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Evolution of organelles

This is group 18 with Matthew Cavaciuti, Sarunas Driezis, Owen Griffiths, Kathryn Rudd, Sarah Somji and Alvin Szeto. Hope you like it.
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Alvin Szeto

on 22 November 2012

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Transcript of Evolution of organelles

Cell membrane Ribosomes Endoplasmic reticulum Mitochondria Chloroplast Golgi References Present cell & Nucleus We start in the Primordial Soup There are two competing theories regarding the formation of the endoplasmic reticulum and the nucleus.
- Autogenous
- Symbiosis Endosymbiosis theory: Methanogenic Archaeon and a fermentative myxobacterium merge to form the Eukaryotic Nucleus. Invagination of the Outer Membrane Endosymbiosis Theory The second theory suggests that the nuclear membrane and endoplasmic reticulum evolved from a inward protrusion from the outer membrane of the cell. Figure 2: The endoplasmic reticulum and nuclear envelope. http://www.tutorvista.com/biology/endoplasmic-reticulum-images# We chose to demonstrate the second because:
In eukaryotes, the signal sequence that causes the signal recognition protein to bind and deliver a protein across the ER, also works as the signal sequence for prokaryotic extra cellular delivery.
In prokaryotes the signal sequence that causes the signal recognition protein to bind and deliver a protein across the outer-membrane, also works as the signal sequence for ER delivery.

Both explain why the nuclear envelope is a double layered membrane, but this theory better takes into account how it is linked with the ER. The ER membranes and nuclear membranes are continuous and their lumens are linked. http://upload.wikimedia.org/wikipedia/commons/3/3c/Translation.gif

In this amazing GIF, you can see the translation of a protein, notice the signal recognition protein that binds to the ribosome mRNA complex (temporarily halting translation)and takes it to be inserted ER about half way through. The outer-membrane of the cell bulges inwards bringing the ribosome lining it closer to the DNA.
It extends, providing more surface area to host more ribosomes in close proximity to the genome.
Eventually it completely surrounds the DNA apart from gaps which go on to be guarded by proteins, forming the nuclear pores.
This compartment is beneficial to the newly eukaryotic cell as it keeps its DNA together, safe, right next to, but importantly separate from, the translation factory and allows a new level of control.
The membrane link connecting the ER/nuclear membranes lumen and the environment outside the cell was then withdrawn leaving the distinct organelles. Figure 4: Electron micrograph of the endoplasmic reticulum and nuclear envelope. Notice that the membranes are linked.
(Gerace, L and Burke, B. 1988) STAGE 1
-Through comparisons of the ribosomal crystal structures, it was found that the center of the ribosome is made up of purely RNA bound together by amine bonds; this suggests that the initial ‘pre-ribosome’ was formed in the RNA world (Fox. 2012).
-The RNA is stabilized by a Mg2+ ion. STAGE 2
-The proto-ribosome begins to increase in size as more molecules of RNA collide and bind.
- RNA only remains part of the structure if it's stable and benefits the transpeptidase function of the ribosome (Bokov et al. 2009). STAGE 3
-Primarily the ribosome is only made of RNA but as it’s size increases it's efficiency in producing proteins also improves.
-These can then bind and become fundamentally important in the tertiary structure allowing protuberances to form (Bokov et al. 2009).
-Leading to the formation of the PTC which eventually leads to tRNA binding (Gutell et al. 2008).
-The complex formed is the large subunit of the ribosome. - The small ribosomal subunit is formed later with a complementary shape to that of the large subunit. STAGE 4
There are two theories present for how the small ribosomal subunit formed. Either by: Addition to the growing ribosome or separately - where it acted as a replicase before becoming recruited to the small subunit (Fox. 2012). Although the second theory appears to be preferred there is a lack of supporting evidence and further research is needed. Figure 1: This diagram shows large ribosomal subunit evolution with the addition of molecules (blue and yellow) to a proto-ribosome precursor. Later the small ribosomal subunit is formed and binds (shown in purple.) (Bokov et al. 2009) Introduction Abodeely,M., DuBois, K. M., Hehl, A., Stefanic, S., Sajid, M., deSouza, W., Attias, M., Engel,J. C., Hsieh, Fetter, R. D., McKerrow, J. H. (2009). A Contiguous Compartment Functions as Endoplasmic Reticulum and Endosome/Lysosome in Giardia lamblia. Eukaryotic Cell. 8(11): 1665–1676
Agnes P. Girard-Egrot, Christophe A. Marquette and Loïc J. Blum (2009). Biomimetic membranes and biomolecule immobilisation strategies for nanobiotechnology applications. International Journal of Nanotechnology.
Allwood, A.C., Grotzinger, J.P., Knoll, A.H., Burch, I.W., Anderson, M.S., Coleman, M. L., Kanik, I. (2009) Controls on development and diversity of Early Archean stromatolites. PNAS, 106 (24). pp. 9548-9555.
Bertoni, Kleinsmith, Hardin. (2012). Becker’s World of the Cell. San Francisco, CA: Peasons Education Ltd.
Beznoussenko, G. V., Mironov, A. A. (2002) Models of intracellular transport and evolution of the Golgi complex Wiley- Liss 268(3): 226-238
Body, A., Gagat, P., Mackiewicz, P. (2012). Organelle Evolution: Paulinella Breaks a Paradigm. Current Biology.22(9):304-306
Bokov, K., Steinberg, S. V. (2009). A Hierarchical Model for Evolution of 23S Ribosomal RNA. Nature. 457:977-980
Duhita, N., Thuy L. H. A., Satoshi, S., Kazuo, H., Daisuke, M., Takao, S. (2010) The origin of peroxisomes: The possibility of an actinobacterial symbiosis. Elsevier 450(1-2) 18-24
Fernando, C., Rowe J. (2006). The Origin of Molecular Autonomous Agents by Natural Selection. PLOS Computational Biology.
Fox, G. E. (2012). Origin and Evolution of the Ribosome. Cold Spring Harbor Perspectives in Biology. 2:1-18
Gabaldón, T., Berend, S., van Zimmeren, F., Hemrika, W., Tabak, H., Huynen, M. A. (2006) Origin and evolution of the peroxisomal proteome. Biol Direct 1:8
Gabaldón, T. (2010) Peroxisome diversity and evolution. Philos Trans R Soc Lond B Biol Sci 365(1541):765-773
Garcia, L and Moreira, D. (2006). BioEssays. Selective forces for the origin of the eukaryotic nucleus. 28, 525–533
Green, B. R. (2011). Chloroplast Genomes of Photosynthetic Eukaryotes. The Plant Journal. 66(1):34-44
Grey, M. W., Burger, G., Lang, B. F. (1999). Mitochondrial Evolution. Science. 283(5407):1476-1481
Gutell, R. R., Hartman, H., Lee, J. C., Smith, T. F. (2008). The Origin of the Ribosome. Biology Direct. 3:16
Gupta, R. S., Aitken, K., Falah, M., Singh, B. (1993). Cloning of Giardia lamblia heat shock protein HSP70 homologs: Implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proceedings of the National Academy of Sciences. 91: 2895-2899
Gunter Blobel (1980).Intracellular protein topogenesis. PNAS 77(3):1496-1500.
Hettema, E. H., Motley, A. M. (2009) How peroxisomes multiply. J Cell Sci 122(14): 2331- 2336
Horiike, T., Hamada, K., Kanaya, S. and Shinozawa, T. (2001). Nature Cell Biology. Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. 3, 210-214.
Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (October 2008). "The Miller volcanic spark discharge experiment". Science 322 (5900): 404.
Karp, G. (2007). Cell and Molecular Biology. 5th ed. New York: J. Wiley p207-208, 318
Keeling, P. J., William, B. A. P. (2003). Cryptic Organelles in Parasitic Protists and Fungi. Advances in Parasitology. 54:9-68
Lake, J. A., Rivera, M. C. (1994). Was the nucleus the first endosymbiont. Proceedings of the National Academy of Sciences. 91:2880-2881
Lujan, H. D., Marotta, A., Mowatt, M. R., Sciaky, N., Lippincott-Schwarts, J., Nash, T. E. (1995), Developmental induction of Golgi structure and function in the primitive eukaryote Giardia lamblia J. Biol. Chem., 270:4612–4618
Martin, W. & Mentel, M. (2010) The Origin of Mitochondria. Nature Education. 3(9):58
Marti, M., Hehl, A. B., (2003) Encystation- specific vesicles in Giardia: a primordial Golgi or just another secretory compartment? Trends in Parasitology 19(10): 440-446
Mereschkowsky C (1905). "Über Natur und Ursprung der Chromatophoren im Pflanzenreiche". Biol Centralbl 25: 593–604.
Miller, Stanley L. (May 1953). "Production of Amino Acids Under Possible Primitive Earth Conditions" . Science 117 (3046): 528–9.
Misteli, T. (2001). Where the nucleus comes from. Trends in Genetics 17:190.
Mowbrey, K., Dacks, J. B., (2009) Evolution and diversity of the Golgi body, Gene 583(23): 3738- 3745
Mulkidjanian A. Y., Galperin M. Y., Koonin E. V. (2009).'' Co-evolution of primordial membranes and membrane proteins''. Trends in Biochemical Sciences 34, (4): 206-215.
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Rossanese, O. W., Soderholm, J., Bevis, B. J., Sears, I. B., O’Connor, J., Williamson, E. K., Glick, B. S. (1999) Golgi structure correlates with transitional endoplasmic reticulum organization in Pichia pastoris and Saccharomyces cerevisiae J. Cell Biol., 145:69–81
Searcy, D. G. (2003). Metabolic Integration During the Evolutionary Origin of Mitochondria. Cell Research. 13: 229 - 238
Schlüter, A., Fourchade, S., Ripp, R., Mandel, J. l., Poch, O., Pujol, A. (2006) The Evolutionary Origin of Peroxisomes: An ER- Peroxisome Connection. Mol Biol Evol 23(4): 838-845
Skelton, P (1993). Evolution : a biological and palaeontological approach. Wokingham, England: Addison-Wesley. 50-59.
Tunnicliffe, V. (1991). The Biology of Hydrothermal Vents: Ecology and Evolution. Oceanography and Marine Biology an Annual Review 29: 319–408.
Wächtershäuser, G. (1990). "Evolution of the First Metabolic Cycles". Proceedings of National Academy of Sciences 87 (1): 200–4.
Wilson, K. and Dawson, S. (2011). Functional evolution of nuclear structure. Journal of Cell biology 2:171-181. This diagram taken from Advances in Parasitology shows step by step the stages of both endosymbiotic events (Keeling et al. 2008).
Stages A – D represent the events of primary endosymbiosis.
Stages E – G represent the events which occurred in secondary endosybiosis There are a number of factors involved in the endosymbiosis and why this event was mutually beneficial. Around 2.7 billion years ago oxygen levels began to rise due to the presence of cyanobacteria; this developed two photosystems that were able to take electrons from water to gain energy and producing a bi-product of water (Green. 2011). The next important step is the acquisition of this cyanobacterium via endosymbiosis. It had been found that two important stages involved endosymbiosis of a uni-cellular organism by a heterotroph (Body et al. 2012). These steps are: The first step is the endosymbiosis of a cyanobacterium into a heterotroph, as seen in sections A - D. This heterotroph was fairly well developed and had already gained mitochondria by this point. The uptaken cyanobacterium was then engulfed but instead of being destroyed by lysosomes it was retained within the cytosol and surrounded by a double membrane. Over time, genes would then be transferred from the endosymbionts circular genome to that of the host nucleus which would lead to the coding of target products for the organelle and new metabolic pathways (Green. 2012). This event is termed ‘Primary Endosymbiosis’ and forms the Plante lineages know as red and green alga. The second step, as seen in sections E - H, is via ‘Secondary Endosymbiosis’ of the alga by another heterotroph. This endosymbiotic event is believed to have occurred in parallel resulting in a number of separate Plant lineages, such as: Chromalveolata through endosymbiosis of red algae and Excavates through uptaken green algae. Again gene transfer between the host and endosymbiont would occur, resulting in new product formation. There is much evidence to support this theory, which was initially suggested by Mereschkowsky in 1905 due to the fact chloroplasts and cyanobacteria have similar structures under a microscope (Mereschkowsky. 1905). This has then been proved by DNA analysis and found that some genes retained within the chloroplast have their origins cyanobactium and also in certain species of algae (Green. 2011). Strictly the ribosome in not classified as an organelle due to the fact it is not membrane enclosed but it is an important sub-cellular component (Bertoni et al. 2012). The role of the ribosome is for protein synthesis and they are found in arachea, bacteria and eukaryotes but these are structurally diverse. However, all ribosomes of these cell types have evolved from one primitive ribosome which was present by the time LUCA had formed (Fox. 2012). Eukaryotic cells are extensively subdivided into functionally distinct membrane-bound compartments called organelles. Each type of organelle houses a unique set of proteins that creates a specific environment, and the presence of all these specialized environments within a single cell allows for a great variety of functions to occur simultaneously. - Archaeal cell moved inside the bacterium
-Archaea used bacteria’s metabolic pathways,
- Eventually lost its not metabolic pathway genes.
- Archaea used its genes to express all processes.
- So over time depended on each other
(Garcia, L and Moreira, D., 2006) Endosymbiosis Eventually, the nucleus formed compartments due to:- The endosymbiosis- Compartmentalization to avoid co-existence of pathways −Recent research shows that Opisthokonts (fungi and metazoan animals) include diverse chromatin-binding membrane proteins and membrane luminal domains could have contributed to the evolution of the nuclear membrane.
- However, this area needs more research! Figure 3: Endosymbiosis of an archaea & bacteria Figure 4: Showing formation of the nuclear envelope Abiogenesis of Organic compounds - Early Earth more than 4 billion years ago contained methane, ammonia gas, hydrogen gas, hydrogen sulphate, carbon monoxide, carbon dioxide, water and small traces of organic molecules originating from meteorites.

- Alexander Oparin's (1950) theory: Inorganic compounds form organic molecules, with help of warm from hydrothermal vents and electric discharge from lighting. Stanley Miller set up an experiment to test this hypothesis in 1953 (Miller 1953). An apparatus was set up so that it fluxes warm water through CH4, NH3 and H2 gas chamber with electrodes. The warm water is that cooled and removed from the apparatus at constant time intervals. When Miller analysed the sample he found that it contained amino acids Glycine and Alanine which are precursors for peptides. In 2008 original samples that Miller made back in 1953 were further analysed using modern techniques and found to contain even a wider range of organic molecules including 19 additional amino acids and five amines
(Johnson 2008). Further studies by Wachtershauser and Tunnicliff suggest that other organic molecules such as lipids, nucleotides, RNA and sugars formed in hydrothermal vents. Then these simple lipids were phosphorylated to form phospholipids
(Tunnicliffe 1991)and(Wächtershäuser 1990). Mulkidjanian et al. (2009) propose that membrane proteins co-evolved with the membrane and its bio-energetics. They talk about the an early membrane being impermeable to large particles and charged ions such as H+ and Na+. The paper mentions membrane pores in the phospholipid bilayer and their evolution to membrane proteins such as ATPases, ion channels and translocation proteins. Blobel (1980) further discusses the evolutionary pathways of membrane proteins such as transport, anchoring, cell signaling and communication proteins that eventually allowed evolution of multi-cellular organisms from their unicellular ancestors. Peroxisome Formation of a Protocell - Its been suggested that the first protocell formed 4 billion years ago and said to be the last universal common ancestor for all living organisms that exist (Allwood et al. 2009).
- It has been proposed that the phospholipid bilayer is self replicating and formed within the primordial soup (Fernando et al. 2006).
-Research by Agnes et al. (2009) explains how such enclosure can be synthesised in laboratory conditions and manipulated by various chemical and physical methods. •Peroxisomes are simple, membrane-bound vesicles. They are around 0.1 to 1.0μm in diameter and contain a dense crystalline core of digestive enzymes (Karp, G. 2007).
Peroxisomes have a single membrane, as are Actinobacteria. Biological similarities such as presence of sterols and phosphatidylinositol lipids which made it possible to be an ancestor of both archaens and eukaryotes. (Duhita, N, et al. 2010) http://erocha.freehosting.net/peroxysomes.htm •Peroxisomes synthesise and degrade hydrogen peroxide which is a highly reactive oxidising agent.
•They oxidise very long chain fatty acids as well as synthesizing plasmalogens which are abundant in myelin sheaths.
•Proteins are imported to the peroxisome post translation after being synthesized on free ribosomes in the cytosol (Karp, G. 2007).
•As the peroxisome membrane is a constituent of the endoplasmic reticulum, they are the latest branch of the endomembrane system. (Hettema, E. 2009) (Campbell & Reece 2007) There are 2 Theories on the evolution of Peroxisomes •Endosymbiosis theory:
as peroxisomes divide from existing ones and import proteins just like the mitochondria and chloroplast. Hypothesis put forward by De Duve (1982) based on the endosymbiosis theory of the mitochondria and chloroplast proposed by Margulis 1970 (Gabaldón, T. 2010).
•According to the scenario (which applies to mitochondria and chloroplast and is widely accepted), the proto-peroxisome would have been acquired when oxygen levels in the atmosphere were increasing and were toxic to organisms (Gabaldón, T. 2010). •Formation though the endo-membrane system:
as a mutant cell that lacks peroxisomes, when given the wild type gene will cause peroxisomes to be formed from the endoplasmic reticulum.There are strong indications that proteins have been re-targeted from the mitochondria rather than having evolved directly from endosymbiosis (Gabaldón, T. 2006).
•Peroxisomes and the endoplasmic reticulum show a homologous relationship between the peroxisome import machinery and those of the ER-associated decay pathway (Gabaldón, T. 2010) VIDEO The golgi was first described by Camillo Golgi. The golgi is the site at which vesicles are sorted and targeted elsewhere within the cell. (Mowbrey, K., Dacks, J. B., 2009)

The separation of the plasma membrane from the endo-membrane system could have required a sorting compartment which became the golgi.

Although there are many proposed mechanisms for the evolution of the Golgi apparatus, the widely accepted theory is the ‘Carrier Maturation Model’ (Beznoussenko et al. 2002). - Mitochondria are organelles used primarily to improve the efficiency of ATP production in a cell. The mitochondria exist as membrane bound organelles ranging in size from 0.5 to 1.0 micrometers
(Embley, T. M. & Martin. W., 2006).
- The use of compartmentalization localizes the metabolic pathway that is oxidative respiration. The enzymes and enzyme substrates are at a higher concentration thus increasing the enzyme activity
(Martin, W. & Mentel, M., 2010). Figure 5: Showing endosymbiosis, forming the mitochondria
(Lopez, G and Moreira, D., 2006) The use of compartmentalization localizes the metabolic pathway that is oxidative respiration. The enzymes and their substrates are at a higher concentration thus increasing the enzyme activity
(Martin, W. & Mentel, M., 2010).
The origin of the mitochondria is via the endosymbiosis of an obligate aerobe similar in physiology and lifestyle to modern Rickettsia (Gray MW, et al. 1999). Alternate theories of mitochondrial origin are the pathogenic infection theory that involves the invasion of a eukaryotic cell by a bacterium that becomes less pathogenic over time. There is also the sulphur syntrophy model that has been experimentally tested to show that H2S can be oxidised by the electron transfer chain in mitochondria. (Chen, Y., 2003) Figure 6: Showing eukaryote diversification
(Embley, T. M. & Martin. W., 2006) -The golgi is often found close to the ER in almost all eukaryotes (Rossanese et al. 1999).
-The protozoic Giardia lamblia is one of the earliest identified eukaryotic lineages and has close links to LUCA.
-By comparing Giardia lamblia to present day cells, it offers an insight into how the golgi evolved
– It is believed that the golgi was already stacked by LUCA (Mowbrey et al. 2009).
-Homologs have been found for specific gene in the plasma membrane, the nuclear envelope and the golgi, suggesting that they are closely related and may have evolved from one another (Lujan et al. 1995). Group18 a.k.a Clay Mason25- Matthew Cavaciuti, Sarunas Driezis, Owen Griffiths, Kathryn Rudd, Sarah Somji, Alvin Szeto. (Campbell & Reece 2007) (Lopez, G and Moreira, D., 2006) (Wilson, K. and Dawson, S., 2011). Figure 7: Electron micrograph of a peroxisome. Figure 8: Showing the budding of the peroxisome Figure 9: Endosymbiosis of chloroplasts Figure 10: Showing formation of Golgi Dedicated to Charles Darwin, Richard Dawkins and The Creator of the Universe. For definition of signal sequencing visit http://www.biology-online.org/dictionary/Signal_sequence http://vimeo.com/53844116 •As peroxisomes lack a genome, it is unable to be analyzed though the classic means and the theory of endosymbiosis cannot be completely ignored (Gabaldón, T. 2010) Links to PDF's can be found here: https://docs.zoho.com/index.do Login details:
Name: Claymason25@gmail.com
Password: Evolution

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