Transposable elements Flashcards
Cut-and-paste transposons
transposable element physically cut out of one site in a chromosome or plasmid and pasted into new site
DNA transposon
Excision and insertion catalyzed by a transposase (synthesized by transposon)
Found in prokaryotes and eukaryotes (e.g. insertion sequence elements in bacteria)
Replicative transponsons
element is replicated with one copy inserted at a new site and one remains at OG site (no excision, unlike cut and paste)
DNA transposon, requires transposase
Only in prokaryotes (e.g. Tn3 element in bacteria)
Retrotransposons
DNA copy of element made by reverse transcription from its RNA and then inserted into a new chromosomal site
Reverse transcriptase is required to transcribe RNA from retrotransposon into DNA
Flow of genetic info from RNA to DNA required RNA-dependent DNA polymerase, this mechanism was discovered in 1970
Only in eukaryotes
Two kinds: retrovirus-like elements and retroposons
Prokaryotic transposable elements (cut-and-paste)
Gene that encodes transposase - a protein required for transposition to occur
Terminal inverted repeats - identical or nearly identical sequences at both ends of element
Target site duplication - short, directly repeated sequences at both ends, result from staggered cleavage of the double stranded DNA at the site of insertion
Insertion sequence elements
simplest type of cut-and-paste transposon, first found in lac- mutations of E. coli
Compactly organized and contain only genes involved in transposition
Inverted terminal repeats are found at the ends
Some IS elements encode transposase, allows transposon to move
IS50 element has a central region with transposase gene, terminal inverted repeats, and target site duplication at either end
Do not memorize sequences, only structure
Insertion of an IS element causes target site duplication
IS elements can be scattered throughout bacterial chromosome, may contain several copies of an IS element, also on plasmids
When a particular IS element found on both a plasmid and a chromosome, homologous recombination may occur, inserting the plasmid into chromosome (changes distribution of IS in cell)
HR between IS elements may involve a non-conjugative resistance plasmid and a conjugative plasmid which can mobilize antibiotic resistance genes within a bacterial population
NOTE: non-conjugative plasmid is a plasmid that cannot be transferred between bacteria through a pilus (aka through conjugation)
HR between these two plasmids yields a larger, antibiotic-resistant coding plasmid
New plasmid has insertion sequence that allows it to enter chromosome, antibiotic resistance gene, and RTF component that allows transfer through conjugation
Because the conjugative plasmid combines with antibiotic resistance, more bacterial cells can be antibiotic resistant
Composite transposons
other type of cut-and-paste transposon, created when two IS elements insert near each other and flank one or more possible antibiotic resistance genes, “capturing” a DNA sequence
IS element excision through transposase cleavage at each end of the transposons can mobilize the entire captured DNA, which may mobilize antibiotic resistance genes
Basically, cuts out resistance gene with IS on either side, moves that chunk somewhere else
Replicative transposons
more complex than the cut-and-paste transposons, found in bacteria
Tn3 is a replicative transposon which can carry and mobilize genes for antibiotic resistance
Tn3 elements are larger than IS elements
Like composite transposons, Tn3 elements often contain additional genes that are not involved in transposition and have simple inverted repeats at each end
Retroviruses
reverse transcriptase enzyme to copy retroviral-like RNA into DNA which then integrates into the chromosome
e.g HIV
Reverse transcriptase catalyzes
reverse flow of genetic info from RNA into DNA
Retroviral-like elements
Very similar to retroviruses but are non-infectious.
General structure of retroviruses
genes that encode reverse transcriptase and integrase: copying RNA into DNA and integration into chromosome
Terminal inverted repeats and target site duplication (see prokaryotic transposable elements) also included in general structure), P in diagram is for promoter
Retrotransposons
Utilize reverse transcriptase to copy retroviral-like RNA into DNA
Resemble integrated retroviruses but do not have terminal inverted repeats
Contain poly A+ tail that is reverse transcribed during transposition
They resemble reverse transcripts of poly A+ mRNA
General structure - genes encode reverse transcriptase & endonuclease activities, 5’ and 3’ untranslated regions (UTR) and poly-A tail
When integrating, they create a target site duplication but have no terminal inverted repeats
Long interspersed nuclear elements
ne of the major transposable LINE sequences in humans is the L1 element
L1 element is a retroposon, human genome contains 3000-5000 complete L1 elements and more than 500 000 truncated L1 elements
Completed L1 elements are about 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
Open reading frame - portion of DNA with no stop codons, usually part of a gene
Short interspersed nuclear elements
SINEs retroposons are the second most abundant class of transposable elements in human genome
SINE families are the Alu, MIR and Ther2/MIR3 elements
Only the Alu elements are transpositionally active
SINEs are usually less than 400 bp long and do NOT encode proteins
The reverse transcriptase required for SINE transposition is provided by a LINE-type element
SINE elements do not encode their own transposase
