GEK1530

1. GEK1530 Nature’s Monte Carlo Bakery:The Story of Life as a Complex System Frederick H. Willeboordse frederik@chaos.nus.edu.sg

2. Evolution and Differentiation Lecture 9 Life started with some form of simple (single)-cellular organism. What are the mechanisms by which this organism evolved and how do cells differentiate.

3. Evolution Overview - Major Transitions Before we investigate the details a bit more, let us have a look at the bigger picture.

4. Fossilisation The oldest fossils (about 3.5Gya) are found in a fine grained quartz called “chert”. Typical Chert Quartz has the chemical formula SiO2 (same as glass). Fossil-bearing cherts are made up of tiny interlocking grains of quartz laid down from solution.The precipitated grains took thousands of years to solidify. As the sedimentary rock formed, the dead microbes trapped in the sediment were petrified, that is turned into stone.

5. Fossilisation The tiny quartz grains (forming inside & around the microbes on all sides) developed so slowly that they grew through the cell walls instead of crushing them. As a result, these fossils are preserved in three dimensions as unflattened bodies. They have quartz-filled interiors & brownish color due to the decomposed organic matter of the cell. The fossils found in cherts resemble present-day microbes.

6. Earliest Known Fossils 3,465±5Gyo Interpretative drawing

7. Earliest Known Fossils Fossils are inside this grain

8. Earliest Known Fossils

9. Earliest Known Fossils Importance of Apex chert fossils Taxonometry: Implies close relationship to modern cyanobacteria. Implies life was flourishing on earth 3.5 Gya, just 200 to 500My after the earth became habitable. Conclusions: The 3.5Gyo fossils are remains of water borne microbes with the following properties. • prokaryotes • phototrophs, • oxygen producers • cyanobacterium-like

10. Evolution Reproduction - Replication It is important to keep in mind that reproduction and replication are not the same in this context. Reproduction: Rough copies are produced, there is no genetic apparatus. Replication: Accurate copies are produced, there is some kind of a genetic apparatus.

11. Evolution Error & Mutation Rates Whether it be reproduction or replication, error and mutation rates play an essential role. Most probably, systems that merely reproduce are significantly more error tolerant. Low error/mutation rates would seem to be good. However, in order for evolution to proceed, some changes and hence errors/mutations are necessary.

12. Evolution New Genes New genes do not appear out of nowhere through spontaneous random combinations of nucleotides. At least no such mechanism is known to exist. New genes are based on existing genes.

13. Evolution New Genes Some genes are more ‘open’ to change than others. This can be understood in the following way: Firstly, we need to consider that there are roughlythree types of mutations: Mutations that are beneficial. These will be passed on to future generations and increase the likelihood its genome will survive. Mutations that cause serious damage. Such mutations will generally lead to the death of the organism and hence not be passed on to future generations. Mutations that make no/little difference in the functioning of the organism. These will be passed on to future generations but no help in its survivability.

14. Evolution New Genes Secondly, we need to consider that not all genes are equally important: Highly optimized, essential segment. Since such an element is highly optimized, the chance of obtaining an even better optimization are extremely small. Changes are most likely to be damaging. Due to the essential nature of the segment, the organism will likely die. Redundant segment. Here changes may continue. Non-essential segment. Changes may or may not work out.

15. Evolution New Genes Consequently: Some ribosomal RNA, e.g., has hardly changed since the first modern cells evolved. This is because the process of translation is absolutely essential for all such cells. And since this process applies to many different types of genes, any error in the ‘translator’ will likely break many functions. This is very helpful when constructing a tree of life.

16. Evolution There are four basic ways to obtain new genes from existing genes: New Genes Old Gene New Gene Intragenic mutation Gene Duplication DNA Segment Shuffling Old Organisms New Organisms Horizontal Transfer

17. Stages Cellular Stage - DNA The division of labor between RNA, DNA and proteins. This led to the common ancestor of all living modern cells which can be classified as belonging to one of three different domains: Archaea Eubacteria Eukaryotes Prokaryotes

18. Stages Symbiosis Lynn Margulis • Most active promoter of the idea that symbiosis played a key role in the evolution of life. • There is plentiful evidence that parts of eukaryotic cells were originally independent organisms (Mitochondrion, Chloroplast).

19. Stages Cellular Stage - Prokaryotes All parts (DNA, RNA, proteins etc) in one compartment – i.e. no nucleus. Single cellular - greatest biochemical diversity Mostly about 1,000 – 4,000 genes. Natural Selection seems to favor the cells that can reproduce the fastest. Hence the fewer nucleotides to copy the better. Consequently, the genomes are usually compact and efficient. Horizontal transfer of genes is relatively common (even among prokaryotes of different species).

20. Stages Prokaryotes - Archaea A fairly recent discovery! Initially found in what we would consider inhospitable environment but now known to be quite widespread Thermophiles Halophiles

21. Stages Prokaryotes – Eubacteria Phototrophic Lithotrophic Organotrophic

22. Stages Cellular Stage – Eukaryotes Eukaryotic cells are generally bigger (often 10 times in length and 1000 times in volume) and more complex than prokaryotic cells. Their genome is usually larger as well. The genome is stored in a separate nucleus. There are organelles (mitochondira/chloroplasts) with their own DNA. Horizontal transfer of genes rather uncommon.

23. Stages Cellular Stage – Eukaryotes

24. Stages Eukaryotes - Kingdoms There are four kingdoms Animals Plants Protists Fungi Multi-cellular Single-cellular

25. Stages Eukaryotes - Protists These are single cellular eukaryotes. Even so, they can be very complex. Protozoa Yeasts Hunters Scavengers Algae Photo-synthesizers

26. Stages Sideline: Horizontal Transfer Perhaps, horizontal transfer was very common among primordial cells. This may explain why eukaryotes are similar to archaea in DNA replication and transcription but similar to eubacteria in metabolism.If eukaryotes, archaea and eubacteria would have branched off a tree, this relationship would be rather unlikely. Eukayotes Archaea Eubacteria

27. Stages Cell Differentiation Plants Appeared about 500 million years ago. Animals Unclear when they first appeared. However, the first vertebrae lived around 540 million years ago.

28. Cell Differentiation The jump from single-cellular life to multi-cellular life is far from trivial! Even so, it appears to have happened 3 times in evolutionary history. Animals Single-Cellular Life Plants Eukaryote Fungi This may have happened about 1 billion years ago

29. Cell Differentiation Or may be it was trivial (this is still unknown) and simply a dynamical response to a changing environment. A key issue here is the level of Oxygen. Obviously, larger organisms need more Oxygen and hence a way to transport that Oxygen to where it is needed. If the concentration of Oxygen is low it is hard to see how compact multi-cellular life can exist since only a few cells will need to absorb the Oxygen for other cells (and this means per definition that those few cells will need to absorb more than an individual cell would).

30. Cell Differentiation There is some indication that early multi-cellular life was very thin so that Oxygen could directly diffuse into the cells (this also makes sense since it would take time for blood vessel-like systems to evolve). In any case, cell differentiation did happen. So what are its mechanisms? Adult human: 1013 cells and ~ 200 cell types.

31. Cell Differentiation Clearly, the cells in multi-cellular organisms not only fulfill different roles but they are also physically different. Different Role Neuron Differentiated Cell Different Physically Hart Muscle From a dynamical systems point of view the above distinction is far from trivial. In computers for example, programs with different roles may still use all the same hardware.

32. Cell Differentiation If the Cells are physically different, how does this difference come about? There are two main options one could think about: Daughter Cell receives only the genes required Parent Cell Daughter Cell receives all the genes but only some are active It turns out that the 2nd option is what happens.

33. Cell Differentiation Although clear evidence needs genetic analysis, it is nevertheless possible to at least suspect that this is correct from daily experience. Cut off tip Plant shoot Grows roots! This is only possible if somehow the tip contains the information for making roots.

34. Cell Differentiation If the DNA of virtually all the cells in a multi-cellular organism is identical then we have to ask: How can it fulfill different roles? Identical DNA How can it lead to differentphysical properties? In a simple (but wrong) computer analogy, one could surmise that there’s a gene for everything as there are subsystems and subroutines for everything in a computer.

35. Cell Differentiation The idea of a gene for everything is untenable, however, since the human genome only contains around 30,000 genes. Since it is also known that DNA by itself is static (it can make nice crystals for example) it seems more likely that: DNA Crystal We can look at the cell as a dynamical system where the DNA interacts with its environment and thus reaches certain stable states. If such a picture is correct, it would fit very nicely with the idea of life as a complex system.

36. Cell Differentiation But what determines the Cell state? It had generally been assumed that genome and environmental state determine the cell state but this turned out to be incorrect however (at least as a generic truth). This can be seen by an experiment with E. coli bacteria. Many people believe(d) that, due to their relative simplicity, the idea of the cell state being determined by the genome and the environment would be true for bacteria. It was found by Ko & Yomo in 1994, however, that even when starting from a single bacterium (assuring identical genomes) resulting colonies could display large variations in enzyme activity.

37. Cell Differentiation They discovered that several switching types occur between cells with low and high enzyme activities. High Low Low High High Low Low Furthermore this switching could affect either all of the cells of a colony or only some. Consequently, cell state is not necessarily determined by genome and environment only.

38. Cell Differentiation The changes in cell state occur spontaneously as they may in a system with chaotic dynamics. Of course, in multi-cellular organisms, cells do not spontaneous-ly change their activity levels in the sense as above but what this experiment provides us with is additional support for viewing the cell as a non-linear dynamical system. If (virtually) all the cells have the same genes, how are they activated? There are regulator genes that can turn other genes on or off. Interestingly, these regulator genes themselves can be turned on or off depending on the presence/absence of inhibitors.

39. Cell Differentiation Consequently, we have a stunning mechanism where: In principle, any chemical can switch on/off any gene! What is noteworthy is that this regulating mechanism already exists in prokaryotes ( )and hence predates multi-cellular life.

40. Cell Differentiation Heredity Thus far it was mentioned that when cells divide, the genes are copied. They then differentiate on the basis of the environment and some internal dynamical state. But there’s one more issue: When one cultures regular cells like fibroblasts, they will remain fibroblasts even when they divide.

41. Cell Differentiation Heredity Hence, there also must be a mechanism for transferring the current state of a cell to a daughter cell. This is achieved by a labeling system where markers are attached to genes. Interestingly enough, this system too exists in prokaryotes.

42. Cell Differentiation Heredity Hence there is a dual system for heredity. Copying of genes Copying of cell state And there’s a mechanism for switching genes on/off. Both these are essential for multi-cellular life in order to allow for cell differentiation and both already exist in prokaryotes. Hence, the evolution of multi-cellular life is perhaps not such a big modification after all.

43. Cell Differentiation Response Gene expression is not solely derived from the parent cell though. Gene expression can change as a response to external inputs. Such change can be quite radical (like in cloning) but usually changes are relatively limited (a kidney cell e.g. will not turn into a neuron … ) First of all it is important to note that many processes are common to all cells e.g. Structural proteins of chromosomes RNA polymerasesDNA repair enzymesRibosomal Proteins …

44. Cell Differentiation How different? Secondly, it is important to note that there are at least 6 main stages where gene expression can be controlled. Transcriptional controlRNA processing control RNA transport and localization control Translation control mRNA degradation control Protein activity control Inside Nucleus Inside Cytosol Hence there is clearly a cascading effect Many of the bigger differences may be explained by the accumulation of smaller differences.

45. Wrapping up Key Points of the Day Give it some thought Is cell differentiation is like moving towards various chaotic attractors? No life without information! References Stephen J. Gould M. Philpott http://www.museum.vic.gov.au/prehistoric/what/eras.html The Cell, Alberts et al4th edition http://www.xenbase.org/ http://www.ucmp.berkeley.edu/