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WELCOME
M RNA PROCESSINGPROKARYOTES AND EUKARYOTES
K.VIJAYREDDY
RNA (Ribonucleic Acid)
RNA is much more abundant than DNAThere are several important differences between RNA and DNA. The pentose sugar in RNA is ribose, in DNA it’s deoxyribose.In RNA, uracil replaces the base thymine (U pairs with A).RNA is single stranded while DNA is double stranded.
Primary structure of RNAA, C, G, and U are linked by 3’-5’ ester bonds between ribose and phosphate.
Secondary structure of RNA
D
A) Single stranded regionsformed by unpaired nucleotides B) Duplexdouble helical RNA (A-form with 11bp
per turn) C) Hairpinduplex bridged by a loop of unpaired nucleotidesD) Internal loopnucleotides not forming Watson-Crick base pairsE) Bulge loopunpaired nucleotides in one strand,other strand has contiguous base pairingF) Junctionthree or more duplexes separated by singlestranded regionsG) Pseudoknottertiary interaction between bases of hairpin loop and outside bases
G
AB
C
DE
F
6
TERTIARY STRUCTUREPrimary: Covalent bonds & Secondary/Tertiary
Non-covalent bonds(H-bonds)
7
D D
obbs ISU - B
CB
444/544X: R
NA
Structure &
FunctionRNA STRUCTURE: 3 LEVELS OF ORGANIZATION
Rob KnightUniv Colorado
8
RNA TYPES & FUNCTIONS Types of RNAs FunctionmRNA - messenger Template for protein synthesis.
rRNA - ribosomal Component of ribosome's (protein synthesis) .
t-RNA - transfer Transfer of amino acid (protein synthesis).
hnRNA - heterogeneous nuclear Precursors & intermediates of mature mRNAs & other RNAs (Premature mRNA).
scRNA - small cytoplasmic Signal Recognition Particle (SRP)tRNA processing .
snRNA - small nuclear snoRNA - small nucleolar
Participate in the splicing and transfer of hnRNA.rRNA processing/maturation/methylation.
miRNA-micro RNA Usually endogenous, induce degradation of targeted mRNA. that block expression of complementary mRNAs.regulation of transcription and translation.
siRNA-small interfering RNA Usually exogenous, induce degradation of targeted mRNA. regulation of transcription and translation.
ncRNA-non-coding RNA (npcRNA, nmRNA, fRNA)
all RNA other than mRNA,functional RNA molecule that is not translated into a protein. longer than 200nt.
Ribosome's are the sites of protein synthesis.They consist of ribosomal RNA (65%) and proteins (35%).They have two subunits, a large one and a small one.
Ribosomal RNA
Smallest RNAThe existence of tRNA was demonstrated by Hoagland in 1957.
Anticodon loop has 3 nucleotides that function as anticodon. .
Thymine loop function as the ribosome attachment region.
The DHU loop serves as the aminoacyl synthetase recognition region.
Base-pairing involving H bonds.
Transfer RNA(tRNA)
tRNA 3-D structuretRNA has a tertiary structure that is L-shaped
MESSENGER RNA (MRNA)
It is a single stranded base for base complementary copy of one DNA strand& provides information for amino acid sequence of a polypeptide.
Carries genetic information from nucleus to cytoplasm
(Template of protein synthesis).
Present in two forms: Active form: actively supports translation.
Inactive form: does not support translation..
Three main parts: 5’ untranslated region (5’ UTR) or leader
sequence
Coding sequence, specifies amino acids to be translated
3’ untranslated region ( 3’ UTR) or trailer sequence
These are catalytic RNAs that mainly participate in the cleavage of RNA.They are not true catalysts because they alter their own structure as a result of catalysis.Example: 1. RNase P is a common ribozyme that matures tRNA that acts as an endonuclease. 2. Self-splicing introns.
Clinical applications:-Used as therapeutic agents in correcting mutant mRNA in human cells and inhibiting unwanted gene expression.Kill cancer cells.Prevent virus replication.Gene inhibitors.Gene amenders.Protein inhibitors.Immuno stimulatory RNA’s.
Ribozymes
Most newly transcribed RNA molecules (primary transcripts) undergo various alterations to yield
the mature product.(or)
RNA processing is the collective term used to describe the molecular events allowing the
primary transcripts to become the mature RNA.(or)
The process of modification, mainly through cleavage & or splicing, of primary RNA
transcripts so as to release functional RNA molecules from them.
It is carried out by ribonucleases (RNases) that cleave RNA.
What is RNA processing……!
These RNases not only process the RNA transcripts, also degrade the tRNA,
mRNA, rRNA, and other RNA molecules as a part of the normal cellular “Turnover
process”.
Turnover process refers to degradation of old molecules and the synthesis of new
molecules to replace them.
Both exo-and endo ribonuclease participate in the turnover process.
Primary transcript
Mature RNA.
Nucleus or NucleolusCytoplasm
RNA processing
Removal of nucleotides
addition of nucleotides to the 5’- or 3’- ends
modification of certain nucleotides
1)Remvoal of nucleotides by both endonucleases and exonucleases.
Endonucleases to cut at specific sites within a precursor RNA.
Exonucleases to trim the ends of a precursor RNA.
2)Addition of nucleotides to 5’-or 3’-ends of the primary transcripts or their cleavage products.
Add a cap and a poly(A) tail to pre-mRNA. AAAAAA3)Modification of certain nucleotides on either
the base or the sugar moiety. Add a methyl group to 2’-OH of ribose in
mRNA and rRNA.
Processing of mRNAhnRNPsnRNP particles5’Capping3’CleavagePolyadenylationSplicingPre-mRNA methylation
mRNA PROCESSING
Genetic information is transferred from genes to the proteins they encode via a “messenger” RNA
intermediate.
Characteristics of the Five RNA Polymerases of Eukaryotes
Enzyme Location Products
RNA polymerase I Nucleolus Ribosomal RNAs, excluding 5S rRNA
RNA polymerase II Nucleus Nuclear pre-mRNAs
RNA polymerase III Nucleus tRNAs, 5S rRNA, and other small nuclearRNAs
RNA polymerase IV Nucleus (plant) Small interfering RNAs (siRNAs)
RNA polymerase V Nucleus (plant) Some siRNAs plus noncoding (antisense)transcripts of siRNA target genes
MRNA PROCESSING IN PROKARYOTES
There is little or no processing of mRNA transcripts in prokaryotes. In fact, ribosomes can assemble proteins before mRNA molecules have not yet been completely synthesized.
Prokaryotic mRNA is degraded rapidly from the 5’-end therefore only be translated for a limited amount of time.
DNA
Cytoplasm
Nucleus
EUKARYOTIC MRNA TRANSCRIPTS ARE PROCESSED
ExportG AAAAAA
RNA
Transcription
Nuclear pores
G AAAAAA
RNAProcessing
mRNA
The mRNA then moves out of the
nucleus and is translated in the
cytoplasm.
mRNA is synthesized by RNA Pol II as longer precursors (pre-mRNA), the population of different RNA Pol II transcripts are called heterogeneous nuclear RNA (hnRNA).
Among hnRNA, those processed to give mature mRNAs are called pre-mRNAs.
Pre-mRNA molecules are again processed to give mature mRNAs by 5’-capping, 3’-cleavage and poly adenylation, splicing and methylation.
Processing of mRNA
HNRNP:- HNRNA + PROTEINS
The hnRNA synthesized by RNA Pol II is mainly pre-mRNA and rapidly becomes covered by proteins to
form heterogeneous nuclear Ribonucleoprotein (hnRNP).
The hnRNP proteins are keep the hnRNA in a single-stranded form and to assist in the various RNA
processing reactions.
SNRNP PARTICLES: SNRNA + PROTEINS
Eukaryotic nuclei contain many discreet small RNA species called small nuclear
RNAs(snRNAs) are rich in the base uracil, which complex with specific proteins to form
snRNPs.
The most abundant snRNP are involved in pre-mRNA splicing, U1,U2,U4,U5 and U6.
snRNAs are synthesized in the nucleus by RNA Pol II and have a normal 5’-cap.
.
Removes the -phosphate
CAPPING – STEP 1
CAPPING –STEP 2
Attaches guanosine nucleotide
OHOH
OHOH
Adds methyl groups to guanine & riboses
CAPPING – STEP 3
OH OCH3
7-Methylguanine
5¢ 3¢
5¢
5¢ 3¢
Endonuclease cleavage occursabout 20 nucleotides downstreamfrom the AAUAAA sequence.
PolyA-polymerase addsadenine nucleotidesto the 3¢ end.
Polyadenylation sequence
PolyA tail
AAAAAAAAAAAA....AAUAAA
AAUAAA
AAUAAA
CLEAVAGE/POLYADENYLATION
G/U
SPLICING The process of cutting the pre-mRNA to
remove the introns and joining together of the exons is called splicing.
It takes place in the nucleus before the mature mRNA can be exported to the cytoplasm.
Most genes have their protein-coding information interrupted by non-coding sequences called “introns”. The coding sequences are then called “exons”.
Introns: non-coding sequences. Exons: coding sequences.
SPLICING BASED ON SECONDARY STRUCTURE:
SPLICEOSOME MEDIATED SPLICING: All the known introns begin with the
dinucleotide GT and end with the dinucleotide AG this is known as GT-AG rule
The GT dinucleotide depicts the donor splicing site and AG dinucleotide depicts the acceptor splicing site
SPLICING – INTRON SEQUENCES
3¢5¢5¢ splice site 3¢ splice siteBranch site
IntronExon ExonPy12N PyAGGA/CGGU Pu AGUA UACUUAUCC
Exon n ……A G G U A A G U …Intron …Y N Y Y R A Y …....Y12 N C A G N ….. Exon n+1 64 73 100 100 62 68 84 63 80 80 87 75 100 95 65 100 100
Branch Point
Yeast consensus
Intron loops out and exons brought closer together
SPLICING OF PRE-MRNAS
SPLICING OF PRE-MRNA
This is a Spliceosome
Composed of five snRNPs (U1, U2, U4, U5 and U6), other splicing factors, and the pre-mRNA being assembled.
Intron will be degraded and the snRNPs used again
SPLICING OF PRE-MRNA
All noncoding introns are spliced out of a pre- mRNA by the Spliceosome.But not all exons are included in the final mRNA.mRNA can undergo alternative splicing.The selective inclusion or exclusion of exons occur.From one pre-mRNA can make many different mRNA(thus different proteins) >50% of human genes undergo alternative splicing.
ALTERNATIVE SPLICING
ALTERNATIVE SPLICING OF TROPOMYOSIN
* Alternative pA*
* Alternative pA*
HOWEVER, MULTIPLE INTRONS MAY BE SPLICED DIFFERENTLY IN DIFFERENT CIRCUMSTANCES, FOR EXAMPLE IN DIFFERENT TISSUES.
1 2 3 5Heart muscle mRNA
1 43 5Uterine muscle mRNA
Thus one gene can encode more than one protein. The proteins are similar but not identical and may have distinct properties.
This is important in complex organisms
3 5421pre-mRNA
Sex in Drosophila is largely determined
by alternative splicing
RNA EDITINGThis is a form of RNA processing in which
the nucleotide sequence of the primary transcript is altered by either
Changing residues,Deleting residues,Inserting residues at specific points
along the moleculeChanging RNA sequence (after
transcription).
Apolipoprotein-B mRNA in mammalian intestine and liver
The mammalian liver cells contain apolipoprotein- B having 4563 amino acids. While in intestine cells this protein has only 2152 amino acids.In intestine cells, the codon 2153 is modified in the mRNA , the C of this codon, CAA, is changed to U to give rise to the codon UAA, which causes chain termination. A guide RNA containing a sequence that is complementary to the correctly edited mRNA provides a mechanism of U insertion or deletion.
Liver Intestine
mRNA processing: overview
POSSIBLE QUESTIONS: Describe in detail about mRNA processing ? Difference between splicing and alternate
splicing? RNA editing?
REFERNCES: GENETICS- B.D.SINGH PRINCIPLES OF GENETICS- SNUSTARD AND SIMMONS
Thank
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