Proteomic analysis of cortical neuronal cultures treated with poly-arginine peptide-18 (R18) and exposed to glutamic acid excitotoxicity

MacDougall, Gabriella; Anderton, Ryan S.; Mastaglia, Frank L.; Knuckey, Neville W.; Meloni, Bruno P.

doi:10.1186/s13041-019-0486-8

Molecular Brain

Table 1 Differentially expressed proteins identified in neurons treated with: R18 (R18), glutamic acid (Glut), or R18 and glutamic acid exposure (R18 + Glut)

From: Proteomic analysis of cortical neuronal cultures treated with poly-arginine peptide-18 (R18) and exposed to glutamic acid excitotoxicity

Gene name	SwissProt Accession Number	Protein	Fold up−/down-regulated^a
Gene name	SwissProt Accession Number	Protein	R18 vs Cont	Glut vs Cont	R18 + Glut vs Glut
Mitochondrial respiration/function
Acly	P16638	ATP-citrate synthase	1.076	−2.399 ^b	1.659
Aco2	Q9ER34	Aconitate hydratase, mitochondrial	−1.028	−3.435	4.285
Atp5a1	P15999	ATP synthase subunit alpha, mitochondrial	−1.472	1.888	−2.421
Atp5b	P10719	ATP synthase subunit beta, mitochondrial	−1.117	2.558	−3.342
Atp5h	P31399	ATP synthase subunit d, mitochondrial	1.076	2.754 ^b	−1.836
Atp5o	Q06647	ATP synthase subunit O, mitochondrial	1.406	2.032 ^b	−1.644
Cat	P04762	Catalase	−1.555	1.138	−1.659 ^b
Cox4i1	P10888	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	−1.259	2.070	−2.704
Idh1	P41562	Isocitrate dehydrogenase [NADP] cytoplasmic	1.066	1.459	−1.486
Mdh2	P04636	Malate dehydrogenase, mitochondrial	−1.247	2.355	−2.535
Ndufs1	Q66HF1	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	1.294	2.443	−5.249
Uqcrc2	P32551	Cytochrome b-c1 complex subunit 2, mitochondrial	−1.247	1.888	−2.704
Proteasome & Protein synthesis
Asns	P49088	Asparagine synthetase [glutamine-hydrolyzing]	2.089	2.228	2.421 ^b
Cct2	Q5XIM9	T-complex protein 1 subunit beta	1.106	−3.802	3.631
Cct3	Q6P502	T-complex protein 1 subunit gamma	−1.158	−4.787	4.207
Cct4	Q7TPB1	T-complex protein 1 subunit delta	1.127	−3.944	3.499
Cct5	Q68FQ0	T-complex protein 1 subunit epsilon	1.096	−2.269	2.291
Psmc1	P62193	26S protease regulatory subunit 4	−1.419	−22.67	18.197
Axonal growth/Neuronal differentiation/Cytoskeletal arrangement
Actr2	Q5M7U6	Actin-related protein 2	−1.355	− 1.271	− 1.459 ^b
Ap2m1	P84092	AP-2 complex subunit mu	1.271	−5.394	6.855
Armc10	B1WBW4	Armadillo repeat-containing protein 10	−1.294	−6.667	2.070
Baiap2	Q6GMN2	Brain-specific angiogenesis inhibitor 1-associated protein 2	−1.331	−90.09	99.083
Basp1	Q05175	Brain acid soluble protein 1	1.343	1.614	−1.270
Cntn1	Q63198	Contactin-1	−1.117	1.977	−1.836
Cttn	Q66HL2	Src substrate cortactin	1.117	−5.345 ^b	3.251
Dcx	Q9ESI7	Neuronal migration protein doublecortin	1.000	−6.139	6.026
Dnm1	P21575	Dynamin-1	−2.148	−4.093	3.076
Dpysl2	P47942	Dihydropyrimidinase-related protein 2	−1.225	1.723	−1.690
Dync1h1	P38650	Cytoplasmic dynein 1 heavy chain 1	−1.087	−8.873	8.472
Fabp7	P55051	Fatty acid-binding protein, brain	−1.028	4.406 ^b	−4.207
Fyn	Q62844	Tyrosine-protein kinase Fyn	1.117	−2.489	2.754 ^b
Gdi1	P50398	Rab GDP dissociation inhibitor alpha	−1.419	1.820	−2.965
Gfap	P47819	Glial fibrillary acidic protein	1.4322	1.906 ^b	−1.159
Kif21b	F1M5N7	Kinesin-like protein KIF21B	−1.282	−17.857	16.444
Krt1	Q6IMF3	Keratin, type II cytoskeletal	−4.055 ^b	−1.236	−6.485
Krt10	Q6IFW6	Keratin, type I cytoskeletal 10	−2.168	−1.722	−16.892 ^b
Map2	P15146	Microtubule-associated protein 2	1.138	−8.628	11.482
Map4	Q5M7W5	Microtubule-associated protein 4	−2.884	−4.488	4.169
Mapt	P19332	Microtubule-associated protein tau	1.077	−7.179	7.379
Myh10	Q9JLT0	Myosin-10	−1.459	−2.466	2.228
Ncam1	P13596	Neural cell adhesion molecule 1	−1.180	2.831	−4.093
Pa2 g4	Q6AYD3	Proliferation-associated protein 2G4	1.202	−2.188	2.489 ^b
Pak3	Q62829	Serine/threonine-protein kinase PAK 3	−2.208	−4.365	5.754 ^b
^bPebp1	P31044	Phosphatidylethanolamine-binding protein 1	1.5276	2.780 ^b	−2.128
Rala	P63322	Ras-related protein Ral-A	−1.236	2.704 ^b	−1.690
Rtn4	Q9JK11	Reticulon-4	1.107	−2.148	2.679
Tpm4	P09495	Tropomyosin alpha-4 chain	−1.097	−2.270	1.738 ^b
Tuba4a	Q5XIF6	Tubulin alpha-4A chain	1.086	−2.679 ^b	2.535
Tubb5	P69897	Tubulin beta-5 chain	−1.038	−18.018	16.444
Vesicular/Transmembrane trafficking
Actn4	Q9QXQ0	Alpha-actinin-4	−1.294	1.906 ^b	−1.381
Actr1a	P85515	Alpha-centractin	−1.738	−3.565 ^b	2.148
Ap2a2	P18484	AP-2 complex subunit alpha-2	1.159	−2.582	3.698 ^b
Atp1a3	P06687	Sodium/potassium-transporting ATPase subunit alpha-3	−2.128	1.660	−2.355
Cadps	Q62717	Calcium-dependent secretion activator 1	−1.486	−11.481	6.194
Camk2a	P11275	Calcium/calmodulin-dependent protein kinase type II subunit alpha	−1.419	−6.667	6.918
Cask	Q62915	Peripheral plasma membrane protein CASK	1.514	1.306	−1.888 ^b
Dpysl5	Q9JHU0	Dihydropyrimidinase-related protein 5	−1.180	1.213	−1.459 ^b
Klc1	P37285	Kinesin light chain 1	1.107	−6.024 ^b	5.058
Nsf	Q9QUL6	Vesicle-fusing ATPase	−1.117	−5.807	4.656
Prkar2b	P12369	cAMP-dependent protein kinase type II-beta regulatory subunit	−1.472	−3.105	1.754
Stx1b	P61265	Syntaxin-1B	1.225	1.600	−1.419
Stxbp1	P61765	Syntaxin-binding protein 1	−1.107	1.600	−2.466
Syn1	P09951	Synapsin-1	−1.786	−3.597 ^b	3.3113
ER proteostasis/Protein modification
Calr	P18418	Calreticulin	1.419	1.871	−1.570
Ddost	Q641Y0	Oligosaccharyl transferase 48 kDa subunit	−1.500	2.466	−2.938
Erp29	P52555	Endoplasmic reticulum resident protein 29	−1.067	2.168 ^b	−3.163
Hsp90aa1	P82995	Heat shock protein HSP 90-alpha	1.038	1.282	−1.446 ^b
Hspa5	P06761	78 kDa glucose-regulated protein	1.038	2.014	−1.542
Hspa8	P63018	Heat shock cognate 71 kDa protein	1.259	−2.208	2.559 ^b
Hspa9	P48721	Stress-70 protein, mitochondrial	1.159	−6.083	8.318
Hspd1	P63039	60 kDa heat shock protein, mitochondrial	1.107	1.486	−1.556
Pdia3	P11598	Protein disulfide-isomerase A3	−1.600	1.614	−1.995
Phb	P67779	Prohibitin	−1.213	1.644	−2.535
Phb2	Q5XIH7	Prohibitin-2	−1.047	3.837	−2.992
Por	P00388	NADPH--cytochrome P450 reductase	−1.107	−1.038	1.343 ^b
Tcp1	P28480	T-complex protein 1 subunit alpha	−1.472	−3.597 ^b	2.911
Uba1	Q5U300	Ubiquitin-like modifier-activating enzyme 1	−1.107	−5.105	4.406
Glycolysis & Carbohydrate metabolism
Alb	P02770	Serum albumin	−1.570	1.722	−5.701
Aldoa	P05065	Fructose-bisphosphate aldolase A	−1.660	1.629	−2.355
Eno1	P04764	Alpha-enolase	1.107	2.911	−1.706
Gapdh	P04797	Glyceraldehyde-3-phosphate dehydrogenase	−1.028	−11.700	10.280
Gpi	Q6P6V0	Glucose-6-phosphate isomerase	−1.318	1.754	−3.435
Hk1	P05708	Hexokinase-1	1.138	2.051 ^b	−1.888
Ldha	P04642	L-lactate dehydrogenase A chain	−1.786	1.028	−1.675 ^b
Pkm	P11980	Pyruvate kinase PKM	−1.009	1.787	−1.941
Taldo1	Q9EQS0	Transaldolase	1.259	−1.837	2.109
Mitochondrial fatty acid synthesis
Acat1	P17764	Acetyl-CoA acetyltransferase, mitochondrial	1.159	2.377	−1.500
Bdh1	P29147	D-beta-hydroxybutyrate dehydrogenase, mitochondrial	−1.213	−5.970	4.246
Fasn	P12785	Fatty acid synthase	−1.117	−3.311	2.704
Got2	P00507	Aspartate aminotransferase, mitochondrial	−1.923	1.213	−2.109 ^b
Ribosome components/RNA trafficking & processing
Aars	P50475	Alanine--tRNA ligase, cytoplasmic	−1.556	−5.495	4.699
C1qbp	O35796	ASF/SF2-associated protein p32	1.213	1.600 ^b	−1.888
Ddx1	Q641Y8	ATP-dependent RNA helicase DDX1	−1.148	−11.173	4.286
Eef1a1	P62630	Elongation factor 1-alpha 1	−1.225	−5.444	4.529
Eef2	P05197	Elongation factor 2	−1.202	−4.131	3.048
Eif4a2	Q5RKI1	Eukaryotic initiation factor 4A-II	−1.057	−3.945	3.02
Eif5a	Q3T1J1	Eukaryotic translation initiation factor 5A-1	1.514	−6.983	9.638
Elavl2	Q8CH84	ELAV-like protein 2	−1.107	−4.405	5.598 ^b
Hnrnpa1	P04256	Heterogeneous nuclear ribonucleoprotein A1	−1.076	−9.911	9.462
Hnrnpa2b1	A7VJC2	Heterogeneous nuclear ribonucleoproteins A2/B1	1.318	−4.325	6.138
Hnrnpa3	Q6URK4	Heterogeneous nuclear ribonucleoprotein A3	1.191	−3.311	4.920
Hnrnpd	Q9JJ54	Heterogeneous nuclear ribonucleoprotein D0	1.202	−5.495	6.252
Hnrnpk	P61980	Heterogeneous nuclear ribonucleoprotein K	−1.057	−8.091	8.872
Hnrnpl	F1LQ48	Heterogeneous nuclear ribonucleoprotein L	−1.028	−2.729	4.207 ^b
Khsrp	Q99PF5	Far upstream element-binding protein 2	1.556	−3.908	8.017 ^b
Matr3	P43244	Matrin-3	−1.500	−3.373 ^b	3.945
Rpl7	P05426	60S ribosomal protein L7	1.225	−2.109	2.188 ^b
Rpl13	P41123	60S ribosomal protein L13	−1.057	−2.377	2.754 ^b
Rplp0	P19945	60S acidic ribosomal protein P0	1.486 ^b	−1.191	−1.076
Rps24	P62850	40S ribosomal protein S24	1.854	−5.754	14.06 ^b
Rps27	Q71TY3	40S ribosomal protein S27	−1.102	−18.18 ^b	5.058
Yars	Q4KM49	Tyrosine--tRNA ligase, cytoplasmic	−1.225	−4.656	3.342
Calcium transport and signalling
Vdac1	Q9Z2L0	Voltage-dependent anion-selective channel protein 1	−1.419	2.466	−2.938
Cacna2d1	P54290	Voltage-dependent calcium channel subunit alpha-2/delta-1	1.306	4.207	−4.018
Gnao1	P59215	Guanine nucleotide-binding protein G(o) subunit alpha	−1.148	−5.152	3.802
Letm1	Q5XIN6	LETM1 and EF-hand domain-containing protein 1, mitochondrial	−3.020	1.459 ^b	−1.236
Nudt3	Q566C7	Diphosphoinositol polyphosphate phosphohydrolase 1	1.459 ^b	1.282	1.117
Ywhaq	P68255	14–3-3 protein theta	−1.087	1.355	−1.615
Miscellaneous
Ak1	P39069	Adenylate kinase isoenzyme 1 (Cellular energy homeostasis)	1.009	−2.938	4.325
Atic	O35567	Bifunctional purine biosynthesis protein PURH (Purine biosynthesis)	1.038	1.923	−2.630 ^b
Dnm1l	O35303	Dynamin-1-like protein (Mitochondrial fission)	−1.820	−7.519 ^b	5.297
Hist1h4b	P62804	Histone H4 (Transcription regulation)	1.754	−3.802	7.516 ^b

^a Statistically significant values (p < 0.05) for fold up−/down-regulation ≥1.3-fold are highlighted in bold. ^b 25 uniquely DEPs in R18 and Glut treatment versus Cont, or R18 + Glut treatment versus Glut

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ISSN: 1756-6606

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