1
Q
Describe how direct reversal of DNA damage works:
A
- there are three types 1) Light dependent repair: direct repair of thymine dimers by enzyme PHOTOLYASE (= photoreactivation, only in prokaryotes), essentially cleaves cross links after being activated by absorption of blue light) 2) Enzymatic removal of alkyl groups from DNA bases: reverses mutagenic effect of alkylation and reestablishes proper base pairing (by Methyltransferase enzyme), prevents transition mutations 3) Ligation of single-stranded nicks in DNA - if broken DNA strand, ligase can seal nick with phosphodiester bond
2
Q
Describe how base excision repair works
A
- BER recognizes and repairs DNA bases damaged bz deamination, alkylation, or oxidation - the specialized DNA glycolyase enzyme recognizes these types of damage, cleaves the phosphodiester bonds 5’ and 3’ of the damaged base by endonuclease and removes deoxyribose sugar, then DNA polymerase fills in the correct nucleotide and ligates the nicked backbone to restore integrity to the DNA chain
3
Q
How does nucleotide excision work?
A
- NER acts to remove thymine dimers and other bulky DNA damage (usually pyrimidine) - slightly different mechanisms in prokaryotes and eukaryotes - more proteins used in mammals - mutation of human NER genes causes Xeroderma pigmentosum - enzyme recognizes distortion, DNA is separated and singel/stranded/binding proteins stabilize strand, enzyme cleaves strand on both sides of damage, gap is filled in by DNA polymerase and sealed by ligase
4
Q
How does mismatch repair work?
A
- MMR system recognizes mismatched base in newly replicated strand through identification of the hemi-methylated GATC sequence, it compares old and new strands based on methylation status of A (new strand is not methylated yet, parental is) - upon detection an exonuclease removes portion of newly-synthesized strand including the incorrect base and the mismatched sequence - DNA polymerase III fills in the longer gap and DNA ligase seals the nick (this is in prokaryotes but similar mechanism also exists in eukaryotes) - this mechanism happens right after replication
5
Q
Describe how recombination can repair DNA damage:
A
- can repair spontaneous or induced DNA double-stranded breaks - two important mechanisms: homologous recombination (HR) and non-homologous end joining (NHEJ)
6
Q
How does translesion DNA polymerase work to repair DNA damage?
A
- replicative polymerases copy chromosomal DNA but pyrimidine dimers and other bulky lesions block it and can result in cell death - then, translesion synthesis (TLS) DNA polymerases are recruited to replicate thru DNA damage and bypass the lesion, normal DNA replication by replicative polymerase follows - but TLS is more error prone at the site of the lesion, therefore, it is a last resort, though some of the errors can be fixed by other mechanisms - sloppy because just inserts random nucleotides, leads to mutation (localized mutagenesis)
7
Q
How does MMR play into genome stability in eukaryotes?
A
defects in human mismatch repair systems result in mutation accumulation and are directly connected to human cancer (10% of colorectal and endometrial cancers are heritable and caused by mutations in human mismatch repair genes - this increases with age too - therefore, mismatch repair is very important to prevent cancer
8
Q
How does homologous recombination repair DNA damage?
A
- often occurs during or after DNA replication - if one sister chromatid has a DSB it can be repaired using the unbroken sister chromatid - therefore, often occurs in S/G2 phase of eukaryotic cell cycle - also ensure proper chromosome separation (dysjunction) during meiosis
9
Q
How does non-homologous end joining repair DNA damage?
A
- this mechanism uses different set of proteins - mechanism is available throughout the rest of the eukaryotic cell cycle (rest means in contrast to homologous recombination that occurs during S/G2 phase)
10
Q
What are DSBs?
A
= double-stranded breaks, can be lethal to cell
11
Q
How exactly does recombination repair occur post-replication?
A
- when leading strand pauses at a bulky lesion (like pyrimidine dimer), a gap in replication can result - if gap not fixed, chromosome broken - the newly-synthesized portion of the leading strand unwinds from the top template strand and pairs w newly-replicated section of lagging strand, which is used as template to proceed past the point were the dimer is located - allows for strand to be fixed and then the pyrimidine dimer can be fixed by mismatch repair or nucleotide excision
12
Q
What kind of a mechanism is recombination repair really?
A
- really, it is a bypass mechanism rather than repair
13
Q
What are the translesion synthesis polymerases in E Coli?
A
= Pol. IV and V (in eukaryotes there are several TLS polymerases)
14
Q
What is the bacterial SOS response?
A
= induced when considerable damage is caused by DNA damaging agents - occurs in E coli - activation of a host of proteins that help with DNA recombination, repair and replication, including TLS polymerase - increases chance of cell survival, but also frequency of errors - but also chance of mutation that helps adapt to environment - eukaryotic cells have similar response mechanism
15
Q
What are transposons?
A
= transposable elements are segments of DNA capable of moving from one location in a chromosome to another, or even a different chromosome (“jumping genes”)
16
Q
Key facts about transposons?
A
= constitute significant fraction of genome (in humans about 40-44%) - can lead to chromosome breakage and mutations - important in generation of some human diseases when they alter gene function - bacterial transposons can carry antibiotic resistance genes
17
Q
What are cut-and-paste transposons?
A
= element that is physically cut out of one site in chromosome or plasmid and pasted into new one - excision and insertion catalyzed by transposase - found in both prokaryotes and eukaryotes
18
Q
What are replicative transposons?
A
= element is replicated with one copy inserted at a new site and one remains at original site - requires transposase - only found in prokaryotes!
19
Q
What are retrotransposons?
A
= DNA copy of element made by reverse transcription from its RNA and then inserted - so an RNA transposon - reverse transcriptase discovered in 1970: reverse flow of genetic info - RNA to DNA - only found in eukaryotes - two kinds: retrovirus-like and retrosposons
20
Q
What are the two main types of bacterial transposons?
A
= cut and paste type (insertion sequences and composite transposons) = replicative transposons (Tn3 elements)
21
Q
What does the general structure of a cut and paste transposon look like?
A
- has a gene that encodes transposase - terminal inverted repeats (identical or nearly identical inverted sequences at both ends of element) - target site duplication: short, directly repeated sequences at both ends resulting from staggered cleavage of double-stranded DNA at site of insertion, so after inverted sequence
22
Q
What is transposase?
A
= a protein required for transposition (movement of transposons) to occur
23
Q
What is an insertion sequence?
A
- and IS element = simplest bacterial transposon - first detected in lac^- mutations of e coli - compactly organized and contain only genes whose products are involved in transposition - inverted terminal repeats are found at the ends - some IS elements encode transposase
24
Q
What does the structure of the IS50 element look like?
A
25
What are target site duplications exactly?
- the staggered cuts made at the new site allow for phosphodiester linkages to bind insertion sequence to strands but causes gaps
- gaps are filled in by replication of singel stranded DNA and creates flanking direct repeats = target site duplications (sequences are identical and in some direction)
- means that afterwards the transposon has the same overall struture as it did in its original position
26
Where in the bacterial chromosome can IS elements be found?
can be found in the plasmid and/or the chromosome
- if found in both (multiple copies or just similar), then homologous recombination can occur and insert the plasmid into the chromosome (result: bacterial chromosome with integrated plasmid)
27
How can antibiotic resistance genes be moblized in a bacterial population?
- if an antibiotic resistance is originally on a nonconjugative R plasmid along with an insertion sequence and the same insertion sequence is on a conjugative plasmid, then homologous recombination allows for the antibiotic resistance gene to be recombined into the conjugative plasmid
- now, the antibiotic resistance gene can be passed on to other bacterial cells b/c located on a plasmid that can udnergo conjugation (has a transfer factor sequences)
28
What are composite transposons?
- Composite transposons (Tn) are created when two IS elements insert near each other and "capture" a DNA sequence
- IS element excision thu transposase cleavage at each end of the transposons can mobilize the entire captured DNA, which may also mobilize resistance genes (can flank one or several)
- essentially the sequence between the composite trnasposons gets moved with them (stuck b/n them)
29
What are replicative transposons in bacteria?
- they are more complex than cut-and-paste and this type of transposon is ONLY found in bacterial cells
- example: Tn3, can carry and mobilize genes for antibiotic resistance
30
Describe the structure of Tn3 elements:
- larger than IS elements
- like composite transposons they often cotnain additional genes that are not involved in transposition
- have simple inverted repeats at each end
- contain transposase gene and resolvase/repressor gene, which are important for movement
31
How does the Tn3 replicative transposable element move?
- it is copied into a co-integrate, then separated by recombination into two molecules each with a copy of Tn3
- essentially it moves through replication, donor plasmid with transposon and recipient plasmid, replication copies replicative transposon into recipient plasmid, forming one big plasmid (the cointegrate: contains two copies now)
- the two copies undergo homologous recombination, which resolves into two smaller plasmids each bearing the replicative transposon (this is facilitated by resolvase)
- if the Tn3 contained any antibiotic resistance genes, they were also copied over
32
How were cut-and-paste transposons in Eukaryotes first discovered?
- by analyzing genetic instabilities in maize
33
Who discovered transposons?
- Barbara McClintock
- studied chromosome breakage in corn (late 1930ies)
- discovered cut-and-paste Ds and Ac transposable elements which cause clear kernels to become mosaics with patches
- her work departed from the idea that genetic material is static and unchanged
- the idea that DNA could be mobile was revolutionary
34
What are the Ac and Ds elements in maize?
- kernel color affected by Cl allele, encodes dominant inhibitor of coloration (which is why color usually clear)
- if Ds transposon is near Cl allele, Ds movement is mediated by Ac element transposase, then loss of Cl allele from chromosome can result in pigmented kernels
- so color is a result of exision of the Ds tranposon from its normal chromosomal site
35
Describe the Ac/Ds system
- Ds = dissociation factor: located at a site on chromosome 9 in mosaic kernels where chromosome breakage occurs
- Ds cannot induce chromosome breakage though
- Activator Factor (Ac) stimulates chromosome breakage at the site of Ds
- Ds has lost transposase function and relies on Ac for it to be able to move, i.e. needs combination of those factors to move and this results in Cl allele loss and ultimately in the mosaic kernels
36
What exactly does the Ac/Ds element do?
- encodes a transposase that is responsible for excision, transposition, and mutation, as well as chromosome breakage
- Ac transposase interacts with sequences at the ends of Ac and Ds elements and catalyzes their movement
- deletions or mutations in Ac gene abolish its catalytic function
37
Describe how retroviruses work
- they use the enzyme reverse transcriptase to copy retroviral-like RNA into DNA, this integrates into the chromosome (inserts) of the host
- reverse transcriptase was discovered by D Baltimore, H Temin, and Satoshi Mizutani in 1970
- it catalyzes reverse flow of genetic information from single-stranded RNA into double-stranded DNA
- retroviruses have an RNA genome
38
What is an example of a retrovirus
- Human Immunodeficiency Virus (HIV), infects immune system cells and causes acquired immunodeficiency syndrome (AIDS) in humans
39
What are retrovirus-like elements?
- similar to retroviruses but non-infectious
- can move around genome and about 8% of our genome is derived from retroviral-like elements
- about 100 retrovirus-like elements in humans, but few are active in transposition
40
What are retrotransposons?
- utilize reverse transcriptase to copy retroviral-like RNA into DNA, which integrates into the chromosome
- resemble integrated retroviruses, but do not have terminal inverted repeats
- contain poly-A tail that is reverse transcribed during transposition, in this way the resemble reverse transcripts of poly A+ mRNA
- are also known as retroposons
41
General structure of a retrovirus/retroviral-like element
- includes gene that encodes reverse transcriptase and integrase: copying RNA into DNA and integrating into chromosome
- terminal inverted repeats
- target site duplication: short directly repeated sequences at both ends - result from staggered cleavage of the double-stranded DNA at the site of insertion
42
Describe the structure of Retroposons
- genes that encode reverse transcriptase and endonuclease activities
- 5' and 3' untranslated regions (UTR) (after promoter) and poly-A tail after the 3'UTR : resemble reverse transcripts of polyA RNA
- create a target site duplication upon integration but they have NO TERMINAL INVERTED REPEATS
43
How do retroviral-like elements move?
- start with an integrated DNA structure (previously copied from RNA genome into DNA and inserted in x)
- this structure is transcribed into RNA, then through reverse transcriptase it is made into DNA, called cDNA (=complementary DNA)
- the ends are processed by endonclease (encoded by retrovirus)
- DNA copy makes break in DNA at target site (by 3'-OH nucleophilic attack)
- produces pair of staggered DNA ends at target site into which ends of cDNA are attached by ligation; the gaps at the ends (2 gaps: 5' overhangs create 3' gaps) are filled in by polymerase and ligated, produces target site duplication in retrovirus DNA structure
44
What are long interspersed nuclear elements?
= LINEs
- L1 element is a major transposable LINE sequence, it is a retroposon
- human genome has 3k-5k complete L1 elements and 500,000+ truncated L1 elements
- complete L1 are 6 kb long, have an internal promoter and two open reading frames that encode a nucleic-acid binding protein and a protein with endonuclease and reverse transcriptase activities
45
What are short interspersed nuclear elements?
= SINEs
- retroposons are second most abundant class of transposable elements in human genome, SINE families are Alu, MIR, Ther2/MIR3 elements
- only Alu elements are transpositionally active
- SINEs are usually less than 400 bp long, do not encode proteins
- reverse transcriptase required for transposition is provided by LINE-type element
46
What are the major components of transposable elements in humans?
LINEs and SINEs account for 33% of transposons in human genome
47
What are minor components of transposable elements in humans?
- defective retrovirus-like elements (8%)
- elements related to cut-and-paste transposons (like Ac/Ds) (approx 3%)
both of these groups are transpositionally-inactive
48
What are genetic and evolutionary signigicance of transposable elements?
1. Transposons are mutagens = Thomas Hunt Morgan studied this in Drosophila, transposon mutagenesis leads to gene disruption
2. Transposons can mobilize foreign genes = antibiotic resistance genes carried by IS elements, transfer of foreing genes by P elements
3. Change genome organization = alterations in x structure (recombination b/n transposable elements can generate x deletions and amplifications)
49
What happens if two transposable elements are in direct orientation?
- means their sequences are in the same direction
- alignment will lead to crossing over and delete a gene sequence between the elements
- results in shortened chromosome
50
What happens if transposable elements are inverted with respect to each other?
- sequences are in opposite direction
- chromosomal segment bends to permit alignment in same direction, corssing ocer inverts original sequence b/n the two transposons and produces an inversion of DNA sequences on the chromosome
51
What happens if transposons located on two different chromosomes undergo crossing over?
- produces a translocation in which one chromsome is shortened and the other one is longer
- can be potentially deleterious, this can be of advantage or can be detrimental, depends on what happens to genes
MBG 2040
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