Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E The Stability of the...

Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E

The Stability of the Genome

Duplication, Deletion, Transposition


Duplication of DNA sequences

• Could result from unequal crossover– chromosomes are not perfectly aligned during

meiosis

– One gets a duplication; the other gets a deletion

– Process continues, to build tandem repeats

• After duplication, base substitutions (variation)

• Multiple gene family members from one ancestral copy - divergence required

Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E Figure 10.24


Evolution of globin genes

• Hemoglobin is tetramer: 4 globin chains

• Globin genes from different vertebrates have common features– All globins have 3 exons & 2 introns

• Globin-like proteins are different

– leghemoglobin from plants; muscle myoglobin

– 4 exons & 3 introns

– ancestral? (4 exons to 3 exons)



• fusion of 2 exons (~800 million years ago)

• Some primitive fish have only one globin gene

• perhaps fish diverged before the first duplication

• First duplication formed & (~500 million yrs ago)

• & separated transposition/translocation

• today's organization humans

– -globin genes clustered on chromosome 16,

– -globin genes clustered on chromosome 11



• Hemoglobin made of 2 pairs of chains

– One pair always family; the other always -family

– Combinations differ with stage of development

– embryonic, fetal, adult

• Clusters also contain pseudogenes

– have mutations that stop function

– evolutionary relics

– widespread in many gene families

– function unknown (junk?)



• Parts of globin genes evolve at very different rates– DNA of coding regions is highly conserved

– Noncoding regions are much more variable

– Coding area changes are most frequently one base substitutions

– Noncoding - often include additions & deletions as well


Evolution of gene families

• Evolving Sequence and Function– Growth hormone & prolactin are pituitary

hormones

• Related amino acid sequences

• Evoke completely different responses from target cells

– Number of changes only ROUGHLY corresponds to time

– Redundant codons allow “silent” substitutions


Transposons

• Described by Barbara McClintock (Cold Spring Harbor, late 1940s)– Nobel Prize – 1983

– Initially ignored: papers (and subject) complex

– Studied patterns & markings in leaf & kernel coloration maize

– Noticed instability in markers in both germ line and soma

– Concluded movement of genetic elements affecting gene expression

– Defined terms: transposition and transposable elements


Transposons

• Eventually (late 1960s) verified transposons in bacteria

– Encode transposase enzyme

– Excision from donor site & insertion at target site

– bind to specific sequences (IR’s) ends of transposon

– complex binds to target DNA

– catalyzes integration

– Integration creates small duplication in target (DR’s)

– “Footprints” left behind when transposon excises


Transposons

• Eukaryotic genomes contain large numbers of transposable elements – ~40% of DNA in human cell nucleus

from transposable elements– Vast majority are crippled by mutation

or suppressed– they insert almost randomly within

target DNA

• sometimes cause mutations in genes

• ~1 in 500 human mutations caused by transposons


Mechanisms of transposition are complex

• Some are excised from donor site and inserted into target– Example: mariner family of transposons

– Found throughout plant & animal kingdoms

• Some are replicated leaving donor site unchanged (bacteria)


Mechanisms of transposition are complex

• Often, transposition in eukaryotes involves RNA intermediate

– DNA transcribed, producing an RNA

– Converted to DNA by reverse transcriptase

– dsDNA copy is integrated into target DNA site

– Retrotransposons sometimes have gene for RVTase

– Retroviruses, like the AIDS virus related to retrotransposons

• Acquired envelope protein genes

• Or, loss of envolope gene could make transposon


Mobile elements and evolution

• Most moderately repeated sequences of genome are – interspersed & arise by transposition

– 2 most common families: Alu & L1 families

– both transpose by means of RNA intermediates



• L1 – ~500,000 copies; ~15% of total nuclear DNA

– Vast majority of these are incomplete & defective

– Likely present in earliest eukaryotic cells (found everywhere)

– Full length, human L1 sequence

• at least 6000 bp in length)

• encodes unique protein with 2 catalytic activities

• Endonuclease activity cleaves target DNA

• Reverse transcriptase activity makes DNA from RNA



• Alu – roughly 1 million copies

– Family of short sequences ~300 bp in length

– Related to 7S RNA

• present in signal recognition particles

• found with membrane-bound ribosomes

– Alu origin: 7S RNA & reverse transcription?

– Amplification aided by L1 endonuclease?

– Seen only in higher primates

– First appearing ~60 million years ago



• Proposed functions of transposable elements– No function - a genetic parasite

– Fuels evolution


Support for evolutionary role

• Found as essential parts of regulatory regions

– Human parathyroid hormone gene expression controlled, in part, by relics of transposable element

• Can clearly reorder genomes

– Domain shuffling using introns as breakpoints

• Transposable elements become useful genes

– Telomerase derived from reverse transcriptase?

– Enzymes involved in antibody gene rearrangement are derived from transposase encoded by ancient DNA transposon


Support for evolutionary role

• Transposable (P) element of Drosophila melanogaster – T. H. Morgan's flies from 1900s devoid of the P

element

– All members of the wild species have it today

– Spread rapidly (80 years)

• Transmission likely mediated by parasites

Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E The Stability of the...

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