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3 Mutations Evolution and Natural Selection

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  • Unity and Diversity of Life

    All cellular organisms share certain traits as a result of sharing (or “descending from”) a common ancestor (the first primitive prokaryotic cells). Yet the incredible diversity of living organisms is astounding. How did such diversity arise?

    The diversity of life is explained by evolution, a change in the genetic makeup of a population of organisms.

    The “raw material” of evolution is genetic variability, the genetic differences between individuals of a population of organisms. How does genetic variability arise?

    Genetic variability arises through random mutations, changes in the nucleic acid sequence of organisms, horizontal gene transfer in microbes and sexual recombination.

    Random mutations: These mutations usually occur when the enzymes which copy genetic information before a cell divides make a mistake. As an example, the enzyme DNA polymerase should copy the DNA sequence below precisely.

    DNA base abbreviations:

    A=adenine T=Thymine G=Guanine C=cytosine

    Original genetic info, DNA base sequence of double stranded DNA

    A-T- C- G- G

    T- A- G- C- C

    Original DNA

    DNA polymerase should make a precise copy of the DNA before the cell divides such that each “daughter” cell receives a precise copy of genetic information from the parent cell:

    A-T- C- G- G

    T- A- G- C- C copy 1

    A-T- C- G- G /T- A- G- C- C --- DNA polymerase copies

    Original DNA \ A-T- C- G- G

    T- A- G- C- C

    copy 2

    When the original cell divides, both “daughter” cells will receive one copy of the DNA, exact copies of the DNA from the “parent” cell

    One source of genetic variability occurs when DNA polymerase makes a mistake copying the original DNA as shown below:

    A-T- C- G- G

    T- A- G- C- G* ,<-mistake=mutation copy 1

    A-T- C- G- G /

    T- A- G- C- C --- DNA polymerase copies

    Original DNA \ A-T- C- G- G

    T- A- G- C- C

    copy 2

    In this case, DNA polymerase made a mistake in copy #1 (instead of a “C”, it used a “G”). This is a mutation, a change in the DNA sequence. As a result, the mutated gene might encode information for a different variety of protein. This different protein could change some feature of the “daughter cell” which receives the mutant DNA copy. This mutant organism might be a better competitor compared to “normal, non-mutant” member of its population (or the mutant might be less able to compete with its “normal” colleagues).

    If resources are limited, “variants” or mutants which are better competitors will survive in higher numbers than their non-mutant neighbors. The mutants will have more offspring than the non-mutant members of the population which are weaker competitors. The mutation which permitted the variant to compete better will be passed on to its offspring. Over time, the mutant form of the genetic information will be carried by a greater proportion of the surviving population, another way of saying the frequency of the mutant gene increases in the population. Thus the gene pool or genetic makeup the population has changed over time and the population of organisms has “evolved” (and the population becomes better adapted to the environment over time) .

    This mechanism above describing “how” evolution occurs is called “natural selection”, a concept developed by Charles Darwin and Alfred Wallace in the 1800’s. (Darwin and Wallace were not the first people to describe evolution, but they were the first describe the process of natural selection).

    Darwin and Wallace’s explanation of evolution by natural selection is based on 5 assumption (source: Keeton and Gould’s Biology 4th edition, Norton Publishers)

    1. Many more individuals are born in each generation than will survive and reproduce (limiting environmental resources, competition for resources)

    2. There is variation among individuals of a population.

    3. Individuals with certain characteristics have a better chance of surviving and reproducing than individuals with other characteristics.

    4. Some of the differences resulting in differential survival and reproduction are heritable

    5. Vast spans of time have been available for change

    Natural selection vs Artificial selection

    When “nature” chooses which variants are best at competing for natural resources, and thus will survive and reproduce at higher rates than other variants , “natural selection” occurs. However if humans selectively breed organisms for specific traits, or if humans purposely change the environment (for example through overuse of antibiotics), “artificial selection” occurs. The overuse/misuse of antibiotics worldwide has artificially selected for a growing number of antibiotic resistant bacteria.

    Evolution of antibiotic resistant bacteria

    As bacteria reproduce so quickly, it does not take “vast spans of time” for their populations to evolve. Antibiotic resistance can evolve within a few years (even within a few weeks) within some populations of bacteria.

    Evolution of variant strains of RNA viruses: HIV and influenza

    Cellular organisms all have DNA as their genetic information. The enzyme which copies DNA, the DNA polymerases, have “high fidelity”, that is these enzymes make relatively few mistakes because they have the ability to “edit or proofread” their work and correct many of their mistakes. Mistake rates fro DNA polymerase are approximately one incorrect nucleotide per 108-109 nucleotides.

    In contrast, some types of viruses (acellular pathogens) use RNA as their genetic information. The enzymes which copy RNA, the RNA polymerases, lack the ability to correct mistakes, therefore RNA polymerases have a very high mistake rate (one incorrect nucleotide every104-105 nucleotides) . Consequently many RNA viruses such as influenza virus and HIV, have very high mutation rates thus “populations” of HIV and influenza viruses evolve quickly. The high mutation rate of these viruses results in rapid drug resistance and huge challenges in vaccine production.

    Natural Selection in a “nutshell”

    1. Each species produces more offspring than can survive

    2. The offspring compete with one another for limited resources

    3. Organisms in every population vary

    4. Organisms with most favorable traits/variations are most likely to survive and produce more offspring

    Result:…..consequently variant genes “spread” through the population over time, genetic makeup of population changes and population changes/evolves over time=”Evolution”

    Horizontal Gene Transfer in Bacteria

    Transfer of genetic material between prokaryotes: transformation, transduction, conjugation

    I. Genetic Recombination and Homologous Recombination an exchange of DNA sequences by crossing over- permits integration of “foreign” homologous DNA into bacterial host chromosome. Replaces bacterial alleles w/ “foreign” alleles.

    1. “Foreign” single stranded homologous chromosomal DNA aligns with homologous sequences of host bacterial chromosomal DNA

    2. DNA fragment of host DNA excised, replaced by foreign DNA sequence-alters cells genotype (“native” allele is replaced w/ a foreign allele)

    3. Requires many enzymes including recombination enzymes/proteins, nucleases, ligases

    II. Transformation: uptake of “naked” DNA from environment by competent bacterial cells.

    1. plasmid DNA or chromosomal DNA

    2. Some bacterial strains naturally competent. Special surface proteins recognize and take-up closely related naked DNA from environment (recall Griffith’s experiments w/ Streptococcus pneumoniae). Other bacterial strains can be made competent by treatment with chemicals (ex cold + calcium chloride treatment used in lab to create competent E. coli cells; permitted uptake of double stranded plasmid DNA)

    3. Competent Streptococcus pneumoniae permit passage of single stranded DNA through cell membrane (2nd strand is usually degraded).

    4. When competent cell is transformed with DNA, the cells are referred to as “transformants. Chromosomal DNA may undergo genetic recombination with bacterial DNA if homologous sequences are present.

    III. Transduction. DNA transfer process in which bacteriophages carry DNA from one bacterium to another bacterium. 2 types: generalized and specialized.

    1. Generalized transduction:(bacterial genes transferred at random) Recall lytic reproductive cycle. Towards end of cycle, bacterial chromosomal DNA is accidentally packaged into phage heads/capsids instead of phage DNA. This creates a defective phage as it lacks its own genetic material, yet it can still be released, attach to new bacterium and inject the DNA into a new host bacterium. This DNA may replace the homologous region of the bacterial chromosome.. The bacterial cell now carries recombinant DNA.

    2. Specialized transduction (only specific bacterial genes are transferred). Requires temperate bacteriophage. Phage DNA integrates into host bacterial chromosome usually at specific site. Later prophage may be induced to enter lytic cycle. When prophage excises from chromosome, sometimes take small stretch of adjacent bacterial DNA. Bacterial genes are packaged w/ phage DNA and injected into new bacterial host.

    IV. Conjugation. Direct transfer of genetic material between 2 bacteria which are temporarily joined. Model uses E. coli (gram positive bacteria use slightly different process).

    1. One-way transfer of DNA: donor cell (male) transfers genetic material to recepient cell (female)

    2. Male uses protein appendages, hollow sex pili, to attach to female

    3. Temporary cytoplasmic bridge forms between 2 cells, providing path for transfer of DNA

    4. “Maleness’, ability to form sex pili and transfer DNA during conjugation, results from presence of special DNA sequence called F factor=Fertility Factor . F factor may exist integrated into chromosome or as a plasmid, therefore it is an episome (episome= genetic element which can replicate either as a plasmid or as part of bacterial chromosome; temperate viruses such as lambda also qualify as episomes).

    5. Recall plasmids are extrachromosomal, self-replicating DNA elements which usually carry “extra’ genes. These genes can confer survival advantages for bacteria living under stressful conditions. For example, “R plasmids” are plasmids carrying genes for antibiotic resistance and permit host cells to survive in presence of antibiotic pressure. F factor facilitates genetic recombination which could be advantageous in a changing environment which no longer favors existing strains of bacteria (Campbell, Biology 5th ed)

    6. F plasmid: The F factor in its plasmid form is called the F plasmid. Consists of approx. 25 genes, most involved in sex pilus production.

    a. F+ cells (males) contain F plasmid; F plasmid is usually replicated and passed to daughter cells. F+ condition is “contagious” as it can be passed to female cells, converting them to F+ males following conjugation

    b. F- cells (females) lack F plasmid

    c. F plasmid is replicated in male and a copy is passed to female, converting her to F+ male. Only F plasmid copy is transferred during F+ x F- conjugation

    7. Hfr and bacterial gene transfer during conjugation

    a. if F factor is integrated into bacterial chromosome, bacterium is referred to as Hfr cell (High frequency of recombination)

    b. Hfr acts as a male, forms sex pilus, copies F factor, starts to transfer copy of F to F- partner, yet now F factor also takes a copy of some of bacterial chromosomal DNA with it

    -temporarily, female is diploid until genetic recombination occurs and segments of DNA are exchanged (excised DNA is degraded)

    -Female becomes recombinant cell; usually mating is interrupted before entire chromosome and F factor are transferred therefore she usually remains female

    V. Resistance Plasmids and Transposons

    1. R =resistance plasmids, carry genes for antibiotic resistance and/or resistance to heavy metals e.g. mercury resistance. Example enzymes to destroy antibiotics. beta-lactamases destroy beta-lactam ring of penicillin, ampiciilin and related antibiotics, mercury reducatase genes.

    2. R plasmids may carry multiple antibiotic resistance genes and can be copied and transferred between bacteria via conjugation and transformation

    3. Some R plasmids carry 10 antibiotic resistance genes; evolution thought linked to transposons

    4. Transposons are transposable genetic elements, pieces of DNA which can move from one location to another (Barbara McClintock’s “jumping genes”1940’s-50’s; Nobel prize 1983 age 81). Some say transposons (“Tn’s”) never exist independently some gram-positive Tn’s may violate this rule.

    5. Transposons may have moved multiple antibiotic resistance genes to R plasmids

    6. Insertion sequences (IS)-simplest transposons. Carry 1 gene only for enzyme transposase bracketed by inverted repeats, upside down, backwards versions of each other . Transposase binds to inverted repeats and recognizes target sites. Transposase cuts target sequences and inserts IS. “Cut and Paste Transposition”

    7. Composite transposons: Additional genes e.g., for antibiotic resistance sandwich between 2 IS. Probably involved in evolution of R plasmids