Transcript Modular proteins II

Modular proteins II
Level 3 Molecular Evolution and
Bioinformatics
Jim Provan
Patthy Sections 8.1.3 – 8.2
Intron phase
Gly
Lys
Val
Asn
Phase 0
GGC AAG gtaagt ................ (Py)nncag GTC AAC
Gln
G
ly
Gln
Phase 1
GG CAA G gtaagt ................ (Py)nncag GT CAA C
Ala
Ar
g
Phase 2
Ser
G GCA AG gtaagt ................ (Py)nncag G TCA AC
Intron phase and evolution of
collagenases
0
2
1
1
1
2
1
2
1
0
2
1
1
1
1
1
1
1
1
1
1
0
2
1
2
1
2
1
1
2
1
2
1
Exon shuffling by intronic
recombination
Middle repetitive sequences flanking an exon may
facilitate “looping out” or insertion of modules by intronic
recombination
Best example of contraction and expansion of a
multidomain protein found in apolipoprotein(a):
Number of tandem kringle domains ranges from 12 to 51 copies
In one variant, 24 of the 37 kringle domains have identical
nucleotide sequences, suggesting very recent duplication
Isoforms containing different numbers of kringle domains do not
follow simple Mendelian patterns of inheritance: offspring often
have apolipoprotein(a) isoforms that differ from those of parents
Such proteins retain interdomain introns: these are responsible for
high levels of gene structure plasticity
Factors favouring intronic
recombination
Only a tiny portion of spliceosomal introns is essential for
splicing:
5’ end, 3’ end and branch site
Separated by very long sequences that are tolerant to insertions
and deletions
Illustrated by comparison of urokinase genes:
Genome organisation of murine, human, porcine and chicken genes
is identical in terms of location and phase class of introns
Chicken urokinase introns show hardly any sequence similarity with
corresponding mammalian introns, except near splicing junctions
and branch sites
Great difference in size of orthologous introns:
—
—
Intron A is 1489 bp in chicken
Only 306 bp in humans
Factors favouring intronic
recombination
Advantages of spliceosomal introns for exon shuffling (large
size, presence of middle repetitive sequences, tolerance to
structural changes) holds primarily for vertebrate genomes:
Fungi and plants have fewer and shorter introns
Genes of best studied invertebrate genomes (C. elegans, D.
melanogaster) also have shorter introns:
—
—
Relatively compact genome may be characteristic of ancestral metazoa
Alternatively, selection may have led to a secondary increase in genome
compactness in these lineages
Since plant spliceosomal introns are shorter than those of
vertebrates, they are less suitable for intronic recombination
Splicing of chimeric introns, an inevitable consequence of
intronic recombination, is impaired in yeast and plants
Acceptance of mutants created by
intronic recombination
Several levels of selection determine whether intronic
recombination mutant will be fixed or rejected:
Chimeric intron must be spliced correctly, otherwise translation will
probably run into a stop codon in the mRNA/intron region and form
a truncated protein
Two non-orthologous introns must be in the same phase class:
—
—
—
Must split the reading frame in the same phase
Downstream exon must be translated in its original phase to prevent
frameshift mutations
Symmetrical exons
New protein must be able to adopt a stable conformation
Selective advantage of having a new functional domain
Impact of exon insertion may initially be mitigated by
alternate splicing
The intron-phase compatibilty rule
Duplication
2
2
2
2
2
2
2
Insertion
Deletion
2
2
Duplication
2
2
0
Deletion
0
1
1
0
Insertion
1
0
The symmetrical exon rule
Insertion, deletion and duplication of a module by intronic
recombination can satisfy the phase compatibility
requirement only if the two introns flanking the module
are of the same phase (symmetrical modules):
Only symmetrical module groups are 0-0, 1-1 and 2-2
Can only be inserted into the compatible intron i.e. 1-1 modules
can only be inserted into phase 1 introns
If the structure of a gene of a modular protein conforms
to these rules, it suggests that the protein has evolved
through exon shuffling
Intron insertion and removal
1
1
1
1
1
1
1
1
1
1
2
Factor XIIIb subunit
1
1
1 2 1
1
1 2 1
C3d/Epstein-Barr virus receptor
1
1 2 1
1
1
1 0
2
Evolution of mobile modules
Conversion of a domain to a module:
Protein domain may be converted to a protomodule if introns of
identical phase are inserted at its boundaries
Tandem duplication may lead to homopolymerisation
New mobile module may be excised and reinserted at a new
location
There is a large variety of class 1-1 modules known, but
relatively few class 2-2 or class 0-0 modules
May be due to initial predominance of class 1-1 modules
by chance
Conversion of a domain to a mobile
module
Example of the modularisation process
The Kunitz type proteinase inhibitor is a single module
protein:
In bovine pancreatic trypsin inhibitor gene, phase 1 intons are
found at both boundaries of the single inhibitor domain
(protomodule stage)
Lipoprotein-associated coagulation inhibitor consists of three
tandem copies of this module (tandem duplication stage) – each
module is encoded by a distinct class 1-1 exon
Kunitz-type inhibitor modules have been inseted into the genes of
other proteins (shuffling stage):
—
—
Amyloid precursos
Collagens
Evolution of exon shuffling
Obvious examples of proteins assembled by exon
shuffling are restricted to animals:
Not surprising, considering that the evolution of introns and
modules is a relatively late development
Recent evolution of spliceosomal pre-mRNA
Large-scale genome projects on model organisms
provides information on modular evolution:
Many examples in metazoa – presence of “vertebrate” modules in
invertebrates suggests mechanism predates split
No evidence in yeast
Only one possible example in Arabidopsis (receptor protein kinase
with two EGF-like domains)
Evolutionary significance of exon shuffling
Number of proteins constructed from modules underlines
value of exon shuffling
Several unique features made this mechanism important:
Large collection of binding specificities can coexist in a single
protein e.g. plasma proteinases
Acquisition of a new domain can bring about a sudden change in
specificity:
—
—
Good example is gelatinase
Insertion of a gelatin-binding FN2 module into an ancestral
metalloproteinase of the collagen family
Could be correlated with metazoan “big bang”
Modular assembly by exonic
recombination
Exon shuffling by intronic recombination may not be the
only way to exchange domains between genes:
Modular protein of the bacteria Peptostreptococcus magnus is the
product of a recent intergenic recombination of two different types
of streptococcal surface proteins
Transfer of one part of a prokaryotic gene to another without the aid
of introns
Multidomain bacterial proteins of the PEP sugar transferase
system:
Three functional domains separated by “unusual” flexible linker
regions
Linkers responsible for frequent rearrangements