??????????????, ??? ???????????? ???????? in silico

1
??????????????, ??? ???????????? ???????? in
silico

• ?.????????
• ??????? ? ???? 7 ?????? 2006

2
?????????? 1

• ??????? ??????
• ????? ??????????????????

3
?????? ?????????????? ?????

• ????? ??????????? ?????? ? ??????
  ??????????????????? ??????? ??????? ??
  ?????????
• ?????????????? ????? (?????????????? ??????)
• ?????????????? ??????? (??????????????? ????????,
  ?????????? ??????? ? ?.?.)

4

• ?????? ?? ?????? ?????????????? ????? ????
  ??????????? ???????????????? 50-75 ????? ? ?????
  ??????
• ??
• 100 ???????????? ????????????? ????? (??? ??
  ?????? ?????????? ???? ??? ????????? ???????)
• ????????? ???????, ??? ??????? ??????????
  ????????????? ? ??????? ????????
• ? ?????? ?????? 5-10 ?????????????? ????? ?
  ??????????? ????????
• ?????? ????????????? ????????????? ? ????????????
  ?????????? (????????????, ??????? ????????????)
• ?????? ????? ???-?? ????????????? ?????

5
How much do we know about the Escherichia coli
proteome?
Characterized experimentally
Function inferred by similarity only
Hypothetical
Conserved hypothetical
6
?????????? 2 ?????? ??????
7
Haemophilus influenzae, 1995
8
Vibrio cholerae, 2000
9
????????????-???????? ???????

• Positional clustering
• Phylogenetic profiling
• Gene fusions

10
Metabolic pathways
11
Functionally dependent genes tend to cluster on
chromosomes in many different organisms
12
More genomes (stronger links) gt highly
significant clustering
13
???????? ? ???????? ????? (??????)
14
????????????? ??????? ?????(??????????? ???
????????????, ?????????? ??? ??????????)
15
Phyletic profiles in the Phe/Tyr pathway
16
Arithmetics of phyletic patterns
3-dehydroquinate dehydratase (EC 4.2.1.10) Class
I (AroD) COG0710 aompkzyq---lb-e----n---i--
Class II (AroQ) COG0757 ------y-vdr-bcefghs-u
j---- Two forms combined aompkzyqvdrlbcefghsnu
j-i--

Shikimate dehydrogenase (EC 1.1.1.25) AroE
COG0169 aompkzyqvdrlbcefghsnuj-i--
Shikimate kinase (EC 2.7.1.71) Typical (AroK)
COG0703 ------yqvdrlbcefghsnuj-i-- Archaeal-type
COG1685 aompkz-------------------- Two
forms combined aompkzyqvdrlbcefghsnuj-i--

5-enolpyruvylshikimate 3-phosphate synthase (EC
2.5.1.19) AroA COG0128 aompkzyqvdrlbcefghsnuj-
i--
Chorismate synthase (EC 2.5.1.19)
AroC COG0082 aompkzyqvdrlbcefghsnuj-i--
17
STRING trpB fusions
18
?????????? ???????
E. chrysanthemi
19
? ????????? ???????????????????
E. chrysanthemi
Y. pestis
K. pneumoniae
20
YpaA ??????????? ???????????

• 5 ????????????? ??-????????? gt ?????????????
  ???????????
• ???????????? RFN-??????? gt ??-????????? ? ??????
  ??????????? ??????????? gt ????????? ???????????
  ??? ???????????????
• S. pyogenes, E. faecalis, Listeria ???? ypaA,
  ??? ????? ?????????? ??????????? gt ?????????
  ???????????
• ???????????? YpaA ?????????????? ???????????
  (Gelfand et al., 1999)
• ????????
• YpaA ????????? ?????????? (???????????? ??????,
  ??????? ? ??., 2000)
• ypaA ???????????? ???????????? (?????? ??????????
  ?? ??????????, Lee et al., 2001 ??????
  ???????????, Winkler et al., 2002).

21
?????????????? ????????????? ???? ??????????
?????? ????????????? ???? ???????????????
????????????? ? B. subtilis ? ???????????
?????????
22
????????????? ???? ??????????????? ?????????????
- 0

• dapD (yquQ)
• ??????? ?????????? ???? E. coli

23
????????????? ???? ??????????????? ?????????????
- 1

• patA
• ???????????-??????-????????? ???????????????? (??
  ?????????)
• ??-???????????? ? ??-???????????? ? ??????
  ?????????? ?????? ?? ?????? ????-?????????????
  ?????????

24
????????????? ???? ??????????????? ?????????????
- 2

• ykuR
• N-????-L-???????????? ?????????????? (??
  ?????????)
• ??-???????????? ? ??-???????????? ? ?????
  ?????????? ?????? dapD ?? ??????
  ????-????????????? ?????????
• ? ????????? ??????? ??????????? ? ????????
  ?????????? ???????, ????????????? LYS-?????????

25
????????????? ???? ??????????????? ?????????????
- 3

• dapX
• dapF ??????????? ? ????????? ????????
  (Staphylococcus aureus, Oenococcus oeni,
  Leuconostoc mesenteroides)
• ?? ???? ???? ??????? ???? dapX, ????????????
  ?????????? ???????? ? ?????? ??????????
• ? S. aureus dapX ??????????? ? ????????
  ?????????? ???????
• ? O. oeni ?????? dapX-asd ????????????
  LYS-?????????

26
????????????? ???????? ?????? ?????????? ?????

• ??? ???? ????? ? ?????????
• ??????????? ? ???-???????????, ?????????,
  ?????????? ??????
• ?????????????? ? ????????? ? ?????? ??????

27
?????????? ? ???????
nZUR-?
nZUR-?
GAAATGTTATANTATAACATTTC
GATATGTTATAACATATC
GTAATGTAATAACATTAC
TTAACYRGTTAA
AdcR
pZUR
TAAATCGTAATNATTACGATTTA
28
???? ? ???????? ?????? ???????
L36 L33 L31 S14
E. coli, S.typhi
K. pneumoniae
Y. pestis,V. cholerae ?
B subtilis
S. aureus
Listeria spp.
E. faecalis ?
S. pne., S. mutans
S. pyo., L. lactis
nZUR
pZUR
AdcR
29
(? ??????? ????? ???????? ?????)
L36 L33 L31 S14
E. coli, S.typhi () ()
K. pneumoniae () ()
Y. pestis,V. cholerae () ? ()
B subtilis () () () ()
S. aureus () () ()
Listeria spp. () () ()
E. faecalis () () ? ()
S. pne., S. mutans () () ()
S. pyo., L. lactis () () ()
nZUR
pZUR
AdcR
30
?????? ??????????

• Makarova-Ponomarev-Koonin, 2001
• L36, L33, L31, S14 ??? ???????????? ??????????
  ?????, ??????????????? ?????, ??? ? ????? ??????
• L36, L33, L31, S14 ?????? ?? ???? ??????????
  ??????, ?????????? ????? ???????? ????? (??????
  ????????)
• ?? ???? (??? ?????) ????? L36, L33, L31, S1,
  ?????? ???? ???????? ????? ???????? ?????, ?
  ?????? ???
• ????? ?????, ?????????? ???????? ??????????
  ??????, ??? ??????? ???? ???????????? ????????
  ???????????, ? ??????????????? ????? ??????? ??
  ????? ?????? ???????? ?????

31
?????? ????????
???????????? ????? ???? ???? ?????????
??????????, ???????? ????????
?????????? ?????
32
??????? ????????
???????????? ????? ????? ??????? ???????? ?????,
?? ?????????? ????? ???????? ??? ?????????
?????????? ?????
33
???????????? ????????
Sufficient Zn
ribosomes
R
repressor
Zn-dependentenzymes
Zn starvation
R
34
???????????? (Proc Natl Acad Sci U S A. 2003
Aug 19100(17)9912-7.)
? ?????????????
(Mol Microbiol. 2004 Apr52(1)273-83.)
35
???????????? ??????? ? ???? ??? ????

• ?????????????? ?????? ????? ??????
  ?????????????-????????
• ????????????? ????????? (????? ????????????????
  ??????? ??????)

36
?????? ????? ????????

• ???????????? ??????????????????????

• ?????????? (???-??????, ?????????????,
  ???-??????????

37
??? ???????????? ????????? ? ??????????
?????????????? ??????????
38
??? ???????? ?? ??????

• ?????????
• ?????????
• ???????????? ????????
• ????
• ??????
• ?????????????? ? ???????????? ???????
• ?????? ???? ?????? ? ??? ? ???? ??????
• ??????????
• ?????-??????? ??????????????
• ?????-???????? ??????????????
• ????????? ????????? (?????????????, ??????? ? ??
  ??????????? ? ?.?.)
• ????????? ????????