A new model argues against Just in time synthesis in M phase

Bjørn Sponberg

Supervisor: Erik L. L. Sonnhammer

Department of Biochemistry and Biophysics

The eukaryotic cell cycle

Just in time synthesis

In all phases!

Classic thinking!

Current view: Just in time synthesis

Problem with transcription in M phase!

Regulatory level 1: DNA level Regulatory level 2. Nucleosome levelRegulatory level 3. 3D level

Hypothesis : Extreme evolutionary pressure on cell cycle speed.

Conclusion: the first unicellular eukaryotic cells were forced to find the fastest division mechanism that was available to them.

P-body vesicles can store and release transcripts.

P-bodies can increase cell cycle speed

Move transcription from M phase to G1 phase

The new model call them: P-body transcripts

To regulate their unique expression route, P-body transcripts should have unique sequence features.

DETECT DIFFERENCES WITH: SVM & BLAST

5’UTR 3’UTRCDS

INTRON

P-Body transcripts

Normal transcripts

METHODS”The wheel”

”The wheel”

M G2M

360°, 0°

22.5°

135°90°

180°

225°270°

315°

G1S

SCORE

67.5°45°

TOOLS:•Support Vector Machine (SVM)Red vs Blue Kmer lengths 7 nucleotidesData classification based on sequence features (kmer’s) in the red and blue datasets.Value: Matthews correlation coefficient (MCC)•BLAST Red Wordsize 7Sequence alignments of all combinations in the red dataset.Value: ScoreBit (sequence similarity score)

460 GENES DOWNLOADED

SVMBLAST

Two plots:SVM: CMassification score (MCC accuracy)BLAST: Sequence similarity score (ScoreBit)

360°

16 positions (22.5°*16 = 360°)

45°

Expected plot

45°90°

135°180°

0° 360°

225°

SVM

BLAST

M G2 0°180°

G1S

Wheel position °

Score

P-body transcripts

Normal transcripts

G2M M

G1S

SVMBLAST

Results

0°

45°135°

225° 315°

67.5°

M

G1S

G2M

SVMBLAST

45°

As hypothesized

M G2M

0°

45°135°90°

180°

225°270°

315°

G1S

SVMBLAST

HOMOLOGY!

M G2M

0°

45°135°90°

180°

225°270°

315°

G1S

•Minor splicesome system!• Active in M phase!• Maybe it is part of the P-body genes?

SVMBLAST

As hypothesized

SURPRISE!

M G2M

0°

45°135°90°

180°

225°270°

315°

G1S

SVMBLAST

So far: 5’UTR and intron have

Not as hypothesized!

Not as hypothesized!

1) 5.73 longer average length in 3’UTR 2) Affects homology/regulatory signal

M G2M

G1S 67.5 °

0 ° HOMOLOGY

REGULATORY

As hypothesized!

As hypothesized!

As hypothesized!Homology!

Summary

As hypothesized(P-body transccripts)

Not as hypothesized (Homology)

As hypothesized(P-body transccripts)

As hypothesized(P-body transccripts)

UTRscan Searching for 46 annotated 3’UTR and 5’UTR regulators

0°180°

G2M M

G1S

SVMBLAST

UTRscan

BOTH REGULATORS ARE INVOLVED IN TEMPORAL TRANSLATION CONTROL!

CONCLUSION

• We have found the possible existence of the hypothesized P-body genes and their localization - as predicted in the new model.

• If so, the P-body transcripts are probably temporally regulated via three gene regions; three prime untranslated region (3'UTR), five prime untranslated region (5'UTR) and introns.

• Musashi binding element (MBE) and Upstream Open Reading Frame (uORF) are potential regulatory candidates in the P-body transcripts 3’UTR and 5’UTR.

References• http://

www.sparknotes.com/biology/cellreproduction/cellcycle/section2.rhtml• de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation

during the yeast cell cycle. Science. 2005 Feb 4;307(5710):724-7.• Rokas A. The origins of multicellularity and the early history of the genetic

toolkit for animal development. Annu Rev Genet. 2008;42:235-51.• Parker R, Sheth U. P bodies and the control of mRNA translation and

degradation. Mol Cell. 2007 Mar 9;25(5):635-46.• David P. Mindell Axel Meyer. Homology evolving Volume 16, Issue 8, 1

August 2001, Pages 434–440.• Charlesworth A, Wilczynska A, Thampi P, Cox LL, MacNicol AM. Musashi

regulates the temporal order of mRNA translation during Xenopus oocyte maturation. EMBO J. 2006 Jun 21;25(12):2792-801.

Acknowledgement

Supervisor: Erik L. L. Sonnhammer