MLS 531 Microbial Genetics (Evolution and Inheritance Mutation) PDF

**LECTURER:** DR JOHN NDUBUISI **COURSE TITLE:** MICROBIAL GENETICS (1 UNIT) **COURSE CODE:** MLS 531 Topic: Evolution and inheritance mutation. Bacterial DNA in hereditary and Evolution. Evolution is a process of gradual change that takes place over many generations, during which species of ani...

**LECTURER:** DR JOHN NDUBUISI **COURSE TITLE:** MICROBIAL GENETICS (1 UNIT) **COURSE CODE:** MLS 531 Topic: Evolution and inheritance mutation. Bacterial DNA in hereditary and Evolution. Evolution is a process of gradual change that takes place over many generations, during which species of animals, plants, or insects slowly change some of their physical characteristics. Evolution is the name given for changes to a species over time. The process of evolution has given rise to [biodiversity](https://en.wikipedia.org/wiki/Biodiversity) at every level of [biological organization](https://en.wikipedia.org/wiki/Biological_organisation). **INHERITANCE** Evolution in organisms occurs through changes in heritable characteristics---the inherited characteristics of an organism. Inherited traits are controlled by genes and the complete set of genes within an organism\'s [genome](https://en.wikipedia.org/wiki/Genome) (genetic material) is called its *[genotype](https://en.wikipedia.org/wiki/Genotype)* (the set of genes in our DNA). The complete set of observable traits that make up the structure and behaviour of an organism is called its *[phenotype](https://en.wikipedia.org/wiki/Phenotype)* (the outward appearance a set of genes displays). Heritable characteristics are passed from one generation to the next via [DNA](https://en.wikipedia.org/wiki/DNA), a [molecule](https://en.wikipedia.org/wiki/Molecule) that encodes genetic information.  **DNA** Properties of DNA Deoxyribonucleic acid (DNA) is the molecule that carries genetic information for the development and functioning of an organism. DNA is made of two linked strands that wind around each other to resemble a twisted ladder --- a shape known as a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases: adenine (A), cytosine (C), guanine (G) or thymine (T). The two strands are connected by chemical bonds between the bases: adenine bonds with thymine, and cytosine bonds with guanine. The sequence of the bases along DNA's backbone encodes biological information, such as the instructions for making a protein or RNA molecule.  Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. **MUTATION** A mutation is a change in [DNA](https://evolution.berkeley.edu/glossaryDNA), the hereditary material of life. An organism's DNA affects how it looks, how it behaves, and its physiology. So a change in an organism's DNA can cause changes in all aspects of its life. Mutations are essential to evolution; they are the raw material of [genetic variation](https://evolution.berkeley.edu/glossary/genetic-variation). Without mutation, evolution could not occur. Mutations can occur spontaneously or be caused by exposure to mutation-inducing agents. Types of mutations ================== There are many different ways that DNA can be changed, resulting in different types of mutation. #### **Substitution**  Substitution mutation is sometimes referred to as point mutation, i.e. when the gene mutation involves only one nucleotide. A substitution is a mutation that exchanges one base for another (i.e., a change in a single "chemical letter" such as switching an A to a G). Such a substitution could: 1. change a codon to one that encodes a different amino acid and cause a small change in the protein produced. For example, [sickle cell anemia](https://evolution.berkeley.edu/glossary/sickle-cell-anemia) is caused by a substitution in the beta-hemoglobin gene, which alters a single amino acid in the protein produced. 2. change a codon to one that encodes the same amino acid and causes no change in the protein produced. These are called silent mutations. 3. change an amino-acid-coding codon to a single "stop" codon and cause an incomplete protein. This can have serious effects since the incomplete protein probably won't function. #### **Insertion** Insertions are mutations in which extra base pairs are inserted into a new place in the DNA. #### **Deletion**  Deletions are mutations in which a section of DNA is lost, or deleted. #### **Frameshift** Since protein-coding DNA is divided into codons three bases long, insertions and deletions can alter a gene so that its message is no longer correctly parsed. These changes are called frameshifts. For example, consider the sentence, "The fat cat sat." Each word represents a codon. If we delete the first letter and parse the sentence in the same way, it doesn't make sense. In frameshifts, a similar error occurs at the DNA level, causing the codons to be parsed incorrectly. This usually generates truncated proteins that are as useless as "hef atc ats at" is uninformative. There are other types of mutations as well, but this short list should give you an idea of the possibilities. The causes of Bacterial DNA Mutations: ====================================== Mutations can result from errors during DNA replication or induced by exposure to mutagens. Results of mutations can produce changes in structural or colony characteristics or loss in sensitivity to antibiotics. Some potential consequences of mutations are as follows: ============================================================================================================================================================================================================================================================================ - Auxotrophs: this arises from mutational changes in the genes that leaves an essential nutrient process dysfunctional. An auxotroph refers to organisms that are defective in certain genes, resulting in its inability to synthesis organic compounds by itself. In order for an auxotroph to grow, such organic compounds need to be supplied in the media. - Resistant mutants: this can withstand the stress of exposure to inhibitory molecules or antibiotics secondary to acquired mutation. - Regulatory mutants: A regulatory mutation is referred to as a type of mutation where changes or alterations in DNA and RNA molecules will lead to an alteration in other gene\'s expression by the cells. Regulatory mutations can disrupt the binding sites of transcription factors or can create or make new binding sites. Any type of mutation (can be insertion or deletion) that occurs in the promoter sequence of a specific gene can have negative impacts on the normal processes related to the activation of genes. - Constitutive mutants: this continuously express genes that usually switch on and off as in operons. It can be also referred to as a mutation that results in an increased constitutive synthesis by a bacterium of several functionally related, inducible enzymes. Such a mutation either modifies an operator gene so that the repressor cannot combine with it or modifies the regulator gene so that the repressor is not formed. In other words, a constitutive mutant is one in which the gene product is produced continually, that is there is no control over its expression. So in these mutants, the mutation must be a gene other than those responsible for the structural genes. **Spontaneous Mutations** Spontaneous mutations occur without mutation induction and are the result of errors during DNA replication. When DNA polymerase III holoenzyme (DNA pol III) synthesizes a new strand of DNA, occasionally, a nucleotide will be mispaired, added, or omitted. Thus, a point mutation will occur. For example, when nucleotides are mispaired, it will appear that one nucleotide substitutes for another leading to one mutated granddaughter DNA strand. **Mutation Induction** Mutagens may be of physical, chemical, or biological origin. Mostly they act on the DNA directly, causing damage, which may result in errors during replication. Although severely damaged DNA can prevent replication and cause cell death. **Physical Mutagens** Examples of physical mutagens include radiation or UV exposure. UV radiation damages DNA by creating covalent linkages between adjacent pyrimidine bases. This pyrimidine dimer cannot fit well in the double helix structure of DNA, thus inhibiting replication and translation. **Chemical Mutagens** Chemical mutagens are agents that either directly or indirectly induce mutations. A chemical mutagen can either replace a base in DNA, alter a base\'s composition and pairing behavior, or damage the base so that it can no longer pair. These include DNA reactive chemicals such as those listed below: **Base Analogs** Structurally similar enough to nucleotides in that they can incorporate into DNA. For example, 5-bromouracil, an analog of thymine, acts as a substrate during DNA replication and causes point mutations. This mispairing occurs because the base analog forms a tautomer and pairs with guanine instead of adenine. **Reactive Oxygen Species** Hydroxyl radicals attack guanine, thereby producing 8-hydroxy-deoxyguanosine (8-OhdG), which mispairs with adenine instead of cytosine, which results in a (G -\> T) transversion during replication. **Deaminating Agents** These agents remove amino groups on nucleotide bases. Deaminating agents produce an adenine species that pairs with cytosine and a cytosine species (uracil) that pairs with adenine. Deamination of guanine results in xanthine, which inhibits replication, thereby not creating a mutation. **Flat Aromatic Compounds** Acridines like ethidium bromide can intercalate with adjacent pyrimidine base pairs. This interaction slightly unwinds the helix and increases the distance between adjacent base pairs. This intercalation disrupts the reading frame during translation and can cause insertions or deletions. **Alkylating Agents** Agents like ethyl methanesulfonate and dimethyl nitrosoguanidine alter the nucleotide base by adding alkyl groups. The nature and position of the alkylation can vary but usually leads to point mutations through base mispairing. However, alkylation can cause crosslink formation, which inhibits replication.  **Biological Mutagens** Biological agents of mutation are sources of DNA from elements like transposons and viruses. Transposons are sequences of DNA that can relocate and replicate autonomously. Insertion of a transposon into a DNA sequence can disrupt gene functionality. **CLINICAL SIGNIFICANCE OF BACTERIAL DNA MUTATION** Antibiotic Resistance. Antibiotics work through a variety of mechanisms: 1. DNA synthesis inhibitors 2. Protein synthesis inhibitors 3. Cell wall synthesis inhibitors 4. RNA synthesis inhibitors 5. Mycolic acid synthesis inhibitors 6. Folic acid synthesis inhibitors ### **GENETIC INFORMATION IN MICROBES**. Genetic information in bacteria and many viruses is encoded in DNA, but some viruses use RNA. Replication of the genome is essential for inheritance of genetically determined traits. Gene expression usually involves transcription of DNA into messenger RNA and translation of mRNA into protein. ### **GENOME ORGANIZATION** The bacterial chromosome is a circular molecule of DNA that functions as a self-replicating genetic element (replicon). Extrachromosomal genetic elements such as plasmids and bacteriophages are nonessential replicons which often determine resistance to antimicrobial agents, production of virulence factors, or other functions. The chromosome replicates semiconservatively; each DNA strand serves as template for synthesis of its complementary strand. **HORIZONTAL GENE TRANSFER IN BACTERIA** Bacteria are able to respond to selective pressures and adapt to new environments by acquiring new genetic traits as a result of mutation, a modification of gene function within a bacterium, and as a result of horizontal gene transfer, the acquisition of new genes from other bacteria. When bacterial populations are under stress, they can greatly increase their mutation rate. Furthermore, most mutations are harmful to the bacterium. Horizontal gene transfer, on the other hand, enables bacteria to respond and adapt to their environment much more rapidly by acquiring large DNA sequences from another bacterium in a single transfer. Horizontal gene transfer, also known as lateral gene transfer, is a process in which an organism transfers genetic material to another organism that is not its offspring. The ability of *Bacteria* and *Archaea* to adapt to new environments as a part of bacterial evolution most frequently results from the acquisition of new genes through horizontal gene transfer rather than by the alteration of gene functions through mutations. (It is estimated that as much as 20% of the genome of *Escherichia coli* originated from horizontal gene transfer.). Horizontal gene transfer is able to cause rather large-scale changes in a bacterial genome. For example, certain bacteria contain multiple virulence genes called pathogenicity islands that are located on large, unstable regions of the bacterial genome. These pathogenicity islands can be transmitted to other bacteria by horizontal gene transfer. However, if these transferred genes provide no selective advantage to the bacteria that acquire them, they are usually lost by deletion. There are three mechanisms of horizontal gene transfer in bacteria: 1. Transformation 2. Transduction 3. Conjugation. The most common mechanism for horizontal gene transmission among bacteria, especially from a donor bacterial species to different recipient species, is conjugation. Although bacteria can acquire new genes through transformation and transduction, this is usually a rarer transfer among bacteria of the same species or closely related species. **Transformation** ------------------ Transformation is a form of genetic recombination in which a DNA fragment from a dead, degraded bacterium enters a competent recipient bacterium and is exchanged for a piece of DNA of the recipient. Transformation usually involves only homologous recombination, a recombination of homologous DNA regions having nearly the same nucleotide sequences. Typically this involves similar bacterial strains or strains of the same bacterial species. -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- A few bacteria, such as *Neisseria gonorrhoeae, Neisseria meningitidis, Hemophilus influenzae, Legionella pneomophila, Streptococcus pneumoniae*, and *Helicobacter pylori* tend to be naturally competent and transformable. Competent bacteria are able to bind much more DNA than noncompetent bacteria. Some of these genera also undergo autolysis that then provides DNA for homologous recombination. In addition, some competent bacteria kill noncompetent cells to release DNA for transformation. ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ **Transduction** ---------------- Transduction involves the transfer of a DNA fragment from one bacterium to another by a bacteriophage. There are two forms of transduction: *generalized transduction* and *specialized transduction*. ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ **Generalized transduction**: This occurs in a variety of bacteria, including *Staphylococcus, Escherichia, Salmonella*, and *Pseudomonas* Generalized transduction is summarized thus: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- - **Step 1**: A bacteriophage adsorbs to a susceptible bacterium. - **Step 2**: The bacteriophage genome enters the bacterium. The genome directs the bacterium\'s metabolic machinery to manufacture bacteriophage components and enzymes. Bacteriophage-coded enzymes will also breakup the bacterial chromosome. - **Step 3: **Occasionally, a bacteriophage capsid mistakenly assembles around either a fragment of the donor bacterium\'s chromosome or around a plasmid instead of around a phage genome. - **Step 4**: The bacteriophages are released as the bacterium is lysed. Note that one bacteriophage is carrying a fragment of the donor bacterium\'s DNA rather than a bacteriophage genome. - **Step 5: **The bacteriophage carrying the donor bacterium\'s DNA adsorbs to a recipient bacterium. - **Step 6: **The bacteriophage inserts the donor bacterium\'s DNA it is carrying into the recipient bacterium. - **Step 7:** Homologous recombination occurs and the donor bacterium\'s DNA is exchanged for some of the recipient\'s DNA. **Specialized transduction:** This may occur occasionally during the lysogenic life cycle of a temperate bacteriophage. During spontaneous induction, a small piece of bacterial DNA may sometimes be exchanged for a piece of the bacteriophage genome, which remains in the bacterial nucleoid. This piece of bacterial DNA replicates as a part of the bacteriophage genome and is put into each phage capsid. The bacteriophages are released, adsorb to recipient bacteria, and inject the donor bacterium DNA/phage DNA complex into the recipient bacterium where it inserts into the bacterial chromosome.  **Conjugation** --------------- Genetic recombination in which there is a transfer of DNA from a living donor bacterium to a living recipient bacterium by cell-to-cell contact. In Gram-negative bacteria it typically involves a *conjugation *or *sex pilus*. -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Conjugation is encoded by plasmids or transposons. It involves a donor bacterium that contains a conjugative plasmid and a recipient cell that does not. A conjugative plasmid is self-transmissible, in that it possesses all the necessary genes for that plasmid to transmit itself to another bacterium by conjugation. **Transposons** (\"jumping genes\") are small pieces of DNA that encode enzymes that enable the transposon to move from one DNA location to another, either on the same molecule of DNA or on a different molecule. Transposons may be found as part of a bacterium\'s chromosome (conjugative transposons) or in plasmids and are usually between one and twelve genes long. A transposon contains a number of genes, such as those coding for antibiotic resistance or other traits.