Bacterial and Viral Genetic Systems Benjamin A. Pierce GENETICS A Conceptual Approach FIFTH EDITION CHAPTER 9 Bacterial and Viral Genetic Systems © 2014 W. H. Freeman and Company

Bacteria account for most of life’s diversity and exist in almost every conceivable environment, including inhospitable habitats such as the highly saline Dead Sea. Molecular techniques aided in our study of bacteria.

When we look at genetic diversity it is very clear that Bacteria and archaea are more diverse than the diversity see in plants, animals, or fungi. In this chapter you will come to understand why.

Figure 9.7 Conjugation, transformation, and transduction are three processes of gene transfer in bacteria. For the transferred DNA to be stably inherited, all three processes require the transferred DNA to undergo recombination with the bacterial chromosome.

Figure 9.11 The F factor is transferred during conjugation between an F+ and F− cell.

Major Ideas from this chapter. What kinds of genes are present on plasmids? How do the processes of Transformation, Transduction, and conjugation contribute to bacterial diversity.? How do bacteria contribute to viral diversity? In cells containing conjugative plasmids ,how do we distinguish between F-, F+ and Hfr cell types?

Figure 9.12 The F factor is integrated into the bacterial chromosome in an Hfr cell.

Figure 9.10 A sex pilus connects F+ and F− cells during bacterial conjugation. [Dr. Dennis Kunkel/Phototake.]

Figure 9. 6 The F factor, a circular episome of E Figure 9.6 The F factor, a circular episome of E. coli, contains a number of genes that regulate transfer into the bacterial cell, replication, and insertion into the bacterial chromosome. Replication is initiated at oriV. Insertion sequences IS3 and IS2 control insertion into the bacterial chromosome and excision from it.

Figure 9.13 Bacterial genes may be transferred from an Hfr cell to an F− cell in conjugation. In an Hfr cell, the F factor has been integrated into the bacterial chromosome.

Characteristics of Bacteria 9.1 Genetic Analysis of Bacteria Requires Special Approaches and Methods All prokaryotes are unicellular and lack a membrane-bound nucleus and membrane-bound organelles Eubacteria Archaea Characteristics of Bacteria Diverse shapes and sizes Some are photosynthetic Replication occur prior to binary fission

Techniques for the Study of Bacteria 9.1 Genetic Analysis of Bacteria Requires Special Approaches and Methods Techniques for the Study of Bacteria Prototrophic: wild type Auxotrophic: mutant type Minimum medium: only required by prototrophic bacteria Complete medium: contain all substances required by all bacteria, including auxotrophic bacteria

Figure 9.1 Bacteria may be grown in both liquid media and on solid media.

Figure 9.3 Mutant bacteria may be isolated based upon their nutritional requirements.

9.1 Genetic Analysis of Bacteria Requires Special Approaches and Methods The bacterial genome: Mostly single, circular DNA molecule/chromosome (Fig. 9.4) Plasmids: Extra chromosome, small circular DNA Episomes—freely replicating plasmids: F (fertility) factor

Figure 9.4 Most bacterial cells possess a single, circular chromosome, shown here emerging from a ruptured bacterial cell. Many bacteria contain plasmids—small, circular molecules of DNA.

Figure 9.5 A plasmid replicates independently of its bacterial chromosome. Replication begins at the origin of replication (ori) and continues around the circle. In this diagram, replication is taking place in both directions; in some plasmids, replication is in one direction only.

Which is true of plasmids? Concept Check 1 Which is true of plasmids? a. They are composed of RNA. b. They normally exist outside of bacterial cells. c. They possess only a single strand of DNA. d. They replicate independently of the bacterial chromosome.

Which is true of plasmids? Concept Check 1 Which is true of plasmids? a. They are composed of RNA. b. They normally exist outside of bacterial cells. c. They possess only a single strand of DNA. d. They replicate independently of the bacterial chromosome.

9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene Transfer in Bacteria Conjugation: direct transfer of DNA from one bacterium to another Transformation: bacterium takes up free DNA Transduction: bacterial viruses take DNA from one bacterium to another

Figure 9.7 Conjugation, transformation, and transduction are three processes of gene transfer in bacteria. For the transferred DNA to be stably inherited, all three processes require the transferred DNA to undergo recombination with the bacterial chromosome.

Which process of DNA transfer in bacteria requires a virus? Concept Check 2 Which process of DNA transfer in bacteria requires a virus? Conjugation Transformation Transduction All of the above

Which process of DNA transfer in bacteria requires a virus? Concept Check 2 Which process of DNA transfer in bacteria requires a virus? Conjugation Transformation Transduction All of the above

Gene Transfer in Bacteria 9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene Transfer in Bacteria Conjugation: Direct transfer via connection tube, one-way traffic from donor cells to recipient cells. It is not a reciprocal exchange of genetic information

Figure 9.7a Conjugation.

Gene Transfer in Bacteria 9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene Transfer in Bacteria Conjugation: Lederberg and Tatum experiment F+ cells: donor cells contain F factor F– cells: recipient cells lacking F factor Sex pilus: connection tube

Figure 9.8 Lederberg and Tatum’s experiment demonstrated that bacteria undergo genetic exchange.

Figure 9.9 Davis’s U-tube experiment

Figure 9.11 The F factor is transferred during conjugation between an F+ and F− cell.

9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene Transfer in Bacteria Conjugation: Hfr cells: (high-frequency strains): donor cells with F factor integrated into the donor bacterial chromosome F prime (F) cells: Contains F plasmid carrying some bacterial genes. Merozygotes: partial diploid bacterial cells containing F plasmid carrying some bacterial genes.

Figure 9.12 The F factor is integrated into the bacterial chromosome in an Hfr cell.

Figure 9.14 An Hfr cell may be converted into an F’ cell when the F factor excises from the bacterial chromosome and carries bacterial genes with it. Conjugation produces a partial diploid.

Concept Check 3 Conjugation between an F+ and F− cell usually results in: two F+ cells. two F− cells. an F+ and an F− cell. an Hfr and an F+ cell.

Concept Check 3 Conjugation between an F+ and F− cell usually results in: two F+ cells. two F− cells. an F+ and an F− cell. an Hfr and an F+ cell.

Gene Transfer in Bacteria 9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene Transfer in Bacteria Conjugation: Mapping bacterial genes with interrupted Conjugation: Distance between genes are measured by the time required for DNA transfer from Hfr cells to F– cells. (Fig. 9.15) Natural Gene Transfer and Antibiotic Resistance Antibiotic resistance comes from the actions of genes located on R plasmids that can be transferred naturally.

Figure 9.15 Jacob and Wollman used interrupted conjugation to map bacterial genes.

Figure 9.16 The orientation of the F factor in an Hfr strain determines the direction of gene transfer.

Gene Transfer in Bacteria 9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene Transfer in Bacteria Conjugation: Natural Gene Transfer and Antibiotic Resistance Antibiotic resistance comes from the actions of genes located on R plasmids that can be transferred naturally. R plasmids have evolved in the past 60 years since the beginning of widespread use of antibiotics. The transfer of R plasmids is not restricted to bacteria of the same or even related species.

9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction A bacterium takes up DNA from the medium. Recombination takes place between introduced genes and the bacterial chromosome.

Figure 9.7b Transformation.

9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Competent cells: cells take up DNA Transformants: cells that receive genetic material Cotransformed: cells that are transformed by two or more genes

Figure 9.18 Bacterial transformation.

Figure 9.19 Transformation can be used to map bacterial genes.

9.2 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Bacterial Genome Sequences: ~ 1-4 million base pairs of DNA Horizontal Gene Transfer: Genes can be passed between individual members of different species by nonreproductive mechanisms.

9.3 Viruses Are Simple Replicating Systems Amenable to Genetic Analysis Virus: Replicating structure (DNA/RNA) + Protein coat. Bacteriophage: bacterial infection virus Virulent phages: reproduce through the lytic cycle, and always kill the host cells. Temperate phages: inactive prophage—phage DNA integrates into bacterial chromosome.

Figure 9. 20 Viruses come in different structures and sizes Figure 9.20 Viruses come in different structures and sizes. (a)T4 bacteriophage (b) Influenza A virus.

Figure 9.21 Bacteriophages have two alternative life cycles: lytic and lysogenic. 50

9.3 Viruses Are Simple Replicating Systems Amenable to Genetic Analysis Transduction: Bacterial viruses (bacteriophage) carries DNA from one bacterium to another. Transduction usually occurs between bacteria of the same or closely related species.

Figure 9.23 The Lederberg and Zinder experiment.

Figure 9.24 Genes can be transferred from one bacterium to another through generalized transduction.

Figure 9.25 Generalized transduction can be used to map genes.

Concept Check 4 In gene mapping experiments using generalized transduction, bacterial genes that are cotransduced are: far apart on the bacterial chromosome. on different bacterial chromosomes. close together on the bacterial chromosome. on a plasmid.

Concept Check 4 In gene mapping experiments using generalized transduction, bacterial genes that are cotransduced are: far apart on the bacterial chromosome. close together on the bacterial chromosome. on different bacterial chromosomes. on a plasmid.

Figure 9.26 Hershey and Rotman developed a technique for mapping viral genes.

Figure 9.28 Benzer developed a procedure for mapping rll phage mutants.

9.3 Viruses Are Simple Replicating Systems Amenable to Genetic Analysis RNA Virus Retrovirus: RNA viruses that have been integrated into the host genome. Reverse Transcriptase: synthesizing DNA from RNA or DNA template. HIV and AIDS

Figure 9.30a A retrovirus uses reverse transcription to incorporate its RNA into the host DNA. (a) Structure of a typical retrovirus. Two copies of the single-stranded RNA genome and the reverse transcriptase enzyme are shown enclosed within a protein capsid. The capsid is surrounded by a viral envelope that is studded with viral glycoproteins.

Figure 9.30b A retrovirus uses reverse transcription to incorporate its RNA into the host DNA. (b) The retrovirus life cycle.

Figure 9.31 HIV-1 evolved from a similar virus found in chimpanzees.

Figure 9.32 HIV attacks helper T cells.

Influenza Rapid changes occur through genetic recombination Three main types: influenza A, influenza B, and influenza C Most cases influenza A: divided into subtypes based upon expression of hemagglutinin (HA) and neuraminidase (NA)