rna protein interaction - tbi

Introduction RNA binding in detail structural analysis Examples

RNA Protein Interaction

Axel Wintsche

February 16, 2009

Axel Wintsche



Table of Contents

1 Introduction

2 RNA binding in detail

3 structural analysis of local contexts of consensus sequences

4 Examples

Axel Wintsche



Introduction

RNA is more than an intermediate step in protein expression

not every RNA is translated (ncRNAs)

RNA can be linked with regulatory processes in cell

UTRs of some mRNAs have conserved regions

carry information important for fitness

Axel Wintsche



Introduction

one way to participate in regulatory mechanisms is to bind toa protein

can induce conformational changes and results in newfunctionality

RNA-protein binding leads to direct regulation of the RNA(translational repression of mRNA)

⇒ understanding of RNA-protein binding is important tounderstand many regulatory processes

prediction of RNA-protein interaction is hard to compute

Axel Wintsche



Introduction

How recognise proteins their RNA targets?

Is RNA sequence and/or RNA structure important for specificbinding?

Axel Wintsche



Two Examples of RNA binding protein domains

RRM: RNA Recognition Motif

The information of structure, RNA binding and pictures are takenfrom [4] and [1]

KH: K Homology Domain

The information of structure, RNA binding and pictures are takenfrom [5] and [2]

Axel Wintsche



RNA Recognition Motif

RRM can be found in all eukaryotic organisms

one of the most widely spread domains in eukaryots(H. sapiens has at least 497 proteins)

often more than one RRM per protein

identified in the 80s while investigating mRNA precursors

RRM is part of many different functions in cell

Axel Wintsche




RRM has a length of about90 AA

it folds into an αβ sandwich(β1α1β2β3α2β4)

spacially arranged in onefour-stranded antiparallelβ-sheet (β4β1β3β2)

Axel Wintsche




RNA binds mainly to theβ-sheet

5’ end is located on β4β1,3’ end on β3β2

sequence specifity bysidechain interaction

β-sheet detects only adinucleotide

Axel Wintsche




additional RRMs allow recognition of longer sequences

RRM of UA1 needs secondary RNA structure to bind(stem loop or internal loop)

Axel Wintsche



K homology domain

first discovered in K-proteins (human hnRNP)

KH is a common and widespread domain

KH exists in all three kingdoms and hence arose early inevolution

most KH-proteins have more than one KH domain

Axel Wintsche



K homology domain

KH has a length of about 70 AAfold into β1α1α2β2β3α3

spacially forming a β1β3β2-sheet

binds RNA in a different manner to RRM, suggesting that thestructural convergence of RNA binding proteins has little todo with RNA recognition

Axel Wintsche



K homology domain

KH has a length of about 70 AAfold into β1α1α2β2β3α3

spacially forming a β1β3β2-sheetbinds RNA in a different manner to RRM, suggesting that thestructural convergence of RNA binding proteins has little todo with RNA recognition

Axel Wintsche



Materials and Software

Materials

Proteins and related RNA consensus sequences [3]

yeast genome from Genbank

yeast mRNA annotations from Genbank

Software

pwmatch: find sequence matches in a genome(treshold parameter 1 = exact match)

RNAfold: predict RNA secondary structure

Axel Wintsche



first simple approach

1 translate rna consenus sequence into PWM

2 search matches on genome with pwmatch

3 select matches laying in annotated mRNAs

4 cut out matches plus offset

5 fold sequences with RNAfold

Example of consensus sequnece to PWM conversion

HUCNBCAWH →

A: 1 0 0 1 0 0 1 1 1C: 1 0 1 1 1 1 0 0 1G: 0 0 0 1 1 0 0 0 0U: 1 1 0 1 1 0 0 1 1

Axel Wintsche



Example Proteins

SCP160

function: involved in the control of mitotic chromosometransmission

contains 7 KH domains

RNA consensus sequence: UUUAAUGA

PIN4

function: involved in normal G2/M phase transition of themitotic cell cycle

contains 1 RRM domain

RNA consensus sequence: KUUWAYBUN

Axel Wintsche



Examples SCP160

AGA

GGGCUAAA

AG

AA

GCU

UCAG

U GC

UU

CU

UCGGGCUGU

GAUUCC

ACUUUC

UUCC

AAAU

U U U AUG A AC

AUG

CCC

UA A A

GG

CA C C

UCG G AUU

U C U C CU U G A

UU A G A U

UA A A C A U C C G

U G UU G G A

U A GC U GG AUA G A

C C U CU G

CUGAG

AUCUUCCGAC

CGUUUGAGC

UCGUUGAUGUC

CAUCG

ACUUCUUGG

CCA

GUC

CC

G UA

AGCCC A

AU

AC

Axel Wintsche



Examples SCP160

AAAAC

GAAA

UA

AAG

AA

GA

AA

GA

UUAU

UA

UUAU U

AG

UU

A CU

UU

UU

UUA U

UG

UACUC

CA

GUAUG

GACC

UCUU

A GG

UG

AGU

GA U

CU

UA

UUA

AA

AA

AA

AU

AAAAAAAAU

AA

A A A A A U A U G A A AA

AA

AAAGAAAA

UU

AA

AA

ACUAAACAAAU U U U A UG A C

AG

GAAUAAAA A C U A U

AAAAAA

UG

AAAAGCAA

AA

AAAAAAA

GG

CU

AC

UG

GA U U U

UU

Axel Wintsche



Examples SCP160

UAUU

GGGCU

UA

CG

GGA

CU

GG

CC

AAGAAG

UCG

AUGGACAUC

AACG

AGC

U CAAA CGGUC

GGAAGAUCUCAG

C AG A G G U C UAU

C C AG C UAUCCAA

CACGG A U G U U U A A U

CU

AA

U

C

AA G

GAG

A AA

UC

CG AGG

UG

CCU U U

AGG

GC

AUGUU

CAUAAAAUU

UG

GAA

GA A

AG

UGGAAU

CACAGCCCG A

AG

AA

GC A

CU

GAAG

CU

UC

UUU

UAGCCC

UCU

U

Axel Wintsche



Examples PIN4

U GUUUGUGAUAA

AUGCAUU

CU

AAAUUUUGCGAGAG

GGAA

GUGCAAAAUGU

UAC A

A C A U U U U G CC A

U U CAAAG

ACA

UGUG

CCGC

AUG

AA

CAUG U

AG

CC

A AG

UUU A A UG

ACAU C G U A

UGC

C A AUG

GA

GG

GU

GG

AG

GC U G

UUU

UU

CCU

AU

UC

UU

AG

AA A

U

A U U U C C G UU A A

CG

AUAA

UACGGGAAUU

AA

CAUUACAAAU G A

AAU

UGAAA

CUG

Axel Wintsche



Examples PIN4

ACA

GUUA

AUAU

GC

CU

U

AA

GUU

CCAU A

CUA

AUACU

GACG

A U G U AGACAA

AGAG

CA

AU U

GA

GGA

CGAUU

AUG A C

UU CUAUAG

UA

A AA

GGACA

A G A G AU

CG

AG

UU

UAA

UGAUGA

CA A

UUUA

UCG

AG

AU UU

UA

UG

AC

GA A

GCGC

UC

AU

AA

GA A A A

GUAU

GUUUUA

AUAAU

AA

AU

UC

GAGGU

AAAAA

CU

UC

AAC

AGC

CU

CAC

CA

GAA

AC A

CA

UU

Axel Wintsche



Examples PIN4

UC G

CUUA

AA

CGAGGUUUUU

CAUAUGCAUGC

UCCA

AGAUA

GGU

ACG

A A CA

AA A A

AG

A G G C AUU G C A UCAAAA

UG

GA

UAG

UUU

CAG

UU U

AUG U

AACAA

AAUCUC

AUU A

AA A A A ACC C U C

UCCUCCUAUGA A G C G G A A

C A GU U

CA

ACUUUUCCGCUU

AG A U G U

U U U AU A

UA

AAA

UUAAAUAA

AUCA

UGGC A U G

ACCUUU

UC

UUCAUAA

AUCC

Axel Wintsche



Literature

A. Clery, M. Blatter, and F.H.T. Allain.

RNA recognition motifs: boring? Not quite.Current Opinion in Structural Biology, 18(3):290–298, 2008.

N.V. Grishin.

KH domain: one motif, two folds.Nucleic Acids Research, 29(3):638–643, 2001.

D.J. Hogan, D.P. Riordan, A.P. Gerber, D. Herschlag, and P.O. Brown.

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an ExtensiveRegulatory System.PLoS Biol, 6(10):e255, 2008.

C. Maris, C. Dominguez, and F.H.T. Allain.

The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional geneexpression.FEBS Journal, 272(9):2118–2131, 2005.

J.M. Perez-Canadillas and G. Varani.

Recent advances in RNA–protein recognition.Current Opinion in Structural Biology, 11(1):53–58, 2001.

Axel Wintsche



Thank you for listening!

Axel Wintsche


rna protein interaction - tbi

Documents