Comparative transcriptomic analysis reveal genes involved in the pathogenicity increase of Streptococcus suis epidemic strains

Figures & data

Table 1. The information of PICGs identified in the SC84 interaction groups.

		Corresponding homologous gene in P1-7 and 89-1591 genomes
Post-interaction	PICGs identified in the SC84 interaction groups	P1-7	89-1591	Annotation of PICGs	NO. of UDC	Subgroup of COGs
2 h	SSUSC84_1405	SSU1375	MUN40_07820	Cystathionine β- lyase	UDC14	E
	SSUSC84_1406	SSU1376	MUN40_07825	Cystathionine γ-synthase		E
	SSUSC84_1600	SSU1574	MUN40_02800	Methionine ABC transporter permease	UDC15	E
	SSUSC84_1601	SSU1575	MUN40_02795	Methionine ABC transporter ATP-binding protein，ATPase component		E
	SSUSC84_1602	SSU1576	MUN40_02790	Peptidase		E
	SSUSC84_1603	SSU1577	MUN40_02785	MetQ		E
	SSUSC84_1605	SSU1579	MUN40_02780	5-methyltetrahydropteroyltriglutamate – homocysteine methyltransferase (MetE)	UDC16	E
	SSUSC84_1606	SSU1580	MUN40_02765	5,10-methylenetetrahydrofolate reductase （MetF）		E
	SSUSC84_1835	SSU1813	-	Homocysteine S-methyltransferase（MmuM）	UDC20	E
	SSUSC84_1836	SSU1814	-	Amino acid transporter（MmuP）		E
4 h	SSUSC84_0130	SSU0135	MUN40_01225	Folate family ECF transporter S component	UDC3	E

-: absent in the corresponding genome.

Table 2. The information of PIRGs identified in the SC84 interaction groups.

		Corresponding homologous gene in P1-7 and 89-1591 genomes
Post-interaction	PICGs identified in SC84 interaction groups	P1-7	89-1591	Annotation of PICGs	NO. of UDC	Subgroup of COGs
2 h	SSUSC84_0164	SSU0171	-	Epf^d		D
	SSUSC84_0178	SSU0186	-	HP197^d		D
	SSUSC84_0242	SSU0253	-	HP272^d		D
	SSUSC84_0314	SSU0327	-	Deoxyguanosinetriphosphatetriphosphohydrolase		F
	SSUSC84_0342	SSU0356	MUN40_00410	Endonuclease		L
	SSUSC84_0347	SSU0361	MUN40_00435	DNA-directed RNA polymerase subunit delta	C1	H
	SSUSC84_0348	SSU0362	MUN40_00440	Substrate-specific component MtsA of methionine-regulated ECF transporter		E
	SSUSC84_0349	SSU0363	MUN40_00445	Hypothetical protein		S
	SSUSC84_0512	SSU0528	MUN40_09220	Acyltransferase^e		M
	SSUSC84_0619	SSU0652	-	Type I restriction modification protein	C3	V
	SSUSC84_0620	SSU0653	-	Type I restriction modification protein		V
	SSUSC84_0621	SSU0654	-	Restriction endonuclease subunit S		V
	SSUSC84_0622	SSU0655	-	Hypothetical protein		S
	SSUSC84_0688	SSU0724	MUN40_04630	Membrane protein		S
	SSUSC84_0772	SSU0809	-	Hypothetical protein		S
	SSUSC84_0777	SSU0814	-	Hypothetical protein	C4	S
	SSUSC84_0778	SSU0815	-	Hypothetical protein		S
	SSUSC84_0932	SSU0887	MUN40_05795	O-acetylhomoserine (thiol)-lyase		E
	SSUSC84_0985	SSU0945	MUN40_06185	CiaR^d		T
	SSUSC84_1029	SSU0991	MUN40_06405	Membrane protein	C5	S
	SSUSC84_1030	SSU0992	MUN40_06410	Transporter		P
	SSUSC84_1333	SSU1303	MUN40_07265	Lipoprotein		S
	SSUSC84_1375	SSU1345	-	Transcriptional regulator	C7	K
	SSUSC84_1376	SSU1346	-	Hypothetical protein		S
	SSUSC84_1664	SSU1639	MUN40_02365	Lipoprotein		G
4 h	SSUSC84_0145	SSU0152	MUN40_01300	Sspep^d		O
	SSUSC84_0242	SSU0253	-	HP272^d		D
	SSUSC84_0249	SSU0260	MUN40_01895	Alcohol dehydrogenase		C
	SSUSC84_0440	SSU0456	MUN40_08175	Membrane protein		S
	SSUSC84_0566	SSU0593	MUN40_05180	Hypothetical protein	C2	S
	SSUSC84_0567	SSU0594	MUN40_05175	Hypothetical protein		S
	SSUSC84_0568	SSU0595	MUN40_05170	Hypothetical protein		S
	SSUSC84_0773	SSU0810	-	Transcriptional regulator		K
	SSUSC84_1072	SSU1034	MUN40_06625	ArsR family transcriptional regulator	C6	K
	SSUSC84_1073	SSU1035	MUN40_06630	MFS transporter		E
	SSUSC84_1501	SSU1473	MUN40_09110	Membrane protein	C8	S
	SSUSC84_1502	SSU1474	MUN40_09115	Hypothetical protein		S
	SSUSC84_1662	SSU1637	MUN40_02375	Pyruvate dehydrogenase E1 component subunit alpha		C
	SSUSC84_1906	SSU1886	-	Major pilus subunitd		D

-: absent in the corresponding genome.

d: known virulence gene.

e: gene of cps locus.

Figure 1. Cog analysis of DEGs in the sc84 interaction groups. A. Upregulated DEGs in the 2 h post-interaction group. B. Downregulated DEGs in the 2 h post-interaction group. C. Upregulated DEGs in the 4 h post-interaction group. D. Downregulated DEGs in the 4 h post-interaction group. The subgroups of cog are indicated in the bars with different colour.

Figure 2. Survival curves of mice injected with 1 × 10⁷ CFU of wild-type strain SC84, △UDC14 mutant, △UDC15 mutant, △UDC16 mutant, △UDC20 mutant, and PBS only as control group (A). Survival rates were calculated via the Kaplan–Meier method. The experiment was performed independently in duplicate. Mean of survival rates were present. The survival rates of different groups were compared using Log-rank test. # significant difference in survival level between the infected group and control group. * significant difference in survival level between the mutant and SC84 infected group. Production of proinflammatory cytokines IL-6 (B) and TNF-α (C) in serum and bacterial loads in peripheral blood (D) of C57BL/6 mice at 8 h post infected with 1 × 10⁶ CFU of wild-type strain SC84 and △udcs mutants. The experiment was repeated twice with similar results. Median of cytokine levels in serum were presented. Peripheral blood bacterial loads were presented in median with interquartile range. Statistical analysis of the cytokine and bacterial counts was performed using the Wilcoxon two-sample test. p <0.05 was considered significant. * the cytokine levels were significantly higher than those of mice infected with wild-type strain SC84. § the cytokine levels were significantly lower than those of mice infected with wild-type strain SC84. # the bacterial loads in blood were significantly lower than those of mice infected with wild-type strain SC84.

Figure 3. Survival curves of zebrafish infected with 3 × 10⁶ CFU (A) and 3 × 10⁵ CFU (B) of wild-type strain SC84 and △UDC20 mutant. PBS only was used in control group. Survival rates were calculated via the Kaplan–Meier method. The experiment was performed independently in duplicate. Mean of survival rate were presented. The survival rates of different groups were compared using Log-rank test. #, significant difference in survival level between infected group and control group. *, significant difference in survival level between △UDC20 mutant and wild-type strain SC84 infected groups. P < 0.05 was considered significant.

Data availability statement

The sequence of the genome sequenced in the study was deposited in the GenBank under accession number PRJNA822771. The transcriptome data obtained in the study were deposited in the GenBank under accession numbers SRR18778325-SRR18778333, SRR18778712 -SRR18778724, and SRR18779406-SRR18779417. The data supporting the results presented in the study are available from the corresponding author upon reasonable request.