andreas bender - research group gisbert schneider - goethe-university frankfurt1 analysis of...

Andreas Bender - Research Group Gisbert Schneider - Goethe-University Frankfurt 1

Analysis of mitochondrial transit peptides

of Plasmodium falciparum

Andreas Bender

Diplomarbeit

Research Group Gisbert Schneider

April 2002 - September 2002

Goethe-University, Frankfurt


Contents

• Why … ?

• Our results – in short

• Biological background

• Data coding and analysis

• Detailed results

• P. falciparum and other organisms

• Summary and outlook


Why … ?

• Why P. falciparum ?– It causes malaria– Genome sequencing recently completed– „Apicoplastic pressure“– Closely related to Toxoplasma gondii etc.


Why … ?

• Why mitochondrial transit peptides?– Recent related work for apicoplast exists– Major compartment– Failure of established tools


Our results – in short

• Artificial neural networks results:– Mathews coefficient cc = 0.74 (test set),

corresponding to ~90% correct predictions– 381 to 1177 mTPs found in 5334 annotated

genes (7% to 22%) of Plasmodium falciparum


Biological background

Female Anopheles



Courtesy of Mark F. Wiser,

Tulane University


Biological background - Targeting

Courtesy of the Division of Biological Sciences, University of Montana



• Mitochondrial targeting signals – Characteristics– N-terminal, internal, C-terminal– Matrix-targeting or IMS-targeting (bipartite)– No sequence conservation– On average 20-30 amino acids– Net positive charge, forms α-Helix– Distinct cleavage site (Arg at -2 or -3,…)


Data coding and analysis

• 3 Lengths: N-terminal 24, 31, 42 residues

• Redundance reduction

• Two representations:– Relative amino acid frequencies (20-dim.)– Physikochemical properties (19-dim.)

• SOM

• ANN

• Variable selection



• Three-layer feed-forward perceptrons

• Input data – N-terminal 24, 31 and 42 amino acids– Coded in relative amino acid frequency and in

physikochemical space

• All parameters varied one-at-a-time

• 10-fold cross-validation, 40 positive examples, 135 negative



0,6

0,65

0,7

0,75

0,8

0,85

24 31 42N-terminal length

Be

st M

ath

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Relative amino acid frequency

Physikochemical properties



• Two ANNs– Best cc: 1177 of 5334 annotated genes have

mTPs (~22%)– High penalty for overpredictions: 381 of 5334

annotated genes have mTPs (~7%)– Arabidopsis thaliana: 8% mTPs– Saccharomyces cerevisiae: 11% mTPs



Matthews cc

Sensitivity Selectivity

MitoProtII 0.49 0.80 0.47

TargetP 0.60 0.55 0.81

PlasMit 0.74 0.94 0.68


P. falciparum and other organisms

0

0,5

1

1,5

2

2,5

3

3,5

G A V L I M F W P S T C Y N Q D E K R HAminosäure (1-Buchstaben-Code)

Rel

ativ

e am

ino

ac

id f

req

uen

cy in

P.

falc

ipa

rum


P. falciparum and other organisms

• 25% G+C-Content in coding regions (sample of chromsome 2 and 3)

• In good agreement with work of Lobry for 50 bacterial genomes


Summary

• Failure of established tools for mTP pred.

• There are general differences in AA usage between P. falciparum and other eukaryotes

• Low G+C-Content of coding regions

• New tool PlasMit outperforms existing algorithms


Outlook

• Question: Why are there so many positive predictions in P. falciparum ?

• Using PlasMit for assembling putative metabolic pathways in the mitochondria will now be possible

• Final goal: Full map of P. falciparum´s metabolism


Thank you!

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