Download RNA Tertiary Structure

RNA Tertiary Structure
Additional Motifs of Tertiary Structure
•
•
•
•
•
•
•
Coaxial helix
A minor motif
Pseudoknots
Tetraloops
Loop-loop
Ribose zipper
Kink turn motif
Coaxial helix
• Two separate helical regions
stack to form coaxial helices
as a pseudo-continuous
(quasi-continuous) helix.
• Coaxial helices are highly
stabilizing tertiary
interactions and are seen in
several large RNA structures,
including tRNA, pseudoknots,
the group I intron P4-P6
domain, and in the Hepatitis
Delta Virus ribozyme.
A-minor motif
• The A-minor motif
involves the
insertion of minor
groove edges of
adenines into the
minor groove of
neighboring helices.
• It has four subtypes
depending on the
position of the
adenine to the
interacting WatsonCrick base pair.
ype 0: The N3 of the A (or other) residue is outside the O2' of the far strand of the
receptor helix.
Type I: The O2' and N3 atoms of the A residue are inside the minor groove of the
receptor helix. The inserted base for the Type I interaction must be an adenine.
Type II: The O2' of the A residue is outside the near strand O2' of the helix and the N3
of the A residue is inside the minor groove. The inserted base for the Type II interaction
must be an adenine.
Type III: The O2' and N3 of the A (or other) residue are outside the near strand O2' of
the receptor helix.
Ribose zipper
• The ribose zipper is a
tertiary interaction
formed by
consecutive
hydrogen-bonding
between the
backbone ribose 2′hydroxyls from two
regions of the chain
interacting in an antiparallel manner.
Pseudoknot
• When bases pair between nucleotides loops
(hairpin or internal) and bases outside the
enclosing loop, they form a pseudoknot.
• This structure often contains coaxial helices.
• It can be a very stable tertiary interaction.
Loop-loop receptor
• The tetraloop-tetraloop receptor was identified
by comparative sequence analysis.
• This tertiary interaction is characterized by
specific hydrogen-bonding interactions between
a tetraloop and a 11-nucleotide internal
loop/helical region that forms the receptor.
• Other kinds of loop and receptor interactions,
such as penta-loop/receptor and hexaloop/receptor, are observed so this motif is call
loop-loop receptor.
tRNA D-loop;T-loop
• The D-loop in tRNA contains the modified
nucleotide dihydrouridine.
• It is composed of 7 to 11 bases and is closed
by a Watson Crick base pair. The TψC-loop
(generally called the T-loop) contains thymine,
a base usually found in DNA and pseudouracil
(ψ).
• The D-loop and T-loop form a tertiary
interaction in tRNA.
Kissing hairpin
• The kissing hairpin complex is a tertiary
interaction formed by base pairing between
the single-stranded residues of two hairpin
loops with complementary sequences
A new concept:
the Ribozyme - enzymic RNA
• Exactly following the definition of an enzyme, the
L-19 IVS RNA
• accelerates the reaction by a factor of
10
around 10 .
• is regenerated after each reaction
each enzyme molecule can react with many
substrate molecules.
Ribozymes - Therapeutic Applications
• Simple structure, site-specific cleavage activity
and catalytic capability, make ribozymes
effective modulators of gene expression.
• Ribozyme-mediated gene modulation can
target cancer cells, foreign genes that cause
infectious diseases as well as other target sites
(current research), and thereby alter the
cellular pathology.
5S rRNA
proteins
A-site tRNA
23S rRNA
peptidyl transfer reaction:
P-site tRNA
Ninety eight percent of the
human genome
does not code for protein. What
is its
function?
How much of human transcribed RNA
results in proteins?
• Of all RNA, transcribed in higher eukaryotes, 98% are
never translated into proteins.
• Of those 98%, about 50-70% are introns
• 4% of total RNA is made of coding RNA
• The rest originate from non-protein genes, including
rRNA, tRNA and a vast number of other non-coding
RNAs (ncRNAs)
• Even introns have been shown to contain ncRNAs, for
example snoRNAs
• It is thought that there might be order of 10,000
different ncRNAs in mammalian genome
RNA functions
• Storage/transfer of genetic information
• Structural
• Catalytic
• Regulatory
22
RNA functions
Storage/transfer of genetic information
• Genomes
• many viruses have RNA genomes
single-stranded (ssRNA)
e.g., retroviruses (HIV)
double-stranded (dsRNA)
• Transfer of genetic information
• mRNA = "coding RNA" - encodes proteins
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
23
RNA functions
Structural
• e.g., rRNA, which is major structural component of
ribosomes
BUT - its role is not just structural, also:
Catalytic
RNA in ribosome has peptidyltransferase activity
• Enzymatic activity responsible for peptide bond formation
between amino acids in growing peptide chain
• Also, many small RNAs are enzymes
"ribozymes”
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
24
RNA functions
Regulatory
Recently discovered important new roles for RNAs
In normal cells:
• in "defense" - esp. in plants
• in normal development
e.g., siRNAs, miRNA
As tools:
• for gene therapy or to modify gene expression
• RNA aptamers
25
RNA types & functions
Types of RNAs
Primary Function(s)
mRNA - messenger
translation (protein synthesis)
regulatory
rRNA - ribosomal
translation (protein synthesis)
t-RNA - transfer
translation (protein synthesis)
<catalytic>
hnRNA - heterogeneous nuclear precursors & intermediates of mature
mRNAs & other RNAs
scRNA - small cytoplasmic
signal recognition particle (SRP)
tRNA processing
<catalytic>
snRNA - small nuclear
snoRNA - small nucleolar
mRNA processing, poly A addition <catalytic>
rRNA processing/maturation/methylation
regulatory RNAs (siRNA,
miRNA, etc.)
regulation of transcription and translation,
other??
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
26
RNA
ncRNA(non-coding RNA)
mRNA
rRNA
Ribosomal
RNA
Participate in
protein synthesis
tRNA
Transfer RNA
Interface
between
mRNA &
amino acids
Transcribed RNA with a structural,
functional or catalytic role
snRNA
Small
nuclear RNA
-Incl. RNA that
form part of
the
spliceosome
snoRNA
Small
nucleolar RNA
Found in
nucleolus,
involved in
modification
of rRNA
stRNA
Small temporal RNA.
RNA with a role in
Developmental timing.
miRNA
Micro RNA
Small RNA
involved
regulation of
expression
Others
Including large
RNA
with roles in
chromotin
structure and
imprinting
siRNA
Small interfering
RNA
Active molecules in
RNA interference
Small Nuclear RNAs
• One important subcategory of small regulatory RNAs
consists of the molecules know n as small nuclear RNAs
(snRNAs).
• These molecules play a critical role in gene regulation
by w ay of RNA splicing.
• snRNAs are found in the nucleus and are typically
tightly bound to proteins in complexes called snRNPs
(small nuclear ribonucleoproteins, sometimes
pronounced "snurps").
• The most abundant of these molecules are the U1, U2,
U5, and U4/U6 particles, w hich are involved in splicing
pre-mRNA to give rise to mature mRNA
MicroRNAs
• RNAs that are approximately 22 to 26 nucleotides in length.
• The existence of miRNAs and their functions in gene regulation w ere
initially discovered in the nematode C. Elegans .
• Have also been found in many other species, including flies, mice, and
humans. Several hundred miRNAs have been identified thus far, and many
more may exist.
• miRNAs have been show n to inhibit gene expression by repressing
translation.
• For example, the miRNAs encoded by C. elegans, lin-4 and let-7, bind to
the 3' untranslated region of their target mRNAs, preventing functional
proteins from being produced during certain stages of larval development.
• Additional studies indicate that miRNAs also play significant roles in cancer
and other diseases. For example, the species miR-155 is enriched in B cells
derived from Burkitt's lymphoma, and its sequence also correlates w ith a
know n chromosomal translocation (exchange of DNA between
chromosomes).
Small Interfering RNAs
• Although these molecules are only 21 to 25 base pairs in
length, they also work to inhibit gene expression.
• siRNAs were first defined by their participation in RNA
interference (RNAi). They may have evolved as a defense
mechanism against double-stranded RNA viruses.
• siRNAs are derived from longer transcripts in a process
similar to that by which miRNAs are derived, and
processing of both types of RNA involves the same enzyme,
Dicer .
• The two classes appear to be distinguished by their
mechanisms of repression, but exceptions have been found
in which siRNAs exhibit behavior more typical of miRNAs,
and vice versa.
miRNA Challenges for Computational Biology
• Find the genes encoding microRNAs
• Predict their regulatory targets
Computational Prediction of MicroRNA Genes & Targets
• Integrate miRNAs into gene regulatory pathways &
networks
Need to modify traditional paradigm of "transcriptional control" by
protein-DNA interactions to include miRNA regulatory mechanisms
C Burge 2005
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
32
C. elegans lin-4 Small Regulatory RNA
lin-4 precursor
lin-4 RNA
target mRNA
V. Ambros lab
“Translational
repression”
lin-4 RNA
We now know that there are hundreds of microRNA genes
(Ambros, Bartel, Carrington, Ruvkun, Tuschl, others)
C Burge 2005
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
33