A. Study design schematic Streptococcus mitis (NCTC-2261) Streptococcus mitis (B6) Streptococcus mitis (SK321) Streptococcus mitis (SK564) Streptococcus

a. Study design schematic

Streptococcus mitis (NCTC-2261)Streptococcus mitis (B6)Streptococcus mitis (SK321)Streptococcus mitis (SK564)Streptococcus mitis (SK597)Streptococcus mitis (ATCC-6249)Streptococcus oralisStreptococcus salivariusStreptococcus sanguinisStreptococcus parasanguinisLactobacillus paracasei (ATCC-27092)Lactobacillus rhamnosus (ATCC-53103)Homo sapiens

Streptococcus mutans serotype c (NN2025)Streptococcus gordoniiLactobacillus acidophilusLactobacillus casei (ATCC-334)Lactobacillus casei (Zhang)Lactobacillus casei (BL23)Lactobacillus salivarius (ATCC-11741)Lactobacillus salivarius (CECT-5713)Lactobacillus salivarius (ACS-116-V-Col5a)Lactobacillus salivarius subsp. salivarius (UCC118)Lactobacillus fermentum (IFO-3956/LMG-18251)Lactobacillus fermentum (ATCC-14931)Lactobacillus fermentum (28-3-CHN)Lactobacillus fermentum (CECT-5716)Bifidobacterium dentium (ATCC-27534)Bifidobacterium longum (strain DJO10A)Veillonella parvula

b. phylogenetic profiles

targ

et s

peci

esan

titar

get

spec

ies

complete proteome sets

Examples of modelable S. mutans virulence factors

Examples of modelable and druggable S. mutans proteins

druggablemutltiple sugar binding protein zDOPE (model reliability) = -1.57drugEBIlity score = 0.76

not druggableproton/lactate pumpzDOPE (model reliability) = -1.73drugEBIlity score = -0.71

favorable profileunknown enzymeresolution = 2.38 ÅdrugEBIlity score = 0.57

comparative modelnonhydrolyzing UDP acetyl-glucosamine epimerasezDOPE (model reliability) = -1.75drugEBIlity score = 0.82

crystal structureglucosamine-6-PO4 deaminaseresolution = 2.03 ÅdrugEBIlity score = 0.77

druggable and favorable profilemajor cell-surface adhesin zDOPE (model reliability) = -1.50drugEBIlity score = 0.41

a. b. c.

d. e. f.

multiple sugar-binding

MS transport ATP-bindingATP-binding transporter

fructose phosphotransferase IIABCfructose phosphotransferase IIBC

fructose phosphotransferase IIAisocitrate dehydrogenase

acetylornithine aminotransferase

purine nucleoside phosphorylaseglycogen synthase

Glu1-PO

4 adenylyltransferasebeta-glucosidase

endoglucanaselactate dehydrogenase

phosphocarrier protein HPr

PEP-phosphotransferaseproton/lactic acid pum

plactose-specific PO

4-transferaseN

'N' D

CHC-sensitive ATPase

signal recognition particleform

yltetrahydrofolate ligasepanthothenate flavoproteinm

alolactic fermentation reg

DN

A-dir RNA polym

eraseglycogen phosphorylase

phosphorylasesucrose phosphorylase

GTF-I 1,3α-branch

glucosyltransferase-SIglucosyltransferase-S

1,4α-glucan branchingdextran glucosidase

glucan-binding protein Asecr peptidoglycan hydrolase

glucan-binding protein CBglB-like G

bp with lipase

GbpC response regulator

major cell-surface adhesin

cell surface antigen I/IIcollagen-binding adhesin

amylase-binding protein A

amylase-binding protein B

ATP-binding transportercom

petence histidine kinasecom

petence transcriptional regbiofilm

regulatory protein Aresponse regulator of BrpA-1response regulator of BrpA-2

lantibiotic mutacin II

lantibiotic mutacin 1140

lantibiotic mutacin M

lantibiotic mutacin B-N

y266bacteriocin Sm

bAbacteriocin secretion protein

bacteriocin peptideundecaprenol kinase

rRNA m

aturation factorm

utacin 1140 modifying enzym

eserine-threonine kinase PknBoxidative stress sensor kinase

collagenase

metabolismattachmentcoordinationproteins by functional similarity

sugar uptake

nutrientuptake

energy storage

acid production

acid tolerance

S. mutans virulence factors

glucan production

glucan attachment

otherattach

quorum sensinglantibioticslantibiotic

regulation

H. sapiensL. rhamnosus (ATCC-53103)L. paracasei (ATCC-27092)S. parasanguinisS. sanguinisS. salivariusS. oralisS. mitis (ATCC-6249)S. mitis (SK597)S. mitis (SK564)S. mitis (SK321)S. mitis (B6)S. mitis (NCTC-2261)

phylogenetic profiles

protein similarity(matching HMM columns / length of protein)

target proteomes

antitarget proteomes

V. parvulaB. longum (strain DJO10A)B. dentium (ATCC-27534)L. fermentum (CECT-5716)L. fermentum (28-3-CHN)L. fermentum (ATCC-14931)L. fermentum (IFO-3956/LMG-18251)L. salivarius subsp. salivarius (UCC118)L. salivarius (ACS-116-V-Col5a)L. salivarius (CECT-5713)L. salivarius (ATCC-11741)L. casei (BL23)L. casei (Zhang)L.casei (ATCC-334)L. acidophilusS. gordoniiS. mutans serotype c (NN2025)

modelable druggable

tractability

Q00749

Q00752

P72477

Q8DUN3

Q8DWE7

Q8DWE6

Q59940

Q59928

Q8DTU4

Q8CWX0

Q8DT53

Q8DUE7

Q8CVC4

P26283

P45596

P45595

P50976

P26426

P95783

Q54431

Q59925

Q8DU74

Q8DWC9

Q8DWG2

Q8DT55

Q8DT31

P10249

P08987

P13470

P49331

Q8DT52

Q99040

Q8DRV2

Q8DWM3

Q8DTF1

Q8DUW9

Q9S151

P11657

P23504

Q76H84

A8AZZ3

A8AUM3

Q8DW05

Q8DS94

Q8DS39

Q8DVR0

Q8DVJ9

Q8DVJ8

O54329

O68586

Q7BV70

P80666

Q5TLL1

Q8DSA3

Q8CVC8

Q05888

Q8DSY7

O68588

Q8DVK1

Q8DT64

Q8DUX4

Adhesin A3VP1 of AntigenI/IIG

lucosamine-6-phosphate deam

inaseM

n-dependent inorganic pyrophosphataseU

nknown function 1377c

Isopropylmalate dehydratase

V-region of antigen I/IIPhosphatase/hydrolase

PhosphataseN

ADP-dependent G

APDH

Unknow

n enzyme

Dihydroorotate dehydrogenase

Dextran glucosidase

Dextran glucosidase

Peptide chain release factorTagatose 1,6-aldolase

Carboxymuconolactone decarboxylase


target proteomes

S. mutans PD

Bsdruggable

3IOX

2RI1

1I74

3L7V

2HCU

1JMM

3L7Y

1WVI

2QE0

3IJT

3OIX

2ZID

2ZIC

1ZBT

3IV3

3LVY


UD

P acetylglucosamine epim

erasePhosphorylase

Trans enoyl ACP reductaseO

ligopeptide ABC transporterAnthranilate phosphoribosyltransferase

Periplasmic ferrichrom

e ABC transporterU

DP acetylglucosam

ine carboxyvinyltransferase 1U

DP acetylglucosam

ine carboxyvinyltransferase 2Adenylate kinase

D-alanine polyligase

dTDP-glucose dehydratase

Dihydroorotate dehydrogenase

Secreted translocaseβ-galactosidase

Imidazole carboxam

ide isomerase

Acetoin dehydrogenaseBifunctional protein glm

UM

ethionyl-tRNA synthetase

Guanylate kinase

Glycerol dehydrogenase

Phosphataseα-acetolactate synthase

Thiazole pyrodixine kinaseG

lutamyl-tRN

A amidotransferase subA

Bisphosphoglycerate mutase

Manganese inorganic pyrophosphatase

Surface protein I/IIResponse regulator

AdcA-like Zn adhesin lipoproteinAcetyltransferaseD

NA polym

eraseIm

idazole glycerol-PO4 synthase

SAM m

ethyltransferaseG

lucanotransferasetRN

A thiouridylase30S ribosom

al proteinD

ihydrodipicolinate synthasePyrim

idine-nucleoside phosphorylaseO

rotidine 5'-phosphate decarboxylaseU

nknown hydrolase/phosphatase

Maltose operon transcriptional repressor

Uracil phosphoribosyltransferase

ATP synthaseLactose phosphotransferase repressor

Catabolite control proteinATP synthase

Malolactic enzym

eLytTr D

NA-binding

Purine operon repressorTryptophan synthase

tRNA YrdC-m

odifierIsopropylm

alate dehydrataseAdenine phosphoribosyltransferase

Deoxycytidylate deam

inaseRN

A-diphosphate reductaseAdenylate kinase

Glycosyltransferase

Anaerobic RNA-triphosphate reductase

ATP-binding ABC transporterdTD

P keto rhamnose reductase

ATP-binding ABC transporterDTD

P keto rhamnose reductase

Hom

oserine succinyltransferaseCarbam

oyl-phosphate synthaseN

ADP-dependent G

APDH

Unique &

uncharacterizedTellurite resistance protein

Ferrous ion transport proteinPhosphopentom

utaseTranscription regulator

Chorismate m

utasePhosphofructokinase

Cysteine synthaseG

lucan glucosidaseH

istidine kinaseCitrate synthase

Dextran glucosidase

Unknow

n hydrolase/phosphataseU

nknown hydrolase/phosphatase

Tagatose diphosphate aldolaseAm

ino acid aminotransferase

Uracil-D

NA glycosylase

DN

A damage sensor

ATP synthase

V. parvulaB. longum (strain DJO10A)B. dentium (ATCC-27534)L. fermentum (CECT-5716)L. fermentum (28-3-CHN)L. fermentum (ATCC-14931)L. fermentum (IFO-3956/LMG-18251)L. salivarius subsp. salivarius (UCC118)L. salivarius (ACS-116-V-Col5a)L. salivarius (CECT-5713)L. salivarius (ATCC-11741)L. casei (BL23)L. casei (Zhang)L. casei (ATCC-334)L. acidophilusS. gordoniiS. mutans serotype c (NN2025)

Q8DTB7

Q8DT31

Q8DSN4

Q8DW25

Q8DVF6

Q8DUD7

Q8DT57

Q8DT24

Q8DS33

Q53526

P95780

Q8DTV0

Q8DSJ6

P50978

Q8DTR2

Q8DTL3

Q8DSX2

Q8DSW8

Q8DVK6

Q8DVJ3

Q8DV60

Q8DTA6

Q8DSS7

Q8DSG5

P59161

O68579

Q9RFI8

Q8DVJ8

Q8DTN1

Q8DSV5

Q8DWN8

Q8DTR3

Q8DTH5

Q8DT30

Q8DRS4

Q8DWB3

Q8DUE5

Q8DU33

Q8DTV1

Q8DTS3

Q8DT29

Q8DST6

P95789

P26422

O07329

A6PY32

Q8DWC7

Q8DVZ8

Q8DVV6

Q8DVF3

Q8DTG7

Q8DTG5

Q8DT95

Q8DSE5

Q8DV42

Q8DTS0

Q8DSH9

Q8DRY2

Q8DW32

Q8DUS5

Q8DTZ7

O33664

Q8DT96

Q8DUP4

Q59931

Q8DTQ1

Q8DSW3

Q8DVC3

Q8DTU0

Q8DTZ5

Q8DTP2

Q8KWU0

Q8DVJ2

Q99040

Q8DT45

Q59939

Q2HWU5

Q8DV06

Q8DUY6

P26425

Q8DWM1

Q8DTV8

Q8DTC4

P95790

S. mutans proteins

modelable druggable

a.b.

-1.57 0.76

-1.02 0.27

-1.25 0.52

-0.30 -0.08

-0.88 0.36

-1.01 0.74

-0.71 0.80

-0.93 -0.85

-0.44 0.36

0.76 0.78

-1.23 -0.15

-1.73 -0.71

-0.85 -0.75

-1.25 0.80

-0.96 0.79

-0.85 0.74

-1.18 0.82

-1.12 0.82

-0.45 -0.70

-0.15 0.39

-0.09 0.80

-0.25 0.77

-1.77 0.55

-0.69 0.77

-1.08 -0.71

-1.59 0.78

-1.50 0.41

-0.37 0.77

-1.88 0.77

0.72 0.81

0.60 -0.97

0.14 -0.41

0.97 0.81

0.86 0.80

0.76 -0.08

0.52 0.80

-0.34 0.80

0.19 0.80

-1.05 0.77

figure 3

-1.75 0.82

-1.12 0.82

-1.01 0.82

-1.13 0.81

-1.33 0.81

-1.46 0.81

-1.10 0.81

-1.18 0.81

-1.44 0.81

-1.04 0.81

-1.82 0.81

-1.35 0.80

-1.23 0.80

-1.87 0.80

-1.14 0.79

-1.04 0.79

-1.03 0.79

-1.09 0.79

-1.36 0.78

-1.20 0.78

-1.38 0.78

-1.24 0.78

-1.27 0.78

-1.13 0.78

-1.20 0.78

-1.50 0.78

-1.17 0.77

-1.88 0.77

-1.37 0.77

-1.23 0.77

-1.36 0.76

-1.47 0.76

-1.41 0.76

-1.08 0.76

-1.20 0.76

-1.71 0.75

-1.63 0.75

-1.07 0.75

-1.45 0.75

-1.82 0.75

-1.63 0.75

-1.39 0.75

-1.14 0.75

-2.20 0.75

-1.11 0.75

-1.47 0.75

-1.14 0.74

-1.12 0.74

-1.22 0.74

-1.06 0.74

-1.63 0.74

-2.10 0.74

-1.30 0.74

-1.19 0.74

-1.15 0.73

-1.10 0.73

-1.13 0.73

-1.08 0.73

-1.14 0.72

-1.58 0.72

-1.19 0.72

-1.39 0.72

-1.32 0.71

-1.30 0.70

-1.40 0.70

-1.41 0.69

-1.30 0.68

-1.95 0.66

-1.90 0.63

-1.43 0.58

-1.13 0.58

-1.13 0.57

-1.17 0.56

-1.77 0.55

-1.30 0.55

-1.35 0.55

-1.74 0.55

-1.59 0.54

-1.18 0.54

-1.94 0.54

-1.25 0.53

-1.53 0.53

-1.52 0.52

-1.42 0.51

figure 4b

0.77

0.77

0.77

0.74

0.74

0.71

0.70

0.70

0.66

0.57

0.56

0.56

0.56

0.56

0.54

0.53

figure 4a

virulence factors 61, literature review

structures81, PDB

proteome2391, UniProt

comparative modeling 616 of 1631, MODELLER

active site analysis110, drugEBIlity

phylogenetic profiles110, HHsearch

uniquecommon rare

metabolism attachment coordinationproteins by functional similarity

sugar uptake

nutrientuptake

energy storage

acid production

acid tolerance

S. m

utan

s viru

lenc

e fa

ctor

s

glucan production

glucan attachment

otherattach

quorum sensing lantibiotics

lantibiotic regulation


phyl

ogen

etic

profi

les


targ

et p

rote

omes

antit

arge

t pro

teom

es

V. parvulaB. longum (strain DJO10A)B. dentium (ATCC-27534)L. fermentum (CECT-5716)L. fermentum (28-3-CHN)L. fermentum (ATCC-14931)L. fermentum (IFO-3956/LMG-18251)L. salivarius subsp. salivarius (UCC118)L. salivarius (ACS-116-V-Col5a)L. salivarius (CECT-5713)L. salivarius (ATCC-11741)L. casei (BL23)L. casei (Zhang)L.casei (ATCC-334)L. acidophilusS. gordoniiS. mutans serotype c (NN2025)

mod

elab

le d

rugg

able

trac

tabi

lity

mul

tiple

sug

ar-b

indi

ngM

S tr

ansp

ort A

TP-b

indi

ngAT

P-bi

ndin

g tr

ansp

orte

rfr

ucto

se p

hosp

hotr

ansf

eras

e IIA

BCfr

ucto

se p

hosp

hotr

ansf

eras

e IIB

Cfr

ucto

se p

hosp

hotr

ansf

eras

e IIA

isoc

itrat

e de

hydr

ogen

ase

acet

ylor

nith

ine

amin

otra

nsfe

rase

purin

e nu

cleo

side

pho

spho

ryla

segl

ycog

en sy

ntha

seG

lu1-

PO4

aden

ylyl

tran

sfer

ase

beta

-glu

cosi

dase

endo

gluc

anas

ela

ctat

e de

hydr

ogen

ase

phos

phoc

arrie

r pro

tein

HPr

PEP-

phos

phot

rans

fera

sepr

oton

/lacti

c ac

id p

ump

lact

ose-

spec

ific

PO4-

tran

sfer

ase

N'N

' DCH

C-se

nsiti

ve A

TPas

esi

gnal

reco

gniti

on p

artic

lefo

rmyl

tetr

ahyd

rofo

late

liga

sepa

ntho

then

ate

flavo

prot

ein

mal

olac

tic fe

rmen

tatio

n re

gD

NA-

dir R

NA

poly

mer

ase

glyc

ogen

pho

spho

ryla

seph

osph

oryl

ase

sucr

ose

phos

phor

ylas

eG

TF-I

1,3α

-bra

nch

gluc

osyl

tran

sfer

ase-

SIgl

ucos

yltr

ansf

eras

e-S

1,4α

-glu

can

bran

chin

gde

xtra

n gl

ucos

idas

egl

ucan

-bin

ding

pro

tein

Ase

cr p

eptid

ogly

can

hydr

olas

egl

ucan

-bin

ding

pro

tein

CBg

lB-li

ke G

bp w

ith li

pase

Gbp

C re

spon

se re

gula

tor

maj

or c

ell-s

urfa

ce a

dhes

ince

ll su

rfac

e an

tigen

I/II

colla

gen-

bind

ing

adhe

sin

amyl

ase-

bind

ing

prot

ein

Aam

ylas

e-bi

ndin

g pr

otei

n B

ATP-

bind

ing

tran

spor

ter

com

pete

nce

histi

dine

kin

ase

com

pete

nce

tran

scrip

tiona

l reg

biofi

lm re

gula

tory

pro

tein

Are

spon

se re

gula

tor o

f Brp

A-1

resp

onse

regu

lato

r of B

rpA-

2la

ntibi

otic

mut

acin

IIla

ntibi

otic

mut

acin

114

0la

ntibi

otic

mut

acin

Mla

ntibi

otic

mut

acin

B-N

y266

bact

erio

cin

SmbA

bact

erio

cin

secr

etion

pro

tein

bact

erio

cin

pepti

deun

deca

pren

ol k

inas

erR

NA

mat

urati

on fa

ctor

mut

acin

114

0 m

odify

ing

enzy

me

serin

e-th

reon

ine

kina

se P

knB

oxid

ative

stre

ss s

enso

r kin

ase

colla

gena

se

Q00749

Q00752

P72477

Q8DUN3

Q8DWE7

Q8DWE6

Q59940

Q59928

Q8DTU4

Q8CWX0

Q8DT53

Q8DUE7

Q8CVC4

P26283

P45596

P45595

P50976

P26426

P95783

Q54431

Q59925

Q8DU74

Q8DWC9

Q8DWG2

Q8DT55

Q8DT31

P10249

P08987

P13470

P49331

Q8DT52

Q99040

Q8DRV2

Q8DWM3

Q8DTF1

Q8DUW9

Q9S151

P11657

P23504

Q76H84

A8AZZ3

A8AUM3

Q8DW05

Q8DS94

Q8DS39

Q8DVR0

Q8DVJ9

Q8DVJ8

O54329

O68586

Q7BV70

P80666

Q5TLL1

Q8DSA3

Q8CVC8

Q05888

Q8DSY7

O68588

Q8DVK1

Q8DT64

Q8DUX4

Adhe

sin

A3VP

1 of

Anti

genI

/II

Glu

cosa

min

e-6-

phos

phat

e de

amin

ase

Mn-

depe

nden

t ino

rgan

ic p

yrop

hosp

hata

seU

nkno

wn

func

tion

1377

cIs

opro

pylm

alat

e de

hydr

atas

eV-

regi

on o

f anti

gen

I/II

Phos

phat

ase/

hydr

olas

ePh

osph

atas

eN

ADP-

depe

nden

t GAP

DH

Unk

now

n en

zym

eD

ihyd

roor

otat

e de

hydr

ogen

ase

Dex

tran

glu

cosid

ase

Dex

tran

glu

cosid

ase

Pepti

de c

hain

rele

ase

fact

orTa

gato

se 1

,6-a

ldol

ase

Carb

oxym

ucon

olac

tone

dec

arbo

xyla

se


3IOX

2RI1

1I74

3L7V

2HCU

1JMM

3L7Y

1WVI

2QE0

3IJT

3OIX

2ZID

2ZIC

1ZBT

3IV3

3LVY


UD

P ac

etyl

gluc

osam

ine

epim

eras

ePh

osph

oryl

ase

Tran

s en

oyl A

CP re

duct

ase

Olig

opep

tide

ABC

tran

spor

ter

Anth

rani

late

pho

spho

ribos

yltr

ansf

eras

ePe

ripla

smic

ferr

ichr

ome

ABC

tran

spor

ter

UD

P ac

etyl

gluc

osam

ine

carb

oxyv

inyl

tran

sfer

ase

1U

DP

acet

ylgl

ucos

amin

e ca

rbox

yvin

yltr

ansf

eras

e 2

Aden

ylat

e ki

nase

D-a

lani

ne p

olyl

igas

edT

DP-

gluc

ose

dehy

drat

ase

Dih

ydro

orot

ate

dehy

drog

enas

eSe

cret

ed tr

ansl

ocas

eβ-

gala

ctos

idas

eIm

idaz

ole

carb

oxam

ide

isom

eras

eAc

etoi

n de

hydr

ogen

ase

Bifu

nctio

nal p

rote

in g

lmU

Met

hion

yl-t

RNA

synt

heta

seG

uany

late

kin

ase

Gly

cero

l deh

ydro

gena

sePh

osph

atas

eα-

acet

olac

tate

syn

thas

eTh

iazo

le p

yrod

ixin

e ki

nase

Glu

tam

yl-t

RNA

amid

otra

nsfe

rase

sub

ABi

spho

spho

glyc

erat

e m

utas

eM

anga

nese

inor

gani

c py

roph

osph

atas

eSu

rfac

e pr

otei

n I/

IIRe

spon

se re

gula

tor

AdcA

-like

Zn

adhe

sin

lipop

rote

inAc

etyl

tran

sfer

ase

DN

A po

lym

eras

eIm

idaz

ole

glyc

erol

-PO

4 sy

ntha

seSA

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V. parvulaB. longum (strain DJO10A)B. dentium (ATCC-27534)L. fermentum (CECT-5716)L. fermentum (28-3-CHN)L. fermentum (ATCC-14931)L. fermentum (IFO-3956/LMG-18251)L. salivarius subsp. salivarius (UCC118)L. salivarius (ACS-116-V-Col5a)L. salivarius (CECT-5713)L. salivarius (ATCC-11741)L. casei (BL23)L. casei (Zhang)L. casei (ATCC-334)L. acidophilusS. gordoniiS. mutans serotype c (NN2025)

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Documents

A. Study design schematic Streptococcus mitis (NCTC-2261) Streptococcus mitis (B6) Streptococcus mitis (SK321) Streptococcus mitis (SK564) Streptococcus