Bacterial and Viral Genetic Systems Benjamin A. Pierce GENETICS A Conceptual Approach SIXTH EDITION CHAPTER 9 Bacterial and Viral Genetic Systems © 2017 W. H. Freeman and Company

Woman with leprosy, a disease caused by the bacterium Mycobacterium leprae. The study of M. leprae DNA isolated from ancient skeletons of medieval Europeans with leprosy has provided information about the evolution of this bacterium. [Reuters/Rupak de Chowdhuri (India).]

Bacterial function in oceans Agriculture Natural flora Disease 9.1 Bacteria and Viruses Have Important Roles in Human Society and the World Ecosystem Bacterial function in oceans Agriculture Natural flora Disease Commercial products

Advantages of using bacteria and viruses for genetic studies TABLE 9.1 Advantages of using bacteria and viruses for genetic studies 1. Reproduction is rapid. 2. Many progeny are produced. 3. The haploid genome allows all mutations to be expressed directly. 4. A sexual reproduction simplifies the isolation of genetically pure strains. 5. Growth in the laboratory is easy and requires little space. 6. Genomes are small. 7. Techniques are available for isolating and manipulating their genes. 8. They have medical importance. 9. They can be genetically engineered to produce substances of commercial value.

Characteristics of bacteria 9.1 Bacteria and Viruses Have Important Roles in Human Society and the World Ecosystem 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 occurs prior to binary fission

9.1 Bacteria may be grown in liquid medium and on solid medium.

Techniques for the study of bacteria 9.2 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: contains all substances required by all bacteria, including auxotrophic bacteria

9. 2 Bacterial colonies have a variety of phenotypes 9.2 Bacterial colonies have a variety of phenotypes. (a) Serratia marcescens with color variation. (b) Bacillus cereus; colony shape varies among different strains of this species. [part a: Dr. Edward J. Bottone. part b: Biophoto Associates/Science Source.]

9.3 Mutant bacterial strains can be isolated on the basis of their nutritional requirements.

9.2 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

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.

9. 5 A plasmid replicates independently of its bacterial chromosome 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.

9. 6 The F factor, a circular episome of E 9.6 The F factor, a circular episome of E. coli, contains a number of genes that regulate transfer into a bacterial cell, replication, and insertion into the bacterial chromosome. Replication is initiated at ori. Insertion sequences (see Chapter 18) IS3 and IS2 control insertion into the bacterial chromosome and excision from it.

Which statement is true of plasmids? Concept Check 1 Which statement 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 statement is true of plasmids? Concept Check 1 Which statement 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.

9.3 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

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

Gene Transfer in Bacteria 9.3 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene Transfer in Bacteria Conjugation: Lederberg and Tatum experiment F+ cells: donor cells containing F factor F– cells: recipient cells lacking F factor Sex pilus: connection tube

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

9.9 Davis’s U-tube experiment.

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

9.11 The F factor is transferred during conjugation between F+ and F− cells.

9.3 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 (Figs. 9.12 and 9.13) F prime (F) cells: contains F plasmid carrying some bacterial genes (Fig. 9.14) Merozygotes: partial diploid bacterial cells containing F plasmid carrying some bacterial genes

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

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.

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.

Characteristics of E. coli cells with different types of F factor TABLE 9.2 Characteristics of E. coli cells with different types of F factor Type F Factor Characteristics Role in Conjugation F+ Present as separate circular plasmid Donor F– Absent Recipient Hfr Present, integrated into bacterial chromosome High-frequency donor F' Present as separate circular plasmid, carrying some bacterial genes

Results of conjugation between cells with different F factors TABLE 9.3 Results of conjugation between cells with different F factors Conjugating Cells Cell Types Present after Conjugation F+ × F− Two F+ cells (F− cell becomes F+) Hfr × F− One Hfr cell and one F− cell (no change)* F' × F− Two F' cells (F− cell becomes F') *Rarely, the F− cell becomes F+ in an Hfr × F− conjugation if the entire chromosome is transferred during conjugation.

Concept Check 3 Conjugation between an F+ and F− cell usually results in which of the following? 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 which of the following? Two F+ cells Two F− cells An F+ and an F− cell An Hfr and an F+ cell

Gene transfer in bacteria 9.3 Bacteria Exchange Genes Through Conjugation, Transformation, and Transduction Gene transfer in bacteria Conjugation: Mapping bacterial genes with interrupted conjugation: Distance between genes is 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.

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

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

Gene transfer in bacteria 9.3 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.

9.3 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.

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

9.17 Genes can be transferred between bacteria through transformation.

9.18 Transformation can be used to map bacterial genes.

9.3 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.

9.4 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: phage DNA integrates into bacterial chromosome where it remains as inactive prophage.

9. 19 Viruses come in different structures and sizes 9.19 Viruses come in different structures and sizes. (a)T4 bacteriophage. (b) Influenza A virus.

9.20 Bacteriophages have two alternative life cycles: lytic and lysogenic. 45

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

9. 21 Plaques are clear patches of lysed cells on a lawn of bacteria 9.21 Plaques are clear patches of lysed cells on a lawn of bacteria. [© Carolina Biological Supply Company/Phototake.]

9.22 The Lederberg and Zinder experiment.

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

9.24 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.

9.25 Hershey and Rotman developed a technique for mapping viral genes.

Progeny phages produced from h− r+ × h+ r− TABLE 9.4 Progeny phages produced from h− r+ × h+ r− Phenotype Genotype Clear and small h– r+ Cloudy and large h+ r– Cloudy and small h+ r+ Clear and large h– r–

9.4 Viruses Are Simple Replicating Systems Amenable to Genetic Analysis RNA virus Retrovirus: RNA virus that has been integrated into the host genome. Reverse transcriptase: synthesizing DNA from RNA or DNA template. HIV and AIDS

9.26 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. (b) The retrovirus life cycle.

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

9.28 HIV attacks helper T cells.

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

Strains of influenza virus responsible for major flu pandemics TABLE 9.5 Strains of influenza virus responsible for major flu pandemics Year Influenza Pandemic Strain 1918 Spanish Flu H1N1 1957 Asian flu H2N2 1968 Hong Kong flu H3N2 2009 Swine flu

9.29 New strains of influenza virus are created by reassortment of genetic material from different strains. A new H1N1 virus (swine flu) that appeared in 2009 contained genetic material from avian, swine, and human viruses.