Chapter 7 Microbial Genetics

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

Figure 7.1 The structure of nucleic acids. Hydrogen bond Sugar Adenine (A) nucleoside Thymine (T) nucleoside Adenine (A) nucleoside Uracil (U) nucleoside Guanine (G) nucleoside Cytosine (G) nucleoside A–T base pair (DNA) A–U base pair (RNA) G–C base pair (DNA and RNA) 5′ end 3′ end 5′ end 3′ end T A G C A T G Guanine Cytosine 3′ end Adenine Thymine 5′ end 3′ end 5 end′ Double-stranded DNA Thymine nucleoside Thymine nucleotide

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

Figure 7.2 Bacterial genome. Nucleoid Bacterium Chromosome Plasmid

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

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

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)

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

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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

Figure 7.7 The bidirectionality of DNA replication in prokaryotes. Origin Parental strand Replication forks Daughter strand Replication proceeds in both directions Termination of replication

Figure 7.15 Ribosomal structures. 13

Figure 7.16 Assembled ribosome and its tRNA-binding sites. Large subunit Large subunit E site P site A site mRNA Nucleotide bases 5′ 3′ Small subunit Small subunit mRNA Prokaryotic ribosome (angled view) attached to mRNA Prokaryotic ribosome (schematic view) showing tRNA-binding sites 14

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

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

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

Figure 7.24 The effects of the various types of point mutations.

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

Figure 7.25 A pyrimidine (in this case, thymine) dimer. Ultraviolet light Thymine dimer T = T G G G C T G T A C G A C A A C C A T

Figure 7.26 The structure and effects of a nucleotide analog.

Figure 7.27 The action of a frameshift mutagen.

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

Figure 7.29 Positive selection of mutants. Penicillin- resistant cell Penicillin- sensitive cells Medium with penicillin (only penicillin-resistant cell grows into colony) Medium without penicillin (both types of cells form colonies) Mutagen induces mutations Penicillin- resistant mutants indistinguishable from nonmutants Medium with penicillin 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

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 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

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

Figure 7.33 Transformation of Streptococcus pneumoniae. Observations of Streptococcus pneumoniae Griffith's experiment: In vitro transformation Living strain R + X X X X Heat-treated dead cells of strain S X X X X Heat-treated dead cells of strain S Live cells Injection DNA broken into pieces Capsule Mouse dies Injection DNA fragment from strain S Living strain R Heat-treated dead cells of strain S Some cells take up DNA from the environment and incorporate it into their chromosomes Injection X X X X Mouse dies Mouse lives Culture of Streptococcus from dead mouse Transformed cells acquire ability to synthesize capsules Strain R live cells (no capsule) Injection Living cells with capsule (strain S) Mouse lives

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)

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 5 Donor DNA is incorporated into recipient's chromosome by recombination. Inserted DNA

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

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

Figure 7.35 Bacterial conjugation. F plasmid Origin of transfer Pilus Chromosome 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 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 2 Cells join via a pilus. F+ cell (Hfr) F recipient – F plasmid 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. – Recombinant cell (still F− )

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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

Figure 7.37 Transposition. Plasmid with transposon Transposon DNA Jumping transposons. Transposons move from one place to another on a DNA molecule. 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.