Genetics Notes PDF

Genetic transfer in bacteria Microscopic image of E. coli bacteria. Credit: National Institutes of Health. Exam 1 Grades posted on Schoology Mean: 79 Median: 79 Max: 94 I will give you time to look at your exam on Thursday. If you want to “visit” your exam before then you can co...

Genetic transfer in bacteria Microscopic image of E. coli bacteria. Credit: National Institutes of Health. Exam 1 Grades posted on Schoology Mean: 79 Median: 79 Max: 94 I will give you time to look at your exam on Thursday. If you want to “visit” your exam before then you can come to office hours or set up a time. (I will not be available in office hours today from 3:00-3:30ish) There will be an opportunity to earn back points, more on this soon! Genetics Reflection 1 – Due October 11 Choose from two podcasts, an article, or a video to connect to class concepts Remember, you will share one of your Genetics Reflections during the Gallery Walk at the end of the semester. Oral Exam 1 Oral Exam 1 on 10/3 (or take it early on 10/2) Schedule: https://calendar.app.google/1Ct N9BzHBaA7x9j66 Questions posted on Schoology Introduction Like eukaryotes, bacteria possess allelic differences that affect their traits. However, these allelic differences (such as different sensitivity to antibiotics, ability to metabolize sugars, etc.) are between different strains of bacteria because bacteria are usually monoploid and clonal. Typically a bacterium has one allele per gene and members of a strain (not species) will (often) have the same allele E. coli (a species) genomes vary tremendously in terms of genes present (range in size from 4-6 Mb) Vertical versus horizontal gene transfer Vertical gene transfer Horizontal gene transfer Parent Peer Peer Horizontal gene transfer occurs between Offspring individuals that are not parents and offspring Overview of Genetic Transfer in Bacteria Like sexual reproduction in eukaryotes, genetic transfer in bacteria enhances genetic diversity. There are three methods of genetic transfer in bacteria: Conjugation - involves direct physical contact Transduction - involves bacteriophages Transformation - involves uptake from the environment Bacterial Conjugation Genetic transfer in bacteria was discovered in Bacterium that cannot 1946 by Joshua Lederberg and Edward Tatum produce leucine (leu-) They were studying strains of E. coli that had different nutritional growth requirements This would be a Auxotrophs cannot synthesize a particular leucine auxotroph nutrient and therefore need it in their growth medium Vitamins biotin (bio) thiamine (thi) Amino acids methionine (met) leucine (leu) threonine (thr) + indicates they can synthesize the nutrient - indicates they are auxotrophs (cannot synthesize the nutrient) Conjugation Bernard Davis set up another experiment using the same strains. Filter has pores that are large enough to allow passage of genetic material, small enough to prevent the passage of cells Nothing grew on plates without amino acids, biotin, thiamine!  Your turn Filter has pores that are large enough to allow passage of genetic material, small enough to prevent the passage of cells Talk to a neighbor: What does this result (the lack of growth) show? Conjugation The term conjugation refers to the transfer of DNA from one bacterium to another following cell-to-cell contact Many (not all!) species of bacteria can conjugate, but only certain strains of bacteria can act as donor cells Conjugation In E. coli certain donor strains contain a plasmid termed an F factor (fertility factor) Link of Schoology if you want to learn more! Conjugation In E. coli certain donor strains contain a plasmid termed an F factor (fertility factor) Strains containing an F factor are designated F+ Those lacking it are F- Conjugation 1. Contact between donor and recipient cells by pilus (plural pili) which act as an attachment site for the F- bacteria 2. Once contact is made, pilus shortens to pull the cells together and a conjugation bridge is formed between the two cells Conjugation 3. The relaxosome (a collection of proteins) recognizes the origin of transfer (a DNA sequence) and makes a cut in the DNA, then most the relaxosome proteins are released Conjugation 4. Relaxase remains bound to the end of the T (transfer) DNA 5. The exporter is a complex of proteins coded by the F factor that pump T DNA and relaxase into recipient cell Conjugation 6. In both the donor and recipient cells, the F factor (plasmid) DNA is replicated, resulting in double stranded DNA. Both cells are now F+ Your turn Discuss with a neighbor: Briefly summarize the process of conjugation. Identify the main steps involved in the transfer of a plasmid from one bacterium to another Mapping using conjugation F’ factors carry genes that were once found on the bacterial chromosome Mapping using conjugation When F factor integrates into the chromosome, it creates an Hfr cell. Mapping using conjugation Conjugation between an Hfr and an F- strain involves the transfer of a portion of the Hfr bacterial chromosome Mapping using conjugation (cannot metabolize lactose or synthesize proline) F- strain is lac-pro- Hfr strain is lac+pro+ (can metabolize lactose and synthesize proline) Mapping using conjugation If conjugation occurs for a short time, only lac+ will be transferred If conjugation occurs for a longer time, both lac+ and pro+ will be transferred Mapping using conjugation Conjugation experiments have been used to map more than 1,000 genes on the E. coli chromosome The E. coli genetic map is 100 minutes long Approximately the time it takes to transfer the complete chromosome in an Hfr mating  Discuss with a neighbor: Do you think this approach to chromosome mapping is useful today with the ability to do whole genome sequencing? What are some benefits and drawbacks to each approach? Transduction Transduction is the transfer of DNA from one bacterium to another via a bacteriophage. A bacteriophage is a virus that infects bacterial cells Transduction In this example, donor cell is his+ and recipient is his- 1. Phage infect the donor cell and the host DNA is digested into fragments Transduction 2. New phages are assembled and occasionally a phage is mispackaged with host cell DNA instead of phage genetic material 3. The mispackaged phage injects the donor cell DNA into the recipient cell. Transduction 4. The donated DNA is recombined into the chromosome of the recipient resulting in a new his+ cell Your turn Discuss with a neighbor: Briefly summarize the process of transduction. Identify the main steps involved in the transfer of genomic DNA from one bacterium to another via bacteriophage. Transformation Transformation is the process by which a bacterium will take up extracellular DNA released by a dead bacterium Bacterial cells able to take up DNA are termed competent cells Cells can be naturally competent or artificially competent Transformation In this example, donor cell was lys+ and recipient is lys- 1. Fragment of DNA bind to a receptor on the cell surface of a competent cell (recipient) 2. An extracellular (outside the cell) nuclease cuts the into smaller fragments Transformation 3. One strand of DNA is degraded and a single strand is transported into the cell via the uptake system (proteins involved in DNA uptake) Transformation 4. The DNA strand aligns with a homologous region on the bacterial chromosome 5. The DNA undergoes homologous recombined and is incorporated into the recipient cell genome  Transformation Step 5 leave a heteroduplex - a region of mismatch caused by sequence differences between the two alleles (lys+ and lys-) 6. The other strand of DNA is repaired so that both strands contain the lys+ DNA We will talk about DNA repair later in the course! Talk to a neighbor: How is this process of transformation different from the transformation process we discussed in lab? Transformation – some variations to note Sometimes, DNA that enters the cell is not homologous to any genes on the chromosome. It may be incorporated at a random site on the chromosome by nonhomologous recombination (this is much less common!) Some bacteria preferentially take up DNA released from dead bacteria of the same or a related species In naturally competent cells, usually small pieces of DNA are taken up, but plasmids can also be taken up by transformation. Why does horizontal gene transfer (HGT) matter? Horizontal gene transfer has dramatically contributed to the phenomenon of acquired antibiotic resistance Antibiotics are widely used to treat human infections and increase health and size of livestock Bacteria can acquire genes that breakdown the antibiotic, pump it out of the cell, or block its inhibiting effects Methicillin resistant Staphylococcus aureus (MRSA) Some S. aureus strains are resistant to methicillin and all beta-lactams These MRSA strains cause serious skin infections Antibiotic resistance evolves quickly https://www.open.edu/openlearn/mod/oucontent/view.php?id=75701&section=3#back_thumbnailfigure_idm259 Transposition Transposition involves the integration of small segments of DNA into a new location in the genome These small, mobile DNA segments are termed transposable elements (TEs) or transposons Transposons were first identified by Barbara McClintock in the early 1950s from her work in corn. Since then transposons have been identified in bacteria, fungi, plants and animals. Types of transposition Simple transposition Retrotransposition “cut-and-paste” “copy-and-paste” Talk to a neighbor: How does the “cut-and-paste” and “copy-and-paste” metaphor related to the action of simple transposition versus retrotransposition?  Transposons Inverted repeats are DNA sequences that are identical (or very similar) but run in opposite directions M. Gurusaran et al., 2013 Transposons The enzyme transposase catalyzes the removal of a transposon and its reinsertion at another location Transposase recognizes the inverted repeats at the ends of a transposon and brings them close together  Transposition and DNA replication Even simple “cut-and-paste” transposition can result in an increase in the number of copies of a transposon. The transposon “jumps” ahead while DNA replication is occurring and gets re-copied Why do transposons exist? The biological significance of transposons in evolution remains a matter of debate The selfish DNA theory They can proliferate within the host as long as they do not harm the host to the extent that they significantly disrupt survival, so they do Transposons offer some advantage Bacterial transposons may carry antibiotic-resistance genes onto conjugative plasmids Increase genetic variability through recombination