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Lecture 03 (3-28-2017) slides


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Microbial Diversity course, UMass Amherst. Covers Brown Ch. 24 & 7

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Lecture 03 (3-28-2017) slides

  1. 1. !"#$%&"'()' *+#&,-+,.,/0',1'23&.0'23&$4' !"#$%&&&%'(%)*%+,-,.-/%)*0%1002%34)$%5674(8#9% :0;'01%3)4%0"#$%&&&% <08*0(8#9%=>4'?%@A%BC+DBE>$% FGF%H-.E% !"#$%%"&'$()"*%%"+,"-%$./-"*(."(01/-2" 304"#$%%"&'$()",04'"54/-60(-7"
  2. 2. Quiz   1.  How  did  Pasteur’s  swan-­‐necked   flask  experiments  disprove  the   theory  of  abiogenesis,  when  this   was  likely  the  origin  of  all  life  on   earth?   a.  Time  (weeks  vs  eons,  billions  of   years)   b.  Redox  potenHal  (oxic  growth  vs   ancient  reducing  environment)   c.  …   2   2.  What  are  some  possible  requirements  for   the  origin  of  life?  
  3. 3. What  are  some  possible  requirements   for  the  origin  of  life?   •  GeneraLon  of  simple  organic  molecules   •  ProducLon  of  complex  organic  molecules  and   metabolic  networks   •  Origin  of  self-­‐replicaLon  -­‐  genotype   •  CompartmentalizaLon  –  cells   •  Linking  genotype  to  phenotype   •  Origin  of  geneLc  code   •  Takeover  of  replicaLon  system  by  DNA   3  
  4. 4. ObjecLves   •  Describe  the  origin  of  life  on  earth,  and   approximate  age  of  origins.   •  Describe  the  major  events  in  the  evoluLon  of   life,  and  when  they  happened.   •  What  do  we  know  about  LUCA?     •  What  is  the  evidence  for  early  life?   •  How  is  it  possible  to  know  what  early  life   forms  were,  and  how  old  they  were?     4  
  5. 5. P4"'Y+/'Y3>/'=3;'(T7Z'-+..+,>'0"3&;'3/,' 23&$4'1,&D"9'X7)X'K03' '['X7)'-+..+,>'0"3&;'['X7)'B'(]' )'
  6. 6. History  of  Earth    •  The  Big  Bang  Theory  is  the  prevailing  cosmological   model  that  describes  the  early  development  of  the   Universe.   –  According  to  the  theory,  the  Big  Bang  occurred   approximately  13.8  billion  years  ago,  which  is  thus   considered  the  age  of  the  universe.     •  The  esLmated  age  of  the  Earth  is  4.54  billion  years   (4.54  ×  10^9  years  ±  1%)   6  
  7. 7. 23&.0'23&$4' ^$4"'e&;$'1"='D+..+,>'0"3&;fc' .J! =KK40L)*%M%gDC3#L>/'-,9+";F'+>#.%9+>/' D,,>'1,&D3L,>' NJ! G0?3CK)$>40((')*%M'2B$&3'/&3E+$0' C&,9%#";'4"3$' BJ! O'P040*L#L)*%M'h,&D3L,>',1'$4"'23&$4<;' 4"3E0'D"$3.'#,&"'3>9'.+/4$'"."D">$'#&%;$' +J! G6)4IC?';08%4#8')Q0*'K%'()I)>0(%M' &"."3;"9'&39+,3#LE+$0'+;'3-;,&-"9' i'
  8. 8. The  Early  days  of  Earth     …  (first  few  million  years)   1.  AccreLon.  ImpacLng  bodies  bombard  the  Earth  and  convert  their  energy   of  moLon  (kineLc  energy)  into  heat.  An  early  collision  with  a  very  large   object  was  responsible  for  the  "extracLon"  of  the  Moon  from  Earth.   2.  Self-­‐compression.  As  the  Earth  gets  bigger,  the  extra  gravity  forces  the   mass  to  contract  into  a  smaller  volume,  producing  heat  (just  like  a  bicycle   pump  gets  hot  on  compression).   3.  DifferenLaLon.  FormaLon  of  the  Earth’s  core:  the  extra  gravity  and  heat   causes  heavy  metals  (iron,  nickel  and  related  elements)  to  be   concentrated  in  the  core  of  the  earth,  whereas  the  light  elements   (oxygen,  silicon,  aluminum,  potassium,  sodium,  calcium  etc.)  were   enriched  in  an  outer  layer  of  the  earth  that  is  now  termed  the  mantle   and  the  crust.   4.  Short-­‐lived  radiogenic  isotopes.  The  surrounding  material  absorbs  the   energy  released  in  radioacLvity,  heaLng  up.   8  
  9. 9. The  Early  days     …  (first  few  million  years)   9  
  10. 10. “You  are  made  of  stars”  –  old  proverb   •  Could  the  process  of  accreLon,  or  impacLng   bodies,  “seeded”  our  planet  with  life?   •  hGp://­‐news/ science-­‐at-­‐nasa/2015/01may_halleyids/   •  In  1986,  Europe's  GioGo  spacecrar   encountered  and  photographed  the  nucleus   of  Halley's  Comet  it  approached  the  sun.     10  
  11. 11. W+;$,&0',1'23&$4' ((' !"#$%&'()*& +,(-./(0-*12& 341&5(1/*& 670819/:-9& ;<19*& =>()*&?1@@)&A>*4&& B>*-?4-9C(>/& =>()*&?1@@)&A>*4&& ?4@-(-,@/)*)&
  12. 12. History  of  Earth   •  Hadeon  Eon   –  4.4  Ga  –  The  oldest  rock,  a  zircon  crystal   –  4.2  Ga  –  earliest  evidence  of  life  (microbial  mat  fossils)   •  Archaean  Eon   –  3.5  Ga  –  First  prokaryotes,  or  the  LUCA   •  Proterozoic  Eon   –  2.5  Ga  –  First  eukaryotes  (cells  with  nucleus)   –  2.3  Ga  –  The  Great  OxygenaLon  Event  begins   –  1.5  Ga  –  First  eukaryotes  with  endosymbioLc  RickeGsiales  (Sar11   clade)  bacteria,  now  mitochondria:  symbiogenesis     –  1.5-­‐1  Ga  –  First  plants  with  endosymbioLc  cyanobacteria,  now   chloroplasts   •  Phanerozoic  Eon   –  60  Ma  –  First  primates   –  1.2  Ma  –  First  genus  Homo  (humans  and  predecessors)…       –  Anthropocene  epoch  –  from  ~1950  to  present     –  *Ga  =  Billion  years  ago,  Ma  =  Million  years  ago     12  
  13. 13. Miller-­‐Urey  experiments   13  
  14. 14. •! S-+,/">";+;'O'.+1"'1&,D',&/3>+#'D3G"&' •! g$'43;'-"">'@>,=>'1,&'="..',E"&'('0"3&;'$43$' D+B$%&";',1'D3>0'$0C";',1';%/3&'D,."#%.";'#3>' -"',-$3+>"9'-0'=3&D+>/'3>'3.@3.+>"';,.%L,>',1' 1,&D3.9"409"F'=4+#4'3.;,'=,%.9'43E"'-"">' 3E3+.3-."',>'$4"'0,%>/'C.3>"$7' •! V>9"&'$4"'&+/4$'#,>9+L,>;';,D"'-%+.9+>/'-.,#@;' ,1'C&,$"+>;F'$4"'3D+>,'3#+9;F'1,&D'"3;+.0'1&,D' ;+DC."&'#4"D+#3.;F'3;'t$3>."0'!7'*+.."&'3>9'W3&,.9' N7'V&"0',1'$4"'V>+E"&;+$0',1'N4+#3/,'9+;#,E"&"9'+>' C+,>""&+>/'"BC"&+D">$;'+>'$4"'(]);' (X'
  15. 15. RNA  the  first  biological  molecule   15  
  16. 16. RNA  the  first  biological  molecule   RNA  likely  was  the  first  biological  molecule   •  exposure  to  ultraviolet  light—intense  solar  UV  rays  hit   shallow  waters  on  the  early  earth—  destroys  the  “incorrect”   nucleoLdes  and  leaves  behind  the  “correct”  ones   •  This  provides  a  clean  route  to  the  C  and  U  nucleoLdes   •  Thus  ribosomes  are  “fossil”  evidence  of  a  primordial  RNA   world   Some  roles  of  modern  RNA   •  TranslaLon   •  DNA  replicaLon   •  Splicing   •  Protein  translocaLon   •  RNA  interference   16  
  17. 17. RNA  as  an  autocatalyLc  network   17  
  18. 18. Layers  of  clay  as  catalysts  for  RNA   polymerizaLon   18  
  19. 19. The  primordial  sandwich  hypothesis   •  Surfaces  can  concentrate  organics  by   adsorpLon   •  PolymerizaLon  is  favored  on  surfaces   •  Surface  chemistry  is  stereospecific   •  AcLvated  precursors  are  not  required   19  
  20. 20. Layers  of  clay  as  catalysts  for  RNA   polymerizaLon   •  Where  do  you  find  clay?  It’s  in  all  soils   •  Soils  are  made  of  minerals  (including  clay),   organic  maGer  (biological  substrates  and   waste  products),  and  microbes   •  clay  minerals  enhance  the  process,  producing   chains  of  up  to  50  or  so  nucleoLdes   20  
  21. 21. CompartmentalizaLon  isolates  a  replicaLng  system,   increasing  self-­‐organizaLon  and  allowing  for  systems   to  become  more  complex.     21  
  22. 22. Protocells  &  assisted  reproducLon     22  
  23. 23. From  protocells  to  bacteria…   23  
  24. 24. 24  
  25. 25. 25  
  26. 26. From  protocells  to  bacteria   1.  First  protocell  is  a  lipid   sack  of  RNA   2.  RNA  catalysis   3.  Metabolism  begins   4.  Proteins  appear   5.  Proteins  take  over   funcLon   6.  DNA  is  created   7.  Bacterial  /  archaeal  world   26  
  27. 27. Hypotheses  on  the  origin  of  viruses   •  The  progressive  hypothesis  states  that  viruses   arose  from  geneLc  elements  that  gained  the   ability  to  move  between  cells   –  HIV  act  like  retrotransposons   •  The  regressive  hypothesis  asserts  that  viruses   are  remnants  from  more  complex  cellular   organisms   –  Mimivirus   •  The  virus-­‐first  hypothesis  states  that  viruses   predate  or  coevolved  with  their  current  cellular   hosts   –  ssRNA  viruses   27  
  28. 28. Hypotheses  on  the  origin  of  viruses   •  progressive  hypothesis     –  Retroviruses  like  HIV  act  a  lot  like  retrotransposons,  mobile   geneLc  elements  that  make  up  42%  of  the  human  genome  &   can  move  within  the  genome  via  an  RNA  intermediate   •  regressive  hypothesis   –  the  nucleocytoplasmic  large  DNA  viruses  (NCLDVs),  illustrate   this  hypothesis.  Ex.  smallpox  virus  and  the  recently  discovered   giant  of  all  viruses,  Mimivirus,  are  much  bigger  than  most   viruses  and  depend  less  on  their  host  compared  to  other  viruses   •  virus-­‐first  hypothesis   –  RNA  pre-­‐dates  DNA,  and  RNA  has  enzymaLc  capabiliLes.   Perhaps  simple  replicaLng  RNA  molecules,  exisLng  before  the   first  cell  formed,  developed  the  ability  to  infect  the  first  cells.     –  today's  single-­‐stranded  RNA  viruses  could  be  descendants  of   these  precellular  RNA  molecules   28  
  29. 29. K&"3$'MB0/">3L,>'2E">$' I]'
  30. 30. Great  Oxygena,on  Event   •  O2  build-­‐up  in  the  Earth's  atmosphere  begins  about  2.3  Ga.   •  Red  and  green  lines  represent  the  range  of  the  es,mates   while  ,me  is  measured  in  billions  of  years  ago  (Ga).   •  Stage  1  (3.85–2.45  Ga):  Prac,cally  no  O2  in  the  atmosphere.   •  Stage  2  (2.45–1.85  Ga):  O2  produced,  but  absorbed  in  oceans   &  seabed  rock.   •  Stage  3  (1.85–0.85  Ga):  O2  starts  to  gas  out  of  the  oceans,  but   is  absorbed  by  land  surfaces.   •  Pre-­‐3.0 Ga  biosphere:  photosynthe,c  bacteria  almost   certainly  employed  photosystem-­‐I    (PS-­‐I)  and  used  H2,  H2S   and/or  Fe2+  to  reduce  CO2  to  organic  maVer   •  Stages  4  &  5  (0.85–present):  O2  sinks  filled  and  the  gas   accumulates.   30  
  31. 31. THE  EVIDENCE  for  Early  Life   1.  Isotopic  record     2.  Rocks  and  Microfossils     3.  Organic  Geochemical  Record,  or  “molecular   fossils”   4.  Molecular  EvoluLon   31  
  32. 32. Isotopic  fracLonaLon   •  Bonds  involving  “light”  isotopes  break  more  readily   than  those  involving  “heavy”  isotopes.   R  is  the  ISOTOPIC  RATIO  e.g.,  (13C/12C)  sample   R  =  HEAVY  ISOTOPE/  LIGHT  ISOTOPE   R  =  RARE  ISOTOPE  /  ABUNDANT  ISOTOPE   32  
  33. 33. Isotopic  fracLonaLon   •  Bonds  involving  “light”  isotopes  break  more  readily  than   those  involving  “heavy”  isotopes.   •  Rate  determining  step  which  includes  breaking  of  bond   dictates  isotopic  fracLonaLon  of  enLre  process   •  Typical  of  processes  which  are  unidirecLonal  and  irreversible     Example:  Breathing  -­‐  we  use  16O  preferenLally  for  respiraLon,  so  17O  and   18O  become  progressively  more  abundant  in  lung  air  and  exhaled  air)   Example:  PreferenLal  incorporaLon  of  12C  in  CO2  fixing  plants  -­‐passed  on  to   herbivores  and  up  the  food  chain   Example:  Methane  has  a  very  light  δ13C  signature,  and  differs  whether  it  is   biogenic  methane  of  −60‰  or  thermogenic  methane  −40‰.     33  
  34. 34. g;,$,C+#';+/>3$%&";'3&"'-3;"9',>'' ;$3-."'#3&-,>'+;,$,C";' l9".$3'(T'N3&-,>n' TX'
  35. 35. Stable  Carbon  Isotopes   •  All  C  atoms  have  a  nucleus  containing  6  protons.  99%  of  these   also  contain  6  neutrons,  mass  is  12:  "carbon-­‐12."     •  The  nuclei  of  1%  of  C  atoms  contain  7  or  8.  They  have  masses   of  13  and  14  respecLvely  and  are  referred  to  as  "carbon-­‐13"   and  "carbon-­‐14."   •  C12  and  C13  are  stable,  C14  is  always  undergoing  radioacLve   decay,  half  life  of  5730  years  →  radiocarbon  daLng   –  A  sample  in  which  14C  is  no  longer  detectable  is  said  to  be   "radiocarbon  dead."  Ex.:  Fossil  fuels.     •  Stable  isotopes  can  be  used  as  a  proxy  for  nutrient  cycling   because  of  isotopic  fracLonaLon  compared  to  a  standard…   35  
  36. 36. t$3-."'+;,$,C";'3;'N'$&3#"&k'' P4"'t$3>93&9'+;':""'Q""'Y"."D>+$"'^:QYc' Td'
  37. 37. Stable  isotopes  as  C  tracer:     The  Standard  is  Pee  Dee  Belemnite  (PDB)   Belemnitella  americana   Is  an  ancient  squid   Belemnitella   americana   is  an  ancient     squid     37  
  38. 38. Stable  isotopes  as  C  tracer:     The  Standard  is  Pee  Dee  Belemnite  (PDB)   •  For  δ13C,  say,  “delta  13  C”  or  “delta  13  Carbon”   •  The  standard  established  for  carbon-­‐13  work  was  the  Pee  Dee   Belemnite  or  (PDB)  and  was  based  on  a  Cretaceous  marine  fossil,   Belemnitella  americana,  which  was  from  the  Pee  Dee  FormaLon  in   South  Carolina.     •  Belemnitella  americana  was  a  squid-­‐like  animal,  probably  related  to   the  ancestors  of  modern  squids  and  cuGlefish   •  This  material  had  an  anomalously  high  13C:12C  raLo  (0.0112372),   and  was  established  as  δ13C  value  of  zero.   –  So  delta13C  =  ((13:12  sample/13:12  std)-­‐1)*1000perml  =   ((0.0112/0.0112)-­‐1)*1000  =  0   •  Most  samples  have  lower  13:12  raLos  than  PDB,  so  that  makes   (13:12  sample/13:12  std)  less  than  one,  so  the  delta  13C  is  always   negaLve.   38  
  39. 39. Isotopic  evidence  for  early  life   •  The    3,416-­‐Myr-­‐old  Buck  Reef  Chert,  South   Africa,  is  marine  sediment,  not  hydrothermal   •  Laminated  mat-­‐like  structures  with  stable   carbon  isotope  signature  suggests  CO2   fixaLon,     –   δ  13C  =  -­‐35  o/oo   –  “...isotopic  composiLon  of  BRC  carbonaceous   maGer  is  consistent  with  fixaLon  by  autotrophs   employing  the  Calvin  cycle.”   •  “Taken  together,  the  carbon  isotopic   composiLon  of  BRC  carbonaceous  maGer,  the   presence  of  siderite  and  lack  of  primary  ferric   oxides,  and  the  restricLon  of  microbial  mats   to  shallow  water  indicate  that  photosyntheLc,   probably  anoxygenic,  microbes  were  acLve  in   the  3,416-­‐Myr-­‐old  ocean.”     –  Tice  &  Lowe,  Nature  431,  549  -­‐  552  (2004)   39   hGps://­‐11-­‐earth-­‐early-­‐ocean-­‐cooled-­‐billion.html  
  40. 40. THE  EVIDENCE  for  Early  Life   1.  Isotopic  record     2.  Rocks  and  Microfossils     3.  Organic  Geochemical  Record,  or  “molecular   fossils”   4.  Molecular  EvoluLon   40  
  41. 41. g;,$,C+#'&"#,&9;',1'D+#&,1,;;+.;' *+#&,1,;;+.;',1'$4"'23&.0'S&#4"3>'SC"B'N4"&$k'R"='2E+9">#"',1'$4"'S>LJ%+$0',1'!+1"' Å7'8+..+3D't#4,C1't#+">#"F'R"='t"&+";F'x,.7'IdF'R,7')(Z7'^SC&7'TF'(]]TcF'CC7'dX?dXd' X('
  42. 42. Isotopic  records  of  microfossils   •  The  sole  source  of  direct,  fossil  evidence  is  from  rocks   deposited  during  the  Archaean  Eon  of  Earth  history   (>2.5  Ga).     •  “In  order  to  establish  the  authenDcity  of  Archean   micro-­‐  fossils,  five  principal  criteria  must  be  saDsfied.   The  putaDve  microfossils  must     –  (I)  occur  in  rocks  of  known  provenance  and     –  (ii)  established  Archean  age;     –  (iii)  be  demonstrably  indigenous  to  and     –  (iv)  syngeneic  with  the  primary  deposiDon  of  the  enclosing   rock;  and     –  (v)  be  of  assured  biological  origin.”   Microfossils  of  the  Early  Archean  Apex  Chert:  New  Evidence  of  the  AnDquity  of  Life   J.  William  Schopf  Science,  New  Series,  Vol.  260,  No.  5108.  (Apr.  30,  1993),  pp.  640-­‐646   42  
  43. 43. THE  EVIDENCE  for  Early  Life   1.  Isotopic  record     2.  Rocks  and  Microfossils     3.  Organic  Geochemical  Record,  or  “molecular   fossils”   4.  Molecular  EvoluLon   43  
  44. 44. “Molecular  fossils”   organic  geochemical  markers   •  Organic  biomarkers  from  2.7  billion  year  old  shales   A.  Steranes  (cholestane)  =  eukaryotes   B.  2-­‐methyl  hopanes  =  cyanobacteria   •  Lots  of  care  has  to  be  taken  to  ensure  organics  are   derived  from  the  rock  was  buried  –  and  not   contaminaLng  material.   •  Hard  stuff  to  do  !!!   –  See  also  Archaean  Molecular  Fossils  and  the  Early  Rise  of  Eukaryotes   Jochen  J.  Brocks,  Graham  A.  Logan,  Roger  Buick,  Roger  E.  Summons   –  Science,  Vol  285,  Issue  5430,  1033-­‐1036  ,  13  August  1999   44  
  45. 45. ]#*808%&4)*%e)4$#L)*(% X)'
  46. 46. Banded  Iron  FormaLons   •  Each  band  is  assumed  to  result  from  cyclic   variaLons  in  available  oxygen.   •  Oxygen  is  released  by  photosyntheLc   cyanobacteria  (bluegreen  algae)  in  sea  water     •  This  oxygen  combines  with  dissolved  iron  in   Earth's  oceans  to  form  insoluble  iron  oxides,   which  precipitated  out,  forming  a  thin  layer  on   the  substrate,  which  may  have  been  anoxic  mud   (forming  shale  and  chert).     •  Bands  may  have  been  seasonal,  or  formed  from   some  other  cycle.   46  
  47. 47. Banded  Iron  FormaLons   •  Very  large  bodies  of  sedimentary   rock  laid  down  some  2.5  –  1.8  billion   years  ago  (Precambrian)   –  Fe2+  very  soluble     –  Fe3+  insoluble,  precipitates  from   soluLon   •  BIF  formaLon  seems  to  require   anoxic  deep  waters  for  formaLon.   Thus,  if  deep-­‐sea  O2  became   abundant,  it  could  inhibit  BIF   formaLon   •  BUT,  alternaLve  theory  suggests  Fe-­‐ sulfides  can  also  highly  insoluble.   Was  it  oxygen  or  sulfide,  that  ended   BIF  deposiLon  ?   47  
  48. 48. Stromatolites   48  
  49. 49. Stromatolites   •  Stromatolites  are  formed  through  the  acLvity  of   primiLve  unicellular  organisms:  cyanobacteria  and   other  algae.     •  These  grow  through  sediment  and  sand,  binding  the   sedimentary  parLcles  together,  resulLng  in  successive   layers.   •  Over  a  long  period  of  Lme,  these  layers  harden  to  form   rock.     •  For  at  least  three-­‐quarters  of  the  earth's  history   stromatolites  were  the  main  reef  building  organisms,   construcLng  large  masses  of  calcium  carbonate.   49  
  50. 50. THE  EVIDENCE  for  Early  Life   1.  Isotopic  record     2.  Rocks  and  Microfossils     3.  Organic  Geochemical  Record,  or  “molecular   fossils”   4.  Molecular  EvoluLon   50  
  51. 51. Molecular  evoluLon:     ReconstrucLng  past  events   51  
  52. 52. Molecular  evoluLon:     ReconstrucLng  past  events   •  model  of  macroevoluLon  including  gene  birth,  transfer,  duplicaLon   and  loss  events  to  map  the  evoluLonary  history  of  3,983  gene   families  across  the  three  domains  of  life  onto  a  geological  Lmeline.     •  Figure  shows  a  gradual  increase  in  the  fracLon  of  enzymes  that   bind  molecular  oxygen  predicted  to  be  present  over  Earth  history   –  David    &  Alm,  Nature  2011;  Rapid  evoluLonary  innovaLon  during  an   Archaean  geneLc  expansion.     –  Colours  indicate  abundance  normalized  to  present-­‐day  values.  Values   in  parentheses  give  the  overall  number  of  gene  families  in  each  group.     •  a  brief  period  of  geneLc  innovaLon  during  the  Archaean  eon,  which   coincides  with  a  rapid  diversificaLon  of  bacterial  lineages,  gave  rise   to  27%  of  major  modern  gene  families.     •  A  funcLonal  analysis  of  genes  born  during  this  Archaean  expansion   reveals  that  they  are  likely  to  be  involved  in  electron-­‐transport  and   respiratory  pathways   52  
  53. 53. ObjecLves   •  Describe  the  major  events  in  the  evoluLon  of   life,  and  when  they  happened.   •  Describe  the  origin  of  life  on  earth,  and   approximate  age  of  origins.   •  What  do  we  know  about  LUCA?     •  What  is  the  evidence  for  early  life?   •  How  is  it  possible  to  know  what  early  life   forms  were,  and  how  old  they  were?     53