TABLE 1

Clostridium butyricum ISS-190 proteins up- or downexpressed under the AE condition

Protein expression
type, category,
and no.
NCBI
accession
no.
Gene nameProtein nameFCaNotesbBiological
process
Upexpressed
    Biological process
not assigned
        1489509402CLP_2689Phage major tail protein1.89Biol GO not assigned
        2489502155CLP_3314Metallophosphoesterase0.69Biol GO not assigned
        3488646122CLP_3861Outer surface protein*Biol GO not assigned
        4489502201CLP_3345Uncharacterized protein1.55Biol GO not assigned
        5489504250CLP_1280Uncharacterized protein1.16Biol GO not assigned
        6489504278CLP_1290Uncharacterized protein1.28Biol GO not assigned
        7489504289CLP_1282Uncharacterized protein*Biol GO not assigned
        8489504297CLP_1288Uncharacterized protein1.31Biol GO not assigned
        9489504751CLP_2775Putative lipoprotein2.24Biol GO not assigned
        10489503695CLP_3097Putative lipoprotein0.70Biol GO not assigned
        11489509462CLP_1648Major capsid protein*Biol GO not assigned
        12489504253CLP_1279Uncharacterized protein1.54Biol GO not assigned:
likely phage
        13489504296CLP_1287Baseplate J family protein1.29Biol GO not assigned:
likely phage
        14237656561CLP_1654Uncharacterized protein*Biol GO not assigned:
likely PTS
    Carbohydrate
metabolism
        15488642402CLP_0032N-Acetylneuraminate lyase (NanA)2.89Carbohydrate metabolism:
sialic acid catabolism
        16489505355CLP_0171N-Acetylmannosamine-6-
phosphate 2-epimerase (NanE)
4.50Carbohydrate metabolism:
sialic acid catabolism
        17489503203CLP_0041Beta-glucosidase*Glycoside hydrolaseCarbohydrate metabolism
        18489502642CLP_0871Alpha,alpha-phosphotrehalase1.32Glycoside hydrolaseCarbohydrate metabolism
        19489505662CLP_1017Alpha amylase, catalytic region1.64Glycoside hydrolaseCarbohydrate metabolism
        20489502184CLP_3347Glycosyl hydrolase family 32, N
domain protein
3.15Glycoside hydrolaseCarbohydrate metabolism
        21488644093CLP_1327Hydroxyacylglutathione hydrolase1.57Carbohydrate metabolism
        22488646082CLP_3906Ribose-5-phosphate isomerase B3.45Carbohydrate metabolism
        23489502147CLP_3305dTDP-4-dehydrorhamnose
3,5-epimerase
1.35Carbohydrate metabolism
        24489503814CLP_3464UDP-N-acetylglucosamine
4,6-dehydratase
*Carbohydrate metabolism
        25489507281CLP_4271Aldose 1-epimerase0.65Carbohydrate metabolism
    Peptidoglycan
metabolism
        26489504484CLP_3010Penicillin-binding protein2.12Peptidoglycan metabolism
        27489502929CLP_0014Cell wall hydrolase/autolysin4.04Peptidoglycan metabolism
    Redox homeostasis
        28488644028CLP_1392FAD-dependent oxidoreductase0.94Fe-SRedox homeostasis
        29488644495CLP_1011ArsC family protein2.63Redox homeostasis
        30488644556CLP_0948Redoxin1.37Redox homeostasis
        31489501807CLP_2414NADH oxidase2.89NADH→NADRedox homeostasis
        32489503213CLP_0082Oxidoreductase NAD-binding
domain protein
2.16NAD→NADHRedox homeostasis
        33489505820CLP_3877FAD-linked oxidase domain
protein
1.58FAD→FADHRedox homeostasis
        34489506590CLP_0595Thioredoxin-disulfide reductase3.25FAD→FADH,
NAD→NADH
Redox homeostasis
        35489506753CLP_0519MviM protein NAD(P)-dependent
oxidoreductase
3.25NADP→NADPHRedox homeostasis
        36489507464CLP_4064Thioredoxin reductase1.74NADP→NADPHRedox homeostasis
        37489510856CLP_0102Rubrerythrin1.45FeRedox homeostasis
        38488644026CLP_1394Zinc finger protein0.67Redox homeostasis
        39489502510CLP_2859Ribosome-binding ATPase YchF3.21Redox homeostasis
    Sulfur metabolism
        40489504716CLP_1763Cystathionine beta-lyase, MetC2.10Sulfur metabolism: amino
acid metabolism
        41489507701CLP_3701S-Adenosylmethionine synthase,
MetK
1.02Sulfur metabolism: Cys
and Met metabolism
        42489505568CLP_1012Sulfite reductase1.25Fe-SSulfur metabolism: H2S
biosynthesis—redox
homeostasis
        43237656426CLP_2257Sulfate adenylyltransferase
subunit 1-bifunctional
enzyme CysN/CysC
2.93Sulfur metabolism: H2S
biosynthesis—sulfate
reduction
        44489501666CLP_2258Sulfate adenylyltransferase
subunit 2-bifunctional
enzyme CysN/CysC
*Sulfur metabolism: H2S
biosynthesis—sulfate
reduction
        45488642894CLP_2741Cysteine desulfurase IscS1.18Fe-SSulfur metabolism: (Fe-S)
cluster biosynthesis
    Transport
        Protein
transport
            46488644099CLP_1321Protein translocase subunit SecD1.20P-P hydrolaseProtein transport
            47489510437CLP_1322Protein-export membrane
protein SecF
0.64P-P hydrolaseProtein transport
            48489504061CLP_3432Chemotaxis protein MotA0.69Protein transport
        Sugar transport
            49488646019CLP_3984Phosphoenolpyruvate-protein
phosphotransferase
1.19Sugar PTSSugar transport
            50489503218CLP_0055PTS, lactose/cellobiose family
IIB component
2.05Sugar PTSSugar transport
            51489505845CLP_3908PTS enzyme IIC component,
galactitol transporter
2.57Sugar PTSSugar transport
            52489505963CLP_3910PTS enzyme IIBC component,
fructose transporter
2.96Sugar PTSSugar transport
            53489507776CLP_3760Lichenan-specific phosphotransferase
enzyme IIA component,
cellobiose transporter
3.21Sugar PTSSugar transport
            54489508885CLP_3296CspC, N-acetylmuramoyl-
l-alanine amidase family
protein
0.88HydrolaseSugar transport:
peptidoglycan
amidohydrolase
            55489501903CLP_2323Putative sugar-binding secreted
protein
4.50ABC transporterSugar transport:
peptidoglycan
amidohydrolase
        Transmembrane
transport
            56489510211CLP_2264Sulfate transporter subunit,
sulfate starvation-induced
protein 2
1.86ABC transporterTransmembrane transport
            57489507313CLP_4206ABC transporter, ATP-binding protein2.04ABC transporterTransmembrane transport
            58489502974CLP_2166Amino acid permease-
associated region
3.44Transmembrane transport
            59489504117CLP_2003Efflux transporter, RND family3.09Transmembrane transport
            60488644700CLP_0371Extracellular solute-binding
protein family 3
0.91Transmembrane transport
            61489506027CLP_3956Extracellular solute-binding
protein, family 1
0.77Transmembrane transport
            62489502966CLP_2159Spermidine/putrescine import
ATP-binding protein PotA
0.86Transmembrane transport
        Membrane
protein
            63489505750CLP_1031ErfK/YbiS/YcfS/YnhG family
protein
1.22Membrane protein
            64488645963CLP_4057PilT protein domain protein1.47Membrane protein
            65489502814CLP_1221V-type ATP synthase subunit D3.67Plasma membrane ATP-
coupled proton transport
    Nucleotide/
nucleoside biosynthesis
        66489510278CLP_1207Pseudouridine synthase, RluA family0.86Nucleoside synthesis
        67488642701CLP_3018Nucleoside diphosphate kinase (NDK)2.09Nucleotide biosynthesis
        68488644020CLP_1400Uridine kinase (UDK)1.27Pyrimidine biosynthesis
        69488646320CLP_4393Oxidoreductase FAD/NAD1.46Fe-S
(oxidoreductase)
Pyrimidine biosynthesis
        70489502503CLP_2848Dihydroorotate dehydrogenase
B [NAD(+)], PyrK
0.84Fe-S
(electron transfer)
Pyrimidine biosynthesis
        71488642810CLP_2846Orotate
phosphoribosyltransferase, PyrE
0.26Pyrimidine biosynthesis
    Translation
        72489504979CLP_2730GTP-binding protein TypA/BipA2.16Translation
        73489502964CLP_2156Helicase domain protein3.82Translation
        74488645666CLP_3735Peptide chain release factor 11.05Translation
        75489506025CLP_3829Asparaginyl/glutamyl-tRNA
amidotransferase GatC
0.92Translation
        76489503907CLP_3482Flagellar assembly factor FliW1.25Translation
    Other
        77489503965CLP_3434Flagellar basal body protein*Bacterial-type flagellum
motility
        78489505096CLP_2731RNase J1.10rRNA processing
        79488642929CLP_2579GTPase Der1.98Ribosome biogenesis
        80489509514CLP_1938Chemotaxis response regulator1.04Stimulus response
        81488644530CLP_0974UspA domain protein1.89Stress response
        82489502173CLP_3317DegT/DnrJ/EryC1/StrS
aminotransferase
0.85Transferase
aminotransferase
        83489510263CLP_2488Protein RecA0.79DNA repair
        84489505855CLP_3987Ribonucleoside-diphosphate
reductase
1.54OxidoreductaseDNA replication
Downexpressed
    Biological process
not assigned
        1488644185CLP_1269Uncharacterized protein−0.64Biol GO not assigned
        2489503664CLP_3067Uncharacterized protein−3.20Biol GO not assigned
        3489504941CLP_2749p-47 protein−2.11Biol GO not assigned
        4489505689CLP_1082Uncharacterized protein*Biol GO not assigned
        5489501399CLP_1582TPR repeat protein*Biol GO not assigned
        6489507297CLP_4257Uncharacterized protein*Biol GO not assigned
        7489510276CLP_2354Uncharacterized protein−1.42Biol GO not assigned
    Carbohydrate
metabolism
        8489509381CLP_1388Propionate CoA-transferase−2.21Likely uses butyryl-
CoA as the
substrate
Carbohydrate metabolism
        9489502979CLP_0779Transaldolase−1.55Carbohydrate metabolism
        10488644944CLP_0793Pyruvate formate-lyase-activating
enzyme
−1.85Fe-SCarbohydrate metabolism
        11489505871CLP_3853Butyryl-CoA dehydrogenase−0.95Carbohydrate metabolism:
butyrate synthesis
pathway
        12489506129CLP_3852Electron transfer flavoprotein,
beta subunit
−1.13Electron transferCarbohydrate metabolism:
butyrate synthesis
pathway
        13906848776CLP_38503-Hydroxybutyryl-CoA dehydrogenase−1.24Carbohydrate metabolism:
butyrate synthesis
pathway
    Translation
        14488643005CLP_250230S ribosomal protein S15−0.78Translation
        15488645977CLP_402830S ribosomal protein S19−1.16Translation
        16488645980CLP_402550S ribosomal protein L16−0.72Translation
        17488645984CLP_402150S ribosomal protein L24*Translation
        18488645990CLP_401530S ribosomal protein S5−0.77Translation
        19488645998CLP_400630S ribosomal protein S13−1.66Translation
        20488646007CLP_399750S ribosomal protein L13−0.87Translation
        21488646008CLP_399630S ribosomal protein S9−0.77Translation
        22488646514CLP_404150S ribosomal protein L10−0.84Translation
        23489502574CLP_287250S ribosomal protein L25−1.72Translation
        24489503008CLP_2520Ribosome-recycling factor*Translation
        25488646138CLP_384460-kDa chaperonin−0.94Protein refoldingTranslation
    rRNA processing
        26488642944CLP_2563Probable dual-specificity RNA
methyltransferase RlmN
*Fe-SrRNA processing
        27489508929CLP_3179rRNA small-subunit methyltransferase*rRNA processing
    Nucleotide/
nucleoside biosynthesis
        28489507369CLP_4280Ribose-phosphate pyrophosphokinase*Nucleotide biosynthesis
        29488642862CLP_27885-(Carboxyamino)imidazole
ribonucleotide mutase, PurE
*Nucleotide biosynthesis
    Other
        30488642931CLP_2577Stage IV sporulation protein A−3.09Sporulation
        31653633918AWN73_
11055
Serine protease−2.83Protein kinase
        32488643856CLP_1581Heat shock protein Hsp20−2.40Stress response
        33489507712CLP_3749Peptidoglycan-binding LysM−2.19Peptidoglycan
metabolism
        34488643009CLP_2498Aspartokinase*Amino acid biosynthesis
        35489504328CLP_3792N-Acetylgalactosamine permease
IID component
*PTSSugar transport
  • a FC is reported as log2 AE/AN ratio, as described in Materials and Methods. * indicates proteins for which FC has not been calculated because they have been detected only in aerobic or anaerobic conditions.

  • b Notes column reports some specific relevant functional protein features discussed in the text.