Genome-Wide Survey and Expression Analysis of P1B-ATPases in Rice, Maize and Sorghum

doi:10.1016/j.rsci.2018.06.004

Abstract

Abstract:

P_1B-type ATPase ion pumps that transport heavy metal ions across cellular membranes are essential for plant growth and development. To date, a genomic comparison overview of the family in rice, maize and sorghum is not yet available. In this study, a total of 31 heavy metal P_1B-type ATPase (HMA) genes were identified, including 9 in rice, 11 each from maize and sorghum. They were classified into two distinct subfamilies based on their sequence composition and phylogenetic relationship. Four pairs of HMA genes were expanded via gene duplication with tandemly duplicated. Comprehensive analyses were performed to investigate the expression profiles of HMA genes in various tissues by using quantitative real-time PCR. Some HMA members exhibited abundant and tissue-specific expression patterns. Moreover, most of the genes were found to be differentially expressed under the Cu/Cd treatment. This study will facilitate further studies on P_1B-type ATPase family and provide valuable hints for the functional validation in rice, maize and sorghum.

Key words: P_1B-type ATPase, rice, maize, sorghum, HMA gene family, expression pattern analysis

Zhiguo E, Tingting Li, Chen Chen, Lei Wang. Genome-Wide Survey and Expression Analysis of P_1B-ATPases in Rice, Maize and Sorghum[J]. Rice Science, 2018, 25(4): 208-217.

Figures/Tables 7

References 26

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Species	Chr	Gene name	Locus name ^a	No. of introns	Amino acid (aa)	TM ^b	Subcellular localization^c	Location (bp)	Strand
Oryza sativa (rice)
	6	OsHMA1	LOC_Os06g47550	12	822	6	Chloroplast	28 797 545-28 789 015	Reverse
	6	OsHMA2	LOC_Os06g48720	8	1 067	6	PM	29 480 905-29 477 949	Reverse
	7	OsHMA3	LOC_Os07g12900	6	1 005	5	Tonoplast	7 409 553-7 405 745	Reverse
	2	OsHMA4	LOC_Os02g10290	8	979	8	PM	5 404 703-5 410 764	Forward
	4	OsHMA5	LOC_Os04g46940	5	1 003	8	PM	27 829 775-27 835 535	Forward
	2	OsHMA6	LOC_Os02g07630	8	1 013	7	PM	3 955 899-3 950 378	Reverse
	8	OsHMA7	LOC_Os08g37950	16	960	7	Chloroplast	24 031 272-24 039 316	Forward
	3	OsHMA8	LOC_Os03g08070	15	886	5	Chloroplast	4 126 933-4 119 945	Reverse
	6	OsHMA9	LOC_Os06g45500	8	1 004	7	PM	27 523 604-27 517 100	Reverse
Zea mays (maize)
	5	ZmHMA1	GRMZM2G067853	12	823	6	Chloroplast	52 117 376-52 139 003	Forward
	5	ZmHMA2	GRMZM2G099191	8	1 099	4	PM	56 423 032-56 429 658	Reverse
	2	ZmHMA3a	GRMZM2G175576	4	993	6	Tonoplast	158 406 991-158 410 957	Reverse
	2	ZmHMA3b	GRMZM2G455491	5	927	5	Tonoplast	158 386 097-158 389 415	Reverse
	5	ZmHMA4	GRMZM2G029951	7	974	8	PM	121 407 958-121 412 467	Reverse
	2	ZmHMA5a	GRMZM2G143512	5	999	8	PM	18 705 084-18 713 162	Reverse
	2	ZmHMA5b	GRMZM2G144083	5	1 001	8	PM	18 620 426-18 626 656	Reverse
	4	ZmHMA6	GRMZM2G010152	8	998	7	PM	235 734 155-235 739 482	Forward
	4	ZmHMA7	GRMZM2G315931	16	928	7	Chloroplast	197 051 975-197 061 374	Forward
	9	ZmHMA9	GRMZM2G404702	5	597	5	PM	109 888 623-109 894 466	Reverse
	7	ZmHMA10	AC205008.4_FG002	5	883	5	Tonoplast	21 633 432-21 636 570	Forward
Sorghum bicolor (sorghum)
	10	SbHMA1	Sb10g028080	12	828	6	Chloroplast	57 972 772-57 985 175	Reverse
	10	SbHMA2	Sb10g028920	8	1069	6	PM	58 715 561-58 722 945	Reverse
	2	SbHMA3a	Sb02g006940	3	895	6	Tonoplast	8 908 023-8 911 069	Forward
	2	SbHMA3b	Sb02g006950	5	933	8	Tonoplast	8 913 910-8 917 295	Forward
	4	SbHMA4	Sb04g006600	7	974	8	PM	6 611 424-6 615 768	Forward
	6	SbHMA5a	Sb06g024900	5	1 002	8	PM	53 929 840-53 937 843	Forward
	6	SbHMA5b	Sb06g024910	5	998	8	PM	53 941 501-53 948 034	Forward
	4	SbHMA6	Sb04g004820	9	1 011	8	PM	4 611 722-4 616 506	Reverse
	7	SbHMA7	Sb07g029010	16	817	6	Chloroplast	64 072 258-64 081 513	Reverse
	1	SbHMA8	Sb01g045340	15	877	6	Chloroplast	68 452 000-68 458 070	Forward
	10	SbHMA9	Sb10g026600	8	996	8	PM	56 024 169-56 030 667	Reverse
Chr, Chromosome; TM, Transmembrane structure; PM, Plasma membrane. ^a Locus identity number of HMAs assigned by Gramene; ^b Prediction of transmembrane helices in proteins using TMHMM Server v.2.0 (http://www.cbs.dtu.dk/services/TMHMM/); ^c Subcellular location prediction using TargetP 1.1 Server (http://www.cbs.dtu.dk/services/TargetP/).

Species	Chr	Gene name	Locus name ^a	No. of introns	Amino acid (aa)	TM ^b	Subcellular localization^c	Location (bp)	Strand
Oryza sativa (rice)
	6	OsHMA1	LOC_Os06g47550	12	822	6	Chloroplast	28 797 545-28 789 015	Reverse
	6	OsHMA2	LOC_Os06g48720	8	1 067	6	PM	29 480 905-29 477 949	Reverse
	7	OsHMA3	LOC_Os07g12900	6	1 005	5	Tonoplast	7 409 553-7 405 745	Reverse
	2	OsHMA4	LOC_Os02g10290	8	979	8	PM	5 404 703-5 410 764	Forward
	4	OsHMA5	LOC_Os04g46940	5	1 003	8	PM	27 829 775-27 835 535	Forward
	2	OsHMA6	LOC_Os02g07630	8	1 013	7	PM	3 955 899-3 950 378	Reverse
	8	OsHMA7	LOC_Os08g37950	16	960	7	Chloroplast	24 031 272-24 039 316	Forward
	3	OsHMA8	LOC_Os03g08070	15	886	5	Chloroplast	4 126 933-4 119 945	Reverse
	6	OsHMA9	LOC_Os06g45500	8	1 004	7	PM	27 523 604-27 517 100	Reverse
Zea mays (maize)
	5	ZmHMA1	GRMZM2G067853	12	823	6	Chloroplast	52 117 376-52 139 003	Forward
	5	ZmHMA2	GRMZM2G099191	8	1 099	4	PM	56 423 032-56 429 658	Reverse
	2	ZmHMA3a	GRMZM2G175576	4	993	6	Tonoplast	158 406 991-158 410 957	Reverse
	2	ZmHMA3b	GRMZM2G455491	5	927	5	Tonoplast	158 386 097-158 389 415	Reverse
	5	ZmHMA4	GRMZM2G029951	7	974	8	PM	121 407 958-121 412 467	Reverse
	2	ZmHMA5a	GRMZM2G143512	5	999	8	PM	18 705 084-18 713 162	Reverse
	2	ZmHMA5b	GRMZM2G144083	5	1 001	8	PM	18 620 426-18 626 656	Reverse
	4	ZmHMA6	GRMZM2G010152	8	998	7	PM	235 734 155-235 739 482	Forward
	4	ZmHMA7	GRMZM2G315931	16	928	7	Chloroplast	197 051 975-197 061 374	Forward
	9	ZmHMA9	GRMZM2G404702	5	597	5	PM	109 888 623-109 894 466	Reverse
	7	ZmHMA10	AC205008.4_FG002	5	883	5	Tonoplast	21 633 432-21 636 570	Forward
Sorghum bicolor (sorghum)
	10	SbHMA1	Sb10g028080	12	828	6	Chloroplast	57 972 772-57 985 175	Reverse
	10	SbHMA2	Sb10g028920	8	1069	6	PM	58 715 561-58 722 945	Reverse
	2	SbHMA3a	Sb02g006940	3	895	6	Tonoplast	8 908 023-8 911 069	Forward
	2	SbHMA3b	Sb02g006950	5	933	8	Tonoplast	8 913 910-8 917 295	Forward
	4	SbHMA4	Sb04g006600	7	974	8	PM	6 611 424-6 615 768	Forward
	6	SbHMA5a	Sb06g024900	5	1 002	8	PM	53 929 840-53 937 843	Forward
	6	SbHMA5b	Sb06g024910	5	998	8	PM	53 941 501-53 948 034	Forward
	4	SbHMA6	Sb04g004820	9	1 011	8	PM	4 611 722-4 616 506	Reverse
	7	SbHMA7	Sb07g029010	16	817	6	Chloroplast	64 072 258-64 081 513	Reverse
	1	SbHMA8	Sb01g045340	15	877	6	Chloroplast	68 452 000-68 458 070	Forward
	10	SbHMA9	Sb10g026600	8	996	8	PM	56 024 169-56 030 667	Reverse
Chr, Chromosome; TM, Transmembrane structure; PM, Plasma membrane. ^a Locus identity number of HMAs assigned by Gramene; ^b Prediction of transmembrane helices in proteins using TMHMM Server v.2.0 (http://www.cbs.dtu.dk/services/TMHMM/); ^c Subcellular location prediction using TargetP 1.1 Server (http://www.cbs.dtu.dk/services/TargetP/).