Chapter 11 Homologous Recombination at the Molecular Level. 吳彰哲 (Chang-Jer Wu) Department of Food Science National Taiwan Ocean University

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1 Chapter 11 Homologous Recombination at the Molecular Level 吳彰哲 (Chang-Jer Wu) Department of Food Science National Taiwan Ocean University 1

Introduction All DNA is recombinant DNA During meiosis homologous recombination results in crossing over = the exchange of genetic material between chromosomes The frequency of crossing over between

2 Introduction All DNA is recombinant DNA During meiosis homologous recombination results in crossing over = the exchange of genetic material between chromosomes The frequency of crossing over between 2 genes depends on the distance between the genes the greater the distance the more frequent the cross-over Homologous recombination is essential to cellular processes and is catalyzed by proteins specific for this function Homologous recombination provides genetic variation, allows repair (replacement) of damaged DNA and can influence gene expression 2

3 DNA breaks are common and initiate recombination DS breaks in DNA occur frequently and cause cell death if not repaired DSB can be repaired by recombination or by NHEJ method In bacteria, repairing DSB is primary role of homologous recombination, also promotes genetic exchange In eukaryotic cells, primary function is in chromosome pairing, although repair is important 3

4 Models of homologous recombination DNA replication is semiconservative Recombination is conservative = direct breakage and rejoining of DNA Recombination also often involves limited destruction and re-synthesis of DNA Current models of recombination include: 1. Alignment of 2 homologous DNA molecules 2. Introduction of ds breaks into DNA 3. Base-pairing between the 2 recombining molecules - strand invasion forms cross structure = Holliday junction or structure 4. Movement of Holliday junction = branch migration 5. Cleavage of Holliday junction = resolution 4

5 Strand invasion is a key early step in homologous recmbination 2 dsdna molecules with different alleles Initiation begins with two nick at the same location in 1 strands (dsdna breaks) DNA near nick is peeled away, freeing strands to invade (pair) with homologous duplex Strand invasion creates a Holliday junction 5

6 Strand invasion is a key early step in homologous recmbination Holliday junction moves along strands = branch migration Migration increases the length of exchanged DNA Exchange of DNA creates heteroduplex DNA 6

7 Holliday model Resolution, finishing recombination, requires cutting of the DNA The location of the cuts determines whether the recombination results in crossover products or patch products 7

8 Holliday model Cutting the strands that were not broken in the initiation reaction results in splice or crossover products = regions of the parental molecules are covalently linked by region of hybrid duplex - reciprocal strand exchange Cutting the strands that were broken in initiation results in patch product = a region of hybrid DNA in otherwise parental chromosomes, no reassortment of flanking genes = non-crossover products 8

9 Double-strand break repair model Current Model - Recombination is often initiated by dsdna breaks in DNA Initiating event is a DSB in 1 of 2 molecules more likely model than Holliday which requires 2 ssdna breaks at same place in 2 molecules Meiotic cells undergo double-strand breakage x the rate in vegetative cells After initiation DNA-cleaving molecules degrade broken DNA to form ssdna tails terminating in 3 OH ends 9

10 Double-strand break repair model ssdna tails invade the unbroken homologous DNA duplex Invasion may be initially by single strand, then 2 invading strands, strands pair with complementary strand Invading strands serve as 3 primers for new DNA synthesis Elongation of 3 ends using the complementary strand as template replaces DNA degraded by processing at break site 10

Double-strand break repair model Region of DNA replaced by new synthesis is lost Gene conversion = replacement of region on one homologous strand with

11 Double-strand break repair model Region of DNA replaced by new synthesis is lost Gene conversion = replacement of region on one homologous strand with sequence from homolog 2 Holliday junctions move by branch migration, extending region of exchange as in Holliday model, and are then resolved by stand cleavage 11

12 Double-strand break repair model Resolution involves cuts are sites 1 or 2 of both junctions If both junctions are cut in the same way (both 1 or both 2) then non-crossover products will be formed If both junctions are cut in different ways (1 and 2 or 2 and 1) then crossover products will be formed 12

13 Homologous recombination protein machines 13

Recombination in E. coli All organisms have genes for products essential for recombination, some genes are homologous, some appear to be convergence on function Best understood model is from E.

14 Recombination in E. coli All organisms have genes for products essential for recombination, some genes are homologous, some appear to be convergence on function Best understood model is from E. coli, the RecBCD pathway RecBCD enzyme processes DNA at DSB site to generate ssdna RecA mediates single-stranded DNA exchange RuvA and RuvB drive branch migration RuvC resolves Holliday junctions 14

15 Recombination in E. coli RecBCD: 1. processes broken DNA to generate ssdna tails the preferred substrate for recombination 2. loads RecA protein onto ssdna 3. selects whether DNA will be recombined or destroyed 15

16 Recombination in E. coli RecBCD is composed of 3 subunits products of the recb, recc and recd genes RecBCD enters DNA from dsdna break and moves along the DNA RecB and RecD are both helicases, unwinding DNA using energy from ATP hydrolysis RecBCD nuclease activity degrades DNA as it is unwound 16

17 Recombination in E. coli At chi (χ) sequence nuclease activity is altered = RecBCD no longer cleaves the 3 to 5 strand, and cleaves the other strand even more This asymmetrical cleavage results in a 3 tail terminating at the chi sequence ideal for assembly of RecA and initiation of recombination Change in nuclease activity appears to be inactivation or loss of RecD subunit 3 overhang could also be coated with SSB (e.g. RPA), interaction of RecBCD and RecA ensures that RecA binds 17

site is a specific sequence (GCTGGTGG), but a common sequence, in fact

coli genome, +1000 instead of the predicted ~80 E.

18 Recombination in E. coli Chi sites increase frequency of recombination at the site 10x Chi site is a specific sequence (GCTGGTGG), but a common sequence, in fact it is overrepresented in the E. coli genome, instead of the predicted ~80 E. coli DNA can, and do, incorporate DNA from other E. coli This E. coli DNA, but not viral or other invading DNA, will have chi sites, DNA without chi sites will be degraded by RecBCD 18

19 Recombination in E. coli RecA binds to ssdna and is a strand-exchange protein, catalyzing the pairing of homologous DNA molecules 19

20 Recombination in E. coli The active form of RecA is a protein-dna filament huge, variable size, 100 subunits of RecA, 300 nucleotides RecA filament can bind 1, 2, 3 or 4 DNA strands DNA in strands is extended 1.5 fold Search for regions of homologous sequence, and then exchange, happens within filament 20

21 Recombination in E. coli RecA binding is cooperative, growing with the addition of subunits to the 3 side of the first subunit - in the 5 to 3 direction = filament ending in a 3 is most likely to be coated by RecA 21

22 Recombination in E. coli RecA binds to ssdna RecA looks for sequence homology using 2 binding sites The ssdna is bound in the primary binding site dsdna can occupy the secondary binding site binding is rapid, weak, transient and sequence independent RecA moves along dsdna scanning for homology base-flipping 22

23 Recombination in E. coli Matches of 15+ bp triggers strand exchange RecA promotes formation of stable complex between two DNA molecules = three-stranded joint molecule containing several 100 bp of hybrid DNA The strand in the primary site is paired with its complement in the duplex bound in the secondary site - breaking and forming hydrogen bonds 23

24 24

25 Recombination in E. coli Strand-exchange proteins in the RecA family are present in all organisms. a) human Rad51 b) E. coli RecA c) archaebacteria RadA All with similar helical structure 25

connected by a Holliday junction Branch migration increases the

specific DNA-binding protein, it binds at junction and recruits

26 Recombination in E. coli After strand invasion, the 2 recombining molecules are connected by a Holliday junction Branch migration increases the amount of genetic material exchanged RuvA is a Holliday junction specific DNA-binding protein, it binds at junction and recruits RuvB to site RuvB is a ATP-dependent hexameric helicase, provides energy to drive exchange of bases along branch 26

27 Recombination in E. coli Completion requires that Holliday junction(s) be resolved RuvC is resolving endonuclease in bacteria, it functions in conjunction with RuvAB complex RuvC recognizes DNA-RuvAB complex and nicks 2 DNA strands with the same polarity, resulting 5 and 3 ends are sealed by DNA ligase Depending on which strands are cut the products may, or may not, be of the crossover type. 27

28 Recombination in E. coli RuvC cleaves DNA at 5 A/T-T-T-G/C 3 sites Sequence is specific, but frequent, ~1/64 nucleotides Modest sequence specificity ensures a certain amount of branch migration before resolution 28

29 Homologous recombination in eukaryotes Homologous recombination is required for DNA repair and restarting replication forks in eukaryotes mutants are hypersensitive to DNA damaging agents and predisposed to certain types of cancer Recombination is also required for proper chromosome pairing in meiosis and reshuffles alleles on parental chromosomes (meiotic recombination) without recombination chromosomes fail to align properly - nondisjunction 29

between the non-sister homologous chromotids Mechanism is unknown, but biological

30 Recombination in eukaryotes Meiotic recombination occurs when there are 4 complete, ds, DNA molecules representing each chromosome Dmc1-dependent recombination is preferentially between the non-sister homologous chromotids Mechanism is unknown, but biological rationale = promote interhomolog connections to assist in alignment of chromosomes for division 30

31 Recombination in eukaryotes Eukaryotes (and not E. coli) have a specific protein to generate dsdna breaks in DNA to initiate recombination = Spo11 Spo11 cuts DNA with little sequence selectivity, but at a specific time = when the replicated homologous chromosomes pair Spo11 also cuts at specific locations, regions of DNA not tightly packed on nucleosomes, e.g. promoters = hot spots for recombination 31

32 Recombination in eukaryotes Specific tyrosine on Spo11 attacks phosphodiester backbone forming a covalent complex between protein and DNA 2 Spo11 subunits make staggered cut protein is related to topoisomerases 5 ends of DNA are bound to Spo11, energy of cleaved bond is stored bound in the protein-dna linkage 32

33 Recombination in eukaryotes DNA ds break is processed by MRXenzyme complex to generate singlestranded regions needed for RecA-like protein, long ssdna terminating in 3 OH MRX is not homologous to RecBCD, but is a multisubunit nuclease Digestions occurs only on the strand with 5 end bound to Spo11, 5 to 3 resection, generating +1kb of ssdna 33

34 Recombination in eukaryotes Eukaryotes have 2 homologs of RecA: Rad51 and Dmc1 Rad51 is expressed in cells undergoing mitosis or meiosis, Dmc1 is expressed only during meiosis Together Rad51 and Dmc1 participate in recombination, but how they interact is not known 34

35 Recombination in eukaryotes Many proteins interact in homologous recombination, likely as a large multicomponent complexes These recombination factories can be visualized in the cell, e.g. colocalization of Rad51 and Dmc1 during meiosis 35

Other recombination proteins in eukaryotes Rad52 interacts with Rad51 to promote formation of Rad51-DNA complexes, antagonizes action of RPA, the normal ssdna

36 Other recombination proteins in eukaryotes Rad52 interacts with Rad51 to promote formation of Rad51-DNA complexes, antagonizes action of RPA, the normal ssdna binding protein The concentration of Rad52 increases after radiation exposure Rad52-GFP foci in nuclei after irradiation - DNA repair and recombination centers 36

37 Recombination in eukaryotes Depending on manner of resolution of junction, recombination can happen without generating crossover products (formation of patch products) Non-crossover recombination can have genetic consequences = gene conversion 37

38 Mating-type switching = gene conversion Homologous recombination can change the DNA sequence at a specific chromosomal location The budding yeast S. cerevisiae (single-celled eukaryote) exists as any 1 of 3 cell types, a and α haploids and a/α diploid a and α haploids mate to form the diploids a can only mate with α, α can only mate with a, homothallism A yeast can switch to α, and vice versa, to allow mating 38

39 Mating-type switching = gene conversion The mating-type genes encode transcriptional regulators that control the expression of sp. target genes that define cell type The mating-type genes that are expressed in a given cell are found at the mating-type locus (MAT locus) In a-cells the a1 gene is at the MAT, in α cells the α1 and α2 are at the MAT In diploids both sets of genes are expressed 39

40 Mating-type switching = gene conversion Cells can switch mating-type by recombination In addition to the MAT locus, there is an additional copy of both the a and α genes present, but not expressed, in the yeast genome Additional, silent, copies are called the HML (α) and HMR (a) loci = silent cassettes Silent cassette loci store genetic information that can be used to switch the mating type 40

41 Mating-type switching = gene conversion HO endonuclease initiates DSB at MAT locus HO endonuclease expression is tightly regulated This is a sequence-specific endonuclease, with sequence only found at mating-type loci Cuts form a staggered break in chromosome, no binding of protein to DNA 41

42 Mating-type switching = gene conversion 5 to 3 resection occurs as in meiosis, a function of MRX protein, specifically degrading 5 ends, forming 3 tails Long 3 tails associate with Rad51 and Rad52 and search for homologous regions of the chromosome to initiate strand invasion and genetic exchange Mating-type switching is unidirectional, seq. information, but not actual DNA, moves to MAT from HMR or HML, never the reverse the HO endonuclease cannot cleave its recognition seq. at either HMR or HML b/c of chromatin packing 42

43 Mating-type switching = gene conversion Rad51-coated 3 ssdna tails from MAT locus choose either the HMR or HML locus for strand invasion if MAT is a invade HML, if α invade HMR This unidirectional movement of information from one site to another is a specialized case of gene conversion 43

44 Mating-type switching = gene conversion Recombination pathway diverges from DSB-repair mechanism Crossover class of recombination products is never observed suggests recombination without Holliday junctions Synthesis-dependent strand annealing (SDSA) model Initiating event is DSB and strand invasion, the invading 3 end serves as primer for DNA synthesis A complete replication fork is assembled at point of strand invasion (unlike in other types of recombination) Both leading and lagging strand synthesis occurs, Both strands are displaced from their templates new ds DNA is synthesized with sequence of template site, replacing MAT sequence 44

45 Mating-type switching = gene conversion 45

46 Consequences of mechanism of recombination Recombination can occur between any 2 regions of DNA with sufficient sequence similarity None of the steps require specific sequence recognition, although some do have sequence preferences The committed step in recombination is strand-exchange, which depends only on the capacity of DNA to base-pair The freq. of recombination between any 2 markers (genes) is generally proportional to the distance between the genes greater distance = more recombination This proportionality allows genetic mapping using recombination freq. 46

47 Consequences of mechanism of recombination Distortions in genetic maps occur when regions differ in the probability of participating in recombination High proportion = Hot Spots genes appear farther apart than they are Low proportion = Cold Spots genes appear closer than they are 47

Consequences of mechanism of recombination Gene conversion is common during normal homologous recombination Example heterozygous Aa individual, after DNA replication, expected to have 4 copies

48 Consequences of mechanism of recombination Gene conversion is common during normal homologous recombination Example heterozygous Aa individual, after DNA replication, expected to have 4 copies of gene: A A a a Gene conversion alters the observed results, e.g. A a a a This can happen through DSB repair if gene is close to break invading strand copies information from other homolog 48

49 Consequences of mechanism of recombination Gene conversion alters the observed results, e.g. A a a a This can happen through DSB repair if gene is close to break invading strand copies information from other homolog Second mechanism involves repair of mismatches in intermediates = A/a heteroduplexes Heteroduplexes may be recognized by mismatch repair enzymes which randomly choose which strand to replace 49

DNA Recombination Biochemistry 302. Bob Kelm February 2, 2005

DNA Recombination Biochemistry 302 Bob Kelm February 2, 2005 Homologous recombination: Why is it advantageous to a cell? Bacterial cell Information exchange during bacterial conjugation (mating) between