Bentley A Fane

Bentley A Fane

Professor, Plant Sciences
Professor, Applied BioSciences - GIDP
Professor, Genetics - GIDP
Professor, Immunobiology
Professor, BIO5 Institute
Primary Department
Department Affiliations
(520) 626-6634

Work Summary

Upon infection, viruses must transport their genomes into cells and produce progeny, often under a strict time deadline. We study how the viral proteins interact with with each other and with host cell proteins to efficiently accomplish these processes.

Research Interest

Bentley A. Fane, PhD, is a Professor in the School of Plant Sciences, College of Agriculture and Life Sciences and holds a joint appointment in the Department of Immunobiology, Arizona College of Medicine. Dr. Fane has an international reputation for his research into virus structure, assembly and evolution. His research focuses on the viruses of the Microviridae, of which he is considered one of the leading experts. He has been instrumental in defining the biochemical and structural parameters that allow these viruses to replicate and produce progeny in as little as five minutes. The rapid lifecycle has facilitated in depth studies into how viruses evolved resistance mechanism to anti-viral proteins targeting particle assembly.He has published over 60 original research paper in leading scientific journals, including Nature, Molecular Cell, and Journal of Virology, in which his publications on the evolution of resistance mechanisms and kinetic traps have been selected by the journal editors as articles of “significant interest.” He is a frequent presenter at national and international meetings, and has been invited to State of the Art and plenary talks at give the American Society for Virology. He presently serves on the Editorial Boards of two leading virology journals: Virology and the Journal of Virology. At the University of Arizona, Dr. Fane has been actively involved in promoting undergraduate research has been honored with teaching awards on the department, college, and university levels. Keywords: Virus structure and assembly, Viral DNA translocation, Viral evolution


Christakos, K. J., Chapman, J. A., Fane, B. A., & Campos, S. K. (2015). PhiXing-it, displaying foreign peptides on bacteriophage ΦX174. Virology, 488, 242-248.
BIO5 Collaborators
Samuel K Campos, Bentley A Fane

Although bacteriophage φX174 is easy to propagate and genetically tractable, it is use as a peptide display platform has not been explored. One region within the φX174 major spike protein G tolerated 13 of 16 assayed insertions, ranging from 10 to 75 amino acids. The recombinant proteins were functional and incorporated into infectious virions. In the folded protein, the peptides would be icosahedrally displayed within loops that extend from the protein׳s β-barrel core. The well-honed genetics of φX174 allowed permissive insertions to be quickly identified by the cellular phenotypes associated with cloned gene expression. The cloned genes were easily transferred from plasmids to phage genomes via recombination rescue. Direct ELISA validated several recombinant virions for epitope display. Some insertions conferred a temperature-sensitive (ts) protein folding defect, which was suppressed by global suppressors in protein G, located too far away from the insertion to directly alter peptide display.

Uchiyama, A., Heiman, P., & Fane, B. A. (2009). N-terminal deletions of the øX174 external scaffolding protein affect the timing and fidelity of assembly. Virology, 386(2), 303-309.

PMID: 19237183;Abstract:

The first α-helices of Microviridae external scaffolding proteins function as coat protein substrate specificity domains. Mutations in this helix can lengthen the lag phase before progeny production. 5′ deletion genes, encoding N-terminal deletion proteins, were constructed on plasmids and in the øX174 genome. Proteins lacking the first seven amino acids were able to rescue a nullD mutant when expressed from a plasmid. However, the lag phase before progeny production was lengthened. The øX174 mutant with the corresponding genomic gene grew very poorly. The molecular basis of the defective phenotype was complex. External scaffolding protein levels were reduced compared to wild-type and most of the viral coat protein in mutant infected cells appears to be siphoned off the assembly pathway. Second-site suppressors of the growth defects were isolated and appear to act via two different mechanisms. One class of suppressors most likely acts by altering mutant external scaffolding protein expression while the second class of suppressors appears to act on the level of protein-protein interactions. © 2009 Elsevier Inc. All rights reserved.

Dalphin, M. E., Fane, B. A., Skidmore, M. O., & Hayashi, M. (1992). Proteolysis of bacteriophage φX174 prohead accessory protein gpB by Escherichia coli OmpT protease is not essential for phage maturation in vivo. Journal of Bacteriology, 174(7), 2404-2406.

PMID: 1532389;PMCID: PMC205867;Abstract:

To examine whether cleavage of the φX174 prohead accessory protein, gpB, by the OmpT protease is required for phage development in vivo, a phage mutant lacking the OmpT cleavage site and an Escherichia coli C ΔompT strain were constructed. The results of burst size experiments suggest that neither the cleavage site nor the OmpT protein is required for φX174 development.

Bernal, R. A., Hafenstein, S., Olson, N. H., Bowman, V. D., Chipman, P. R., Baker, T. S., Fane, B. A., & Rossmann, M. G. (2003). Structural studies of bacteriophage α3 assembly. Journal of Molecular Biology, 325(1), 11-24.

PMID: 12473449;Abstract:

Bacteriophage α3 is a member of the Microviridae, a family of small, single-stranded, icosahedral phages that include φX174. These viruses have an ssDNA genome associated with approximately 12 copies of an H pilot protein and 60 copies of a small J DNA-binding protein. The surrounding capsid consists of 60 F coat proteins decorated with 12 pentameric spikes of G protein. Assembly proceeds via a 108 S empty procapsid that requires the external D and internal B scaffolding proteins for its formation. The α3 "open" procapsid structural intermediate was determined to 15 Å resolution by cryo-electron microscopy (cryo-EM). Unlike the φX174 "closed" procapsid and the infectious virion, the α3 open procapsid has 30 Å wide pores at the 3-fold vertices and 20 Å wide gaps between F pentamers as a result of the disordering of two helices in the F capsid protein. The large pores are probably used for DNA entry and internal scaffolding protein exit during DNA packaging. Portions of the B scaffolding protein are located at the 5-fold axes under the spike and in the hydrophobic pocket on the inner surface of the capsid. Protein B appears to have autoproteolytic activity that cleaves at an Arg-Phe motif and probably facilitates the removal of the protein through the 30 Å wide pores. The structure of the α3 mature virion was solved to 3.5 Å resolution by X-ray crystallography and was used to interpret the open procapsid cryo-EM structure. The main differences between the α3 and φX174 virion structures are in the spike and the DNA-binding proteins. The α3 pentameric spikes have a rotation of 3.5° compared to those of φX174. The α3 DNA-binding protein, which is shorter by 13 amino acid residues at its amino end when compared to the φX174 J protein, retains its carboxy-terminal-binding site on the internal surface of the capsid protein. The icosahedrally ordered structural component of the ssDNA appears to be substantially increased in α3 compared to φX174, allowing the building of about 10% of the ribose-phosphate backbone. © 2002 Elsevier Science Ltd. All rights reserved.

Garner, S. A., Everson, J. S., Lambden, P. R., Fane, B. A., & Clarke, I. N. (2004). Isolation, molecular characterisation and genome sequence of a bacteriophage (Chp3) from Chlamydophila pecorum. Virus Genes, 28(2), 207-214.

PMID: 14976421;Abstract:

Chlamydiae are obligate intracellular pathogens that have a unique developmental cycle. Thirty nine viable isolates representing all nine currently recognised chlamydial species were screened by immunofluorescence with a cross-reacting chlamydiaphage monoclonal antibody. A novel chlamydiaphage (Chp3) was detected in C. pecorum, a chlamydial species not previously known to carry bacteriophages. Chp3 belongs to the Microviridae, members of this virus family are characterised by circular, single-stranded DNA genomes and small T = 1 icosahedral capsids. Double-stranded replicative form Chp3 DNA was purified from elementary bodies and used as a template to determine the complete genome sequence. The genome of Chp3 is 4,554 base pairs and encodes eight open reading frames organised in the same genome structure as other chlamydiaphages. An unrooted phylogenetic tree was constructed based on the major coat proteins of 11 members of the Microviridae and Chp3. This showed that the Microviridae are clearly divided into two discrete sub-families; those that infect the Enterobacteriaceae e.g. ØX174 and the bacteriophages that infect obligate intracellular bacteria or mollicutes including SpV4 (Spiroplasma melliferum), ØMH2K (Bdellovibrio bacteriovorus) and the chlamydiaphages. Comparative analyses demonstrate that the chlamydiaphages can be further subdivided into two groupings, one represented by Chp2/Chp3 and the other by ØCPG1/ØCPAR39.