ArticleCASPubMed Google Scholar
Duda, R. L., Hendrix, R. W., Huang, W. M. & Conway, J. F. Shared architecture of bacteriophage SPO1 and herpesvirus capsids. Curr. Biol.16, R11–R13 (2006). ArticleCASPubMed Google Scholar
Liu, X. et al. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nature Struct. Mol. Biol.17, 830–836 (2010). ArticleCAS Google Scholar
Effantin, G., Boulanger, P., Neumann, E., Letellier, L. & Conway, J. F. Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships. J. Mol. Biol.361, 993–1002 (2006). ArticleCASPubMed Google Scholar
Dai, W. et al. Three-dimensional structure of tropism-switching Bordetella bacteriophage. Proc. Natl Acad. Sci. USA107, 4347–4352 (2010). ArticleCASPubMedPubMed Central Google Scholar
Cerritelli, M. E. et al. Encapsidated conformation of bacteriophage T7 DNA. Cell91, 271–280 (1997). ArticleCASPubMed Google Scholar
Leforestier, A. & Livolant, F. Structure of toroidal DNA collapsed inside the phage capsid. Proc. Natl Acad. Sci. USA106, 9157–9162 (2009). ArticleCASPubMedPubMed Central Google Scholar
Agirrezabala, X. et al. Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery. J. Mol. Biol.347, 895–902 (2005). ArticleCASPubMed Google Scholar
Cerritelli, M. E. et al. A second symmetry mismatch at the portal vertex of bacteriophage T7, 8-fold symmetry in the procapsid core. J. Mol. Biol.327, 1–6 (2003). ArticleCASPubMed Google Scholar
Tang, J. et al. Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in P22. Structure19, 496–502 (2011). ArticleCASPubMedPubMed Central Google Scholar
Black, L. W. & Silverman, D. J. Model for DNA packaging into bacteriophage T4 heads. J. Virol.28, 643–655 (1978). CASPubMedPubMed Central Google Scholar
de Frutos, M., Letellier, L. & Raspaud, E. DNA ejection from bacteriophage T5: analysis of the kinetics and energetics. Biophys. J.88, 1364–1370 (2005). ArticleCASPubMed Google Scholar
Leforestier, A. & Livolant, F. The bacteriophage genome undergoes a succession of intracapsid phase transitions upon DNA ejection. J. Mol. Biol.396, 384–395 (2010). ArticleCASPubMed Google Scholar
Sao-Jose, C., de Frutos, M., Raspaud, E., Santos, M. A. & Tavares, P. Pressure built by DNA packing inside virions: enough to drive DNA ejection in vitro, largely insufficient for delivery into the bacterial cytoplasm. J. Mol. Biol.374, 346–355 (2007). ArticleCASPubMed Google Scholar
Letellier, L., Boulanger, P., Plancon, L., Jacquot, P. & Santamaria, M. Main features on tailed phage, host recognition and DNA uptake. Front. Biosci.9, 1228–1339 (2004). ArticleCASPubMed Google Scholar
Casjens, S. & Molineux, I. in Viral Molecular Machines (eds Rossmann, M. & Rao, V.) (Springer, New York, in the press).
Casjens, S. R. Comparative genomics and evolution of the tailed-bacteriophages. Curr. Opin. Microbiol.8, 451–458 (2005). ArticleCASPubMed Google Scholar
Hendrix, R. W. Bacteriophages: evolution of the majority. Theor. Popul. Biol.61, 471–480 (2002). ArticlePubMed Google Scholar
Kochan, J., Carrascosa, J. L. & Murialdo, H. Bacteriophage lambda preconnectors: purification and structure. J. Mol. Biol.174, 433–447 (1984). ArticleCASPubMed Google Scholar
Driedonks, R. A., Engel, A., tenHeggeler, B. & van Driel, R. Gene 20 product of bacteriophage T4 its purification and structure. J. Mol. Biol.152, 641–662 (1981). ArticleCASPubMed Google Scholar
Carazo, J. M., Donate, L. E., Herranz, L., Secilla, J. P. & Carrascosa, J. L. Three-dimensional reconstruction of the connector of bacteriophage φ29 at 1.8 nm resolution. J. Mol. Biol.192, 853–867 (1986). ArticleCASPubMed Google Scholar
Lurz, R. et al. Structural organisation of the head-to-tail interface of a bacterial virus. J. Mol. Biol.310, 1027–1037 (2001). ArticleCASPubMed Google Scholar
Doan, D. N. & Dokland, T. The gpQ portal protein of bacteriophage P2 forms dodecameric connectors in crystals. J. Struct. Biol.157, 432–436 (2007). ArticleCASPubMed Google Scholar
Morais, M. C. et al. Defining molecular and domain boundaries in the bacteriophage φ29 DNA packaging motor. Structure16, 1267–1274 (2008). This investigation uses cryo-electron microscopy to obtain a three-dimensional reconstruction of the phage φ29 procapsid with the TerL ATPase bound to it. ArticleCASPubMedPubMed Central Google Scholar
Olia, A., Prevelige, P. E. Jr, Johnson, J. & Cingolani, G. Three-dimensional structure of a viral genome-delivery portal vertex. Nature Struc. Mol. Biol.18, 597–604 (2011). This article describes the most recent of the three X-ray structures of portal protein rings (see also references 55 and 56). ArticleCAS Google Scholar
Cuervo, A., Vaney, M. C., Antson, A. A., Tavares, P. & Oliveira, L. Structural rearrangements between portal protein subunits are essential for viral DNA translocation. J. Biol. Chem.282, 18907–18913 (2007). ArticleCASPubMed Google Scholar
Chen, D. H. et al. Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc. Natl Acad. Sci. USA108, 1355–1360 (2011). This paper describes the highest-resolution asymmetrical three-dimensional reconstruction of procapsids that has been obtained to date by cryo-electron microscopy. ArticleCASPubMedPubMed Central Google Scholar
Bazinet, C. & King, J. Initiation of P22 procapsid assembly in vivo. J. Mol. Biol.202, 77–86 (1988). ArticleCASPubMed Google Scholar
Weigele, P., Sampson, L., Winn-Stapley, D. & Casjens, S. Molecular genetics of bacteriophage P22 scaffolding protein's functional domains. J. Mol. Biol.348, 831–844 (2005). ArticleCASPubMed Google Scholar
Baumann, R. G., Mullaney, J. & Black, L. W. Portal fusion protein constraints on function in DNA packaging of bacteriophage T4. Mol. Microbiol.61, 16–32 (2006). ArticleCASPubMed Google Scholar
Hugel, T. et al. Experimental test of connector rotation during DNA packaging into bacteriophage φ29 capsids. PLoS Biol.5, e59 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Ding, F. et al. Structure and assembly of the essential RNA ring component of a viral DNA packaging motor. Proc. Natl Acad. Sci. USA108, 7357–7362 (2011). ArticleCASPubMedPubMed Central Google Scholar
Reid, R., Zhang, F., Benson, S. & Anderson, D. Probing the structure of bacteriophage φ29 prohead RNA with specific mutations. J. Biol. Chem.269, 18656–18661 (1994). CASPubMed Google Scholar
Zhang, C., Tellinghuisen, T. & Guo, P. Confirmation of the helical structure of the 5′/3′ termini of the essential DNA packaging pRNA of phage φ29. RNA1, 1041–1050 (1995). CASPubMedPubMed Central Google Scholar
Casjens, S. & Gilcrease, D. in Bacteriophages: Methods and Protocols (eds Clokie, M. & Kropinski, A.) 91–111 (Humana, Totowa, New Jersey, 2009). Book Google Scholar
Jackson, E. N., Jackson, D. A. & Deans, R. J. _Eco_RI analysis of bacteriophage P22 DNA packaging. J. Mol. Biol.118, 365–388 (1978). ArticleCASPubMed Google Scholar
Tye, B. K., Huberman, J. A. & Botstein, D. Non-random circular permutation of phage P22 DNA. J. Mol. Biol.85, 501–528 (1974). ArticleCASPubMed Google Scholar
Adams, M. B., Hayden, M. & Casjens, S. On the sequential packaging of bacteriophage P22 DNA. J. Virol.46, 673–677 (1983). CASPubMedPubMed Central Google Scholar
Mousset, S. & Thomas, R. Ter, a function which generates the ends of the mature λ chromosome. Nature221, 242–245 (1969). ArticleCASPubMed Google Scholar
Poteete, A. R. & Botstein, D. Purification and properties of proteins essential to DNA encapsulation by phage P22. Virology95, 565–573 (1979). ArticleCASPubMed Google Scholar
Al-Zahrani, A. S. et al. The small terminase, gp16, of bacteriophage T4 is a regulator of the DNA packaging motor. J. Biol. Chem.284, 24490–24500 (2009). ArticleCASPubMedPubMed Central Google Scholar
Nemecek, D. et al. Subunit conformations and assembly states of a DNA-translocating motor: the terminase of bacteriophage P22. J. Mol. Biol.374, 817–836 (2007). ArticleCASPubMedPubMed Central Google Scholar
Gual, A., Camacho, A. G. & Alonso, J. C. Functional analysis of the terminase large subunit, G2P, of Bacillus subtilis bacteriophage SPP1. J. Biol. Chem.275, 35311–35319 (2000). ArticleCASPubMed Google Scholar
Leffers, G. & Rao, V. B. Biochemical characterization of an ATPase activity associated with the large packaging subunit gp17 from bacteriophage T4. J. Biol. Chem.275, 37127–37136 (2000). ArticleCASPubMed Google Scholar
Maluf, N. K., Yang, Q. & Catalano, C. E. Self-association properties of the bacteriophage l terminase holoenzyme: implications for the DNA packaging motor. J. Mol. Biol.347, 523–542 (2005). ArticleCASPubMed Google Scholar
Sun, S. et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell135, 1251–1262 (2008). This study uses cryo-electron microscopy to obtain a three-dimensionsal reconstruction of the phage T4 procapsid with the TerL ATPase bound to it. ArticleCASPubMed Google Scholar
Burroughs, A. M., Iyer, L. M. & Aravind, L. Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems. Genome Dyn.3, 48–65 (2007). ArticleCASPubMed Google Scholar
Mitchell, M. S., Matsuzaki, S., Imai, S. & Rao, V. B. Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Nucleic Acids Res.30, 4009–4021 (2002). ArticleCASPubMedPubMed Central Google Scholar
Guo, P., Peterson, C. & Anderson, D. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage ϕ29. J. Mol. Biol.197, 229–236 (1987). ArticleCASPubMed Google Scholar
Hwang, Y. & Feiss, M. Mutations affecting the high affinity ATPase center of gpA, the large subunit of bacteriophage l terminase, inactivate the endonuclease activity of terminase. J. Mol. Biol.261, 524–535 (1996). ArticleCASPubMed Google Scholar
Morita, M., Tasaka, M. & Fujisawa, H. DNA packaging ATPase of bacteriophage T3. Virology193, 748–752 (1993). ArticleCASPubMed Google Scholar
Oliveira, L., Henriques, A. O. & Tavares, P. Modulation of the viral ATPase activity by the portal protein correlates with DNA packaging efficiency. J. Biol. Chem.281, 21914–21923 (2006). ArticleCASPubMed Google Scholar
Goetzinger, K. R. & Rao, V. B. Defining the ATPase center of bacteriophage T4 DNA packaging machine: requirement for a catalytic glutamate residue in the large terminase protein gp17. J. Mol. Biol.331, 139–154 (2003). ArticleCASPubMed Google Scholar
Duffy, C. & Feiss, M. The large subunit of bacteriophage l's terminase plays a role in DNA translocation and packaging termination. J. Mol. Biol.316, 547–561 (2002). ArticleCASPubMed Google Scholar
Kondabagil, K. R., Zhang, Z. & Rao, V. B. The DNA translocating ATPase of bacteriophage T4 packaging motor. J. Mol. Biol.363, 786–799 (2006). ArticleCASPubMed Google Scholar
Tsay, J. M. et al. Mutations altering a structurally conserved loop-helix-loop region of a viral packaging motor change DNA translocation velocity and processivity. J. Biol. Chem.285, 24282–24289 (2010). ArticleCASPubMedPubMed Central Google Scholar
Tsay, J. M., Sippy, J., Feiss, M. & Smith, D. E. The Q motif of a viral packaging motor governs its force generation and communicates ATP recognition to DNA interaction. Proc. Natl Acad. Sci. USA106, 14355–14360 (2009). ArticleCASPubMedPubMed Central Google Scholar
Alam, T. I. et al. The headful packaging nuclease of bacteriophage T4. Mol. Microbiol.69, 1180–1190 (2008). CASPubMed Google Scholar
Hwang, Y., Hang, J. Q., Neagle, J., Duffy, C. & Feiss, M. Endonuclease and helicase activities of bacteriophage l terminase: changing nearby residue 515 restores activity to the gpA K497D mutant enzyme. Virology277, 204–214 (2000). ArticleCASPubMed Google Scholar
Oliveira, L., Alonso, J. C. & Tavares, P. A defined in vitro system for DNA packaging by the bacteriophage SPP1: insights into the headful packaging mechanism. J. Mol. Biol.353, 529–539 (2005). ArticleCASPubMed Google Scholar
de Beer, T. et al. Insights into specific DNA recognition during the assembly of a viral genome packaging machine. Mol. Cell9, 981–991 (2002). ArticleCASPubMed Google Scholar
Hanagan, A., Meyer, J. D., Johnson, L., Manning, M. C. & Catalano, C. E. The phage lambda terminase enzyme: 2. Refolding of the gpNu1 subunit from the detergent-denatured and guanidinium hydrochloride-denatured state yields different oligomerization states and altered protein stabilities. Int. J. Biol. Macromol.23, 37–48 (1998). ArticleCASPubMed Google Scholar
Nemecek, D., Lander, G. C., Johnson, J. E., Casjens, S. R. & Thomas, G. J. Jr. Assembly architecture and DNA binding of the bacteriophage P22 terminase small subunit. J. Mol. Biol.383, 494–501 (2008). ArticleCASPubMedPubMed Central Google Scholar
Zhao, H. et al. Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine. Proc. Natl Acad. Sci. USA107, 1971–1976 (2010). This report presents the only currently known X-ray structure of TerS, the protein that is responsible for recognition of the DNA that will be packaged. ArticleCASPubMedPubMed Central Google Scholar
Lin, H., Simon, M. N. & Black, L. W. Purification and characterization of the small subunit of phage T4 terminase, gp16, required for DNA packaging. J. Biol. Chem.272, 3495–3501 (1997). ArticleCASPubMed Google Scholar
Chai, S., Lurz, R. & Alonso, J. C. The small subunit of the terminase enzyme of Bacillus subtilis bacteriophage SPP1 forms a specialized nucleoprotein complex with the packaging initiation region. J. Mol. Biol.252, 386–398 (1995). ArticleCASPubMed Google Scholar
Casjens, S. R. & Thuman-Commike, P. A. Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology411, 393–415 (2011). ArticleCASPubMed Google Scholar
Casjens, S. in Virus Structure and Assembly (ed. Casjens, S.) 75–148 (Jones and Bartlett, Boston, 1985). Google Scholar
Maluf, N. K., Gaussier, H., Bogner, E., Feiss, M. & Catalano, C. E. Assembly of bacteriophage lambda terminase into a viral DNA maturation and packaging machine. Biochemistry45, 15259–15268 (2006). ArticleCASPubMed Google Scholar
Chemla, Y. R. et al. Mechanism of force generation of a viral DNA packaging motor. Cell122, 683–692 (2005). ArticleCASPubMed Google Scholar
Smith, D. et al. The bacteriophage φ29 portal motor can package DNA against a large internal force. Nature413, 748–752 (2001). This important paper describes the first application of single-molecule optical tweezer technology to phage DNA packaging. It describes the basic rate and force properties of the phage ϕ29 motor. ArticleCASPubMed Google Scholar
Gope, R. & Serwer, P. Bacteriophage P22 in vitro DNA packaging monitored by agarose gel electrophoresis: rate of DNA entry into capsids. J. Virol.47, 96–105 (1983). CASPubMedPubMed Central Google Scholar
Yang, Q., Catalano, C. E. & Maluf, N. K. Kinetic analysis of the genome packaging reaction in bacteriophage l. Biochemistry48, 10705–10715 (2009). ArticleCASPubMed Google Scholar
Laemmli, U. K. & Favre, M. Maturation of the head of bacteriophage T4. I. DNA packaging events. J. Mol. Biol.80, 575–599 (1973). ArticleCASPubMed Google Scholar
Fuller, D. N. et al. Measurements of single DNA molecule packaging dynamics in bacteriophage l reveal high forces, high motor processivity, and capsid transformations. J. Mol. Biol.373, 1113–1122 (2007). This study defines the basic rate and force parameters of the phage λ packaging motor. ArticleCASPubMedPubMed Central Google Scholar
Fuller, D. N., Raymer, D. M., Kottadiel, V. I., Rao, V. B. & Smith, D. E. Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proc. Natl Acad. Sci. USA104, 16868–16873 (2007). This investigation defines the basic rate and force parameters of the phage T4 packaging motor. ArticleCASPubMedPubMed Central Google Scholar
Rickgauer, J. P. et al. Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage φ29. Biophys. J.94, 159–167 (2008). ArticleCASPubMed Google Scholar
Moffitt, J. R. et al. Intersubunit coordination in a homomeric ring ATPase. Nature457, 446–450 (2009). This important work refines optical tweezer analysis to be able to study the step size of DNA packaging (10 bp) and the coordination of the 2.5-bp substeps. ArticleCASPubMedPubMed Central Google Scholar
Yu, J., Moffitt, J., Hetherington, C. L., Bustamante, C. & Oster, G. Mechanochemistry of a viral DNA packaging motor. J. Mol. Biol.400, 186–203 (2010). ArticleCASPubMed Google Scholar
Draper, B. & Rao, V. B. An ATP hydrolysis sensor in the DNA packaging motor from bacteriophage T4 suggests an inchworm-type translocation mechanism. J. Mol. Biol.369, 79–94 (2007). ArticleCASPubMed Google Scholar
Ray, K., Sabanayagam, C. R., Lakowicz, J. R. & Black, L. W. DNA crunching by a viral packaging motor: compression of a procapsid-portal stalled Y-DNA substrate. Virology398, 224–232 (2010). ArticleCASPubMed Google Scholar
Ortega, M. E., Gaussier, H. & Catalano, C. E. The DNA maturation domain of gpA, the DNA packaging motor protein of bacteriophage lambda, contains an ATPase site associated with endonuclease activity. J. Mol. Biol.373, 851–865 (2007). ArticleCASPubMedPubMed Central Google Scholar
Ghosh-Kumar, M., Alam, T. I., Draper, B., Stack, J. D. & Rao, V. B. Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4. Nucleic Acids Res.39, 2742–2755 (2011). ArticleCASPubMed Google Scholar
Yang, Q. & Catalano, C. E. A minimal kinetic model for a viral DNA packaging machine. Biochemistry43, 289–299 (2004). ArticleCASPubMed Google Scholar
Gao, S. & Rao, V. B. Specificity of interactions among the DNA-packaging machine components of T4-related bacteriophages. J. Biol. Chem.286, 3944–3956 (2011). ArticleCASPubMed Google Scholar
Woods, L., Terpening, C. & Catalano, C. E. Kinetic analysis of the endonuclease activity of phage l terminase: assembly of a catalytically competent nicking complex is rate-limiting. Biochemistry36, 5777–5785 (1997). ArticleCASPubMed Google Scholar
Gaussier, H., Ortega, M. E., Maluf, N. K. & Catalano, C. E. Nucleotides regulate the conformational state of the small terminase subunit from bacteriophage lambda: implications for the assembly of a viral genome-packaging motor. Biochemistry44, 9645–9656 (2005). ArticleCASPubMed Google Scholar
Oram, M., Sabanayagam, C. & Black, L. W. Modulation of the packaging reaction of bacteriophage T4 terminase by DNA structure. J. Mol. Biol.381, 61–72 (2008). ArticleCASPubMedPubMed Central Google Scholar
Leffers, G. & Rao, V. B. A discontinuous headful packaging model for packaging less than headful length DNA molecules by bacteriophage T4. J. Mol. Biol.258, 839–850 (1996). ArticleCASPubMed Google Scholar
Xin, W. & Feiss, M. Function of IHF in l DNA packaging: I. Identification of the strong binding site for integration host factor and the locus for intrinsic bending in cosB. J. Mol. Biol.230, 492–504 (1993). ArticleCASPubMed Google Scholar
Wu, H., Sampson, L., Parr, R. & Casjens, S. The DNA site utilized by bacteriophage P22 for initiation of DNA packaging. Mol. Microbiol.45, 1631–1646 (2002). ArticleCASPubMed Google Scholar
Bukhari, A. I., Froshauer, S. & Botchan, M. Ends of bacteriophage Mu DNA. Nature264, 580–583 (1976). ArticleCASPubMed Google Scholar
Groenen, M. A. & van de Putte, P. Mapping of a site for packaging of bacteriophage Mu DNA. Virology144, 520–522 (1985). ArticleCASPubMed Google Scholar
Harel, J., Duplessis, L., Kahn, J. S. & DuBow, M. S. The _cis_-acting DNA sequences required in vivo for bacteriophage Mu helper-mediated transposition and packaging. Arch. Microbiol.154, 67–72 (1990). ArticleCASPubMed Google Scholar
Casjens, S. et al. The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging. J. Mol. Biol.339, 379–394 (2004). ArticleCASPubMed Google Scholar
Casjens, S. R. et al. The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J. Bacteriol.187, 1091–1104 (2005). ArticleCASPubMedPubMed Central Google Scholar
Black, L. W. & Peng, G. Mechanistic coupling of bacteriophage T4 DNA packaging to components of the replication-dependent late transcription machinery. J. Biol. Chem.281, 25635–25643 (2006). ArticleCASPubMed Google Scholar
Zhang, X. & Studier, F. W. Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection. J. Mol. Biol.340, 707–730 (2004). ArticleCASPubMed Google Scholar
Chung, Y. B., Nardone, C. & Hinkle, D. C. Bacteriophage T7 DNA packaging. III. A “hairpin” end formed on T7 concatemers may be an intermediate in the processing reaction. J. Mol. Biol.216, 939–948 (1990). ArticleCASPubMed Google Scholar
Xin, W., Cai, Z. H. & Feiss, M. Function of IHF in l DNA packaging: II. Effects of mutations altering the IHF binding site and the intrinsic bend in cosB on l development. J. Mol. Biol.230, 505–515 (1993). ArticleCASPubMed Google Scholar
Droge, A. & Tavares, P. in Viral Genome Packaging Machines: Genetics, Structure, and Mechanism (ed. Catalano, C.) 89–101 (Landes Bioscience, Georgetown, Texas, 2005). Book Google Scholar
Feiss, M. & Catalano, C. in Viral Genome Packaging Machines: Genetics, Structure, and Mechanism (ed. Catalano, C.) 5–39 (Landes Bioscience, Georgetown, Texas, 2005). Book Google Scholar
Frackman, S., Siegele, D. A. & Feiss, M. A functional domain of bacteriophage l terminase for prohead binding. J. Mol. Biol.180, 283–300 (1984). ArticleCASPubMed Google Scholar
Morita, M., Tasaka, M. & Fujisawa, H. Structural and functional domains of the large subunit of the bacteriophage T3 DNA packaging enzyme: importance of the C-terminal region in prohead binding. J. Mol. Biol.245, 635–644 (1995). ArticleCASPubMed Google Scholar
Oliveira, L., Cuervo, A. & Tavares, P. Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein. J. Biol. Chem.285, 7366–7373 (2010). ArticleCASPubMedPubMed Central Google Scholar
Lin, H., Rao, V. B. & Black, L. W. Analysis of capsid portal protein and terminase functional domains: interaction sites required for DNA packaging in bacteriophage T4. J. Mol. Biol.289, 249–260 (1999). ArticleCASPubMed Google Scholar
Casjens, S. et al. Bacteriophage P22 portal protein is part of the gauge that regulates packing density of intravirion DNA. J. Mol. Biol.224, 1055–1074 (1992). ArticleCASPubMed Google Scholar
Isidro, A., Santos, M. A., Henriques, A. O. & Tavares, P. The high-resolution functional map of bacteriophage SPP1 portal protein. Mol. Microbiol.51, 949–962 (2004). ArticleCASPubMed Google Scholar
Wieczorek, D. J. & Feiss, M. Defining cosQ, the site required for termination of bacteriophage l DNA packaging. Genetics158, 495–506 (2001). CASPubMedPubMed Central Google Scholar
Cardarelli, L. et al. The crystal structure of bacteriophage HK97 gp6: defining a large family of head–tail connector proteins. J. Mol. Biol.395, 754–768 (2010). ArticleCASPubMed Google Scholar
Lhuillier, S. et al. Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating. Proc. Natl Acad. Sci. USA106, 8507–8512 (2009). ArticleCASPubMedPubMed Central Google Scholar
Olia, A. S. et al. Binding-induced stabilization and assembly of the phage P22 tail accessory factor gp4. J. Mol. Biol.363, 558–576 (2006). ArticleCASPubMed Google Scholar
Olia, A. S., Bhardwaj, A., Joss, L., Casjens, S. & Cingolani, G. Role of gene 10 protein in the hierarchical assembly of the bacteriophage P22 portal vertex structure. Biochemistry46, 8776–8784 (2007). ArticleCASPubMed Google Scholar
Olia, A. S., Casjens, S. & Cingolani, G. Structure of phage P22 cell envelope-penetrating needle. Nature Struct. Mol. Biol.14, 1221–1227 (2007). ArticleCAS Google Scholar
Chattoraj, D. K. & Inman, R. B. Location of DNA ends in P2, 186, P4 and lambda bacteriophage heads. J. Mol. Biol.87, 11–22 (1974). ArticleCASPubMed Google Scholar
Saigo, K. & Uchida, H. Connection of the right-hand terminus of DNA to the proximal end of the tail in bacteriophage lambda. Virology61, 524–536 (1974). ArticleCASPubMed Google Scholar
Thomas, J. O., Sternberg, N. & Weisberg, R. Altered arrangement of the DNA in injection-defective lambda bacteriophage. J. Mol. Biol.123, 149–161 (1978). ArticleCASPubMed Google Scholar
Israel, V. E proteins of bacteriophage P22. I. Identification and ejection from wild-type and defective particles. J. Virol.23, 91–97 (1977). CASPubMedPubMed Central Google Scholar
Wikoff, W. R. et al. Topologically linked protein rings in the bacteriophage HK97 capsid. Science289, 2129–2133 (2000). ArticleCASPubMed Google Scholar
Gilcrease, E. B., Winn-Stapley, D. A., Hewitt, F. C., Joss, L. & Casjens, S. R. Nucleotide sequence of the head assembly gene cluster of bacteriophage L and decoration protein characterization. J. Bacteriol.187, 2050–2057 (2005). ArticleCASPubMedPubMed Central Google Scholar
Tang, L., Gilcrease, E. B., Casjens, S. R. & Johnson, J. E. Highly discriminatory binding of capsid-cementing proteins in bacteriophage L. Structure14, 837–845 (2006). ArticleCASPubMed Google Scholar
Qin, L., Fokine, A., O'Donnell, E., Rao, V. B. & Rossmann, M. G. Structure of the small outer capsid protein, Soc: a clamp for stabilizing capsids of T4-like phages. J. Mol. Biol.395, 728–741 (2010). ArticleCASPubMed Google Scholar
Sathaliyawala, T. et al. Functional analysis of the highly antigenic outer capsid protein, Hoc, a virus decoration protein from T4-like bacteriophages. Mol. Microbiol.77, 444–455 (2010). ArticleCASPubMedPubMed Central Google Scholar
Yang, Q., Maluf, N. K. & Catalano, C. E. Packaging of a unit-length viral genome: the role of nucleotides and the gpD decoration protein in stable nucleocapsid assembly in bacteriophage l. J. Mol. Biol.383, 1037–1048 (2008). ArticleCASPubMed Google Scholar
Lee, T. J., Schwartz, C. & Guo, P. Construction of bacteriophage φ29 DNA packaging motor and its applications in nanotechnology and therapy. Ann. Biomed. Eng.37, 2064–2081 (2009). ArticlePubMedPubMed Central Google Scholar
Branton, D. et al. The potential and challenges of nanopore sequencing. Nature Biotech.26, 1146–1153 (2008). ArticleCAS Google Scholar
Sun, S., Kondabagil, K., Gentz, P. M., Rossmann, M. G. & Rao, V. B. The structure of the ATPase that powers DNA packaging into bacteriophage T4 procapsids. Mol. Cell25, 943–949 (2007). ArticleCASPubMed Google Scholar
Casjens, S. in Structural Biology of Viruses (eds Chiu, W., Burnett, R. & Garcea, R.) 3–37 (Oxford Univ. Press, Oxford, 1997). Google Scholar
Fuller, D. N. et al. Ionic effects on viral DNA packaging and portal motor function in bacteriophage ϕ29. Proc. Natl Acad. Sci. USA104, 11245–11250 (2007). This paper describes the X-ray structure of phage T4 TerL, the ATPase that powers DNA packaging. ArticleCASPubMedPubMed Central Google Scholar