Chapter 7 Microbial Genetics 2015 Pearson Education Inc

The Structure and Replication of Genomes • Genetics • Study of inheritance and inheritable traits as expressed in an organism's genetic material • Genome • The entire genetic complement of an organism • Includes its genes and nucleotide sequences © 2015 Pearson Education, Inc.

Figure 7. 1 The structure of nucleic acids. Hydrogen bond Sugar Thymine (T) nucleoside Adenine (A) nucleoside A–T base pair (DNA) 5′ end 3′ end A–U base pair (RNA) Cytosine (G) nucleoside Guanine (G) nucleoside G–C base pair (DNA and RNA) 5′ end 3′ end A T G A Uracil (U) nucleoside Adenine (A) nucleoside C T G Guanine 3′ end 5′ end Double-stranded DNA Cytosine Adenine 3′ end Thymine 5 end′ Thymine nucleoside Thymine nucleotide © 2015 Pearson Education, Inc.

The Structure and Replication of Genomes • The Structure of Prokaryotic Genomes • Prokaryotic chromosomes • Main portion of DNA, along with associated proteins and RNA • Prokaryotic cells are haploid (single chromosome copy) • Typical chromosome is circular molecule of DNA in nucleoid © 2015 Pearson Education, Inc.

Figure 7. 2 Bacterial genome. Nucleoid Bacterium Chromosome Plasmid © 2015 Pearson Education, Inc.

The Structure and Replication of Genomes • The Structure of Prokaryotic Genomes • Plasmids • Small molecules of DNA that replicate independently • Not essential for normal metabolism, growth, or reproduction • Can confer survival advantages • Many types of plasmids © 2015 Pearson Education, Inc.

Plasmids • Types of plasmids • Fertility factors • carries genes for a variety of functions not essential for cell growth (e. g. conjugation) • result in the expression of sex pili • Resistance factors • Bacteriocin factors • carries genes for proteinaceous toxins • Virulence plasmids • turn bacteria into pathogen © 2015 Pearson Education, Inc.

The Structure and Replication of Genomes • The Structure of Eukaryotic Genomes • Nuclear chromosomes • Typically have more than one chromosome per cell • Chromosomes are linear and sequestered within nucleus • Eukaryotic cells are often diploid (two chromosome copies) © 2015 Pearson Education, Inc.

The Structure and Replication of Genomes • The Structure of Eukaryotic Genomes • Extranuclear DNA of eukaryotes • DNA molecules of mitochondria and chloroplasts • Resemble chromosomes of prokaryotes • Code only for about 5% of RNA and proteins • Some fungi, algae, and protozoa carry plasmids © 2015 Pearson Education, Inc.

The Structure and Replication of Genomes • DNA Replication • Other characteristics of bacterial DNA replication • Bidirectional • Gyrases and topoisomerases remove supercoils in DNA • DNA is methylated • Control of genetic expression • Initiation of DNA replication • Protection against viral infection • Repair of DNA © 2015 Pearson Education, Inc.

Figure 7. 7 The bidirectionality of DNA replication in prokaryotes. Origin Parental strand Replication forks Daughter strand Replication proceeds in both directions © 2015 Pearson Education, Inc. Termination of replication

Figure 7. 15 Ribosomal structures. © 2015 Pearson Education, Inc.

Figure 7. 16 Assembled ribosome and its t. RNA-binding sites. Large subunit m. RNA Nucleotide bases 5′ E P A sitesite t. RNAbinding sites 3′ Small subunit Prokaryotic ribosome (angled view) attached to m. RNA © 2015 Pearson Education, Inc. m. RNA Small subunit Prokaryotic ribosome (schematic view) showing t. RNA-binding sites

Gene Function • Regulation of Genetic Expression • Most genes are expressed at all times • Other genes are transcribed and translated when cells need them • Allows cell to conserve energy • Quorum sensing regulates production of some proteins • Detection of secreted quorum-sensing molecules can signal bacteria to synthesize a certain protein © 2015 Pearson Education, Inc.

Mutations of Genes • Mutation • Change in the nucleotide base sequence of a genome • Rare event • Almost always deleterious • Rarely leads to a protein that improves ability of organism to survive © 2015 Pearson Education, Inc.

Mutations of Genes • Types of Mutations • Point mutations • One base pair is affected • Substitutions and frameshift mutations • Frameshift mutations • Nucleotide triplets after the mutation are displaced • Creates new sequence of codons © 2015 Pearson Education, Inc.

Figure 7. 24 The effects of the various types of point mutations. © 2015

Mutations of Genes • Mutagens • Radiation • Ionizing radiation • Nonionizing radiation • Chemical mutagens • Nucleotide analogs • Disrupt DNA and RNA replication • Nucleotide-altering chemicals • Alter the structure of nucleotides • Result in base-pair substitutions and missense mutations • Frameshift mutagens • Result in nonsense mutations © 2015 Pearson Education, Inc.

Figure 7. 25 A pyrimidine (in this case, thymine) dimer. Ultraviolet light Thymine dimer

Figure 7. 26 The structure and effects of a nucleotide analog. © 2015 Pearson

Figure 7. 27 The action of a frameshift mutagen. © 2015 Pearson Education, Inc.

Mutations of Genes • Frequency of Mutation • Mutations are rare events • Otherwise, organisms could not effectively reproduce • About 1 of every 10 million genes contains an error • Mutagens increase the mutation rate by a factor of 10 to 1000 times • Many mutations stop transcription or code for nonfunctional proteins © 2015 Pearson Education, Inc.

Figure 7. 29 Positive selection of mutants. Penicillinresistant cell Medium with penicillin (only penicillin-resistant cell grows into colony) Penicillinsensitive cells Medium without penicillin (both types of cells form colonies) Mutagen induces mutations Penicillinresistant mutants indistinguishable from nonmutants Medium with penicillin © 2015 Pearson Education, Inc. Medium without penicillin

Genetic Recombination and Transfer • Exchange of nucleotide sequences often occurs between homologous sequences • Recombinants • Cells with DNA molecules that contain new nucleotide sequences © 2015 Pearson Education, Inc.

Figure 7. 32 Genetic recombination. Homologous sequences 3′ DNA A 5′ 3′ DNA B 5′ Enzyme nicks one strand of DNA at homologous sequence. A B Recombination enzyme inserts the cut strand into second molecule, which is nicked in the process. Ligase anneals nicked ends in new combinations. Molecules resolve into recombinants. Recombinant A © 2015 Pearson Education, Inc. Recombinant B

Genetic Recombination and Transfer • Horizontal Gene Transfer Among Prokaryotes • Vertical gene transfer • Passing of genes to the next generation • Horizontal gene transfer • Donor cell contributes part of genome to recipient cell • Three types • Transformation • Transduction • Bacterial conjugation © 2015 Pearson Education, Inc.

Genetic Recombination and Transfer • Horizontal Gene Transfer Among Prokaryotes • Transformation • Recipient cell takes up DNA from the environment • Provided evidence that DNA is genetic material • Cells that take up DNA are competent • Results from alterations in cell wall and cytoplasmic membrane that allow DNA to enter cell © 2015 Pearson Education, Inc.

Figure 7. 33 Transformation of Streptococcus pneumoniae. Observations of Streptococcus pneumoniae Live cells Living strain R Injection Capsule Heat-treated dead cells of strain S Griffith's experiment: Mouse dies + In vitro transformation XX XX Heat-treated dead cells of strain S Injection X Heat-treated XX X DNA broken into pieces dead cells of strain S DNA fragment from strain S Living strain R Injection XX XX Mouse dies Some cells take up DNA from the environment and incorporate it into their chromosomes Mouse lives Culture of Streptococcus from dead mouse Strain R live cells (no capsule) Injection Living cells with capsule (strain S) Mouse lives © 2015 Pearson Education, Inc. Transformed cells acquire ability to synthesize capsules

Genetic Recombination and Transfer • Horizontal Gene Transfer Among Prokaryotes • Transduction • Transfer of DNA from one cell to another via replicating virus • Virus must be able to infect both donor and recipient cells • Virus that infects bacteria called a bacteriophage (phage) © 2015 Pearson Education, Inc.

Figure 7. 34 Transduction. Bacteriophage Host bacterial cell (donor cell) Bacterial chromosome 1 Phage injects its DNA. 2 Phage enzymes degrade host DNA. Phage DNA Phage with donor DNA (transducing phage) 3 Cell synthesizes new phages that incorporate phage DNA and, mistakenly, some host DNA. Transducing phage Recipient host cell 4 Transducing phage injects donor DNA. Transduced cell Inserted DNA © 2015 Pearson Education, Inc. 5 Donor DNA is incorporated into recipient's chromosome by recombination.

Genetic Recombination and Transfer • Horizontal Gene Transfer Among Prokaryotes • Transduction • Generalized transduction • Transducing phage carries random DNA segment from donor to recipient • Specialized transduction • Only certain donor DNA sequences are transferred © 2015 Pearson Education, Inc.

Genetic Recombination and Transfer • Horizontal Gene Transfer Among Prokaryotes • Conjugation • Genetic transfer requires physical contact between the donor and recipient cell • Donor cell remains alive • Mediated by conjugation (sex) pili © 2015 Pearson Education, Inc.

Figure 7. 35 Bacterial conjugation. F plasmid Origin of transfer Chromosome Pilus 1 Donor cell attaches to a recipient cell with its pilus. F+ cell _ F cell 2 Pilus may draw cells together. 3 One strand of F plasmid DNA transfers to the recipient. Pilus 4 The recipient synthesizes a complementary strand to become an F+ cell with a pilus; the donor synthesizes a complementary strand, restoring its complete plasmid. F+ cell © 2015 Pearson Education, Inc. F+ cell

Figure 7. 36 Conjugation involving an Hfr cell. Donor chromosome Pilus F+ cell 1 F plasmid integrates into chromosome by recombination. Hfr cell Pilus F+ cell (Hfr) F plasmid 2 Cells join via a pilus. F – recipient Donor DNA Part of F plasmid 3 Portion of F plasmid partially moves into recipient cell trailing a strand of donor's DNA. Incomplete F plasmid; cell remains F − 4 Conjugation ends with pieces of F plasmid and donor DNA in recipient cell; cells synthesize complementary DNA strands. 5 Donor DNA and recipient DNA recombine, making a recombinant F –cell. © 2015 Pearson Education, Inc. Recombinant cell (still F − )

Genetic Recombination and Transfer • Transposons and Transposition • Transposons • Segments of DNA that move from one location to another in the same or different molecule • Result is a kind of frameshift insertion (transpositions) • Transposons all contain palindromic sequences at each end © 2015 Pearson Education, Inc.

Figure 7. 37 Transposition. Transposon Jumping transposons. Transposons move from one place to another on a DNA molecule. © 2015 Pearson Education, Inc. Plasmid with transposon DNA Replicating transposons. Transposons may replicate while moving, resulting in more transposons in the cell. Transposons can move onto plasmids. Transposons moving onto plasmids can be transferred to another cell.