1. Prokaryotes First cellular life form over 3.5 billion years ago

2. 演化樹 （種族發生樹 - phylogenetic tree ） 最古老的兩「界」（ kingdom ）觀： – 動物 （ Animalia ） – 植物 （ Plantae ） 改良的五界觀： – 動物 （ Animalia ） – 植物 （ Plantae ；包括藍綠藻 － 原核） – 黴菌 （ Fungi ） – 原生生物（ Protists ；單細胞的真核生物） – 單原生物（ Monera ；單細胞的原核生物） 較新的兩個「超級界」觀念：（風行約三十年） – 真核生物 （ Eukaryotes ） – 原核生物（ Prokaryotes ；﹦細菌？） 最新的三「領域」（ domain ）觀念： – 真核生物 （ Eucarya; eukaryotes ） – 真細菌 （ Bacteria; eubacteria ） – 古生物（ Archaea; archaebacteria 古細菌）

3. Tree of life (based on rRNA sequences)

4. origin vertebrate eukaryotes invertebrate dinosaurs human Prokaryotes only 40 億年 生物演化時間略表

5. 典型的細菌？ 1 µM Fig. 18.1

6. The genetic materials E. coli chromosome: 4.6 Mb = 4.6 x 10 6 bp x 3.4 Å = 1.6 x 10 7 Å = 1.6 x 10 -3 m = 1.6 mm = 1,600¨µm Plasmids are about 100 times smaller. 1 µm Highly packed chromosomal DNA

7. Prokaryotes lack nuclear membrane nucleoid

8. Anatomy of a bacterial cell

9. Cell envelope

10. Gram-negative cell envelope

11. Cell Wall

12. Flagella and pili

13. 與真核生物比較 個體的結構較簡單較小，但是 ⋯ 細胞中分子結構及生物化學一樣複雜 細胞形態高度多樣性 能適應的生態環境寬廣得多 – 「無所不在」 遺傳物質內容變化較大 – 快速的複製，快速的演化

14. 原核生物是地球生命的基礎 光合作用 固氮 有氧的大氣層 地球的表面溫度 生物演化 生物循環 生物共生

15. Photosynthetic bacteria Purple sulfur bacteria Purple nonsulfur bacteria Photosynthetic purple and green bacteria

16. Cyanobacteria 藍綠藻（菌） Extremephile habitats Ancestors of chloroplasts in plants Biochemically, cyanobacteria are very similar to the chloroplasts of red algae (Rhodophyta)

17. 細菌的固氮 植物生長依賴固氮作用 –25% 催化合成，化學肥料 –15% 閃電及其他步驟 –60% 細菌固氮 固氮的細菌 – 水稻田中的 cyanobacteria 很多都不須要施肥 – 某些植物根瘤中的 Rhizobium （最重要的） 輪耕的重要 – 其他共生及自生的細菌

18. 細菌與人類 健康（腸子中的好菌、「養樂多」、 yoghurt ） 疾病醫療（抗生素 ⋯） 形象（口臭、放屁？ ⋯） 環境及生態（被忽略的要素 ⋯） 文明、戰爭、瘟疫等社會大變遷 能源（以色列第一任總統、⋯） 科技（生物技術 ⋯） 飲食 （酸菜、日本納豆 ⋯） 文學藝術 （林黛玉 ⋯）

19. Bacteria we eat Bacillus subtilis 發酵的黃豆：納豆 Sporulation

20. 歷史上的瘟疫 黑死病（ black death ） –Yersinia pestis –1347 年起四分之三世紀中，毀滅四分之三歐洲人口 – 文藝復興的契機？（如自然的山火？） 肺炎（ tuberculosis ） –Mycobacterium tuberculosis – 歷史上最大殺手 — 一億人！ – 剋星居然是同樣屬於放線菌（ Actinomycetes ）的鏈黴 菌（ Streptomyces ）產生的鏈黴素（ streptomycin ）及 rifampicin 。

21. Bacillus anthracis (Robert Koch, 1876) Koch's Postulates: microbiological standard to demonstrate that a specific microbe is the cause of a specific disease

22. 細菌對抗細菌 — 抗生素 抗生素 – 生物所合成（並分泌），殺死或抑制起它生物 的物質；大都是二級代謝物（一級代謝的衍生 物） – 已知約六千種 約三分之二為鏈黴菌所產生 生產菌也會對自己的產生的抗生素敏感 – 抗藥性基因與合成基因在一起，一起表現 – 抗藥性基因擴散到它類細菌（特別是後抗生素 期的病源菌）

23. Actinomycetes Soil habitat Gram positive Differentiation: spores, substrate mycelia, aerial mycelia Linear chromosomes and linear plasmids

24. 腸子中的細菌 腸氣 – 胃及小腸中沒有消化吸收的醣 Raffinose, stachyose, verbascose （豆類中豐富） – 在大腸中被細菌發酵，產生腸氣 抑制其他細菌 酸菜、酸奶、優酪乳（ yoghurt ）、養樂多 –Probiotics Lactobacillus –‘competitive exclusion’

25. 歷史性契機 第一次世界大戰英國火藥原料 acetone 危機 – 俄裔猶太移民 Chaim Weizmann （ Manchester 大學） –Clostridium acetobutylicus 發酵 acetone –1917 年 Balfour 宣言：巴列斯坦為猶太人建國之 地 – 三十年後以色列建國， Weizmann 成為第一任 總統。 – 今日 Weizmann Institute

26. Bacterial insecticide Bacillus thuringiensis Toxin: spore crystal proteins

27. 扭轉歷史的細菌 — 威力強過槍炮 — 傷寒菌 –Rickettsia prowazekii ( 紀念兩位因研究喪生的科 學家 Ricketts 及 Prowazek ） 瓦解拿破崙大軍 –1526 年法國圍攻 Naples 失敗 –1566 年德國放棄進攻奧圖曼帝國 –1812 年拿破崙遠征俄國大敗（最慘）

28. 這方面有趣的讀物 Power Unseen –(Dixon, B. 1994) 以歷史或時事為例子說明微生物的與人類之間的密切關係 The outer reaches of life –(Postgate ， 1994) 生動地描述生活在極端環境的微生物 肺結核之戰（絲路） – 抗生素發展史事 演化之舞（ Microcosmos ） – （ Margulies 與 Sagan 著，王文祥譯， 1995 ，天下）提出了生命共生理論， 認為地球上所有生命形式的根基就是細菌。 瘟疫與人（ Plagues and Peoples ） – （ McNeill 著，楊玉齡譯， 1997 ）傳染病放到歷史的詮釋領域裡，審視傳染 病在歷史所扮演的角色 槍炮、病菌與鋼鐵 (Guns, Germs and Steel) – （ Diamond 著，王道還、廖月娟 譯，時報， 1998 ）槍炮、病菌與鋼鐵是怎 樣成為族群鬥爭的利器

29. Bacterial Genetics

30. Evolution of the genomes The concept of ‘genome’ –The whole set of genetic elements in an organism Chromosomes Extrachromosomal elements (‘episomes’) –Plasmids –Mitochondrial chromosomes and plasmids –Chloroplast chromosomes and plasmids The contents of genomes change by: –Mutation –Recombination (broad sense)

31. The first genetic exchange programs The concept of ‘genome’ –The whole set of genetic elements in an organism Chromosomes Extrachromosomal elements (‘episomes’) –Plasmids –Mitochondrial chromosomes and plasmids –Chloroplast chromosomes and plasmids Two kinds of exchanges –The whole molecules (Assortments) –Sequence rearrangements (Recombination) Between homologous DNA ‘Homologous recombination’ Between non-homologous DNA –Site-specific recombination, transposition, illegitimate recombination

32. Recombination or mutation? Fig. 18.12 Frequencies of occurrences Proper controls

33. 1952: Lederberg 將此染 色體外之遺傳物質命名為 Plasmid （質體） 質體引導細菌染色體的重組

34. 細菌的「變性」 Fig. 18.14

35. Fig. 18.15a Conjugal transfer of plasmid

36. Hfr (High frequency of recombination) 1950 Luca Cavalli-Sforza –HfrC 1953 William Hayes –HfrH Fig. 18.15b

37. Fig. 18.15c Mobilization of Hfr chromosomes

38.  染色體從「供給者」到「接受者」有順序的 傳遞 — 可以用來進行遺傳定位  大腸桿菌的染色體是環狀的 用打斷交配 (interrupted mating) 做遺傳 定位

39. Elie Wollman & Jacob, 1955 用果汁機打斷細菌的鴛鴦美夢

40. Plasmids 質體 Universal presence –Prokaryotic cell Bacterial Archaea –Eukaryotic cell Cytoplasm Mitochondria Chloroplast Most are circular and some are linear –Promoters of genetic exchanges –Carriers of useful genes Drug resistance, metabolite degradation, etc.

41. Bacteriophages (phages) 噬菌體 - bacterial viruses 病毒 Fig. 18.2d

42. An infection cycle Fig. 18.3

43. Two kinds of phage based on cycles Lytic (virulent) phages –Only lytic pathway Lysis of the host cells Lysogenic (temperate) phages –Two pathways Lytic pathway Lysogenic pathway –Formation of lysogens –Inactive phage genomes (prophage) »Usually integrated »Some are freely replicating

44. Fig. 18.4

45. Bacteriophage lambda Fig. 18.5

46. Virus infection is specific Host range –‘Lock and key’ fit between virus and receptors on the host’s surface –Some viruses have a broad host ragne, and other infect only a single species Most eukaryotic viruses attack specific tissues.

47. Phage-mediated gene transfers Transduction

48. Generalized vs. specialized transduction

49. Three kinds of genetic exchanges between prokaryotes Three kinds –Transformation Mediated by free DNA –Conjugation Mediated by plasmids –Transduction Mediated by phages All involving merozygote (partial diploid) All require even number of crossovers

50. Transposable elements Insertion sequence Fig. 18.16 Fig. 18.18

51. A transposable element, TE (not transposon), is a piece of DNA that can move from one location to another in a cell’s genome. Transposon movement occurs as a type of recombination between the transposon and another DNA site, a target site. –The target may be the chromosome, a plasmid, a virus, or even another TE. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

52. Some TE (not transposons) jump from one location to another (cut-and-paste transposition). However, in replicative transposition, the transposon replicates at its original site, and a copy inserts elsewhere. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

53. The simplest bacterial transposon, an insertion sequence, consists only of the DNA necessary for the act of transposition. The insertion sequence consists of the transposase gene, flanked by a pair of inverted repeat sequences. –The 20 to 40 nucleotides of the inverted repeat on one side are repeated in reverse along the opposite DNA strand at the other end of the transposon. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

54. The transposase enzyme recognizes the inverted repeats as the edges of the transposon. Transposase cuts the transposon from its initial site and inserts it into the target site. –Gaps in the DNA strands are filled in by DNA polymerase, creating direct repeats, and then DNA ligase seals the old and new material. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 18.17

55. Transposable elements Responsible for most spontaneous mutations fin many bacteria –60% in E. coli Natural genetic engineers —Promote deletions, inversion, translocation, replicon fusion B. subtilis does not have transposable elements!

56. Natural genetic engineers Create mutations –Mostly bad –Rarely good - become conserved Promote genome rearrangements and exchanges –Same or similar TE sequences provide sustrates for homologous recombination –Sometimes transposition itself causes rearrangement

57. Transposable elements, plasmids, viruses They are all mobile elements They close related in evolution Some transposable elements (Tn916) are also conjugative plasmids Some prophages (N15) are like like plasmids Some phages (Mu) are transposable elements

58. The newest phase in bacterial genetics The genomic approach

59. Carl Woese, 1977 第三個領域古生物 –Archaea 最初結論的根據－ ribosomal RNA 序 列 古生物 真核生物 細菌

60. C. Venter, H. Smith, C. Fraser 等， 1995 第一套生物體基因組序列 –Haemophilus influenza 目前進展（ 2000 年底） –6 個古生物 （ archae ） –26 個細菌（ eubacteria ） 約 160 個原核基因組在定序中 – 三年內將超過 200 Mb 200,000 基因 約人類基因的三倍

61. 細菌基因組學（ Genomics ） 細菌遺傳學的大革命 不需藉助生化學就（部份）了解生理學 醫療、工業、農業等應用 給《細菌演化學》研究帶來實質的基礎 幫助對整個生物界的了解

62. Bacterial Genomics A revolution in the practice of bacteriology Learning the life style without biochemistry Evolution studies becoming practical Contribution to our vision of the whole living world

63. Metabolism with doing chemistry Primary metabolism –Energy management –Body building Information process –Replication –Transcription –Translation –Repair Pathogenicity Secondary metabolites What is absent is as interesting as what is present

64. 新陳代謝重建 Physiology without biochemistry Metabolic reconstructio n from the genomes

65. Genome sizes and content Sizes: 0.6 kb - 9.4 Mb, about 1.0 - 1.1 kb/gene The larger the genomes, the more complex the life styles The larger the genomes, the more paralogous genes G+C content: 25 - 75% Topology: Circular vs. linear Single or multiple chromosomes and plasmids

66. 見樹見林

67. GC skew with respect to replication

68. 基因組學與演化分析 《 演化學 》 依賴 《 分類學 》 傳統的《 分類學 》 依賴 《 形態學 》 及 《 生化學 》 – 對大型生物非常成功 – 對微生物非常不可靠 … 微小突變可能造成巨大變化 基因組與蛋白質組（ proteome ） – 記載著演化過程的痕跡 – 分析演化的最直接數據

69. Studies of evolution relationship Conservation of protein families Diversity of gene repertoires and organizations Incongruities abundant in the phylogenetic tree Common and intensive horizontal gene transfers –between bacteria and between bacteria and Archeae –Mosaic nature of genomes ‘Gene evolution does not equal species evolution’ Which set of parameters to rely on for a particular task?

70. Proteobacteria 的「內共生」發生

71. Thermophilic ancestors?

72. The third domains — Archeae Originally based on rRNA sequences –Carl Woese Bacteria-type morphology and yet different inside –Genetic system (Replication, transcription, translation -Eukaryotic-like –Metabolic system - bacterial-like

73. 快速擴張的 Phylogenetic Tree

74. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

75. Virus infection by membrane fusion Fig. 18.6 Viruses equipped with an outer envelope –Glycoproteins on the envelope bind to specific receptors on the host’s membrane. The envelope fuses with the host’s membrane, transporting the capsid and viral genome inside. –The viral genome duplicates and directs the host’s protein synthesis machinery to synthesize its own proteins. –After the capsid and viral genome self- assemble, they bud from the host cell covered with an envelope derived from the host’s plasma membrane, including viral glycoproteins. These enveloped viruses do not necessarily kill the host cell.

76. Some viruses have envelopes that are not derived from plasma membrane. –The envelope of the herpesvirus is derived from the nuclear membrane of the host. –Herpesvirus DNA, like many viral DNA, may become integrated into the cell’s genome as a provirus. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

77. RNA viruses In some with single-stranded RNA (class IV), the genome acts as mRNA and is translated directly. In others (class V), the RNA genome serves as a template for mRNA and for a complementary RNA. –This complementary strand is the template for the synthesis of additional copies of genome RNA. All viruses that require RNA -> RNA synthesis to make mRNA use a viral enzyme that is packaged with the genome inside the capsid.

78. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Retroviruses (class VI) Retroviruses have the most complicated life cycles. –These carry an enzyme, reverse transcriptase, which transcribes DNA from an RNA template. –The newly made DNA is inserted as a provirus into a chromosome in the animal cell. –The host’s RNA polymerase transcribes the viral DNA into more RNA molecules.

79. Human immunodeficiency virus (HIV), the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus. The viral particle includes an envelope with glyco- proteins for binding to specific types of red blood cells, a capsid containing two identical RNA strands as its genome and two copies of reverse transcriptase. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 18.7a

80. The reproductive cycle of HIV illustrates the pattern of infection and replication in a retrovirus. After HIV enters the host cell, reverse transcriptase synthesizes double stranded DNA from the viral RNA. Transcription produces more copies of the viral RNA that are translated into viral proteins, which self-assemble into a virus particle and leave the host. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 18.7b

81. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Tumor viruses 1911, Peyton Rous discovered that a virus causes cancer in chickens. Tumor viruses include retrovirus, papovavirus, adenovirus, and herpesvirus types. Viruses appear to cause certain human cancers. –The hepatitis B virus is associated with liver cancer. –The Epstein-Barr virus, which causes infectious mononucleosis, has been linked to several types of cancer in parts of Africa, notably Burkitt’s lymphoma. –Papilloma viruses are associated with cervical cancers. –The HTLV-1 retrovirus causes a type of adult leukemia.

82. All tumor viruses transform cells into cancer cells after integration of viral nucleic acid into host DNA. –Viruses may carry oncogenes that trigger cancerous characteristics in cells. These oncogenes are often versions of proto- oncogenes that influence the cell cycle in normal cells. Proto-oncogenes generally code for growth factors or proteins involved in growth factor function. –In other cases, a tumor virus transforms a cell by turning on or increasing the expression of proto- oncogenes. It is likely that most tumor viruses cause cancer only in combination with other mutagenic events. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

83. Plant viruses can stunt plant growth and diminish crop yields. Most are RNA viruses with rod-shaped capsids produced by a spiral of capsomeres. 6. Plant viruses Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 18.9a

84. Plant viral diseases spread by two major routes. In horizontal transmission, a plant is infected with the virus by an external source. –Plants are more susceptible if their protective epidermis is damaged, perhaps by wind, chilling, injury, or insects. –Insects are often carriers of viruses, transmitting disease from plant to plant. In vertical transmission, a plant inherits a viral infection from a parent. –This may occurs by asexual propagation or in sexual reproduction via infected seeds. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

85. Viroids and prions are infectious agents even simpler than viruses Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

86. Viroids Smaller and simpler than viruses Tiny naked circular RNA molecules (several hundred nt) that infect plants –No protein-coding sequence –Can replicate in the host The RNA molecules disrupt plant metabolism and stunt plant growth, perhaps by disturbing the regulatory systems.

87. Prions Prions are infectious proteins. A prion is a misfolded form of a normal brain protein. It can convert a normal protein into the prion version, creating a chain reaction. –degenerative brain diseases such as scrapie in sheep, “mad cow disease”, and Creutzfeldt-Jacob disease in humans. Fig. 18.10