46

Rgn13

46. Partial sequences of rice cDNAs putatively identified as encoding protein kinases

H. itadani, K. yamamoto and T. sasaki

Rice Genome Research Program, National Institute of Agrobiological Resources / Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305, Japan

Protein kinases play important roles in a variety of signal transduction pathways in eukaryotes. In plants, it has been shown that protein kinases are involved in disease resistance and hormone response. For example, the rice disease resistance gene Xa21 has been isolated and shown to encode a receptor kinase-like protein (Song et al. 1995).

In the Rice Genome Research Program, a large-scale sequence analysis of rice cDNAs has been progressing (Sasaki et al. 1994). The cDNA libraries were constructed from various tissues (root, green shoot, etiolated shoot and panicle) and calli grown under 4 different conditions. The cDNA clones were randomly selected from each library, and partially sequenced from their 5' ends. The deduced amino acid sequences of the expressed sequence tags (ESTs) were compared with those in the NBRF-PIR database using the FASTA algorithm or with those in the GenPept database using the BLAST algorithm.

As of March 1996, we have analyzed approximately 27,000 cDNAs. Clones with FASTA optimized scores or with BLAST high scores of 100 or more, have been regarded as having significant similarity to known proteins or genes. In this way, we putatively identified 243 ESTs as encoding protein kinases (Table 1), although we did not confirm whether they contain kinase domains. Five of the 243 clones have already been sequenced completely and shown to contain kinase domains (Hamada et al., in preparation).

We also determined the 3' partial nucleotide sequences of 236 of the 243 clones. By comparing the 3' sequences, we classified the 236 partially sequenced and the 5 completely sequenced clones (total 241 clones) into 159 groups (Table 1). Among these groups, 110 were non-redundant, i.e., consisting of only a single clone. Since the 3' untranslated regions of the cDNA clones are expected to contain gene-specific sequences, we conclude that at least 159 species of protein kinase genes are expressed in rice.

Research Notes 151

Table 1. Isolated clones putatively identified as encoding protein kinases

clone	group 1)	5'sequence 2)	3'sequence 3)	clone	group 1)	5'sequence 2)	3'sequence 3)
C12544	1	C22375	C22376	C11084	10	C22347	C22348
C12931	1	C22385	C22386	C12351	10	C22373	C22374
C50128	1	C22401	C22402	R1477	11	D24178	C22586
C50132	l	C22403	C22404	R2568	11	D24794	C22596
E10839	1	C22546	C22547	R2573	11	D24798	C22597
E20312	1	C22554	C22555	S14264	12	D48183	C22634
E20926	1	C22558	C22559	S15319	12	C22645	C22646
E21082	1	C22562	C22563	S15625	12	D49016	C22650
E10076	2	C22526	C22527	C11129	13	D22444	C22350
E10225	2	C22532	C22533	C52856	13	C22423	C22424
E10295	2	C22534	C22535	C62887	13	C22460	C22461
E10484	2	C22538	C22S39	R1468	14	D24174	C22585
E10485	2	C22540	C22541	R2396	14	D24699	C22593
E10572	2	C22542	C22543	R2531	14	D24771	C22594
S3742	2	C22681	C22682	R2595	15	D24813	C22598
C86	3	D15115	C22468	R2596	15	D24814	C22599
C1224	3	D15773	C22474	S12662	15	D47346	C22625
C52043	3	C22417	C22418	C12916	16	C22383	C22384
C52244	3	C22419	C22420	C62514	16	C22447	C22448
S4284	3	D41644	C22684	C62706	16	C22451	C22452
E10808	4	C22544	C22545	C61495	17	C22441	C22442
S2513 4)	4	D40490	-	C61663	17	C22443	C22444
S2514	4	D40491	C22675	S 12429	18	D47219	C22623
S3433	4	D41138	C22680	S13441	18	D47760	C22627
C 12723	5	C22377	C22378	R3156	19	D25101	C22607
R2856	S	D24965	C22601	S11141	19	D46450	C22617
S504	5	C22661	C22662	S1 1007	20	D46376	C22616
S15276	5	D48835	C22644	S14063	20	C22631	C22632
C12283	6	C22371	C22372	C11404	21	C22357	C22358
S2674	6	D40598	C22676	C63066	21	C22464	C22465
S4276	6	D41640	C22683	C10173	22	D22009	C22342
S 10770	6	D46231	C22615	R639	22	D23945	C22580
E128	7	C22492	C22493	S15608	23	S 11344 4)	C22648
E40064	7	C22564	C22565	SI 5622	23	D49013	C22649
E40372	7	C22566	C22567	C11283	24	C22352	C22351
E40953	7	C22574	C22575	C12741	24	C22381	C22382
C10220	8	D22039	C22343	R1424	25	D24144	C22583
C10769	8	D22341	C22346	S 11344- 4)	25	D46580	-
C62653	8	C22449	C22450	C1255	26	D22766	C22475
E3742	9	C22518	C22519	C1315	26	D15811	C22476
E40433	9	C22568	C22569	C3080	27	D23606	C22486
E40447	9	C22570	C22571	C3119	27	D23628	C22487
C10148	10	D21988	C22341	C2476	28	D38918	C22479

152 Rice Genetics Newsletter Vol. 13

Table 1. (continued)

clone	group 1)	5'sequence 2)	3'sequence 3)	clone	group 1)	5'sequence 2)	3'sequence 3)
R2644	28	D39154	C22600	S964	49	D39547	C22664
S 14383	29	D48259	C22636	S994	49	D39557	C22665
S15160	29	D48767	C22643	C417	50	D 15294	C22469
E4214	30	C22522	C22523	C846	51	D15569	C22471
E4289	30	C22524	C22525	C915	52	D15597	C22472
C60057	31	C22427	C22428	C2851	53	D16072	C22480
C60091	31	C22429	C22430	C2939	54	D23521	C22481
R1440	32	D24156	C22584	C2985	55	D23546	C22482
R2208	32	D24581	C22589	C3014	56	C22483	C22484
C3015	33	D23565	C22485	C10415	57	D22146	C22344
C11368	33	C22353	C22354	C10624	58	D22261	C22345
C60578	34	C22431	C22432	010846 4)	59	-	.
C60633	34	C22433	C22434	C11110	60	D22431	C22349
S1296	35	D39722	C22668	C11378	61	C22355	C22356
S14403	35	D48272	C22637	C11461	62	C22359	C22360
E10203	36	C22530	C22531	C11781	63	C22361	022362
E10468	36	C22536	C22537	C11876	64	C22365	C22366
C510	37	D15355	C22470	C12126	65	C22367	C22368
C2195	37	D23102	C22478	C12239	66	C22369	C22370
C1083	38	D15682	C22473	C12740	67	C22379	C22380
R3332	38	D25141	C22610	C12955	68	C22387	C22388
R1035	39	D24062	C22582	C20074	69	C22392	C22391
S15511	39	D48931	C22647	C30013	70	C22393	C22394
E46	40	C22488	C22489	C30123	71	C22398	C22397
E3925	40	C22520	C22521	C50102	72	C22399	C22400
E41082	40	C22576	C22577	C50171	73	C22405	C22406
C1429	41	D15862	C22477	C50665	74	C22407	C22408
S12552	41	D47273	C22624	C50914	75	C22409	C22410
C61277 4)	42	-	-	C51033	76	C22411	C22412
S4972	42	D41944	C22686	C51107	77	C22413	C22414
S5976	43	C22695	C22696	C51452	78	C22415	C22416
S6530	43	C22697	C22698	C53374	79	C22425	C22426
C30026	44	C22395	C22396	C60738	80	C22435	C22436
S343	44	D39382	C22660	C60871	81	C22437	C22438
C20001	45	C22390	C22389	C60933	82	C22439	C22440
C52767	45	C22421	C22422	C61761	83	C22445	C22446
E829	46	C22508	C22509	C62707	84	C22453	C22454
E20101	46	C22550	C22551	C62806"	85	C22455	-
E40620	46	C22572	C22573	C62833	86	C22456	C22457
S1 129	47	D39614	C22666	C62866	87	C22458	C22459
S1175	47	D39639	C22667	C62984	88	C22462	C22463
C11824	48	C22363	C22364	C63827	89	C22466	C22467
C12534 4)	48	-	-	E81	90	C22491	C22490

Research Notes 153


clone	group 1)	5'sequence 2)	3'sequence 3)	clone	group1)	5'sequence 2)	3'sequence 3)
E142	91	C22494	C22495	S782	126	D39451	C22663
E235	92	C22496	C22497	S1522	127	D39876	C22669
E250	93	C22498	C22499	S1604	128	D39928	C22670
E341	94	C22500	C22501	S1616	129	D39936	C22671
E417	95	C22502	C22503	S1617	130	D39937	C22672
E507	96	C22504	C22505	S1676	131	D39976	C22673
E612	97	C22506	C22507	S1756	132	D40033	C22674
E880	98	C22510	C22511	S2867	133	D40733	C22677
E3310	99	C22512	C22513	S2901	134	D40757	C22678
E3477	100	C22514	C22515	S3027	135	D40851	C22679
E3727	101	C22516	C22517	S4655	136	D41826	C22685
E10087	102	C22528	C22529	S5163	137	C22687	C22688
E12066	103	C22548	C22549	S5274	138	C22690	C22689
E20128	104	C22552	C22553	S5450	139	C22691	C22692
E20342	105	C22556	C22557	S5627	140	C22693	C22694
E21042	106	C22560	C22561	S10057	141	C22614	C22613
F10028	107	C22579	C22578	SI 1172	142	D46473	C22618
R758	108	D23998	C22581	S11214	143	C22619	C22620
R1804	109	D24372	C22587	SI 1867	144	D46911	C22621
R1985	110	D24464	C22588	S12158	145	D47063	C22622
R2278	111	D24627	C22590	S13157	146	D47575	C22626
R2291	112	D24638	C22591	S13752	147	D47944	C22628
R2394	113	D24697	C22592	S13788	148	D47967	C22629
R2554	114	D24784	C22595	S13814	149	D47980	C22630
R2873	115	D24973	C22602	S 14245	150	D48170	C22633
R2875	116	D24975	C22603	S14275	151	D48189	C22635
R2916	117	D24997	C22604	S14591	152	D48412	C22638
R2976	118	D25047	C22605	S14618	153	D48429	C22639
R3104	119	D25069	C22606	S14663	154	D48459	C22640
R3192	120	D25110	C22608	S 14969	155	D48640	C22641
R3214	121	D39262	C22609	S15001	156	D48660	C22642
R3342	122	D39328	C22611	S 15955	157	C22651	C22652
R3369	123	D39340	C22612	S16515	158	D49304	C22653
S14	124	C22657	C22656	S16656	159	C22654	C22655
S83	125	C22659	C22658

Table 1. (continued)

241 isolated cDNA clones that showed significant similarities to protein kinases, the accession numbers of their 5' and 3' partial sequences in DDBJ, and the non-redundant groups to which the clones were classified are indicate)

1) The clones marked by the same group number were classified into the same non-redundant group.

2), 3) The accession number of 5' (2) and 3' (3) partial sequences of the clone, rspectively.

4) A clone whose full nucleotide sequences has been determined.

5) The clone, C62806 has not been sequenced from the 3' end because the 5' partial sequence extends to a poly(A) tail.

154 Rice Genetics Newsletter Vol. 13

References

Sasaki, T., J. Song, Y. Koga-Ban, E. Matsui, F. Fang, H. Higo, H. Nagasaki, M. Hori, M. Miya, E. Murayama-Kayano, T. Takiguchi, A. Takasuga, T. Niki, K. Ishimaru, H. Ikeda, Y. Yamamoto, Y. Mukai, I. Ohta, N. Miyadera, 1. Havukkala and Y. Minobe, 1994. Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J. 6: 615-624.

Song, W.Y., G.L. Wang, L.L. Chen, H.S. Kirn, L.Y. Pi, T. Holsten, J. Gardner, B. Wang, W.X. Zhai, L.H. Zhu, C. Fauquet and P. Ronald, 1995. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270: 1804-1806.