Systematic identification of regulatory proteins critical for T-cell activation

Chu, Peter; Pardo, Jorge; Zhao, Haoran; Li, Connie C; Pali, Erlina; Shen, Mary M; Qu, Kunbin; Yu, Simon X; Huang, Betty CB; Yu, Peiwen; Masuda, Esteban S; Molineaux, Susan M; Kolbinger, Frank; Aversa, Gregorio; de Vries, Jan; Payan, Donald G; Liao, X Charlene

doi:10.1186/1475-4924-2-21

Journal of Biology

Table 1 Overview of identified molecular targets

From: Systematic identification of regulatory proteins critical for T-cell activation

Known to function in TCR pathway
Gene	Domain homology	Direction	Accession number*	Relative to ORF*	Frequency*	Phenotype transfer
TCRβ	Receptor	Sense	Numerous	Partial	46	On hold
ZAP70	Tyrosine kinase	Sense	L05148.1	-147, +787 nt	12	Yes
ZAP70 (long)	Tyrosine kinase	Sense	L05148.1	-21, +809 nt	17	TBD
Syk	Tyrosine kinase	Sense	L28824.1	-27, +1012 nt	2	Yes
Lck	Tyrosine kinase	Sense	U23852.1	-59, +799 nt	4	Yes
PLCγ1	Tyrosine kinase	Sense	NM_002660.1	+1409, +2282 nt	3	Yes
SHP-1/PTP1C	Protein-tyrosine phosphatase	Sense	X62055.1	+472, >+2021 nt	1	Yes
Csk	Tyrosine kinase	Sense	NM_004383.1	-55, +1285 nt	1	TBD
PAG	Transmembrane adaptor	Sense	NM_018440.2	-237, +644 nt	1	Yes
Nucleolin	RNA-binding	Sense	NM_005381.1	-136, +479 nt	1	No
Enzymes and receptors
TCPTP/PTPN2	Protein-tyrosine phosphatase	Sense	NM_002828.1	-58, +1108 nt	20	Yes
PAK2	p21-activated kinase 2	Sense	NM_002577.1	-50, +339 nt	18	Yes
PAK2 (long)	p21-activated kinase 2	Sense	NM_002577.1	-42, +670 nt	1	Yes
A-Raf-1	Serine/threonine kinase	Sense	X04790.1	-4, +456 nt	5	Yes
EDG1	G-protein-coupled receptor	Sense	NM_001400.2	<-244, +942 nt	4	Yes
EDG1 (long)	G-protein-coupled receptor	Sense	NM_001400.2	<-244, +1037 nt	1	TBD
TRAC-1	RING finger ubiquitin ligase	Sense	NM_017831.1	-254, +510 nt	1	Yes
IL-10Rα	Receptor	Sense	NM_001558.1	+689, +1350 nt	1	Yes
Integrin α₂	Receptor	Sense	NM_002203.2	+3348, +3914 nt	1	Yes
Enolase 1α	Phosphopyruvate hydratase	Sense	NM_001428.1	+703, +1374 nt	2	No
DUSP1	Dual-specificity phosphatase	Sense	NM_004417.2	+817, +1112 nt	1	No
KIAA0251	Pyridoxal-dependent decarboxylase	Sense	D87438.1	nt 2098-2370^†	1	No
Adaptors and transcription factors
Grb7	Adaptor	Sense	NM_005310.1	+1268, +1912 nt	3	Yes
GG2-1	TNF-induced protein	Sense	AF070671.1	-97, +1795 nt	2	Yes
SH2-B	Adaptor	Sense	AF227968.1	+1352, +1960 nt	1	Yes
RERE	Transcriptional factor	Sense	AB036737.1	+914, +1202 nt	3	No
SudD	Serine/threonine rich	Sense	NM_003831.1	-93, +413 nt	1	No
Ku 70	DNA-PKc subunit	Sense	S38729.1	+1026, +2069 nt	1	No
Novel (130 amino acids; no homology)	Unknown	Sense	AC005321.1	nt 33543-33938^‡	1	No
Novel signaling molecule	GYF domain	Sense	NM_022574.1	+1, +121 nt	1	No
SCAMP2	Secretory carrier membrane protein	Sense	AF005038.2	-5, +833 nt	1	No
KIAA1228	C2 domain (Ca²⁺- or IP-binding)	Sense	AB033054.2	nt 1439-2163^†	1	No
EST from clone 2108068	LPP20 lipoprotein precursor	Sense	Al357532.1	Novel isoform	1	No
RNH	Ribonuclease/angiogenin inhibitor	Sense	NM_002939.1	-22, +713 nt	1	No
Cytoskeleton
Moesin	Moesin	Sense	NM_002444.1	-93, +1534 nt	1	Yes
Vimentin	Intermediate filament	Sense	NM_003380.1	-98, +374 nt	1	Yes
Others
Alu repeat					5	On hold
CpG island? (clone 550H1)			AL035420.1		1	On hold
IgG2 heavy chain	Ig superfamily	Sense		Partial	1	On hold
Ig light chain	Ig superfamily	Sense		Partial	1	On hold
18S rRNA		Sense	M10098.1	Partial	2	On hold
28S rRNA		Sense		Partial	1	On hold

*For each identified clone, the GenBank database [51] accession number is given, followed by the first and last nucleotide (nt) positions relative to the initiation codon (ATG being the +1, +2, +3 nts, respectively); Frequency indicates the number of original cell clones expressing the specific hit. ^†Relative to the EST itself because the start codon is not identified. ^‡Relative to the genomic clone itself. Ig, Immunoglobulin; TBD, to be determined.

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