BENSON RESEARCH SUMMARY
The research interests of the Benson laboratory involve the use of X-ray crystallography as a tool to understand biological structures and processes. Our major focus is the structural organization of viruses, in particular double-stranded (ds)DNA icosahedral viruses. A major emphasis has been on the major coat proteins of dsDNA viruses that appear, from structures and sequences, to be evolutionarily related. However, other viral proteins from these viruses are more species specific allowing the viruses to selectively interact with their hosts. Structural data can further elucidate similarities and differences between these dsDNA viruses. Another area of great interest to our group is how mutations in human enzymes lead to metabolic disorders.
Viruses are extremely diverse and have devised many interesting methods of stably encapsulating their genomes to be successfully transferred through harsh external environments, yet remaining capable of releasing their genomes when they contact a susceptible host. They are essentially little capsules containing a blue print (the genome) that carries the plans for reproducing their capsules for further “exploration”. Some interesting ideas arise from the study of viruses, such as how they find their host, how the individual structural proteins (for spherical viruses) form the viral capsid, and how is the genome packaged and delivered?
Bacteriophage PRD1, a virus that infects bacteria, has provided the springboard for our research interests. PRD1 has some interesting characteristics, such as not containing a tail as most dsDNA bacteriophage, and having a lipid membrane beneath its icosahedral capsid.
The capsid of PRD1 is icosahedral with 240 copies of the major coat protein P3 and a protein complex composed of a pentamer of P31, trimer of P5, and a monomer of P2 at the vertices. The X-ray structure of the major coat protein has been determined. The structure revealed P3 to be a trimer with each subunit composed of two viral jelly rolls - a double-barrel trimer (green and blue below). At the time it was determined, this arrangement had only been seen in one other molecule, the major coat protein hexon of the human adenovirus.
The striking structural similarity between the major coat proteins of these two viruses, even though they infect hosts from very different domains of life and they have no evident sequence similarity, suggests that they are evolutionarily related. This discovery has led to the search for additional members of the lineage. One potential member is another bacteriophage, Bam35, which is in the same family as PRD1 but infects Gram-positive bacteria as opposed to Gram-negative bacteria. We are investigating the major coat protein of Bam35 to see if our prediction that the sequence, though only showing 16% identity to P3, is able to conform to the P3 structure.
We are also interested in how the viruses interact with their hosts. As these components would be host specific, it is expected that there would be more divergence in their structure. The receptor-binding protein of PRD1 has been determined. Bam35 does not seem to contain a similar gene and its method of host identification is probably quite different. More structural information is needed to compare how the viruses in this developing lineage are the same and how they differ.
Human enzymes involved in metabolic disorders
Another focus of the laboratory is enzymes involved in human metabolic processes. Mutations in these important enzymes lead to genetic disease. We are studying the structure of the glycosylated a-galactosidase A (AGA), which is involved in the breakdown of glycolipids and glycoproteins. Over 300 mutations have been documented that destroy AGA function and lead to Fabry disease. The structure determination of AGA has proven challenging, and a lower resolution structure is available, but the additional information from a better determined structure is critical in further understanding the function of AGA. We have also looked at human a-N-acetylgalactosaminidase, which is very similar to AGA, to better understand this class of enzymes.
- Benson, S.D., Bamford, J.K.H., Bamford, D.H. and Burnett, R.M. (1999). Viral Evolution Revealed by Bacteriophage PRD1 and Human Adenovirus Coat Protein Structures. Cell 98, 825-833.
- Xu, L., Butcher, S.J., Benson, S.D., Bamford, D.H. and Burnett, R.M. (2001). Crystallization and X-ray Analysis of Receptor-Binding Protein P2 of Bacteriophage PRD1. J. Struct. Biol. 131, 159-163.
- Benson, S.D., Bamford, J.K.H., Bamford, D.H. and Burnett, R.M. (2002). The X-ray Crystal Structure of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1, at 1.65 Å Resolution. Acta Crystallogr. D58, 39-59.
- Xu, L., Benson, S.D., Butcher, S.J., Bamford, D.H. and Burnett, R.M. (2003). The Receptor Binding Protein P2 of PRD1, a Virus Targeting Antibiotic-Resistant Bacteria, has a Novel Fold Suggesting Multiple Functions. Structure 11, 309-322.
- Yasuda, M., Shabbeer, J., Benson, S.D., Maire, I., Burnett, R.M. and Desnick, R.J. (2003). Fabry disease: Characterization of a-galactosidase A double mutations and the D313Y plasma enzyme pseudodeficiency allele. Hum. Mut. 22, 486-492.
- Strömsten, N.J., Benson, S.D., Burnett, R.M., Bamford, D.H. and Bamford, J.K.H. (2003). The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J. Bacteriol. 189, 6985-6989.
- Benson, S.D., Bamford, J.K.H., Bamford, D.H. and Burnett, R.M. (2004). Does common architecture reveal a viral lineage spanning all three domains of life? Mol. Cell 16, 673-685.