A hierarchical model for evolution of ribosomal RNA

Konstantin Bokov and Sergey Steinberg

Université de Montréal

11

SMALLSUBUNIT

LARGESUBUNIT

The ribosome is a universal machine producing proteins

TRANSPORTRNA

MESSENGERRNA

- addition of new peptides to the growing protein chain (in PTC);

- correct decoding of the messenger RNA (in DR);

- precise movement along the messenger RNA;

- coordination of the work of all co-factors and ligands;

GROWINGPROTEIN

PTC

DR

225’

P A

The evolution of Life on Earth directly depends on the emergence of the ribosome !

33

Protein World

The ribosome and LUCA

LastUniversalCommonAncestor

Bacteria Archaea Eukarya

44

Functionality of the ribosome depends primarily on its RNA

Large subunit

RNA proteins++

Small subunit

++RNA proteins

RNA-bodyRNA-body

RNA+proteinsRNA+proteins

RNA-WORLD

Protein-WORLD

55

MODERNRIBOSOME

F

Major periods in the evolution of the ribosomal RNA

PROTORIBOSOME

Unlimited reshuffling of RNA chains

F FRestricted step-wise increase of the ribosome size

66

insertion gene sequence

5’ 3’ 5’3’

Preserve functional structure !

77

Accommodation of an insertion

Broken Unstable Stable

insertion

gene sequence

gene sequence

88

General principle of insertion:

Structural integrity of more ancient elements cannot be dependent on the presence of more recently acquired elements.

99

Integrity of each strand of a double helix depends on the presence of the other strand

1010

5’

3’5’

3’

The A-minor motif as an evolutionary determinant

A-minor motif

Nissen, P., Ippolito, J.A., Ban. N., Moore, P.B., Steitz, T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc Natl Acad Sci U S A. No 98(9), pp. 4899-4903.

1111

23S rRNA23S rRNA

In a newly emerged element:

1. The 3’- and 5’-termini must be close to each other2. For each double helix, both strands must be present3. When such element forms an A-minor interaction with the other elements of the ribosome, it must provide the adenosine stack and not the double helix

1212

Dismantling the ribosomal RNA: removal of those elements that are qualified as the most recent acquisitions of the ribosomal structure

1313

MODERNRIBOSOME PROTO-

RIBOSOME

core

Last acquisitions 2-nd last acquisitions

Dismantling the structure of the 23S rRNA

1414

Inter-domain A-minor interactions

double helix

stack of adenosines1515

A-minA-min

Dismantling the structure of the 23S rRNA

1616

The symmetrical structure in Domain V is the proto-ribosome

t-RNA

1717

A-site

P-site

The network of dependencies does not contain cycles

181859 54

If the orientations of all A-minor interactions in the 23S rRNA were chosen randomly, the probability of a cycle-free arrangement would be P< 10-9.

The absence of cycles of dependency is a fundamental characteristic of the 23S rRNA, which is directly related to the particular trajectory of its emergence.1919

Growing support for PTC

2020

Appearance of the protuberances and of the small subunit

2222

What about 16S rRNA?

2121

LSUSSU

The hypothetical structure of the primordial ribosome and two tRNAs

2525

Small world...

2626

Acknowledgment

We appreciate the help ofNSERC and CIHR for financing this project.

presentationpresentation

Non-covalent dependency

Double helix is older than stack of A-s packing in its minor groove

H71

H68

H69

A-stack (in red)

H92

H93

H95

A-stack (in red) A-stack (in red)

H74

H69

H71

H93

H92H68

H95H74

E-coli, 23S E-coli, 23S E-coli, 23S

Chain of A-minor interactions

AA

Pseudoknot

The loop of a stem-loop structure (A) forms a double-helix (B) with a region outside this stem-loop

A

B

C

for example with another stem-loop (C)BB

Pseudoknots in the 23S rRNA

CC

- local- non-local

Long-distance pseudoknots in the 23S rRNA

DD

40 40

33

The approach is applicable

H2

(G-C) H25

(G-U)

Along-groove packing” motif as a mean of structural fitting

H2 minor groove

H25 minor groove

G17-C523

G539-U554

Along-groove packing motif

E-coli, 23S

FF

Along-groove packing motif

GG

AGPM-s in 23S rRNA

HH

What about evolutionary deletions ?

A

C=A-D

evolution

B

LL

X

?

Accommodation must not provoke structure weakening

MM

Notion of dependency

C

A

B

Additional

E-coli, 23S

A

B

C

Covalent dependency

The new RNA insertion covalently depends on the structure where it emerged

Core

Core

Non-covalent dependency (A-min)

D

E

E-coli, 23SB

A

yellowA-stacks

A

B

C

D

E

C

The element containing stack of adenosines is non-covalently dependent on its complimentary WC helix

In PCKWC helices

A A

NN

Domain-V is the most ancient part of the ribosome

PP

16S mitochondrial versus prokaryotes

Only prokaryotes

Mito and prokaryotesRR

23S mitochondrial versus prokaryotes

Only prokaryotesMito and prokaryotesSS

Dismantling versus evolution

TT

MODERNRIBOSOME PROTO-

RIBOSOME

PROTO-RIBOSOME

MODERNRIBOSOME

19 54 26 26 11 11 25 47

36 27 45 57 40 51 20 40

AGPMs in the ribosome of E.coli

The evolution of Life on Earth directly depends on the emergence of the ribosome !

22

Protein World