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The
Library of Congress in Washington DC was designed as a
showplace as well
as a repository. The main reading room looks as
much like a museum or
a cathedral as it does a library. If I could
figure out how to get away with
it, I would live in the LOC.
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In a way, you can think of the molecular workings of the
cell like the Library of Congress. You need information storage – these are the
books. In each book (chromosome or parts of a chromosome) contain the instructions
(genes) needed to make products (proteins) the cell may need.
Each time you want to make a certain molecule, you must
consult the book (chromosome) that has the correct instruction page (DNA gene). But
you may be making many copies of your product in a short period, so one book
might not be enough.
You could keep many copies of each book, maybe thousands,
but this would take up too much room. The LOC already covers 2.1 million sq.
feet (and that’s just one main building). What if you needed 1500 copies of One Good Turn (and interesting book
about the history of the screw and screwdriver) because at some time or
another, 1500 people wanted to learn how to build a square screwdriver?
To avoid this need for extra space, you make
copies of pages (mRNA) from the books (chromosomes) that can be taken out of
the library (nucleus) and used for making the products. Each time you want a
product, a translator (tRNA and ribosome) must be used. This converts the
copied instructions (mRNA) into a usable product (protein).
When one or several translations have been made, the copied
instructions start to tear and get worn, and finally break down. Good thing we
still have the original copy of the book stored in the nucleus… I mean library.
We can go back and make more copies later if we need them. Humans are amateurs,
we only have about 25,000 sets of instructions stored in 46 books, nowhere near
the 155.3 million of the LOC.
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The
central dogma of molecular biology says that DNA is replicated to
DNA,
so daughter cells get a full set of instructions. DNA is also
transcribed
to mRNA, which is a copied message of the instructions to
build
one protein. Finally, the mRNA acts as a code that is translated
into
an amino acid polymer – a protein. HIV and other retroviruses
laugh
at the central dogma, going the opposite direction, RNA to
DNA. Retrotransposons laugh at HIV, as they can do all that and more.
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Ever here of small nuclear RNAs, or micro RNAs, or plasmid
DNAs for that matter? We have talked about plasmids as extrachromosomal pieces
of DNA that can code for genes, especially antibiotic resistance genes in
prokaryotes.
But the list of RNAs is far more impressive. There are
regulatory RNAs that control gene expression (whether or not a protein is made
from a gene), RNAs that control modification of other RNAs or work in DNA
replication. There are even RNAs that are parasitic, like some viral genomes
(RNA viruses) and retrotransposons.
Of these, retrotransposons
may be the most interesting. A transposon is a piece of DNA that can jump
around from place to place in the chromosomes of a cell. Barbara McClintock won
a Nobel Prize for identifying transposable elements were responsible for the
different colors of corn kernels in maize.
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Ancient
viral RNA got inserted into plant and animal genomes. The
retrotransposon
can be transcribed to mRNA, and then could be
reverse
transcribed back into DNA or translated into protein. The
DNA
can then insert itself anywhere in the genome. Since several
mRNA
transcripts can be made from one transcribed retrotransposon,
and
since several pieces of DNA can be reverse transcribed from just
one
mRNA, we have the potential for millions of retrotransposons in
the
genome – and that’s exactly what we have found. The bottom
cartoon
shows HIV. Since reverse transcription makes more mistakes
than
DNA replication, many more mutants can be produced. This is
one
reason HIV is so hard to treat – it’s always changing.
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In and of themselves, retrotransposons represent an
exception in nucleic acids. They are mRNA sequences that can turn back into DNA.
Transcription is the process of
using DNA to produce an mRNA, so going the opposite direction is called reverse transcription. This is also
what retroviruses like HIV do.
In this way, retrotransposons can make more copies of themselves and end
up all over the chromosomes of the organism. Mutation occurs at a higher rate
in reverse transcription than in DNA replication because reverse transcriptase
makes more mistakes than replication enzymes. This is why HIV is so hard to
treat; it mutates so often that drug design can’t keep up with the changes in the
viral proteins.
So how can the same mRNA sometimes be translated, and other
times end up in a new place on the DNA? A 2013 study has investigated how one type of retrotransposon manages these different outcomes. The BARE
retrotransposon of plants has just one coding sequence for a protein, but the
study results show that it actually makes three distinct mRNAs from this one
piece of DNA.
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Sam
Kean is the author of The Violinist’s Thumb, a very readable
book
on molecular biology. He goes through how fruit flies were
recruited
to disprove DNA heredity and ended up as the strongest
evidence
for it; how DNA is linked very strongly to linguistics and
math;
and how Stalin tried to breed a race of half human - half
chimps.
This is in addition to showing how most DNA on Earth is
descended
from viruses.
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If plants have so much nucleic acid in the form of
retrotransposons, could these be the remnants of ancient viral infections? You
betcha, and it doesn’t stop with plants. In his fascinating book, The Violinist’s Thumb, Sam Kean lays out
a compelling argument that most human DNA is actually just viral nucleic acid
remnants, much of it being mutated versions of old RNAs.
Old RNA is probably the best way to describe all nucleic
acids, because the generally accepted view of the evolution of life on Earth is
that everything started with RNA. This called the RNA world hypothesis and professes that the job that DNA does now was
first done by RNA.
The hypothesis also says that what those that protein
enzymes now do - cutting things up, putting things together, and modifying
existing structures - was originally done by RNAs as well, called catalytic RNAs.
We have evidence for this hypothesis, specifically, we know
of many RNAs that have enzymatic activity. Called ribozymes (a cross between ribo
for RNA, and zyme for enzyme), some
RNAs carry out enzymatic roles in our cells and the cells of every eukaryote
and prokaryote ever analyzed for their presence.
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Ribozymes,
a form of catalytic RNA, are present in most cells. They come
in
two flavors based on what someone thought their secondary structure
looked
like – the hammerhead or the hairpin. Scientists aren’t the most
imaginative
when it comes to naming things. They both sit down on an
RNA
where they recognize their specific sequence, and make a cut in the
strand.
In the cartoon, N stands for any nucleotide, and X stands for
unknown.
On the right side is a diagram showing how one ribozyme can
act
again and again to cleave RNAs.
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One essential ribozyme function is the synthesis of protein.
The ribosome (a riboprotein because it is made up of many RNAs and proteins)
translates the codons of mRNA into a sequence of amino acids. It uses the RNA
to link the individual amino acids together via peptide bonds. I’d say that’s
essential.
Other ribozymes work on themselves. Many mRNAs, when first
copied from DNA have sequence within them that is not used in the final
product. These are called intervening sequences (or introns), and are cut out (spliced) as part of the transcript processing.
Group I and II introns are self-splicing. They fold over on themselves and
cause their own excision from the RNA of which they are part!
Group I introns can be found in the mRNAs, rRNAs, and tRNAs
of most prokaryotes and lower eukaryotes, but the only place we have found them
so far in higher eukaroytes are the introns of plants and the introns of
mitochondrial and chloroplasts genomes. Yet more evidence for the plastid endosymbiosis hypothesis.
If the RNA world hypothesis is to be strengthened, we must
find a catalytic RNA that can replicate long strings of RNA “genes.” If RNA was
both the storage material and the enzymatic material, there must have been an
RNA-dependent, RNA polymerase that was itself a piece of RNA. An RNA replicase
has not been found, probably because life moved on to using DNA as the long-term
repository of genetic information, But we should be able to make an RNA
replicase as a proof of concept.
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The
RNA world hypothesis is an idea of how early life on Earth transmitted
information
and carried out functions. RNA did everything, stored info.,
replicated
itself, and carried out enzymatic activity. A – E represent a
possible
sequence, although no times can be assigned yet. According to this
theory
– the last thing that developed was enzymatic proteins – but new
evidence
suggests that proteins were important for the development of
tRNAs
so they must have been around earlier. Step B is an area of interest,
as
scientists are trying to make an RNA that could replicate any RNA, even itself.
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Then a study was published showing that a modification of
R18 could synthesize much longer strings and could replicate many different RNA
templates. In this publication, the authors could synthesize ribonucleic acids
of 95 bases, almost as long as the R18 replicase itself. Another study has
shown that some catalytic RNAs can self-replicate at an exponential rate,
making thousands of copies of themselves while still having catalytic function.
It seems that the RNA hypothesis is getting stronger, but
there remain some hurdles.
A July, 2013 study shows that primitive protein enzymes
(called urenzymes, where ur = primitive) activate tRNAs much faster
than do ribozymes. These primitive proteins date to before the last common
ancestor, so they have been around nearly as long as life itself. tRNA urenzymes
suggest a tRNA-enzyme co-evolution, providing evidence that catalytic proteins
and the conventional central dogma were important in early life – a result that
does not support the RNA world hypothesis. I’m glad – the hunt goes on.
In the next weeks, let’s take a look at nucleic acid structures and
their building blocks. Think DNA is double stranded? – not always. Think A, C,
G, T, and U are the only nucleotides life uses? – not even close.
For
more information or classroom activities, see:
Nucleic
acids –
Central
dogma of molecular biology –
Types
of RNA –
Retrotransposons
–
RNA
world hypothesis –
Catalytic
RNA (ribozymes) –
