The transcriptomic and proteomic responses of Daphnia pulex to changes in temperature and food supply comprise environment-specific and clone-specific elements

Becker, Dörthe; Reydelet, Yann; Lopez, Jacqueline A.; Jackson, Craig; Colbourne, John K.; Hawat, Susan; Hippler, Michael; Zeis, Bettina; Paul, Rüdiger J.

doi:10.1186/s12864-018-4742-6

Table 3 Differentially expressed proteins (DEPs) in the D. pulex clones G and M under heat stress

From: The transcriptomic and proteomic responses of Daphnia pulex to changes in temperature and food supply comprise environment-specific and clone-specific elements

Spot ID	Gene ID	Function	R	P	R	P	SP	M_re	M_rp	pIe	pIp	SC (%)	NP
			24 h		48 h
743	306433	20S Proteasome, A and B subunits	0.5	0.00	0.7	0.14	–	34.3	28	5.3	5.3	35.9	8
520	300012	Actin and related proteins	3.1	0.06	2.4	0.04	–	62.6	41.8	5.5	5.3	30.0	8
3309	306442	Actin and related proteins	1.3	0.03	1.4	0.00	–	62.6	41.9	5.4	5.2	30.8	8
417	100611	α-Tubulin	2.2	0.02	2.0	0.00	–	82.3	46.1	5.4	5.0	23.8	8
405	301837	α-Tubulin	2.1	0.00	1.7	0.01	–	81.9	49.9	5.3	5.0	33.0	16
416	301837	α-Tubulin	1.9	0.00	1.7	0.02	–	81.9	49.9	5.2	5.0	11.8	6
757	220693	Arginine kinase	0.9	0.35	1.5	0.01	–	28.8	39.9	5.4	5.5	36.3	9
796	220693	Arginine kinase	0.6	0.03	0.6	0.01	–	24.4	39.9	5.1	5.5	34.9	10
438	300845	β-Tubulin	1.6	0.01	1.3	0.09	–	78.8	50.1	5.1	4.7	19.9	10
463	210624	Calreticulin	1.7	0.03	1.2	0.44	16	72.4	46.6	4.7	4.5	48.3	18
742	303899	Carboxypeptidase A2	0.8	0.06	0.6	0.01	17	30.0	46.1	4.8	5.2	29.6	14
609	304126	FOG, leucine-rich repeat	1.7	0.00	2.0	0.00	22	47.2	42.1	4.6	4.7	18.6	7
801	303282	Glutathione transferase	1.3	0.07	1.6	0.00	–	24.2	24.8	5.3	5.4	36.8	12
794	317266	Glutathione transferase	1.0	0.84	1.4	0.05	–	25.0	25	5.4	5.2	67.3	18
472	300366	Glycoside hydrolase, family 7	0.5	0.07	0.5	0.02	19	70.2	50.3	4.8	4.8	21.5	8
600	303,036	Glycoside hydrolase, family 16	0.3	0.01	0.3	0.00	19	47.5	40.4	4.9	4.8	30.1	12
441	309746	H⁺-transporting two-sector ATPase	1.9	0.00	1.4	0.07	–	78.1	56.8	5.2	5.5	43.8	16
466	309746	H⁺-transporting two-sector ATPase	2.2	0.00	1.8	0.00	–	71.4	56.8	5.2	5.5	79.4	56
23,222	309746	H⁺-transporting two-sector ATPase	0.5	0.09	0.5	0.02	–	66.8	56.8	5.1	5.5	65.5	23
293	9558	Ubiquitin and ubiquitin-like proteins	0.8	0.63	0.4	0.04	–	107.3	5.7	5.1	5.2	35.3	2
845	9558	Ubiquitin and ubiquitin-like proteins	0.9	0.59	0.6	0.01	–	18.3	5.7	4.9	5.2	35.3	2
937	308693	Vitellogenin	1.4	0.08	1.4	0.05	20	12.1	191.9	4.7	6.5	11.3	16
Spot ID	Gene ID	Function	R	P	R	P	SP	M_re	M_rp	pIe	pIp	SC (%)	NP
			24 h		48 h
520	300012	Actin and related proteins	0.5	0.04	0.4	0.00	–	62.6	41.8	5.5	5.3	30.0	8
724	305550	Actin and related proteins	1.7	0.02	1.5	0.04	–	32.0	41.8	5.7	5.4	37.9	12
405	301837	α-Tubulin	1.8	0.01	1.5	0.01	–	81.9	49.9	5.3	5.0	33.0	16
438	300,845	β-Tubulin	1.5	0.01	1.0	0.80	–	78.8	50.1	5.1	4.7	19.9	10
742	303899	Carboxypeptidase A2	0.5	0.03	0.7	0.05	17	30.0	46.1	4.8	5.2	29.6	14
383	301074	Chaperonin ATPase, Cpn60/Hsp60p	5.1	0.01	3.1	0.04	–	89.1	61.4	5.6	5.8	31.2	22
908	300446	Cytosolic fatty-acid binding protein	0.5	0.04	0.8	0.25	–	26.1	14.8	6.0	5.3	31.1	4
609	304126	FOG, leucine-rich repeat	3.0	0.00	5.6	0.00	22	47.2	42.1	4.6	4.7	18.6	7
784	305501	Glutathione transferase	1.6	0.06	1.8	0.03	–	25.3	25.2	5.8	5.6	36.2	10
794	317266	Glutathione transferase	1.5	0.03	1.3	0.02	–	25.0	25	5.4	5.2	67.3	18
600	303036	Glycoside hydrolase, family 16	0.5	0.14	0.6	0.03	19	47.5	40.4	4.9	4.8	30.1	12
415	306451	H⁺-transporting two-sector ATPase	3.2	0.03	2.7	0.02	–	66.9	55.5	5.7	5.5	57.6	56
779	309746	H⁺-transporting two-sector ATPase	1.8	0.01	1.6	0.10	–	26.5	56.8	5.9	5.5	64.2	20
439	234212	Protein disulfide isomerase	2.0	0.00	1.3	0.23	15	78.1	58.3	5.0	4.8	44.4	22
635	251885	Serine endopeptidase	0.4	0.16	0.4	0.01	19	41.5	39.6	4.4	5.0	12.7	6
641	251885	Serine endopeptidase	0.6	0.21	0.4	0.01	19	41.2	39.6	4.5	5.0	12.7	6
270	219769	Vitellogenin fused with SOD	3.4	0.05	4.2	0.02	17	110.9	223	5.6	6.5	12.3	22
301	219769	Vitellogenin fused with SOD	4.4	0.02	5.3	0.00	17	107.0	223	5.6	6.5	13.3	34
305	219769	Vitellogenin fused with SOD	2.5	0.04	3.0	0.00	17	104.8	223	5.5	6.5	12.5	23
322	219769	Vitellogenin fused with SOD	5.1	0.06	9.3	0.01	17	102.6	223	5.6	6.5	12.3	21
576	219769	Vitellogenin fused with SOD	1.6	0.31	3.2	0.05	17	51.9	223	5.7	6.5	7.5	18
580	219769	Vitellogenin fused with SOD	2.2	0.13	2.4	0.04	17	51.8	223	5.6	6.5	9.9	22
689	219769	Vitellogenin fused with SOD	0.9	0.87	0.3	0.01	17	38.1	223	5.7	6.5	12.9	25
1545	219769	Vitellogenin fused with SOD	2.7	0.05	3.3	0.01	17	51.8	223	5.6	6.5	9.9	22

D. pulex clone G on top, D. pulex clone M at the bottom. From left to right: Spot identity (ID), gene ID (JGI_V11_gene ID), protein function (described in the protein sequence database of the Daphnia pulex genome assembly v1.0), expression ratios (R) contrasting stress (24 h or 48 h at 30 °C, ad libitum feeding) and control (20 °C, ad libitum feeding) conditions and associated P values (t-tests), predicted length of N-terminal signal peptides (SP), experimental and predicted molecular masses (M_re, M_rp) and isoelectric points (pIe, pIp) of the mature protein (without signal peptide), sequence coverage (SC; percentage of the predicted protein sequence covered by matching peptide sequences), and number of matching peptides (NP). Bold R and P values indicate statistical significance. Number of gels (biological replicates, 25-30 animals each) for clone G or M: control (5 or 4) and 24 h (4 or 3) or 48 h (6 or 10) of stress

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ISSN: 1471-2164

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