Download The RNA World

The
RNA
World
E. Westhof
http://www-ibmc.u-strasbg.fr/upr9002/westhof/
Stabilization of
Fossils of
the hydrosphere
stromatolites
Decrease in the
Organic matter
Earth
Number of
From living organisms
Formation
Meteorite impacts
4.5
4.2
4.0
3.8
RNA WOLRD
3.6
3.4
(x 109 ans)
Global overview of all life
RNA World
The RNA World
• Origin of life / central dogma
paradox
• DNA needs proteins to replicate
• Proteins coded for by DNA
• RNA can be code and machinery
• Selex, aptamers
• RNAs are remnants
• Ancient and Essential
RNA, Parts
O
O
H
H
N
O
Bases
N
N
O
N
OH
OH
O
O
O
O
O
O
P
O
5’
Sugar (ribose)
O
-
O
Phosphate
P
O
-
3’
DNA = modified RNA
O
-O
P
O
O
O-
P
O
H
OH
H
H
OH
OH
Thioredoxine
(-SH)2
NADP+
NADPH
+ H+
O-
RNA
O
O
P
Ribonucleoside
triphosphates
Ribonucleoside
diphosphate
réductase
Thioredoxine
-(S-S-)
-O
Base
O
O
P
O
Base
O
H
OH
OH
H
H
H
Deoxyribonucleoside
triphosphates
DNA
O3'
O
P
O
O3'
O
P
P
O5'
O
O3'
O
O5'
O
O5'
Nucleic acids are negatively charged
biopolymers ...
5!’
ADENINE (A)
O
O
P
O
O
O
O
P
THYMINE (T)
OH
O
O
(Uracil)
O
O
O
P
GUANINE (G)
OH
O
O
O
O
OH
O
O
P
O
CYTOSINE (C)
O
O
RNA
O
O
P
O
O
OH
3!’
Conformations of RNA
•Primary structure of RNA similar to DNA
•RNA, like DNA, can be single or double stranded, linear
or circular.
•Unlike DNA, RNA can exhibit different foldings
•Different folds permit the RNAs to carry out specific
functions in the cell
H
H
H
N
N
C
Charge
delocalization
C
H
N
N
imine
énamine
H
H
O
O
C
C
N
lactame (forme céto)
N
H
H
lactime (forme énol)
N
+
N
C
C
H
Tautomeric
forms
H
N
N
O
C
H
N
O
H
+
N
C
Cytidine
H
H
N
H
H
H
Uridine
H
H
N
O
S
O
O
pKa = 9,2
3
H
N
O
H
N
S
H
H
N
N
N
N
H
H
H
N
N
H
O
N
N
O
O
H
pKa = 2,1
H
H
H N
H+
H N
N
1
6
S
N
N
pKa = 9,2
N
H
H
N
N
H+
H N
N
N
H
H
H
H+
S
N
7
N
+
N
N
S
Guanosine
H
N
pKa = 3,5
1
H
H+
H
N
S
H
Protonation
possibilities
H
+
N
H+
H
N
S
H
O
Adénosine
H
N
+
N
N
pKa = 4,2
3
O
H
N
S
S
H
Guanine
H
Always
N
H
O
O
1
N
N
6
N
H
H
N
H
N
N
N
H
H
S
S
Adénine
H
H
H
N
N
seen
Never
seen
N
N
N
N
6
1
H
N
N
H
H
N
N
N
N
S
S
Uracile
H
H
N
H
H
H
4
3
O
O
O
N
N
ou
2
O
H
N
O
H
N
O
H
N
H
S
S
S
Cytosine
H
H
H
N
3
4
H
N
N
H
H
N
H
H
N
N
ou
2
O
N
H
O
N
H
O
N
H
S
S
S
H
H
H
O
N
H3C
N
Modified bases
have different
…
CH3
N
H
N
N
H
H
H
N
N
N
N
N
H
S
S
1-méthyladénine
7-méthylguanine
O
CH3
N
H
N
H
H
H3C
N
N
H
N
O
H
N
N
CH3
N
O
O
S
…
electronic
properties
N
H
N
2,2,7-triméthylguanine
H
H
H
N
N
N
H
N
H
H
8-oxoadénine
H
N
8-oxoguanine
H
N
O
H
N
O
N
H
N
H
H
H
O
N
N
N
H
Fapy-adénine
H
H
H
N
H
N
N
H
Fapy-guanine
H
H-bond characteristics
N
N
H
H
N
H
N
O
O
H
1,8 - 2 Å
d-
d+
d-
N
H
N
donneur
accepteur
N
C
2,8 - 3 Å
H
N
Horizontal
Interactions
Base pairing.
In helices
Complementary
Watson-Crick
C
H
4
3N
O6
H
N1
N
G
N
N
O
2
H N
2
H
H
O
4
U
N
3N
H
H
N6
N1
N
N
A
N
N
O
H3C
H
O
4
T
3N
N
H
H
N6
N
1
N
A
N
N
O
55 °
55 °
10.5 Å
Vertical interactions : stacking
H
O
N
N
N
O
H
H
N
N
N
O
O
N
N
H
N
N
H
N
N
N
N H
H
H
H
H
N
N
O
O
H
H
O
N
O
N
N
O
N
O
N
N
N
H N
N
O
N
H
H
H
Stacking forces
• Driving Force : hydrophobic effect.
• Not very specific
•Partition in
very polar regions (phosphates) &
less polar ones (exocyclic groups of bases)
History of the many roles of
RNA
Central dogma
The flow of genetic information
transcription
DNA
translation
RNA
Protein
DNA notoriety
Short history of RNA
• Late 1800’s - 2nd kind of nucleic acid not in
the nucleus (rRNA)
• 1920’s - sugar for DNA vs RNA
• 1958 - tRNA (Hoagland)
Relative Amount of
• 1960’s - mRNA
RNA in E. coli
rRNA 80%
tRNA 15%
mRNA 5%
RNA
•“Three” different types of RNA
•mRNA - messenger RNA,
specifies order of amino acids
during protein synthesis
•tRNA - transfer RNA, during
translation mRNA information is
interpreted by tRNA
•rRNA – ribosomal RNA,
combined with proteins aids
tRNA in translation
Ribosomal RNA (rRNA)
Phylogeny of Life using SSU rRNA
Discovery of catalytic RNA
•
•
•
•
Early 1980’s :
Tom Cech & Sidney Altman
Self-splicing group I introns and
Ribonuclease P
360
P9.2
P9.1
P9.1a
370
380
AG
G C G U A U G UU U A A U C A A G G G U C GC C G
G U CA C A A
A
C 350
• • • •
A • • • • • • • • • • • • • • • • • • • • • •
G
G
U
A
U
A
U
G
A
U
U
A
G
U
U
U
C
U
A
G
CG
G
A
G
U
G
P13''
A
AU GA
AU
U
390
400
340
P9b
330
P9a
U
A G G G AG U G G A
G
A
A UC C UC
UC C
C
U
320
A
G AC A
G C
3´ g
5´ U
P5a G C
C G
U
a
U 130
U A
u
A
200
A U
G C
g
C
120
G C
G U
P10 C
g
190 U A
P5 U G
a
U
U
C G
C G
20 U
a 410 A
G
C G
u
G
U
A U
U
C
A
A
G u
A
U
U A P9.0
A
G c
A
A
GC G
A
P1 A u
A
C G
G c
U A
C G
G u
210 A
G C
G c
260
G C
180
110
G
C
C
G
P5c
A
U
P4 G C
CA
C G
A A AG G G U A
C G
U
310 U
A
170 C
A
A U
G C P7
G U C CG G
A 140
A U
U
U G
P14''
A U A
A U
U
P6 G U
U
A
160 G C
C G
A
A 270
C
A
A U
A
A U
A
P5b G C
C
A
C
G
A
U A
G
U
U
G
220
U G
G U
100 G C
A
U G
U A
C G P3
A
C G
P6a C G
C G
G 150
C G 250
A
A U
A A
U
U
G C
A
A
A
300 U
A G
G U
C G 280
U A
U G
C G
C G P8
230 A U
U A
A U
U A
P6b C G
C G
A U
U A
G C 240
U
U
290 A UG
U
A
U CU
A
P13'
A A
80
90
40
30
A A
AC
A
C
CGU
G G A C UA U UG A
C G GA A A U U U G G U A
U
• • • • • • • • • •
• • • • • • • • • • •
U
G
C
C
U
G
G
U
A
G
C
U
A
G U C UU U A A A C C A AU
P14'
CA
AGA
50
70
60
P2
P2.1
P13
P8
P14
P2
Group I self-splicing introns
Core structure
9
5
5'
3'
P10
P5
P9.0
G
P1
C
P4
G
5'
P7
7
P6
P3
3
P8
2
6
8
Catalytic
Catalytic Core
Core of
of Group
Group II
introns
introns
Réaction de
Transesterification
transestérification
Ribozyme
N
P
O
HO
N
G
O
O
O
O
O
N
OH
N
O
P
O
O
O
O
P
3'
OH
O
OH
O
U
O
O
P
OH
O
O
O
U
O
Exon 5'
H N
H
O
H
O
O
5'
!
Second discovery of RNA
• ncRNAs - functional RNA molecules rather than
proteins; RNA other than mRNA (ex.XIST)
• RNAi - RNA interference
• siRNA- active molecules in RNA interference; degrades
mRNA (act where they originate)
• miRNAs - tiny 21–24-nucleotide RNAs; probably
acting as translational regulators of protein-coding mRNAs
(regulate elsewhere)
Other Roles of RNA
• stRNA - Small temporal RNA; (ex. lin-4 and let-7 in
Caenorhabditis elegans : development
• snRNA - Small nuclear RNA; includes spliceosomal RNAs
• snoRNA - Small nucleolar RNA; most known snoRNAs are
involved in rRNA modification
• RNA world - RNA as catalyst
Central dogma
The flow of genetic information
transcription
DNA
translation
RNA
X
Protein
ncRNA genes
• Genomic dark matter
• Ignored by gene prediction methods
• Not in EnsEMBL
• Computational complexity
• ~10% of human gene count?
RNA interference
Intricate maturation pathways
Implicated
in
chromatine
remodelling
Cleavage part of DICER
Measuring device for 21 nt
ONE Role of RNA in cells
1 Transcription
DNA
tRNA
DNA
mRNA
RNA
polymerase
RNAr
1
anticodon
protein
RNA
Polypeptide
chain
nucleotides
2
Proteins
Amino
acids
2 Translation
mRNA
codon
ribosome
Versatility of RNA functions
• Not only messenger RNAs (alternative
splicing)
• Number & variety of non-coding RNAs :
ribosomal RNAs, snRNAs, snoRNAs,and
numerous regulator RNAs..
• Cofactor RNAs : telomerase,
• …… to be discovered
Properties of RNA molecules
Assemble in double-starnded helices like DNA
Carry GENETIC INFORMATION like DNA
Fold in complex tertiary architectures like proteins
Perform CHEMICAL CATALYSIS like proteins
Catalytic RNAs
• Ribonuclease P
• Self-splicing introns
• Hepatitis delta virus
• The ribosome and peptide bond
formation
• The spliceosome (not fully proven yet)
• and ...
Great diversity of RNA functions
and architectures
Genome
Transfer
RNA
Ribozyme
2D
Different
levels of
organization
possibly
hierarchically
structured.
3D
The bacterial ribosome :
270 000 atoms (C,N, O, P)
55 proteins
3 RNA (4600 nucleotides)
Ribosome active site
30S
50S
Nissen et al. (2000) Science, 289
H. F. Noller, T. A. Steitz, P. B. Moore, A.Yonath, V.
Ramakrishnan
Luc Jaeger ©
Only
RNA
in
the
reaction
site
Comparisons of
3D structures
Comparisons of
sequences
((((
(((
GCUG UUAGG GGA GUUUUA
GCCG UUAGG GGA GUUUCA
GUUG UAGG GGA GUCUCA
GCUG GAGG GAA GC AA
ACUU CAGU GGA GC AA
ACUU CAGU GGA GC AA
GAUG GAGG UUG G AAA
GGGC CAGG GGU G AAA
GGCC UAGG UCG G AAA
GGCC CAGG UCG G AAA
GGCC CAGG UCG G AAA
GGCC CAGG UCG G AAA
GGCC CAGG UCG G AAA
)))
UCC
UCC
UCC
UUC
UCC
UCC
CAA
ACC
CGG
CGG
CGG
CGG
CGG
)))-)
AGCGU CAG-C
AGCGA UGG-C
AGCA CAA-C
AGCA CAG-C
AGCA GAGAU
AGCA GAGAU
UGCA CAU-C
AGCA GCC-A
AGCA GGU-C
AGCA GGU-C
AGCA GGU-C
AGCA GGU-C
AGCA GGU-C
Biological sequence analysis
Protein easy
RNA hard
Watson-Crick base paired helices
Internal loops (symmetric,
Asymmetric, bulge)
Hairpin loops
Single-strands junctions
2D
RNA alignments
• RNA sequences are aligned/compared differently
because sequence variation in RNA maintain
base-pairing patterns
• Thus an alignment will
exhibit covariation at
interacting basepairs
• RNA specifying genes
will have conserved
regions reflecting
common ancestry
Main building block :
the RNA double helix
held together by
Watson-Crick pairs