. 2023 Aug 28;14:1020275. doi: 10.3389/fpls.2023.1020275

Table 2.

Top 110 tomato stromal proteins.

Tomato Gene ID^A	Protein name^B	Gene product^C	Ranking (Mol %)	Mol %	Arabidopis homolog^D,E	Arabidopsis abundance class^F
544163620	ATPB	ATP synthase CF1 beta subunit	1	13.886	Atcg00480	4
544163621	RBCL	RuBisCo large subunit	2	10.412	Atcg00490	1
544163653	RPS19	Ribosomal protein S19	3	6.442	Atcg00820	4
Solyc06g073260	CSP41B	41-kDa chloroplast stem-loop binding protein	4	4.477	At1g09340	3
544163671	RPS15	Ribosomal protein S15	5	4.062	Atcg01120	4
Solyc06g007760	YCF54	Ycf54 protein, Low chlorophyll accumulation (LCAA)	6	4.062	At5g58250	nd
Solyc01g087040	TL19	Thylakoid lumenal 19-kDa protein	7	2.033	At3g63540	nd
Solyc10g076350	–	Macrophage migration inhibitory factor family protein	8	2.033	At5g01650	nd
Solyc08g074630	PPO-F^K	Polyphenol oxidase F	9	1.948	–	–
Solyc08g074620	PPO-E	Polyphenol oxidase E	10	1.507	–	–
Solyc06g071790	EF-TuB	Elongation factor TuB	11	1.335	At4g20360	2
Solyc10g086150	CP29B^H	29-kDa RNA-binding protein B, HopU1 effector target	12	1.202	At2g37220	4
Solyc10g086580	RCA2A^G	RuBisCo activase	13	1.169	At2g39730	2
Solyc09g007850	CP29A^H	29-kDa RNA-binding protein A	14	1.069	At2g37220	4
Solyc03g095180	Fe-SOD2^L	Superoxide dismutase	15	1.016	At4g25100 (At5g51100)	3
544163678	RPL23	Ribosomal protein L23	16	0.940	Atcg01300	nd
Solyc02g083500	AANH-like	Adenine nucleotide alpha hydrolase family protein	17	0.853	At5g66090	3
Solyc03g112150	EF-TuA	Elongation factor TuA	18	0.797	At4g20360	2
Solyc09g065180	CSP41A	41-kD chloroplast stem-loop binding protein	19	0.738	At3g63140	3
Solyc09g011080	RCA2B^G	RuBisCo activase	20	0.710	At2g39730	2
544163619	ATPE	ATP synthase CF1 epsilon subunit	21	0.638	Atcg00470	nd
Solyc02g079950	OEE3	Oxygen-evolving enhancer protein 3, PsbQ	22	0.638	At4g21280 (At4g05180)	4
Solyc02g086740	RPL12-A^O	50S ribosomal protein L12-A	23	0.638	At3g27830	nd
544163598	ATPA	ATP synthase CF1 alpha subunit	24	0.506	Atcg00120	nd
Solyc04g007010	KIROLA-like^P	KIROLA-like, Major latex-like protein 43-like	25	0.433	At1g70890	nd
Solyc12g056830	ATPD	ATP synthase delta subunit	26	0.433	At4g09650	nd
Solyc12g042060	CLPC1^N	Clp protease subunit CLPC1	27	0.408	At5g50920	3
Solyc01g080280	GS2	Glutamine synthetase	28	0.400	At5g35630	1
Solyc02g086730	RPL12-C	50S ribosomal protein L12-C	29	0.400	At3g27840	nd
Solyc12g013810	TRX-m4.1^J (Trx-m1/4)	Thioredoxin m	30	0.400	At1g03680 (At3g15360)	4
Solyc01g057830	RPS1A	30S ribosomal protein S1	31	0.393	At5g30510	nd
Solyc01g106430	PPA6	Inorganic pyrophosphatase family protein	32	0.387	At5g09650	3
Solyc01g103450	HSC70-2^I	Chloroplast heat shock protein 70	33	0.375	At5g49910	4
Solyc07g066610	cpPGK1	Phosphoglycerate kinase1	34	0.343	At1g56190	2
Solyc07g062060	MSRB1	Peptide methionine sulfoxide reductase B	35	0.328	At1g53670	nd
Solyc02g020940	GAPA-2	Glyceraldehyde-3-phosphate dehydrogenase	36	0.317	At1g12900	2
Solyc02g086820	CA1	Carbonic anhydrase 1, SA-binding protein 3	37	0.317	At3g01500	2
Solyc08g006070	AIG2-like	AIG2-like protein	38	0.293	At4g31310	nd
Solyc10g018300	TKL1	Transketolase 1	39	0.293	At3g60750	2
Solyc03g118240	CHLM	Magnesium-protoporphyrin IX methyltransferase	40	0.280	At4g25080	nd
Solyc02g083810	LFRN^R PETH	Ferredoxin–NADP reductase	41	0.275	At1g20020	3
Solyc02g084440	FBA3^M	Fructose-bisphosphate aldolase	42	0.270	At4g38970	2
Solyc08g076220	PRK	Phosphoribulokinase/uridine kinase	43	0.265	At1g32060	3
544163637	CLPP1	Clp protease proteolytic subunit P1	44	0.250	Atcg00670	3
Solyc02g080540	ATPC	ATP synthase gamma chain	45	0.250	At4g04640	nd
Solyc04g009030	GAPA-1	Glyceraldehyde-3-phosphate dehydrogenase subunit 2	46	0.250	At3g26650	2
Solyc11g066390	SOD3	Superoxide dismutase	47	0.250	At2g28190	nd
Solyc07g056540	GLO1	Glycolate oxidase 1	48	0.238	At3g14420	nd
Solyc07g044860	OEE2	Oxygen-evolving enhancer protein 2, PsbP	49	0.229	At1g06680	2
Solyc11g069790	CPN60A2	Chaperonin - RuBisCo LS binding protein (A	50	0.228	At2g28000	3
Solyc04g074750	CP33C	Polyadenylate-binding protein 1-A	51	0.225	At4g09040	nd
Solyc12g010840	-	Ketol-acid reductoisomerase	52	0.222	At3g58610	3
Solyc01g097460	RPI3	Ribose-5-phosphate isomerase	53	0.216	At3g04790	nd
544163595	RPS16	Ribosomal protein S16	54	0.197	Atcg00050	nd
Solyc01g009990	CYP20-2 (PNSL5)	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type	55	0.197	At5g13120	nd
Solyc04g008710	-	Glutamic acid-rich protein-like	56	0.197	At3g24506	nd
Solyc05g005480	-	NADPH-dependent alkenal/one oxidoreductase	57	0.197	At1g23740	3
Solyc05g009030	IMDH	3-isopropylmalate dehydrogenase	58	0.197	At1g31180	4
Solyc05g052710	RPS31 (PSRP4)	30S ribosomal protein S31	59	0.197	At2g38140	nd
Solyc08g006780	STIC2-like	Suppressor of Tic40-2	60	0.197	At4g30620	nd
Solyc08g081570	MeCPS	2-C-methyl-D-erythritol 2 4-cyclodiphosphate synthase	61	0.197	At1g63970	nd
Solyc08g079180	EF-G	Elongation factor G	62	0.179	At1g62750	3
Solyc01g100520	CLPP5	Clp protease proteolytic subunit P5	63	0.177	At1g02560	3
Solyc03g121910	TS1	Threonine synthase	64	0.177	At4g29840	nd
Solyc01g108600	PREP1	Presequence protease	65	0.174	At1g49630	nd
Solyc03g007110	CLPT1	Clp protease T1 subunit	66	0.173	At4g25370	5
Solyc06g048410	Fe-SOD2 (PAP9)	Superoxide dismutase	67	0.167	At5g51100	nd
Solyc03g118340	CLPC2^N	Clp protease C2 subunit	68	0.151	At5g50920	3
Solyc12g010380	AK5	Adenylate kinase-like protein	69	0.151	At5g35170	nd
Solyc06g048730	UROD2 (HEME2)	Uroporphyrinogen decarboxylase	70	0.146	At2g40490	nd
Solyc05g005880	RPS13	30S ribosomal protein S13	71	0.143	At5g14320	nd
Solyc01g079790	APL1	Glucose-1-phosphate adenylyltransferase	72	0.140	At5g19220	5
Solyc03g063560	GLU1	Ferredoxin-dependent glutamate synthase	73	0.134	At5g04140	3
Solyc01g009080	-	FHA domain containing protein	74	0.132	At2g21530	nd
Solyc01g111120	pdTPI-2A	Plastid triosephosphate isomerase	75	0.132	At2g21170	2
Solyc05g052600	SBPase	Sedoheptulose-1,7-bisphosphatase	76	0.132	At3g55800	2
Solyc07g025520	-	Methyltransferase type 11	77	0.132	At4g29590	nd
Solyc07g053280	-	Ketol-acid reductoisomerase	78	0.132	At3g58610	3
Solyc07g063190	Trx-m4.3	Thioredoxin	79	0.132	At3g15360	nd
Solyc11g006020	NDHO	NAD(P)H-quinone oxidoreductase subunit O	80	0.132	At1g74880	nd
Solyc12g094640	GAPB^S	Glyceraldehyde-3-phosphate dehydrogenase B	81	0.132	At1g42970	2
Solyc02g086910	CYP38	Peptidyl-prolyl cis-trans isomerase cyclophilin-type	82	0.127	At3g01480	3
Solyc04g009200	GSA	Glutamate-1-semialdehyde-2 1-aminomutase	83	0.127	At5g63570	4
Solyc01g028810	CPN60B2	Chaperonin, RuBisCo LS-binding protein	84	0.127	At3g13470	3
Solyc01g110360	FBA1^M	Fructose-bisphosphate aldolase	85	0.122	At4g38970	2
Solyc02g085100	-	Putative glucose-6-phosphate 1-epimerase	86	0.122	At5g66530	4
Solyc03g111840	-	28-kDa ribonucleoprotein	87	0.122	At4g24770	3
Solyc03g120430	GLYK	Glycerate kinase	88	0.122	At1g80380	nd
Solyc04g082630	GAPB	Glyceraldehyde-3-phosphate dehydrogenase B	89	0.121	At1g42970	2
Solyc06g053600	At1g04420-like1	Oxidoreductase aldo/keto reductase family protein	90	0.120	At1g04420	4
Solyc01g006980	MCAT	Malonyl CoA-acyl carrier protein transacylase	91	0.118	At2g30200	4
Solyc01g108630	NIR	Nitrite reductase	92	0.118	At2g15620	4
Solyc03g120850	CPN60B1	Chaperonin - RuBisCo LS binding protein	93	0.118	At1g55490	3
Solyc06g076790	-	Uncharacterized protein	94	0.118	At3g47070	nd
Solyc09g008670	OMR1A	Threonine dehydratase 2	95	0.116	At3g10050	nd
Solyc02g062340	FBA2^M	Fructose-bisphosphate aldolase	96	0.116	At4g38970	2
544163615	RPS4	Ribosomal protein S4	97	0.114	Atcg00380	2
Solyc02g088610	CLPB3	ATP-dependent chaperone ClpB	98	0.111	At5g15450	4
Solyc01g105060	-	Thioesterase superfamily protein	99	0.108	At5g10160	nd
Solyc10g054870	pdTPI-2B	Triosephosphate isomerase	100	0.108	At2g21170	2
Solyc12g010020	LapA1	Leucyl aminopeptidase A1	101	0.108	At4g30920-like	nd
Solyc12g089210	OTC2	Ornithine carbamoyltransferase	102	0.108	At1g75330	4
Solyc12g094430	GSTF5	Glutathione S-transferase	103	0.108	At2g30860	nd
Solyc01g005520	MET1	Tetratricopeptide TPR2 repeat protein	104	0.105	At1g55480	nd
Solyc01g006560	LOXF TomLoxF	Lipoxygenase	105	0.105	At3g45140	3
Solyc03g111610	-	HAD-superfamily hydrolase subfamily protein	106	0.104	At3g48420	3
Solyc02g065400	PSBO-1 OEE1-1	PS II Oxygen-evolving enhancer protein 1	107	0.101	At3g50820	3
Solyc04g007790	KIROLA-like	KIROLA-like protein, Major latex-like protein	108	0.101	At1g70890	nd
Solyc04g015040	FKBP16-3	Peptidyl-prolyl cis-trans isomerase	109	0.101	At2g43560	nd
Solyc06g072470	RPL29	50S ribosomal protein L29	110	0.101	At5g65220	nd

^A Tomato gene IDs are from Sol Genomics.

^B Names of tomato genes were curated from the literature, Sol Genomics database, NCBI and/or were guided by names of Arabidopsis orthologs. See Table S2 for NCBI accessions and literature citations. Several genes had two or three paralogs in tomato versus a single gene in Arabidopsis.

^C Identities of tomato proteins were confirmed by reciprocal BLASTP searches for the tomato and Arabidopsis homologs at NCBI and Sol Genomics.

^D Some tomato proteins do not have orthologs in Arabidopsis. These proteins are designated with a dash (-).

^E For proteins in multigene families, the closest Arabidopsis ortholog is provided. However, there were cases when an Arabidopsis ortholog was not detected by Peltier et al. (2006). In these cases, the next mostly closely-related homolog (name in parentheses) was identified using BlastP searches and its corresponding rank provided.

^F Peltier et al. (2006) classified 241 proteins into concentration ranking groups 1 (most abundant) and 4 (least abundant). When the Arabidopsis homolog of a tomato protein was not detected it is indicated by “nd”.

^G There are two tomato RuBisCo activase proteins similar to At2g39730 (AtRCA2) in tomato (Solyc10g086580 -RCA2A and Solyc09g011080-RCA2B). A third tomato RCA protein (RCA1) is similar to At1g73110 (AtRCA1).

^H There are two 29-kDa RNA-binding proteins (A and B) in tomato. In Arabidopsis, these proteins are also a HopU1 effector target.

^I There are two chloroplast Hsc70-2 genes in tomato (Solyc01g103450 and Solyc11g020040) that are more similar to the Arabidopsis Hsc70-2 (At5g49910) than Hsc70-1 (At4g24280). Phylogenetic analysis of the tomato Hsc70 protein family was performed by Vu et al. (2019), but gene names were not assigned.

^J TRX-m gene family is expanded relative to Arabidopsis. The TRX-m nomenclature is based on reciprocal BLAST-P searches of tomato TRX-m and Arabidopsis TRX-m proteins and names were based on relatedness and phylogenetic trees of homologs. TRX-m4 was previously designated as TRX-m1/4 (Cheng et al., 2014). Current phylogenic trees unambiguously classify this protein as a TRX-m4. Gene family names are found in Table S2 and Table S10 (protein folding).

^K PPO gene nomenclature was previously established by Newman et al. (1993).

^L The tomato SOD gene family is expanded relative to Arabidopsis. While Arabidopsis has one Fe-SOD2 gene, there are two Fe-SOD2 genes in tomato. SOD proteins detected in tomato’s stromal proteome are found in the Redox Table ( Table S9D ).

^M FBA gene nomenclature was based on Cai et al. (2016).

^N In our hands, there are two tomato CLPC1 proteins with greatest protein identity to Arabidopsis’ CLPC1 (At5g0920) and a weaker identity to AtCLPC2 (At3g11830). This differs from the analyses of D’Andreas et al. (2018); despite this, we have used the D’Andreas et al. CLPC nomenclature.

^O There are two RPL12 genes in tomato. Names are based on Sol Genomics designations. Solyc02g086740 encodes RPL12-A and Solyc02g086730 encodes RPL12-C.

^P Four major latex proteins (MLPs) were identified in the tomato stromal proteome ( Table S2 ). NCBI designates them as KIROLA or KIROLA-like and we have retained this nomenclature.

^Q Based on reciprocal BLASTP searches there is only one PETE gene in tomato, while there are two in Arabidopsis. The tomato PETE is mostly closely related to ATPETE2.

^R There are two leaf ferredoxin NADP reductases (LFNR, PETH) in tomato (Solyc02g083810, Solyc02g062130) that are similar to the AtLFNR2 (AtFNR2, At1g20020) and AtLFNR1 (FNR1, AT5G66190).

^S Based on reciprocal BLASTP searches there are two GAPB paralogs in tomato, while there is one in Arabidopsis (At1g42970).