Chapter 23
Catalytic RNA
23.1 Introduction
23.2 Group I introns undertake self-splicing by
transesterification
23.3 Group I introns form a characteristic secondary
structure
23.4 Ribozymes have various catalytic activities
23.5 Some introns code for proteins that sponsor
mobility
23.6 The catalytic activity of RNAase P is due to RNA
23.7 Viroids have catalytic activity
23.8 RNA editing occurs at individual bases
23.9 RNA editing can be directed by guide RNAs
The idea that only proteins have enzymatic activity
was deeply rooted in biochemistry,
The enzyme ribonuclease P is a ribonucleoprotein that
contains a single RNA molecule bound to a protein.
Small RNAs of the virusoid class have the ability to
perform a self-cleavage reaction.
Introns of the group I and group II classes possess the
ability to splice themselves out of the pre-mRNA that
contains them.
23.1 Introduction
The common theme of these reactions is that the
RNA can perform an intramolecular or
intermolecular reaction that involves cleavage or
joining of phosphodiester bonds in vitro,
RNA splicing is not the only means by which
changes can be introduced in the informational
content of RNA.
23.1 Introduction
Figure 23.1 Splicing of the
Tetrahymena 35S rRNA precursor
can be followed by gel
electrophoresis,The removal of
the intron is revealed by the
appearance of a rapidly moving
small band,When the intron
becomes circular,it
electrophoreses more slowly,as
seen by a higher band.
23.2 Group I introns undertake self-
splicing by transesterification
Figure 23.2 Self-splicing
occurs by
transesterification
reactions in which bonds
are exchanged directly,
The bonds that have
been generated at each
stage are indicated by
the shaded boxes.
23.2 Group I introns undertake self-
splicing by transesterification
Figure 23.3 The excised
intron can form circles by
using either of two internal
sites for reaction with the 5
end,and can reopen the
circles by reaction with
water or oligonucleotides.
23.2 Group I
introns undertake
self-splicing by
transesterification
Figure 23.8 The L-19 linear
RNA can bind C in the
substrate-binding site; the
reactive G-OH 3 end is
located in the G-binding site,
and catalyzes transfer reactions
that convert 2 C5
oligonucleotides into a C4 and
a C6 oligonucleotide.
23.2 Group I introns
undertake self-
splicing by
transesterification
Figure 23.4 Group I introns have a
common secondary structure that is
formed by 9 base paired regions,
The sequences of regions P4 and
P7 are conserved,and identify the
individual sequence elements P,Q,
R,and S,P1 is created by pairing
between the end of the left exon
and the IGS of the intron; a region
between P7 and P9 pairs with the 3'
end of the intron.
23.3 Group I introns form a
characteristic secondary structure
Figure 23.5 Placing the
Tetrahymena intron within the
b-galactosidase coding sequence
creates an assay for self-splicing
in E,coli,Synthesis of b-
galactosidase can be tested by
adding a compound that is
turned blue by the enzyme,The
sequence is carried by a
bacteriophage,so the presence
of blue plaques indicates
successful splicing.
23.3 Group I introns form a
characteristic secondary structure
Figure 23.6 Excision of the
group I intron in Tetrahymena
rRNA occurs by successive
reactions between the occupants
of the guanosine-binding site and
substrate-binding site,The left
exon is red,and the right exon is
purple.
23.4 Ribozymes have
various catalytic
activities
Figure 23.2 Self-splicing
occurs by
transesterification
reactions in which bonds
are exchanged directly,
The bonds that have
been generated at each
stage are indicated by the
shaded boxes.
23.4 Ribozymes have various catalytic activities
Figure 23.7 The position
of the IGS in the tertiary
structure changes when
P1 is formed by substrate
binding.
23.4 Ribozymes have various catalytic activities
Figure 23.3 The excised intron
can form circles by using either
of two internal sites for reaction
with the 5 end,and can
reopen the circles by reaction
with water or oligonucleotides.
23.4 Ribozymes have
various catalytic activities
Figure 23.8 The L-19 linear
RNA can bind C in the
substrate-binding site; the
reactive G-OH 3 end is
located in the G-binding site,
and catalyzes transfer
reactions that convert 2 C5
oligonucleotides into a C4
and a C6 oligonucleotide.
23.4 Ribozymes have
various catalytic activities
Figure 23.9 Catalytic
reactions of the ribozyme
involve transesterifications
between a group in the
substrate-binding site and a
group in the G-binding site.
23.4 Ribozymes have
various catalytic activities
Figure 23.10 Reactions catalyzed by RNA have the same features
as those catalyzed by proteins,although the rate is slower,The KM
gives the concentration of substrate required for half-maximum
velocity; this is an inverse measure of the affinity of the enzyme for
substrate,The turnover number gives the number of substrate
molecules transformed in unit time by a single catalytic site.
23.4 Ribozymes have various catalytic activities
Figure 23.11 An intron
codes for an
endonuclease that
makes a double-strand
break in DNA,The
sequence of the intron
is duplicated and then
inserted at the break.
23.5 Some introns code for proteins
that sponsor mobility
Figure 23.11 An intron
codes for an
endonuclease that
makes a double-strand
break in DNA,The
sequence of the intron
is duplicated and then
inserted at the break.
23.5 Some introns code for proteins
that sponsor mobility
Figure 16.18
Retrotransposition of non-
LTR elements occurs by
nicking the target to
provide a primer for
cDNA synthesis on an
RNA template.
23.5 Some introns code for
proteins that sponsor mobility
Figure 23.12 Reverse
transcriptase coded by
an intron allows a copy
of the RNA to be
inserted at a target site
generated by a double-
strand break.
23.5 Some introns code
for proteins that
sponsor mobility
Viroid is a small infectious
nucleic acid that does not
have a protein coat.
23.6 RNA can have
ribonuclease activities
Figure 23.10 Reactions catalyzed by RNA have the same features
as those catalyzed by proteins,although the rate is slower,The KM
gives the concentration of substrate required for half-maximum
velocity; this is an inverse measure of the affinity of the enzyme for
substrate,The turnover number gives the number of substrate
molecules transformed in unit time by a single catalytic site.
23.4 Ribozymes have various catalytic activities
Figure 12.16 The
rolling circle
generates a
multimeric single-
stranded tail.
23.6 RNA can have
ribonuclease activities
Figure 23.13 Self-cleavage
sites of viroids and virusoids
have a consensus sequence
and form a hammerhead
secondary structure by
intramolecular pairing,
Hammerheads can also be
generated by pairing between
a substrate strand and an
"enzyme" strand.
23.6 RNA can have
ribonuclease activities
Figure 23.14 A
hammerhead ribozyme
forms a V-shaped tertiary
structure in which stem 2 is
stacked upon stem 3,The
catalytic center lies
between stem 2/3 and stem
1,It contains a magnesium
ion that initiates the
hydrolytic reaction.
23.6 RNA can have
ribonuclease activities
Figure 23.15 The sequence
of the apo-B gene is the
same in intestine and liver,
but the sequence of the
mRNA is modified by a
base change that creates a
termination codon in
intestine.
23.7 RNA editing
utilizes information
from several sources
Figure 23.16
Editing of
mRNA
occurs when
a deaminase
acts on an
adenine in an
imperfectly
paired RNA
duplex
region.
23.7 RNA editing utilizes
information from several sources
Figure 23.17 The mRNA for the trypanosome coxII gene
has a -1 frameshift relative to the DNA; the correct
reading frame is created by the insertion of 4 uridines.
23.7 RNA editing utilizes information
from several sources
Figure 23.18 Part of the mRNA sequence of T,brucei coxIII
shows many uridines that are not coded in the DNA (shown
in red) or that are removed from the RNA (shown as T).
23.7 RNA editing utilizes information
from several sources
Figure 23.19 Pre-edited
RNA base pairs with a
guide RNA on both sides
of the region to be edited,
The guide RNA provides
a template for the
insertion of uridines,The
mRNA produced by the
insertions is
complementary to the
guide RNA.
23.7 RNA editing utilizes information
from several sources
Figure 23.20 The Leishmania genome contains genes
coding for pre-edited RNAs interspersed with units that
code for the guide RNAs required to generate the correct
mRNA sequences,Some genes have multiple guide RNAs.
23.7 RNA editing utilizes information
from several sources
Figure 23.21 Addition or
deletion of U residues
occurs by cleavage of
the RNA,removal or
addition of the U,and
ligation of the ends,The
reactions are catalyzed
by a complex of
enzymes under the
direction of guide RNA.
23.7 RNA editing
utilizes information
from several sources
23.8 Summary
Catalytic RNA
23.1 Introduction
23.2 Group I introns undertake self-splicing by
transesterification
23.3 Group I introns form a characteristic secondary
structure
23.4 Ribozymes have various catalytic activities
23.5 Some introns code for proteins that sponsor
mobility
23.6 The catalytic activity of RNAase P is due to RNA
23.7 Viroids have catalytic activity
23.8 RNA editing occurs at individual bases
23.9 RNA editing can be directed by guide RNAs
The idea that only proteins have enzymatic activity
was deeply rooted in biochemistry,
The enzyme ribonuclease P is a ribonucleoprotein that
contains a single RNA molecule bound to a protein.
Small RNAs of the virusoid class have the ability to
perform a self-cleavage reaction.
Introns of the group I and group II classes possess the
ability to splice themselves out of the pre-mRNA that
contains them.
23.1 Introduction
The common theme of these reactions is that the
RNA can perform an intramolecular or
intermolecular reaction that involves cleavage or
joining of phosphodiester bonds in vitro,
RNA splicing is not the only means by which
changes can be introduced in the informational
content of RNA.
23.1 Introduction
Figure 23.1 Splicing of the
Tetrahymena 35S rRNA precursor
can be followed by gel
electrophoresis,The removal of
the intron is revealed by the
appearance of a rapidly moving
small band,When the intron
becomes circular,it
electrophoreses more slowly,as
seen by a higher band.
23.2 Group I introns undertake self-
splicing by transesterification
Figure 23.2 Self-splicing
occurs by
transesterification
reactions in which bonds
are exchanged directly,
The bonds that have
been generated at each
stage are indicated by
the shaded boxes.
23.2 Group I introns undertake self-
splicing by transesterification
Figure 23.3 The excised
intron can form circles by
using either of two internal
sites for reaction with the 5
end,and can reopen the
circles by reaction with
water or oligonucleotides.
23.2 Group I
introns undertake
self-splicing by
transesterification
Figure 23.8 The L-19 linear
RNA can bind C in the
substrate-binding site; the
reactive G-OH 3 end is
located in the G-binding site,
and catalyzes transfer reactions
that convert 2 C5
oligonucleotides into a C4 and
a C6 oligonucleotide.
23.2 Group I introns
undertake self-
splicing by
transesterification
Figure 23.4 Group I introns have a
common secondary structure that is
formed by 9 base paired regions,
The sequences of regions P4 and
P7 are conserved,and identify the
individual sequence elements P,Q,
R,and S,P1 is created by pairing
between the end of the left exon
and the IGS of the intron; a region
between P7 and P9 pairs with the 3'
end of the intron.
23.3 Group I introns form a
characteristic secondary structure
Figure 23.5 Placing the
Tetrahymena intron within the
b-galactosidase coding sequence
creates an assay for self-splicing
in E,coli,Synthesis of b-
galactosidase can be tested by
adding a compound that is
turned blue by the enzyme,The
sequence is carried by a
bacteriophage,so the presence
of blue plaques indicates
successful splicing.
23.3 Group I introns form a
characteristic secondary structure
Figure 23.6 Excision of the
group I intron in Tetrahymena
rRNA occurs by successive
reactions between the occupants
of the guanosine-binding site and
substrate-binding site,The left
exon is red,and the right exon is
purple.
23.4 Ribozymes have
various catalytic
activities
Figure 23.2 Self-splicing
occurs by
transesterification
reactions in which bonds
are exchanged directly,
The bonds that have
been generated at each
stage are indicated by the
shaded boxes.
23.4 Ribozymes have various catalytic activities
Figure 23.7 The position
of the IGS in the tertiary
structure changes when
P1 is formed by substrate
binding.
23.4 Ribozymes have various catalytic activities
Figure 23.3 The excised intron
can form circles by using either
of two internal sites for reaction
with the 5 end,and can
reopen the circles by reaction
with water or oligonucleotides.
23.4 Ribozymes have
various catalytic activities
Figure 23.8 The L-19 linear
RNA can bind C in the
substrate-binding site; the
reactive G-OH 3 end is
located in the G-binding site,
and catalyzes transfer
reactions that convert 2 C5
oligonucleotides into a C4
and a C6 oligonucleotide.
23.4 Ribozymes have
various catalytic activities
Figure 23.9 Catalytic
reactions of the ribozyme
involve transesterifications
between a group in the
substrate-binding site and a
group in the G-binding site.
23.4 Ribozymes have
various catalytic activities
Figure 23.10 Reactions catalyzed by RNA have the same features
as those catalyzed by proteins,although the rate is slower,The KM
gives the concentration of substrate required for half-maximum
velocity; this is an inverse measure of the affinity of the enzyme for
substrate,The turnover number gives the number of substrate
molecules transformed in unit time by a single catalytic site.
23.4 Ribozymes have various catalytic activities
Figure 23.11 An intron
codes for an
endonuclease that
makes a double-strand
break in DNA,The
sequence of the intron
is duplicated and then
inserted at the break.
23.5 Some introns code for proteins
that sponsor mobility
Figure 23.11 An intron
codes for an
endonuclease that
makes a double-strand
break in DNA,The
sequence of the intron
is duplicated and then
inserted at the break.
23.5 Some introns code for proteins
that sponsor mobility
Figure 16.18
Retrotransposition of non-
LTR elements occurs by
nicking the target to
provide a primer for
cDNA synthesis on an
RNA template.
23.5 Some introns code for
proteins that sponsor mobility
Figure 23.12 Reverse
transcriptase coded by
an intron allows a copy
of the RNA to be
inserted at a target site
generated by a double-
strand break.
23.5 Some introns code
for proteins that
sponsor mobility
Viroid is a small infectious
nucleic acid that does not
have a protein coat.
23.6 RNA can have
ribonuclease activities
Figure 23.10 Reactions catalyzed by RNA have the same features
as those catalyzed by proteins,although the rate is slower,The KM
gives the concentration of substrate required for half-maximum
velocity; this is an inverse measure of the affinity of the enzyme for
substrate,The turnover number gives the number of substrate
molecules transformed in unit time by a single catalytic site.
23.4 Ribozymes have various catalytic activities
Figure 12.16 The
rolling circle
generates a
multimeric single-
stranded tail.
23.6 RNA can have
ribonuclease activities
Figure 23.13 Self-cleavage
sites of viroids and virusoids
have a consensus sequence
and form a hammerhead
secondary structure by
intramolecular pairing,
Hammerheads can also be
generated by pairing between
a substrate strand and an
"enzyme" strand.
23.6 RNA can have
ribonuclease activities
Figure 23.14 A
hammerhead ribozyme
forms a V-shaped tertiary
structure in which stem 2 is
stacked upon stem 3,The
catalytic center lies
between stem 2/3 and stem
1,It contains a magnesium
ion that initiates the
hydrolytic reaction.
23.6 RNA can have
ribonuclease activities
Figure 23.15 The sequence
of the apo-B gene is the
same in intestine and liver,
but the sequence of the
mRNA is modified by a
base change that creates a
termination codon in
intestine.
23.7 RNA editing
utilizes information
from several sources
Figure 23.16
Editing of
mRNA
occurs when
a deaminase
acts on an
adenine in an
imperfectly
paired RNA
duplex
region.
23.7 RNA editing utilizes
information from several sources
Figure 23.17 The mRNA for the trypanosome coxII gene
has a -1 frameshift relative to the DNA; the correct
reading frame is created by the insertion of 4 uridines.
23.7 RNA editing utilizes information
from several sources
Figure 23.18 Part of the mRNA sequence of T,brucei coxIII
shows many uridines that are not coded in the DNA (shown
in red) or that are removed from the RNA (shown as T).
23.7 RNA editing utilizes information
from several sources
Figure 23.19 Pre-edited
RNA base pairs with a
guide RNA on both sides
of the region to be edited,
The guide RNA provides
a template for the
insertion of uridines,The
mRNA produced by the
insertions is
complementary to the
guide RNA.
23.7 RNA editing utilizes information
from several sources
Figure 23.20 The Leishmania genome contains genes
coding for pre-edited RNAs interspersed with units that
code for the guide RNAs required to generate the correct
mRNA sequences,Some genes have multiple guide RNAs.
23.7 RNA editing utilizes information
from several sources
Figure 23.21 Addition or
deletion of U residues
occurs by cleavage of
the RNA,removal or
addition of the U,and
ligation of the ends,The
reactions are catalyzed
by a complex of
enzymes under the
direction of guide RNA.
23.7 RNA editing
utilizes information
from several sources
23.8 Summary
