Lambda Phage

12 Key excerpts on "Lambda Phage"

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  Quantitative Biology

  From Molecular to Cellular Systems

  • Michael E. Wall(Author)
  • 2012(Publication Date)
  • CRC Press

    (Publisher)

  This allows a principled approach both to construction of models and testing their predictions. Finally, λ offers the opportunity to relate decisions made at the molecular level to the behavior of populations and eventually to evolutionary strategies for optimizing viral behavior, particularly when taken together with the behavior of other related viruses. Experimental characterization of λ is deep at multiple levels, making it an excellent candidate for developing multiscale models that range from dynamics of regulatory networks to population genetics. Few biological systems offer this prospect. 12 .2 Phage λ Gene Regulatory Circuitry Phage λ is a bacterial virus, or bacteriophage, that infects host cells (Hendrix et al ., 1983; Ptashne, 2004). After infection, most phages follow a so-called lytic pathway, in which a temporal pattern of gene expression occurs, leading to synthesis of new copies of the viral genome, followed by packaging these copies into mature virus particles, which are then released from the host cell, usually by lysis of the cell. Although λ can follow this same lytic pathway, it has an alternative mode of existence, the lysogenic state, in which the viral genome is physically integrated into the genome of the host, and expression of the lytic genes is blocked by the action of a master regulatory protein termed λ repressor or CI (“see-one,” not “see-eye”) (Figure 12.1). The lysogenic state is extremely stable. It can switch to the lytic pathway, but in the absence of perturbations it does so at an almost undetectably low rate, probably < 10 –8 per cell generation (Little and Michalowski, 2010). Switching can be extremely efficient, however, when the host SOS response is triggered by treatments that damage DNA or inhibit DNA replication (Little and Mount, 1982; Little, 1993). A key part of this host response is activation of the host RecA protein to a form that can mediate the proteolytic cleavage of the host LexA repressor.

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  Recombinant DNA Principles and Methodologies

  • James Greene(Author)
  • 2021(Publication Date)
  • CRC Press

    (Publisher)

  Lambda II are chapters on lambda basics (Arber 1983), lambda as a cloning vector (Murray 1983), and lambda experimental methods (Arber et al. 1983)

  B. Lambda Biology

  Lambda virions consist of a head, which contains the DNA molecules, and a tail, which is used for cell adsorption and is likely the conduit through which the DNA is injected into the cell. The lambda chromosome is a single double-stranded DNA molecule some 48,502 bp long. At the 5′ ends of the DNA strands are complementary single-strand extensions that are 12 bases long. These extensions, the cohesive ends, anneal following injection of the chromosome into a cell, thus cyclizing the molecule. The annealed cohesive ends create a site, cos, at which staggered nicks are introduced during lytic growth to regenerate the cohesive ends.

  When lambda infects a cell, two outcomes are possible. The first is lytic development, which results in the production of 100 progeny virions and cell lysis, all within about an hour. Alternatively the lambda chromosome carries out the lysogenic response, in which the lytic genes become repressed and the lambda DNA is recombined into the host chromosome. The recombination occurs between the phage attP site (Figure 1 ) and a site on the bacterial chromosome, attB, thus forming an integrated prophage which can be passively replicated for many generations as part of the bacterial chromosome. Integration requires the phage-encoded Int protein (integrase), whereas excision of a lambda prophage from the bacterial chromosome requires both Int and an excision protein, Xis. The 60-some genes of the lambda chromosome (Figure 1 ) are grouped according to function, with the leftmost 10 genes (Nul through FII) encoding the proteins involved assembling the head shell and DNA packaging. The second block of genes contains 11 essential genes (Z through J) involved in assembly of the tail of the virion. To the right of att are two genes, int and xis, involved in the site-specific recombination that occurs between the lambda and E. coli DNAs during prophage integration and excision. Three genes, the red genes, exo and bet, and gam, are involved in general recombination. Genes N and Q control early and late transcription during lytic development, and the immunity region is concerned with repression of lytic genes, that is, with maintenance of the lysogenic state. Genes O and P are involved in DNA replication, which is initiated at ori. Finally, genes S, R, and RZ

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  Bacteriophages

  Biology and Applications

  • Elizabeth Kutter, Alexander Sulakvelidze, Elizabeth Kutter, Alexander Sulakvelidze(Authors)
  • 2004(Publication Date)
  • CRC Press

    (Publisher)

  3.6.1. PHAGES OF GRAM-NEGATIVE BACTERIA

  Lambda (λ), a 48,502-bp siphovirus, is the best-studied of the temperate coliphages; its key early role in understanding gene regulation and integration in lysogeny has been explored earlier in this chapter. From the beginning, it was a primary vector in genetic engineering work. Its efficient system for generalized recombination is the basis for the recombineering system that has revolutionized the construction of transgenic systems, from bacteria to mice (Court et al., 2002). It was one of the first phages sequenced (Sanger et al., 1982), and the intensely explored lambdoid phage group has strongly influenced our view of phage evolution (Chapter 5). Many λ-like phages carry toxin genes and other genes associated with pathogenicity, as discussed in Chapter 8 .

  Mu is a temperate generalized transducing myovirus with a broad host range that includes E. coli, Salmonella, Citrobacter, and Erwinia. It integrates into the genome at quite random sites, which led to its being called Mu, for mutator, and takes with it stretches on both sides when it is packaged, as discussed in Chapter 7. Mu is unusual in that its DNA replication does not occur in a free state, but rather is associated with transposition to random sites within the host chromosome. The first round (lysogenization) occurs by conservative transposition. Further rounds of replication are replicative, with transposed copies of Mu DNA interspersed within host DNA sequences. The mature Mu particle has 37 kbp of conserved Mu-specific DNA flanked on the left by 50–150 bp of host DNA and on the right by 0.5 to 3.0 kbp of host DNA. These random samples of host DNA sequence are incorporated during packaging of the phage DNA, which occurs directly from the host-integrated form. This property is also seen in coliphage D108, a number of Pseudomonas phages including phage D3112, and the levivirus Vibrio cholera phage VcA1. The transposable Pseudomonas prophages are all inducible by DNA-damaging agents, whereas Mu and D108 are not. Mu and D108 expand their host ranges by making two forms of the tail fibers responsible for host recognition; the orientation of an invertible stretch of DNA called the G-loop determines which is expressed. Genes expressed in one orientation are responsible for adsorption to E. coli K-12; genes expressed in the other orientation permit adsorption to other gram-negative bacteria such as Erwinia and Citrobacter freundii. N4 E. coli bacteria such as Erwinia and Citrobacter freundii

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  Discover the World of Microbes

  Bacteria, Archaea, Viruses

  • Gerhard Gottschalk(Author)
  • 2012(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Figure 42 ). Next, both rings open and interfuse to form a figure eight. In this way, phage DNA is integrated into the bacterial chromosome. Such integrated bacteriophages are called temperate. Temperate-phage DNA is replicated along with that of the bacterial chromosome, so any bacterial offspring are temperate-phage carriers. Events such as exposure to toxins or deterioration of bacterial living conditions may activate regulatory signals and lead to excision of lambda-phage DNA, separating it from the bacterial chromosome. The Lambda Phage then becomes lytic like the T4 phage.

  Figure 42  Integration of phage DNA into the E. coli chromosome. The two circles, the E. coli DNA (large) and the phage DNA (small) associate in a region of homology, between the chromosomal regions gal and bio . Then both rings open up and interfuse to form a figure eight. Unfolding of this structure gives a larger circular DNA molecule carrying the integrated DNA molecule.

  (Drawing: Anne Kemmling, Goettingen, Germany.)

  The lambda bacteriophage has been and still is an important tool in gene technology. In the early development of gene technology, a special property of this bacteriophage was used to introduce foreign DNA into E. coli cells. During assembly of lambda-phage particles, the head is filled with phage DNA. However, there is no mechanism by which foreign DNA can be excluded by the head-filling machinery, which merely requires the presence of two lambda-specific regions. Between these regions, some of the lambda-phage DNA may have been excised and replaced by DNA encoding for nonlambda protein, much like the cuckoo that lays its eggs in the nests of other birds. Such altered phages retain their infectious potential, however. After infecting a bacterial host, they become temperate phages. When the host DNA is replicated along with the “smuggled” DNA, the information is transcribed and translated into proteins. Obviously, it’s the end of the line for such phages because some of the information required for viral replication is missing, so there can be no active descendents.

  This Is Another Process that Would Be Considered by Most People As a Delusion of Molecular Genetics Experts.

  Perhaps these processes will be more plausible when we discuss restriction enzymes in Chapter 25.

  Bacteriophages were major objects of research in the 1940s and 1950s, the early days of molecular genetics. To give an example, Max Delbrueck (1906–1981) and Salvador Luria (1912–1991) (Nobel laureates in 1969) did experiments on the emergence of phage-resistant E. coli cells. The results led them to conclude that mutations are not induced but occur spontaneously. In an elegant analysis they showed that phage-resistant mutants arise irrespective of the presence of phages. The phages were simply required in the experiments to demonstrate the presence of such mutants. To give another example: during growth of E. coli , a variety of mutants is generated, among them are some resistant against the antibiotic Steptomycin. They appear spontaneously, but for the demonstration of their presence, Streptomycin has to be added to an agar medium. Growth of E. coli

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  International Congress for Microbiology

  Moscow, 1966

  • Sam Stuart(Author)
  • 2014(Publication Date)
  • Pergamon

    (Publisher)

  We shall first describe some experiments pertaining to the nature of this virulent control mechanism and later show that the bacterial host, E. coli, differs in its response to lytic infection by the temperate phage λ. A second major control mechanism is evidenced by the sequential synthesis of T-even phage enzymes and structural proteins (2). Experiments will be described which demonstrate that regulation is exerted at the level of both transcription of the phage genome into mRNA and translation of this RNA into enzymes. A third type of control mechanism is exhibited by the lysogenic cell, E. coli (λ). Although the prophage λ DNA is attached to the cell's genome, it is normally repressed. Except under certain conditions which cause induction of λ development, the cell does not produce λ proteins or DNA even when it is super-infected by λ phage (1, 3). This repression is under control of the G region of the λ genome and its repressor product. Studies on the derepression of the λ genome and induction of phage development have led us to hypothesize a bifunctional role for the λ repressor and to gain some insight into its chemical properties. 1 Abbreviations used: mRNA, messenger RNA; CAP, chloramphenicol; UV, ultraviolet. — 509 — 510 I. INHIBITION OF ESCHERICHIA COLI AND BACTERIOPHAGE LAMBDA (λ) MESSENGER RNA SYNTHESIS BY T4 It is conceivable to suppose that in the course of evolution, certain bacterio-phages acquired genetic properties that enabled them to gain complete command of the biochemical machinery of their hosts. Examples of such phages are T2, T4, and T6, which are known to turn off all macromolecular syntheses directed by their host, Escherichia coli, while producing their own enzymes, somatic proteins, DNA, and mRNA (2). In order to gain some information about the nature of this control mechanism, we entertained the following question.

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  Snyder and Champness Molecular Genetics of Bacteria

  • Tina M. Henkin, Joseph E. Peters(Authors)
  • 2020(Publication Date)
  • ASM Press

    (Publisher)

  Gottesman , Suggested Reading).

  Figure 7.21 gives an overview of the two life cycles of which λ is capable and the fate of the DNA in each cycle, while Figure 7.22 gives a more detailed map of the phage genome for reference. As described above, phage λ DNA is linear in the phage head, and the map shows how it exists in the head. Immediately after the DNA is injected into the cell to initiate the infection, the DNA cyclizes, that is, forms a circular molecule, by pairing between the cos sites at the ends (Figure 7.9 ). This brings the lysis genes (S and R) and the head and tail genes (A to J) of the phage together and allows them all to be transcribed from the late promoter pR ′, as discussed above. This circular DNA can then either integrate into the host chromosome (lysogenic cycle) or replicate and be packaged into phage heads to form more phage (lytic cycle). Which decision is made depends on the physiological state of the cell, as we discuss below. Later, the integrated DNA in a lysogen can also be excised, replicate, and form more phage (induction).

  THE LYSIS-LYSOGENY DECISION

  Figure 7.23 illustrates the process of forming a lysogen after λ infection, how the cI, cII, and cIII gene products are involved, and the central role of the CII protein. After λ infects a cell, the decision about whether the phage enters the lytic cycle and makes more phage or forms a lysogen depends on the outcome of a competition between the product of the cII gene, which acts to form lysogens, and the products of the cro gene and of genes in the lytic cycle that replicate the DNA and make more phage particles. Which pathway wins most often depends on the conditions of infection. At a low multiplicity of infection (MOI; see “Multiplicity of Infection” below), the lytic cycle usually wins, and in as many as 99% of the infected cells, the λ DNA replicates and more phage are produced. However, for reasons we explain below, at a high MOI, the CII protein wins more often, and as many as 50% of the infected cells can form lysogens. The richness of the medium also plays a role. One reason is that cells that are growing very fast in rich medium have more RNase III (see chapter 2 ) than if they are growing more slowly, and more RNase III means more N protein, which favors lytic development (see “λ N-Mediated Antitermination” above; Court et al ., Suggested Reading). The reason they have more N protein is that the leftward transcript from pL contains the nutL site just upstream of the translational initiation region (TIR) for the N gene (Figure 7.10 ). The Nus factors and N protein bound to the nutL site inhibit N translation from the nearby TIR for the N gene, so less N protein is made. There is a cleavage site for RNase III between the nutL site and the TIR for gene N, and the higher concentrations of RNase III when the cells are growing rapidly cleave the mRNA at a hairpin between the nutL site and the TIR for gene N, separating the nutL site from the N

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  Fundamentals of Molecular Virology

  • Nicholas H. Acheson(Author)
  • 2012(Publication Date)
  • Wiley

    (Publisher)

  REVIEW QUESTIONS 1. Lambda Phage infection of E. coli can have two possible outcomes. What are they? 2. What is induction? 3. What affects the phage’s decision to go lytic or lysogenic? 4. What is the role of CII? 5. Lambda DNA replication is directed by the early genes O and P, but what is the role of host cell proteins? 97 C H A P T E R 9 Viruses of Archaea David Prangishvili Archaea (singular: archaeon) From Greek archaios, “ancient” THE THREE DOMAINS OF LIFE: ARCHAEA, BACTERIA, EUKARYA Archaea are unicellular organisms lacking a nucleus that are phylogenetically distinct from bacteria and eukaryotes • Cell walls made of S layer of protein • Ether linkages in phospholipids • Proteins initiated with methionine, not N-formyl methionine • RNA polymerase and promoters resemble eukaryotic transcriptional machinery Many archaea thrive in extreme environments • Thermophiles (45C) and hyperthermophiles (80C): volcanic hot springs • Acidophiles (pH 0–3): volcanic hot springs • Halophiles (high salt concentrations): salt lakes • Anaerobic environments (methanogens) Two major phyla of archaea: Crenarchaeota and Euryarchaeota. VIRUSES OF ARCHAEA HAVE UNUSUAL MORPHOLOGIES Lemon, droplet, rod, or bottle shapes with surface fibers. All viruses have double-stranded DNA genomes except for one single-stranded DNA virus. Most have internal or external lipid envelopes. Crenarchaeota are hosts for seven distinct virus families, based on virion morphology and genome sequences. Euryarchaeota are hosts for a reduced morphologi- cal spectrum of viruses, some which are related to head–tail bacteriophages. LIFE CYCLES OF VIRUSES OF ARCHAEA Many are temperate viruses that integrate their genome into host cell DNA and replicate without killing the host cell. Some produce unique pyramidal structures that lead to exit of virions and cell death. One virus develops long tails at both ends of virion after release from cell.

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  Desk Encyclopedia Animal and Bacterial Virology

  • Brian W.J. Mahy, Marc H.V. van Regenmortel(Authors)
  • 2010(Publication Date)
  • Academic Press

    (Publisher)

  New York: Oxford University Press. Greive SJ and von Hippel PH (2005) Thinking quantitatively about transcriptional regulation. Nature Reviews Molecular Cell Biology 6(3): 221–232. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, and Ruger W (2003) Bacteriophage T4 genome. Microbiology and Molecular Biology Reviews 67(1): 86–156. Oppenheim AB, Kobiler O, Stavans J, Court DL, and Adhya S (2005) Switches in bacteriophage lambda development. Annual Review of Genetics 39: 409–429. Ptashne M (2004) A Genetic Switch. Phage Lambda Revisited. Cold Spring Harbor, NY: Cold Spring Harbor Press. Virus Evolution: Bacterial Viruses R W Hendrix, University of Pittsburgh, Pittsburgh, PA, USA ã 2008 Elsevier Ltd. All rights reserved. Glossary Chromosome The physical DNA or RNA molecule present in the virion and containing the information of the genome. The chromosome can differ from the genome by, for example, having a terminal repetition of part of the genomic sequence or being circularly permuted relative to other chromosomes in the population. Genome The totality of the genetic complement of a virus. The genome is a conceptual object usually expressed as a sequence of nucleotides. Homologous Having common ancestry. Homology of two sequences is often inferred on the basis of a high percentage of identity between the sequences, but homology itself is either present or not and is not expressed as a percentage. Novel joint A novel juxtaposition of sequences in a genome resulting from a nonhomologous recombination event. Virus Evolution: Bacterial Viruses 571 Bacteriophage Evolution Bacterial viruses (‘bacteriophages’ or ‘phages’ for short) have probably been evolving for 4 billion years or more, but it is only in recent years that we have come to a relatively detailed view of the genetic mechanisms that underlie phage evolution.

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  Mobile Genetic Elements

  • James Shapiro(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  In my judgment, the actual data fit much better with the idea that they are deletion derivatives of lambdoid phages. 2. BACTERIOPHAGE λ 95 Β. Distinction between Host Modules and Defective Prophages I have not tried to justify my evaluation of the data on λ-related phages and phage-related DNA segments. These issues have been discussed in more detail elsewhere (Campbell, 1977). However, in the case of phage-related segments, it is important to explain what question is really being asked, and why it seems necessary to ask that question rather than some other one. Most scientists distrust concepts that cannot be translated rather directly into experimental operations. If we ask whether portions of a viral genome can originate from host genes, we might hope to settle the matter by showing that a DNA segment that consists of host genes at the beginning of an experiment can become part of a viral genome during the experiment. However, to define the question in that manner would require us to conclude that viruses originate from host genes every time a lysogenic bacterium is induced, because the genes of the prophage behave as host genes, operationally defined. Few virologists would want to equate induction of a lysogen with the origin of a virus. Because bacteria can become lysogenic in the laboratory by infection, we suspect (although we cannot prove) that most naturally lysogenic bacteria likewise acquired the viral genome through infection. The prophage is therefore treated as a stage in the phage life cycle, rather than as an evolutionary precursor of the phage. To anyone taking the opposite view, the problem of the origin of viruses is of course already solved. Although the distinction just made may appear obvious and trivial, it needs to be stated explicitly before we consider the subject of natural strains carrying defective or incomplete prophages.

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  Mechanisms of Adaptation

  • J.R. Spkatch(Author)
  • 2014(Publication Date)
  • Academic Press

    (Publisher)

  Lysogenic conversion clearly provides a mechanism by which a temperat e phage may be of net benefit to a host. In addition, both transduction by addition and lysogenic con-version provide 4 source of extra DNA for bacteria l or viral evolution. IV. Specific Examples of Bacteriophage Growth A. P HAGE λ— V ARIETY I N L IFE S TYLE 1. G ENERAL O U T L I N E OF P HAGE λ D EVELOPMENT The temperat e phage λ has been the most extensively studied of all bacteriophage , characterized fondly in a biography (Hershey, 1971) and numerous recent review articles (Echols, 1971a, 1972, 1973, 1974; Hersko-witz, 1973; Weisberg et al., 1977). In this section, I will use λ to show how the general framework described in Section III is executed in a particular case. For more details and a more extensive reference list, the reader should consult the review articles noted above. In Section IV,B I will outline the productive growth of the virulent phages Ml 3, T7, and T4. Bacteriophage A is a phage of moderate structura l complexity with an icosahedra l head about 54 nm in diameter and a tail of 150 nm, terminating in a short tail fiber; the genome is a double-strande d D N A molecule of MW 30 χ 10 6 with a 12-base complementary single-stranded region at each 502 HARRISON ECHOLS end that provides for intracellular circularization of the DNA by pairing of these cohesive sites. When λ DNA is injected into a cell, the first events are formation of a molecule and limited transcription of a small region of the λ DNA, princi-pally the Ν and cro genes (Fig. 5). Following this immediat e early period the Ν protein (product of the Ν gene) activates the delayed early stage of viral development in which leftward transcription extends through the recombination genes and rightward transcription is enhanced from the replication genes and extends through gene Q (Echols, 1971b; Thomas, 1971).

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  Thinking Like a Phage

  The Genius of the Viruses That Infect Bacteria and Archaea

  • Merry Youle, Leah L Pantéa(Authors)
  • 2017(Publication Date)
  • Wholon

    (Publisher)

  1 continues to grow and can give rise to multiple generations of descendants, each with a phage on board. Meanwhile, this resident phage, termed a prophage, considers that it has committed to only a moment-to-moment lease. When conditions threaten the virocell’s viability, the prophage opts out and resumes lytic replication.

  Note: This chapter focuses almost exclusively on temperate phages that infect Bacteria. Although many archaeal phages are non-lytic, we know little about their cooperative ways.

  Unmasking Lysogeny

  Nearly a hundred years ago, early phage researchers observed something very puzzling. Some bacterial strains cultured in the lab, apparently virus-free, could give rise to phages. Such strains were termed lysogenic, i.e., capable of lysing and releasing phage. What was going on? Clues accumulated. The researchers could convert a non-lysogenic strain into a lysogenic one by infecting a culture with one of these phages. However, when they ruptured the lysogens and looked inside for phage, they found no infectious particles. Their conclusion? The phage persisted in the cells in some non-infectious form until something prompted them to produce new particles. More evidence of their intracellular persistence: the phage particles released by these lysogens were new entities, but they were always of the same type as those that had originally infected that bacterial culture generations ago. Apparently whatever produced those virus particles had become part of the cell’s heredity. Also, the lysogens could be routinely induced to release infectious particles on demand by damaging their chromosomes with UV irradiation or chemical mutagens. This was all quite mysterious. Bear in mind that this initial sleuthing was done before DNA had been identified as the genetic material in cells.2

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  Phage Display of Peptides and Proteins

  A Laboratory Manual

  • Brian K. Kay, Jill Winter, John McCafferty(Authors)
  • 1996(Publication Date)
  • Academic Press

    (Publisher)

  CHAPTER 1

  Biology of the Filamentous Bacteriophage

  Robert E. Webster

  INTRODUCTION TO THE LIFE CYCLE OF THE BACTERIOPHAGE

  A number of filamentous phage have been identified which are able to infect a variety of gram negative bacteria. They have a single-stranded, covalently closed DNA genome which is encased in a long cylinder approximately 7 nm wide by 900 to 2000 nm in length. The best characterized of these phage are M13, fl, and fd, which infect Escherichia coli containing the F conjugative plasmid. The genomes of these three bacteriophage have been completely sequenced and are 98% homologous (

  Van Wezenbeek et al ., 1980

  ; Beck and Zink, 1981 ; Hill and Petersen, 1982 ). Because of their similarity and their dependence on the F plasmid for infection, M13, fl, and fd are collectively referred to as the Ff phage.

  Infection of E. coli by the Ff phage is initiated by the specific interaction of one end of the phage with the tip of the F pilus. This pilus is encoded by genes in the tra operon on the F conjugative plasmid (Fig. 1 ). The F pilus is required for conjugal transfer of the F plasmid DNA or chromosomal DNA containing the integrated plasmid DNA into recipient bacteria lacking the plasmid DNA (Willetts and Skurray, 1987 ; Ippen-Ihler and Maneewannekul, 1991 ;

  Frost et al ., 1994

  ). It consists of a protein tube which is assembled and disassembled by a polymerization and depolymerization process from pilin subunits in the bacterial inner membrane (Frost, 1993) . Conjugation is thought to be initiated by interaction of the tip of the F pilus and the envelope of the recipient bacteria. Pilus retraction, by depolymerization of pilin subunits into the inner membrane, then draws the donor (F plasmid containing) and recipient bacteria together to facilitate the processes required for DNA transfer (Ippen-Ihler and Manneewannekul, 1991) .

  FIGURE 1

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