. 2022 Jun 14;13:927746. doi: 10.3389/fpls.2022.927746

TABLE 1.

Overview of protein domain organization, membrane topology, subcellular localization, structural features indicative for regulated intramembrane proteolysis (RIP) and alternative transcripts of membrane-bound TFs in Arabidopsis (atMB-TFs).

Protein name	TMD position relative to the TFFD	TMD score prediction^a	Membrane topology^b	Position^c (AA) of		Subcellular localization^d	Postranslational modifications^e	Helix-breaking residues in the TMD^f	No. positively charged AA (K,R) in the^g		No. alternative transcripts resulting in TMD loss Yao et al., 2017
				TFFD	TMD	Predicted\| \| experimental			TMD	20-AA TM-flanking region
AIL6	N	0.702	I	389-440	301-321	mt, nuc\| \| mt	ph(4)		0	K(3) R(1)	2
ANAC028	C	0.570		6-143	609-630	Nuc	nt(1)^*		K(2)	K(5) R(1)
AT2G13960	N	0.582	II	40-86	9-29	sec, nuc, PM		[GxxN]	0	K(4)^*
AT2G29660	N	0.477	I	126-149	9-29	sec, mt, nuc	ph(1)^*		R(1)	K(6) R(4)^*
AT3G04930	C	0.486	II	137-235	372-395	nuc\| \| PM	ph(5)^*		0	K(1)	1
AT5G25475	N	0.606	I	78-155	52-75	Mt		[PxxN]	K(1)	K(1)R(5)^*	2
AT5G63280	C	0.836	II	105-128	223-246	sec, nuc	nt(1) ng(1)^* ac(1) ro(1)		0	K(4) R(1)^*
bHLH035	C	0.581	II	58-101	203-224	Nuc	ph(1)^*		0	K(2)	3
		0.360	II		190-213				K(1)	K(2) R(1)
		0.871	I		214-245			[PN]	R(1)
bHLH115	C	0.363		136-182	190-211	Nuc			K(5)	K(1) R(2)
bHLH131	N	0.463		1351-1397	1242-1262	nuc, sec\| \| pl and mt	ph(1)		0	K(2)	2
		0.341			1277-1297				0
bZIP7	N	0.662		197-254	38-59	Nuc	ph(3)^* ng(1)		K(1)	0	3
bZIP17	C	0.798	I	226-287	364-387	nuc\| \| ER, PM, nuc [1]	ph(1)	[GA]	K(1)	K(7)^*
bZIP28	C	0.848	I	192-237	321-344	nuc, sec, ER\| \| ER, PM, nuc [2]			K(1)	K(7) R(1)^*
bZIP49	C	0.755	I	172-219	286-309	Nuc		[GA]	K(1)	K(6) R(1)^*
bZIP60	C	0.693	II	141-183	217-240	Nuc			0	K(2) R(1)
CAMTA1	C	0.380	I	81-188	192-211	Nuc	ph(10)^* na(1) nt(1)		R(1)	K(1) R(3)
CAMTA5	C	0.683		30-146	579-600	nuc\| \| Golgi(4), PM, nuc	ph(3)^* sm(1)		0	K(4)	1
FRF3	C	0.424		25-110	115-136	mt, cyt			R(1)	K(2) R(1)	1
GPL2	C	0.786		61-155	328-348	Nuc	ph(4)^*	[PxxP]	0	0
HHO5	N	0.567		218-272	64-85	Nuc	ph(1)		R(1)	K(3) R(1)	3
LD	C	0.496		66-122	222-243	Nuc	ph(2)^* ub(1)		K(1)	K(2) R(1)
LHL2	N	0.537		529-566	123-144	nuc\| \| nuc [3]			0	K(1) R(4)	2
LOL1	N	0.488	II	70-171	24-47	sec, nuc			0	K(3) R(1)
MAMYB	N	0.770	I	159-193	35-55	nuc\| \| ER(2), Golgi(4), PM(3), nuc [4]	ph(14)^* na(1)		0	K(1)
		0.575	II		61-84			[PxxP]	K(1)
NFXL2	C	0.462	II	247-452	840-863	Nuc	ph(1)^*		K(1)	K(2) R(2)
NGAL2	C	0.469	II	29-142	198-221	Nuc			0	K(2)	2
NLP3	N	0.550	I	495-546	41-64	mt, nuc			0	0
NOK	N	0.345		57-155	30-51	nuc\| \| nuc [5]	nt(1)		K(1) R(1)	K(1) R(1)
NTL1	C	0.792	I	10-135	497-520	nuc\| \| ER, PM, nuc [6]		[GA]	0	K(7) R(1)^*
NTL2	C	0.760	II	24-151	605-625	nuc\| \| ER, PM, nuc [6]			0	K(5) R(1)^*
NTL3	C	0.718	II	17-143	535-555	nuc\| \| ER, PM, nuc [6]		[GA]	K(1)	K(2) R²
NTL4	C	0.714	II	9-136	522-545	nuc, PM\| \| ER, PM, nuc [6]			K(1)	K(1)
NTL5	C	0.528	II	15-140	316-334	nuc\| \| ER, PM, nuc [6]			R(1)	K(1) R(1)
NTL6	C	0.523	II	13-141	442-462	nuc\| \| ER, PM, nuc [6]	ph(9)^*		R(1)	K(3) R(1)
NTL7	C	0.856	II	17-143	525-548	nuc, cyt\| \| ER, PM, nuc [6]	ph(1)^*	[GA]	R(1)	K(3) R(2)
NTL8	C	0.759	II	14-140	312-332	nuc, PM\| \| ER, PM, nuc [6]			0	K(4) R(2)
NTL9	C	0.528	II	9-135	488-511	nuc, Golgi\| \| ER, PM, nuc [6]			K(1) R(1)	K(2) R(5)^*
NTL10	C	0.773	II	5-138	410-428	nuc\| \| ER, PM, nuc [6]	ph(3)^*		0	K(2)
NTL11	C	0.571	II	9-136	541-564	nuc\| \| ER, PM, nuc [6]	ph(2)^*		K(1) R(1)	K(1)
NTL13	C	0.480	II	22-147	319-339	nuc\| \| ER, PM, nuc [6]			0	K(2) R(1)
NTM1	C	0.432	II	6-136	445-468	nuc\| \| ER, PM, nuc, cytoskeleton [6]	ph(4)^*		K(2) R(2)	K(4) R(2)
OBP3	N	0.595		118-177	42-62	mt, nuc	ph(2)^*		0	0	5
RLT2	C	0.554		18-74	518-539	nuc\| \| Golgi	ph(24)^* ac(1)^*		R(1)	K(4)	3
SCP	N	0.550	II	36-136	14-37	sec, nuc\| \| nuc [7]		[GA]	R(1) K(1)	K(1) R(3)
SPL1	C	0.641	II	105-182	835-858	nuc\| \| ER, PM, nuc [8]	ph(3)^*		R(1)	K(2) R(2)
SPL7	C	0.627	II	137-213	762-782	nuc\| \| nuc [9]	ph(1)^*		0	K(2) R(3)
SPL12	C	0.641	I	126-203	881-904	nuc\| \| ER, PM, nuc [8]	ph(10)^*		R(1)	K(3) R(1)
SPL14	C	0.614	II	119-196	995-1018	nuc\| \| ER, PM, nuc [8]	ph(3)^*		0	K(1) R(3)
SPL16	C	0.614	II	82-158	978-1001	nuc\| \| PM			0	K(2) R(3)
SRS8	C	0.375	II	46-140	144-164	Nuc	ph(1)		0	K(1) R(1)	3
WIP4	N	0.468		256-362	42-63	nuc, sec			0	K(1) R(1)
ZFN2	C	0.720		45-334	444-465	Nuc	ph(8)^* na(1) nt(1) my(1) ub(1)		K(1)	0	2

cyt, cytosol; pl, plastid; nuc, nucleus; sec, secretory pathway; PM, plasma membrane; mt, mitochondria; ph, phosphorylation; na, N-terminal acetylation; nt, N-terminus proteolysis; ng, N-glycosylation; ac, lysine acetylation; ro, reversible cysteine oxidation; sm, lysine SUMOylation; ub, lysine ubiquitination; my, myristolysation.

^aMean hydrophobicity within the TMD obtained from Aramemnon (Schwacke et al., 2003), with mean hydrophobicity value > 0.68 representing a high score and < 0.42 representing a low score.

^bMembrane topology prediction obtained from TMHMM (Krogh et al., 2001), with type-I and type-II referring to a membrane-bound protein with the C-terminus and the N-terminus in the cytosol, respectively.

^cPosition of the TFFD and TMD obtained from the PlnTFDB v5.0 database (Riaño-Pachón et al., 2007) and TMHMM (Krogh et al., 2001) or from Aramemnon (Schwacke et al., 2003), respectively.

^dThe predicted subcellular localization obtained from SeqNLS (Lin et al., 2012), SignalP 6.0 (Teufel et al., 2022), DeepSig (Savojardo et al., 2018), and Aramemnon (Schwacke et al., 2003) is presented in Supplementary Table 2; the experimentally determined subcellular localization based on fluorescent protein fusion (regular text), mass spectrometry analysis of subcellular fractions (bold) and both methods (underlined) was obtained from SUBA4 [2] Liu et al. (2007); [7]Oh et al. (2010); [1] Liu et al. (2008); [4] Slabaugh et al. (2011); [3] Ohashi-Ito et al. (2013); [6] Liang et al. (2015); [8] Chao et al. (2017), Hooper et al. (2017); [9] Ramamurthy et al. (2018); [5] Hong et al. (2021).

^eBetween parentheses, the number of modifications; *indicates that at least one of them is present in between the TMD and TFFD, with the amino acid positions indicated in Supplementary Table 3.

^fAmino acid position in the TMD are presented in Supplementary Table 4.

^gNumber of lysines (K) and number of arginine (R) are indicated between parentheses; *significantly enriched compared to the Arabidopsis proteome or compared to the TMD regions encompassing the 5–, 10–, 15– or 20-amino-acid flanking regions of the Arabidopsis membrane-bound proteome (Bonferroni-corrected hypergeometric P values < 0.05)., with corresponding P values presented in Supplementary Table 7.