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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #343893

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: The plastid and mitochondrial peptidase network in Arabidopsis thaliana: a foundation for testing genetic interactions and functions in organellar proteostasis

item MAJSEC, KRISTINA - University Of Zagreb
item BHUIYAN, NAZMAL - Cornell University - New York
item SUN, QI - University Of Zagreb
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item Ware, Doreen
item VAN WIJK, KLAAS - Cornell University - New York

Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2017
Publication Date: 9/25/2017
Citation: Majsec, K., Bhuiyan, N., Sun, Q., Kumari, S., Kumar, V., Ware, D., Van Wijk, K. 2017. The plastid and mitochondrial peptidase network in Arabidopsis thaliana: a foundation for testing genetic interactions and functions in organellar proteostasis. The Plant Cell.

Interpretive Summary: This study provides a compendium for all putative peptidases and auxiliary factors in Arabidopsis, and their tentative assignments to plastids and mitochondria, and includes all proteins that have an assigned clan and family in the MEROPS database (an online database for peptidases, their substrates and their inhibitors).

Technical Abstract: Plant plastids and mitochondria have dynamic proteomes. To maintain their protein homeostasis, a proteostasis network containing protein chaperones, peptidases and their substrate recognition factors exists, but many peptidases, their functional connections and substrates are poorly characterized. This study provides a systematic insight in the organellar peptidase network in Arabidopsis. After compiling all Arabidopsis (putative) peptidases and inhibitors, the distribution of plastid and mitochondrial peptidases across the total peptidase complement was compared to MEROPS clans and families and showed striking biases, such as the (near) absence of cysteine and aspartic peptidases, and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based co-expression dataset was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases, and to generate a co-expression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network showed 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The complete peptidase compendium, including the autophagy and proteosomal systems, annotated based on the MEROPS nomenclature of clans and families, is incorporated into the Plant Proteome Database, PPDB.