Artificial bio-nanomachines based on protein needles derived from bacteriophage T4
Bacteriophage T4 is a natural bio-nanomachine which achieves efficient infection of host cells via cooperative motion of specific three-dimensional protein architectures. The relationships between the protein structures and their dynamic functions have recently been clarified. In this review we summarize the design principles for fabrication of nanomachines using the component proteins of bacteriophage T4 based on these recent advances. We focus on the protein needle known as gp5, which is located at the center of the baseplate at the end of the contractile tail of bacteriophage T4. This protein needle plays a critical role in directly puncturing host cells, and analysis has revealed that it contains a common motif used for cell puncture in other known injection systems, such as T6SS. Our artificial needle based on the β-helical domain of gp5 retains the ability to penetrate cells and can be engineered to deliver various cargos into living cells. Thus, the unique components of bacteriophage T4 and other natural nanomachines have great potential for use as molecular scaffolds in efforts to fabricate new bio-nanomachines.
KeywordsBacteriophage T4 Gp5 β-Helix Protein needle Cell penetration
This work was supported by a Research Fellowship for Young Scientists of JSPS for H.I. (No. 4240) and by JSPS KAKENHI grant nos. JP13F03343, JP16H04177, JP16K13095, JP23350080, and JP26102513 and from Mochida Memorial Foundation for Medical and Pharmaceutical Research for T.U.
Compliance with ethical standards
Conflict of interest
Hiroshi Inaba declares that he has no conflict of interest. Takafumi Ueno declares that he has no conflict of interest.
This article does not contain any studies with human participants or animals performed by the authors.
- Aksyuk AA, Bowman VD, Kaufmann B, Fields C, Klose T, Holdaway HA, Fischetti VA, Rossmann MG (2012) Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Proc Natl Acad Sci USA 109:14001–14006. https://doi.org/10.1073/pnas.1207730109 CrossRefPubMedPubMedCentralGoogle Scholar
- Bebeacua C, Bron P, Lai L, Vegge CS, Brøndsted L, Spinelli S, Campanacci V, Veesler D, van Heel M, Cambillau C (2010) Structure and molecular assignment of lactococcal phage TP901-1 baseplate. J Biol Chem 285:39079–39086. https://doi.org/10.1074/jbc.M110.175646 CrossRefPubMedPubMedCentralGoogle Scholar
- Granell M, Namura M, Alvira S, Kanamaru S, van Raaij MJ (2017) Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fiber protein gp34. Viruses. https://doi.org/10.3390/v9070168
- Harada K, Yamashita E, Nakagawa A, Miyafusa T, Tsumoto K, Ueno T, Toyama Y, Takeda S (2013) Crystal structure of the C-terminal domain of mu phage central spike and functions of bound calcium ion. Biochim Biophys Acta 1834:284–291. https://doi.org/10.1016/j.bbapap.2012.08.015 CrossRefPubMedGoogle Scholar
- Heymann JB, Bartho JD, Rybakova D, Venugopal HP, Winkler DC, Sen A, Hurst MR, Mitra AK (2013) Three-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila. J Biol Chem 288:25276–25284. https://doi.org/10.1074/jbc.M113.456145 CrossRefPubMedPubMedCentralGoogle Scholar
- Kageyama Y, Murayama M, Onodera T, Yamada S, Fukada H, Kudou M, Tsumoto K, Toyama Y, Kado S, Kubota K, Takeda S (2009) Observation of the membrane binding activity and domain structure of gpV, which comprises the tail spike of bacteriophage P2. Biochemistry 48:10129–10135. https://doi.org/10.1021/bi900928n CrossRefPubMedGoogle Scholar
- Karam JD, Drake JW, Kreuzer KN, Mosig G, Hall DH, Eiserling FA, Black LW, Spicer EK, Kutter E, Carlson K, Miller ES (eds) (1994) Molecular biology of bacteriophage T4. American Society for Microbiology, Washington D.C.Google Scholar
- Koshiyama T, Ueno T, Kanamaru S, Arisaka F, Watanabe Y (2009) Construction of an energy transfer system in the bio-nanocup space by heteromeric assembly of gp27 and gp5 proteins isolated from bacteriophage T4. Org Biomol Chem 7:2649–2654. https://doi.org/10.1039/b904297k CrossRefPubMedGoogle Scholar
- Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley SK, Almo SC, Mekalanos JJ (2009) Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. Proc Natl Acad Sci USA 106:4154–4159. https://doi.org/10.1073/pnas.0813360106 CrossRefPubMedPubMedCentralGoogle Scholar
- Nakayama K, Takashima K, Ishihara H, Shinomiya T, Kageyama M, Kanaya S, Ohnishi M, Murata T, Mori H, Hayashi T (2000) The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol Microbiol 38:213–231. https://doi.org/10.1046/j.1365-2958.2000.02135.x CrossRefPubMedGoogle Scholar
- Pukatzki S, Ma AT, Revel AT, Sturtevant D, Mekalanos JJ (2007) Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci USA 104:15508–15513. https://doi.org/10.1073/pnas.0706532104 CrossRefPubMedPubMedCentralGoogle Scholar
- Rao VB, Black LW (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 200:475–488. https://doi.org/10.1016/0022-2836(88)90537-2 CrossRefPubMedGoogle Scholar
- Rossmann MG, Rao VB (eds) (2012) Viral molecular machines. Springer, New YorkGoogle Scholar
- Sciara G, Bebeacua C, Bron P, Tremblay D, Ortiz-Lombardia M, Lichière J, van Heel M, Campanacci V, Moineau S, Cambillau C (2010) Structure of lactococcal phage p2 baseplate and its mechanism of activation. Proc Natl Acad Sci USA 107:6852–6857. https://doi.org/10.1073/pnas.1000232107 CrossRefPubMedPubMedCentralGoogle Scholar
- Spínola-Amilibia M, Davó-Siguero I, Ruiz FM, Santillana E, Medrano FJ, Romero A (2016) The structure of VgrG1 from Pseudomonas aeruginosa, the needle tip of the bacterial type VI secretion system. Acta Crystallogr D Struct Biol 72:22–33. https://doi.org/10.1107/S2059798315021142 CrossRefPubMedGoogle Scholar
- Sun S, Kondabagil K, Draper B, Alam TI, Bowman VD, Zhang Z, Hegde S, Fokine A, Rossmann MG, Rao VB (2008) The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135:1251–1262. https://doi.org/10.1016/j.cell.2008.11.015 CrossRefPubMedGoogle Scholar
- Sun L, Zhang X, Gao S, Rao PA, Padilla-Sanchez V, Chen Z, Sun S, Xiang Y, Subramaniam S, Rao VB, Rossmann MG (2015) Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Nat Commun 6:7548. https://doi.org/10.1038/ncomms8548 CrossRefPubMedPubMedCentralGoogle Scholar
- Takeda S, Arisaka F, Ishii S, Kyogoku Y (1990) Structural studies of the contractile tail sheath protein of bacteriophage T4. 1. Conformational change of the tail sheath upon contraction as probed by differential chemical modification. Biochemistry 29:5050–5056. https://doi.org/10.1021/bi00473a008 CrossRefPubMedGoogle Scholar
- Vafabakhsh R, Kondabagil K, Earnest T, Lee KS, Zhang Z, Dai L, Dahmen KA, Rao VB, Ha T (2014) Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4. Proc Natl Acad Sci USA 111:15096–15101. https://doi.org/10.1073/pnas.1407235111 CrossRefPubMedPubMedCentralGoogle Scholar
- Xu J, Xiang Y (2017) Membrane penetration by bacterial viruses. J Virol 91:e00162–17. https://doi.org/10.1128/JVI.00162-17
- Yamashita E, Nakagawa A, Takahashi J, Tsunoda K, Yamada S, Takeda S (2011) The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure. Acta Crystallogr Sect F Struct Biol Cryst Commun 67:837–841. https://doi.org/10.1107/S1744309111005999 CrossRefPubMedPubMedCentralGoogle Scholar
- Yokoi N, Inaba H, Terauchi M, Stieg AZ, Sanghamitra NJM, Koshiyama T, Yutani K, Kanamaru S, Arisaka F, Hikage T, Suzuki A, Yamane T, Gimzewski JK, Watanabe Y, Kitagawa S, Ueno T (2010) Construction of robust bio-nanotubes using the controlled self-assembly of component proteins of bacteriophage T4. Small 6:1873–1879. https://doi.org/10.1002/smll.201000772 CrossRefPubMedGoogle Scholar
- Yokoi N, Miura Y, Huang C-Y, Takatani N, Inaba H, Koshiyama T, Kanamaru S, Arisaka F, Watanabe Y, Kitagawa S, Ueno T (2011) Dual modification of a triple-stranded b-helix nanotube with Ru and re metal complexes to promote photocatalytic reduction of CO2. Chem Commun 47:2074–2076. https://doi.org/10.1039/c0cc03015e CrossRefGoogle Scholar