Modular proteins I

Presentation Transcript

Level 3 Molecular Evolution and Bioinformatics

Jim Provan

Patthy Sections 8.1.1 – 8.1.3

Folded structures of proteins that are larger than 200-300 residues generally consist of multiple structural domains:

Compact, stable units with a unique three-dimensional structure
Interactions within a domain are more significant than those between domains
Fold independently i.e. structural domains are also folding domains
If domain performs distinct function which remains intact in the isolated domain, then it is also a functional domain

Many multidomain proteins are homomultimeric i.e. contain multiple copies of a single type of structural domain:

Example is plasminogen activator where a trypsin-like serine protease is joined to kringle, finger and EGF domains
May occur by fusion of two or more genes (chimeric proteins)
Also known as modular proteins, with domains known as modules

Suggests mechanisms to facilitate duplication and dispersal
“Building blocks” of different types of multidomain proteins are known as mobile protein modules
Frequency of transfer and incorporation into new protein reflects fixation probability

Gilbert suggested that recombination within introns could assort exons independently
Idea of rapid construction of novel genes from parts of old ones led to the formulation of the exon-shuffling hypothesis

According to “introns early” theories, all extant genes were constructed from a limited number of exon types
Under the “introns late” theory, intronic recombination and exon shuffling could not have played a major role in the assembly of the earliest genes
Original theory was that exons corresponded directly to modules and/or structural motifs

In the case of many genes, no obvious correspondence was observed between protein structure and intron location
It is now known that introns can also be inserted into genes i.e. structure of a gene may not be its original structure
Introns suitable for exon shuffling did not originate until a relatively late stage of eukaryotic evolution
Exon shuffling has only been conclusively demonstrated in “young” proteins unique to higher eukaryotes
Only a special group of exons, the “symmetrical” modules, are really valuable for exon shuffling. Intron phase distribution is also a crucial factor.

Does not require an external cofactor: 2’-OH of an adenine within the intron cuts the 5’ splice site
2’5’ phosphodiester bond (branch site) forms the lariat structure
Although folding is still crucial, chemistry, sequence of events and lariat formation are similar to nuclear spliceosomal introns

Spliceosomal introns are only spliced in the presence of a complex of specific proteins and RNA known as a spliceosome
Majority of intron is unimportant: as long as the 5’ and 3’ splice sites and the branch site are conserved, splicing can take place:

Large insertions into spliceosomal introns, or deletions do not affect splicing efficiency
Chimeric introns, containing the 5’ end of one intron and the 3’ end of another, are also properly spliced
Mutations (directed or otherwise) in these regions lead to aberrant splicing

Spliceosomal intron plays a minor role in its own splicing: the actual spliceosome complex is more important

Both group I and group II self-splicing mechanisms resemble spliceosome catalysed splicing:

Initial step is attack by ribose hydroxyl group on 5’ splice site
In each case, reactions are transesterifications where phosphate moieties are retained in products
In group II and spliceosomal introns, intron is released as a lariat

Accepted that spliceosomal-catalysed splicing evolved from group II self-splicing introns :

Key step was transfer of catalytic role from intron to other molecules
Formation of spliceosome gave spleceosomal introns structural freedom as they no longer had to fulfil the catalytic function

Generally found only in nuclear genomes of higher eukaryotes (plants, animals and fungi)

Plays a significant role in changing exon-intron structure of genes
Introns may be eliminated through mechanism that gives rise to processed genes (retroposition)
Reverse transcription can also lead to loss of only some introns:

Reverse transcription of perfectly spliced mRNA and recombination with the functional gene: mutates original gene
Partially processed pre-mRNA could give rise to a semi-processed gene: generates a new paralogue

Believed that insertion of exons may occur by the same mechanism as insertion of introns:

Exon shuffling may be a consequence of the occasional inclusion of exon sequences in the insertion cycle of introns
Alternative splicing (exon skipping during splicing) may yield exons with flanking introns
If such a composite is inserted into the genome by the same mechanism that inserts single introns (reverse splicing) we have exon shuffling

Key difference between intronic recombination model and retrotransposition model:

In first case, insertion occurs into a pre-existing intron of same phase as introns flanking exon
Retrotransposition model does not have this requirement