A briefing document prepared for the Royal Society
and Association of British Science Writers
by Dr Elizabeth Fisher
April 1995
The Royal Society's two day meeting brought together scientists from many different areas, and the interest and discussion it generated indicates how molecular and cell biology have come of age, and are now addressing one of the most fundamental issues of science and human thought: our evolution.
Conclusions The meeting was all about eukaryotic cells, that is plant and animal cells rather than bacterial cells. There are some fundamental differences between eukaryotic cells compared to bacterial cells and the thrust and debate of the presentations concerned how these differences could have evolved, and why we are not all single cell beings encased in a cellulose wall and asexually dividing in a nutrient rich broth.
Professor John Gerhart(1) summed up the meeting by concluding that while we understand some of the biology of how eukaryotic cells function, and we are beginning to understand how some eukaryotic cell processes might have arisen, we are a long way from understanding which key changes led eukaryotic cells to evolve from bacterial cells. From the talks presented there are examples of either conservation or, conversely, of diversification of systems between eukaryotes and bacterial cells, and we have to understand the significance of these before we fully comprehend the evolution of eukaryotic cellular processes and therefore eukaryotic cells.
Background Current thinking in molecular evolution is that plant and animal cells, 'eukaryotic cells', evolved from bacterial cells. However, plant and animal cells are different from bacterial cells in several fundamental aspects. Most obvious of these is that bacteria are encased in a stiff cellulose wall and bacterial cells do not have a nucleus or a cell membrane, instead the chromosomes are free within the cell. Eukaryotic cells have a nucleus which contains the chromosomes, and the cells are encased in a cell membrane which is a dynamic structure that has enabled eukaryotic cells to come together into multicellular organisms (although plant cells also have a cellulose cell wall).
Bacteria and eukaryotes differ in many other respects, (such as mode of cell division), and some of these were examined in this meeting. If eukaryotic cells evolved from an ancestral bacterial cell, then some of the original bacterial cell functions have changed into what we now recognise as eukaryotic cell functions. How could this happen and why did it occur?
Presentations The introduction to this meeting was presented by one of the organizers, Professor Lewis Wolpert of University College London(2). (Professor Wolpert is well known for his work in various media to make science, in particular biological sciences, more accessible to the general public.) Here he presented an overview of the history of our ideas about how cells work. Professor Wolpert started with the Greeks and made the point that there was little progress in the development of our ideas about cells up until the 19th century, although Hooke had described cells in 1665. As microscopes improved scientists began to describe different cell types and to discern internal structures, such as the nucleus. By 1838 the idea that cells are the universal units was proposed by Schleiden and Schwann, but it took over a decade before Remak and Virchow established that cells divide into new cells, and are not simply formed de novo from basic components. Gradually over the course of the last 150 years we have come to understand more of cell structures and how cells function, both in bacteria and eukaryotes.
One remarkable leap in our understanding of bacterial and eukaryotic cells was described by Dr Russell Doolittle (3) who stated that in 1977 life on earth was reclassified and split not just into two groups, but into three groups: study of nucleic acids in a variety of organisms showed that the earth contains three kingdoms of living things - eukaryotes (plants and animals) and two types of bacteria: eubacteria and archaebacteria. Eighteen years later the three groups have become established in our biological dogma, but we are still arguing about how they are related. One way of assessing the relationships between organisms is to look at how similar their proteins are. Many proteins are common to all three kingdoms, but a few proteins exist in eukaryotes and archaebacteria that have never been found in the eubacteria. For example, a protein called tubulin, which is important for cell division, is known only in eukaryotes. This leaves us with the puzzle of trying to work out where the gene encoding tubulin came from, particularly as tubulin is very similar in all eukaryotes, implying that it is produced by a gene which has changed very little during the course of animal and plant cell evolution. This gene should clearly also be present in bacteria. One clue which is helping to unravel this puzzle comes from new studies of the three dimensional structure of proteins.
As we learn more about the shapes of different proteins we are starting to notice similarities between proteins previously thought to be unrelated. These relationships had been overlooked because the DNA and amino acid structures are too different to show the similarities - but the 3D structure has been maintained. So we are finding more genes in eubacteria that are related to genes in eukaryotes. In the case of actin for example, we are left then with another puzzle: if actin changes so slowly in eukaryotes, why have the related sequences diverged so much in eubacteria? As Dr Doolittle stated, "natural selection is much more subtle than anything we can achieve in the lab".
Another presentation, studying the evolution of DNA sequences by comparing related sequences from different organisms, was presented by Professor Paul Sharp of Nottingham University (4). Different codons in DNA can code for the same amino acid, and each organism has its favourite codon for any particular amino acid. This is called the 'codon usage' of the organism. Professor Sharp has found that codon usage is determined by a number of factors. One factor in mammals is that the genome, the DNA, appears to be roughly divided into regions which are more GC rich and regions which are more AT rich. As more genomes are being sequenced, we are finding these regions of GC abundance in an increasing number of organisms. This affects codon usage, but other factors will also be involved.
Still on the subject of the DNA in cells, Professor Adrian Bird (5) from Edinburgh reiterated that "evolutionary questions are now the big questions in biology" and went on to suggest how a modification of DNA, called methylation, might have led to the evolution of eukaryotes from bacteria, and the evolution of vertebrates (animals with backbones) from other eukaryotes. DNA that is methylated has a chemical modification made to the C nucleotide. Vertebrate DNA is methylated all over the genome, but methyl groups are subject to a high rate of mutation, and for example, the price we pay for such methylation is that one third of all mutations in human genetic diseases are due to methyl C mutations. So, why do vertebrates methylate their DNA? Professor Bird says we know vertebrates have 60,-70,000 genes; invertebrates have only 10-20% of this number, and other organisms have considerably less. Therefore we vertebrates have a considerable problem in keeping all our genes switched off, because most genes only function to produce protein in a few specific tissues. From experiments in Professor Bird's laboratory, and elsewhere, we know that methylation turns off genes. So methylation is our noise reduction control. It turns off all our extra genes when they're not needed. This mechanism has allowed vertebrates to have more genes and be more complex than invertebrates.
Other mechanisms of noise reduction occur between eukaryotes and bacteria, and these have allowed eukaryotes generally to have more genes than bacteria and thus develop into more complex organisms.
Consideration of gene transcription in eukaryotes and bacteria was continued by Dr Mark Ptaschne (6) who proposed that although the details may be different, both types of organisms have similar mechanisms for regulating genes. He again referred to a theme running through the meeting by quoting E.O. Wilson: "Molecular biologists, as they promised, have taken up evolutionary studies, making important contributions whenever they find systematists to tell them the names of organisms...". The investigation of gene transcription was also discussed by Dr Mike Levine (7) who studies the early development of the fruit fly, Drosophila. Dr Levine proposed that one form of evolution of gene function might be provided by not altering the proteins themselves, but by altering their gene regulatory elements and thereby altering where proteins are produced and are active. This point was picked up later by Dr Mike Akam (8), a Cambridge scientist also studying Drosophila. Speculation on the use of regulatory sequences in evolution led to a lively debate between scientists working on organisms as diverse as humans through to bacteriophage, on whether any general principles could be drawn from this work. It is too early to conclude this debate but Professor Bird pointed out that 'bacteria are as successful as we are, and are not trying to turn into men'.
Dr Akam who is an expert in Drosophila development, considered the evolution of arthropods - who are segmental animals (such as lobsters and insects etc) - and who like all animals have a set of genes called hox genes, which lay down some of the basic patterns during development. He compared a crustacean, the shrimp artemia, with the fruit fly and concluded that the hox genes existed in their full complement in a common ancestor. Most importantly, what has changed between artemia and Drosophila is not the numbers of genes but is the controlling elements that regulate where the genes are expressed. Such changes would be a very strong force for altering the basic body plan of an animal.
Still on the subject of DNA, but turning to look at the chromosomes of the eukaryotic cell, Dr Kim Nasmyth (9) speculated on the evolution of the cell cycle and chromosome division in eukaryotes compared to bacteria (Dr Nasmyth studies yeast which is a eukaryote). Dr Nasmyth highlighted many differences between eukaryotes and both types of bacteria (eubacteria and archaebacteria) which have a functional significance.
For example, eukaryotes have their DNA split into multiple chromosomes whereas bacteria tend to have just one chromosome; eukaryotic chromosomes replicate from multiple sites on each chromosome, bacterial chromosomes replicate from just one origin only. Possibly some of these differences arise from fundamental differences in how the chromosomes separate during cell division in eukaryotic and bacterial cells. Once we fully understand these mechanisms we will understand more of how the eukaryotic cell cycle has evolved from the bacterial cell cycle.
In addition to DNA and RNA, other aspects of how eukaryotic cells might have evolved were considered by Professor Wilfred Stein (10) who pointed out that a fundamental difference between plants and animals is that animals can move. Pictures of moving animals and non-moving trees were used to illustrate this point. What causes this difference in mobility may be the massive cellulose wall that surrounds plant and bacterial cells. This cell wall allows the cells to keep their shape, particularly important to bacteria where the water gradient is always into the cell. Because of the cell wall, bacteria - and similarly plant cells - do not flood and explode. Animal cells approach this problem of osmosis differently, by using a sodium pump to alter the ionic strength in the cell. This pump is unique to animal cells and may be the change that allows us a cell membrane, which does not restrain shape, and so enables us to move. This particular sodium pump is only found in animal cells and Professor Stein speculates, "basic to the evolution of animal cells is development of the sodium pump", and "the primary role of the sodium pump in cell volume regulation has evolved to provide the basis for an enormous variety of physiological functions".
Other cellular processes of the eukaryote were described by Professor Henry
Bourne (11) who discussed signal transduction, the passing of
information through the intracellular medium. 'G proteins' are examples of
signal transduction molecules. Most G proteins are made up of three subunits and
Professor Bourne emphasised these subunit components are different in G proteins
doing slightly different jobs. So the eukaryotic cell has built a system of
great subtlety and flexibility from simple components. Dr Graham Warren (12)
continued the theme of looking at the contents of the eukaryotic cell by
discussing the membrane apparatus inside the
cell and how plants and animals have evolved different arrangements of this
membrane apparatus, which might be due to different arrangements of the
microtubules in the cells. Dr Gerald Edelman (13) then
described the cell adhesion molecules which are large cell surface proteins,
coupled to the internal cytoskeleton, that effect some cell-cell interactions.
These molecules are thought to have arisen from a common precursor, which also gave rise to many other molecules involved in the function of the immune system. Dr Tim Mitchison (14) discussed another element of the eukaryotic cell, the microtubule system, and how this might have evolved. Microtubules, such as those seen at the spindles during mitosis, are polymers and in addition they are dynamic in that they use energy to form at one end and degrade at the other (a 'treadmill' effect). Dr Mitchison discussed how, in the transition from bacterial to eukaryotic cells, an individual protein could have mutated into a shape which allowed it to form polymers and then incorporated an energy using function. Such an addition to an early eukaryotic cell might have been one of the first steps in allowing the cell to move.
Dr Laurence Hurst (15) who is an evolutionary geneticist discussed a fundamental determinant of evolution: when considering a trait the question is not "is the trait good for the individual?", but "will the trait spread through the population?". As an example he considered selfish genetic elements. Such elements can spread through a population because they may replicate much more quickly than other DNAs. Also they may spread because they have a deleterious effect on other elements so they remove the other elements from the population - as is the case with mitochondrial DNAs in cells, for example. If different cells fuse, as during sexual reproduction, only one type of mitochondria will be passed to the resulting organism (mitochondria are small organelles within cells and contain their own DNA). In humans we only ever inherit our maternal mitochondria, and in extreme cases such as some single cell animals, the mitochondria from one strain kill those of a second strain, when the cells fuse. This could be taken as an example of the spread of selfish DNA.
This example is particularly important to eukaryotes because in organisms where cells fuse and cytoplasmic (outside the nucleus) organelles which contain DNA might mix, there are only ever two sexes, because it turns out this is the most stable state. Organisms such as mushrooms, which undergo sexual reproduction without the mixing of cytoplasmic organelles such as mitochondria, can - and do - have many sexes.
In considering the general process of how multicellular organisms have evolved from a bacterial precursor, one of the organisers, Professor Marc Kirschner (16) stated that multicellular animals make use of a wide range of 'exploratory processes' which are non-deterministic, but are wasteful and to some extent random.
These processes achieve a desired outcome by a large degree of variation,
followed by selection acting to produce the desired outcome. He cited many
examples in biology to prove his point. These included the development of the
fine scale capillary system in mammals or the tracheal system in flies (which
supplies oxygen to the cells): at a fine level no plan is laid down for these
systems, the vessels grow and are maintained in response to low oxygen tension,
or factors given off by target tissues. Other examples of the stabilisation of
random processes come in the nervous system. In many systems the growth of
neurones or neuronal processes is
excessive, and the final connections are only established by stabilisation of
functional interactions. For example, as tadpoles metamorphose into frogs no new
nerve cells are formed, but previously existing cells are 'reprogrammed' for
their new environment. This is also true in the immune system where specific
responses are generated by variation and selection. These exploratory processes
are very robust and make the organism or cell capable of responding to damage,
or variability in the environment.
Speakers
1. Professor John Gerhart
Department of Molecular and Cell Biology
University of California
Berkeley
California 94720 tel: 00 1 510 642
6382
UNITED STATES OF AMERICA fax: 00 1 510 643 6791
2. Professor Lewis Wolpert
University College and Middlesex School of Medicine
Windeyer Building
Cleveland Street tel: 0171 380 9345
London W1P 6DB fax: 0171 380 9346
3. Dr Russell Doolittle
Centre for Molecular Genetics
University of California San Diego
9500 Gilman Drive
La Jolla
CA 92093 0634 tel: 00 1 619 534 4417
UNITED STATES OF AMERICA fax: 00 1 619 534 4985
4. Professor Paul Sharp
Department of Genetics
University of Nottingham
Queen's Medical Centre
Clifton Boulevard tel: 0115 970 9263
Nottingham NG7 2UH fax: 0115 970 9906
5. Professor Adrian Bird
Institute of Cell and Molecular Biology
University of Edinburgh
Mayfield Road tel: 0131 650 5670
Edinburgh EH9 3JR fax: 0131 650 5379
6. Dr Mark Ptaschne
Department of Biochemistry and Molecular Biology
Harvard University
7 Divinity Avenue
Cambridge
MASS 02138 tel: 00 1 617 495
1000
UNITED STATES OF AMERICA fax: 00 1 617 495 0758
7. Dr Mike Levine
Department of Biology
University of California San Diego
Pacific Hall
9500 Gilman Drive
La Jolla
CA 92093 0322 tel: 00 1 619 534 2230
UNITED STATES OF AMERICA fax: 00 1 619 534 0555
8. Dr Mike Akam
Wellcome-CRC Institute of Cancer and Developmental
Biology
Tennis Court Road tel: 01223 334142
Cambridge CB2 1QR fax: 01223 334089
9. Dr Kim Nasmyth
Research Institute for Molecular
Pathology
Dr Bohr Gasse 7
1030 Vienna tel: 00 43 1 797 3060
AUSTRIA fax: 00 43 1 798 7153
10. Professor Wilfred Stein
Department of Biochemistry
Silberman Institute of Life Sciences
Hebrew University of Jerusalem
Jerusalem 91904 tel: 00 972
2525 649
ISRAEL fax: 00 972 2666 804
11. Professor Henry Bourne
Department of Pharmacology
University of California San Diego
Box 0450
513 Parnassus
San Francisco
CA 94143 0450 tel: 00 1 415 476 8161
UNITED STATES OF AMERICA fax: 00 1 415 476 5292
12. Dr Graham Warren
Imperial Cancer Research Fund
Lincoln's Inn Fields
London tel: 0171 269 3561
WC2A 3PX fax: 0171 269 3417
13. Dr Gerald Edelman
Department of Neurobiology
The Scripps Research Institute
10666 North Torrey
Pines Road
La Jolla
CA 92037 tel: 00 1 619 554 3600
UNITED STATES OF AMERICA fax: 00 1 619 554 6660
14. Dr Tim Mitchison
Department of Pharmacology
University of California
San Francisco
CA 94143 0450 tel: 00 1 415 476 2869
UNITED STATES OF AMERICA fax: 00 1 415 476 5292
15. Dr Laurence Hurst
Department of Genetics
University of Cambridge
Downing Street
Cambridge tel: 01223 333999
CB2 3EH fax: 01223 333992
16. Professor Marc Kirschner
Department of Cell Biology
Harvard Medical School
25 Shattuck Street
Boston
MASS 021115 tel: 00 1 617 432 2200
UNITED STATES OF AMERICA fax: 00 1 617 432 0420
Enquiries to: Ref: PR 17 (95)
Miss Anna Link
Science Promotion Section
The Royal Society
6 Carlton House Terrace
London
SW1Y 5AG
Telephone: 0171-839 5561 ext 315 27th April 1995
INFORMATION NOTE
Why aren't we all bacteria?
On 22nd and 23rd February 1995, the Royal Society held a scientific meeting on The Evolution of Eukaryotic Cellular Processes. The enclosed document was prepared after the meeting to summarize key issues raised by the speakers and to provide a list of helpful contacts for future reference.
This document does not necessarily constitute the views of the Royal Society, and views expressed in it should not be attributed to the Society. The document is free of copyright and may be used without reference to source.