Presentation on theme: "Recombination and Repair Chaper 14 高雄醫學大學 生物醫學暨環境生物學系 張學偉 助理教授."— Presentation transcript:
Recombination and Repair Chaper 14 高雄醫學大學 生物醫學暨環境生物學系 張學偉 助理教授
Homologous Recombination occur between any two highly similar regions of DNA, regardless of the sequence Non-homologous (Site-Specific) Recombination (SSR) occur between two defined sequences elements. Transposition (Tn) occur between one specific seq and non-specific DNA sites. Concept for chapter 14 & 15
Fig14.1 Two crossovers result in recombination. In all cases of recombination, two DNA molecules are broken and rejoined to each other forming a crossover. Single crossover usually forms short-lived hybrid DNA molecules. promoter recombination of linear chromosomes. cannot cause recombination between two circular DNA molecules. Double crossovers forms recombination. Overview of Recombination
Fig14.2 Homologous vs non-homologous recombination. [E.Coli] [site-specific recombination] Specific recognition protein Rarer than HR (HR)
Molecular Basis of Homologous Recombination
Fig Formation of a crossover. Crossover due to base homology may occur in DNA as 20-30bases, however, bases is reasonable frequency.
heteroduplex: is any region of double- stranded nucleic acid (DNA, RNA), where the two strands come from two different original molecules.
Fig14-4. Rearrangement and Resolution of a Holliday Junction RuvC, RecG act as resolvase. Patch recombinants Short parch of heteroduplex remains in each molecule. Formation of two hybrid DNA molecules by crossing-over
Fig Migration of a Holliday Junction. Bind to Junction Drive migration
5 key steps in Homologous recombination (i) alignment of 2 homologous chromosomes (ii) introduction of breaks in DNAs (iii) formation of initial short regions of base pairing between the two recombining DNA molecules (strand invasion) (iv) movement of Holliday junctions by repeat melting and formation of base pair (branch migration) (v) cleavage (or resolution) of Holliday junctions
Single-strand invasive and Chi sites 5’-GCTGGTGG-3’ Chi sites naming
Fig14-6. RecBCD recognized Chi sites. Immune response of E.coli (protect from foreign DNA)
Fig14-7. RecA promote strand invasion. 3’ tail
Where is the dsb appeared? Bacterial is haploid. [no HR in sexual reproduction] Bacterial recombination occurs between resident bacterial chrosome and shorter incoming DNA. e.g, transformation, transduction, conjugation. In transformation, a cell can absorb and integrate fragments of DNA from their environment. In conjugation, one cell directly transfers genes (e.g., plasmid) to another cell. In transduction, viruses transfer genes between prokaryotes.
DNA bacterial viruses = bacteriophages
Conjugation = plasmid-directed transfer of DNA from one cell to another.
Site-specific Recombination (non-homologous recombination) Phage DNA properties is linear inside the virus particle it circularizes upon entering bacterial cells& before integration
Fig14-8. Integration of Lambda DNA-overview. att = attachment site INT = integrase O = center core of 15 bases = the same in phage & bacterial B,P = different in size and sequence in bacterial & phage dsDNA XIS = Excisionase The control of INT & XIS activity determines it latency or not.
Fig14-8. Integration of Lambda DNA-Detail of crossover.
Fig Timeline of Eukaryotic Recombination in Yeast. Eukaryotic recombination occurs in a span of ~2 hours. resolution Recombination in Higher Organisms
Spo11 make dsb Rad51 ~= RecA Rad = response for recombination and repair Fig Spo11 promotes dsb (double strand breaks)
Overview of DNA repair Different repair enzymes deal with different DNA damages included: Overall distortion of DNA structure. Mismatched RS( more sensitive than ERS) & Excision RS Specific chemical defects. Lead to mutation.
Not included the synthetic enzymes and enzymes also used in normal DNA replication
DNA Mismatch Repair System
Fig Principle of Mismatch Repair Mismatch Repair Gap filled by DNA Pol III. Note! most repair system using Pol I to replace short damaged region of DNA. Cut out part of DNA strand containing wrong base.
Fig Methylated Bases-Chemical Structure. Dam Protein (product of dam gene) DNA adenine methylase Dcm Protein (product of dcm gene) DNA cytosine methylase Recognition site is “Sequence-specific” & “Palindromic” Not perturb base pairing GATCCCTGG Sequence unique for E.Coli
Fig Hemimethylated DNA Palindrome make the DNA methylated equally on both strands. Not perturb base pairing [delay in fully methylation] 1.During this period, many repair systems check DNA. 2.Control the initiation of new round of bacterial DNA replication Function of methylation Tell which is old, correct strand.
The major mismatch repair system of E.Coli is MutSHL. Consist of MutS, MutH, MutL (proteins) Note! Genes are mutS, mutH, mutL ( 寫法不一樣 ) mut = mutator, def in mut high mutation rate
Fig MutSHL mismatch Repair System L = hold together H = find the nearest GATC site & nick the non-CH3 strand Pol III attach & repair the gap created by MutSHL system.
General Excision Repair System (“Cut and Patch” Repair) 1. The most widely distributed sysytem for DNA repair. 2. Recognize the bulge of DNA strand. e.g., UV (TT dimer) 3. Defect UV sensitive (uvr = UV resistence) 4. Not detect mismatches, base analogs, certain methylated bases.
Fig UvrABC Excision Repair System Helicase Single strand Pol; 5’exonuclease Nick are closed by DNA ligase
DNA repair by Excision of Specific Bases (chemical changed bases, CH3, O2 ) Adenine Hypo-xanthine Guanine Xanthine Cytosine Uracil deamination Removal by DNA glycosylase (- bases) Uracil-N-glycosylase (Ung protein)
Fig Removal of unnatural bases. 3’-OH Pol I 1. recognizes the 3’-OH 2. replaces a strench of ssDNA with AP site. a-purine/ a-pyrimidine Pol; 5’exonuclease
Fig dealing with oxidized guanine. Prevent incorporation of preformed 8-oxoG into DNA. MutT, MutM, MutY
Specialized DNA repair mechanisms. 5-methylcytosine leads to mutational hot-spots. Deamination of 5-methylcytosine:G T:G 1. Occur spontaneously at any time and rarely during replication. 2. Often goes unrepair 3. If occur at Dcm recognition site, it is repaired by “ very short patch repair” (Vsr) system [nicking by Vsr endonuclease] Short length of strand remove by DNA pol I
Fig Suicide demethylase for O-methyl bases. O 6 -CH 3 -G O 4 -CH 3 -T
Fig Ada plays a dual role in removing alkyl groups Ada = Adaptation to alkylation Note! ~CH 3 at N- and C- has different effects.
Photoreactivation cleaves thymine dimers Uvr excision repair system alsoPS:
Fig Photoreactivation cleaves pyrimidine dimers. No DNA synthesis nm photolyase Bind to dimer in dark but lack energy to remove crosslink
Transcriptional coupling of repair Preferential repair of transcribed template DNA strand. Non-template strand is less likely to be repaired. Bacteria: Transcription-repair coupling factor (TRCF) can detect a stalled RNA pol & direct UrvAB to block site.
Fig Eukaryotic transcription-coupled excision repair. helicase Recruit the repair protein Nick at the junction between ds and ssDNA.
Repair by Recombination
Fig RecA and recombination repair. TT dimer is still unrepaired in this process. Old template is still damaged, but new made is correct.
SOS Error Prone Repair in Bacteria Allow DNA replication to proceed through severely damaged zones, even at the cost of introducing mutations [error prone repair]
Fig RecA and LexA control the SOS system.
Fig DNA polymerase V is part of the SOS system. umu = UV mutagenesis DNA pol V: 1.Subunits encoded by umu C and umu D 2. lack of proofreading subunit 3. Prefer GA rather than AA to pair TT dimer For time to repair [no pol activity]
Like E.Coli, yeast, flies, and human all have error-prone DNA polymerase. In higher organisms, these repair enzymes are more specialized and less error-prone. Human error-prone pol, eta, can replicate past TT dimer.
Repair in Eukaryotes Human MutS homologue = hMSH2 ~= E.Coli MutS BRCA1 (breast cancer A1) def breast & ovarian ca
Double-strand Repair in Eukaryotes by Non-homologous End Joining
Fig Non-homologous End Joining in Mammals. XRCC4 protein recruits DNA ligase IV to join two broken ends.
Gene conversion Nonreciprocal step in DSB-repair sometimes result in gene conversion. Gene conversions are “not” associated with crossing over. Occur at Yeast mating-type switching at Bacterial genetic exchange via transduction or conjugation at eukaryote homologous recombination in meiosis
Fig Gene Conversion Following Crossing over.
Comparison between gene conversion and DNA crossover. (a) Two DNA molecules. (b) Gene conversion - the red DNA donates part of its genetic information (e-e' region) to the blue DNA. (c) DNA crossover - the two DNAs exchange part of their genetic information (f-f' and F-F').
An origin of gene conversion. (a) Heteroduplexes formed by the resolution of Holliday structure or by other mechanisms. (b) The blue DNA uses the invaded segment (e') as template to "correct" the mismatch, resulting in gene conversion. (c) Both DNA molecules use their original sequences as template to correct the mismatch. Gene conversion does not occur.