Using the SUBcellular database for Arabidopsis proteins to localize the Deg protease family

Abstract

Sub-functionalization during the expansion of gene families in eukaryotes has occurred in part through specific subcellular localization of different family members. To better understand this process in plants, compiled records of large-scale proteomic and fluorescent protein localization datasets can be explored and bioinformatic predictions for protein localization can be used to predict the gaps in experimental data. This process can be followed by targeted experiments to test predictions. The SUBA3 database is a free web-service at http://suba.plantenergy.uwa.edu.au that helps users to explore reported experimental data and predictions concerning proteins encoded by gene families and to define the experiments required to locate these homologous sets of proteins. Here we show how SUBA3 can be used to explore the subcellular location of the Deg protease family of ATP-independent serine endopeptidases (Deg1–Deg16). Combined data integration and new experiments refined location information for Deg1 and Deg9, confirmed Deg2, Deg5, and Deg8 in plastids and Deg 15 in peroxisomes and provide substantial experimental evidence for mitochondrial localized Deg proteases. Two of these, Deg3 and Deg10, additionally localized to the plastid, revealing novel dual-targeted Deg proteases in the plastid and the mitochondrion. SUBA3 is continually updated to ensure that researchers can use the latest published data when planning the experimental steps remaining to localize gene family functions.

SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations

“…The latter resources and knowledge were used in over 900 downstream studies. More recently, SUBA has played a pivotal role in estimating plant cell energy budgets (14), exploring sugar metabolism networks in barley (15) and demonstrating sub-functionalization of gene family expansions (16). The breath of work benefitting from SUBA highlights the importance of ongoing efforts in developing this central subcellular resource.…”

Differential Roles of the Thylakoid Lumenal Deg Protease Homologs in Chloroplast Proteostasis

“…These proteins are characterized by an N-terminal protease domain with a Ser-His-Asp catalytic triad, a C-terminal PDZ domain(s) involved in protein-protein interaction, and an oligomeric structure associated with their active state. The Arabidopsis (Arabidopsis thaliana) genome contains 16 Deg genes, some of which are suspected to be pseudogenes (Schuhmann and Adamska, 2012;Tanz et al, 2014). The remaining gene products are distributed among chloroplasts, mitochondria, peroxisomes, and the nucleus.…”

The contribution of individual domains of chloroplast protein AtDeg2 to its chaperone and proteolytic activities

“…Sixteen genes coding for proteins orthologous to E.coli Deg proteases (DegP, DegQ, and DegS) have been identified in the A. thaliana nuclear genome and marked AtDEG1-16 [4]. It has been confirmed both by GFP tagging and by proteomic studies that products of AtDEG 1,2,5,8, and 13 are targeted exclusively to chloroplasts with AtDeg2 being sorted to stromal side and AtDeg1, 5, and 8 to luminal side of thylakoid membrane [5][6][7][8]. Contrarily, no data on intrachloroplast location of AtDeg13 has been published.…”

“…Contrarily, no data on intrachloroplast location of AtDeg13 has been published. As judged by the results of studies based on GFP tagging approach, remaining AtDEG genes code for proteins which are targeted to mitochondria (AtDeg6, 11, 12, and 14), nucleus (AtDeg9), peroxisome (AtDeg15), or have a dual chloroplast/mitochondrion (AtDeg3 and 10) or nucleus/mitochondrion location (AtDeg7), whereas two of the sixteen genes seem to be pseudogenes (AtDEG4 and AtDEG16) [8]. An ability of a majority of chloroplast AtDegs to degrade in vitro artificial protein substrates has been convincingly proven.…”