Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots.
Manganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn. Using an integrated RNA-based transcriptomic and high-throughput shotgun proteomics approach, we generated a comprehensive inventory of transcripts and proteins that showed altered abundance in response to Mn deficiency in roots of the model plant Arabidopsis. A suite of 22,385 transcripts was consistently detected in three RNA-seq runs; LC-MS/MS-based iTRAQ proteomics allowed the unambiguous determination of 11,606 proteins. While high concordance between mRNA and protein expression (R = 0.87) was observed for transcript/protein pairs in which both gene products accumulated differentially upon Mn deficiency, only approximately 10% of the total alterations in the abundance of proteins could be attributed to transcription, indicating a large impact of protein-level regulation. Differentially expressed genes spanned a wide range of biological functions, including the maturation, translation, and transport of mRNAs, as well as primary and secondary metabolic processes. Metabolic analysis by UPLC-qTOF-MS revealed that the steady-state levels of several major glucosinolates were significantly altered upon Mn deficiency in both roots and leaves, possibly as a compensation for increased pathogen susceptibility under conditions of Mn deficiency.
Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan.
Jorge
J
Rodríguez-Celma
Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan.
Yi-Hsiu
YH
Tsai
Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan.
Tuan-Nan
TN
Wen
Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan.
Yu-Ching
YC
Wu
Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Institut National pour la Recherche Agronomique, Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, INRA/SupAgro, Université Montpellier 2, Montpellier, France.
Catherine
C
Curie
Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan.|Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.|Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan.
Wolfgang
W
Schmidt
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002851:Chromatography, High Pressure Liquid; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005961:Glucosinolates / Q000032:analysis / Q000378:metabolism; D008345:Manganese / Q000172:deficiency* / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D018749:RNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D017423:Sequence Analysis, RNA; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D053719:Tandem Mass Spectrometry
D029681:Arabidopsis Proteins; D005961:Glucosinolates; D020543:Proteome; D018749:RNA, Plant; D008345:Manganese