Ig

Figure 12-1 Filamentous phage f1/M13/fd: genes and gene products. pII binds to a sequence (the + strand origin) in the intergenic region (IG) of double-stranded DNA and nicks the (+) strand; the original (+) strand is displaced by Rep helicase as a new (+) strand is elongated from the 3' end of the nick by host DNA polymerase III, using the (—) strand as template. pX, which is identical to the C-terminal third of pII, is required for the accumulation of single-stranded DNA, as is pV. Dimers of pV bind cooperatively to single-stranded DNA, which collapses the circular genome into a flexible rod with the packaging signal (PS) exposed at one end of the filament. pVII and pIX are small coat proteins located at the tip of the virus that is first to emerge from the cell during assembly. pVIII is the major coat protein, several thousand copies of which form the cylinder that encases the single-stranded DNA phage genome. pIII and pVI are located at the end of the virion where they mediate termination of assembly and release of the virion from the cell membrane. pIII is also necessary for phage infectivity. pI may hydrolyze ATP to promote assembly; pXI is identical to the C-terminal third of pI; it lacks the cytoplasmic domain and may play a structural role as part of an oligomeric pI/pXI complex. pIV is a multimeric outer membrane channel through which the phage exits the bacterium.

seal the tips of the tube. The genome consists of a dozen or fewer closely packed genes and an intergenic (IG) region that contains sequences necessary for DNA replication and encapsidation. Unlike most bacterial viruses, filamentous phage are produced and secreted from infected bacteria without cell killing or lysis. Rather, they assemble at and are secreted across the cell membrane(s). Readers are referred to several other reviews on filamentous phage (4, 82, 101, 106,112) for more comprehensive information and citations of the primary literature than are given here.

Most information about filamentous phages derives from those that infect Eschericia coli (f!/M13/fd, and to a lesser extent Ike and I2-2). Structural analysis of several others has shown that the packing density (protein:DNA mass ratio in the particle) can vary, as can the symmetry of the particles. Those defined as class I, including the E. coli phages, have a 5-fold rotation axis combined with a 2-fold screw axis, while class II phage like Pseudomonas phages Pf1 and Pf3 have a simple one-start helix (107). The mechanism of assembly is likely to be fundamentally the same for both classes; perhaps differences in the primary sequences of the major coat proteins account for the different subunit packing. DNA sequences reveal the modular nature of phage evolution and other variations. Phages I2-2 and IKe are highly homologous over the two thirds of their genomes that encode capsid and morphogenetic proteins, whereas the remaining portions, containing the replication origins and replication genes, are unrelated (153). Although Pf3 has a gene IV it is in a different position in the genome than in other filamentous phages. Vibrio cholerae CTXF lacks gene IV (162, 163), which encodes an outer membrane assembly protein that is essential in the E. coli phages; instead, it uses the homologous host protein, EpsD (26). EpsD, one of three Vibrio pIV homologs (members of the widespread "secretin" family), is also required for secretion of cholera toxin (133, 143). B5, the recently discovered filamentous phage that infects the Gram-positive Propionibacterium freuden-reichii, also lacks a gene IV (18); since Gram-positive bacteria lack an outer membrane, presumably neither pIV nor a bacterial equivalent is necessary. Whereas adjacent genes encode two small minor coat proteins (pVII and pIX) located at the same end of the particle in E. coli phages, a single gene is located in the analogous region of the Pf3 and some other phage genomes, which may encode a functionally equivalent fused minor coat protein. The major coat proteins of the E. coli phages are synthesized with a signal sequence, while those of Pf3 (90), PH75, a filamentous phage of Ther-mus thermophilus (119), and B5 (18) are not. Several filamentous phages of Vibrio and Xanthomonas, but not those of E. coli or Pseudomonas aeruginosa, lysogenize their host (10, 93,163). Finally, CTXF is so far unique among filamentous phages (although not among phages in general) in carrying additional genes, in this case the genes that encode cholera toxin (163). Unless specified, the properties of filamentous phage described below refer to the almost identical f1, M13, and fd (the "Ff," for F-specific filamentous phage, see "Infection" below).

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