A comparative proteome approach to decipher the mechanism of rice adaptation to phosphorous deficiency

Abstract

Mineral deficiency limits crop production in most soils and in Asia alone, about 50% of rice lands are phosphorous deficient. In an attempt to determine the mechanism of rice adaptation to phosphorous deficiency, changes in proteome patterns associated with phosphorous deficiency have been investigated. We analyzed the parental line Nipponbare in comparison to its near isogenic line (NIL6-4) carrying a major phosphorous uptake QTL (Pup1) on chromosome 12. Using 2-DE, the proteome pattern of roots grown under 1 and 100 microM phosphorous were compared. Out of 669 proteins reproducibly detected on root 2-DE gels, 32 proteins showed significant changes in the two genotypes. Of them, 17 proteins showed different responses in two genotypes under stress condition. MS resulted in identification of 26 proteins involved in major phosphorous deficiency adaptation pathways including reactive oxygen scavenging, citric acid cycle, signal transduction, and plant defense responses as well as proteins with unknown function. Our results highlighted a coordinated response in NIL in response to phosphorous deficiency which may confer higher adaptation to nutrient deficiency.

Stress Response Versus Stress Tolerance: A Transcriptome Analysis of Two Rice Lines Contrasting in Tolerance to Phosphorus Deficiency

“…In a similar experiment, NILs segregating for the Pup1 locus (+Pup1: NILs 6-4, Y-4, 14-4; −Pup1: NILs 26-6, 28-10, and Nipponbare) were grown for 50 days in either Pdeficient or P-fertilized soil, and root material was sampled and immediately shock-frozen in liquid N. Some genotype information on these NILs can be found in Heuer et al (2009), Torabi et al (2009), and Wissuwa et al (2002. Total RNA was extracted and used to compare the relative expression of XTH and NAD(P)H-dependent oxidoreductase genes through RT-qPCR.…”

“…In addition, two genes potentially linked to the hormonal regulation of root growth, an IAA-amino acid hydrolase ILR1 precursor and a gibberellin receptor GID1L2, were among the genes expressed at a higher level in NIL6-4 roots. The higher expression for many root cell- Only genes with informative annotation and that are "present" in at least one tissue are shown a Localized within Kasalath introgressions present on chromosomes 1, 7, 10, and 12 (Torabi et al 2009) b Genes present in shoot and root Only genes with informative annotation and that are "present" in at least one tissue are shown a Localized within Kasalath introgressions present on chromosomes 1, 7, 10, and 12 (Torabi et al 2009) b Genes present in shoot and root wall-associated genes would support our third hypothesis that tolerance to P deficiency in NIL6-4 is due to modifications in root growth that maximize Pi interception. This is further corroborated by phenotypic data showing that the most consistent difference between Nipponbare and NIL6-4 is a far more pronounced reduction in root biomass and surface area due to P deficiency in Nipponbare (Wissuwa and Ae 2001b;Wissuwa 2005).…”

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants

“…Transcript accumulation for genes associated with the oxidative stress response is a hallmark of P i deficiency gene expression experiments (Misson et al, 2005;Hernández et al, 2007;Torabi et al, 2009). Metabolic pathways continuously produce ROS as by-products.…”

“…These ROS are usually scavenged by antioxidants, but abiotic/biotic and nutrient stresses can disrupt the equilibrium of ROS formation and detoxification, resulting in oxidative stress. ROS are known to both induce oxidative damage to cellular components and serve as signaling molecules in signaling cascades (Shin et al, 2005;Torabi et al, 2009). Those authors (Shin et al, 2005;Torabi et al, 2009) found the severity of P i deficiency directly correlated with the severity of the oxidative stress.…”

Complementary Proteome and Transcriptome Profiling in Phosphate-deficient Arabidopsis Roots Reveals Multiple Levels of Gene Regulation

“…Generally, because of post-translational turnover and alternate translation efficiency, mRNA abun-dance is not a reliable proxy of protein abundance, and modest congruency of the two levels has been reported except for high abundance transcripts and "molecular machines" (16 -22). Much has been learned regarding P i deficiency responses from proteomic approaches (23)(24)(25). Despite these efforts, data sets on P i deficiency-induced changes in the proteome remained somewhat patchy, because of a skew toward highabundant proteins and work carried out on different species.…”