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Morphological and physiologicalcharacteristics used in classification
• Oxygen relationship• Energy sources• Electron sources• Carbon sources• Fermentation products• Cell wall components• Temp and pH optima• Osmotic tolerance• Photosynthetic mechanism• Secondary metabolites• Sensitivity to antibiotics
Hybridization based oncomplementarity of DNA sequences
Mem
bran
e Test DN
A
Small ribosomal subunit RNA
Fig. 19.9
DNA sequencing
Fig. 15.2
Fig. 11.6
Fig. 11.15
ddATP= stops DNA elongation
Fig. 15.1
Fig. 11.15
DNA sequencing
Fig. 15.2
Whole genome sequencing
Fig. 15.3
69 Complete Microbial Genomes(as of 12/17/01) [A] - Archaea - 12 species[B] - Bacteria - 57 species
224 Complete Microbial Genomes(as of 2/17/05) [A] - Archaea - 21 species[B] - Bacteria - 203 species
Map of Mycoplasma genitalium
Fig. 15.5
What do you get from sequencedata?
• Evolutionary relatedness based onseveral loci
• Infer function of proteins encoded bygenes
+ Consensus #1
- - - M - G Y R - - - - - - - S N V P K V R L T T D R I V L R L V H E R D A V R - L A D Y Y A E N R A F L E P W E P V R D E S H C Y R S G W Q A R L G M I - - S Consensus #1- - - M - G Y R - - - - - - - S N V P K V R L T T D R I V L R L V H E R D A V R - L A D Y Y A E N R A F L E P W E P V R D E S H C Y R S G W Q A R L G M I - - S Majority
10 20 30 40 50 60 70 80
- - - M F G Y R - - - - - - - S N V P K V R L T T D R L V V R L V H D R D A W R - L A D Y Y A E N R H F L K P W E P V R D E S H C Y P S G W Q A R L G M I - - N 1 rimJ-CDS- - - M F G Y R - - - - - - - S N V P K V R L T T D R L V V R L V H D R D A W R - L A D Y Y A E N K A F L K P W E P V R D D S H C Y P S G W Q A R L S M I - - A 1 rimJ-K. pneumoniae-CDS- - - M F G Y R - - - - - - - S N V P K V R L T T D R L V V R L V H E R D A W R - L A D Y Y A E N R H F L K P W E P V R D E S H C Y P S G W Q A R L G M I - - G 1 rimJ-S. typhi-CDS- - - M N G L N - - - - - - - S E C H F Y Q - T D G D I V V R C A Q I N D A E R - L S Q Y F V D N R S H L I E W E P R R E A E F F T E S G W L Q R L I K L - - N 1 rimJ-V.cholerae-CDS- - - L P G N R - - - - - - - R Q V P I L H R D A D - F L L R A L Q P D D F V R - T S R Y E N A N R E H L A P W E P L R D P G Y F S V D N A R A R T L L Q - - V 1 rimJ-P. aeruginosa-CDS/revcomp- - - M F G Y H - - - - - - - T A T P K V H L T T D R M S L R L V H E R D A Y R - L A E Y Y A E N Q V F L K P W E P V R D Q S H C M P S G W Q A R L G M I - - M 1 rimJ-Y. pestis-CDS- GOODV S V L L P F L - - - - - - - S P R P R L R L Q G R A V Y L R P P M Q R D Y A P - W A A L R S R S R A F L E P W E P T W P E H D L S R A A F R A R L A A Y - - A 1 rimJ-C. crescentus-CDS/revcompM - - - - - - - - - - - - - - - - - - - - - L K G K T I Y V R P L E V T D A E E - N L G L Q S E N R D F F E Q F S M I R A D D Y Y T V E G Q R K R I T E Y - - Q 1 rimJ-B. subtilis-CDS/revcompL V T L L R F N A R H P G W P S N V G P L R V P A G V I R L R A V R L R D G V Q - W S R I R L A D R A Y L E P W E P S T E G D W V V R H S V I A W Q V L C - - S 1 rimJ-M. leprae-CDSM P - - - H T P P R H L A E G P R V G I R H F S H A D A A E F T A R A R Q S K D - L H H P W L F P P E S V Q A Y E A Y A A - - R L I E D R T K A G F L V C - - E 1 rimJ-S. coelicolor-CDSM A - - - - - - - - - - - - - - - V G P L R V S A G V I R L R P V R M R D G V H - W S R I R L A D R A H L E P W E P S A D G E W T V R H T V A A W P A V C - - S 1 rimJ-M. tuberculosis-CDSM E T L - - Y T E - - - - - - - - - - - - - - - - - R L T L R K M - E L E D A D V L C Q Y W S D P E V T K Y M N I T P F T D V S Q A R D M I Q M I N D L - - - - 1 rimJ-B. lichenformis-CDSM I N I - G Y L H - - - - - - T T F P V F D L - - G N I V L R E L A E S D V Q D Y L C - Y M S R S E M G L Y I - - - - - T E S N R P K D L E E A R K E I F Y W S 1 rimj-R. prowezekki-CDS-revcomp
+ Consensus #1
E L H K Q G S A F Y F G L L D P E E - - G E I I G V A N F S N V V R G S F H A C Y L G Y S L G E A A Q G Q G L M T E A L T L A I R Y M F R T L G L H R I E A N V Consensus #1E L H K Q G S A F Y F G L L D P E E - - G E I I G V A N F S N V V R G S F H A C Y L G Y S L G E A A Q G Q G L M T E A L T L A I R Y M F R T L G L H R I E A N V Majority
90 100 110 120 130 140 150 160
E F H K Q G S A F Y F G L F D P D E - - K E I I G V A N F S N V V R G S F H A C Y L G Y S I G Q K W Q G K G L M F E A L T A A I R Y M Q R T Q H I H R I M A N Y 202 rimJ-CDSE F H K Q G S A F Y F A L L D P E E - - K E I I G V A N F S N V V R G S F H A C Y L G Y S I G E K W Q G Q G L M F E A L T S A I R Y M Q R T Q H I H R I M A N Y 202 rimJ-K. pneumoniae-CDSE F H K Q G S A F Y F A L L D P E E - - K E I I G V A N F S N V V R G S F H A C Y L G Y S I A Q E W Q G Q G L M F E A L T A A I R Y M Q R T Q H I H R I M A N Y 202 rimJ-S. typhi-CDSE L H K M K L G Y Y L L I L D A Q N - - D A M L G T I S F S N I I R F P F H A C N V G Y S L A Y E A Q G K G I M T R A L T M A C Q Y M F S E H N M H R I M A S Y 199 rimJ-V.cholerae-CDSA S M D E G E A L L L L L L D P D D - - G E V L G R C S Y T N I V R G V F Q A C H L G F S L A A A A Q G R G L M A R A L R V A N R Y C F E Q L G L H R I M A S H 199 rimJ-P. aeruginosa-CDS/revcompE L Q K Q G S A Y Y F I L L D P E E - - K E V R G V A N F S N V L R G S F H A C F L G Y S L G E R W Q G Q G L M F E A L Q P L I R Y M Q R Q E R M H R I M A N Y 202 rimJ-Y. pestis-CDS- GOODR E L E L G E A Y P F F I F R R E D - - D A L L G A I R L F H V R R G V S L T G T I G Y W L G E P Y V R Q G H M A D A V E T L I R F A F H G L G L H R L E A A C 211 rimJ-C. crescentus-CDS/revcompE R L E K D E E Y H F G I F T A S D - - D R L I G T V S L F Q I I R G A L Q T A F I G Y F L D K A H N G K G I M T E A V R L V V D Y A F H E L K L H R I E A G V 169 rimJ-B. subtilis-CDS/revcompS L R S E A R K G R M L P Y A - I E L D G N F C G Q L T I G N V T H G A L R S A W I G Y W V S S S A T G G G V A T G A L A L G L D H C F G P V M L H R V E A T V 232 rimJ-M. leprae-CDSK - D T E A T D G A G G P A G P V P D G G S I A G F V N I N N I V E G G F L S G A L G Y G A F A H A A G R G L M R E G L D L V V R Y A F G P M R L H R L E I N V 217 rimJ-S. coelicolor-CDSG L R S E A R N G R M L P Y V - I E L D G Q F C G Q L T I G N V T H G A L R S A W I G Y W V P S A A T G G G V A T G A L A L G L D H C F G P V M L H R V E A T V 187 rimJ-M. tuberculosis-CDSS L E G Q A N R F - - S I I - - V K E T D E V I G T C G F - N M I D Q E N G R A E I G Y D L G R N H W G K G F A S E A V Q K L I D Y G F T S L N L N R I E A K V 169 rimJ-B. lichenformis-CDSN L Y T L H R S F Y W G I A - - L K T D N K L I G T A G F - N I I N L E H H R A E I S Y D L D P N F W G Q G I M L K S I K N I L K F A - D C I G I I R V Q A T V 196 rimj-R. prowezekki-CDS-revcomp
+ Consensus #1
M P H N A R S G A L L A R L G F E K E G Y A K D Y L L I D G A W R D H V L T A L T T P E - - - - - - - - - - - - - - - - W - - - - - - Consensus #1M P H N A R S G A L L A R L G F E K E G Y A K D Y L L I D G A W R D H V L T A L T T P E - - - - - - - - - - - - - - - - W - - - - - - Majority
170 180 190 200 210 220
M P H N K R S G D L L A R L G F E K E G Y A K D Y L L I D G Q W R D H V L T A L T T P D - - - - - - - - - - - - - - - - W T P G R . 436 rimJ-CDSM P H N Q R S G A L - A R L G F E K E G Y A K D Y L L I D G Q W R D H V L T A L T T P D - - - - - - - - - - - - - - - - W S A G R . 436 rimJ-K. pneumoniae-CDSM P H N K R S G A L L A R L G F E K E G Y A K D Y L L I D G Q W R D H V L T A L T T P L - - - - - - - - - - - - - - - - W T P G R . D 436 rimJ-S. typhi-CDSI P H N K R S E N V L K R V G F V L E G H A K D Y L L I N G K W E D H N L T S L I N P N - - - - - - - - - - - - - - - - W K E . 433 rimJ-V.cholerae-CDSL P R N A R S E R L L E S L G F E K E G Y A R A Y L K I A G V W E D H V L R A L V D A - - - - - - - - - - - - - - - - - - - - P R . I 433 rimJ-P. aeruginosa-CDS/revcompM P H N H R S G N L L A R L G F E R E G Y A K D Y L M I D G Q W R D H V L T A L T N K E - - - - - - - - - - - - - - - - W A S T R . 436 rimJ-Y. pestis-CDS- GOODM P E N H A S A A L L A K C G F S E E G Y A H A Y L K I N G A W R D H R L F G L V A P E . 445 rimJ-C. crescentus-CDS/revcompM P R N L G S M R V L E K A G F H K E G I A R K N V K I N G V W E D H Q V L A I L N P D - - - - - - - - - - - - - - - - - - D E Q . 403 rimJ-B. subtilis-CDS/revcompR P A N V A S R A V L A K V G F R E E G L L R R Y L E V D R A W R D H L L M A L T I E E V S G S V T S N L V R A G R A S W L . I 469 rimJ-M. leprae-CDSQ P G N A A S I A L A R A C G F H L E G F S P R M L Y I D G A W R D H Q R W A I T A E T V T S - - - - - - - - - - - - - - - - - - G . 454 rimJ-S. coelicolor-CDSR P E N A A S R A V L A K V G F R E E G L L R R Y L E V D R A W R D H L L M A I T V E E V Y G S V A S T L V R A G H A S W P . 424 rimJ-M. tuberculosis-CDSE P E N T P S I K L L N S L S F Q K E G L L R D Y E K A K G R L I D V Y M F S L L K R E Y A G . 394 rimJ-B. lichenformis-CDSI T D N F R S V N L L E R C G F S K E G I L K K Y E I I A N K H K D Y Y M Y A R V - - - - - V . 424 rimj-R. prowezekki-CDS-revcomp
Consensus 'Consensus #1': When all match the residue of the Consensus show the residue of the Consensus, otherwise show '.'.
Decoration 'Decoration #1': Shade (with solid black) residues that match rimJ-CDS exactly.
Red= conserved in RimJ and 13 putative prokaryotic acetylasesYellow=conserved in RimJ and 11 putative prokaryotic acetylasesBl ue = rimJ mutations that cause a loss of papBA thermoregulationGr een= motifs conserved in N-acetyltransferase (GNAT) superfamily
The RimJ protein
Fig.15.6
Map of Haemophilus influenzae
Bergey’s Manuals
• Manual of Determinative Bacteriology– used for identification of bacterial species
• Manual of Systematic Bacteriology– more thorough taxonomic classification– 1st edition= phenetic classification– 2nd edition= phylogenetic classification