Bioinformatics and Evolutionary Genomics

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Bioinformatics and Evolutionary Genomics
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Request

• We have a small group
• and also heterogeneous with respect to previous
  knowledge
• PLEASE interrupt / ask questions when I am going
  to fast, when I use jargon, when I make
  jumps/conclusions that to me seem obvious 100
  logical, but to your are erratic please point
  out my implicit assumptions regarding what
  everybody knows

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Lectures and computer exercises

• Homology, trees,
• Genomic context , genome evolution, pathway
  evolution
• HTP data
• Eukaryotic Genome Evolution, tree of life.
• Exercises basic abilities, plus impression of
  what is possible / how type of research is done
  (albeit on a larger scale)

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Literature Discussion

• Each (set of) articles will be introduced
  (presentation) by a 1 / 2 persons, presentation
  should last approximately half an hour, followed
  by a discussion
• What to discuss
• What are the articles actually saying? What have
  authors done? (so that everybody knows)
• What does this mean in a larger context? (e.g. a
  discussion of the discussion)

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Homology and Domains
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Gene / protein sequence evolution what is
homology

• Definition homology (biology)
• structures are said to be homologous if they are
  alike because of shared ancestry.
• Classic arms bird wings bat wings,
• Genes/proteins/stretches of dna sequence
  similarity because derived from the same
  ancestral sequence
• Instead of analogous with sequences we have
  convergence, but thought to be limited to
  specific cases (e.g. coiled-coil, regulatory
  motifs) but with function we have analogy e.g.
  analogous enzymes

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Why are we interested in homology

• Function prediction ? Homologous proteins tend to
  have similar functions
• Evolutionary dynamics ? Tracing the evolution of
  genes (duplication, gene trees, origin of new
  gene families)

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How do we detect homology

• Similarity of
• 3D structure ? most conserved aspect, yet not
  all structures are available. Structures are
  compared and classified by eye and software
  packages (Dali). (NB classical homology)
  criterion shared idiosyncratic features that
  are not strictly necessary for function
  sequence features
• Sequence ? less conserved, many sequences are
  however available. Homology determination is
  mainly based on models of sequence evolution and
  the likelihood that when you compare a sequence
  to a database you will find a sequence of at
  least that similarity.
• NB Manually curated databases of 3D structure
  similarity are used as a benchmark for detection
  of homology by sequence similarity (SCOP,
  Blundels Bus).

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Gene / protein evolution beyond blast, distant
homology

• Not obvious by blast
• Substantial divergence, due to time and/or speed
• Use profile (HMMer or PSI-BLAST),
• In general work better because

ECGHR ECGHR C G TCQQL SIGNL
ECNHN ECNHN
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Gene / protein evolution beyond blast, distant
homology

• PSI-BLAST a multiple sequence alignment is
  generated on the fly to detect which
  residues/positions characterize the family.
• OR use CDD, PFAM or SMART
• Experts have collected representative and
  divergent members of a gene family and use HMMer
  or RPS-BLAST to see if your query sequence
  belongs to this gene family (i.e. is homologous
  to the members)
• clearer/cleaner than psi-blast or blast.

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How to detect very distant homology /
superfamilies

• When two protein families are homologous but the
  homology is not obvious they are part of the same
  so called superfamily
• How to detect
• In depth PSI-BLAST
• Reciprocal
• Use of right seed
• hopping (homology is by definition transitive)

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Gene / protein evolution Distant homology

• alignment-vs-alignment, Profile-vs-profile, HMM
  vs HMM comparison (whereas HHMer, PSI-BLAST
  compare a profile to a single sequence)
• Unfortunately statistic are still poor
• works because

ACRNG ACRNG ACGNR ACGNR C C TCQQL TCQQL
TFQQI TCILL
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Gene / protein evolution Distant homology

• 3D structure comparison/alignment plus visual
  inspection of multiple sequence alignment by
  Alexey Murzin
• The results of this are stored in the SCOP
  database
• (Blundels bus)

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Structural alignment

• Secondary structure elements
• Alpha-helices
• Beta strands (beta sheets)
• Loops
• Fold vs superfamily?

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An example of distant homology

• E.g. superfamily P-loop containing nucleoside
  triphosphate hydrolase
• In humans AAA 130, ABC_tran 182, SMC_N 29
• Zot UPF0079 TraG SMC_N SKI Sigma54_activat
  Rep_fac_C Rad17 NACHT Mg_chelatase MCM
  KTI12 IstB GSPII_E DUF853 DNA_pol3_delta
  Bac_DnaA APS_kinase ABC_tran AAA_PrkA AAA_5
  AAA_3 AAA_2 AAA

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Apart from sequence and structural features
conservation of basic molecular function
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Distant HomologyApplications to function
prediction

• Bacterial protein of unknown function (DUF853)
• Member of the P-loop containing nucleoside
  triphosphate hydrolase superfamily
• Thus thought to be an ATPase

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Relevance of homology for function prediction
Similar function What is function ?

• Various levels of description
• Sequence similarity, Homology has the largest
  relevance for Molecular Function. This is aspect
  of protein function that is best conserved,
  protein sequence, structure can often be
  interpreted in terms of function.

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Using distant homology for function prediction
example from (just) before PSI-BLAST HMMer

• Secreted Fringe-like Signaling Molecules May Be
  Glycosyltransferases. 
• Cell. 1997 Jan 1088(1)9-11.
• Y. Yuan, J. Schultz, M. Mlodzik, P. Bork

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Distant Homology Application to evolution

• Invention vs (duplication and) divergence
• First determine homology before putting sequences
  in multiple sequence alignment tree building
  software
• Two (or more) Proteins families that are present
  in all three kingdoms of life and which can be
  determined to be homologous to each other
  Information from before the Last Universal Common
  Ancestor, information about very early evolution

b
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Protein domains structural definition separate
in structure

• a structural domain ("domain") is an element of
  overall structure that is self-stabilizing and
  often folds independently of the rest of the
  protein chain

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Protein domains sequence/evolutionary
definition Separate in evolution

• Homologous parts of proteins that occur with
  different partners
• Mobile
• Modules
• Almost always same as structural definition

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Implications of domains for homology

• The shared ancestry is not a property of the
  whole gene but only of part of the gene.
• When studying the evolution of gene families,
  consider fusions / domain combinations (also when
  making trees etc.)

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Domain repeats. Homology?

• Blast homology vs the real homology unit
• Q8TKV1 (Methanosarcina acetivorans)
• ?

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Q8TKV1
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Ramifications for function prediction
understanding of cellular processes one domain
one (molecular) function (in contrast to one
gene one function)

• This bit does this and that bit does that
• E.g.
• multidomain enzymes
• Transcriptional regulators

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Example multidomain enzyme TrpG E.coli
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Ramifications for function prediction when doing
blast mind the domains

• Protein B is wrongly annotated as having the
  function of domain 1, based on homology with the
  multidomain protein A, but not with domain 1
• (multi-domain architecture problem for annotating
  proteins via blast)

1 2
A
B
B
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Ramifications for function prediction when doing
blast mind the domains

• Protein B is incompletely annotated as having the
  function of domain 2, based on homology with the
  single domain protein A, the second domain is
  missed in the annotation

2
1
A
B
B
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Ramifications for function predictionwhen doing
blast do psi-blast, cdd / pfam instead.

• Rather than discover the domain structure by
  blast yourself, use e.g. SMART / PFAM / CDD to do
  it for you
• NB CDD

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Domains and distant homologies

• Promiscuous domains (i.e. that are present in
  many proteins), are often quite diverged and
  thus need sensitive homology detection tools in
  order to be recognized..
• Moreover it is often only the most general
  functional property of the domain that is
  conserved over such long evolutionary distances
• Over long evolutionary distances genes are often
  only homologous in the sense that they share a
  domain, rather than being full length homologous
• We THUS use PFAM/SMART etc. for
• The domains
• And to improve upon BLAST / be cleaner than
  PSI-BLAST
• And because most of the sequences are covered by
  these database. No need to reinvent the wheel.
  The ones that are not, are often non globular,
  recent inventions, or very fast evolving

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Disclaimer non-globular regions

• Low complexity
• Unstructured, Elongated (as opposed to globular)
• Many polar/charged residues few hydrophobic
  residues
• parts of proteins that do not posses a clear 3D
  structure
• Convergence
• Do not obey PAM or BLOSUM

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Disclaimer Coiled coil

• All alpha thought to arise independently
  (convergence)
• Hypothesis reservoir for new folds all alpha
  folds (Koonin EV)
• E.g. ras / rho / rab / ran / -GAPs

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Disclaimer Other protein motifs

• Signal peptides
• Lipid anchoring
• Convergence yet still important to predict
• Trans-membrane?

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Interesting result on protein evolution regarding
domains and duplications neutral?
Black observed Blue model of recombination
duplication separate Red also duplication of
combinations
b