Сравнительная геномика и метаболическая реконструкция бактериальных патогенов

,-

XII

: (, -, ) : - - ( ) () : : , ,

: : - - ( ) : : : , ( , ) , , ( , ) ,

acpPfabDaccAaccDaccBaccCfabHfabFfabGfabZfabIGene fabI of Enoyl-ACP reductase (EC 1.3.1.9) is missing in the genome 12B, and a number of StreptococcifabI (Enoyl-ACP reductase, EC 1.3.1.9), . : ,

FabR (Tr?, HTH)HTHfabKfabHacpPfabGfabFaccAaccDaccCaccBfabZfabDFad (42.1.17)1234

CONSENSUS

acTTTGAtwaTCAAAgt

E. faecalis

HTH-1

AgTTTGggTATCAAAGT

E. faecalis

HTH-2

AgTTTGAacATCAAAtg

E. faecalis

HTH-3

GtTTTGATAATCAAAGT

E. faecium

HTH-1

ACTTTGATAATCAAAaT

E. faecium

HTH-2

AgTTTGAacATCAAAag

E. faecium

HTH-3

gaTTTGATAATCAAAcT

S. pyogenes

4.2.1.17

GaTTTGATTATCAAAtg 1

S. pyogenes

HTH-1

AaTTTGATTgTCAAAGT 2

S. pyogenes

fabK-1

CtTTTGATAtTCAAAtT 3

S. pyogenes

fabK-2

AgTTTGATTATCAAAtT 4

S. pneumoniae

4.2.1.17

ACTTTGAcAgTgAAAta

S. pneumoniae

HTH-1

gtTTTGATTgTaAAAGT

S. pneumoniae

fabK-1

AgTTTGAcTgTCAAAtT

S. mutans

4.2.1.17-1

ACTTTGATTtTCAAAcT

S. mutans

4.2.1.17-2

AaTTTGATTATCttAaT

S. mutans

HTH-1

ACTTTGATAgTCAAAGT

S. mutans

fabK-1

AgTTTGAcAtTCAAAtc

S. mutans

fabK-2

AgTTTGAcTgTCAAAtT

( / )thiN (confirmed)(Gram-positive bacteria)(Gram-negative bacteria)Transport of HMPTransport of HETPurine pathway

, - +

1

S. pneumoniaeS. pyogenesS. equiS. uberisS. agalactiaeS. mutansS. thermophilusS. suisL. lactisL. caseiL. gasseriL. delbrueckiiP. pentosaceusL. brevisL. mesenteroidesOenococcus oeni

arabinose

arbutin

cellobiose

dextranFragmentary biochemical data

esculinExperimentally verified genes

fructoseOnly genomic prediction

fucoseBiochemical data and genomic prediction

galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

2


amygdalin+++++/-

arabinose++/---+/-++

arbutin+++++++/-

cellobiose-+++-++++/-

dextran+++++

esculin+?+-++++/-+

fructose+*+++++++++++

fucose++----

galactose+*++++++/-+++++++

glucose++++++++++++++++

inulin+--+/--+++++-

lactose+++/-++/-++++++++++/-

maltose+++?++++-++++-++

mannitol---+-++-+/-++-+?+/-

mannose+?+++-++++

melibiose-+/-++-/++/-

N-AcGlu++++++

pullulan++?+

raffinose++--+/--+++-/++/-

ribose-*-+/-+/-+-+++

salicin-++++/-+++++++/-

sorbitol--+/-+-++--++

sorbose-----++-

sucrose+*++++++++++-+

tagatose--?+-

trehalose+*+-++/-++?-+/-++-+

xylose+---++/-++/-++++/-

3


unknown

arabinose

arbutin

cellobiose





galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

1


arabinose

arbutin

cellobiose





galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

2


amygdalin+++++/-


arbutin+++++++/-


dextran+++++

esculin+?+-++++/-+

fructose+*+++++++++++

fucose++----

galactose+*++++++/-+++++++

glucose++++++++++++++++

inulin+--+/--+++++-

lactose+++/-++/-++++++++++/-

maltose+++?++++-++++-++

mannitol---+-++-+/-++-+?+/-

mannose+?+++-++++


N-AcGlu++++++

pullulan++?+

raffinose++--+/--+++-/++/-

ribose-*-+/-+/-+-+++

salicin-++++/-+++++++/-

sorbitol--+/-+-++--++

sorbose-----++-

sucrose+*++++++++++-+

tagatose--?+-

trehalose+*+-++/-++?-+/-++-+

xylose+---++/-++/-++++/-

3

1


arabinose

arbutin

cellobiose





galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

2


amygdalin+++++/-


arbutin+++++++/-


dextran+++++

esculin+?+-++++/-+

fructose+*+++++++++++

fucose++----

galactose+*++++++/-+++++++

glucose++++++++++++++++

inulin+--+/--+++++-

lactose+++/-++/-++++++++++/-

maltose+++?++++-++++-++

mannitol---+-++-+/-++-+?+/-

mannose+?+++-++++


N-AcGlu++++++

pullulan++?+

raffinose++--+/--+++-/++/-

ribose-*-+/-+/-+-+++

salicin-++++/-+++++++/-

sorbitol--+/-+-++--++

sorbose-----++-

sucrose+*++++++++++-+

tagatose--?+-

trehalose+*+-++/-++?-+/-++-+

xylose+---++/-++/-++++/-

3

1


arabinose

arbutin

cellobiose





galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

2


amygdalin+++++/-


arbutin+++++++/-


dextran+++++

esculin+?+-++++/-+

fructose+*+++++++++++

fucose++----

galactose+*++++++/-+++++++

glucose++++++++++++++++

inulin+--+/--+++++-

lactose+++/-++/-++++++++++/-

maltose+++?++++-++++-++

mannitol---+-++-+/-++-+?+/-

mannose+?+++-++++


N-AcGlu++++++

pullulan++?+

raffinose++--+/--+++-/++/-

ribose-*-+/-+/-+-+++

salicin-++++/-+++++++/-

sorbitol--+/-+-++--++

sorbose-----++-

sucrose+*++++++++++-+

tagatose--?+-

trehalose+*+-++/-++?-+/-++-+

xylose+---++/-++/-++++/-

3

1


arabinose

arbutin

cellobiose





galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

2


amygdalin+++++/-


arbutin+++++++/-


dextran+++++

esculin+?+-++++/-+

fructose+*+++++++++++

fucose++----

galactose+*++++++/-+++++++

glucose++++++++++++++++

inulin+--+/--+++++-

lactose+++/-++/-++++++++++/-

maltose+++?++++-++++-++

mannitol---+-++-+/-++-+?+/-

mannose+?+++-++++


N-AcGlu++++++

pullulan++?+

raffinose++--+/--+++-/++/-

ribose-*-+/-+/-+-+++

salicin-++++/-+++++++/-

sorbitol--+/-+-++--++

sorbose-----++-

sucrose+*++++++++++-+

tagatose--?+-

trehalose+*+-++/-++?-+/-++-+

xylose+---++/-++/-++++/-

3

S. pneumoniaeS. pyogenesS. equiS. agalactiaeS. suis

1


arabinose

arbutin

cellobiose





galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

2


amygdalin+++++/-


arbutin+++++++/-


dextran+++++

esculin+?+-++++/-+

fructose+*+++++++++++

fucose++----

galactose+*++++++/-+++++++

glucose++++++++++++++++

inulin+--+/--+++++-

lactose+++/-++/-++++++++++/-

maltose+++?++++-++++-++

mannitol---+-++-+/-++-+?+/-

mannose+?+++-++++


N-AcGlu++++++

pullulan++?+

raffinose++--+/--+++-/++/-

ribose-*-+/-+/-+-+++

salicin-++++/-+++++++/-

sorbitol--+/-+-++--++

sorbose-----++-

sucrose+*++++++++++-+

tagatose--?+-

trehalose+*+-++/-++?-+/-++-+

xylose+---++/-++/-++++/-

3


unknown

arabinose

arbutin

cellobiose





galactose

glucose

inulin

lactose

maltose

mannitol

mannose

melibiose

N-AcGlu

raffinose

ribose

salicin

sorbitol

sorbose

sucrose

tagatose

trehalose

xylose

S. pyogenes, S. agalactiaeS. equiS. pneumoniae TIGR4S. suisS. pneumoniae R6

3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine PTS transporterhydrolaseisomeraseoxidoreductasedehydrogenasekinasealdolasepyruvate + D-glyceraldehyde 3-phosphate

- 2S. pyogenes, S. agalactiaeS. equiS. pneumoniae TIGR4S. suisS. pneumoniae R6

- -

: ,

:

: -, , ..

:

nZUR FUR family???AdcR ? MarR familypZUR FUR family

nZUR-nZUR-AdcRpZURTTAACYRGTTAAGATATGTTATAACATATCGAAATGTTATANTATAACATTTCGTAATGTAATAACATTACTAAATCGTAATNATTACGATTTA

AdcABC YciC AdcABC YciC

zinT: zinT is isolated fusion: adcA-zinTE. coli, S. typhi, K. pneumoniaeGamma-proteobacteriaAlpha-proteobacteriaB. subtilis, S. aureusS. pneumoniae, S. mutans, S. pyogenes, L. lactis, E. faecalisBacillus groupStreptococcus groupzinT is regulated by zinc repressors (nZUR-, nZUR-, pZUR)adcA-zinT is regulated by zinc repressors (pZUR, AdcR) (ex. L.l.)A. tumefaciens, R. sphaeroides

ZinT: E. coli, S. typhi, K. pneumoniae, A. tumefaciens, R. sphaeroides, B. subtilisL. lactisY. pestis, V. cholerae, B. haloduransTMZnAdcAS. aureus, E. faecalis, S. pneumoniae, S. mutans, S. pyogenesZinT

ZinT: zinT adcAzinT ZinT ( )ZinT - ZinT: ZinT - ABC-

, PHT- (pneumococcal histidine triad) S. pneumoniaeS. equiS. agalactiaephtEphtBphtAlmbphtDS. pyogenesphtYlmbphtD

PH-PHT- HxxHxHPHT- S. pneumoniae - (65-95% )Sec- N- PHT- S. pneumoniae

PH-: PHT- PHT- PHT- - :PHT-

- :

EEEHEEHDHGEHEHSH

HSHEEHGHEEDDHDHSHEEHGHEEDDHHHHHDED

DEHGEGHEEEHGHEH

(--) :

HGDHYHY7 out of 21HGDHYHF2 out of 21HGNHYHF2 out of 21HYDHYHN2 out of 21HMTHSHW2 out of 21

( )

PH- () phtD lmb Lmb: , PhtY S. pyogenes: phtY AdcRPhtY :4 HIS TRIADS

PH-: -2PHT- PHT- PHT- - phtD PhtY , PHT- , ,

nZURpZURAdcR

L36L33L31S14E. 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 +

(Makarova-Ponomarev-Koonin, 2001)nZURpZURAdcR

L36L33L31S14E. 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()() () +

:Makarova-Ponomarev-Koonin, 2001:L36, L33, L31, S14 , L36, L33, L31, S14 , ( ) ( ) L36, L33, L31, S14 , , , () ,

ribosomesZn-dependent enzymesRSufficient ZnZn starvationRrepressor

(Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9912-7.) (Mol Microbiol. 2004 Apr;52(1):273-83.)

() () () ( UCLA, USA) .. () () ( LORIA, France)Howard Hughes Medical Institute Ludwig Institute of Cancer Research ( ) (Burnham Institute, San-Diego, USA) ( )

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Сравнительная геномика и метаболическая реконструкция бактериальных патогенов