Bacteriophages

Instances of bacteriophage-induced stuck MLF appear to be random in occurrence. This may result from the relatively low bacterial population density (10 -10 CFU/mL) compared with starter cultures at 10 CFU/mL. Because phage infection requires identification of unique receptor site(s) on the bacterial cell wall, the use of alternate or multiple-strain LAB cultures may preclude or mitigate stuck MLF (Cone, 1995 personal communication). 

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Nucleoproieins. The prosthetic group of the nucleoproteins is nucleic acid, often linked through salt linkages with protamines or histones. The nucleoproteins are present in the nuclei of all cells. Chromasomes are largely nucleoproteins and some plant viruses and bacteriophages have been shown to be pure nucleoproteins. See also histones. 

Ikai A, Yoshimura K, Arisaka F, Ritani A and Imai K 1993 Atomic force microscopy of bacteriophage T4 and its tube-baseplate complex FEBS Lett. 326 39... 

Bacterms Bacteriocide Bacteriocms Bacteriophage lambda Bacteriophages Bacteriorhodopsin... 

Fig. 4. Construction of recombinant phage in vectors derived from bacteriophage lambda where E represents the enzyme EcoRl. Other terms are defined...

Knots nd Ca.tena.nes, Closed-circular DNA hehces can cross over one another three or more times to form topological knots. These stmctures are not common, but have been found to occur naturally in some bacteriophage DNAs. 

Hydroxymethylcytosine (967) was isolated only in 1952 from the T-even bacteriophages of Escherichia coli, in which it occurs instead of cytosine in the 2-deoxyribonucleic acid (65MI21304). Of several syntheses described, the most convenient is probably that beginning with ethyl 4-amino-2-methylthiopyrimidine-5-carboxylate which is reduced by LAH to 4-amino-2-methylthiopyrimidin-5-ylmethanol followed by hydrolysis to 5-hydroxymethyl-cytosine (967) (B-68MI21302, B-68MI21306). 

SY Chung, S Subbiah. The use of side-chain packing methods m modeling bacteriophage repressor and cro proteins. Pi-otem Sci 4 2300-2309, 1995. 

In the first edition of this book this chapter was entitled "Antiparallel Beta Structures" but we have had to change this because an entirely unexpected structure, the p helix, was discovered in 1993. The p helix, which is not related to the numerous antiparallel p structures discussed so far, was first seen in the bacterial enzyme pectate lyase, the stmcture of which was determined by the group of Frances Jurnak at the University of California, Riverside. Subsequently several other protein structures have been found to contain p helices, including extracellular bacterial proteinases and the bacteriophage P22 tailspike protein. 

A more complex p helix is present in pectate lyase and the bacteriophage P22 tailspike protein. In these p helices each turn of the helix contains three short p strands, each with three to five residues, connected by loop regions. The p helix therefore comprises three parallel p sheets roughly arranged as the three sides of a prism. However, the cross-section of the p helix is not quite triangular because of the arrangement of the p sheets. Two of the sheets are... 

The number of helical turns in these structures is larger than those found so far in two-sheet p helices. The pectate lyase p helix consists of seven complete turns and is 34 A long and 17-27 A in diameter (Figure 5.30) while the p-helix part of the bacteriophage P22 tailspike protein has 13 complete turns. Both these proteins have other stmctural elements in addition to the P-helix moiety. The complete tailspike protein contains three intertwined, identical subunits each with the three-sheet p helix and is about 200 A long and 60 A wide. Six of these trimers are attached to each phage at the base of the icosahedral capsid. 

Bacteriophage repressor proteins provide excellent examples of sequence-specific interactions between the side chains of a protein and bases lining the floor of the major groove of B-DNA. As we shall see, to fit the protein s recognition module into this groove it has to be made even wider in other words, the B-DNA has to be distorted. 

Certain strains of Escherichia coli can be stimulated by irradiation with a moderate dose of ultraviolet (UV) light to stop normal growth and start producing bacteriophages that eventually lyse the bacterium. Bacteria of these so-called lysogenic strains carry the DNA of the phage integrated into their own... 

Figure 8.1 A region of DNA in the related bacteriophages lambda, 434, and P22 that controls the switch for synthesis of new phage particles. Two structural genes are involved in this switch one coding for a repressor protein and one coding for the Cro protein. Between these genes there is an operator region (OR) that contains three protein binding sites—ORl, OR2, and OR3.

Table 8.1 The nucleotide sequences of the three protein-binding regions ORl, OR2, and OR3 of the operator of bacteriophage lambda...

Figure 8.3 The DNA-binding protein Cro from bacteriophage lambda contains 66 amino acid residues that fold into three a helices and three P strands, (a) A plot of the Ca positions of the first 62 residues of the polypeptide chain. The four C-terminal residues are not visible in the electron density map. (b) A schematic diagram of the subunit structure. a helices 2 and 3 that form the helix-turn-helix motif ate colored blue and red, respectively. The view is different from that in (a), [(a) Adapted from W.F. Anderson et al., Nature 290 754-758, 1981. (b) Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.]...

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

Anderson, J.E., Ptashne, M., Harrison, S.C. Stmeture of the repressor-operator complex of bacteriophage 434. Nature 326 846-8S2, 1987. 

Anderson, W.F., et al. Structure of the Cro repressor from bacteriophage X and its interaction with DNA. 

Ohlendorf, D.H., et al. Comparison of the structures of Cro and X repressor proteins from bacteriophage X. 

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