Chapter 9 Eukaryotic Cells and Multicellular Organisms

1. Chapter 9Eukaryotic Cells andMulticellularOrganisms Figure CO: Oblong shaped Giardia Courtesy of Dr. Stan Erlandsen/CDC

2. Overview • The origin of cells with eukaryotic organization, some 2.5 Bybp, facilitated the evolution of multicellularity • Endosymbiosis was important in the origin of eukaryotes • Five (or more) supergroups of eukaryotes are recognized • DNA in eukaryotic cells is dispersed among several linear chromosomes • There are separate mitochondrial and chloroplast genomes • Meiosis and some form of sexual reproduction are almost universal in eukaryotes • Some eukaryotes are multicellular

3. Evolution of Eukaryotes • As early as 1.5 Bya eukaryotic cells appear as fossils Figure 01A: Microfossils of probable eukaryotic cells Figure 01B: Microfossils of probable eukaryotic cells Figure 01C: Microfossils of probable eukaryotic cells Reproduced from Schopf, J.W., Scientific American 239 (1978): 111-138. Courtesy of J. William Schopf, Professor of Paleobiology & Director of IGPP CSEOL

4. Evolution of Eukaryotes • Grypania spiralis has been found in ancient rocks in Michigan • This fossil species is preserved because it formed simple shells

5. Still Another Tree of Life • A Tree of Life was established using nucleotide sequences from 5S rRNA of over 30 species of prokaryotes and eukaryotes • This tree is from 1979 • There are still three grades recognized here: animals, plants and fungi • Unfortunately, protistans are omitted from this analysis Figure 02: Phylogenetic tree Adapted from Hori, H. and S. Osawa, Proc. Natl Acad. Sci. USA 76 (1979): 381-385.

6. Single-Celled Eukaryotes: Protistans • Early eukaryotes were single-celled organisms or simple filaments • Today, most eukaryotes are multicellular • All unicellular eukaryotes can be classified in the kingdom Protista • Endosymbiotic events provided mitochondria and chloroplasts • Microtubules drive the nuclear chromosomal divisions (mitosis and meiosis) • But the Kindgom Protista does not appear to be monophyletic

7. Five Eukaryotic Supergroups alveolates chromalveolates * * Others would establish six supergroups Figure B01: Eukaryotic tree of life Adapted from Keeling, P.J., et al., Trends Ecol. Evol. 20 (2005): 670-676.

8. Five Eukaryotic Supergroups • Plantae = Archaeplastida: Charophyta (stem group), red algae, green algae, and land plants • Excavata: Various Protistans, many with parasitic lifestyles (e.g., Giardia, Trichomonas, Trypanosoma) • Chromalveolata: Many of the algae, heterotrophic ciliates, and other Protistan parasites such as Plasmodium falciparum • Rhizaria: A group advocated for by Cavalier-Smith containing heterotrophic Protistans such as foraminiferans and radiolarians • Unikonta: Still other parasitic Protistans, choanoflagellates, fungi, animals, and amebozoans including slime molds

9. Five Eukaryotic Supergroups:Plantae = Archaeplastida Charophyta (stem group) red and green algae Red algae Chlorophytes Viridiplantae Charophytes Streptophyta land plants Plantae Embryophytes

10. Five Eukaryotic Supergroups: Excavata Trichomonas vaginalis Giardia lamblia Trypanosoma sp.

11. Five Eukaryotic Supergroups: Chromalveolata dinoflagellates brown algae diatoms Plasmodium falciparum water molds

12. Five Eukaryotic Supergroups: Rhizaria foraminiferans Figure B03: Diversity of forms of foraminiferans radiolarians Reproduced from E. Haeckel. Art Forms in Nature. New York: Dover Publications, Inc., 1974.

13. Five Eukaryotic Supergroups: Unikonta choanoflagellates animals amoeba cellular slime mold plasmodial slime mold fungi

14. Six Eukaryotic Supergroups As more data is collected, especially DNA sequence data, from more example organisms, and more data about Horizontal Gene Transfer, these groups will be revised -- probably many times Unikontans Figure B02: Eukaryotic tree of life Adapted from Adl, S.M., Simpson, A.G.B., et al., J. Eukaryot. Microbiol. 52 (2005): 399-451.

15. Unikontans & Bikontans one flagellum and basal body versus two Lots of competing hypotheses!

16. Unikontans & Bikontans

17. Origin of the Eukaryotes? We may never know the correct pathway or how many steps were involved Endosymbiosis is very likely an important part of this process Which came first: the nucleus, mitochondria or chloroplasts as organelles?

18. Origin of the Eukaryotes • Free-living bacteria developed mutually beneficial relationships within a host prokaryotic cell • Some aerobic bacteria developed into mitochondria and cyanobacteria into chloroplasts, eventually producing the eukaryotic cells of animals and plants

19. Origin of the Eukaryotes

20. Origin of the Eukaryotes

21. Origin and Evolution of Mitochondria and Chloroplasts • Ancient anaerobic eukaryotic cells evolved the ability to engulf (endocytose or phagocytize) prokaryotes Figure 03: Symbiotic relationships between a eukaryote and its photosynthetic organelles The ciliate Paramecium bursaria houses hundreds of symbiotic green algae which can be liberated from the Protistan cell and the algal cells will live independently Courtesy of Anthony L. Swinehart, Hillsdale College

22. Organelle DNA Differsfrom Nuclear DNA • In location: organelle vs. nucleus • In organization: single circular vs. multiple linear strands • In function: which proteins are coded for and how are they regulated • In mode of replication and inheritance: organelle DNA transmitted maternally during cell division during cytokinesis while nuclear DNA is sorted during nuclear division (mitosis and meiosis)

23. Mitochondrial DNA (mtDNA) • Mt DNA is a single double-stranded circular DNA molecule • There are several copies in each mitochondrion and there are many mitochondria in each eukaryotic cell • Mt DNA is similar to prokaryotic DNA: there are no histones or any other protein associated with mt DNA and Mt DNA genes contain no introns • Because Mt DNA is in a highly oxidizing environment, Mt DNA has a much higher mutation rate than nuclear DNA • Mt DNA genes code for mitochondrial ribosomes and transfer RNAs • Some Mt DNA genes code for polypeptide subunits of the electron transport chain common to all mitochondria • Mt DNA relies on nuclear gene products for replication and transcription

24. Chloroplast DNA (cpDNA) • CP DNA is a single double-stranded circular DNA molecule (the smallest of the three plant genomes) • 20-200 copies in every chloroplast; several thousand copies in each green leaf cell; CP DNA constitutes one-fourth of all DNA in a plant cell • Consists of large (LSC) and small (SSC) single-copy regions separated by two inverted repeat regions • Inherited uniparentally from the maternal (seed) parent • CP DNA contains some 113 genes, 20 of which contain introns; most of these genes are involved with photosynthesis and plastid gene expression • Structural rearrangments of the genome are rare (but when they occur, they are useful in establishing relationships phylogenetically; e.g., losses of genes and introns, inversions, IR expansions or contractions)

25. Origin of VariousPhotosynthetic Eukaryotes The Origin of early Eukaryotic Ancestors leading to the lineages of animals and fungi was probably an independent event from that of the origin of plants Figure 04: Primary, secondary and tertiary endosymbiosis Adapted Cracraft, J. and M. J. Donoghue (Eds). Assembling the Tree of Life. Oxford University Press, 2004.

26. Transfer of Genes Between Organelles and Nucleus • Many genes were transferred to the eukaryotic nucleus; conversely, some nuclear genes were transferred to organelle genomes • Two examples are genes for anaerobic glycolysis and genes for amino acid synthesis • Chloroplasts synthesize only a small portion of the proteins they use • The transfer of nuclear genes coding for symbiotic organelle proteins improves efficiency and reduce the likelihood of mutations

27. Transfer of Genes Between Organelles and Nucleus • Genes transferred to and from the eukaryotic nucleus and internal organelles are a form of horizontal gene transfer • The transfer of genes between the nucleus and the organelles complicates their use in establishing phylogenies • Despite many potential problems, DNA sequences have become important characters in the study of evolutionary relationships

28. The Molecular Clock • Molecular clocks use mutations to estimate evolutionary time • Mutations add up at a “constant rate” in related species • This rate is the ticking of the molecular clock • As more time passes, there will be more mutations • Scientists estimate mutation rates by linking molecular data and real (geological) time

29. Organelle DNA as a Molecular Clock When a stretch of DNA serves as molecular clock, it becomes a powerful tool for estimating the dates of lineage-splitting events • Imagine that a length of DNA found in two species differs by four bases and we know that this entire length of DNA changes at a rate of approximately one base per 25 million years • That means that the two DNA versions differ by 100 million years of evolution and that their common ancestor lived 50 million years ago • Since each lineage experienced its own evolution, the two species must have descended from a common ancestor that lived at least 50 million years ago

30. Mitochondrial DNA and Ribosomal RNA Provide Two Types of Molecular Clocks Mutations add up at a fairly constant rate in the DNA of species that evolved from a common ancestor. Ten million years later— one mutation in each lineage Another ten million years later— one more mutation in each lineage . • Different molecules have different mutation rates • higher rate, better for studying closely related species • lower rate, better for studying distantly related species • Ribosomal RNA is used to study distantly related species • many conservative regions because the shape is so important • lower mutation rate than most DNA loci The DNA sequences from two descendant species show mutations that have accumulated (black). The mutation rate of this sequence equals one mutation per ten million years. DNA sequence from a hypothetical ancestor

31. grandparents mitochondrial DNA nuclear DNA parents Mitochondrial DNA is passed down only from the mother of each generation, so it is not subject to recombination. child Nuclear DNA is inherited from both parents, making it more difficult to trace back through generations. Organelle DNA as a Molecular Clock • Mitochondrial DNA is used to study closely related species • Mt DNA’s mutation rate is ten times faster than that of nuclear DNA due to the reactive oxygen species in the mitochondrial matrix • Mt DNA is passed down from mother to offspring without recombination

32. Using DNA as a Molecular Clock • It is relatively easy to use DNA from living species to draw conclusions about phylogeny and times of divergence • It is more difficult to use DNA from preserved museum and fossil material • First, museum and fossil material may be contaminated by other DNA, especially microbial DNA • Second, fossil material is likely to have only tiny quantities of original DNA from which to work

33. DNA Reveals the Aboriginal Australians Are the First Humans to Leave Africa • An international team of researchers has for the first time sequenced the genome of a man who was an Aboriginal Australian (Science: 22 September 2011) • They have shown that modern day Aboriginal Australians are the direct descendents of the first people who arrived on the continent some 50,000 years ago and that those ancestors left Africa earlier than their European and Asian counterparts • Although there is good archaeological evidence that shows humans in Australia around 50,000 years ago, this genome study re-writes the story of their journey there • The study provides good evidence that Aboriginal Australians are descendents of the earliest modern explorers, leaving Africa around 24,000 years before their Asian and European counterparts • This is contrary to the previous and most widely accepted theory that all modern humans derive from a single out-of-Africa migration wave into Europe, Asia, and Australia The study derived from a lock of hair collected by a British anthropologist one hundred years ago from an Aboriginal man from the Goldfields region of Western Australia in the early 20th century

34. The Polymerase Chain Reaction Figure B04A: The polymerase chain reaction

35. Eukaryote Origins Remain Unclear Which came first – nucleus or organelle? Other details of the transition?

36. Eukaryote Characteristics • DNA organized as linear chromosomes; various states of ploidy • many cytoplasmic membrane-bound organelles • eukaryotic cytoskeleton (microtubules, actin, and intermediate filaments) • eukaryotic ribosomes • presence of external cell wall - variable • sexual reproduction predominates and various means of gene recombination are available • unicellular or multicellular organisms

37. Eukaryotes

38. There Is No Generalized Eukaryotic Protistan Cell

39. Generalized Eukaryotic Cell (Animal) • Plasma Membrane • microvilli • Cytoplasm • Cytoplasmic Organelles • cytoskeleton • ribosomes • mitochondria • rough endoplasmic reticulum • smooth endoplasmic reticulum • Golgi apparatus • lysosomes, etc. • Nuclear Envelope with pores • Nucleoplasm and nucleoli • DNA in chromosomes

40. Generalized Eukaryotic Cell (Plant) • The same basic components and organelles as the animal cell with the addition of a cellulose cell wall, a central water vacuole, which sequesters various chemicals, and chloroplasts that carry out photosynthesis

41. Generalized Eukaryotic Cell (Fungus) The same basic components and organelles as the plant cell but the substitution of a chitin cell wall and no central water vacuole

42. Eukaryotes Package DNA Differently

43. Transcription and Translation in Prokaryotes and Eukaryotes • Prokaryote genes lack introns and, therefore, no pre-mRNA processing is required • Prokaryotes have no nucleus, no separation between DNA and the cytoplasm • Prokaryotic ribosomes are different in structure • Methods of gene regulation differ (prokaryotic operons)

44. Review: Gene Expression • DNA contains a sequence of nitrogenous bases which codes for the sequence of amino acids in a protein • A triplet code, in which each codon is composed of 3 nitrogenous bases, forms the “genetic code” • During transcription • one strand of DNA serves as a template for formation of messenger RNA • mRNA has bases complementary to the base sequence in the DNA • Messenger RNA is processed, with intron removal, before leaving the nucleus

45. Review: Gene Expression (cont.) • mRNA carries the codon sequence to the ribosomes (rRNA and protein) in the cytoplasm • Each tRNA carries a particular kind of amino acid • each tRNA also carries a 3-base anticodon which pairs complementarily to a codon of the mRNA • During translation • the linear sequence of codons in the mRNA determines the order of tRNAs and their attached amino acids • sequential peptide bond formation produces the primary structure of the protein at the ribosome

46. Oxidative Nutrient Metabolism • Breakdown products of carbohydrates, fats, and proteins enter various metabolic pathways where energy is harvested • Oxygen (O2) is used up; carbon dioxide (CO2) is given off

47. Nutrient Catabolism Pathways Are All Interconnected Nucleic acids can also be broken down and the products sent to these or related pathways

48. Photosynthesis

49. Photosynthesis • Plant cells contain numerous chloroplasts • In chloroplasts, light energy is used eventually to produce energy transfer molecules, ATP and NADP+ • These energy transfer molecules power the Calvin cycle, which in turn produces glucose • Glucose is used in cellular respiration and starch synthesis

50. Landmarks in Time • As early as ~3.5 Bya, some prokaryotes develop early photosynthetic metabolism • ~ 2.0 Bya: eukaryotes develop from prokaryotes by complex means including endosymbiosis • ~ 2.0 Bya : eukaryotes develop sexual reproduction and colonial lifeforms • ~1.8 Bya : O2 levels rise sufficiently that the atmosphere becomes oxidizing • ~1.3 – 0.6 Bya : multicellular (metazoan) life evolves, perhaps several times