How the DNA got into the killer machine
Today biolution released a new video visualising the assembly of T4 phage, one of the pets of molecular geneticists. Despite extensive work on these nano machines some mnysteries remain, for example how exactly the DNA is prepared for entering the prophage capsid. In a bacterium infected by T4, new bacteriophages are assembled in a stepwise process: the shaft builds up, DNA is replicated and the empty pro-head assembles as an empty shell. But how does the DNA get into the prohead?
For a quick answer see our video here: https://youtu.be/RbL3BZCGPA4
The initiation of DNA import is not entirely clear, but once DNA, the packaging motor and pro-head interact the DNA is rapidly threaded through a pore in the circular motor at the speed of 2000 basepairs a second.
Once the head is full, the packaging motor cuts the DNA and the complex falls off an expanded head, which has changed in shape. The shaft and long tail fibres are attached to complete the infectious particle. Within 1 hour more than 100 new phages are released from a single infected bacterium which makes the T4 phage one of the most efficient but also fascinating killing machines.
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Model of the T4 Phage
The T4 phage depicted in this video corresponds widely to the current status of research. The model was assembled using structural data available from public databases (see below) and benefitted greatly from the following publications:
Leiman PG, Arisaka F, van Raaij MJ, Kostyuchenko VA, Aksyuk AA, Kanamaru S, Rossmann MG. Morphogenesis of the T4 tail and tail fibers. Virol J. 2010 Dec 3;7:355. doi: 10.1186/1743-422X-7-355.
Eric S. Miller, Elizabeth Kutter, Gisela Mosig, Fumio Arisaka, Takashi Kunisawa, Wolfgang Rüger. Bacteriophage T4 Genome MMBR, Mar. 2003, p. 86–156 Vol. 67, No. 1 doi: 10.1128/MMBR.67.1.86-156.2003
Siying Lin, Tanfis I. Alam, Vishal I. Kottadiel, Carl J. VanGessel, Wei-Chun Tang, Yann R. Chemla and Venigalla B. Rao. Altering the speed of a DNA packaging motor from bacteriophage T4 Nucleic Acids Res. 2017 Nov 2; 45(19): 11437–11448. doi: 10.1093/nar/gkx809
EMDB:EMD-2774, EMD-6079, EMD-6080, EMD-6081, EMD-6082, EMD-6083: Hu B, Margolin W, Molineux IJ, Liu J, Structural remodeling of bacteriophage T4 and host membranes during infection initiation. PNAS 112 e4919-e4928 (2015) doi: 10.1073/pnas.1501064112EMD-8661: Chen Z, Sun L, Zhang Z, Fokine A, Padilla-Sanchez V, Hanein D, Jiang W, Rossmann MG, Rao VB, Cryo-EM structure of the bacteriophage T4 isometric head at 3.3- angstrom resolution and its relevance to the assembly of icosahedral viruses. PNAS 114 E8184-E8193 (2017) doi: 10.1073/pnas.1708483114
These included the following PDB codes:
5VF3 Bacteriophage T4 isometric capsid
3FOH Fitting of gp18M crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 extended tail
5IV5 Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex
2XGF Structure of the bacteriophage T4 long tail fibre needle-shaped receptor-binding tip
Retrieved from EMDB.org:
PDB consortium, Protein Data Bank: the single global archive for 3D macromolecular structure data (2019). Nucleic acids research Volume 47 p.D520-D528 doi: 10.1093/nar/gky949
Retrieved from rcsb.org
Stephen K Burley, Helen M. Berman, et al. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy (2019) Nucleic Acids Research 47: D464–D474; doi: 10.1093/nar/gky1004.
Modelling and Animation: Christian Müller
Idea, Scientific Advice, Text and Narrator:Stefan Grünert
MusicChad Crouch – Headwaters Instrumental https://freemusicarchive.org/music/Chad_Crouch