2016 일반생물학 Ch.16 Prokaryote

The Origin and Evolution of Microbial Life: Prokaryotes and Protists Chapter.16 Introduction: How Ancient Bacteria Changed the World

• Virtually all metabolic pathways on Earth evolved in prokaryotic cells, before the evolution of eukaryotes • The products generated by prokaryotic metabolism changed the Earth’s atmosphere and rocks • Fossilized stromatolites from 3 billion years ago contain the fossils of photosynthetic cyanobacteria – These bacteria produced O2 and made Earth’s atmosphere aerobic

• Prokaryotes lived alone on Earth for over 1 billion years – They remain the most numerous and widespread organisms on Earth – The total biomass of prokaryotes is ten times that of eukaryotes – Most prokaryotes are 1–5 µm in diameter (vs. 10–100 µm for eukaryotic cells) – More prokaryotes live in your mouth than the total number of humans that have ever lived – There are ten times as many prokaryotes living in and on your body as the number of cells in your body

• Prokaryotes live in cold, hot, salty, acidic, and alkaline habitats • Although some bacteria are pathogenic (pathogen) and cause disease, most bacteria on our bodies are benign or beneficial ! Several hundred species of bacteria live in and on our bodies, • decomposing dead skin cells, • supplying essential vitamins, and • guarding against pathogenic organisms. • Prokaryotes in soil decompose dead organisms, sustaining chemical cycles

• The two prokaryotic domains, Bacteria and Archaea, diverged soon after life on Earth arose • Present day Archaea and Eukarya evolved from a common ancestor, complicated by gene transfer between prokaryotic lineages • Some genes of Archaea are similar to bacterial genes, some are similar to eukaryotic genes, and some are unique to Archaea External features

! Prokaryotic cells have three common cell shapes. • Cocci are spherical prokaryotic cells. They sometimes occur in chains that are called streptococci. • Bacilli are rod-shaped prokaryotes. Bacilli may also be threadlike, or filamentous. • Spiral prokaryotes are like a corkscrew. – Short and rigid prokaryotes are called spirilla. – Longer, more flexible cells are called spirochetes.

7 Cocci Bacilli Spirochete

8 External features

! Nearly all prokaryotes have a cell wall. Cell walls • provide physical protection and • prevent the cell from bursting in a hypotonic environment. ! When stained with Gram stain, cell walls of bacteria are either • Gram-positive, with simpler cell walls containing peptidoglycan – Penicillin class antibiotics for Gram positive • Gram-negative, with less peptidoglycan, and more complex and more likely to cause disease. • More toxic due to lipid molecule functioning as a toxin ! The cell wall of many prokaryotes is covered by a capsule, a sticky layer of polysaccharides or protein. ! The capsule • enables prokaryotes to adhere to their substrate or to other individuals in a colony and • shields pathogenic prokaryotes from attacks by a hosts immune system.

9 LPS : endotoxin External features

! Some prokaryotes have external structures that extend beyond the cell wall. • Flagella help prokaryotes move in their environment. • Hairlike projections called fimbriae enable prokaryotes to stick to their substrate or each other.

11 Rapid adaptation in the environment

! Prokaryote population growth • occurs by binary fission, • can rapidly produce a new generation within hours, and • can generate a great deal of genetic variation – by spontaneous mutations, – increasing the likelihood that some members of the population will survive changes in the environment. ! The genome of a prokaryote typically • has about one-thousandth as much DNA as a eukaryotic genome and • is one long, circular chromosome packed into a distinct region of the cell. ! Many prokaryotes also have additional small, circular DNA molecules called plasmids, which replicate independently of the chromosome.

12 13

15 Various structural features contribute to the success of prokaryotes

• Some prokaryotes stick to the substrate or each other with hair-like appendages called pili – Sex pili join prokaryotes during conjugation • Transfer DNA • The flagella of Bacteria and Archaea allow them to move in response to chemical and physical signals in their environment • The prokaryotic flagellum is a naked protein without microtubules – The flagellum rotates like a propeller • Are prokaryotic flagella homologous or analogous to eukaryotic flagella? • Fast cell division : 2n – A single prokaryote could give rise to a colony outweighing Earth in only three days! Flagellum

Plasma membrane Cell wall

Rotary movement of each flagellum Various structural features contribute to the success of prokaryotes

• Some prokaryotes can withstand harsh conditions by forming endospores within an outer cell – The endospore has a thick protective coat – It can dehydrate and is tolerant of extreme heat or cold – Hard to kill the most of these resistant cells by boiling – Autoclave : 121C with high pressure steam – High gamma radiation (44kGy) for space food • When conditions improve, the endospore absorbs water and resumes growth, sometimes after centuries

• Some prokaryotic cells have specialized membranes that perform metabolic functions – Aerobic prokaryotes carry out cellular respiration on infoldings of the plasma membrane – Cyanobacteria carry out photosynthesis on infolded thylakoid membranes • Prokaryotic DNA forms a circular chromosome – Smaller rings of DNA called plasmids carry genes that may provide resistance to antibiotics or metabolize rare nutrients, among other metabolic activities • Many prokaryotes can transfer genes, such as antibiotic resistance genes, within or between species

Thylakoid membrane Prokaryotes obtain nourishment in a variety of ways

• Nutrition diversity of prokaryote :diverse Energy and carbon source – Source of Energy • Sunlight: phototrophic • Chemicals (inorganic or organics): chemotrophic ! Two sources of carbon are used by prokaryotes. • Autotrophs obtain carbon atoms from carbon dioxide. • Heterotrophs obtain their carbon atoms from the organic compounds present in other organisms. • Mode of nutrition – Photo-autotrophs, Photo-heterotrophs, Chemoautotrophs, Chemo-heterotrophs ENERGY SOURCE Sunlight Chemicals Photoautotrophs Chemoautotrophs

2 CO

Oscilliatoria Unidentified rock-eating bacteria Photoheterotrophs Chemoheterotrophs CARBONSOURCE

Rhodopseudomonas A Bdellovibrio attacking a Organic compounds larger cell Biofilm

• In some prokaryotes, metabolic cooperation occurs in surface-coating colonies called biofilms – Biofilms form when cells in a colony secrete signaling molecules that recruit nearby cells – Channels in the biofilm allow nutrients and wastes to move inside and outside the biofilm • Biofilms cause ear and urinary tract infections and the dental plaque that produces tooth decay (ex. Dental plaque) ! Prokaryotes attach to surfaces and form biofilm communities that • are difficult to eradicate and • may cause medical and environmental problems. ! Biofilms are large and complex “cities” of microbes that • communicate by chemical signals, • coordinate a division of labor and defense against invaders, and • use channels to distribute nutrients and collect wastes. ! Biofilms • clog and corrode pipes, • gum up filters and drains, and • Coat the hulls of ships.

28 29 30 Prokaryotes help clean up the environment

! Prokaryotes are useful for cleaning up contaminants in the environment because prokaryotes • have great nutritional diversity, • are quickly adaptable, and • can form biofilms. ! Bioremediation is the use of organisms to remove pollutants from soil, air, or water. ! Prokaryotic decomposers are the mainstays of sewage treatment facilities. • Raw sewage is first passed through a series of screens and shredders. • Solid matter then settles out from the liquid waste, forming sludge. • Sludge is gradually added to a culture of anaerobic prokaryotes, including bacteria and archaea. • The microbes decompose the organic matter into material that can be placed in a landfill or used as fertilizer.

31 Biomediation

• Bioremediation is becoming an important tool for cleaning up toxic chemicals released into the soil and water by industrial processes. • Environmental engineers change the natural environment to accelerate the activity of naturally occurring prokaryotes capable of metabolizing pollutants.

32 33 Archeae

! New studies of representative genomes of prokaryotes and eukaryotes strongly support the three-domain view of life. • Prokaryotes are now classified into two domains: – Bacteria and – Archaea. • Archaea have at least as much in common with eukaryotes as they do with bacteria.

34 35 Archaea thrive in extreme environments—and in other habitats

• Archaea are among the most abundant cells on Earth • They are a major life-form in the oceans – Extreme halophiles • Salt-loving archaes, ex. Halobacterium halobium – Extreme theromophiles • Heat-loving archaes, ex. Sulfolobus – Taq polymerase (from thermophilic bacterium, Themus aquaticus) vs Pfu DNA polymerase (from hyperthermophilc archaeon, Pyrococcus furious) – Methanogens • Live in anaerobic environments and give off methane as a waste product – the digestive tracts of cattle and deer and – decomposing materials in landfills. • Extremophiles 37 BioEssays 25:1119–1128, 2003.

38 Bacteria include a diverse assemblage of prokaryotes

The domain Bacteria is currently divided into five groups, based on comparisons of genetic sequences. 1. Proteobacteria – are all gram negative, – share a particular rRNA sequence, and – represent all four modes of nutrition. – Include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter

39 Bacteria include a diverse assemblage of prokaryotes

2. Gram-positive bacteria – rival proteobacteria in diversity and – include the Actinobacteria, streptomyces common in soil. • Produce Secondary metabolites (high pharmacological and commercial interest) ex. Actinomycin, hundreds of natural antibiotics – Streptomyces is often cultured by pharmaceutical companies as a source of many antibiotics. (ex. Streptomycin : Binds to bacterial ribosome to inhibit protein synthesis) – A few pathogens such mycobacterium • M.tuberculosis (tuberculosis) and M.leprae (leprosy:Hansen’s disease) – Abnormal cell wall structure (neither gram positive nor negative) – resistant to penicillin and other antibiotics » Waxy coating on cell surface (mycolic acid) : resistant to drug entry – Hard to be cured. Takes several months for successful treatment – Treated by Bacterial RNA polymearse inhibitor : Rifamycins or fatty acid synthase inhibitor, Isoniazid (inhibiting mycolic acid)

40 Actinomycin D: polypeptie antibiotics from Streptomyces - Anti-cancer activity - By inhibiting transcription - Block to form the transcription initiating complex to prevent RNA elongation 에덴의 마지막날

Streptomycin

41 Bacteria include a diverse assemblage of prokaryotes

! 3. Cyanobacteria • Cyanobacteria are the only group of prokaryotes with plantlike, oxygen-generating photosynthesis. • Some species, such as Anabaena, have specialized cells that fix nitrogen. ! 4. Chlamydias • Chlamydias live inside eukaryotic host cells. • Chlamydia trachomatis – is a common cause of blindness in developing countries and – is the most common sexually transmitted disease in the United States. ! 5. Spirochetes are • helical bacteria and • notorious pathogens, causing – syphilis and – Lyme disease. 42 Some bacteria cause disease

• Pathogenic bacteria cause disease by producing poisonous exotoxins or endotoxins – Exotoxins are proteins secreted by bacterial cells – Some of the most powerful toxins known are exotoxins, including the toxin that causes lockjaw (due to sustained spasm of the jaw muscle, Costridium tetani) – Staphylococcus aureus produces several exotoxins, including one that causes deadly toxic shock syndrome (TSS) when it enters the body through a wound "Septic shock • Ex. Methicillin resistant S. aureus : MRSA – Hospital infection – Exotoxin producing E.Coli : O157:H7 • Causes a number of outbreaks of bloody diarrhea and hundreds of deaths 44 Foodborne illness, hemorrhagic diarrhea and kidney failure. Transmission to fecal-oral route

45 46 Some bacteria cause disease

• Endotoxins are components of the outer membrane of gram-negative bacteria, released when the cell dies or is digested by a defensive cell – Endotoxins produce septic shock, bacterial meningitis (Neisseria meningitidis) , and food poisoning (salmonella) – The most widespread pest-carried disease in the United States is Lyme disease, caused by the spirochaete Borrelia burgdorferi – Debilitating arthritis, heart disease, nervous disorder – Avoiding tick bites • Exotoxin : a toxin secreted by a bacteria or fungi. – Botulinum toxin from Clostridium botulium, Corynebacterium diphtheriae • Most potent toxin (LD50 : 1.3-2.1ng/kg) • Botox for cosmetic or medical procedure • Antibiotic resistant bacteria • Education for preventing sexually transmitted diseases

49 Koch’s postulates

! Kochs postulates are four essential conditions used to establish that a certain bacterium is the cause of a disease. They are 1. find the bacterium in every case of the disease, 2. isolate the bacterium from a person who has the disease and grow it in pure culture, 3. show that the cultured bacterium causes the disease when transferred to a healthy subject, and 4. isolate the bacterium from the experimentally infected subject. ! Kochs postulates were used to demonstrate that the bacterium Helicobacter pylori is the cause of most peptic ulcers. ! The 2005 Nobel Prize in Medicine was awarded to Barry Marshall and Robin Warren for this discovery.

50 51 Bacteria can be used as biological weapons

• The bacterium that causes anthrax can be used as biological weapons – Bacillus anthracis forms hardy endospores – Weaponizing anthrax involves manufacturing endospores that disperse easily in air, where they are inhaled and germinate in the lungs • Bacillus anthracis killed five people in the United States in 2001. • Yersinia pestis bacteria – are typically carried by rodents and transmitted by fleas, causing the plague and – can cause a pneumonic form of plague if inhaled. ! Clostridium botulinum produces the exotoxin botulinum, the deadliest poison on earth. ! Botulinum blocks transmission of nerve signals and prevents muscle contraction.

• Prokaryotes are key participants in chemical cycles, making nitrogen available to plants and thus animals • They also decompose organic wastes and dead organisms to inorganic chemicals • Bioremediation is the use of organisms to remove pollutants from soil, air, or water – Prokaryotes are decomposers in sewage treatment and can clean up oil spills and toxic mine waste • Oil-eating bacteria – Genetically Engineered bacteria for higher efficiency • Thiobacillus for removing toxic mine waste

• Protists constitute several kingdoms within the domain Eukarya • are a diverse collection of mostly unicellular eukaryotes, • may constitute multiple kingdoms within the Eukarya, and • refer to eukaryotes that are not – Plants, animals, or fungi. – Many aquatic protists are plankton: Free-floating aquatic organisms. (photosynthetic plankton : phytoplankton) ! Protists obtain their nutrition in many ways. Protists include • autotrophs, called algae, producing their food by photosynthesis, • heterotrophs, called protozoans, eating bacteria and other protists, • heterotrophs, called parasites, deriving their nutrition from a living host, and • mixotrophs, using photosynthesis and heterotrophy.

Caulerpa, a green alga Giardia, a parasite Euglena Pathogenic protozoans

62 Protists are an extremely diverse assortment of eukaryotes

• Symbiosis is a close association between organisms of two or more species – Endosymbiosis—living within another – Termite endosymbionts digest cellulose in the wood eaten by the host – The protists have endosymbiotic prokaryotes that metabolize the cellulose • Protists are eukaryotes, with – Membrane-bound chromosomes – Multiple chromosomes – Flagella or cilia with 9 + 2 pattern of microtubules • Some protists have a very high level of cellular complexity

• The endosymbiont theory explains the origin of mitochondria and chloroplasts. • Eukaryotic cells evolved when prokaryotes established residence within other, larger prokaryotes. • This theory is supported by present-day mitochondria and chloroplasts that • have structural and molecular similarities to prokaryotic cells and • replicate and use their own DNA, separate from the nuclear DNA of the cell.

2 3 Autotrophic 4 Heterotrophic 5 1 Nucleus eukaryotes eukaryotes Heterotrophic eukaryote

Chloroplast Red alga 66 • Primary endosymbiosis gave rise to chloroplasts of “green algae” (chlorophytes and charophytes) and the red algae. • Photosynthetic land plants arose from a green algal ancestor. • Red algal chloroplasts retain some pigments that were present in the original cyanobacterium. • Secondary and tertiary endosymbiosis gave rise to chloroplasts in the other photosynthetic eukaryotes. • The euglenid ancestor engulfed a chlorophyte, retaining the chloroplasts. • Euglenid chloroplasts have the same pigments as green algae and land plants, and have a third membrane.

67 Mixotricha paradoxa - No mitochondria - Bacterial symbiont for functioning mitochondria - Five genomes due to symbiogenesis

68 • Uncertainties remain about the origins of eukaryotic cells. • Lateral gene transfer complicates the study of relationships, and accounts for the number of bacterial genes being found in eukaryotes. • A recent suggestion is that Eukarya arose from the fusion of a Gram-negative bacterium and an archaean.

69 A tentative phylogeny of eukaryotes

• The taxonomy of protists remains a work in progress – The names, boundaries, and placement of clades will continue to change as genomes of more protists are sequenced and compared

Alveolates Alveolates Dinoflagellates Apicomplexans Ciliates Stramenopiles Stramenopiles Diatoms

Brown algae Water molds

Forams Radiolarians Red algae Green algae Chlorophytes Charophytes

Amoebozoans Land plants

Amoebas

Slime molds

Fungi

Choanoflagellates Animals Diplomonads and parabasalids have modified mitochondria

• Diplomonads may be the most ancient surviving lineage of eukaryotes – They have modified mitochondria without DNA or electron transport chains (mitosome), no golgi complex – Most are anaerobic • Parabasalids are heterotrophic protists with modified mitochondria that generate some energy anaerobically – The parasite Trichomonas vaginalis is sexually transmitted, feeding on white blood cells and bacteria living in the cells lining the vagina – Small population in male urethra due to lack of food supply • But can repeatedly infect the female partner • Metronidazole

Undulating membrane Euglenozoans have flagella with a unique internal structure

• Euglenozoans are a diverse clade of protists – Their common feature is a crystalline rod of unknown function inside their flagella • Euglenozoans include heterotrophs, photosynthetic autotrophs, and pathogenic parasites – Trypanosome for sleeping sickness (African trypanosomiasis) – Fatal disease spread by the African tsetse fly Trypanosoma brucei

75 Malaria

• A mosquito-borne infections disease caused by eukaryotic protists (Plasmodium falciparum, Plasmodium malariae) • Act as parasites within RBCs, causing fever, headache, shivering, vomiting, hemolytic anemia, jaundice, renal damage, coma or death • 655,000 people died in 2010 (mostly under 5 years old) • No vaccine therapy, anti-malarial medications • Quinine treatment and resistance has been developed. – Until 1940s, Quinine was the anti-malarial drug of choice • Plasmodium’s complex life cycle makes it difficult to control. • Best strategy—remove stagnant water where mosquitoes breed. Insecticides are also used. • The genomes of Plasmodium falciparum, and Anopheles gambiae have now been sequenced.

76 77 Life Cycle of the Malarial Parasite (Part 1) Quinine

Isolated from Cinchona’s bark Originally discovered by Quechua (Inca) peoples of Peru and Bolivia and later introduced to Europe by the Jesuit missionaries (Jesuit’s bark) and used for anti-malaria in 17th century

Chloroquine 79 Alveolates have sacs beneath the plasma membrane

• Alveolates have membrane-enclosed sacs or alveoli beneath the plasma membrane • Dinoflagellates are important members of marine and freshwater phytoplankton – Some live within coral animals, feeding coral reef communities – Dinoflagellate blooms cause red tides • Ciliates use cilia to move and feed. • Apicomplexans are animal parasites such as Plasmodium, which causes malaria

• Stramenopiles are named for their “hairy” flagellum, usually paired with a “smooth” flagellum – Water molds are fungus-like and decompose dead organisms in freshwater habitats – Diatoms are unicellular, with silicate cell walls – Brown algae are large, complex algae called seaweeds; all are multicellular and most are marine Amoebozoans have lobe-shaped pseudopodia

• Amoebas move and feed by means of pseudopodia • Members of the clade amoebozoans include many free-living amoebas, some parasitic amoebas, and slime molds – All have lobe-shaped pseudopodia Amoebozoans have lobe-shaped pseudopodia

• A plasmodial slime mold is an amoebozoan that forms a plasmodium, a multinucleate mass of cytoplasm – The plasmodium extends pseudopodia through soil and rotting logs, engulfing food by phagocytosis as it grows – Under adverse conditions, the plasmodium forms reproductive structures that produce spores • Cellular slime molds live as solitary amoeboid cells – When food is scarce, the amoeboid cells swarm together, forming a slug-like aggregate that migrates, before forming a fruiting body borne on a stalk

• Foraminiferans and radiolarians move and feed by means of threadlike pseudopodia • Foraminiferans live in marine and freshwater – They have porous tests composed of calcium carbonate, with small pores through which pseudopodia extend • Radiolarians produce an internal silicate skeleton – The test is composed of organic materials

• Red algae are typically soft-bodied, but some have cell walls encrusted with hard, chalky deposits • Green algae split into two groups, the chlorophytes and the charophytes – The charophytes are the closest living relatives of land plants

• The life cycles of most green algae involve the alternation of generations, in which a haploid (n) gametophyte alternates with a diploid (2n) sporophyte generation • Alternation of generations: A multicellular diploid spore-forming organism gives rise to a multicellular haploid gamete-forming organism. • When haploid gametes fuse (fertilization or syngamy) a diploid individual is formed. • The haploid or diploid organism, or both, may also reproduce asexually. • Forms multicellular haploid (n) : gametrophyte • Mulicellular diploid (2n) : sporophyte • The generations may be different morphologically—heteromorphic. • Isomorphic—the generations have similar morphology.

Copyright © 2009 Pearson Education, Inc. • Specialized cells in the sporophyte (sporocytes) divide meiotically to produce haploid spores. • The spores germinate and divide mitotically to produce the haploid gametophyte generation. • Gametes produced by the gametophyte generation must fuse to form a new sporophyte generation.

87 88 Mitosis Male gametophyte Spores Mitosis Gametes

Female gametophyte Meiosis

Fusion of gametes

Sporophyte Zygote

Key Mitosis Haploid (n) Diploid (2n)

Multicellularity evolved several times in eukaryotes

• Multicellularity evolved in several different lineages, probably by specialization of the cells of colonial protists. – Stramenopile lineage " brown algae – Unnamed lineage " red algae, green algae, land plants – Opisthokont lineage " fungi and animals • Multicellular life arose over a billion years ago. • By 543 million years ago, diverse animals and multicellular algae lived in aquatic environments; plants and fungi colonized land 500 million years ago

Locomotor cells Somatic 1 2 3 cells Food- synthesizing cells Unicellular Colony Early multicellular organism Later organism that protist with specialized, interdepen- produces gametes dent cells