Identification of two new capsid proteins in bacteriophage M13

Regulation of filamentous bacteriophage length by modification of electrostatic interactions between coat protein and DNA

Bacteriophage fd gene VIII, which encodes the major capsid protein, was mutated to convert the serine residue at position 47 to a lysine residue (S47K), thereby increasing the number of positively charged residues in the C-terminal region of the protein from four to five. The S47K coat protein underwent correct membrane insertion and processing but could not encapsidate the viral DNA, nor was it incorporated detectably with wild-type coat proteins into hybrid bacteriophage particles. However, hybrid virions could be constructed from the S47K coat protein and a second mutant coat protein, K48Q, the latter containing only three lysine residues in its C-terminal region. K48Q phage particles are approximately 35% longer than wild-type. Introducing the S47K protein shortened these particles, the S47K/K48Q hybrids exhibiting a range of lengths between those of K48Q and wild-type. These results indicate that filamentous bacteriophage length (and the DNA packaging underlying it) are regulated by unusually flexible electrostatic interactions between the C-terminal domain of the coat protein and the DNA. They strongly suggest that wild-type bacteriophage fd makes optimal use of the minimum number of coat protein subunits to package the DNA compactly.

Pore-forming properties of the adsorption protein of filamentous phage fd

The gene 3-encoded adsorption protein (g3p) of filamentous phage fd has been purified to homogeneity by using high-performance liquid chromatography. Removal of SDS from the SDS-solubilized g3p results in spontaneous oligomerization of the g3p. Reconstitution into artificial lipid bilayer membranes shows that the oligomer forms large aqueous pores that remain open for seconds and are insensitive to changes in membrane potential. The estimated diameter of the pores suggest that they are large enough to allow passage of phage single-stranded DNA. The implications of these findings for phage infection are discussed.

Dual importance of positive charge in the C-terminal region of filamentous bacteriophage coat protein for membrane insertion and DNA-protein interaction in virus assembly

Gene VIII encoding the procoat protein of the Class II filamentous bacteriophage Pf1 (infecting Pseudomonas aeruginosa) has been cloned and expressed in Escherichia coli and subjected to site-directed mutagenesis. The two positively charged residues clustered near the C-terminus, arginine-44 and lysine-45, were systematically converted to uncharged residues and serine-41 was converted to an arginine residue. Removal of positive charge in the C-terminal region of the molecule seriously impaired the ability of the procoat molecule to undergo insertion at the E. coli cell inner membrane, as manifested by the diminished processing of the N-terminal leader peptide. The basic amino acids near the C-terminus of the coat protein are also involved in neutralizing the negatively charged viral DNA during virus assembly. However, despite its additional positive charge, the S41R mutant protein was unable to participate in the assembly of Class I bacteriophage fd in E. coli. This dual requirement of positively charged residues in the C-terminal region of the coat protein for membrane processing and insertion and for electrostatic neutralization of the encapsidated DNA poses important constraints on the evolution of filamentous bacteriophages with two different helical symmetries.

Variable electrostatic interaction between DNA and coat protein in filamentous bacteriophage assembly

A restriction fragment carrying the major coat protein gene (gene VIII) was excised from the DNA of the class I filamentous bacteriophage fd, which infects Escherichia coli. This fragment was cloned into the expression plasmid pKK223-3, where it came under the control of the tac promoter, generating plasmid pKf8P. Bacteriophage fd gene VIII was similarly cloned into the plasmid pEMBL9+, enabling it to be subjected to site-directed mutagenesis. By this means the positively charged lysine residue at position 48, one of four positively charged residues near the C terminus of the protein, was turned into a negatively charged glutamic acid residue. The mutated fd gene VIII was cloned back from the pEMBL plasmid into the expression plasmid pKK223-3, creating plasmid pKE48. In the presence of the inducer isopropyl-beta-D-thiogalactoside, the wild-type and mutated coat protein genes were strongly expressed in E. coli TG1 cells transformed with plasmids pKf8P and pKE48, respectively, and the product procoat proteins underwent processing and insertion into the E. coli cell inner membrane. A net positive charge of only 2 on the side-chains in the C-terminal region is evidently sufficient for this initial stage of the virus assembly process. However, the mutated coat protein could not encapsidate the DNA of bacteriophage R252, an fd bacteriophage carrying an amber mutation in its own gene VIII, when tested on non-suppressor strains of E. coli. On the other hand, elongated hybrid bacteriophage particles could be generated whose capsids contained mixtures of wild-type (K48) and mutant (E48) subunits. This suggests that the defect in assembly may occur at the initiation rather than the elongation step(s) in virus assembly. Other mutations of lysine-48 that removed or reversed the positive charge at this position in the C-terminal region of the coat protein were also found to lead to the production of commensurately longer bacteriophage particles. Taken together, these results indicate direct electrostatic interaction between the DNA and the coat protein in the capsid and support a model of non-specific binding between DNA and coat protein subunits with a stoicheiometry that can be varied during assembly.

Cloning and expression of the filamentous bacteriophage Pf1 major coat protein gene in Escherichia coli. Membrane protein processing and virus assembly

A restriction fragment carrying the major coat protein gene (gene VIII) was excised from the replicative form (RF) DNA of the class II filamentous bacteriophage Pf1, which infects Pseudomonas aeruginosa. This fragment was cloned into the expression plasmid pKK223-3, where it came under the control of the tac promoter. In transformed Escherichia coli JM101 cells, in the presence of the inducer isopropyl-beta-D-thiogalactoside, the bacteriophage Pf1 gene was strongly expressed. The bacteriophage Pf1 coat protein displays the same pattern of negatively charged N-terminal region, hydrophobic middle region and positively charged C-terminal region as that of its counterpart in the class I bacteriophage fd, which infects E. coli, but otherwise the two proteins have no sequence homology. However, the Pf1 procoat protein was found to undergo processing and insertion into the E. coli cell inner membrane, like its fd counterpart, demonstrating that this part of the assembly process is the same for these different bacteriophages. The complete transcriptional unit, incorporating the tac promoter and rrnB transcription terminators flanking the Pf1 coat protein gene, was excised from the expression plasmid and cloned into the intergenic space of bacteriophage R252, an fd bacteriophage that carries an amber mutation in its own major coat protein gene. The Pf1 coat protein gene was again well expressed in infected E. coli cells but the chimeric bacteriophage had growth properties identical to those of the parent bacteriophage R252 on suppressor and non-suppressor strains of E. coli. The class I bacteriophage Pf1 coat protein evidently cannot be recognized by the class I bacteriophage assembly complex at or in the E. coli cell inner membrane, either at the point of initiation of assembly or during the elongation process.

The major coat protein gene of the filamentous Pseudomonas aeruginosa phage Pf3: absence of an N-terminal leader signal sequence

From in vitro protein synthesis studies and nucleotide sequence analysis it has been deduced that, unlike the major coat proteins of the hitherto studied filamentous bacterial viruses Ff (M13, fd and f1), IKe and Pf1, the major coat protein of the filamentous Pseudomonas aeruginosa virus Pf3 is not synthesized as a precursor containing a leader signal polypeptide at its N-terminal end. From the elucidated nucleotide sequence of the Pf3 major coat protein gene it follows that the coat protein is 44 amino acid residues long (mol.wt. 6425). No sequence homology was observed with the major coat protein genes of either the Ff group or IKe but, similar to these phages, 3' ward of the Pf3 coat protein gene a DNA sequence is located which has many characteristics in common with rho-independent transcription termination signals.

Nucleotide sequence of bacteriophage f1 DNA

The nucleotide sequence of the DNA of the filamentous coliphage f1 has been determined. In agreement with earlier conclusions, the genome was found to comprise 6,407 nucleotides, 1 less than that of the related phage fd. Phage f1 DNA differs from that of phage M13 by 52 nucleotide changes, which lead to 5 amino acid substitutions in the corresponding proteins of the two phages, and from phage fd DNA by 186 nucleotide changes (including the single-nucleotide deletion), which lead to 12 amino acid differences between the proteins of phages f1 and fd. More than one-half of the nucleotide changes in each case are found in the sequence of 1,786 nucleotides comprising gene IV and the major intergenic region between gene IV and gene II. The sequence of this intergenic region (nucleotides 5501 to 6005) of phage f1 differs from the sequence reported by others through the inclusion of additional single nucleotides in eight positions and of a run of 13 nucleotides between positions 5885 and 5897, a point of uncertainty in the earlier published sequence. The differences between the sequence of bacteriophage f1 DNA now presented and a complete sequence for the DNA previously published by others are discussed, and the f1 DNA sequence is compared with those of bacteriophages M13 and fd.

Oligonucleotide-directed mutagenesis of gene IX of bacteriophage M13

The synthetic oligodeoxyribonucleotide pCGAAAGACTACAC has been applied as a site-specific mutagen to introduce a T leads to G transversion mutation at nucleotide position 1223 of the M13 DNA sequence. The in vitro-induced conversion of a TAT codon into a TAG at this position resulted in gene IX mutants with an amber mutant character thereby confirming that this reading frame defines a gene of an essential phage protein. The gene IX amber mutants obtained grew well on SuI (Ser) and SuIII (Tyr) suppressing strains but could not be propagated on SuII (Gln) and SuVI (Leu) strains. Complementation studies show that amber mutants in genes V and VII exert a polar effect on gene IX expression suggesting that these three contiguous genes form an operon. In addition, we demonstrate the in vitro synthesis of gene IX-protein in a coupled transcription-translation system.

Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd

The DNA sequence of the filamentous phage F1, consisting of 6407 nucleotides, has been determined. When compared with the DNA sequence of the related filamentous phage fd (Beck et al., 1978), the f1 sequence is one nucleotide shorter and differs in 180 positions from the fd DNA. Only ten of these base exchanges cause amino acid exchanges in the known gene products. Most of the exchanges in f1 are the same as in M13 (Van Wezenbeek et al., 1980), showing a near identity of these two phage (there are only 59 nucleotide differences). Regulatory units for replication, transcription, and translation are in their essential parts identical in all three phage.

Structure and architecture of the bacterial virus fd. An infrared linear dichroism study

Oriented gels of intact bacterial virus fd have been invetigated by infrared linear dichroism. Infrared absorption band maxima and dichroism indicate an alpha-helix content of the major coat protein of 95-100%. The alpha-helical rods of the coat protein are aligned parallel to the long axis of the virion with an inclination roughly estimated to approximately 37 degree. The presence of DNA infrared bands at 968, 885, 830 and 799 cm-1, the absence of a band at 860 cm-1 and the perpendicular polarization of the symmetric PO-2 stretching vibration at 1085 cm-1 are all indicative of a B-type backbone conformation in the single-stranded DNA. We find no evidence for specific interaction between aromatic side groups (phenylalanine, tyrosine) and the DNA bases. Our results independently confirm most features of the model of Marvin and co-workers [2,15 ] based on low-resolution X-ray diffraction studies. However, our findings contradict their suggestion of an A-type DNA in the bacterial virus fd. Two results are consistent with rigid and stable order in the virus. First, over a 4-day period, 65% of the peptide hydrogens remain unexchanged with deuterium. Second, changes in the relative humidity of the sample do not result in any shifts in the DNA spectrum that are characteristic of free DNA.

Genes VI, VII, and IX of phage M13 code for minor capsid proteins of the virion

The minor capsid proteins C and D from phage M13 have been characterized by differential amino acid labeling and amino-terminal sequence analysis. We demonstrate that D protein (Mr 12,260) is the product of gene VI, whereas the C component is composed of the products of both gene VII (Mr 3580) and gene IX (Mr 3650). Our data further show that the proteins of genes VI, VII, and IX are not subject to proteolytic processing but are packaged into mature virions as their primary translational products. On the basis of incorporation of specific amino acids, the copy numbers of these proteins in M13 virions could be estimated relative to the number of A protein molecules. The M13 phage contains on the average 5 molecules of A protein, 5 molecules of VI protein and 3-4 molecules of both VII protein and IX protein. These copy numbers remained unchanged in M13 recombinant phages of up to two times the length of wild-type phages, a fact that indicates that these minor capsid proteins are located at either one or both ends of the phage filament.

Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd

The 6407 nucleotide-long sequence of bacteriophage M13 DNA has been determined using both the chemical degradation and chain-termination methods of DNA sequencing. This sequence has been compared with that of the closely related bacteriophage fd (Beck et al., 1978). M13 DNA appears to be only a single nucleotide shorter than fd DNA. There is an average of 3.0% of nucleotide-sequence differences between the two genomes, but the distribution of these changes is not random; the sequence of some genes is more conserved than of others. In contrast, the nucleotide sequences and positions of the regulatory elements involved in transcription, translation and replication appear to be identical in both filamentous phage DNA genomes.