5
Ribosomes and the RNA World
Peter B. Moore
Departments of Chemistry and of Molecular
Biophysics and Biochemistry
Yale University
New Haven, Connecticut 06511
The hypothesis that all modern organisms are descendants of an ancient,
self-replicating entity that depended on RNA both for its genetic material
and for catalysis has gained a large following over the past decade, as the
existence of this volume attests. This idea, also known as the RNA world
hypothesis, has been around in various forms for almost 30 years, and it
has been known for most of that time that RNA can serve a DNA-like
function. The reason there is so much interest in the RNA world
hypothesis today is that we now know something our predecessors did
not, namely, that RNAs are capable of catalyzing biochemical reactions.
Boiled down to its essence, the RNA world hypothesis is a proposal
for the origin of life that explains why RNA is so important for gene expression in modern organisms but has no role in any other aspect of metabolism. Ribosomes are important for two reasons in this context. First,
because ribosomal RNA accounts for about 80% of the RNA in most
modern cells, the RNA world hypothesis either makes sense of them or
fails entirely. Second, again because the ribosome contains so much
RNA, information about its structure and function has to be an important
part of the input used for formulating all such theories.
This paper is intended to provide the reader with a broadbrush picture
of the ribosome field that emphasizes the findings that bear most directly
on evolutionary issues. Readers wishing to find out more about the topics
covered here, as well as about the ribosome field in general, should consult the symposium volumes that have appeared at irregular intervals
since the late 1960s (Nomura et al. 1974; Chambliss et al. 1980; Hardesty and Kramer 1986; Hill et al. 1990), which are excellent summaries
of the field's progress.
The information we now have about ribosomes points to three conclusions that are important for theories about the origin of life. In order of
increasing controversiality they are (1) that the Last Common Ancestor
(LCA) of all modern organisms had ribosomes, (2) that the ribosomes of
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the LCA were nucleoprotein complexes, and (3) that the concept that the
progenitors of the LCA had protoribosomes made entirely of RNA is
supportable, but irrelevant to the RNA World Hypothesis.
A SHORT SCIENTIFIC HISTORY OF THE RIBOSOME
The Ribosome Is Discovered
The ribosome field is rooted in observations made long before it was
recognized as a distinct biochemical subdiscipline. The word "ribosome"
was coined in 1958 (Roberts 1958), about 20 years after the first observations that led to the development of the field (see Tissieres 1974).
The origins of the ribosome field can be traced back to histological
studies made before World War II that established several important
facts about eukaryotic cells: (1) DNA is a nuclear substance (Feulgen et
al. 1937), (2) most of the RNA in both plant and animal cells is cytoplasmic, and (3) the amount of RNA a cell contains is correlated with its activity in protein synthesis (Brachet 1941; Caspersson 1941, 1950). Cell
fractionation techniques, which were developed in the late 1930s,
enabled Claude to identify an RNA-rich, particulate fraction from
cytoplasmic extracts called "microsomes" (see, e.g., Claude 1941), and
by 1942, Jeener and Brachet were convinced that microsomes were universal in eukaryotic cells and important for protein synthesis (Jeener and
Brachet 1941, 1942).
Ultracentrifugation and electron microscopy, technologies that entered common use in the years immediately after the war, had a revolutionary impact on cytology. Through their use, it was soon demonstrated
that the RNA in eukaryotic microsomes is associated with the discrete
ribonucleoprotein particles we now call ribosomes (Palade 1955; Palade
and Siekevitz 1956) and that bacterial cells also contain ribosomes (Luria
et al. 1943; Schachman et al. 1952).
Physical studies soon demonstrated that the ribosomes in any given
organism are all the same size and are roughly half protein and half
RNA. They are more or less spherical, with diameters in the neighborhood of 250 A and molecular weights of several million. Furthermore, all
ribosomes are 1:1 complexes of two nonequivalent subunits that associate in a magnesium-dependent way (Chao 1957).
Radioisotopes also became available to the biochemical world in the
early postwar years, and they were used to test the hypothesis that microsomes are involved in protein synthesis. Whole-animal experiments done
around 1950 supported that theory (see Tissieres 1974), but definitive
proof was not obtained until several years later when Zamecnik and his
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merits which demonstrated that nascent polypeptides form on ribosomes
(Littlefield et al. 1955).
Nothing that has happened since has shaken the general conclusions
drawn in those early years. All cellular life forms that have been examined so far contain ribosomes, and the only known function of ribosomes
is protein synthesis. Both because ribosomes are universal and because
the role they play in metabolism is so basic, the conclusion that the LCA
must also have made proteins using ribosomes is all but inescapable and
is widely accepted.
The Function of the Ribosome Is Defined
From the mid-1950s until the late 1960s, elucidation of the role of the
ribosome in protein synthesis was a central issue in biochemistry. Most
of the work done in that period depended on cell-free systems that
synthesize proteins in vitro. A perusal of Zamecnik's 1969 review of
those years will remind the reader just how difficult it was to develop
such systems (Zamecnik 1970). It could never have been done without
radioisotopes, since cell-free systems efficient enough to make more than
traces of product were not available then or for many years thereafter.
The knowledge gleaned from these systems was of the utmost importance; we note only those findings that are important here.
One of the first fruits of the cell-free work was the demonstration that
aminoacyl-tRNAs are the activated amino acid intermediates used by the
protein-synthesizing system (Hoagland et al. 1957, 1958). These were
the molecules called for by Crick's adapter hypothesis (Crick 1958), and
the proof of their existence provided by Zamecnik's group and others
launched the tRNA/aminoacyl-tRNA synthetase field, which is as active
today as ever. The significance of the synthetases is that they are the
entities that actually "read" the code; once an amino acid is attached to a
tRNA, its fate is sealed.
Although it was clear from the outset that ribosomes have to be included in a cell-free system, it was not clear precisely what they contribute. Since the Central Dogma was well established by the late 1950s (see
Crick 1958), the presence of RNA in ribosomes was not a source of
anxiety. After all, DNA makes RNA makes protein. However, up until
1960 or so, many thought that the RNA in ribosomes was informational
(see Zamecnik 1970). The ribosome was envisioned as a segment of
sequence-specifying RNA around which a set of proteins clustered busily
translating RNA sequence information into amino acid sequences. There
even was a phase where the notion that ribosomes are built like little
viruses was entertained (Crick 1958).
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P.B. Moore
Even then there were reasons for feeling uncomfortable with the idea
that rRNA is informational. The rRNAs in an organism do not vary from
one tissue type to the next. They are uniform in size, and base compositional data alone suggested that their sequences do not vary from tissue
to tissue and certainly indicated that their sequences are not representative of the genomes with which they are associated (see Spirin 1964).
Both characteristics were worrying, since it was already known that
proteins vary enormously in chain length and sequence. One's expectation, therefore, was that there ought to be a corresponding variability in
rRNA size and base composition. The theory that rRNA is informational
was put to rest for good in 1961 by the announcement of the discovery of
messenger RNA (Brenner et al. 1961; Gros et al. 1961; Jacob and Monod
1961).
By the close of play in 1961, one knew that the protein-synthesizing
apparatus is programmed by mRNA and that the interactions between
mRNA and tRNAs that lead to protein synthesis occur on the ribosome.
The final chapter of the basic story was put in place a few years later by
Monro and co-workers (Monro 1967; Maden et al. 1968), who demonstrated that the activity responsible for peptide bond formation, i.e. peptidyl transferase, is an intrinsic part of the large ribosomal subunit.
The Ribosome Is a Polymerase
The pace of discovery in the protein synthesis field was so rapid that by
1964 or so, one could confidently write a reaction scheme for the
ribosomal steps of protein synthesis
template
Ai(aminoacyl-tRNA) + 2«GTP
^
(amino acid) + ntRNA +2«P
r i b o s o m e + protein factors
n
;
+ 2nGDP
When the corresponding reaction scheme is written for DNA (or RNA)
polymerase the result is the following
template
«dXTP
—>
(dXMP)„ + «P;Pj
DNA polymerase + protein factors
The parallels are obvious. DNA polymerase is an enzyme that catalyzes
the formation of heteropolymers, starting with activated monomers, and
the sequences of the polymers it makes are determined by polynucleotide
templates. If you replace "DNA polymerase" with "the ribosome," the
sentence still works.
The ribosome is not an organelle, a term one still sees attached to it in
the literature; it is not comparable in any way to intracellular entities like
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the mitochondrion or the lysozome, which are organelles. It is an enzyme. It would make sense to rename the ribosome to reflect that fact;
"polypeptide polymerase" would be appropriate (see Moore 1986). However, the weight of tradition is such that it would be folly to agitate for
reform at this late date —even a reform as sensible as this.
Ribosomes Contain Many Proteins
By 1966 or so, a lot of the biochemistry connected with the ribosomal
phase of gene expression had been worked out, but not as thoroughly,
perhaps, as many thought at the time. Important new observations continue to be made. Our understanding of the elongation phase of protein
synthesis —which biochemists who do not work on protein synthesis
have regarded as a closed book for 25 years —has changed significantly
(see Nierhaus 1990).
Nevertheless, starting in the late 1960s, the focus of the ribosome
field began to shift from pathway elucidation toward structure determination and the study of the relationship between ribosome structure and
function. From about 1965 to 1980, most questions of this kind were addressed using the particles from Escherichia coli, and by 1980, their
chemical structure was fully understood. The ribosomes from this
organism contain 3 RNA molecules: 16S rRNA, which is part of the
small ribosomal subunit, and 23S and 5S rRNAs, which are found only
in the large ribosomal subunit. All three are present in 1 mole per mole
of ribosomes (see Van Holde and Hill 1974).
5S rRNA was sequenced in 1968 (Brownlee et al. 1968), and although progress was made with the large rRNAs by direct sequencing
methods, their sequences were not completed until their genes were analyzed in the late 1970s (Brosius et al. 1978, 1980; Carbon et al. 1979).
Even though E. coli has several genes for each of its rRNAs, the sequence differences between their products are slight, one or two residues
per hundred, and have no known physiological significance. From the
point of view of the RNAs they contain, all ribosomes in E. coli are equivalent.
Starting in the early 1960s, methods were gradually worked for isolating the components of the protein mixture that is found in ribosome preparations. The invention of acrylamide gel electrophoresis, which occurred at about that time, provided a convenient means for identifying individual proteins and assessing the purity of ribosomal protein preparations. Despite some confusion, it was evident quite early that ribosomal
protein mixtures are very complicated (Waller and Harris 1961; Waller
1964). Approximately 56 different proteins associate strongly with the
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P.B. Moore
ribosomes from E. coli (see Wittmann-Liebold 1986). Their average
molecular weight is about 15,000, and they range in molecular weight
from about 8,000 to about 65,000.
By 1984, sequences were available for all of the ribosomal proteins
from E. coli. Sequence comparisons proved what the fingerprinting
studies done almost 20 years earlier had indicated (Traut et al. 1967);
every one of the ribosomal proteins is a distinct species. The differences
between these proteins are so large that the extent of homologies between them is still uncertain (see Wittmann-Liebold 1986).
The stoichiometry of the proteins in the ribosome was a bone of contention in the late 1960s and early 1970s, but when the dust cleared, the
consensus was that almost all ribosomal proteins occur in single copies
in the ribosome in vivo (Hardy 1975). The exception is the acidic, large
subunit protein, L7/L12, which occurs in four copies per ribosome (Subramanian 1975; Marquis and Fahnestock 1978). Normal preparations
contain substoichiometric amounts of many proteins because ribosomes
shed proteins as they are purified.
Bacterial Ribosomes Self-assemble
In the late 1960s, Nomura and colleagues discovered that the small subunit from bacterial ribosomes will reassemble from its dissociated macromolecular components in vitro (Traub and Nomura 1968). Techniques
were worked out subsequently for reconstituting the large subunit as well
(Nomura and Erdmann 1970; Nierhaus and Dohme 1974). Reconstitution
provided the field with a powerful experimental tool that is still bearing
fruit. Shortly after its discovery, a series of experiments was done that
answered an important question about the distribution of proteins in
ribosome populations.
The stoichiometric data require that every small subunit have one
copy of 16S rRNA and that every large subunit have a single 23S rRNA
molecule, because both molecules account for more than half the mass of
the particles to which they belong. Although the stoichiometric data also
tell us that there is one copy of every protein per particle, they do not require that every particle have one copy of every protein. Some particles
could carry two copies of protein x and none of protein y, provided
others had two copies of y and none of x, etc.
The single protein omission experiments done by Nomura's group on
the small subunit settled the issue for a significant number of proteins
(Mizushima and Nomura 1970; Held et al. 1974). They found that the
omission of any one of many ribosomal proteins led to complete failure
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of reconstitution; no normally sedimenting particles would form. This
proved that every normal subunit had to contain (at least) one copy of
each protein whose omission has this effect on reconstitution. Everything
that has been learned since supports the idea that each subunit in vivo
carries one copy of every protein (except L7/L12), not just the proteins
essential for normal reconstitution.
The Ribosome Is a Single-site Enzyme
Any macromolecular complex that contains single copies of effectively
all of its components is asymmetric and can have no equivalent sites,
formally speaking. Consistent with this inference, all the experiments
that have ever been done to measure the number of active sites of a given
kind on the ribosome have produced one as their answer. The ribosome
has one peptidyl transferase site, one mRNA-binding site, one A-type
site for tRNA binding, etc. It follows that when one is thinking of allprotein enzymes to compare to the ribosome, the molecules to think
about are small enzymes like RNase A or lysozyme, which have single
active sites, not large, multi-enzyme complexes like pyruvate dehydrogenase, which are comparable to the ribosome in size, but which have
multiple copies of every site.
There is every reason to believe that E. coli ribosomes are typical.
The qualitative conclusions we have just discussed would have emerged
had the ribosomes from any other organism been subjected to comparable scrutiny.
A R E RIBOSOMES RIBOZYMES?
As soon as one realizes that the ribosome is an enzyme, the following
question arises. Why does it contain RNA? After all, RNA and DNA
polymerase, which have analogous functions, get along quite well
without it.
Some have attempted to explain the presence of RNA in ribosomes by
arguing that base-pairing is the most economical way to obtain the
substrate-enzyme interactions required during the ribosomal phase of
protein synthesis, because all the substrates involved are nucleic acids.
Although this argument has some force, it does not carry the day. Given
the versatility of proteins, there is no reason to believe that an all-protein
catalyst could not have evolved to perform the same function. Since there
is no compelling chemical explanation for rRNA, the reason it exists
must have an evolutionary explanation.
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P.B. Moore
Do Proteins Do It or Does the RNA?
Two extreme hypotheses can be entertained for the function of the
rRNAs. On the one hand, all the important catalytic functions of the
modern ribosome could be mediated by its proteins, and its RNA might
serve only as a scaffold on which proteins are hung (see, e.g., Fellner
1974). Alternatively, rRNA could be responsible for all important
ribosomal functions, with the proteins serving only auxiliary functions.
Someone evaluating the merits of these two models in 1970 would
have noted with satisfaction that the first model ascribes catalytic activity
to molecules of a class well known for it, but its defect would have been
equally obvious. What purpose is served by attaching catalytic proteins
to large pieces of RNA? If the primordial ribosome was an all-protein assembly, how did it ever acquire RNA components (Crick 1968; Woese
1980)?
The ribocentric model is easier to rationalize from an evolutionary
point of view. If the primordial protein-synthesizing system depended on
a catalytic RNA, the retention of RNA in the modern ribosome reflects
nothing more than the conservatism of evolution. Furthermore, no difficulties are created by proposing that proteins were added to the
ribosome as time went on to improve the functional properties of the
RNA that is its core. The only difficulty the ribocentric picture posed for
the biochemist of 1970 was its implication that RNAs are catalytic, a
concept for which there was no precedent.
The collective response of the ribosome field to this conundrum was
not as perverse as some who have written about it since enjoy making it
sound. Yes, the field did concentrate on ribosomal proteins from about
1968 until 1978. This does not imply, however, that the field had collectively decided in favor of the proteocentric ribosome. Biochemistry is a
technique-driven science. One deals today with those problems that
today's technology gives one a chance of solving, not necessarily with
those problems one would like most to solve.
There were sound, practical reasons for working on ribosomal
proteins in that era: (1) Ribosomal proteins could be purified, (2) proteins
could be sequenced, and (3) protein activities could be examined one by
one using reconstitution techniques. Nothing half so interesting was possible with rRNA. If the members of the field had been polled on the
RNA-protein question in that era, many (myself included) would have
claimed to be agnostics.
Today, as a result of the revolution in molecular biology, RNA is
much easier to work with than protein, and most ribosome workers are
using those technologies to study the involvement of rRNA in protein
synthesis to the exclusion of all else. Furthermore, since it is now clear
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that some RNAs have catalytic properties, the conceptual block that earlier held the ribocentric model at bay has disappeared. Now that the
pendulum has swung decisively in favor of the ribocentric ribosome, it
would be wise to review the evidence on which those who profess that
doctrine base their beliefs.
The Last Common Ancestor's Ribosomes Were
Ribonucleoproteins
I can remember wondering in the mid-1970s whether ribosome structure
really is conserved across major phylogenetic boundaries. On the one
hand, we all knew that every ribosome has two unequal subunits, that the
subunits played distinctive roles that are the same from one species to the
next, and that the protein synthesis pathway is basically the same in all
species, granted, of course, the substantial mechanistic differences between prokaryotes and eukaryotes. We also were pretty sure that the
three-dimensional structure of 5S RNAs does not vary from one
taxonomic group to the next (Fox and Woese 1975). All these observations argued for conservation. On the other hand, eukaryotic ribosomes
are almost twice as big as their prokaryotic counterparts, and the few experiments that had been done suggested that parts were not interchangeable between eukaryotic and prokaryotic ribosomes (see, e.g., Wrede and
Erdmann 1973). Moreover, the protein sequence comparisons one could
do (which were not very numerous) suggested that there might be substantial differences between major phylogenetic groups in this regard,
too.
The nucleic acid sequencing revolution of the late 1970s immediately
resolved this problem. Sequences began pouring in for the large rRNAs
from species belonging to all kingdoms. In addition, the number of different 5S rRNA sequences available skyrocketed (see Specht et al. 1990).
Cross-species comparisons led to several important conclusions. First, it
was confirmed that all 5S rRNAs are homologous. Second, it was established that the two large rRNAs from E. coli have homologs in the
ribosomes of all other species, which had not been quite so obvious. We
know the latter is true because all of the sequences available can be
folded into similar secondary structures that place conserved sequences
at corresponding locations (see Noller 1984). Thus, there is no doubt that
the ribosomes in the LCA had rRNAs whose secondary structures
resembled those of their descendants. Because this is so, rRNA sequence
comparisons have become extremely important for determining phylogenetic relationships (see Woese and Pace, this volume).
The existence of strong homologies at the RNA level and their appar-
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ent absence at the protein level was taken by some (myself included) as
evidence for the paramount importance of RNA in ribosome function.
Despite the obscurity that had descended over their activities, the
ribosomal protein-sequencing laboratories continued beavering away,
and as a result of their efforts, the picture has recently become more interesting than that. In the last few years, enough protein sequences from
eubacteria, archaebacteria, and eukaryotes have become available to
make meaningful searches for sequence homologies possible across
kingdom boundaries. They exist, and there are quite a lot of them (Wool
et al. 1990; LO. Wool, pers. comm.).
This discovery has many interesting implications. If ribosomal
proteins were "invented" after the three kingdoms diverged, there should
be no homologies. Every kingdom should have its own set whose members would bind to rRNA in their own ways at their own special locations. The existence of homologies thus argues powerfully that ribosomal
proteins appeared before the great divergence; the LCA had ribosomal
proteins. Furthermore, because we expect that homologous proteins will
bind to rRNAs at homologous locations, another implication of the existence of protein homologies is that ribosome structure should be conserved at the quaternary level, as well as at the primary, secondary, and
tertiary levels. Thus, the LCA's ribosomes must have had a threedimensional structure we would recognize as ribosomal today - if only
we knew what any modem ribosome's structure looks like in three
dimensions.
The reasons the field has been so slow coming to these conclusions
are both technological and scientific. The technological reason is the difficulty connected with sequencing proteins; proteins are harder to sequence than RNAs. The scientific problem has to do with the fact that the
rules that relate sequence to structure in proteins are much less well understood than they are in nucleic acids. Thus, the sequence database for
ribosomal proteins was, and remains, thin compared to that for rRNAs,
and its meaning is much harder to read. Let me add that until we have
determined the structures of ribosomes from organisms belonging to at
least two different kingdoms, it is unlikely that we will fully understand
the extent of the homology that exists between the ribosomal proteins
from different kingdoms.
Ribosome Function Does Not Depend Absolutely
on Its Proteins
Clearly, evidence other than sequence comparisons must be appealed to
in order to decide whether RNA is functionally more important than
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protein in the ribosome. Fortunately, there is a lot of non-sequence data
that speaks to this point, and it all points in the same direction —toward
RNA. Only the most decisive data are summarized here due to limitations of space; a more complete analysis may be found elsewhere (Moore
1986).
The genetic studies of Dabbs have provided the strongest evidence we
have on the nonessentiality of the ribosomal proteins for ribosome function. He has constructed deletion mutations for 16 of the 56 ribosomal
proteins in E. coli and found that none of them are lethal (see Dabbs
1991). Cells that lack specific ribosomal proteins usually grow slowly,
but they do grow, and that means that their ribosomes make protein.
To the list of proteins Dabbs has identified as nonessential for activity
mutationally, we can add the species identified as nonessential by
reconstitution techniques (Held et al. 1973; Held and Nomura 1975;
Ramakrishnan et al. 1986). These experiments, as well as many others,
indicate that there are no ribosomal proteins that make all-or-none contributions to ribosome activity. There are no serine hydroxyl groups or
histidine imidazole groups that are absolutely required by the catalytic
mechanism of the ribosome.
Ribosomal proteins do have a function, however. Modern rRNAs are
incapable of assuming the conformations they display in the ribosome in
the absence of ribosomal proteins, and many of the proteins identified as
nonessential by experiments of the types just described catalyze assembly. Thus, efficient ribosome assembly depends on ribosomal proteins. It
is also certain that ribosomal proteins are the means by which the structure of the ribosome is tuned for optimal function, and the selective pressure for optimization is overwhelming (see Kurland et al. 1990).
RNA Is Directly Involved in Most Ribosomal Functions
The only aspect of protein synthesis that we know for certain depends
exclusively on RNA-RNA interactions is the one identified by Shine and
Dalgarno (1974) many years ago. The pairing between the 3 ' e n d of 16S
rRNA and upstream sequences in bacterial mRNAs which they postulated is responsible for aligning mRNAs on ribosomes during initiation
has been amply documented (see Steitz 1980; Hui and de Boer 1987;
Jacob et al. 1987). The impact this discovery made on the RNA-protein
controversy was modest, however, because the process it explained is
peripheral to decoding and peptide transfer, which are the essence of
protein synthesis.
Although proof of exclusively RNA-based mechanisms is lacking for
other aspects of protein synthesis, the list of processes in which RNA is
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P.B. Moore
known to be intimately involved is a long one. It includes: (1) peptidyl
transferase (Barta et al. 1984), (2) the decoding center on the 30S
ribosomal subunit (Prince et al. 1982), (3) the thiostrepton site (Cundliffe
1986), (4) the a-sarcin-ricin site (Endo and Wool 1982; Endo et al.
1987), and (5) the colicin E3 site (Bowman et al. 1971; Senior and Holland 1971), to name a few. Either RNA is a part of each of these sites, or
the properties of the site are altered by RNA mutation, or damage to the
RNA in the region in question blocks ribosome activity. Structurefunction studies directed at the rRNAs have often led to the sort of all-ornone results that those studying ribosomal proteins in the 1970s wanted
but never obtained.
The most ambitious effort to demonstrate rRNA involvement in
ribosome activity to date has been undertaken by the Noller group at
Santa Cruz, which has been trying to show that the large ribosomal subunit RNA alone will catalyze the fragment reaction of peptidyl transferase (Noller 1991). They have managed to strip almost all the proteins
from the large ribosomal subunit of Thermus aquaticus by a combination
of detergent and protease treatments without destroying its fragment
reaction activity. Unfortunately, some protein resists removal, and as
long as any is present, absolute proof that the peptidyl transferase is
RNA will be lacking. Nevertheless, the finding that a particle that has
lost most of its protein retains transferase activity strongly suggests that
the peptidyl transferase is indeed made of RNA.
The answer to the question raised at the beginning of this section is
thus clear. Ribosomes contain RNA because RNA is directly involved in
many of the interactions on which ribosomal activity depends. "Many"
may ultimately have to be replaced by "all."
CONCLUDING COMMENTS
Three basic messages that advocates of the RNA world should be receiving from their friends and colleagues who work on ribosomes are: (1)
Ribosomes are enzymes, (2) ribosomal RNA is vital for the enzymatic
activity of ribosomes, and (3) the LCA had ribonucleoprotein ribosomes.
How these nuggets of wisdom get incorporated into one's personal
theory about the origin of life is a matter of taste, both because the constraints placed on theories about the early history of this planet by the
evidence available are few, and because hypotheses about the origin of
life are impossible to prove. In addition, origin theories have always had
a disconcerting tendency to ebb and flow with intellectual fashion. It is
wise to regard all of them with skepticism —even the entirely sound and
well-supported theory that is the subject of this volume.
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Of one thing we can be certain: The RNA world —if it ever existed —
was short-lived. The earth came into existence about 4.5 x 1 0 years ago,
and fossil evidence suggests that cellular organisms resembling modern
bacteria existed by 3.6 x 10 years before the present (Schopf 1983).
There are even hints that those early organisms engaged in oxygenic
photosynthesis, which is likely to have been a protein-dependent process
then, as it is now. Thus, it appears likely that organisms with sophisticated, protein-based metabolisms existed only 0.9 x 1 0 years after the
planet's birth.
The "window of opportunity" for the RNA world was much shorter
than 0.9 x 1 0 years. The earth's surface was uninhabitable at the beginning due to the heat generated by meteoric bombardment and its geological differentiation. The oldest rocks discovered so far, which date to only
3.9 x 1 0 years before the present, could be remnants of the planet's
original crust. Moreover, we have to allow some time for cellular forms
to evolve the photosynthetic apparatus that they may have had by 0.9 x
10 years after the beginning. Thus, the interval in which the biosphere
could have been dominated by RNA-based life forms may be less than
100 million years. Incidentally, when one starts thinking along these
lines, one must consider the unthinkable, i.e., that the length of time that
RNA-based organisms bestrode the earth might actually be zero.
9
9
9
9
9
9
Did the denizens of the fleeting, transient RNA world have
ribosomes? Absolutely not. Any entity that contains structures that can
be identified as protoribosomes must be making proteins, and if so, it is
not a bona fide member of the RNA world. It is instead a participant in
the brave new Protein world, as indeed the LCA certainly was. Thus, the
question of what the first ribosomes were like, although of the utmost interest, has not got much to do with the RNA world per se.
In fact, it is quite easy to account for the presence of RNA in modern
ribosomes. Simply postulate that the first useful peptidyl transferase to
evolve was made of RNA, not protein. In addition, it is easy to understand how such a thing might have arisen in a biosphere where RNA was
much more important than it is today, i.e., in the RNA world. Nevertheless, there is no need to propose that the first ribosomes were made
entirely of RNA. Proteins must have come before ribosomes. After all,
why would a device for making polypeptides evolve in an organism that
had no use for protein? A protoribosome that contained both RNA and
protein is thus entirely plausible.
ACKNOWLEDGMENT
This work was supported by a grant from the National Institutes of
Health (AI-09167).
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132
P.B. Moore
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