Common peptides study of aminoacyl-tRNA synthetases

Assaf Gottlieb, Milana Frenkel-Morgenstern,Mark Safro, David Horn, Plos One, 2011

* Figure from Prous science

Aminoacyl-tRNA synthetases (aaRSs)

Rosetta stone

aaRS classes• Divided into two classes (I & II),

characterized by different structures and distinguishing motifs

NameClass

Threonyl tRNA synthetaseII

Lysyl tRNA synthetase *II

Alanyl tRNA synthetaseII

Seryl tRNA synthetaseII

Aspartatyl tRNA synthetaseII

Glycyl tRNA synthetaseII

Prolyl tRNA synthetaseII

Phenylalanyl tRNA synthetaseII

Histidyl tRNA synthetaseII

Asparaginyl tRNA synthetaseII

NameClass

Tyrosyl tRNA synthetaseI

Tryptophanyl tRNA synthetaseI

Leucyl tRNA synthetaseI

Isoleucyl tRNA synthetaseI

Valyl tRNA synthetaseI

Methionyl tRNA synthetaseI

Cysteinyl tRNA synthetaseI

Glutamyl tRNA synthetaseI

Glutaminyl tRNA synthetaseI

Arginyl tRNA synthetaseI

• DataData

• Method

• Results

Data

• 5,406 non-redundant aaRS protein sequences

• ~500 species

• 22 aaRSs – 20 standard– Pyrrolysine– O-phosphoseryl-tRNA synthetase (SepRS))

• Data

• MethodMethod

• Results

MEX-Motif Extraction algorithm

a l i c e w a s b e g i n n i n g t o g e t v e r y t i r e d o f s i t t i n g b y h e r s i s t e r o n t h e b a n k a n d o f h a v i n g n o t h i n g t o d o o n c e o r t w i c e

s h e h a d p e e p e d i n t o t h e b o o k h e r

s i s t e r w a s r e a d i n g b u t i t h a d n o p i c t u r e s o r c o n v e r s a t i o n s i n i t a n d w h a t i s t h e u s e o f a b o o k t h o u g h t a l i c e w i t h o u

t p i c t u r e s o r c o n v e r s a t i o n

Find patterns in strings of lettersalicewas beginning toget verytiredof sitting by hersister onthebank and of having nothing todo onceortwice shehad peep ed intothe book hersister was reading butit hadno pictures or conversation s init and what is

theuseof abook thoughtalice without pictures or conversation

Initially developed for learning text.

given a sequence of lettersgiven a sequence of letters

• = ∑ {a-z}

Creating the graph…

e

h

d

v

ab

c

g

fu

t

s

r

qp

on

ij

km l

w

xy

zbeginend

)1,1(

)1,2(

)1,3(

)1,4(

)1,5()1,6(

• alice

• was

)2,1(

)2,2(

)2,3()2,4(

structured graph

a

b

c

d

e

f

g

h

i

j

k

l

m

n

o

p

{1003;3}

{1002;1}

{1002;2}

{1003;4}

{1003;5}

{1003;6}

{1003;8}

{1003;7}

{1003;9}

{1003;10}

{1003;11}

{1003;12}

{1003;13}

{1003;14}

Creating the graph… - cont’d

MEX algorithm for proteins

Finds deterministic motifs (peptides)

Method of Common Peptides (CPs)

• Extract per-aaRS peptides to form 22 per-aaRS peptide lists

• Merge the 22 lists

• Search the merged list peptides on all aaRSs

• CP-space: 5,406 sequences x 10,612 CPs.

• Data

• Method

• ResultsResults

Inter-aaRSs similarity

Heat map of Pearson cross-correlations of different aaRSs according to their shared CPs.

* Self correlations were left out for cleaner view.

Class I

Class II

BLAST provides a complementary view

-lo

g (

E-v

alu

e)

aaRSs similarity-Eukaryotes

aaRSs similarity - Archaea

aaRSs similarity - Mitochondria

CPs & Mitochondrial aaRSs• Tested enrichment of mitochondrial CPs in

kingdom-specific CPs.

• 16 mitochondrial aaRSs enriched in Bacteria, 13 in α-proteobacteria

• 4 aaRSs enriched in Eukaryotes, none in Archaea

• Assessed which gene was retained for 5/8 aaRSs with single nuclear genes in higher eukaryotes.

Biotin-[acetyl-CoA carboxylase] synthetase (birA) and aaRSs

• Structural similarity between birA and class II aaRSs was reported, but no sequence homology.

• Extracted CPs from 1,630 birA sequences.

• 28 CPs are common (p<2e-5)

birA and aaRSs, contd.

CP(alternatives)

Structuralproperties

# of aaRSsoccurrences

# of birAoccurrences

# of class Ioccurrences

# of class IIoccurrences

GILIE (GILVEGILTE)

Biotin binding site in birA, ThrAMS binding site in ThrRS

21982113

GALRL(GALLL)

Binding site for 4AD in AspRS

132042

GEALG(GETLG)

Helix-turn-Helix in birA

422131

CPs as novel class signatures CP

# of class I aaRSs

# of class I occurrences

# of class II aaRSs

# of class II occurrences

TADEI**84711ALADE83712

KSLGN750022SKSKG729900SKGNV718200DVIAR**77300DVVAR**76012ADAIR73900

GLDLL73511GVERL*00892DLVEE*13766GLDRI*11743AEAVL12724ERISA*00724LRLAE**00638AAGVR22647

*Overlap a binding site** less than four residues apart from a binding site

Class I signatures Class II signatures

Functional role of CPs

• 29/50 prevalent CPs overlap known catalytic and binding sites (p<e-5)

• Additional 8 <4 residues from site (p<e-10)

• Most hit amino acid esterification sites• Other hit tRNA or ions binding sites.

Summary

• CP methodology identifies significant deterministic motifs.

• These motifs characterize family and class specific sequences.

• CPs can find subtle evolutionary traces

• CPs overlap functional sites

Thank you