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Are There Enough Known Parameters to Construct a Probability 41stSaas‐Fee course from Planets to Life 3‐9 April 2011 Lecture 9A. The probability of acquiring life elsewhere and the origin of eukaryotes • Are there enough known parameters to construct a probability equaon for an origin of an Earth life? • What is required to get a eukaryoc cell? • What drives mulcellularity? • Are these extremely rare events? 41stSaas‐Fee course from Planets to Life 3‐9 April 2011 Lecture 9 B – The origin of eukaryotes • The endosymbiosis theory for the origin of eukaryotes • Symbiosis today – a couple of examples • The early stages in the formaon of eukaryotes is not a rare event Important differences between eukaryotes and prokaryotes • Unity of biochemistry and genec code • Eukaryotes have mulple chromosomes, prokaryotes have a singular circular chromosome • Eukaryotes genomes are full of non‐coding DNA and genes encoding RNA • Eukaryoc translaon and transcripon are separate, prokaryotes they happen concomitantly • Eukaryoc informaon genes are Archaea, operaonal genes are Bacteria • Most eukaryote genes have no known prokaryoc homologues • Archaea are adapted to energy stress and can make due with lile free energy; Bacteria and eukaryotes reproduce using reliable energy sources Important differences between eukaryotes and prokaryotes • Unity of biochemistry and genec code • Eukaryotes have mulple chromosomes, prokaryotes have a singular circular chromosome • Eukaryotes genomes are full of non‐coding DNA and genes encoding RNA • Eukaryoc translaon and transcripon are separate, prokaryotes they happen concomitantly • Eukaryoc informaon genes are Archaea, operaonal genes are Bacteria • Most eukaryote genes have no known prokaryoc homologues • Archaea are adapted to energy stress and can make due with lile free energy; Bacteria and eukaryotes reproduce using reliable energy sources If this tree is correct and there was extensive genec exchange (lateral gene transfer) then it is likely that there was only one tree of life since any new genec innovaon that increased survival was rapidly transmied to other “organisms” What is lateral gene transfer and symbiosis? A reculated version of the tree of life, displaying at its boom the last common community (LCC) instead of the last common organism. Implicaon is that lateral gene transfer and symbiosis were (and sll is) a dominant mechanism for creang diversity and complexity (from Boa, 2004) The first stages in the development of eukaryotes • A fusion of archaea and bacteria Nature 431, 2004 Four schemes of natural order in the microbial worlds. a. The three‐domain proposal based on the ribosomal RNA tree, as rooted with data from anciently duplicated protein genes. b. The two empire proposal, separang eukaryotes from prokaryotes and eubacteria from archaebacteria, c. The three domain proposal with connuous lateral gene transfer among domains. d. the ring of life, incorporang lateral gene transfer but preserving the prokaryote divide Rivera and Lake – fusion of bacteria and archaea to form a eukaryote • What kind of bacteria and archaea fused? The three domain The three domain tree Euryarchaeota tree shows eukaryotes and root archaea are Eubacteria Crenarchaeota Archaea separate groups that share a common ancestor Eukaryotes to the esclusin of The Eocyte tree the eubacteria Euryarchaeota root Eubacteria Crenarchaeota The “eocyte” tree has eukaryotes originang within the archaea and Eukaryotes sharing a common Cox et al., 2008 used the sequence of 53 proteins from all ancestor with the three domains involved in transcripon, translaon and Crenarchaeota (eocyte) replicaon to show the eocyte tree is favored The second phase of eukaryoc development • The acquision of the mitochondria and the chloroplast – early symbiosis – The mitochondria are gram‐negave bacteria that probably evolved around 2.5 Ga – The chloroplasts are cyanobacteria that evolved around 2.7 Ga The evoluon of oxygenic photosynthesis (Calvin Bensen Cycle) and the mitochondria (controversy about the original mirochondria but all mulcellular organisms use mitochondria for respiraon involving oxygen and the Tricarboxylic Acid Cycle (TCA) From Hedges et al., Evol. Biol., 2001 Summary diagram showing relationship between timing of evolutionary events (Table 2) and that of Earth and atmospheric histories. Time estimates are shown with ± 1 standard error (thick line) and 95% confidence interval (narrow line). The phylogenetic tree illustrates the radiation of extant eubacterial lineages (blue), and dashed lines with arrows indicate the origin of eukaryotes (BK-o) and origin of mitochondria (BK-m). The earliest divergence (last common ancestor) was not estimated but is placed (arbitrarily) just prior to the AK divergence. The increasing thickness of the eukaryote lineage represents eubacterial genes added to the eukaryote genome through two major episodes of horizontal gene transfer. The rise in oxygen represents a change from <1% to >15% present atmospheric level [34,52], although the time of the transition period and levels have been disputed [19,53]. Yeast cell (~5µm) Centric diatom (~10 µm) The mitochondria and chloroplasts come from symbiosis with cyanobacteria and an alpha‐ proteobacteria Previously Proposed Models i. genome fusion ii. unidenfied host cell acquires nucleus from archaeon, mitochondria from bacterium iii. archaeon engulfs bacterium iv. protoeukaryote (genome with lineage disnct from archaeal or bacterial) engulfs bacterium Model i aempts to explain genomic evidence Models ii‐iv are theories on the origin of the nucleus and/or mitochondria Poole and Penny (2007) Bioessays Koonin, Senkevich, Dolja 2006. Biology Direct. Symbiosis is a very common phenomenon in nature Animal symbiosis • Definion of symbiosis • Examples of symbiosis – A look at our future – Light for all reasons • Symbiosis at vents – Riia symbiosis – aquiring the symbiont – Other animals • Concluding comments Expanded terminology on organism interactions with other organisms • Symbiosis: An associaon between two or more species • Endosymbiont: A symbiont that lives inside of its host, oen within host cells (intracellular symbiont) • Facultave mutualist: A beneficial symbiont that associates with the host, but can also live apart from it. Examples include Rhizobium species that associate with legumes, but also have a free‐living stage in their life cycle. • Obligate mutualist: A beneficial symbiont that lives exclusively with its host and depends on the host for survival. Examples include many nutrional symbionts of insects, which cannot survive outside the insect host cell. These associaons are reciprocally obligate when the host cannot live without the endosymbiont. • Parasite: A symbiont that has a negave effect on host fitness, in contrast to a mutualist that enhances host fitness • Reproducve parasite: a symbiont that manupulates host reproducon to its own benefit. Reproducve parasites usually bias offspring to infected females PNAS, Nov. 2008 The sea slug Elysia chloroca acquires plasds by ingeson of its algal food source Vaicheria litorea. Organelles are sequestered in the mollusc’s digesve epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plasd metabolism depends on the nuclear genome for >90% of the needed proteins. The findings indicate that the sea slug provides the essenal plasd proteins. Genes supporng photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plasd. The source of the photogenec Elysia chloroca genes in the sea slug is from V. litorea. Predaon, horizontal gene transfer results in a “green animal”. Next step is “green humans”. Rowher and Thurber (2009) state that the presence of viruses in both the chloroplast and the nucleus provides a possible mechanism for HGT of photosynthec genes to the host. Viruses would have two roles: They dramacally alter the slug’s life history, and they are probably the vector for HGT between an animal and a plant Two very different sea slugs have evolved ways of using the ability of plants to convert the sun's energy into sugars and other nutrients. In simple terms they have become “photosynthec”. The aeolid nudibranch Pteraeolidia ianthina which "farms" colonies of brown single‐celled algae (zooxanthellae) in its The sacoglossan Placida cf. dendrica body. showing the green network of ducts which contain the green chloroplasts from its algal food. In a symbioc mutualism, the clownfish feeds on small invertebrates which otherwise potenally could harm the sea anemone, and the fecal maer from the clownfish provides nutrients to the sea anemone. The clownfish is addionally protected from predators by the anemone's snging cells, to which the clownfish is immune. Marine animals that use luminescent as part of their behavior and survival Most involve symbioc luminescent bacteria Taningia danae ‐ a female 7 m long filmed off the coast of Japan at 240‐940 m depths Photograph of Watasenia scinllans taken by its own light, showing The Hawaaiian bobtail squid (Euprymna luminescing organs of arms and body scolopes) (ventral view) This blackdevil angler fish, Melanocetus johnsonii, has a luminescent lure that she uses to attract prey and to identify herself to potential mates. Flashlight fish refer to a family of fish, the Anomalopidae, also known as the lantern‐eye fish. Most are in the genus Photoblepharon and the one in the picture is P. steinitzi. The bacterial symbiont is a Photobacterium species. Photographs of Photoblepharon congregated along the reefs on the
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