Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Triclocarban wikipedia , lookup
Microorganism wikipedia , lookup
Human microbiota wikipedia , lookup
Magnetotactic bacteria wikipedia , lookup
Horizontal gene transfer wikipedia , lookup
Bacterial taxonomy wikipedia , lookup
Bacterial morphological plasticity wikipedia , lookup
生物學 Lecture 5: From prokaryotes y to eukaryotes 生物醫學系 羅時成老師 [email protected] ext: 3295 Prokaryotes and Eukayrotes • 學習目標: • To know differences between cells with and without nucleus and understand the endosymbiosis hypothesis Prokaryotes y and Eukaryotes y • 1. Three domains of classification---Bacteria,, Archaea, and Eukaryotes, • 2. 2 H How bacteria b t i cause diseases di (Koch’s (K h’ postulation). • 3. The beneficial of microorganisms and genetic engineering. • 4. How prokaryotes and eukaryotes were coevolved (endosymbiosis ( i i hypothesis). i) Eukarya Land plants Green algae Cellular slime molds Dinoflagellates Forams Ciliates Red algae Diatoms Amoebas Euglena Trypanosomes yp Leishmania Animals Fungi Green nonsulfur bacteria Sulfolobus Thermophiles (Mitochondrion) Spirochetes Halophiles COMMON ANCESTOR OF ALL LIFE Methanobacterium Archaea Chlamydia Green sulfur lf bacteria b t i Bacteria Cyanobacteria (Plastids, including chloroplasts) Euryarchaeotes C Crenarchaeotes h t UNIVERSAL ANCESTOR Nanoarchaeotes Do omain Arrchaea Korarchaeotes Doma ain Eukarrya Eukaryotes Proteobacteria Spirochetes Cyanobacteria Gram-positive Gram positi e bacteria Domain Bacteria Chlamydias Figure 21.UN01 Bacteria Genome size Number of genes Gene density Introns Other noncoding DNA Archaea Most are 16 Mb 1,5007,500 Higher than in eukaryotes None in protein-coding t i di genes Present in some genes Very little Eukarya Most are 104,000 Mb, but a few are much larger 5,00040,000 Lower than in prokaryotes (Within eukaryotes, lower density is correlated with larger genomes.)) Unicellular eukaryotes: t but b t prevalent l t only l in i present, some species Multicellular eukaryotes: present in most genes Can be large amounts; generally more repetitive noncoding di DNA iin multicellular eukaryotes Table 27.2 (A) Mimivirus (arrows) in cytocentrifuged y g A. ppolyphaga yp g cells, seen as Gram-positive p particles about mycoplasma size and appearance (B) Electron microscopy of stained mimivirus and U. urealyticum (a cell) (C) Phylogenetic tree from alignment of ribonucleotide reductase small subunit sequences Genome Size Comparison Science 341, 226 Acanthamoeba polyphaga, the host eukaryote k cell ll ● ● ● Most common protist in soil Bacterivores Cause amoebic keratitis and encephalitis N. Philippe et al. (19 July 2013) Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb. Science 341 (6143 cover), 281 Transmission electron microscopy of a Pandoravirus particle (length: 1.2 μm) Explaination: Despite obeying all criteria to discriminate viruses from cells (no ribosomes, no ATP A production, i no cell division), these Acanthamoeba vviruses, uses, u unrelated e ated to p previously ev ous y recognized virus families, have genomes of up to 2.5 megabases, and d more genes (CDS (CDSs)) th than some microsporidia eukaryotic cells. Phylogeny of the DNA polymerases hinting at the existence of 4th domain in the Tree of Life Endosymbiosis in Eukaryotic Evolution • There is now considerable evidence that much protist diversity has its origins in endosymbiosis • Endosymbiosis is the process in which a unicellular organism engulfs another cell, which becomes an endosymbiont and then organelle in the host cell • Mitochondria evolved by endosymbiosis of an aerobic prokaryote k t • Plastids evolved by endosymbiosis of a photosynthetic cyanobacterium © 2011 Pearson Education, Inc. Figure 28.2 Plastid Dinoflagellates Membranes are represented d k li lines in i as dark the cell. Secondary endosymbiosis Apicomplexans Red alga Cyanobacterium 1 2 3 Primary endosymbiosis Heterotrophic eukaryote Stramenopiles Secondary endosymbiosis One of these membranes was lost in red and green algal d descendants. d t Plastid Euglenids Secondary endosymbiosis Green alga Chlorarachniophytes Figure 28.2a Membranes are represented as dark lines in the cell. Red alga C Cyanobacterium b t i 1 2 3 Primary endosymbiosis Heterotrophic eukaryote One off these O th membranes was lost in red and green algal l l descendants. Green alga Figure 28.2b Plastid Dinoflagellates Secondary endosymbiosis A i Apicomplexans l Red alga Stramenopiles Figure 28.2c Secondary endosymbiosis Plastid Euglenids Secondary endosymbiosis d bi i Green alga Chlorarachniophytes • The plastid-bearing plastid bearing lineage of protists evolved into red and green algae • The DNA of plastid genes in red algae and green algae closely resemble the DNA of cyanobacteria • On O severall occasions i during d i eukaryotic k ti evolution, l ti redd and green algae underwent secondary endosymbiosis, i which in hi h they th were ingested i t d by b a heterotrophic h t t hi eukaryote © 2011 Pearson Education, Inc. Five Supergroups of Eukaryotes • It is no longer thought that amitochondriates (lacking mitochondria) are the oldest lineage of eukaryotes • Many have been shown to have mitochondria and have been reclassified • Our O understanding d t di off the th relationships l ti hi among protist ti t groups continues to change rapidly • One hypothesis divides all eukaryotes (including protists) into five supergroups © 2011 Pearson Education, Inc. Diplomonads Parabasalids Euglenozoans Excavata Figure 28.3a Apicomplexans Ciliates Diatoms Stramenopilles Golden algae Brown algae Chromalveolata Alveolates s Dinoflagellates Oomycetes Forams Radiolarians Gre een alg gae Chlorophytes Charophytes Land plants Archaeplastida Red algae Rhizariia Cercozoans Gymnamoebas Entamoebas Opis sthokonts Nucleariids Fungi Choanoflagellates Animals Unikonta a Amo oebozoans Slime molds Craig Venter creates ssynthetic nthetic life form • Craig Venter and his team have b il the built h genome off a bacterium b i from scratch and incorporated it into a cell to make what they call the world's first synthetic life form • O On May ay 21,, 2010 0 0 Synthetic Biology • Mycoplasma laboratorium is a planned partially synthetic species of bacterium derived from the genome of Mycoplasma genitalium. This effort in synthetic biology is being undertaken at the J. C i Venter Craig V Institute I i b a team off approximately by i l 20 scientists headed by Nobel laureate Hamilton Smith and including DNA researcher Craig Smith, Venter and microbiologist Clyde A. Hutchison III. Mycoplasma genitalium was chosen as it was the species i with i h the h smallest ll number b off genes known k at that time. Dictyostelium y discoideum 黏菌 http://www.youtube.com/watch?V=bkVhLJLG7ug Overview: Masters of Adaptation • Utah’s Utah s Great Salt Lake can reach a salt concentration of 32% • Its pink color comes from living prokaryotes © 2011 Pearson Education, Inc. • Prokaryotes thrive almost everywhere, including places too acidic, salty, cold, or hot for most other organisms • Most prokaryotes are microscopic, but what they lack in size they make up for in numbers • There are more in a handful of fertile soil than the number b off people l who h have h ever lived li d • Prokaryotes are divided into two domains: bacteria and archaea © 2011 Pearson Education, Inc. Concept: Structural and functional adaptations contribute to prokaryotic success • E Earth’s th’ fi firstt organisms i were likely lik l prokaryotes k t • Most prokaryotes are unicellular, although some species i form f colonies l i • Most prokaryotic cells are 0.5–5 µm, much smaller th the than th 10–100 10 100 µm off many eukaryotic k ti cells ll • Prokaryotic cells have a variety of shapes • The three most common shapes are spheres (cocci), rods (bacilli), and spirals © 2011 Pearson Education, Inc. 1 m 1 m 3 m Figure 27.2 ((a)) Spherical p ((b)) Rod-shaped p ((c)) Spiral p Cell-Surface Structures • An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, protects the cell cell, and prevents it from bursting in a hypotonic environment • Eukaryote cell walls are made of cellulose or chitin • Bacterial cell walls contain peptidoglycan, a network off sugar polymers l cross-linked li k d bby polypeptides l id © 2011 Pearson Education, Inc. • Archaea contain polysaccharides and proteins but lack peptidoglycan • Scientists use the Gram stain to classify bacteria by cell wall composition • Gram-positive G iti bacteria b t i have h simpler i l walls ll with ith a large amount of peptidoglycan • Gram-negative bacteria have less peptidoglycan and an outer membrane that can be toxic © 2011 Pearson Education, Inc. Figure 27.3 (a) Gram-positive bacteria: peptidoglycan traps crystal violet. Gram-positive bacteria (b) Gram-negative bacteria: crystal violet is easily rinsed away, revealing red dye. Gram-negative bacteria Carbohydrate portion of lipopolysaccharide Cell wall Peptidoglycan layer Cell wall Plasma membrane 10 m Outer membrane Peptidoglycan layer Plasma membrane • Many antibiotics target peptidoglycan and damage bacterial cell walls • Gram-negative Gram negative bacteria are more likely to be antibiotic resistant • A polysaccharide l h id or protein t i layer l called ll d a capsule l covers many prokaryotes © 2011 Pearson Education, Inc. Figure 27.4 Bacterial cell wall Bacterial capsule Tonsil cell 200 nm • Some prokaryotes have fimbriae, fimbriae which allow them to stick to their substrate or other individuals in a colony • Pili (or sex pili) are longer than fimbriae and allow prokaryotes to exchange DNA © 2011 Pearson Education, Inc. Figure 27.5 Fimbriae 1 m Motility • In a heterogeneous environment, environment many bacteria exhibit taxis, the ability to move toward or away from a stimulus • Chemotaxis is the movement toward or away from a chemical stimulus © 2011 Pearson Education, Inc. • Most motile bacteria propel themselves by flagella scattered about the surface or concentrated at one or both ends • Flagella of bacteria, archaea, and eukaryotes are composed of different proteins and likely evolved independently © 2011 Pearson Education, Inc. Figure 27.6 Flagellum Filament Hook Motor Cell wall Plasma as a membrane Rod Peptidoglycan p gy layer 20 nm Figure 27.6a 20 nm Hook Motor Evolutionary Origins of Bacteria Flagella • Bacterial flagella are composed of a motor, motor hook, hook and filament flagella s proteins are modified versions • Many of the flagella’s of proteins that perform other tasks in bacteria • Flagella likely evolved as existing proteins were added to an ancestral secretory system exaptation where existing • This is an example of exaptation, structures take on new functions through descent with modification © 2011 Pearson Education, Inc. Internal Organization and DNA • Prokaryotic cells usually lack complex compartmentalization • Some prokaryotes do have specialized membranes that perform metabolic functions ese aree usually usu y infoldings o d gs of o thee plasma p s membrane e b e • These © 2011 Pearson Education, Inc. Figure 27.7 1 m 0.2 m Respiratory membrane b Thylakoid membranes (a) Aerobic prokaryote (b) Photosynthetic prokaryote • The prokaryotic genome has less DNA than the eukaryotic genome • Most of the genome consists of a circular chromosome • The Th chromosome h is i nott surrounded d d by b a membrane; b it is located in the nucleoid region • Some species of bacteria also have smaller rings of DNA called plasmids © 2011 Pearson Education, Inc. Figure 27.8 Chromosome Plasmids 1 m • There are some differences between prokaryotes and eukaryotes in DNA replication, transcription, and translation • These allow people to use some antibiotics to inhibit bacterial growth without harming themselves © 2011 Pearson Education, Inc. Reproduction and Adaptation • Prokaryotes reproduce quickly by binary fission and can divide every 1–3 hours • Key features of prokaryotic reproduction: – They are small – They h reproduce d bby bi binary fission fi i – They have short generation times © 2011 Pearson Education, Inc. • Many prokaryotes form metabolically inactive endospores, which can remain viable in harsh conditions for centuries © 2011 Pearson Education, Inc. Figure 27.9 Endospore Coat 0.3 m • Their short generation time allows prokaryotes to evolve quickly – For example example, adaptive evolution in a bacterial colony was documented in a lab over 8 years • Prokaryotes are not “primitive” primitive but are highly evolved © 2011 Pearson Education, Inc. Concept: p Rapid p reproduction, p , mutation, and genetic recombination promote genetic diversity in prokaryotes k t • Prokaryotes k have h considerable id bl genetic i variation i i • Three factors contribute to this genetic diversity: – Rapid reproduction – Mutation utat o – Genetic recombination © 2011 Pearson Education, Inc. Rapid Reproduction and Mutation • Prokaryotes reproduce by binary fission, and offspring cells are generally identical • Mutation rates during binary fission are low, low but because of rapid reproduction, mutations can accumulate rapidly in a population • High diversity from mutations allows for rapid evolution l ti © 2011 Pearson Education, Inc. Genetic Recombination • Genetic recombination, recombination the combining of DNA from two sources, contributes to diversity • Prokaryotic DNA from different individuals can be brought together by transformation, transduction, and conjugation • Movement of genes among individuals from different species i is i called ll d horizontal h i t l gene transfer t f © 2011 Pearson Education, Inc. Transformation and Transduction • A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment in a process called transformation • Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria) © 2011 Pearson Education, Inc. Figure 27.11-4 Phage A B Donor cell A B A Recombination A A B A B Recipient R i i t cell Recombinant cell Conjugation and Plasmids • Conjugation is the process where genetic material is transferred between prokaryotic cells • In bacteria bacteria, the DNA transfer is one way • A donor cell attaches to a recipient by a pilus, pulls it closer, l andd transfers t f DNA • A piece of DNA called the F factor is required for the production of pili © 2011 Pearson Education, Inc. Figure 27.12 1 m Sex pilus The F Factor as a Plasmid • Cells containing the F plasmid function as DNA d donors dduring i conjugation j ti • Cells without the F factor function as DNA recipients during conjugation g conjugation j g • The F factor is transferable during © 2011 Pearson Education, Inc. Figure 27.13 Bacterial chromosome F plasmid F cell (donor) F cell Mating bridge F cell (recipient) F cell Bacterial chromosome (a) Conjugation and transfer of an F plasmid Hfr cell (donor) A A A F factor F cell (recipient) A A A A (b) Conjugation and transfer of part of an Hfr bacterial chromosome A A A Recombinant F bacterium The F Factor in the Chromosome • A cell with the F factor built into its chromosomes f ti functions as a ddonor dduring i conjugation j ti • The recipient becomes a recombinant bacterium, with DNA from two different cells © 2011 Pearson Education, Inc. R Plasmids and Antibiotic Resistance • R plasmids carry genes for antibiotic resistance • Antibiotics kill sensitive bacteria, but not bacteria with specific R plasmids • Through natural selection, the fraction of bacteria with genes for resistance increases in a population exposed to antibiotics • Antibiotic-resistant strains of bacteria are becomingg more common © 2011 Pearson Education, Inc. Concept : Diverse nutritional and metabolic adaptations have evolved in prokaryotes • Prokaryotes can be categorized by how they obtain energy and carbon – – – – Phototrophs obtain energy from light Chemotrophs obtain energy from chemicals Autotrophs require CO2 as a carbon source Heterotrophs require an organic nutrient to make organic compounds © 2011 Pearson Education, Inc. • Energy and carbon sources are combined to give four major modes of nutrition: – – – – Photoautotrophy Chemoautotrophy Ph t h t t h Photoheterotrophy Chemoheterotrophy © 2011 Pearson Education, Inc. Table 27.1 The Role of Oxygen in Metabolism • Prokaryotic metabolism varies with respect to O2 – Obligate aerobes require O2 for cellular respiration – Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration – Facultative F lt ti anaerobes b can survive i with ith or without ith t O2 © 2011 Pearson Education, Inc. Nitrogen Metabolism • Nitrogen is essential for the production of amino acids and nucleic acids • Prokaryotes can metabolize nitrogen in a variety of ways • In I nitrogen it fixation, fi ti some prokaryotes k t convertt atmospheric nitrogen (N2) to ammonia (NH3) © 2011 Pearson Education, Inc. Metabolic Cooperation • Cooperation between prokaryotes allows them to use environmental resources they could not use as individual cells • In the cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing nitrogen fixing cells called heterocysts (or heterocytes) exchange metabolic products © 2011 Pearson Education, Inc. Ecological Interactions • Symbiosis is an ecological relationship in which two species live in close contact: a larger host and smaller symbiont • Prokaryotes often form symbiotic relationships with larger organisms © 2011 Pearson Education, Inc. • In mutualism, mutualism both symbiotic organisms benefit • In commensalism, one organism benefits while neither harmingg nor helping p g the other in anyy significant way • In parasitism, an organism called a parasite harms b ddoes not kill its but i host h • Parasites that cause disease are called pathogens • The ecological communities of hydrothermal vents depend on chemoautotropic bacteria for energy © 2011 Pearson Education, Inc. Concept: Prokaryotes have both beneficial and harmful impacts on humans • S Some prokaryotes k are hhuman pathogens, h bbut others h have positive interactions with humans © 2011 Pearson Education, Inc. Mutualistic Bacteria • Human intestines are home to about 500 500–11,000 000 species of bacteria • Many of these are mutalists and break down food that is undigested by our intestines • Probiotics i i are microorganisms i i that h provide id health benefits when consumed • Prebiotics is a general term to refer to chemicals that induce the growth and/or activity of commensal microorganisms (e.g., b t i andd fungi) bacteria f i) that th t contribute t ib t to t © 2011 Pearson Education, Inc. microbiota • Human beings have clusters of bacteria in different parts of the body, such as in the p layers y of skin (skin ( surface or deep microbiota), the mouth (oral microbiota), the vagina (vaginal microbiota) microbiota), and so on. on GUT MICROBIOTA • Gut microbiota (formerly called gut flora) is the name given today to the microbe population living in our intestine. It contains tens of trillions of microorganisms, including at least 1000 different species i off known k bacteria b i with i h more than h 3 million genes (150 times more than human genes). Microbiota can, can in total, total weigh up to 2 kg. kg One third of our gut microbiota is common to most people, while two thirds are specific to each one of us. In I other h words, d the h microbiota i bi in i your intestine i i is like an individual identity card. Pathogenic Bacteria • Prokaryotes cause about half of all human diseases – For example example, Lyme disease is caused by a bacterium and carried by ticks (15,000 to 20,000 people infected) – Two million people die in Mycobacterium tuberculosis and another 2 million die from diarrheal caused by various bacteria © 2011 Pearson Education, Inc. • Pathogenic prokaryotes typically cause disease by releasing exotoxins or endotoxins • Exotoxins are secreted and cause disease even if the prokaryotes that produce them are not present Cholera o e toxin, o , causes c uses diarrheal d e disease d se se too stimulate s u e • C intestine cells to release chloride ions. • Endotoxins are released onlyy when bacteria die and their cell walls break down • Horizontal ggene transfer: O157:H7 ((1387 ggenes not found in the 5416 genes of K12 . © 2011 Pearson Education, Inc. • Horizontal gene transfer can spread genes associated with virulence • Some pathogenic bacteria are potential weapons of bioterrorism © 2011 Pearson Education, Inc. Prokaryotes in Research and Technology • Experiments using prokaryotes have led to important advances in DNA technology – For example, E. coli is used in gene cloning – For example, Agrobacterium tumefaciens is used to produce transgenic p g plants p • Bacteria can now be used to make natural plastics © 2011 Pearson Education, Inc. • Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from the environment • Bacteria can be engineered to produce vitamins, antibiotics and hormones antibiotics, • Bacteria are also being engineered to produce ethanol f from waste t biomass bi © 2011 Pearson Education, Inc. Figure 27.21 (a) (c) (b) Robert Koch (11 December 1843 – 27 May 1910) Koch’s postulations • • • • The microorganism must be found in abundance in all organisms g sufferingg from the disease,, but should not be found in healthy organisms. The microorganism must be isolated from a diseased organism and grown in pure culture. culture The cultured microorganism should cause disease when introduced into a healthy organism. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as beingg identical to the original g specific p causative agent. g Koch’ss postulates for the 21st Koch century: • A nucleic l i acid id sequence belonging to a putative pathogen should be present in most cases of an infectious disease. Microbial nucleic acids should be found preferentially in those organs or gross anatomic sites known to be diseased, and not in those organs that lack pathology. p gy Koch’ss postulates for the 21st Koch century: • Fewer, or no, copies of pathogen-associated nucleic acid sequences should occur in hosts or tissues without disease. • With resolution of disease, disease the copy number of pathogen-associated nucleic acid sequences should decrease or become undetectable. With clinical relapse, the opposite should occur. Koch’ss postulates for the 21st Koch century: • When sequence detection predates disease, or sequence copy number correlates with severity of disease or pathology, the sequence-disease association is more likely to be a causal relationship. • The nature of the microorganism inferred from the available sequence should be consistent with the known biological g characteristics of that group g p of organisms. Koch’ss postulates for the 21st Koch century: • Tissue-sequence correlates should be sought at the cellular level: efforts should be made to demonstrate specific in situ hybridization of microbial sequence to areas of tissue pathology andd to visible i ibl microorganisms i i or to areas where h microorganisms are presumed to be located. • These sequence sequence-based based forms of evidence for microbial causation should be reproducible Detection of bacteria- or virus-infection Immunology method S Serum—serology l ( (sero-typing) yp g) Immuno-diffusion RIA radio immunoassay RIA—radio-immunoassay EIA (ELISA) Nucleic acid method Hybridization PCR or RT-PCR S Sequencing i Figure 28.6 9 m Figure 31.1 Figure 31.22 Figure 31.27 Staphylococcus Penicillium Zone of inhibited growth Figure 30.2 PLANT GROUP Mosses and other nonvascular plants Gametophyte Dominant Sporophyte Ferns and other seedless vascular plants Seed plants (gymnosperms and angiosperms) Reduced, independent (photosynthetic and free-living) Reduced (usually microscopic), dependent on surrounding sporophyte tissue for nutrition Reduced, dependent on Dominant gametophyte for nutrition Dominant Gymnosperm Sporophyte (2n) Sporophyte (2n) Microscopic female gametophytes (n) inside ovulate cone Gametophyte (n) Angiosperm Microscopic female gametophytes (n) inside these parts of flowers Example Gametophyte (n) Microscopic male gametophytes (n) i id pollen inside ll cone Sporophyte (2n) Microscopic male gametophytes (n) inside parts these p of flowers Sporophyte (2n) Figure 32.11 Ct Ctenophora h Eumeta azoa Me etazoa ANCESTRAL COLONIAL FLAGELLATE Porifera Cnidaria Acoela Bilateria Chordata Platyhelminthes L Lophotro ochozoa a Ecdysozoa Deute erostomiia Echinodermata Rotifera Ectoprocta Brachiopoda Mollusca Annelida Nematoda Arthropoda