Structure and organization of bacteriophage Pf3 probed by Raman and ultraviolet resonance Raman spectroscopy

The Pseudomonas bacteriophage Pf3 is a long and narrow filament consisting of a covalently closed DNA single strand of 5833 bases sheathed by similar to 2500 copies of a 44-residue subunit. Ultraviolet resonance Raman spectra excited at 257, 244, 238, and 229 nm and off-resonance Raman spectra excit ed at 514.5 nm are reported for Pf3 in both H2O and D2O solutions. The key Raman bands are assigned to specific protein and DNA groups of the native V irion assembly. The results are compared with proposed assembly models and Raman spectra recently reported for the isomorphous (class ii) Pseudomonas phage Pf1 and the morphologically distinct (class I) coliphage fd [Wen, Z. Q., Overman, S. A., and Thomas, G. J., Jr. (1997) Biochemistry 36, 7810-782 0; Wen, Z. Q., Armstrong, A., and Thomas, G. J., Jr. (1999) Biochemistry 38 , 3148-3156]. Surprisingly, deoxynucleosides of the packaged DNA genome of Pf3 adopt the same conformation (C3'-endolanti) found for DNA packaged in t he class I fd virion rather than that (C2'-endolanti) associated with DNA i n the isomorphous Pf1 virion. However, DNA base stacking in Pf3, as judged by Raman hypochromic effects, differs significantly from that occurring in either Pf1 or fd. Thus, the single-stranded DNA genomes of Pf3, Pf1, and fd are all organized differently within their respective capsids, implying th at local subunit-DNA interactions may be important in determining the struc ture specific to each native assembly. The present study confirms a complet ely alpha -helical secondary structure for the Pf3 subunit and an unusual i ndolyl ring environment for the subunit tryptophan residue (Trp-38).