The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis
Kristina Majseca b, Nazmul H. Bhuiyanc d, Qi Sune f, Sunita Kumarig h, Vivek Kumarg h, Doreen Wareg h, Klaas Jan van Wijkc d
- aFaculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- baFaculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- cSchool for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
- dbSchool for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
- eComputational Biology Service Unit, Cornell University, Ithaca, New York 14853
- fcComputational Biology Service Unit, Cornell University, Ithaca, New York 14853
- gCold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
- hdCold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
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Abstract
We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows 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 coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 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 peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.
TL;DRThis review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana and shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidasing inhibitors, whereas other peptid enzyme families were exclusively organellar; reasons for such biases are discussed. (Semantic Scholar)