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Chapter 56 : SPO1 and Related Bacteriophages

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Abstract:

SPOl, SP82, Fe, 2C, SP8, H1, and SP5C constitute a family of large, virulent bacteriophages of whose distinguishing feature is the complete replacement of thymine by hydroxymethyluracil in their DNA. This chapter focuses on SPO1, about which the most is known, but will also discuss data for the other phages that can illuminate areas not studied with SPO1. Gene product 28 substitutes for the host sigma factor, changing the specificity of the RNA polymerase so that it now transcribes the middle genes, which include genes 33 and 34. The products of these genes then modify the RNA polymerase so that it transcribes the late genes. The gene 27 mutant is also deficient in DNA replication, and neither deficiency appears to be an indirect result of the other. Thus, gp27 may play a direct role in both replication and late transcription, although it remains possible that either deficiency is the result of a polar effect on a downstream gene. All major early promoters are located in the terminal redundancy, as determined either by binding RNA polymerase to specific restriction fragments or by the formation of ternary complexes of restriction fragments, RNA polymerase, and nascent RNA. Recombination is essential for transfection by the DNA of hydroxymethyluracil (hmUra) phages. As shown primarily for SP82, transfecting DNA is susceptible to a host nuclease that causes sufficient damage that recombination between several genomes is necessary to form a single intact genome.

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56

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DNA Polymerase III
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DNA Polymerase I
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DNA Polymerase III
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DNA Polymerase I
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DNA Polymerase III
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DNA Polymerase I
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DNA Polymerase III
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Figures

Image of Figure 3
Figure 3

Map of the SPO1 terminal redundancy. Data for the restriction map are from references , and and from E. P. Geiduschek ( ). Small adjustments have been made to reconcile differences in positions reported by different groups. Restriction sites: B, NI; Bs, EII; E, RI; H, W; h, II; Ha, III; K, I; T, I; X, I. The numbers of the RI fragments are indicated above the line. Positions of early promoters ( ) are indicated by arrows labeled El through E12, corresponding to P1 through P12. Positions of two possible middle promoters are indicated by arrows labeled M. The leftmost of these is a middle promoter sequence ( ) not known to be functional, and the rightmost is inferred from Perkus and Shub's ( ) conclusion that gene el 6 is expressed from a middle promoter. Its position is shown just to the right of that of el6, but it could also be farther to the right. (Some evidence suggests the presence of more than one middle promoter in this region [ ].) The direction of transcription driven by each promoter is indicated by an arrow. The positions of transcription terminators ( ) are indicated by straight lines descending from the map. Those designated H are heavy-strand terminators that terminate rightward transcription; the light-strand terminators, designated L, terminate leftward transcription. The efficient terminators in the central termination region are emphasized with longer lines. Transcription from each rightward promoter is terminated at the efficient terminator H3, and that from each leftward promoter is terminated at L1, with intermediate terminators functioning less efficiently or under particular conditions. The gene positions are from references and . Placements are based on the best arguments available, but in some cases, those arguments are not conclusive, so placements should be considered approximations. Where there is no basis for determining the order of two genes, they are placed in parentheses. The length of the box for each gene represents the size of the gene calculated from the molecular weight of the gene product as estimated by gel electrophoresis (except that e4 has been shortened by about 18% to permit consistency with the restriction enzyme inactivation data without invoking overlapping genes). In the e9 to el5 and el6 to e20 regions, the indicated genes occupy nearly all the space available, assuming no overlapping. There is an indication of another open reading frame just downstream of P4 ( ), so the space between el5 and e3 is probably occupied as well. In the e7-e21-el2 region, the dashed box represents space unaccounted for by known genes. Any of those three genes could be anyplace within that dashed region instead of at their indicated positions, with the only constraints being that e 12 is to the right of e7 and e21 and that e21 cannot overlap a W or EW site. Markers in genes 35 and 36 are located in RI* fragment 18 ( ). That in gene 35 is in the terminal redundancy ( ), and that in gene 36 behaves as if it is, too ( ), so they are probably both in RI*-20, which is the portion of fragment 18 that is in the redundant region. It is unlikely that either of these genes is e9, since gene 36 apparently is expressed from RI*-18 ( ), whereas e9 is not expressed from RI*-20 ( ), and since e9 is an early gene, whereas gene 35 is required for viral assembly ( ) and is therefore probably a late gene. Therefore, genes 35 and 36 are placed to the left of e9. There is no basis for estimating the size of genes 35 and 36, so the dashed box merely indicates the region within which they are found.

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56
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Image of Figure 4
Figure 4

Map of gene 28 to 34 region. All of the known genes in this region are indicated by numbers immediately below the line (except that the TF1 gene is indicated by the letter T, and the unidentified open reading frame next to gene 30 is indicated by the letter O). Those genes enclosed in boxes have been completely sequenced ( ). Genes 29 and 32 have not been located precisely. Brackets enclose regions within which at least part of those genes must be located according to marker rescue activity associated with specific restriction fragments ( ). The shaded region between the two halves of gene 31 represents the intron. The more lighdy shaded portion is the open reading frame within the intron. Restriction sites are indicated by letters above the line: B, II; Bs, EII; E, RI; H, III; K, I S, I; X, I. The numbers of the RI fragments are given above the lines. The locations of restriction sites within the sequenced regions have been determined precisely from the sequence. Others have been determined by restriction mapping and are not as precise ( ). The Seal map is incomplete, as most of the unsequenced region has not been tested for Seal sites. The Seal site indicated within RI fragment 23 is actually two sites 78 bp apart. Parentheses around one Bs indicate that the location of that EII site is not precise, so its relationship to M13 and El 5 is not known. The locations of all of the known promoters in the region are shown below the line, with directions of transcription indicated by arrows. M3 through M13 are middle promoters P3 through P13, and E13 through E15 are early promoters P13 through P15. Their locations were determined by Chelm et al. ( ), with additional information about certain promoters coming from sequence information and from Scarlato et al. ( ). All locations were determined with reference to the RI* restriction map ( ), using fragment sizes from reference .

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56
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Image of Figure 5
Figure 5

Map of a region of middle transcription. All information was taken from Lee and Pero ( ). Restriction sites: Bs, EII; E, RI; H, II; Hh, I; S, 3A. The numbers of the RI fragments are given above the line. The four middle promoters are designated P. Arrows indicate directions of transcription driven by each promoter. No genes on these fragments have been identified.

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56
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Image of Figure 6
Figure 6

Map of a region of late transcription. All data are taken from Costanzo ( ). Restriction sites: A, I; B, NI; Bs, EII Bg, II; E, RI; H, II; h, III; S, 3A; T, I. The numbers of the RI fragments are given above the line. Five late promoters are indicated by P, with arrows showing directions of transcription. Genes known from marker rescue experiments to be (at least partially) on these fragments include genes 13 and 14 on RI fragment 16, genes 16 and 16.5 on fragment 13b, and gene 17 on fragment 17 ( ). Since their locations are not known more precisely, the genes are not shown.

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56
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Image of Figure 1
Figure 1

Restriction and genetic maps of the SPO1 genome (taken from references , and ). Arrows indicate positions of the terminal redundancy. The RI* site between RI*-3 and RI*-22b is not there in some strains of SPO1 (e.g., see reference ). Where the order of two or more adjacent genes or fragments with respect to each other has not been determined, their numbers are placed one above the other. The positions of genes 6, 7, 10, 15, 22, 23, 24, 25, and 26 have been determined only by genetic mapping; those of all other genes have been determined from the positions of the restriction fragments on which they are located ( ). In most cases, the latter positions are the same as those determined by genetic mapping, but when those determinations differ, the positions given are those determined from the restriction map. For several pairs of genes (genes 1 and 2, 8 and 9, and 20 and 21a), their positions with respect to the rest of the genome were determined from the restriction map, but their positions with respect to each other were determined only from the genetic map. Mutation CI was mapped adjacent to gene 32 but was not shown to be in a separate gene ( ). Eleven additional genes have been located to the right of genes 35 and 36 in the terminal redundancy by in vitro expression from specific restriction fragments, although none of them has been defined by mutation ( ). Their positions are shown in an expanded map of the terminal redundancy in Fig. 3 . All locations are determined with respect to the RI restriction map ( ), using fragment sizes from reference . This map was published previously ( ) and has been reproduced with permission from Plenum Press.

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56
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Image of Figure 2
Figure 2

General locations of early, middle, and late sequences on the SPO1 genome. Thick, thin, and dotted line represent relative amounts of early, middle, and late labeled RNA that hybridize to each of the indicated RI restriction fragments. RI fragments 13a and 13b and fragments 14 and 15 were not resolved on these Souther blots, so the hybridized RNAs for these bands were arbitrarily assigned to one or both members of each pair < DNAs on the basis of the amount of RNA hybridizing to restriction fragments neighboring each member of the paii Data are from references and , and the figure has been reproduced with permission from the America Society for Microbiology.

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56
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Tables

Generic image for table
Table 1

Consensus sequences of SPO1 promoters

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56
Generic image for table
Table 2

Summary of genes of SPO1

Citation: Stewart C. 1993. SPO1 and Related Bacteriophages, p 813-829. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch56

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