Overview of introns and their structure

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Overview of introns and their structure
DNA Helix Mosaic featured on the cover of
Nature, February 15, 2001
Mathieu Lajoie
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Discovery of introns

• 1977
• Research Groups working on adenovirus at MIT and
  Cold Spring Harbor reported that mRNAs were
•  mosaic molecules consisting of sequences
  complementary to several non-contigous segments
  of the viral genome 
• Phil Sharp (MIT) Rich Roberts (CSH)
• Nobel prize in Medecine 1993

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Discovery of introns

• 1978
• Pierre Chambon demonstrated the existence of
  introns in the ovalbumine gene.

Ovalbumine is the protein contained in the white
part of the eggs so its easy to get a lot of
its mRNA. Chambon hybridized this mRNA with the
gene DNA and got the following image by
electronic microscopy
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Discovery of introns

• 1978
• Pierre Chambon demonstrated the existence of
  introns in the ovalbumine gene.

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Discovery of introns

• 1978
• Pierre Chambon demonstrated the existence of
  introns in the ovalbumine gene.

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Classification of introns

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Spliceosomal introns
Phylogenetic distribution

• Eukarya

Location

• Protein coding gene in nucleus

Size

• 25 nt over 500 000 nt (TRPM3 human chr 9)

Adapted from http//mips.gsf.de/proj/yeast/review
s/intron/major_classes.html
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Spliceosomal introns
Sequence constrain very limited
Splice site
Splice site
AG GUPuAGPy PyPyPyPyPyAG
5
3
consensus sequence (vertebrate)
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Spliceosomal introns
Splicing mecanism

• Spliceosome 5 snRNP more than 760 proteins
• snRNP snRNA 7 proteins
• Needs ATP
• Produce a lariat

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Spliceosomal introns
Splicing mecanism

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Spliceosomal introns
Exemple
The dystrophin gene 2400 kb contains 78 introns
wich represent 99.5 of his length. Only 0.5
of the gene is coding !
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Spliceosomal introns
Utility ?

• Could protects gene families against unequal
  recombination

• Alternative splicing

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tRNA introns
Phylogenetic distribution

• Eukarya
• Archaea
• Eubacteria

Location

• Nuclear tRNA genes

Size

• 15 nt 60 nt

Splicing

• Three protein enzymes a site-specific
  endonuclease, a tRNA ligase, and a
  phosphotransferase

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Group I introns
Phylogenetic distribution

• Fungal mitochondria
• Plant mitochondria and chloroplasts
• Nuclear genome of some protists and fungi
  Eubacterial bacteriophage genomes.
• Not found in vertebrate genes.

Adapted from http//mips.gsf.de/proj/yeast/review
s/intron/major_classes.html
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Group I introns
Location

• Mitochondrial mRNA and rRNA genes
• Chloroplastic rRNA and tRNA genes
• Nuclear rRNA genes
• mRNA genes of phage
• tRNA genes of bacteria

Adapted from http//mips.gsf.de/proj/yeast/review
s/intron/major_classes.html
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Group I introns
Structure

• Four blocks of conserved sequences in the
  catalytic core
• No splice site consensus
• Well defined secondary structure
• Size range from 68 to 3000 nt
• Most are over 400 nt

Adapted from http//mips.gsf.de/proj/yeast/review
s/intron/major_classes.html
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Newer representation
Old style drawing
Exon seq. in lower case and boxed
Shows how splice sites can be brought close
together by internal guide sequence.
splice site
Conserved core
Cr.LSU intron
http//www.esb.utexas.edu/herrin/bio344/lectures/P
T3_Splicing1rev.ppt
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3-D Model of Tetrahymena rRNA Intron
Catalytic core consists of two stacked helices
domains 1. P5 P4 P6 P6a (in green) 2. P9
P7 P3 P8 (in purple) The substrate is
the P1 P10 domain (in red and black), it
contains both the 5 and 3 splice sites.
http//www.esb.utexas.edu/herrin/bio344/lectures/P
T3_Splicing1rev.ppt
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Group I introns
Splicing mecanism
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Group I introns
Splicing mecanism

• Needs external G nucleotide cofactor

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Group I introns
Splicing mecanism

• Needs external G nucleotide cofactor

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Group I introns
Splicing mecanism

• Needs external G nucleotide cofactor

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Group I introns
Splicing mecanism

• Needs external G nucleotide cofactor
• Produce a linear intron

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Group I introns
Splicing mecanism

• Needs external G nucleotide cofactor
• Produce a linear intron
• Most can splice without protein
• Doesnt need ATP
• Splicing modulated by some proteins

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Group I introns
Mobility
Group I intron
Exon n
Exon n1
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Group I introns
Mobility
Group I intron
Exon n
Exon n1
ORF
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Group I introns
Mobility
Group I intron
Exon n
Exon n1
ORF
 homing endonuclease 
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Group I introns
Mobility
Group I intron
Exon n
Exon n1
ORF
 homing endonuclease 
Gene with target sequence without group I intron
Exon n
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Group I introns
Mobility
Group I intron
Exon n
Exon n1
ORF
 homing endonuclease 
Gene with target sequence without group I intron
Exon n
Exon n
Exon n1
ORF
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Group II introns
Phylogenetic distribution

• Organellar genome of lower eukaryotes
• Eubacteria
• Archaebacteria

Location

• Organelle mRNA
• Eubacteria mostly outside ORF
• Archea inside other introns (twintrons)

Dai, L., Toor, N., Olson, R., Keeping, A., and
Zimmerly, S. (2003). Database for mobile group II
introns. Nucleic Acids Res. 31 424-426
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Group II introns
Phylogenetic distribution

• Organellar genome of lower eukaryotes
• Eubacteria
• Archaebacteria

Location

• Organelle mRNA
• Eubacteria mostly outside ORF
• Archea inside other introns (twintrons)

Dai, L., Toor, N., Olson, R., Keeping, A., and
Zimmerly, S. (2003). Database for mobile group II
introns. Nucleic Acids Res. 31 424-426
32
Group II introns
2D structure

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Group II introns
2D structure

RT Reverse Transcriptase X Maturase D DNA
binding En Endonuclease
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Group II intronssplicing

No protein is required in vitro
Very similar to spliceosomal splicing
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Group II intronssplicing

Reverse transcriptase is required in vivo
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Group IImobility
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Group IImobility

• Such process occurind at specific sites (highly
  efficient)
• is called retrohoming
•  Invasion  into unrelated sites (low
  frequencies) is called
• retrotransposition

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Group IIevolution
Dai, L., Toor, N., Olson, R., Keeping, A., and
Zimmerly, S. (2003). Database for mobile group II
introns. Nucleic Acids Res. 31 424-426
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Group II evolution
It is widely accepted that group II introns are
the ancestors of slpiceosomal nuclear introns
foung in higher eukaryote, including humans.

• Common splicing mecanism
• Structural similarities between group II introns
  and snRNA-intron-exon pairings in spliceosome.

Dai, L., Toor, N., Olson, R., Keeping, A., and
Zimmerly, S. (2003). Database for mobile group II
introns. Nucleic Acids Res. 31 424-426
44
Group II evolution
LINE 20 of Human genome
Dai, L., Toor, N., Olson, R., Keeping, A., and
Zimmerly, S. (2003). Database for mobile group II
introns. Nucleic Acids Res. 31 424-426
45
Group IIevolution
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Group II evolution
Might group II intron confer an advantage to
the host genome ?

• For
• Exon shuffling might creates new genes
• Alternative splicing increase proteome (in
  Euglena ct)
• Spread of genes contained in introns

• Against
• Genome instability senescence (In Podospora mt)
  
• Generation of scrambled genes (in Chlamydomonas)

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Classification of introns

http//mips.gsf.de/proj/yeast/reviews/intron/major
_classes.html