Assignment for Friday:

Assignments for Monday

Slides on introns

See here for the splice site consensus in Arabidopsis

Discuss non-sense mediated decay pathway (Wikipedia, review article)

 

Introns and Their Evolution

 


Three groups of introns based on their splicing mechanisms:

group I and II are self-splicing [have different splicing mechanism: see this figure for comparison of splicing]:
BOOK2


group III introns are present in eukaryotic nucleus, need spliceosomes to splice out:

BOOK

Where different groups of introns occur?

  • Group I: were discovered in ciliated protozoan Tetrahymena; found also in Physarum, fungal and algal and plant mitochondria and in phage T4, rare in Bacteria, one is present in Thermotoga 23SrRNA. Similar to inteins, they often rely on Homing Endonucleases to invade a host gene.
  • Group II: common in Bacteria, and so far found only in one Archaeal genus, Methanosarcina
  • Spliceosomal Introns: present throughout eukaryotes, but more common in "crown-group" eukaryotes

Where do spliceosomal introns come from and how the splicing machinery evolved?

Hypothesis:

Spliceosomal introns evolved from Class II introns; the function of some of the internal loops of the class II introns are taken over by the spliceosomal snRNA (small nuclear RNA).

Support:

Gratuitous complexity hypothesis for evolution of spliceosomal machinery: See reading assignment on WebCT [the portions for the reading are highlighted in the PDF file]

Problem:

class II introns are found in bacteria, and only in one Archaeal genus, Methanosarcina; why is it that predominately "crown-group" eukaryotes have introns?

Not much of a splice site consensus (exon1 GT-intron-AT exon2, see here for the splice site consensus in Arabidopsis)

Group I introns often have homing endonucleases.
Homing endonucleases and intron mobility. Spread in populations, selective pressure on endonuclease. See the excellent paper by Goddard and Burt on the reinvasion cycle.

Also: reverse splicing

Possible benefits of having introns:

Exon shuffling, alternative splicing (1 gene -> different protein products) ....

Two rival hypotheses: Intron Early vs. Intron Late

Intron early:

Protein diversity arose in analogy to exon shuffling in the generation of antibody diversity (see your biochemistry or genetics textbook on the maturation of the immune system).

Claims:

Intron late:

Present day introns are late invaders of already functional genes. Exon shuffling might play some role in eukaryotes, but most of protein diversity arose before introns invaded protein coding genes.

Claims:
  • distribution of introns mapped on phylogenetic trees unambiguously points towards late invasion (and here).
  • The correlation between structure and intron position is not unambiguous.
  • The finding that introns in mitochondrial (eubacterial) and nucleocytoplasmic genes have introns in the same location could reflect a preferred intron integration site. The phase pattern is also observed in vertebrate genes, in which the introns are of late origin.
  • Exon shuffling requires introns located in the same phase, but there might be other reasons for having a slight excess of introns in the same phase. For introns to frequently invade genes, there needs to be mechanisms for introns to find new "homes" (see above).

Compromise:

mixed model of intron evolution
  • version 1 - while some introns are recent, most are old. E.g.: [Roy, 2003].
  • version 2 - while most introns are recent, some are older, but not necessarily very old. E.g.: [Rogozin et al., 2003]

Else:

it was suggested that class II introns were the reason for the separation between transcription and translation in Eukaryotes (accomplished through the nuclear envelope). Martin and Koonin's hypothesis suggests that class 2 introns were brought into the eukaryotic cell by the mitochondrial endosymbiont.

 

 

 

Discussion - two debate teams on the function of introns in evolution:
Team A) Introns Early versus Team B) Introns Late

1) discuss arguments within group (5 minutes)
2) present arguments in favor of your thesis (each site, one person one argument)
3) discuss counter arguments within group (3 minutes)
4) present arguments against opposing teams evidence

 

 

 

Goals class 16:

 

 

 

 

 

 

 

 

 

 

PRO INTRONS EARLY:

 

PRO INTRONS LATE :

 

 

 

 

 

From:<http://dml.cmnh.org/2002Jul/msg00351.html>

----- Original Message -----
From: <Dinogeorge@aol.com>
Sent: Thursday, July 11, 2002 6:47 PM
Subject: Re: New finds

 

> > --+--+-----------A
> >   |  `--+--+-----B
> >   |     |  `--+--C
> >   |     |     `--D
> >   |     `--------E
> >    `--------------F
>
> This is >not< a Hennigian comb. Only the entire ABCDE clade and the F
lineage
> make a (two-toothed) Hennigian comb in this cladogram. In a Hennigian comb
> the side branches are left unbranched, like the teeth of a comb. Hence the
> name.

This _is_ a Hennigian comb, because in a cladogram, _only_ topology counts.
A cladogram is a mobile. Look at the following -- it's exactly the same
cladogram as above:

--+--F
  `--+--A
     `--+--E
        `--+--B
           `--+--D
              `--C

... what a side branch is lies completely in the hand of the presentator.
All I did was I rotated a few stems around their long axes.

 

sequence space slides

Intro to phylogenetic reconstruction

Phylogenetic analysis is an inference of evolutionary relationships between organisms.
Those relationships are usually represented by tree-like diagrams.
Note:
the assumption of exclusively tree-likeliness of evolution is not justified.

Steps of the phylogenetic analysis:


Compilation of sequence dataset
Alignment
Determination of substitution model
Tree building
Tree evaluation

 

 

 

 

Why phylogenetic reconstruction of molecular evolution?

A) Systematic classification of organisms

      e.g.: Who were the first angiosperms? (i.e. where are the first angiosperms located relative
      to present day angiosperms?)

      Where in the tree of life is the last common ancestor located?

B) Evolution of molecules

e.g.: domain shuffling, reassignment of function, gene duplications, horizontal gene transfer, drug targets, detection of genes that drive evolution of a species/population (e.g. influenca virus, see here for more examples)

C) Identification of organisms

e.g., phylotyping in microbiom samples),
origin
of genes and viruses (e.g. recent ebola out break)

How:

1) Obtain sequences

Sequencing

Databank Searches -> ncbi a) entrez, b) BLAST, c) blast of pre-release data

Friends

 

2) Determine homology (see notes for earlier classes for practical implementation)

Reminder on Definitions:
Homology: Two sequences are homologous, if there existed an ancestral molecule in the past that is ancestral to both of the sequences

3) Align sequences

(most algorithms used for phylogenetic reconstruction require a global alignment. An exception is statalign
from Thorne JL, and Kishino H, 1992, Freeing phylogenies from artifacts of alignment. Mol Bio Evol 9:1148-1162)

Some evolutionary biologists recommend to select only the part of the alignment that is reliable. (Discuss!) Modify alignment, if necessary.

 

4) Reconstruct evolutionary history

    A) Distance analyses

      1. calculate pairwise distances
        (different distance measures, correction for multiple hits, correction for codon bias)
      2. make distance matrix (table of pairwise corrected distances)
      3. calculate tree from distance matrix
i) using optimality criterion
(e.g.: smallest error between distance matrix
and distances in tree), or use
ii) algorithmic approaches (UPGMA or neighbor joining)

    B) Parsimony analyses

      find that tree that explains sequence data with minimum number of substitutions

      (tree includes hypothesis of sequence at each of the nodes)

       

    C) Maximum Likelihood analyses

      given a model for sequence evolution, find the tree that has the highest probability under this model.

      This approach can also be used to successively refine the model.

      Bayesian statistics use ML analyses to calculate posterior probabilities for trees, clades and evolutionary parameters. Especially MCMC approaches have become very popular in the last year, because they allow to estimate evolutionary parameters (e.g., which site in a virus protein is under positive selection), without assuming that one actually knows the "true" phylogeny.

       

      D - ...) Else:
      spectral analyses, evolutionary parsimony, i.e., look only at patterns of substitutions, supertrees from many gene trees.

Another way to categorize methods of phylogenetic reconstruction is to ask if they are using

  • an optimality criterion (e.g.: smallest error between distance matrix and distances in tree, least number of steps), or
  • algorithmic approaches (UPGMA or neighbor joining)

5) Interpret the result.

It is especially important to consider artifacts that might originate in phylogenetic reconstruction, and to asses the reliability of your results.

 

6) Discussion: How can a tree be rooted?

Slides