The Regulation of Bacterial Gene Expression

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1 The Regulation of Bacterial Gene Expression Constitutive genes are expressed at a fixed rate Other genes are expressed only as needed Inducible genes Repressible genes Catabolite repression

2 Pre-transcriptional Control Repression inhibits gene expression and decreases enzyme synthesis Mediated by repressors, proteins that block transcription Default position of a repressible gene is on Induction turns on gene expression Initiated by an inducer Default position of an inducible gene is off

3 The Operon Model of Gene Expression Promoter: segment of DNA where RNA polymerase initiates transcription of structural genes Operator: segment of DNA that controls transcription of structural genes Operon: set of operator and promoter sites and the structural genes they control

4 The Operon Model of Gene Expression In an inducible operon, structural genes are not transcribed unless an inducer is present In the absence of lactose, the repressor binds to the operator, preventing transcription In the presence of lactose, lactose (inducer) binds to the repressor; the repressor cannot bind to the operator and transcription occurs

5 Figure 8.12 An inducible operon (1 of 3). Operon Control region Structural genes I P O Z Y A DNA Regulatory gene Promoter Operator Structure of the operon. The operon consists of the promoter (P) and operator (O) sites and structural genes that code for the protein. The operon is regulated by the product of the regulatory gene (I)

6 Figure 8.12 An inducible operon (2 of 3). RNA polymerase I P Z Y A Transcription Repressor mrna Translation Active repressor protein Repressor active, operon off. The repressor protein binds with the operator, preventing transcription from the operon.

7 Figure 8.12 An inducible operon (3 of 3). I P O Z Y A Transcription Operon mrna Allolactose (inducer) Translation Inactive repressor protein Transacetylase Permease β-galactosidase Repressor inactive, operon on. When the inducer allolactose binds to the repressor protein, the inactivated repressor can no longer block transcription. The structural genes are transcribed, ultimately resulting in the production of the enzymes needed for lactose catabolism.

8 The Operon Model of Gene Expression In repressible operons, structural genes are transcribed until they are turned off Excess tryptophan is a corepressor that binds and activates the repressor to bind to the operator, stopping tryptophan synthesis

9 Figure 8.13 A repressible operon (1 of 3). Operon Control region Structural genes DNA I P O E D C B A Regulatory gene Promoter Operator Structure of the operon. The operon consists of the promoter (P) and operator (O) sites and structural genes that code for the protein. The operon is regulated by the product of the regulatory gene (I)

10 Figure 8.13 A repressible operon (2 of 3). RNA polymerase I P O E D C B A Transcription Repressor mrna Translation Operon mrna Inactive repressor protein Polypeptides comprising the enzymes for tryptophan synthesis Repressor inactive, operon on. The repressor is inactive, and transcription and translation proceed, leading to the synthesis of tryptophan.

11 Figure 8.13 A repressible operon (3 of 3). I P E D C B A Active repressor protein Tryptophan (corepressor) Repressor active, operon off. When the corepressor tryptophan binds to the repressor protein, the activated repressor binds with the operator, preventing transcription from the operon.

12 Check Your Understanding

13 Positive Regulation Catabolite repression inhibits cells from using carbon sources other than glucose Cyclic AMP (camp) builds up in a cell when glucose is not available camp binds to the lac promoter, initiating transcription and allowing the cell to use lactose

14 Figure 8.14 The growth rate of E. coli on glucose and lactose. Bacteria growing on glucose as the sole carbon source grow faster than on lactose. Glucose Lactose Glucose used All glucose consumed Lag time Lactose used Bacteria growing in a medium containing glucose and lactose first consume the glucose and then, after a short lag time, the lactose. During the lag time, intracellular camp increases, the lac operon is transcribed, more lactose is transported into the cell, and β-galactosidase is synthesized to break down lactose.

15 Figure 8.15 Positive regulation of the lac operon. Promoter lacl DNA CAP-binding site camp Active CAP lacz Operator RNA polymerase can bind and transcribe Inactive lac repressor camp cyclic AMP CAP catabolic activator protein Inactive CAP Lactose present, glucose scarce (camp level high). If glucose is scarce, the high level of camp activates CAP, and the lac operon produces large amounts of mrna for lactose digestion. DNA lacl CAP-binding site Promoter lacz Operator RNA polymerase can't bind Inactive CAP Inactive lac repressor Lactose present, glucose present (camp level low). When glucose is present, camp is scarce, and CAP is unable to stimulate transcription.

16 Epigenetic Control Methylating nucleotides turns genes off Methylated (off) genes can be passed to offspring cells Not permanent

17 Post-Transcriptional Control micrornas (mirnas) base pair with mrna to make it double-stranded Double-stranded RNA is enzymatically destroyed, preventing production of a protein

18 Figure 8.16 MicroRNAs control a wide range of activities in cells. DNA Transcription of mirna occurs. mirna mirna binds to target mrna that has at least six complementary bases. mrna mrna is degraded.

19 Changes in Genetic Material Mutation: a permanent change in the base sequence of DNA Mutations may be neutral, beneficial, or harmful Mutagens: agents that cause mutations Spontaneous mutations: occur in the absence of a mutagen

20 Types of Mutations Base substitution (point mutation) Change in one base in DNA

21 Figure 8.17 Base substitutions. Parental DNA Replication During DNA replication, a thymine is incorporated opposite guanine by mistake. Daughter DNA Daughter DNA If not corrected, in the next round of replication, adenine pairs with the new thymine, yielding an AT pair in place of the original GC pair. Daughter DNA Replication Granddaughter DNA mrna When mrna is transcribed from the DNA containing this substitution, a codon is produced that, during translation, encodes a different amino acid: tyrosine instead of cysteine. Transcription Translation Amino acids Cysteine Tyrosine Cysteine Cysteine

22 Types of Mutations Missense mutation Base substitution results in change in an amino acid

23 Figure 8.18a-b Types of mutations and their effects on the amino acid sequences of proteins. DNA (template strand) Transcription mrna Translation Amino acid sequence Met Lys Phe Gly Stop Normal DNA molecule DNA (template strand) mrna Amino acid sequence Met Lys Phe Ser Stop Missense mutation

24 Types of Mutations Nonsense mutation Base substitution results in a nonsense (stop) codon

25 Figure 8.18a-c Types of mutations and their effects on the amino acid sequences of proteins. DNA (template strand) Transcription mrna Translation Amino acid sequence Met Lys Phe Gly Stop Normal DNA molecule Met Stop Nonsense mutation

26 Types of Mutations Frameshift mutation Insertion or deletion of one or more nucleotide pairs Shifts the translational "reading frame"

27 Figure 8.18a-d Types of mutations and their effects on the amino acid sequences of proteins. DNA (template strand) Transcription mrna Translation Amino acid sequence Met Lys Phe Gly Stop Normal DNA molecule Met Lys Leu Ala Frameshift mutation

28 Chemical Mutagens Nitrous acid: causes adenine to bind with cytosine instead of thymine Nucleoside analog: incorporates into DNA in place of a normal base; causes mistakes in base pairing

29 Figure 8.19a Oxidation of nucleotides makes a mutagen.

30 Figure 8.19b Oxidation of nucleotides makes a mutagen.

31 Figure 8.20 Nucleoside analogs and the nitrogenous bases they replace.

32 Radiation Ionizing radiation (X rays and gamma rays) causes the formation of ions that can oxidize nucleotides and break the deoxyribose-phosphate backbone UV radiation causes thymine dimers

33 Radiation Photolyases separate thymine dimers Nucleotide excision repair: Enzymes cut out incorrect bases and fill in correct bases

34 Figure 8.21 The creation and repair of a thymine dimer caused by ultraviolet light. Ultraviolet light Thymine dimer Exposure to ultraviolet light causes adjacent thymines to become cross-linked, forming a thymine dimer and disrupting their normal base pairing. An endonuclease cuts the DNA, and an exonuclease removes the damaged DNA. New DNA DNA polymerase fills the gap by synthesizing new DNA, using the intact strand as a template. DNA ligase seals the remaining gap by joining the old and new DNA.

35 The Frequency of Mutation Spontaneous mutation rate = 1 in 10 9 replicated base pairs or 1 in 10 6 replicated genes Mutagens increase the mutation rate to 10 5 or 10 3 per replicated gene

36 Identifying Mutants Positive (direct) selection detects mutant cells because they grow or appear different than unmutated cells Negative (indirect) selection detects mutant cells that cannot grow or perform a certain function Auxtotroph: mutant that has a nutritional requirement absent in the parent Use of replica plating

37 Figure 8.22 Replica plating. Handle Velvet surface (sterilized) Sterile velvet is pressed on the grown colonies on the master plate. Master plate with medium containing histidine Cells from each colony are transferred from the velvet to new plates. Plates are incubated. Petri plate with medium containing histidine Auxotrophic mutant Colony missing Petri plate with medium lacking histidine Growth on plates is compared. A colony that grows on the medium with histidine but could not grow on the medium without histidine is auxotrophic (histidine-requiring mutant).

38 Identifying Chemical Carcinogens The Ames test exposes mutant bacteria to mutagenic substances to measure the rate of reversal of the mutation Indicates degree to which a substance is mutagenic

39 Figure 8.23 The Ames reverse gene mutation test. Experimental sample Suspected mutagen Rat liver extract Experimental plate Incubation Cultures of histidine-dependent Salmonella Media lacking histidine Colonies of revertant bacteria Control (no suspected mutagen added) Rat liver extract Incubation Control plate Two cultures are prepared of Salmonella bacteria that have lost the ability to synthesize histidine (histidinedependent). The suspected mutagen is added to the experimental sample only; rat liver extract (an activator) is added to both samples. Each sample is poured onto a plate of medium lacking histidine. The plates are then incubated at 37 C for two days. Only bacteria whose histidine-dependent phenotype has mutated back (reverted) to histidinesynthesizing will grow into colonies. The numbers of colonies on the experimental and control plates are compared. The control plate may show a few spontaneous histidine-synthesizing revertants. The test plates will show an increase in the number of histidine-synthesizing revertants if the test chemical is indeed a mutagen and potential carcinogen. The higher the concentration of mutagen used, the more revertant colonies will result.

40 Genetic Transfer and Recombination Genetic recombination: exchange of genes between two DNA molecules; creates genetic diversity Crossing over: Two chromosomes break and rejoin, resulting in the insertion of foreign DNA into the chromosome

41 Figure 8.24 Genetic recombination by crossing over. DNA from one cell aligns with DNA in the recipient cell. Notice that there is a nick in the donor DNA. Donor DNA Recipient chromosome DNA from the donor aligns with complementary base pairs in the recipient's chromosome. This can involve thousands of base pairs. RecA protein catalyzes the joining of the two strands. RecA protein The result is that the recipient's chromosome contains new DNA. Complementary base pairs between the two strands will be resolved by DNA polymerase and ligase. The donor DNA will be destroyed. The recipient may now have one or more new genes.

42 Genetic Transfer and Recombination Vertical gene transfer: transfer of genes from an organism to its offspring Horizontal gene transfer: transfer of genes between cells of the same generation

43 Transformation in Bacteria Transformation: genes transferred from one bacterium to another as "naked" DNA

44 Figure 8.25 Griffith's experiment demonstrating genetic transformation.

45 Figure 8.26 The mechanism of genetic transformation in bacteria. Recipient cell a b c d A B D C DNA fragments from donor cells Chromosomal DNA Recipient cell takes up donor DNA. 5' 3' a b c d A B D C Donor DNA aligns with complementary bases. 5' 3' b c d A B D C Recombination occurs between donor DNA and recipient DNA. Degraded unrecombined DNA a B D C Genetically transformed cell

46 Conjugation in Bacteria Conjugation: plasmids transferred from one bacterium to another Requires cell-to-cell contact via sex pili

47 Figure 8.27 Bacterial conjugation. Sex pilus Mating bridge F cell F + cell Sex pilus Mating bridge

48 Conjugation in Bacteria Donor cells carry the plasmid (F factor) and are called F + cells Hfr cells contain the F factor on the chromosome

49 Figure 8.28a Conjugation in E. coli. RECOMBINATION Bacterial chromosome Mating bridge Replication and transfer of F factor F factor F + cell F cell When an F factor (a plasmid) is transferred from a donor (F + ) to a recipient (F ), the F cell is converted to an F + cell. F + cell F + cell

50 Figure 8.28b Conjugation in E. coli. RECOMBINATION Recombination between F factor and chromosome, occurring at a specific site on each Insertion of F factor into chromosome Integrated F factor F + cell Hfr cell When an F factor becomes integrated into the chromosome of an F + cell, it makes the cell a high frequency of recombination (Hfr) cell.

51 Figure 8.28c Conjugation in E. coli.

52 Conjugation in Bacteria Conjugation can be used to map the location of genes on a chromosome

53 Figure 8.29 A genetic map of the chromosome of E. coli. bp kbp 1160 kbp kbp Amino acid metabolism DNA replication and repair Carbohydrate metabolism Membrane synthesis Lipid metabolism

54 Transduction in Bacteria DNA is transferred from a donor cell to a recipient via a bacteriophage Generalized transduction: Random bacterial DNA is packaged inside a phage and transferred to a recipient cell Specialized transduction: Specific bacterial genes are packaged inside a phage and transferred to a recipient cell

55 Figure 8.30 Transduction by a bacteriophage. The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted. Restart your computer, and then open the file again. If the red x still appears, you may have to delete the image and then insert it again. RECOMBINATION Phage protein coat Phage DNA Bacterial chromosome Donor cell A phage infects the donor bacterial cell. Phage DNA and proteins are made, and the bacterial chromosome is broken into pieces. Phage DNA Bacterial DNA Recipient cell Occasionally during phage assembly, pieces of bacterial DNA are packaged in a phage capsid. Then the donor cell lyses and releases phage particles containing bacterial DNA. A phage carrying bacterial DNA infects a new host cell, the recipient cell. Recombinant cell reproduces normally Donor bacterial DNA Recipient bacterial DNA Recombination can occur, producing a recombinant cell with a genotype different from both the donor and recipient cells. Many cell divisions

56 Plasmids Plasmids are self-replicating circular pieces of DNA 1 to 5% the size of a bacterial chromosome Often code for proteins that enhance the pathogenicity of a bacterium

57 Figure 8.31 R factor, a type of plasmid. Origin of replication Mercury resistance Pilus and conjugation proteins RTF Sulfonamide resistance Streptomycin resistance Chloramphenicol resistance Origin of transfer Tetracycline resistance

58 Plasmids Conjugative plasmid: carries genes for sex pili and transfer of the plasmid Dissimilation plasmids: encode enzymes for the catabolism of unusual compounds Resistance factors (R factors): encode antibiotic resistance

59 Transposons Transposons are segments of DNA that can move from one region of DNA to another Contain insertion sequences (IS) that code for transposase that cuts and reseals DNA Complex transposons carry other genes (e.g, in antibiotic resistance)

60 Figure 8.32a Transposons and insertion. IS1 Transposase gene Inverted repeat Inverted repeat An insertion sequence (IS), the simplest transposon, contains a gene for transposase, the enzyme that catalyzes transposition. The tranposase gene is bounded at each end by inverted repeat sequences that function as recognition sites for the transposon. IS1 is one example of an insertion sequence, shown here with simplified IR sequences.

61 Figure 8.32b-c Transposons and insertion. Transposase gene Transposase cuts DNA, leaving sticky ends. IS1 Tn5 Kanamycin resistance Complex transposons carry other genetic material in addition to transposase genes. The example shown here, Tn5, carries the gene for kanamycin resistance and has complete copies of the insertion sequence IS1 at each end. IS1 IS1 Sticky ends of transposon and target DNA anneal. IS1 Insertion of the transposon Tn5 into R100 plasmid

62 Genes and Evolution Mutations and recombination create cell diversity Diversity is the raw material for evolution Natural selection acts on populations of organisms to ensure the survival of organisms fit for a particular environment

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