Archaea Cell Biology PDF

Archaea cell biology © ISTOCK.COM/NANOSTOCKK Overview • • • • Discovery of Archaea Distinctive properties of Archaea Archaeal cell structure Diversity of Archaea Divisome Bacterial sell : formation mediates Flagella membrace -> -> Wooclap Notary of septur Motor doesn't prevent ,...

Archaea cell biology © ISTOCK.COM/NANOSTOCKK Overview • • • • Discovery of Archaea Distinctive properties of Archaea Archaeal cell structure Diversity of Archaea Divisome Bacterial sell : formation mediates Flagella membrace -> -> Wooclap Notary of septur Motor doesn't prevent , Proton Motor mechanical Force damage & compress : on The phylogenetic tree (tree of life) has evolved through time Originally based on morphology, anatomy, biochemistry, … 2 main domains of life: prokaryotes and eukaryotes Ernst Haeckel’s rendering of the tree of life, from his 1866 book General Morphology of Organisms Archaea and the tree of life https://youtu.be/hw-ij3822DY Molecular biology reveals a new vision of microbiology and microbial diversity • Used genetics to compare different organisms • Common cellular ancestry means certain molecules are shared between all living organisms • Such as molecules that form parts of the transcriptional machinery, including ribosomal RNA. I recommend The Tangled Tree by David Quammen Carl Woese Archaea phylogeny • Seven major phyla identified (so far) • Only 5 of these phyla have species we can grow in a lab • Most know are: • Euryarchaeota (methanogens, halophiles, thermophiles) lacking genes -> • TACK (Crenarchaeota, thermophiles) • Asgard (ancestral eukaryotes?) • DPANN (obligate symbionts?-gene loss) ↳ live with with or other associated cells To learn more: Archaea and the tree of life, by Dipti Nayak, iBiology v 19.1 Archaeal Diversity at a glance Share with buctail X • Archaea share many metabolic traits, such as redox metabolism, with bacteria. • Other core traits of DNA-RNA machinery are shared with eukaryotes. • Whilst gene regulation looks more like that of bacteria. • Key traits such as ether-linked membrane lipids are found only in archaea, and in a few bacteria that received them by horizontal gene flow from archaea. • These distinctive features are called “archaeal signatures.” Bacteria metabol traits gene regulation looks 1 ! Ke Enkalotes DNA-RNA machinery : Polymase I migre ether 8 linked membrane lipids ↳D in bacteria through horizontal gene Flow Archaeal Traits The cell wall (envelope) is the most distinctive feature of Archaea 9 Distinctive properties of Archaea • Often associated with extreme environments, but they do grow in temperate marine, soil and freshwater (a few in or on us) • Structure • Size is usually 0.5 to 5 μm in diameter. cell • Similar shapes to Bacteria/Eukarya • Archaea, as for bacteria, are prokaryote, ie have no nucleus • The Archaea plasma membrane structure is unique to this domain. qun S Halococcus salifodinae, microbiologyonline.org Thermococcus gammatolerans, wiki commons Sulfolobus, microbiologyonline.org Methanosarcina rumen (green with red cell walls), microbiologyonline.org Distinctive properties of Archaea • Genetically different from bacteria and eukarya, with a distinct genome structure: Both Archaea and Bacteria usually possess singular, circular chromosomes and lack a membrane-bound nucleus. • Archaeal DNA is complexed with histones (like eukaryotes). • Many of the DNA replication enzymes of Archaea look like those of Eukarya. • http://www.biologyreference.com/Ar-Bi/Archaea.html Archaea cytoplasm: general properties • Inclusion bodies such as gas vacuoles or carbon storage have been observed in some Archaea. • Protein content similar as in Bacteria (ribosomes, enzymes, etc…). • Cytoskeleton formed of protein that have homologues in both bacterial and eukarial cells. • No Archaea is known to form spores. • No nucleus means the DNA is within the region called the nucleoid. Inclusion bodies (lipids) Rice Uni Openstax Chap 3.3 Archaeal cytoplasm: cytoskeleton • Cytoskeletal homologues are found in both Bacteria and Archaea. • Homologues/orthologues: FtsZ/TubZ/tubulin MreB/crenactin/actin Microtubules CreS/ - /IF ESCRT no homologues, completely different system Intermediate filaments (IF) Actin microfilament The evolution of the cytoskeleton, Bill Wickstead, Keith Gull, The Journal of Cell Biology Aug 2011, 194 (4) 513-525; DOI: 10.1083/jcb.201102065 Archaeal cell membrane Archaeal cytoplasmic membranes have different lipid constituents and chemistry but are structurally similar Archaea can form membranes with lipid bilayers but with monolayers too! bead 2 I PhosphateasicI perce Fatty Source: Khan Academy "met-inte wi : inks Archaeal cell membrane Isoprene chains instead of fatty acids in bacteria and eukaryotes https://courses.lumenlearning.com/sunyosbiology2e/chapter/structure-ofprokaryotes-bacteria-and-archaea/ between chals Lipids Carbon 2 ta like zb - Ze & Satarond ↳tragtens Ether linkages instead of ester linkage in bacteria and eukaryotes Archaeal cell wall: pseudomurein Har of With pseudomurein -Dis like NAM S-Layer Source: IPY programs is MERGE: Microbiological and Ecological Responses to Global Environmental Archea No peptidoglycan! Just Euryarchaeota -> Pseudomurein: • found in cell walls of certain methanogenic Archaea • polysaccharide similar to peptidoglycan • Immune to lysozymes and penicillin • composed of NAT and NAG: Nacetylglucosamine (in peptidoglycan) and N-acetyltalosaminuronic acid (different, replaces N-acetylmuramic acid) • β-1,3 glycosidic bonds instead of β-1,4 • amino acids all L-stereoisomer attacks4 - B 1 - lik Archaeal cell wall: pseudomurein With pseudomurein S-Layer Source: IPY programs is MERGE: Microbiological and Ecological Responses to Global Environmental No peptidoglycan! S-layer: • most common cell wall type • consist of protein or glycoprotein • paracrystalline structure of various symmetry: hexagonal, tetragonal, or trimeric • in many organisms, S-layers present in addition to other cell wall components, usually polysaccharides • always Generally outermost layer • Resist osmotic pressure in extreme environment, more flexible than peptidoglycan cell wall Archaeal cell wall • No peptidoglycan layer! • Other proteins or glycoproteins possible • Methanochondroitin: looks a little like chondroitin found in connective tissues in animals • Protein sheath: Often found covering multiple cells forming a chain instead of a single cell. http://library.open.oregonstate.edu/microbiology/chapter/archaea/ Cell surface structures Hami Archaeal “grappling hooks” assist in surface attachment, forming biofilms. Sandy Y. M. Ng et al. J. Bacteriol. 2008;190:6039-6047 Structure of Archaella -> like Flagella • Simpler then bacterial or eukaryotic flagella • Uses ATP rather then the proton motive force as energy source • Rotating flagella (eukaryotes have whip-like flagella) Enkaryotic Bacterin Archea : : Whi Notating : Polaths ATP , Proton Motor Force / , ATP Archaea are the only known organisms capable of methanogenesis Whether they are is swamps or in animal guts, archaea are responsible for the methane production in our atmosphere. Chemolithotrophy: ATP H2 + CO2 Chemoorganotrophy: CH4 ATP Methanol CH4 ATP Acetate CH4 Methanogens contribute to gas house emissions UAF - 2010 - Hunting for methane with Katey Walter Anthony. 1:54min Retinal-Based Photoheterotrophy • Most haloarchaea are photoheterotrophs. • Haloarchaea respire with oxygen or anaerobically with nitrate. • Supplement their utilization of organic substrate energy by using light-driven ion pumps. • Do not fix carbon (like photosynthesis) • Do not produce O2 • Use light-driven ion pumps capture light energy. • • • • Bacteriorhodopsin (BR) pumps out H+. Halorhodopsin (HL) pumps in Cl–. Both increase proton motive force. Other rhodopsins signal to the archellum. • • Phototaxis Blue versus red light alter archellar rotation. 23 Halocrchea Light-Driven Ion Pumps and Sensors light Ex xHtenergy ↑ ↓, Since Erease Flagella rotate swim laumfal n V E destYYNA a bead 24 Flagella tumble swe away - -> =ATP I redlight Pylue 3 light rhodspin Retinal-Based Photoheterotrophy – Animation 25 Some Archaea can use light to power ATP production without doing photosynthesis Using bacteriorhodopsin: • structurally similar to rhodopsin, which is a lightgathering pigment found in vertebrate eyes • cytoplasmic membrane proteins that can absorb light energy and pump protons across the membrane 1. Bacteriorhodopsin absorbs light (replaces ETC) 2. Retinal (actually purple) is excited by rhodopsin and 3. Changes conformation from trans to cis 4. Retinal transformation coupled to one proton being pumped outside of the cell 5. ATP synthase can use proton gradient to produce ATP Brock Microbiology, Pearson, Chap 17 Bacteriorhodopsin in haloarchaea and proteorhodopsin in bacteria. Go figure! Archaeal Gene Structure and Regulation Genomes of archaea resemble those of bacteria in gene size and density. However, certain features of genome structure more closely resemble those of eukaryotes: Ebaster :a • Certain tRNA genes are interrupted by introns. • DNA and RNA polymerases and transcription factors are similar to those of eukaryotes • Archaea contain histone homologs. - Certain features are unique to archaea: ↑ negative bacter : in a W • Certain thermophiles possess a reverse gyrase that introduces positive supercoils in chromosomal DNA, which helps protect it against high temperatures. 27 carry bigger genome Genetics of archaea Stacked nucleosomes ↑ than bactin Histones L Chromatin structure: Histones form tetramers around which DNA wraps around (instead of the eukaryotic octamers). • The nucleosome structure allows stacking of units, or superhelix (something prevented by histone structure in eukaryotes) • Histone tails may allow for some epigenetic modifications (Dec 2018, one • DNA Nucleosome Archaeal nucleosomes HHMI.org paper) Eukaryotic nucleosomes Methanococcus jannaschii complete genome Genetics of archaea Genomic structure: • • Not a whole lot of whole genome sequencing, ~150 genomes (mostly Euryarchaeota) Presence of introns In Methanocaldococcus jannaschii: • 1.66Mbp, circular genome • ~1700 genes • Homology to bacterial genes (mostly genes encoding central metabolic pathways and cell division) • Homology to eukaryotic genes (genes encoding molecular processes like transcription and translation) • 40% of genome with no homology to any living organism (methanogenesis and unknown functions) http://bacmap.wishartlab.com/maps/NC_000909/index.html Genetics of archaea Equivalent to general transcription factors (like TFIIB) in eukaryote Gene structure : • Promoters resemble that of eukaryotic cells: Presence of a TATA box • Presence of a BRE • Formation of a pre-initiation complex (RNA pol II needs to be recruited by general transcription factors (TBP, TFBs)) • Transcription Regulation in the Third Domain, Elizabeth A. Karr, Advances in Applied Microbiology, Volume 89, 2014, Pages 101-133 BRE: B-recognition element TBP: TATA-binding protein TFB: Archaeal transcription factor B In shorts, bacteria-like regulators must interact with a scaled-down version of a eukaryotic transcription machinery and gene structure Archaeal Gene Regulation • • • • • RNA pol II structure similar to that of eukaryotes Multiple regulatory elements (binding sites) direct gene expression Activators and repressors resemble more that of bacterial DNA binding proteins then eukaryotic transcription factors However, the domain arrangements and sensing domains (in response to environment) are often unique to the archaeal domain of life Distinctive modified bases in their tRNA molecules • Archaeosine, a guanosine analog 31 Cell division in Archaea Cell cycles and cell division in the archaea. Rachel Y Samson and Stephen D Bell, Current Opinion in Microbiology Volume 14, Issue 3, June 2011, Pages 350-356. • Very much research in progress. • Only possible to study archaea we can culture, lack of genetic tools, growth in esoteric conditions. • Members of distinct phyla have very different chromosome copy numbers, replication control systems and even employ distinct machineries for cell division. • Sometimes these processes seem more bacteria-like or more eukaryote-like depending on archaeal species. Why don’t Archaea cause disease? Next class Viruses!