TABLE 1.

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

Protein expression type, category, and no.	NCBI accession no.	Gene name	Protein name	FCa	Notesb	Biological process
Upexpressed
Biological process not assigned
1	489509402	CLP_2689	Phage major tail protein	1.89		Biol GO not assigned
2	489502155	CLP_3314	Metallophosphoesterase	0.69		Biol GO not assigned
3	488646122	CLP_3861	Outer surface protein	*		Biol GO not assigned
4	489502201	CLP_3345	Uncharacterized protein	1.55		Biol GO not assigned
5	489504250	CLP_1280	Uncharacterized protein	1.16		Biol GO not assigned
6	489504278	CLP_1290	Uncharacterized protein	1.28		Biol GO not assigned
7	489504289	CLP_1282	Uncharacterized protein	*		Biol GO not assigned
8	489504297	CLP_1288	Uncharacterized protein	1.31		Biol GO not assigned
9	489504751	CLP_2775	Putative lipoprotein	2.24		Biol GO not assigned
10	489503695	CLP_3097	Putative lipoprotein	0.70		Biol GO not assigned
11	489509462	CLP_1648	Major capsid protein	*		Biol GO not assigned
12	489504253	CLP_1279	Uncharacterized protein	1.54		Biol GO not assigned: likely phage
13	489504296	CLP_1287	Baseplate J family protein	1.29		Biol GO not assigned: likely phage
14	237656561	CLP_1654	Uncharacterized protein	*		Biol GO not assigned: likely PTS
Carbohydrate metabolism
15	488642402	CLP_0032	N-Acetylneuraminate lyase (NanA)	2.89		Carbohydrate metabolism: sialic acid catabolism
16	489505355	CLP_0171	N-Acetylmannosamine-6- phosphate 2-epimerase (NanE)	4.50		Carbohydrate metabolism: sialic acid catabolism
17	489503203	CLP_0041	Beta-glucosidase	*	Glycoside hydrolase	Carbohydrate metabolism
18	489502642	CLP_0871	Alpha,alpha-phosphotrehalase	1.32	Glycoside hydrolase	Carbohydrate metabolism
19	489505662	CLP_1017	Alpha amylase, catalytic region	1.64	Glycoside hydrolase	Carbohydrate metabolism
20	489502184	CLP_3347	Glycosyl hydrolase family 32, N domain protein	3.15	Glycoside hydrolase	Carbohydrate metabolism
21	488644093	CLP_1327	Hydroxyacylglutathione hydrolase	1.57		Carbohydrate metabolism
22	488646082	CLP_3906	Ribose-5-phosphate isomerase B	3.45		Carbohydrate metabolism
23	489502147	CLP_3305	dTDP-4-dehydrorhamnose 3,5-epimerase	1.35		Carbohydrate metabolism
24	489503814	CLP_3464	UDP-N-acetylglucosamine 4,6-dehydratase	*		Carbohydrate metabolism
25	489507281	CLP_4271	Aldose 1-epimerase	0.65		Carbohydrate metabolism
Peptidoglycan metabolism
26	489504484	CLP_3010	Penicillin-binding protein	2.12		Peptidoglycan metabolism
27	489502929	CLP_0014	Cell wall hydrolase/autolysin	4.04		Peptidoglycan metabolism
Redox homeostasis
28	488644028	CLP_1392	FAD-dependent oxidoreductase	0.94	Fe-S	Redox homeostasis
29	488644495	CLP_1011	ArsC family protein	2.63		Redox homeostasis
30	488644556	CLP_0948	Redoxin	1.37		Redox homeostasis
31	489501807	CLP_2414	NADH oxidase	2.89	NADH→NAD	Redox homeostasis
32	489503213	CLP_0082	Oxidoreductase NAD-binding domain protein	2.16	NAD→NADH	Redox homeostasis
33	489505820	CLP_3877	FAD-linked oxidase domain protein	1.58	FAD→FADH	Redox homeostasis
34	489506590	CLP_0595	Thioredoxin-disulfide reductase	3.25	FAD→FADH, NAD→NADH	Redox homeostasis
35	489506753	CLP_0519	MviM protein NAD(P)-dependent oxidoreductase	3.25	NADP→NADPH	Redox homeostasis
36	489507464	CLP_4064	Thioredoxin reductase	1.74	NADP→NADPH	Redox homeostasis
37	489510856	CLP_0102	Rubrerythrin	1.45	Fe	Redox homeostasis
38	488644026	CLP_1394	Zinc finger protein	0.67		Redox homeostasis
39	489502510	CLP_2859	Ribosome-binding ATPase YchF	3.21		Redox homeostasis
Sulfur metabolism
40	489504716	CLP_1763	Cystathionine beta-lyase, MetC	2.10		Sulfur metabolism: amino acid metabolism
41	489507701	CLP_3701	S-Adenosylmethionine synthase, MetK	1.02		Sulfur metabolism: Cys and Met metabolism
42	489505568	CLP_1012	Sulfite reductase	1.25	Fe-S	Sulfur metabolism: H2S biosynthesis—redox homeostasis
43	237656426	CLP_2257	Sulfate adenylyltransferase subunit 1-bifunctional enzyme CysN/CysC	2.93		Sulfur metabolism: H2S biosynthesis—sulfate reduction
44	489501666	CLP_2258	Sulfate adenylyltransferase subunit 2-bifunctional enzyme CysN/CysC	*		Sulfur metabolism: H2S biosynthesis—sulfate reduction
45	488642894	CLP_2741	Cysteine desulfurase IscS	1.18	Fe-S	Sulfur metabolism: (Fe-S) cluster biosynthesis
Transport
Protein transport
46	488644099	CLP_1321	Protein translocase subunit SecD	1.20	P-P hydrolase	Protein transport
47	489510437	CLP_1322	Protein-export membrane protein SecF	0.64	P-P hydrolase	Protein transport
48	489504061	CLP_3432	Chemotaxis protein MotA	0.69		Protein transport
Sugar transport
49	488646019	CLP_3984	Phosphoenolpyruvate-protein phosphotransferase	1.19	Sugar PTS	Sugar transport
50	489503218	CLP_0055	PTS, lactose/cellobiose family IIB component	2.05	Sugar PTS	Sugar transport
51	489505845	CLP_3908	PTS enzyme IIC component, galactitol transporter	2.57	Sugar PTS	Sugar transport
52	489505963	CLP_3910	PTS enzyme IIBC component, fructose transporter	2.96	Sugar PTS	Sugar transport
53	489507776	CLP_3760	Lichenan-specific phosphotransferase enzyme IIA component, cellobiose transporter	3.21	Sugar PTS	Sugar transport
54	489508885	CLP_3296	CspC, N-acetylmuramoyl- l-alanine amidase family protein	0.88	Hydrolase	Sugar transport: peptidoglycan amidohydrolase
55	489501903	CLP_2323	Putative sugar-binding secreted protein	4.50	ABC transporter	Sugar transport: peptidoglycan amidohydrolase
Transmembrane transport
56	489510211	CLP_2264	Sulfate transporter subunit, sulfate starvation-induced protein 2	1.86	ABC transporter	Transmembrane transport
57	489507313	CLP_4206	ABC transporter, ATP-binding protein	2.04	ABC transporter	Transmembrane transport
58	489502974	CLP_2166	Amino acid permease- associated region	3.44		Transmembrane transport
59	489504117	CLP_2003	Efflux transporter, RND family	3.09		Transmembrane transport
60	488644700	CLP_0371	Extracellular solute-binding protein family 3	0.91		Transmembrane transport
61	489506027	CLP_3956	Extracellular solute-binding protein, family 1	0.77		Transmembrane transport
62	489502966	CLP_2159	Spermidine/putrescine import ATP-binding protein PotA	0.86		Transmembrane transport
Membrane protein
63	489505750	CLP_1031	ErfK/YbiS/YcfS/YnhG family protein	1.22		Membrane protein
64	488645963	CLP_4057	PilT protein domain protein	1.47		Membrane protein
65	489502814	CLP_1221	V-type ATP synthase subunit D	3.67		Plasma membrane ATP- coupled proton transport
Nucleotide/ nucleoside biosynthesis
66	489510278	CLP_1207	Pseudouridine synthase, RluA family	0.86		Nucleoside synthesis
67	488642701	CLP_3018	Nucleoside diphosphate kinase (NDK)	2.09		Nucleotide biosynthesis
68	488644020	CLP_1400	Uridine kinase (UDK)	1.27		Pyrimidine biosynthesis
69	488646320	CLP_4393	Oxidoreductase FAD/NAD	1.46	Fe-S (oxidoreductase)	Pyrimidine biosynthesis
70	489502503	CLP_2848	Dihydroorotate dehydrogenase B [NAD(+)], PyrK	0.84	Fe-S (electron transfer)	Pyrimidine biosynthesis
71	488642810	CLP_2846	Orotate phosphoribosyltransferase, PyrE	0.26		Pyrimidine biosynthesis
Translation
72	489504979	CLP_2730	GTP-binding protein TypA/BipA	2.16		Translation
73	489502964	CLP_2156	Helicase domain protein	3.82		Translation
74	488645666	CLP_3735	Peptide chain release factor 1	1.05		Translation
75	489506025	CLP_3829	Asparaginyl/glutamyl-tRNA amidotransferase GatC	0.92		Translation
76	489503907	CLP_3482	Flagellar assembly factor FliW	1.25		Translation
Other
77	489503965	CLP_3434	Flagellar basal body protein	*		Bacterial-type flagellum motility
78	489505096	CLP_2731	RNase J	1.10		rRNA processing
79	488642929	CLP_2579	GTPase Der	1.98		Ribosome biogenesis
80	489509514	CLP_1938	Chemotaxis response regulator	1.04		Stimulus response
81	488644530	CLP_0974	UspA domain protein	1.89		Stress response
82	489502173	CLP_3317	DegT/DnrJ/EryC1/StrS aminotransferase	0.85		Transferase aminotransferase
83	489510263	CLP_2488	Protein RecA	0.79		DNA repair
84	489505855	CLP_3987	Ribonucleoside-diphosphate reductase	1.54	Oxidoreductase	DNA replication
Downexpressed
Biological process not assigned
1	488644185	CLP_1269	Uncharacterized protein	−0.64		Biol GO not assigned
2	489503664	CLP_3067	Uncharacterized protein	−3.20		Biol GO not assigned
3	489504941	CLP_2749	p-47 protein	−2.11		Biol GO not assigned
4	489505689	CLP_1082	Uncharacterized protein	*		Biol GO not assigned
5	489501399	CLP_1582	TPR repeat protein	*		Biol GO not assigned
6	489507297	CLP_4257	Uncharacterized protein	*		Biol GO not assigned
7	489510276	CLP_2354	Uncharacterized protein	−1.42		Biol GO not assigned
Carbohydrate metabolism
8	489509381	CLP_1388	Propionate CoA-transferase	−2.21	Likely uses butyryl- CoA as the substrate	Carbohydrate metabolism
9	489502979	CLP_0779	Transaldolase	−1.55		Carbohydrate metabolism
10	488644944	CLP_0793	Pyruvate formate-lyase-activating enzyme	−1.85	Fe-S	Carbohydrate metabolism
11	489505871	CLP_3853	Butyryl-CoA dehydrogenase	−0.95		Carbohydrate metabolism: butyrate synthesis pathway
12	489506129	CLP_3852	Electron transfer flavoprotein, beta subunit	−1.13	Electron transfer	Carbohydrate metabolism: butyrate synthesis pathway
13	906848776	CLP_3850	3-Hydroxybutyryl-CoA dehydrogenase	−1.24		Carbohydrate metabolism: butyrate synthesis pathway
Translation
14	488643005	CLP_2502	30S ribosomal protein S15	−0.78		Translation
15	488645977	CLP_4028	30S ribosomal protein S19	−1.16		Translation
16	488645980	CLP_4025	50S ribosomal protein L16	−0.72		Translation
17	488645984	CLP_4021	50S ribosomal protein L24	*		Translation
18	488645990	CLP_4015	30S ribosomal protein S5	−0.77		Translation
19	488645998	CLP_4006	30S ribosomal protein S13	−1.66		Translation
20	488646007	CLP_3997	50S ribosomal protein L13	−0.87		Translation
21	488646008	CLP_3996	30S ribosomal protein S9	−0.77		Translation
22	488646514	CLP_4041	50S ribosomal protein L10	−0.84		Translation
23	489502574	CLP_2872	50S ribosomal protein L25	−1.72		Translation
24	489503008	CLP_2520	Ribosome-recycling factor	*		Translation
25	488646138	CLP_3844	60-kDa chaperonin	−0.94	Protein refolding	Translation
rRNA processing
26	488642944	CLP_2563	Probable dual-specificity RNA methyltransferase RlmN	*	Fe-S	rRNA processing
27	489508929	CLP_3179	rRNA small-subunit methyltransferase	*		rRNA processing
Nucleotide/ nucleoside biosynthesis
28	489507369	CLP_4280	Ribose-phosphate pyrophosphokinase	*		Nucleotide biosynthesis
29	488642862	CLP_2788	5-(Carboxyamino)imidazole ribonucleotide mutase, PurE	*		Nucleotide biosynthesis
Other
30	488642931	CLP_2577	Stage IV sporulation protein A	−3.09		Sporulation
31	653633918	AWN73_ 11055	Serine protease	−2.83		Protein kinase
32	488643856	CLP_1581	Heat shock protein Hsp20	−2.40		Stress response
33	489507712	CLP_3749	Peptidoglycan-binding LysM	−2.19		Peptidoglycan metabolism
34	488643009	CLP_2498	Aspartokinase	*		Amino acid biosynthesis
35	489504328	CLP_3792	N-Acetylgalactosamine permease IID component	*	PTS	Sugar transport

^aFC 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.

^bNotes column reports some specific relevant functional protein features discussed in the text.