Converging antigenic structure of a recombinant viral peptide displayed on different frameworks of carrier proteins

A peptide reproducing the G-H loop amino acid sequence of foot-and-mouth disease virus VP1 protein was fused to the solvent-exposed C-terminus of the bacteriophage P22 tailspike protein [Carbonell and Villaverde (1996) Gene, in press], a homotrimeric polypeptide with a strong beta-helical structure. This fusion does not interfere with the biological activities of the phage tail. The antigenic profile of the complex antigenic site A within the G-H loop has been determined by competitive ELISA with a panel of monoclonal antibodies directed against different overlapping B-cell epitopes. The antigenic data have been compared with those obtained with a set of 12 chimeric beta-galactosidases displaying the G-H loop on different exposed regions. A high coincidence has been evidenced between the antigenicity of the viral peptide fused to the phage protein and that of some peptides inserted in an exposed loop of the activating interface of beta-galactosidase. This indicates that completely different structural frameworks of carrier proteins can provide similar constraints that allow the recombinant peptide to successfully mimic the antigenicity, and probably conformational features, of the natural peptide on the virion surface.

Mutations that stabilize folding intermediates of phage P22 tailspike protein: folding in vivo and in vitro, stability, and structural context

The folding of the trimeric phage P22 tailspike protein is affected by single amino acid substitutions designated temperature-sensitive folding (tsf) mutations. Their phenotypes are alleviated by two repeatedly isolated global suppressor (su) mutations (su V331A and su A334V) and by two additional substitutions (su V331G and su A334I), accessible through site-directed mutagenesis. We investigated the influence of the suppressor mutations on tailspike refolding in vitro, on its maturation at high expression levels in vivo, and on the rates of thermal unfolding of the native protein. All su mutations improved the folding efficiency in vitro and in vivo, but the relative effects of substitutions at position 334 were more pronounced in vivo, whereas the 331 substitutions were more effective in vitro. V331G caused the strongest increase in refolding yields of any single mutation, and was as effective as the V331A/A334V double mutation, where the two single mutations exhibited an additive effect. Both V331A and V331G retarded thermal denaturation, while A334V did not affect, and A334I accelerated unfolding. A334I is the first mutation found to affect the folding of the tailspike and the thermal stability of the native protein in opposite directions. The observed effects can be rationalized on the basis of the recently determined crystal structure of an N-terminally shortened tailspike. As the backbone dihedral angles of Val331 (phi = -119 degrees, psi = -142 degrees) are unusual for non-glycine residues, V331G and V331A may remove steric strain and thereby stabilize folding intermediates and the native protein. The beta-branched side-chains of Val and Ile substituted for Ala334 in the interior of the protein may improve a hydrophobic stack of residues in the large parallel beta-helix. This is likely important in loosely structured early folding intermediates, but not in the very rigid native structure, where the side-chain of Ile can hardly be accommodated.

Multimeric intermediates in the pathway to the aggregated inclusion body state for P22 tailspike polypeptide chains

The failure of newly synthesized polypeptide chains to reach the native conformation due to their accumulation as inclusion bodies is a serious problem in biotechnology. The critical intermediate at the junction between the productive folding and the inclusion body pathway has been previously identified for the P22 tailspike endorhamnosidase. We have been able to trap subsequent intermediates in the in vitro pathway to the aggregated inclusion body state. Nondenaturing gel electrophoresis identified a sequential series of multimeric intermediates in the aggregation pathway. These represent discrete species formed from noncovalent association of partially folded intermediates rather than aggregation of native-like trimeric species. Monomer, dimer, trimer, tetramer, pentamer, and hexamer states of the partially folded species were populated in the initial stages of the aggregation reaction. This methodology of isolating early multimers along the aggregation pathway was applicable to other proteins, such as the P22 coat protein and carbonic anhydrase II.

Nascent chains: folding and chaperone interaction during elongation on ribosomes

Monoclonal antibodies that detect folding intermediates in vitro were used to monitor the appearance of folded polypeptide chains during their synthesis on the ribosomes. Nascent immunoreactive chains of the bacteriophage P22 tail-spike protein and of the Escherichia coli beta 2 subunit of tryptophan-synthase were thus identified, suggesting that they can fold on the ribosomes. Moreover, the immunoreactivity of ribosome-bound tryptophan-synthase beta-chains of intermediate lengths was shown to appear with no detectable delay compared to their synthesis. This suggested that beta-chains start folding during their elongation on the ribosomes. However, newly synthesized incomplete beta-chains were shown to interact with chaperones while still bound to the ribosome. Because of the peculiar properties of the epitope recognized by the anti-tryptophan-synthase monoclonal antibody used, it could not be concluded whether the immunoreactivity of the nascent beta-chains resulted from their ability to fold cotranslationally or from their association with chaperones which might maintain them in an unfolded, immunoreactive state.

Selective in vivo rescue by GroEL/ES of thermolabile folding intermediates to phage P22 structural proteins

The in vivo conformational substrates of the GroE chaperonins have been difficult to identify, in part because of limited information on in vivo polypeptide chain folding pathways. Temperature-sensitive folding (tsf) mutants have been characterized for the coat protein and tailspike protein of phage P22. These mutations block intracellular folding at restrictive temperature by increasing the lability of folding intermediates without impairing the stability or function of the native state. Overexpression of GroEL/ES suppressed the defects of tsf mutants at 17 sites in the coat protein, by improving folding efficiency rather than assembly efficiency or protein stability. Immunoprecipitation experiments demonstrated that GroEL interacted transiently with newly synthesized wild-type coat protein and that this interaction was prolonged by the tsf mutations. Folding defects of the tailspike polypeptide chains were not suppressed. A fraction of the tsf mutant tailspike chains bound to GroEL but were inefficiently discharged. The results suggest that 1) thermolabile folding intermediates are natural substrates of GroEL/ES; 2) although GroEL may bind such intermediates for many proteins, the chaperoning function is limited to a subset of substrate proteins; and 3) a key reason for the heat-shock response may be to stabilize thermolabile folding intermediates at elevated temperatures.

Phage tailspike protein. A fishy tale of protein folding

The crystal structure of bacteriophage P22 tailspike protein reveals a striking fold with a distinctive, fish-like appearance, and helps explain many of the properties of this unusual molecule and its folding pathway.

Intracellular trapping of a cytoplasmic folding intermediate of the phage P22 tailspike using iodoacetamide

Critical steps in polypeptide chain folding within the bacterial cytoplasm have been difficult to identify. Salmonella cells infected with temperature-sensitive folding mutants of the P22 tailspike protein at restrictive temperature accumulated a metastable folding intermediate with a half-life of 6 min at 39 degrees C. The native trimeric tailspike contains 24 buried cysteines (8/chain) but neither disulfide bonds nor active site cysteines. Eighteen of the 24 cysteines are involved in strong hydrogen bonds (Thomas, G. J., Jr., Becka, R., Sargent, D., Yu, M.-H., and King, J. (1990) Biochemistry 29, 4181-4187). Cyanide and iodoacetamide prevented the folding and association of the restrictive temperature folding intermediate to the native state after shift to permissive temperature. The cytoplasmic folding intermediate was covalently modified by iodoacetamide within infected cells. Chains which had reacted with iodoacetamide were unable to proceed through the folding pathway. Iodoacetamide also reacted with a folding intermediate during the refolding of purified tailspike chains in vitro, inhibiting further folding. No reaction occurred with native tailspike in vivo or in vitro. The target residues in the intermediates were in the carboxyl terminus of the chain and may be a unique set of cysteine residues that are activated during protein folding, but not in the native state.

Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer

The tailspike protein (TSP) of Salmonella typhimurium phage P22 is a part of the apparatus by which the phage attaches to the bacterial host and hydrolyzes the O antigen. It has served as a model system for genetic and biochemical analysis of protein folding. The x-ray structure of a shortened TSP (residues 109 to 666) was determined to a 2.0 angstrom resolution. Each subunit of the homotrimer contains a large parallel beta helix. The interdigitation of the polypeptide chains at the carboxyl termini is important to protrimer formation in the folding pathway and to thermostability of the mature protein.

In vitro and ribosome-bound folding intermediates of P22 tailspike protein detected with monoclonal antibodies

It remains unclear whether polypeptide chains renaturing in vitro from strong denaturants proceed through the same folding pathway as chains released from ribosome within cells. Folding intermediates formed both in vivo and in vitro have been examined using three monoclonal antibodies shown previously to recognize different epitopes of the native P22 tailspike protein (Friguet, B., Djavadi-Ohaniance, L., Haase-Pettingell, C. A., King J., and Goldberg, M. E. (1990) J. Biol. Chem. 265, 10347-10351). The tailspike protein was reconstituted from polypeptide chains unfolded by urea as described by Fuchs et al. (Fuchs, A., Seiderer, C., and Seckler, R. (1991) Biochemistry 30, 6598-6604), and the appearance of immunoreactive forms during the refolding was monitored. The three antibodies discriminated intermediates at different stages in the folding pathway. On the basis of the reconstitution pathway determined from spectroscopic and hydrodynamic measurements by Fuchs et al. (1991), monoclonal antibody (mAb) 236-3 recognized partially folded monomers, mAb 155-3 recognized folded protomers in a protrimer species, and mAb 33-2 recognized the native trimer. The kinetics of appearance of the immunoreactive forms during the in vitro refolding of the protein in crude extracts of phage-infected cells was similar to that observed with the pure tailspike. Thus, the antibodies provided probes for the chain folding and association pathway in vivo. The conformation of the ribosome-bound tailspike polypeptide chains of the infected cells was analyzed with the three antibodies. The antibodies recognizing native trimer and the protrimer did not bind chains associated with the ribosomes. Antibody 236-3, which recognized structured monomers in vitro, bound to the polypeptide chains still associated with ribosomes. This result suggests that steps that take place in solution during in vitro refolding may occur in a ribosome-bound state in vivo.

Isolation of suppressors of temperature-sensitive folding mutations

Mutations in the tailspike gene (gene 9) of Salmonella typhimurium phage P22 have been used to identify amino acid interactions during the folding of a polypeptide chain. Since temperature-sensitive folding (tsf) mutations cause folding defects in the P22 tailspike polypeptide chain, it is likely that mutants derived from these and correcting the original tsf defects (second-site intragenic suppressors) identify interactions during the folding pathway. We report the isolation and identification of second-site revertants to tsf mutants.

Mechanism of phage P22 tailspike protein folding mutations

Temperature-sensitive folding (tsf) and global-tsf-suppressor (su) point mutations affect the folding yields of the trimeric, thermostable phage P22 tailspike endorhamnosidase at elevated temperature, both in vivo and in vitro, but they have little effect on function and stability of the native folded protein. To delineate the mechanism by which these mutations modify the partitioning between productive folding and off-pathway aggregation, the kinetics of refolding after dilution from acid-urea solutions and the thermal stability of folding intermediates were analyzed. The study included five tsf mutations of varying severity, the two known su mutations, and four tsf/su double mutants. At low temperature (10 degrees C), subunit-folding rates, measured as an increase in fluorescence, were similar for wild-type and mutants. At 25 degrees C, however, tsf mutations reduced the rate of subunit folding. The su mutations increased this rate, when present in the tsf-mutant background, but had no effect in the wild-type background. Conversely, tsf mutations accelerated, and su mutations retarded the irreversible off-pathway reaction, as revealed by temperature down-shifts after varied times during refolding at high temperature (40 degrees C). The kinetic results are consistent with tsf mutations destabilizing and su mutations stabilizing an essential subunit folding intermediate. In accordance with this interpretation, tsf mutations decreased, and su mutations increased the temperature resistance of folding intermediates, as disclosed by temperature up-shifts during refolding at 25 degrees C. The stabilizing and destabilizing effects were most pronounced early during refolding. However, they were not limited to subunit-folding intermediates and were also observable during thermal unfolding of the native protein.

Temperature-sensitive mutations and second-site suppressor substitutions affect folding of the P22 tailspike protein in vitro

One of the central problems in protein folding is how amino acid sequences within polypeptide chains direct polypeptide chain folding and avoid off-pathway aggregation both in intracellular environments and in the test tube. The tailspike protein of phage P22 is a model system for which genetic analysis has permitted mutational dissection of the role of amino acid positions in the polypeptide chain in directing its in vivo folding. Two classes of mutations that affect intracellular folding and aggregation have been characterized; temperature-sensitive folding (tsf) mutants and second-site suppressors of tsf mutants. Here we report the effects of these mutations on the in vitro refolding and aggregation pathway of the purified proteins. The tsf mutations reduced refolding yields at high temperature and increased aggregation, while second-site suppressors enhanced refolding and inhibited aggregation in the test tube. For both types of mutations, the strength of the effects observed in vitro correlated with their in vivo phenotypes. The results confirm that the mutations act intrinsically on the folding pathway of the tailspike polypeptide and not through accessory proteins.

DNA inversion regions Min of plasmid p15B and Cin of bacteriophage P1: evolution of bacteriophage tail fiber genes

Plasmid p15B and the genome of bacteriophage P1 are closely related, but their site-specific DNA inversion systems, Min and Cin, respectively, do not have strict structural homology. Rather, the complex Min system represents a substitution of a Cin-like system into an ancestral p15B genome. The substituting sequences of both the min recombinase gene and the multiple invertible DNA segments of p15B are, respectively, homologous to the pin recombinase gene and to part of the invertible DNA of the Pin system on the defective viral element e14 of Escherichia coli K-12. To map the sites of this substitution, the DNA sequence of a segment adjacent to the invertible segment in the P1 genome was determined. This, together with already available sequence data, indicated that both P1 and p15B had suffered various sequence acquisitions or deletions and sequence amplifications giving rise to mosaics of partially related repeated elements. Data base searches revealed segments of homology in the DNA inversion regions of p15B, e14, and P1 and in tail fiber genes of phages Mu, T4, P2, and lambda. This result suggest that the evolution of phage tail fiber genes involves horizontal gene transfer and that the Min and Pin regions encode tail fiber genes. A functional test proved that the p15B Min region carries a tail fiber operon and suggests that the alternative expression of six different gene variants by Min inversion offers extensive host range variation.

DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages

We have determined the DNA sequence of the bacteriophage P2 tail genes G and H, which code for polypeptides of 175 and 669 residues, respectively. Gene H probably codes for the distal part of the P2 tail fiber, since the deduced sequence of its product contains regions similar to tail fiber proteins from phages Mu, P1, lambda, K3, and T2. The similarities of the carboxy-terminal portions of the P2, Mu, ann P1 tail fiber proteins may explain the observation that these phages in general have the same host range. The P2 H gene product is similar to the products of both lambda open reading frame (ORF) 401 (stf, side tail fiber) and its downstream ORF, ORF 314. If 1 bp is inserted near the end of ORF 401, this reading frame becomes fused with ORF 314, creating an ORF that may represent the complete stf gene that encodes a 774-amino-acid-long side tail fiber protein. Thus, a frameshift mutation seems to be present in the common laboratory strain of lambda. Gene G of P2 probably codes for a protein required for assembly of the tail fibers of the virion. The entire G gene product is very similar to the products of genes U and U' of phage Mu; a region of these proteins is also found in the tail fiber assembly proteins of phages TuIa, TuIb, T4, and lambda. The similarities in the tail fiber genes of phages of different families provide evidence that illegitimate recombination occurs at previously unappreciated levels and that phages are taking advantage of the gene pool available to them to alter their host ranges under selective pressures.

Molecular properties of global suppressors of temperature-sensitive folding mutations in P22 tailspike endorhamnosidase

Two global suppressors (Val-331 greater than Ala and Ala-334 greater than Val) have been identified for temperature-sensitive folding (tsf) mutations in gene 9 of bacteriophage P22 (Mitraki, A., Fane, B., Haase-Pettingell, C., Sturtevant, J., and King, J. (1991) Science 253, 54-58). We have introduced 19 different single amino acid substitutions at the two global suppressor sites independently and examined the effects on the tailspike formation in Escherichia coli. Folding and maturation patterns of the various substitutions at the two global suppressor sites in the wild-type background suggest that Val-331 is located on the protein surface and Ala-334 is in the hydrophobic region. In combination with a tsf mutation, tsfH304 (Gly-244 greater than Arg), only Gly at 331 and Ile at 334, the substitutions that have similar side chain properties to the original suppressor sequences, were active as tsf suppressors. The newly identified suppressors of tsfH304 could also alleviate the tsf defect of three other mutations. The mutant carrying both Val-331 greater than Ala and Ala-334 greater than Val substitutions was also a global suppressor and was more active in suppressing the tsf defect than mutants carrying only one substitution. The suppressors may act by increasing the stability of an intermediate in the productive pathway of folding and maturation of the mutant polypeptides.

Global suppression of protein folding defects and inclusion body formation

Amino acid substitutions at a site in the center of the bacteriophage protein P22 tailspike polypeptide chain suppress temperature-sensitive folding mutations at many sites throughout the chain. Characterization of the intracellular folding and chain assembly process reveals that the suppressors act in the folding pathway, inhibiting the aggregation of an early folding intermediate into the kinetically trapped inclusion body state. The suppressors alone increase the folding efficiency of the otherwise wild-type polypeptide chain without altering the stability or activity of the native state. These amino acid substitutions identify an unexpected aspect of the protein folding grammar--sequences within the chain that carry information inhibiting unproductive off-pathway conformations. Such mutations may serve to increase the recovery of protein products of cloned genes.

In vitro folding pathway of phage P22 tailspike protein

The intracellular chain folding and association pathway of the thermostable, trimeric phage P22 tailspike endorhamnosidase has been the subject of a previous detailed study employing temperature-sensitive folding mutants. Recently, reconstitution of native tailspikes from completely unfolded polypeptides has been accomplished, providing a model system to compare protein folding pathways in vivo and in vitro. The in vitro reconstitution pathway of the protein after dilution from guanidine hydrochloride or acid-urea solutions at 10 degrees C was characterized by spectroscopic and hydrodynamic techniques, and may be summarized as an ordered sequence of folding, association, and folding reactions. Multiphasic folding of monomers was indicated by changes in circular dichroism and fluorescence, with a rate constant of k = 1.6 X 10(-3) s-1 for the slowest phase observed spectroscopically. Trimerization of structured monomers was followed by size-exclusion HPLC and was completed within 1.5 h at a protein concentration of 20 micrograms/mL. Although at this time trimers did not exchange subunits, they were readily dissociable by dodecyl sulfate in the cold. Formation of native, detergent-resistant trimers was only completed after 3 days of reconstitution at 10 degrees C. The reconstitution pathway of the tailspike protein closely resembles its intracellular maturation path. Thus, the in vitro reconstitution system, as a valid model of chain folding and association in vivo, should provide the tools to localize the steps or intermediates on the pathway that are the targets of temperature-sensitive folding mutations.

Identification of global suppressors for temperature-sensitive folding mutations of the P22 tailspike protein

Suppressor mutations which alleviate the defects in folding mutants of the P22 gene 9 tailspike protein have recently been isolated (Fane, B. and King, J. (1991) Genetics 127, 263-277). The starting folding defects were in missense polypeptide chains generated by host amino acid insertions at different amber mutant sites. Fragments of genes carrying the amber mutations with and without their independently isolated suppressor mutations were cloned and sequenced. The parental nonsense mutations were located at Q45, K122, E156, W202, W207, Y232, and W365. Their conformational suppressors were single amino acid substitutions at a limited set of sites, V84 greater than A, V331 greater than A, and A334 greater than V. The V331 greater than A or A334 greater than V suppressors were independently recovered starting with different mutant sites suggesting that they acted by some global or general mechanism. When the V331 greater than A and A334 greater than V mutations were crossed into well-characterized temperature-sensitive folding (tsf) mutants at various sites in the tailspike protein, they suppressed all of the eight tsf mutants tested. Since the tsf defects destabilize folding intermediates rather than the native conformation, this result implies that the suppressors act in the folding pathway. Strains carrying the isolated suppressor mutations displayed no obvious phenotypic defect and formed native biologically active tailspikes. Thus, these single amino acid substitutions have striking influences on the efficiency of intracellular chain folding, without causing functional defects in the native protein.

Single mutations in a gene for a tail fiber component of an Escherichia coli phage can cause an extension from a protein to a carbohydrate as a receptor

The T-even type Escherichia coli phage Ox2 recognizes the outer membrane protein OmpA as a receptor. This recognition is accomplished by the 266 residue protein 38, which is located at the free ends of the virion's long tail fibers. Host-range mutants had been isolated in three consecutive steps: Ox2----Ox2h5----Ox2h10----Ox2h12, with Ox2h12 recognizing the outer membrane protein OmpC efficiently and having lost some affinity for OmpA. Protein 38 consists, in comparison with these proteins of other phages, of two constant and one contiguous array of four hypervariable regions; the alterations leading to Ox2h12 were all found within the latter area. Starting with Ox2h12, further host-range mutants could be isolated on strains resistant to the respective phage: Ox2h12----h12h1----h12h1.1----h12h1.11----h12 h1.111. It was found that Ox2h12h1.1 (and a derivative of Ox2h10, h10h4) probably uses, instead of OmpA or OmpC, yet another outer membrane protein, designated OmpX. Ox2h12h1.11 was obtained on a strain lacking OmpA, -C and -X. This phage could not grow on a mutant of E. coli B, possessing a lipopolysaccharide (LPS) with a defective core oligosaccharide; Ox2h12h1.111 was obtained from this strain. It turned out that the latter two mutants used LPS as a receptor, most likely via its glucose residues. Selection for resistance to them in E. coli B (ompA+, ompC-, ompX-) yielded exclusively LPS mutants, and in another strain, possessing OmpA, C and X, the majority of resistant mutants were of this type. Isolated LPS inactivated the mutant phages very well and was inactive towards Ox2h12. By recombining the genes of mutant phages into the genome of parental phages it could be shown that the phenotypes were associated with gene 38. All mutant alterations (mostly single amino acid substitutions) were found within the hypervariable regions of protein 38. In particular, a substitution leading to Ox2h12h1.11 (Arg170----Ser) had occurred at the same site that led to Ox2h10 (His170----Arg), which binds to OmpC in addition to OmpA. It is concluded that not only can protein 38 gain the ability to switch from a protein to a carbohydrate as a receptor but can do so using the same domain of the polypeptide.

Requirement of the SecB chaperone for export of a non-secretory polypeptide in Escherichia coli

The SecB protein of Escherichia coli is a cytosolic component of the export machinery which can prevent some precursors from prematurely folding into export-incompatible conformations by binding to the newly synthesised polypeptide. The feature(s) of target proteins recognised by SecB, however, are unclear and have been a matter of controversy. Also, it has not been asked if binding of SecB is specific for secretory proteins. We demonstrate here that a non-secretory polypeptide, a fragment of a tail fiber protein of phage T4, fused to the signal peptide of the outer membrane protein OmpA has a very strong SecB requirement for export and that the signal peptide itself cannot, at least not alone, be responsible for this action of SecB. The data reported, together with those of the literature, suggest that SecB recognizes the polypeptide backbone of the target protein.

Nucleotide sequence of the genes encoding the major tail sheath and tail tube proteins of bacteriophage P2

The major structural components of the contractile tail of bacteriophage P2 are proteins FI and FII, which are believed to be the tail sheath and tube proteins, respectively. Both proteins were mapped previously to the P2 late gene F, based on the pattern of protein synthesis in various P2 amber mutants. In order to clarify the gene arrangement and to provide a basis for structural comparisons with other contractile phage tails, we have determined the nucleotide sequence of the region of the P2 genome encoding these two proteins. The coding regions were confirmed by location of the Fam4 mutation and by N-terminal amino acid sequencing of both proteins. The molecular weight and amino acid composition predicted by each of the coding regions correspond well to those determined experimentally for each protein. FII is encoded by a newly identified P2 late gene. These proteins bear little resemblance to their functional homologues in bacteriophage T4.

Cloning, sequencing, and recombinational analysis with bacteriophage BF23 of the bacteriophage T5 oad gene encoding the receptor-binding protein

Binding of bacteriophage T5 to its receptor, the Escherichia coli FhuA protein, is mediated by tail protein pb5. In this article we confirm that pb5 is encoded by the T5 oad gene and describe the isolation, expression, and sequencing of this gene. In order to locate oad precisely, we analyzed recombinants between BF23, a T5-related phage with a different host range, and plasmid clones containing segments of the T5 chromosome. This analysis also showed that oad has little or no homology with hrs, the analogous BF23 gene. We were able to overproduce a protein that comigrates with pb5 after fusing a 2-kb segment containing oad to a phage T7 promoter. This segment contains an open reading frame that can encode a protein of the appropriate size. Its deduced amino acid sequence does not closely resemble that of any other protein in the database. The sequence upstream of the open reading frame shows typical characteristics of a promoter region with two overlapping, divergently orientated promoters.

Intragenic suppressors of folding defects in the P22 tailspike protein

Within the amino acid sequences of polypeptide chains little is known of the distribution of sites and sequences critical for directing chain folding and assembly. Temperature-sensitive folding (tsf) mutations identifying such sites have been previously isolated and characterized in gene 9 of phage P22 encoding the tailspike endorhamnosidase. We report here the isolation of a set of second-site conformational suppressors which alleviate the defect in such folding mutants. The suppressors were selected for their ability to correct the defects of missense tailspike polypeptide chains, generated by growth of gene 9 amber mutants on Salmonella host strains inserting either tyrosine, serine, glutamine or leucine at the nonsense codons. Second-site suppressors were recovered for 13 of 22 starting sites. The suppressors of defects at six sites mapped within gene 9. (Suppressors for seven other sites were extragenic and distant from gene 9.) The missense polypeptide chains generated from all six suppressible sites displayed ts phenotypes. Temperature-sensitive alleles were isolated at these amber sites by pseudoreversion. The intragenic suppressors restored growth at the restrictive temperature of these presumptive tsf alleles. Characterization of protein maturation in cells infected with mutant phages carrying the intragenic suppressors indicates that the suppression is acting at the level of polypeptide chain folding and assembly.

Reduced tendency to form a beta turn in peptides from the P22 tailspike protein correlates with a temperature-sensitive folding defect

A family of mutants of the P22 bacteriophage tailspike protein has been characterized as temperature sensitive for folding (tsf) by King and co-workers [King, J. (1986) Bio/Technology 4, 297-303]. There is substantial evidence that the tsf mutations alter the folding pathway but not the stability of the final folded protein. Several point mutations are known to cause the tsf phenotype; most of these occur in regions of the tailspike sequence likely to take up reverse turns. Hence, it has been hypothesized that the correct folding of the P22 tailspike protein requires formation of turns and that the mutations causing tsf phenotypes interfere at this critical stage. We have tested this hypothesis by study of isolated peptides corresponding to a region of the P22 tailspike harboring a tsf mutation. Comparison of the tendencies of wild-type and tsf sequences to adopt turn conformations was achieved by the synthesis of peptides with flanking cysteine residues and the use of a thiol-disulfide exchange assay. We find that the wild-type sequence, either as a decapeptide (Ac-CVKFPGIETC-CONH2) or as a dodecapeptide (Ac-CYVKFPGIETLC-CONH2), has a 3-5-fold greater tendency for its termini to approach closely enough to form the intramolecular disulfide than do the peptide sequences corresponding to the tsf mutant sequences, which have a Gly----Arg substitution (Ac-CVKFPRIETC-CONH2 or Ac-CYVKFPRIETLC-CONH2). A peptide with a D-Arg substituted for the Gly has a slightly higher turn propensity than does the wild type. Together with data from nuclear magnetic resonance analysis of the oxidized peptides, this suggests that a type II beta turn is favored by the wild-type sequence. Our results on isolated peptides from the P22 tailspike protein support the model for its folding that includes reverse turn formation as a critical step.

Intragenic suppression of a capsid assembly-defective P22 tailspike mutation

The tailspike protein of bacteriophage P22 assembles with mature capsids during the final reaction in phage morphogenesis. The gene 9 mutation hmH3034 synthesizes a tailspike protein with a change at amino acid 100 from Asp to Asn. This mutant form of trimeric tailspike protein fails to assemble with capsids in vivo. By using in vitro quantitative tailspike-capsid assembly assays, this mutant tailspike trimer can be shown to assemble with capsids at very high tailspike concentrations. From these assays, we estimate that this single missense mutation decreases by 100-500-fold the affinity of the tailspike for capsids. Furthermore, hmH3034 tailspike protein has a structural defect which makes the mature tailspike trimers sensitive to SDS at room temperature and causes the trimers to "partially unfold." Spontaneously arising intragenic suppressors of the capsid assembly defect have been isolated. All of these suppressors are changes at amino acid 13 of the tailspike protein, which substitute His, Leu or Ser for the wild type amino acid Arg. These hmH3034/sup3034 mutants and the separated sup3034 mutants form fully functional tailspike proteins with assembly activities indistinguishable from wild type while retaining the SDS-sensitive structural defect. From the analysis of the hmH3034 mutant and its suppressors, we propose that in the wild-type tailspike protein, the Asp residue at position 100 and the Arg residue at position 13 form an intrachain or interchain salt bridge which stabilizes the amino terminus of the tailspike protein and that the unneutralized positive charge at amino acid 13 in the hmH3034 protein is the cause of the assembly defect of this protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Properties of monoclonal antibodies selected for probing the conformation of wild type and mutant forms of the P22 tailspike endorhamnosidase

Eleven species of monoclonal antibodies directed against the trimeric P22 tailspike endorhamnosidase have been selected and characterized. Seven of these antibodies recognize the native tailspike, both isolated and assembled onto the virion, and prevent phage infection. Four antibodies react with denatured forms of the tailspike as well as with the plastic absorbed tailspike. Three of these latter prevent the tailspike from assembling onto the phage head. The antibodies have been tested against tailspike proteins carrying single amino acid substitutions at 15 different sites on the protein. Two of these mutations interfere with binding by a set of the monoclonals, indicating that they disrupt the epitopes for these antibodies. Since amino acid replacements corresponding to the temperature-sensitive folding mutations do not change the conformation of the native protein, these mutant proteins may be particularly useful for mapping epitopes. Amber fragments of the tailspike chain are recognized predominantly by the anti-denatured antibodies suggesting either that they are conformationally closer to folding intermediates than to the native tailspike or that the epitopes recognized by anti-native antibodies are carried by the C-terminal end of the native protein. Immunochemical detection by an anti-denatured antibody, after sucrose gradient sedimentation of a large 55-kDa amber fragment, indicates a monomeric rather than a trimeric state. This suggests that the missing C-terminal region is important for the trimerization reaction. Such N-terminal amber fragments may be useful models for studying with the monoclonal antibodies the nascent chain emerging from the ribosome.

Structural studies of the contractile tail sheath protein of bacteriophage T4. 2. Structural analyses of the tail sheath protein, Gp18, by limited proteolysis, immunoblotting, and immunoelectron microscopy

The molecular structure of the T4 phage tail sheath protein, gp18, was studied by limited proteolysis, immunoblotting, and immunoelectron microscopy. Gp18 is extremely resistant to proteolysis in the assembled form of either extended or contracted sheaths, but it is readily cleaved by proteases in the monomeric form, giving rise to stable protease-resistant fragments. Limited proteolysis with trypsin gave rise to a trypsin-resistant fragment, Ala82-Lys316, with a molecular weight of 27K. Chymotrypsin- and thermolysin-resistant fragments were also mapped close to the trypsin-resistant region. The time course of trypsin digestion of the monomeric gp18 as monitored by SDS-polyacrylamide gel electrophoresis and immunoblotting of the gel revealed that the polypeptide chain consisting of 658 amino acid residues is sequentially cleaved at several positions from the C terminus. The N-terminal portion, Thr1-Arg81, was then removed to form the trypsin-resistant fragment. Immunoelectron microscopy revealed that the polyclonal antibodies against the trypsin-resistant fragment bound to the tail sheath. This supported the idea that at least part of the protease-resistant region of gp18 constitutes the protruding part of the sheath protein as previously revealed with three-dimensional image reconstruction from electron micrographs by Amos and Klug [Amos, L. A., & Klug, A. (1975) J. Mol. Biol. 99, 51-73].

Structural studies of the contractile tail sheath protein of bacteriophage T4. 1. Conformational change of the tail sheath upon contraction as probed by differential chemical modification

Differential chemical modifications of tyrosine residues of the tail sheath protein, gp18, were performed to elucidate the structural change of the tail sheath upon contraction. Tyrosine residues of monomeric gp18, extended tail sheath, and contracted tail sheath were nitrated by tetranitromethane, and the modified tyrosine residues in each state of the sheath protein were identified by peptide mapping and amino acid sequence analyses of the isolated peptides. Of 31 tyrosine residues in gp18 monomer or in the extended sheath, 12 or 13 residues (Tyr63 and/or -73, -225, -254, -270, -304, -455, -460, -493, -532, -535, -569, and -590) were modified. When photo-CIDNP difference spectra were measured with monomeric gp18, two peaks, which are due to highly exposed tyrosine residues on the molecular surface of gp18, were observed. These two peaks disappeared when the monomeric gp18 was nitrated. With contracted sheath, however, only eight tyrosine residues (Tyr225, -254, -270, -455, -460, -493, -532, and -535) were nitrated on the contracted sheath. Chemical modification of cysteine residues by sulfhydryl group specific reagent ABD-F [(4-aminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole] revealed that, among five cysteine residues, Cys377, Cys477, and Cys607 have a sulfhydryl group. Cys402 and Cys406 were modified only under reducing conditions, which strongly suggested the presence of a disulfide bond between these two residues.

Conformational stability of P22 tailspike proteins carrying temperature-sensitive folding mutations

The thermostable tailspike endorhamnosidase of Salmonella phage P22 provides a model system for comparing the role of amino acid sequences in determining the intracellular folding pathway with their role in stabilizing the mature structural protein. Complete Raman band assignments are given here for the native form of the tailspike trimer in aqueous solution. Once correctly folded and assembled, the wild-type and two well-characterized mutant proteins, tsfIle258----Leu and tsfGly323----Asp, exhibit the same secondary structure in solution, consisting predominantly of beta-strand (56 +/- 5%) and turns (17 +/- 2%). Raman bands that are sensitive indicators of hydrogen-bonding interactions of tyrosine (phenolic OH) and tryptophan (indole NH) are unchanged between 30 and 80 degrees C in both wild type and tsf mutants. Similarly, Raman bands that are sensitive to changes in the hydrophobic environment of nonpolar side chains exhibit no significant temperature dependence in wild type and tsf mutants. In contrast, these conformational features are greatly altered by chemical denaturation of the tailspike with lithium halide and guanidine hydrochloride. In the chemically denatured tailspike, the beta-strand structure is substantially converted to irregular or "random coil" conformation. These findings confirm conclusions from physiological studies that the three-dimensional structures of the tsf mutants, once stabilized at permissive temperatures, are equivalent to the native structure of the wild type, and this structure is maintained at temperatures far above those that block the folding of the chain into the final native conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Expression and regulation of genes coding for three bacteriophage T4 tail tube-associated proteins

The assembly and length regulation of the tail tube of bacteriophage T4 requires the function of three proteins: gp29, 48, and 54. Six copies of each protein are found in the completed tail, and the genes for these proteins are adjacent on the T4 genome. Evidence is presented here that gp54 is also a tail tube-associated protein that remains bound to the tail tube after the baseplate is removed by guanidine hydrochloride, suggesting that all three proteins interact structurally. There is a strong polar effect of translation termination mutants in gene 48 upon the expression of the adjacent gene 54, in cis-trans tests. Gene dosage experiments that assay the in vivo expression of these genes show that only gene 48 is expressed at slightly higher than stoichiometric levels during T4 infection. Genes 48 and 54 were placed under the control of a T7 promoter and the corresponding proteins identified. When a frameshift mutation was introduced into gene 48, neither gp48 nor gp54 was made. Transcriptional termination was not the explanation of this result because genes distal to 48 and 54 in the plasmid were expressed. These data suggest that expression of genes 48 and 54 is translationally coupled.

Characterization of bacteriophage P22 tailspike mutant proteins with altered endorhamnosidase and capsid assembly activities

The tailspike protein of Salmonella typhimurium phage P22 is a multifunctional homotrimer which is involved in the terminal reaction of phage assembly, the adsorption of the phage to susceptible cells, and the hydrolysis of the Salmonella O-antigen during the first steps of phage infection. The proteins made from 15 mutant tailspike structural genes carried on high level expression plasmids have been analyzed with respect to their in vivo stability, quaternary structure, capsid assembly activity, and enzymatic activity. Nine mutants synthesize tailspike proteins which fail to accumulate to any appreciable level in vivo, and thus these proteins are probably degraded. Four other altered proteins accumulate in vivo as soluble monomers. The remaining two altered proteins accumulate in vivo as stable trimers. Each of these two proteins is defective for at least one of the known functions of the tailspike protein. One is defective in the capsid assembly reaction and shows an unusual quaternary structural defect but is normal with respect to the enzymatic hydrolysis of O-antigen. The other is defective in the enzymatic hydrolysis of O-antigen but is normal with respect to its capsid assembly activity and quaternary structure. The known sequence changes which give rise to these altered proteins and those of previously identified mutants allow the description of possible functional and structural "domains" of this multifunctional protein.

Irreversible binding of bacteriophage T5 to its FhuA receptor protein is associated with covalent cross-linking of 3 copies of tail protein pb4

Irreversible binding of bacteriophage T5 to its FhuA receptor protein is characterized by a high activation energy, typical for reactions where covalent bonds are formed [Zarnitz, M.L. and Weidel, W. (1963) Z. Naturforsch. 18b, 276-280]. Upon binding of radiolabeled T5 phages to FhuA formation of a new protein of 250 kDa was observed. Using electrophoretical and Western blotting techniques this protein was shown to be formed by cross-linking of 3 copies of tail protein pb4, rather than by cross-linking of FhuA and the receptor-binding protein.

Reconstitution of the thermostable trimeric phage P22 tailspike protein from denatured chains in vitro

Intermediates in the intracellular chain folding and association pathway of the P22 tailspike endorhamnosidase have been identified previously by physiological and genetic methods. Conditions have now been found for the in vitro refolding of this large (Mr = 215,000) oligomeric protein. Purified Salmonella phage P22 tailspikes, while very stable to urea in neutral solution, were dissociated by moderate concentrations of urea at acidic pH. The tailspike protein was denatured to unfolded polypeptide chains in 6 M urea, pH 3, as disclosed by analytical ultracentrifugation, fluorescence, and circular dichroism. Upon dilution into neutral buffer at 10 degrees C, the polypeptides fold spontaneously and associate to form trimeric tailspikes with high yield. Like native phage P22 tailspikes, the reconstitution product is resistant to denaturation by dodecyl sulfate in the cold and displays endorhamnosidase activity. Sedimentation coefficients, electrophoretic mobility, and fluorescence emission maxima of native and reconstituted tailspikes are identical within experimental error. By characterization of intermediates, localization of temperature-sensitive steps, and analysis of the effect of previously identified folding mutations, the reconstitution system described should allow comparison of in vivo and in vitro folding pathways of this large protein oligomer.

Thermostability of temperature-sensitive folding mutants of the P22 tailspike protein

Temperature-sensitive folding mutations (tsf) of the thermostable P22 tailspike protein prevent the mutant polypeptide chain from reaching the native state at the higher end of the temperature range of bacterial growth (37-42 degrees C). At lower temperatures the mutant polypeptide chains fold and associate into native proteins. The melting temperatures of the purified native forms of seven different tsf mutant proteins have been determined by differential scanning calorimetry. Under conditions in which the wild type protein had a melting temperature of 88.4 degrees C, the melting temperatures of the mutant proteins were all above 82 degrees C, more than 40 degrees C higher than the temperature for expression of the folding defect. Because the folding defects were observed in vivo, the thermostability of the native protein was also examined with infected cells. Once matured at 28 degrees C, intracellular tsf mutant tailspikes remained native when the cells were transferred to 42 degrees C, a temperature that prevents newly synthesized tsf chains from folding correctly. These results confirm that the failure of tsf polypeptide chains to reach their native state is not due to a lowered stability of the native state. Such mutants differ from the class of ts mutations which render the native state thermolabile. The intracellular folding defects must reflect decreased stabilities of folding intermediates or alteration in the off-pathway steps leading to aggregation and inclusion body formation. These results indicate that the stability of a native protein within the cells is not sufficient to insure the successful folding of the newly synthesized chains into the native state.

The isolation and sequence of missense and nonsense mutations in the cloned bacteriophage P22 tailspike protein gene

Twenty-seven new mutations in the structural gene for the Salmonella typhimurium bacteriophage P22 tailspike protein have been isolated, mapped using a powerful plasmid-based genetic system and their DNA sequence changes determined. The mutations were generated by hydroxylamine treatment of the cloned gene on a plasmid expression vector. Assaying the activity of the tailspike protein produced from this plasmid and screening for plasmid mutants were accomplished by the in situ complementation of P22 capsids imbedded in soft agar to produce infectious phage. Deletion mutations in the cloned gene have been constructed by a two step procedure involving oligonucleotide linker insertion and in vitro deletion by restriction endonuclease digestion. The deletions, whose physical endpoints were determined by DNA sequencing, define 12 genetic and physical intervals into which the new mutations were mapped by marker rescue experiments. These deletions were transferred to phage P22 by recombination and used to map mutations carried on plasmids. Following mapping, the nucleotide change for each of the mutations was determined by DNA sequencing. The majority were absolute missense mutations although both amber and ochre nonsense mutations were also identified in the protein coding portion of the gene. The suppression pattern of the nonsense mutations was determined on several nonsense suppressors. Four of the mutations cause severely depressed levels of tailspike protein expression from both the cloned gene on the plasmid expression vector and from P22 phage carrying these mutations. These mutations were identified as nucleotide changes in what is probably the P22 late operon transcription terminator which immediately follows the tailspike protein coding sequence.

Organization of the bacteriophage P1 tail-fibre operon

The revised sequence of a bacteriophage P1 DNA fragment containing the 5' end of the tail-fibre gene, gene 19, revealed that this gene is closely preceded by another open reading frame (ORF) of 432 bp. We have designated this ORF as gene R. The tail-fibre gene and gene R are transcriptionally and translationally coupled. Thus, the tail-fibre operon of bacteriophage P1 consists of three genes: gene R, gene 19 (or gene S) and gene U.

Fine structure genetic and physical map of the phage P22 tail protein gene

Bacteriophage P22 which are incapable of making functional tail protein can be propagated by the addition of purified mature tail protein trimers to either liquid or solidified medium. This unique in vitro complementation condition has allowed us to isolate 74 absolute lethal tail protein mutants of P22 after hydroxylamine mutagenesis. These phage mutants have an absolute requirement for purified P22 tail protein to be present in a soft agar overlay in order to form plaques and do not grow on any nonsense suppressing strains of Salmonella typhimurium. In order to genetically map and physically locate these mutations we have constructed two complementary sets of fine structure deletion mapping strains using a collection of Tn1 insertions in gene 9, the structural gene for the tail protein. Fourteen bacteriophage P22 strains carrying unique Tn1 transposon insertions (Ap phage) in gene 9 have been crossed with Ap phage carrying Tn1 insertions in gene 20. Phage carrying deletions that arose from homologous recombination between the Tn1 elements were isolated as P22 lysogens. The deletion prophage were shown to be missing all genetic information bracketed by the parental Tn1 elements and thus form a set of deletions into gene 9 from the 5' end of the gene. From the frequency of production of these deletion phage the orientation of the Tn1 insertions in gene 9 could be deduced. The genetic end points of the deletions in gene 9 and thus the order of Tn1 insertions were determined by marker rescue experiments using the original Ap phage. The genetic end points of the deletions in gene 20 were determined in similar experiments using nonsense mutations in gene 20. To locate the physical end points of these deletions in gene 9, DNA containing the Tn1 element has been cloned from each of the original Ap phage into plasmids. The precise point of insertion of Tn1 into gene 9 was determined by restriction enzyme mapping and DNA sequencing of the relevant portions of each of these plasmids. In vitro deletion of different 3' gene 9 sequences in the plasmid clones was accomplished through the use of unique restriction endonuclease sites in Tn1. The resulting plasmids form a set of deletions extending into the 3' end of the gene which are complementary compared to the deletion lysogens.(ABSTRACT TRUNCATED AT 400 WORDS)

Nucleotide sequence of the tail tube structural gene of bacteriophage T4

The nucleotide sequence of gene 19 of bacteriophage T4, the structural gene of the tail tube protein, was determined by both the dideoxy and the Maxam-Gilbert methods. The predicted Mr of tube protein gene product 19 is 18,842. The N-terminal amino acid of the tube protein was determined by Edman degradation, and the C-terminal sequence was confirmed by isolation of the C-terminal tryptic peptide. In the noncoding region between genes 18 and 19, there are two late-T4-promoter consensus sequences, 51 bases apart. The implication of the two late promoter sequences was examined by an S1 nuclease protection experiment. Both serve as weak promoters, but the bulk of the transcripts arise from further upstream of the two promoters.

Three-alpha-helical coiled-coil, as a proposed model for a thin rod segment of bacteriophage T3 tail fibers

Three-stranded alpha-helical coiled-coil was considered as a model for a thin proximal rod of T3 phage tail fiber on the basis of amino acid sequence. A segment of residues from ca. 130th to 270th was shown to have a unique feature to satisfy the required conditions of the coiled-coil, and to give the observed geometry.

Fusions of bacteriophage P22 late genes to the Escherichia coli lacZ gene

The late genes of bacteriophage P22 were fused to lacZ to study their differential expression from the late operon transcript. No instances of posttranscriptional regulation were uncovered, thus supporting the model that the late genes are expressed, by and large, in fixed ratios based on their translational efficiency and message stability.

Identification of sites influencing the folding and subunit assembly of the P22 tailspike polypeptide chain using nonsense mutations

Amber mutations have been isolated and mapped to more than 60 sites in gene 9 of P22 encoding the thermostable phage tailspike protein. Gene 9 is the locus of over 30 sites of temperature sensitive folding (tsf) mutations, which affect intermediates in the chain folding and subunit association pathway. The phenotypes of the amber missense proteins produced on tRNA suppressor hosts inserting serine, glutamine, tryosine and leucine have been determined at different temperatures. Thirty-three of the sites are tolerant, producing functional proteins with any of the four amino acids inserted at the sites, independent of temperature. Tolerant sites are concentrated at the N-terminal end of the protein indicating that this region is not critical for conformation or function. Sixteen of the sites yield temperature sensitive missense proteins on at least one nonsense suppressing host. Most of the sites with ts phenotypes map to the central region of the gene which is also the region where most of the tsf mutations map. Mutations at 15 of the sites have a lethal phenotype on at least one tRNA suppressor host. For nine out of ten sites tested with at least one lethal phenotype, the primary defect was in the folding or subunit association of the missense polypeptide chain. This analysis of the tailspike missense proteins distinguishes three classes of amino acid sites in the polypeptide chain; residues whose side chains contribute little to folding, subunit assembly or function; residues critical for maintaining the folding and subunit assembly pathway at the high end of the temperature range of phage growth; and residues critical over the entire temperature range of growth.

[Structure and regulation of the assembly of bacteriophage T4 fibrillar proteins. II. Isolation and initial structural characteristics of whiskers]

A procedure for purification of bacteriophage T4 whiskers and it's monomeric subunits--gene product wac--has been developed. We have shown, that the whiskers are composed of two identical copies of gene product wac with molecular weight of 56 kDa each. The dimer of gene product wac is a highly ordered structure and it's length is about 70.0 +/- 10.0 nm, as revealed by electron microscopy. The amino acid composition of whiskers is very similar to that of watersoluble keratins. We have proposed a new term for the definition of the whiskers--the fibritin.

[Structure and regulation of the assembly of bacteriophage T4 fibrillar proteins. I. Isolation and spectral properties of long fibers]

A preparative procedure for purification of the biological active proximal (A) and distal (BC') parts of bacteriophage T4 long-tail fibers is described. Absorption spectra of these proteins in the near ultraviolet region were measured. The absorption coefficients were determined on the basis of the nitrogen content, the absorption coefficient for the A part is epsilon 0.1% 277 nm = 0.93 +/- 0.06 and for the BC' part is epsilon 0.1%, 277,5 nm = 1.01 +/- 0.08. Calculations of the secondary structure from CD spectra show that there is a high content of beta-structure: 41% in the A part and 51% in the BC' part,--and also that alpha-helix are present in the native complex: 20% in A and 7% in BC'. A model for the spatial organisation of long fibers is proposed.

Receptor-recognizing proteins of T-even type bacteriophages. Constant and hypervariable regions and an unusual case of evolution

Proteins 38 of bacteriophages T2, K3, Ox2 and M1 are located at the free ends of their long tail fibers and function as adhesins, i.e. they mediate binding to the bacterial receptors. The latter three phages use the Escherichia coli outer membrane protein OmpA as a receptor, while T2 uses the outer membrane proteins OmpF or Ttr. The DNA sequences of genes 38 of phages Ox2 and M1 have been determined and are compared with those known for T2 and K3. The genes encode 262(T2), 260(K3), 266(Ox2) and 262(M1) amino acid residues. Three domains are distinguishable in these proteins. There are two conserved regions encompassing about 120 NH2-terminal and about 25 CO2H-terminal residues, respectively. The area between these was found to be hypervariable, and it is shown that a very large number of amino acid substitutions, deletions and/or insertions have occurred. Glycine-rich stretches are present within and flanking these areas. Their positions are essentially conserved, indicating an important structural role in receptor recognition. The hypervariability, most likely caused by a constant struggle with bacterial phage-resistant mutants, is so drastic that one cannot discern that T2 uses different receptors from those of the other phages. The partially known sequence of gene 38 of phage T4 has been completed. The gene encodes a protein consisting of 183 amino acid residues. The amino acid composition and sequence of this protein is completely different from those of phages T2, K3, Ox2 and M1. Also, the protein is functionally unrelated to the other proteins 38: it is not present in phage T4 and, unlike the other proteins 38, is required for the efficient dimerization of protein 37. All phages under study are of the same morphology and the genomic organization of the tail fiber genes is identical, with genes 36, 37 and 38 most likely representing, in this order, a transcriptional unit. Sequence similarities between the CO2H-termini of genes 37 of the non-T4 phages and gene 38 of phage T4 were found; this part of gene 37 does not exist in T4. It is suggested that gene 38 of phage T4 originated from a segment of gene 37 of a T2-type phage. Gene 38 of phage T4 is not unique, DNA-DNA hybridization experiments indicated that two other T-even type phages, TuIa and TuIb, possess a T4-type gene 38.

Determination of bacteriophage lambda tail length by a protein ruler

How the size and shape of living structures are determined by genetic information is one of the fundamental problems in biology. Here I describe a study in which the size of a biological supramolecular structure was changed in a predictable way by in vitro genetics, with the size both before and after manipulation being exactly determined. I have studied the tail of bacteriophage lambda, whose length is determined by the length of the 'ruler protein', the product of gene H. The length of the tail can be decreased or increased by deleting the middle part of gene H or by forming a small duplication there, and the length of the tail is proportional to the size of the protein. These results can be regarded as a special case of protein engineering, namely supramolecular protein engineering.

Predicted structure of tail-fiber proteins of T-even type phages

The sequences of the tail fiber protein 36 of the phages T4, T2, K3, and Ox2 were analyzed for homologies and for folding patterns using structure prediction methods. No repeating motif was found. A model for the fiber structure is proposed in which beta-strands of about 6 amino acids are separated by turns. In the beta-strand, hydrophobic amino acids are found alternating with hydrophilic ones. Such amphipathic beta-strands can be stabilized by dimer formation. The dimerization occurs in a parallel fashion so that both N-termini are at one end of the dimer. This structure represents a rigid fiber. Our model is consistent with electron microscopic data and electron diffraction patterns for the T4 tail fiber. The observation that all fiber components are found as dimers supports our model. Sequences of the receptor recognition proteins 38 of T-even type phages reveal an architecture different from the architecture of the fiber proteins 36 and 37 of these phages.

Location of genes D16, D17, and N4 encoding tail proteins on the physical map of bacteriophage T5

Bacteriophage T5 DNA fragments were cloned into plasmid pBR322. Recombinant plasmids complementing T5 amber mutants were isolated, and used as hybridization probes with T5 DNA in Southern blots. Employing this approach the three T5 genes D16, D17, and N4 were mapped with respect to the physical map of T5, and shown to be located at 74%, 72%, and 82% of the genome, respectively.

Cloning and expression of the ltf gene of bacteriophage T5

The unique 5-kilobase BamHI fragment of bacteriophage T5 was cloned into plasmid pBR322. Location of the intact ltf gene on the cloned fragment was demonstrated by complementation of the ltf mutation of phage T5hd-2, identification of a plasmid-coded polypeptide of the same molecular weight as the polypeptide forming the L-shaped tail fibers, which binds to anti-T5 antibodies; and analyses of transposon Tn1000 insertions.

Subunit arrangement of the tail fiber of bacteriophage T3

A tail fiber of phage T3 is a trimer of the product of gene 17 (gp17). Treatment of T3 phage particles with chymotrypsin resulted in cleavage of only the tail fiber protein, at a site near the distal end of the fiber, causing a decrease of about 10% in the size of gp17 in the treated virion. The N-terminal amino acid sequences of intact and cleaved tail fiber proteins were identical and corresponded to that deduced from the nucleotide sequence of gene 17 except for the absence of the initiation Met residue. These results indicate that cleavage of the tail fiber occurred near the C terminus and suggest that gp17 polypeptides are oriented parallel to each other in the tail fiber. Association of tail fibers with the tail involves the N-terminal region of gp17. Under mild conditions of SDS-polyacrylamide gel electrophoresis, intact tail fibers dissociated from virions but cleaved ones did not. The nucleotide sequences indicate that T3 and T7 gp17 contain many sites that are potentially sensitive to chymotrypsin. In fact, free tail fibers, purified from T3-infected cells, were cleaved to many smaller fragments by chymotrypsin. These results suggest that the attachment of the tail fibers to the tail may induce a change(s) in the configuration and/or arrangement of gp17 to mask the sensitive sites from cleavage by chymotrypsin.

Potential length determiner and DNA injection protein is extruded from bacteriophage T4 tail tubes in vitro

Bacteriophage T4 tails contain a set of extended protein molecules in the central channel of the tail tube through which the DNA must exit during infection. Treatment of tails with guanidine hydrochloride separates the baseplates, leaving the tail tube and several specific tube-associated proteins. Methods were developed to purify these structures. Using specific antisera, immunoblotting, and electrophoretic analysis, these structures were shown to contain proteins gp19, 29, and 48. Electron microscopy showed specifically defined stain penetration into the tail tube, a bulge at one end, and a short fiber extruded from the tube. These structures could be removed by proteases but the gp19 tube itself was resistant. Structural studies of tails and intact phage show that the bulge and fiber are at the end of the tube that interacts with the cell membrane during infection. Since the fiber did not protrude from baseplates or from incomplete (short) tube-baseplates, we propose that it is first assembled as a compact structure formed of six copies of a tube-associated protein, which elongates during tail tube formation to fill the central channel, span the length of the tube, and regulate its length. We suggest that the exit of this fiber during infection signals DNA ejection.