1. Origin of the Taxa Examples of Protista Topic 6 BOT 3015 Bill Outlaw, Instructor

2. Lecture Outline (a) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

3. Lecture Outline (a) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

4. Chronology (a-1) BYBP EVENT

5. Chronology (a-2) BYBP EVENT

6. Chronology (a-3) BYBP EVENT

7. Chronology (a-4) BYBP EVENT

8. Chronology (a-5) BYBP EVENT

9. Chronology (b-1) BYBP EVENT

10. Chronology (b-2) BYBP EVENT

11. Chronology (b-3) BYBP EVENT

12. Chronology (b-4) BYBP EVENT

13. Chronology (b-5) BYBP EVENT

14. Chronology (b-6) BYBP EVENT

15. Chronology (b-7) BYBP EVENT

16. Chronology (b-8) BYBP EVENT

17. Schopf and His Fossils

18. Microfossils (~3.5 BYBP, Australia)

19. Lecture Outline (b) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

20. Origin of the Major Groups (a) Bacteria, Archaea, Eukarya 1. An unknown protobiont evolved two lineages—one leading to Bacteria and a second leading to the progenitor of Archaea and Eukarya. Or,... Credit: Andrew White, Staffordshire University, UK

21. Origin of the Major Groups (b-1) Bacteria, Archaea, Eukarya 2. Bacteria and Archaea arose (either independently or from a single unknown ancestor). A single Bacterial cell fused with a single Archaeal cell, creating the proto-eukaryal cell. Bacterium Archaeaon ? Whole-cell Fusion Proto-eukaryal cell idea from Lynn Margulis

22. Origin of the Major Groups (b-2) Bacteria, Archaea, Eukarya Bacterium **Membrane lipids **Many/most cytosolic metabolic pathways (e.g. glycolysis) Archaeaon **Transcription/DNA compaction **Translation machinery **ATPases (except organellar) **Many enzymes Whole-cell Fusion

23. Origin of the Major Groups (c) Bacteria, Archaea, Eukarya Summary Both explanations are essentially based on inferences from present-day organisms. Both explanations have strong advocates. Interpretations must have reservations. (For example, whole-cell fusion, a common ancestor, or lateral gene transfer could account for a trait in Eukarya.)

24. Lecture Outline (c) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

25. Phagocytosis as a means of horizontal gene transfer. PNAS 100: 7419 In part, as a lead-in to endosymbiosis....

26. Basic Outline of (Primary) Endosymbiosis using the plastid as an example The bulk of evidence (more later) indicates that all chloroplasts resulted from a single primary endosymbiotic event (=monophyletic origin of plastids).

27. In virtually all ways: chloroplasts = mitochondria = bacteria Basis for the Endosymbiosis Mechanism (a) **size **ribosomes size & sensitivity antibiotics (implying homologous function)/translation **... and other features such as bias towards certain lipids in membranes **DNA packaging/transcription **... and, as expected, all the above being in agreement with sequence data (more later)

28. In virtually all ways: chloroplasts = mitochondria = bacteria...but they are not identical: Basis for the Endosymbiosis Mechanism (b) **DNA-containing organelles are only semiautonomous For example, a chloroplast may contain ~100 ORF, but requires ~1000 polypeptides for function. (Some of the missing genes were transferred to the nucleus and some—being redundant with those of the host—were lost.) ** loss of function/features (e.g. cell wall) is the rule (again, a reason for loss of genes).

29. The details... Endosymbiosis—The devil is in the details. **all chloroplasts are not the same. (more later) **all mitochondria are not the same. For example, the typical mammalian mitochondrial genome has only 0.017 MB, but those of some plant mitochondria have up to 2.5 MB.

30. Secondary Endosymbiosis At least three separate secondary endosymbiotic events led to plastids in different groups of algae. Some odd algae even have two kinds of chloroplasts—either from tertiary endosymbiosis or serial acquisition of chloroplasts.

31. Endosymbiosis—Summary and BOT 3015 Focus Primary Secondary Green Alga/Plant Red Alga CryptomonadHeterokont Expert opinion, but not inclusive of all opinions.

32. The historical way to think of gene transfer is vertically: 1. Asexual (e.g., division of a single-celled organism to form two daughter organisms by mitosis) 2. Sexual (i.e., formation of gametes followed by syngamy) Gene transfer... Summary (a) In this historical way of thinking, gene transfer is linear. One can thus construct a tree in which there are unambiguous lines of descent. --------------------------------------------------------------------------- “Life” is not so simple because of horizontal (=lateral) gene transfer.

33. Mechanisms for horizontal gene transfer: Gene transfer... Summary (b) **conjugation, phagocytosis, & endosymbiosis (as shown earlier) ** bacterial transformation (=uptake of naked DNA). Natural (complex cell machinery required) and artificial (e.g., by treatment with membrane-permeabilizing agent); more later ** bacterial transduction (gene introduction by virus) ** “Transformation” is used broadly in most genetic engineering literature to mean a stable change in genetic potential. In plants, e.g., introduction of a novel gene is usually accomplished by (a) transfer of a gene via a recombinant plasmid from the crown gall bacterium, Agrobacterium; (b) biolistics (“gene gun”); electroporation or chemically induced membrane pores; (d) microfibers (stabbing cells with gene-coated fibers.)

34. How important is gene-by-gene horizontal gene transfer in evolution? Gene transfer... Summary (c) **central force of evolution of many different prokaryotes. ** occurs across domains ** role in eukaryotes less certain, but evidence is accumulating in some groups, particularly phagocytotic algae. (E.g., in one study, 21% of nuclear genes for plastid-targeted proteins were derived by horizontal gene transfer.)

35. Lecture Outline (d) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

36. Chloroplasts are one kind of plastid

37. Green Algal and Plant Chloroplast PS II (LHCII with chl b— regions of membrane appression) PSI & most ATPase Calvin Cycle & Starch Storage Two limiting membranes

38. Chloroplast Types (a) Red Algae (most similar to Cyanobacteria) Green Algae & Plant (share recent common ancestor) Secondary Endosymbiosis (Both these particular examples result from engulfing a Red Alga) Brown Algae (and others) (example of heterokont & meiotic gametogenesis) Cryptomonad (convincing example of surviving nucleomorph)

39. Proximal Chl a-complex Two types of chl a-binding proteins (also carotenes); role is to harvest light and transfer energy. Organization of PS II light-harvesting pigments Three types of antenna complexes involved in light harvesting. Reaction Center Complex A few Chl a, other electron- transfer reagents, 5 proteins; role is charge separation. Core Complex = The above two complexes—sufficient for photosynthesis. Essentially the same in all photosynthetic eukaryotes. *** phycobilisomes, cyanobacteria and red algae *** LHCII (chl a/b binding), plants & green algae *** fucoxanthin/chl a/c complex, brown algae

40. Organization of PS II light-harvesting pigments Three types of antenna complexes involved in light harvesting. *** phycobilisomes, cyanobacteria and red algae Extrinsic (little proteinaceous knobs on membrane); no lateral heterogeneity in thylakoid membranes; associated with linear pigments (phycocyanin and phycobilins) Integral complexes. No lateral heterogeneity in thylakoid membranes. *** fucoxanthin/chl a/c complex, brown algae *** LHCII (chl a/b binding), plants & green algae Integral complexes that migrate between photosystems to balance light, thus stacking and unstacking thylakoids. (Recall, stacked and unstacked regions have different functions.)

41. Lecture Outline (e) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

42. Plastidic and other 16S rRNA phylogeny

43. 18S rRNA phylogeny Plants and Green Algae Animals and Fungi Phototrophic & Heterotrophic Heterokonts

44. Summary of Relationships ***Chloroplasts have a monophyletic origin (All plastidic16S rRNA sequences more similar to each other than to any extant cyanobacterium; gene clusters in chloroplasts similar to each other but different to cyanobacteria; similarity of protein import machinery) ***The eukaryotic portions of heterokonts share a common history, regardless of whether photosynthetic or not (morphology, 18S rRNA sequence, much more) ***Fungi and animals share a “recent” common ancestor not shared by other eukaryotes (18S rRNA and much more) ***Green Algae and plants share a recent common ancestor not shared by other groups (chloroplast structure, chemistry, 16S & 18S rRNA sequences)

45. Diversification of plastids The large diversity of plastids, assumed to have been achieved since the seminal endosymbiotic event, obviously raises questions because no single extant cyanobacterium contains the range of light- absorbing pigments found in algae.... but the biosynthetic pathways leading to pigments are similar, and, moreover, the engulfed cyanobacterium might have had the range of pigments, which have been subsequently lost.

46. Lecture Outline (f) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

47. Examples of Green Algae: Colonial Forms These panels depict three species (Gonium, Pandorina, Eudorina) that comprise a colonial series made up of Chlamydomonas-type cells. The pinnacle in this dead-end evolutionary series is Volvox, which is made of thousands of cells.

48. Examples of Green Algae: Siphonous Form Acetabularia

49. Examples of Green Algae: Parenchytamous Forms Ulva

50. Chlamydomonas sp.

51. Chlamydomonas asexual life cycle

52. Chlamydomonas sexual life cycle

53. Lecture Outline (g) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes)

54. Examples of Red Algae: Bonnemaisonia

55. Examples of Red Algae: coralline alga (calcified walls)

56. Examples of Red Algae: Batrachospermum

57. Lecture Outline (h) Chronology of life and life processes on Earth Possible origins of the proto-eukaryal cell Endosymbiosis and other methods for non-vertical gene transfer Morphology and function of chloroplasts 16(18)S rRNA sequence analysis Green Algae Red Algae Heterokonts (Brown Algae and Oomycetes )

58. Heterokont (=different flagella) Image from Graham & Wilcos “Tinsel-type” flagellum with two rows of stiff glycoproteinaceous hairs. Shorter, smooth flagellum, often with a basal swelling that is involved in light sensing.

59. Examples of Brown Algae: Durvillea, New Zealand

60. Examples of Brown Algae: Laminaria

61. Examples of Brown Algae: Macrocystis

62. Examples of Brown Algae: Fucus (Rockweed)

63. Fucus sexual life cycle

64. Phytophthora infestans on potato

65. Phytophthora life cycle

66. End