High resolution viruses.
Cryo-electron microscopy to reproduce the atomic structure of a staphylococcal bacteriophage in high resolution.
Cryo-electron microscopy performed by researchers at the University of Alabama in Birmingham has revealed the structure of a bacterial virus in unprecedented detail. This is the first structure of a virus capable of infecting Staphylococcus epidermidis. The possibility of knowing in detail, and in high resolution, this structure is a key link between viral biology and the potential therapeutic use of the virus to counteract bacterial infections.
Bacteriophages or “phages” is the term used for viruses that infect bacteria. The UAB researchers, led by Terje Dokland, in collaboration with Asma Hatoum-Aslan, of the University of Illinois Urbana-Champaign, described atomic models for 11 different structural proteins of the phage named Andhra . The study is published in Science Advances. Andhra is a member of the picovirus group . The range of hosts it infects is limited to S. epidermidis,mostly benign skin bacterium which, however, is also a major cause of medical device infections. “Picoviruses are rarely found and remain understudied and underused for therapeutic applications,” said Hatoum-Aslan, a phage biologist at the University of Illinois. With the emergence of antibiotic resistance of both S. epidermidis and its related pathogen, Staphylococcus aureus, researchers have renewed interest in the potential use of bacteriophages in the treatment of bacterial infections.
These viruses always kill the cells they infect, after binding to the bacterial cell wall, enzymatically breaking through it, penetrating the cell membrane, and injecting the viral DNA into the cell. They also have other characteristics that make them attractive candidates for therapeutic use, including a small genome and an inability to transfer bacterial genes.
Knowledge of the structure of Andhra proteins and understanding how these structures allow the virus to infect a bacterium will make it possible to produce bacteriophages tailored to a specific purpose using genetic manipulation. “With this study, we have gained a better understanding of the structures and functions of Andhra gene products and the determinants of host specificity, paving the way for a more rational design of customized phages for therapeutic applications. Our results clarify the critical characteristics for the assembly of the virion (name of the single viral particle, in this form the virus is inactive and physically isolable. A virion, infecting a single host cell, is capable of producing thousands of copies of itself itself using DNA replication mechanisms), host recognition and penetration,” said Dokland, professor of microbiology at the UAB
The structure of Andhra
The general structure of Andhra consists of a 20-sided icosahedral capsid which contains the viral genome. The capsid is connected to a short tubular tail. The tail of viruses has appendages that serve to bind to the bacterial surface. Also in the case of Andhra, its tail is largely responsible for the binding with S. epidermidis and for the enzymatic breakdown of the cell wall of the bacterium.
The 11 different proteins that make up each virus particle are found in multiple copies that assemble together. The capsid (protein structure that encloses the nucleic acid and protects it from the external environment) of Andhra is composed of copies of two proteins (235 copies for each of the two), while the other nine proteins of the virion have a number of copies it ranges from two to 72. In total, the virion is made up of 645 pieces of protein that include two copies of a twelfth protein, the structure of which was predicted using the protein structure prediction program AlphaFold .
Researchers described how each protein binds to other copies of the same protein type, for example to form the hexameric and pentameric faces of the capsid, as well as how each protein interacts with different types of adjacent proteins.
The cryo-electron microscopy
Electron microscopes use a beam of electrons to illuminate an object, providing much higher resolution than the light microscope. Cryo-electron microscopy adds the element of super-cold temperatures , making it particularly useful for resolving the near-atomic structure of larger proteins, membrane proteins or lipid-containing samples, such as membrane-bound receptors, and complexes multiple biomolecules together. Over the past eight years, new electron detectors have created a huge leap in resolutionfor cryo-electron microscopy compared to normal electron microscopy. Advanced computing merges thousands of images to generate high-resolution three-dimensional structures. Graphics processing units are used to process terabytes of data. The microscope stage that holds the specimen can also be tilted during image acquisition, allowing for three-dimensional tomographic construction, similar to a CT scan in a hospital.
The analysis of the Andhra virion structure carried out by UAB researchers started from 230,714 particle images. Molecular reconstruction of the capsid, tail, distal tail, and tail tip began with 186,542, 159,489, 159,489, and 159,489 images, respectively. Resolution ranged from 3.50 to 4.90 angstroms (a metric unit of length equal to 0.1 nanometers).