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Author Singh A., Giri J., Kapoor S., Akhilesh K Tyagi, Girdhar K Pandey
Title Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development.
Abstract:
Protein phosphatases are the key components of a number of signaling pathways where they modulate various cellular responses. In plants, protein phosphatases constitute a large gene family and are reportedly involved in the regulation of abiotic stress responses and plant development. Recently, the whole complement of protein phosphatases has been identified in Arabidopsis genome. While PP2C class of serine/threonine phosphatases has been explored in rice, the whole complement of this gene family is yet to be reported. In silico investigation revealed the presence of 132-protein phosphatase-coding genes in rice genome. Domain analysis and phylogenetic studies of evolutionary relationship categorized these genes into PP2A, PP2C, PTP, DSP and LMWP classes. PP2C class represents a major proportion of this gene family with 90 members. Chromosomal localization revealed their distribution on all the 12 chromosomes, with 42 genes being present on segmentally duplicated regions and 10 genes on tandemly duplicated regions of chromosomes. The expression profiles of 128 genes under salinity, cold and drought stress conditions, 11 reproductive developmental (panicle and seed) stages along with three stages of vegetative development were analyzed using microarray expression data. 46 genes were found to be differentially expressing in 3 abiotic stresses out of which 31 were up-regulated and 15 exhibited down-regulation. A total of 82 genes were found to be differentially expressing in different developmental stages. An overlapping expression pattern was found for abiotic stresses and reproductive development, wherein 8 genes were up-regulated and 7 down-regulated. Expression pattern of the 13 selected genes was validated employing real time PCR, and it was found to be in accordance with the microarray expression data for most of the genes. Exploration of protein phosphatase gene family in rice has resulted in the identification of 132 members, which can be further divided into different classes phylogenetically. Expression profiling and analysis indicate the involvement of this large gene family in a number of signaling pathways triggered by abiotic stresses and their possible role in plant development. Our study will provide the platform from where; the expression pattern information can be transformed into molecular, cellular and biochemical characterization of members belonging to this gene family.
Journal BMC Genomics
Country India
Volume 11
Pages 435
Year 2010
PubMed ID 20637108
PubMed Central ID 3091634
DOI 10.1186/1471-2164-11-435
URL -
Relation
Gene ABI1 ABI2 BIPP2C1 DCW11 FH12 GL3.1 OSKAPP PP100 PP101 PP103 PP104 PP106 PP112 PP113 PP115 PP117 PP118 PP119 PP123 PP124 PP125 PP127 PP128 PP13 PP130 PP132 PP14 PP16 PP17 PP23 PP2A-1 PP2A-3 PP2C1 PP2C1 PP2C10 PP2C11 PP2C12 PP2C14 PP2C15 PP2C16 PP2C17 PP2C18 PP2C19 PP2C2 PP2C20 PP2C21 PP2C22 PP2C23 PP2C24 PP2C25 PP2C26 PP2C27 PP2C28 PP2C29 PP2C30 PP2C31 PP2C32 PP2C33 PP2C34 PP2C36 PP2C37 PP2C38 PP2C39 PP2C4 PP2C40 PP2C41 PP2C42 PP2C43 PP2C44 PP2C45 PP2C46 PP2C47 PP2C48 PP2C49 PP2C5 PP2C50 PP2C52 PP2C53 PP2C54 PP2C55 PP2C56 PP2C57 PP2C58 PP2C59 PP2C6 PP2C61 PP2C62 PP2C63 PP2C64 PP2C65 PP2C66 PP2C67 PP2C69 PP2C7 PP2C70 PP2C71 PP2C72 PP2C73 PP2C74 PP2C75 PP2C77 PP2C78 PP2C8 PP2C9 PP32 PP38 PP41 PP44 PP47 PP5 PP52 PP53 PP56 PP57 PP58 PP73 PP74 PP77 PP82 PP83 PP99 SAL1 SEX4 STR19 XA46 XB15 _ _ _ _ _ _
INSD -
Strain Wild Core Collection -
Induced Mutation Lines(NIG Collection) -
Sterile Seed Strain -
Lethal Embryo
Mutantion Strain 		-
Stages in Each Organ
- Muant Lines (Gene) 		-
Cultivated Varieties(NIG Collection) -
Stages in Each Organ -
/rice/oryzabase