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Chapter 39 : Genetic Exchange and Homologous Recombination

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Abstract:

After , is genetically the best-characterized bacterium. Homologous recombination has been an essential tool in the genetic analysis of , and in turn the availability of powerful genetic tools has facilitated investigation of the exchange of DNA-encoded information in this organism. This review summarizes the present state of knowledge concerning several modes of homologous genetic exchange and places emphasis on natural competence, about which much is known. A section discusses our understanding of the genetics and biochemistry of homologous recombination per se. Another provides an overview of the essential properties of these systems. The chapter emphasizes the newer work that concerns the regulation of competence and the nature of transformation-specific gene products. Competence is widespread in both gram-positive and gram-negative bacteria. The best-studied systems are those of , , , , and . Several competence loci have been identified following the isolation of commutants. The authors propose that the five small ComG proteins assemble to form part of a cell surface-associated structure for the binding and uptake of transforming DNA. The implications of competence- linked induction of DNA repair genes and a possible mechanism for competence-linked induction of the SOS system are also discussed.

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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Image of Figure 1
Figure 1

Genetic map of competence genes. Known competence loci are indicated on the outside of the circle. Italicized markers on the inside are included for reference. Boldface type without underlining indicates regulatory loci. Boldface underlined type indicates late competence loci. Normal type indicates loci that may include either regulatory or late competence genes. The order of the cluster relative to flanking markers is not known.

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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Image of Figure 2
Figure 2

Numerical representation of similarities of products to protein members of the pullulanase secretion, pilin assembly and synthesis, and Ti plasmid systems. The numbers are ? values obtained by using the RDF program ( ) with 100 randomizations of the Com amino acid sequences. ? values in excess of 10 standard deviations are regarded as highly significant, and values of 5 to 10 standard deviations are regarded as possibly significant.

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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Image of Figure 3
Figure 3

Similarities of ComG ORF3, ORF4, and ORF5 ( ) to protein members of the pullulanase secretion system ( ) and to type IV pilins from ( ) and ( ). Amino acid identities are indicated by shading whenever at least three amino acids in the same position are identical except in the last few lines, in which two identical amino acids are indicated. The residue number of the first amino acid on each line is indicated. Type IV pilins are processed by cleavage between the conserved Gly (residues 6 and 7) and Phe (residues 7 and 8).

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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Figure 5

Similarities of the C-terminal 71 amino acid residues of ComA ( ) to C-terminal moieties of other suspected and known transcription factors. Amino acid similarities are indicated by shading when six or more of them occur at the same position. For this purpose, the amino acids are grouped as follows: M, L, I, and V; ?, K, and R; D and E; Q and N; A, G, S, and T; F, W, and ?; P; C. Locations of the region 4 helix-turn-helix ( ) of SigB ( ), based on comparison of factors, and of the proposed helix-turn-helix of ComA are indicated. Additional protein sequences and their sources are GerE ( ), DegU ( ), NarL ( ), MalT ( ), BvgA ( ), ORF2-UvrC ( ), LuxR ( ), RcsB ( ), and NodW ( ).

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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Figure 6

Comparison of proposed CTF-binding sites upstream from , and Identities in at least three of the four sequences are indicated by underlining. Arrows indicate partial dyad symmetries. A deletion extending from the left to position -97 has no effect on expression of , whereas a deletion extending to -79 reduces expression ( ). Positions of the centers of proposed dyad symmetries relative to transcriptional start sites (+1) are indicated to the right. Dotted lines indicate a consensus site upstream from the promoter ( ).

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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Figure 4

Genetic and physical maps of the region of the chromosome. The ORFB determinant was previously called ( ) but is now known not to be a competence gene ( ). The DNA sequence of the entire 8-kb region has been determined. References are given in the text. BH, HI;H, III; EV, RV; , I. The positions of promoters (P) and terminators (ter) are given. The determinant encodes a 46-amino-acid peptide and is not drawn to scale.

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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Figure 7

Regulation of competence: schemes of signal transduction and information flow. Each boldface S indicates a likely point at which signals might be received by the regulatory apparatus. Arrows and lines terminated by perpendiculars indicate positive and negative regulation, respectively. DegU is in parentheses because its location in the scheme is not certain. (A and B) Alternative arrangements that are consistent with the available data as outlined in the text. The schemes differ in one respect: whether the signal is transduced through sin and/or (A) or whether an independent signal is relayed through some combination of the products of these genes that then acts, directly or indirectly on in combination with the signal (B). (C) Summary of two possible pathways of negative control. Spo0A is required to downregulate the expression of , which can act negatively as well as positively on competence (see panels A and B). Since activation of DegU may act negatively on competence, DegS may be considered a negative regulator. The latter mechanism is speculative, since the exact roles of phosphorylated and unphosphorylated DegU in competence are unclear (see text).

Citation: Dubnau D. 1993. Genetic Exchange and Homologous Recombination, p 555-584. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch39
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