The crystal structure of Deg9 reveals a novel octameric-type HtrA protease

Abstract

The high temperature requirement A (HtrA) proteases (also termed Deg proteases) play important roles in diverse organisms by regulating protein quality and quantity. One of the 16 Arabidopsis homologs, Deg9, is located in the nucleus where it modulates cytokinin- and light-mediated signalling via degrading the ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). To uncover the structural features underlying the proteolytic activity of Deg9, we determined its crystal structure. Unlike the well-established trimeric building block of HtrAs, Deg9 displays a novel octameric structure consisting of two tetrameric rings that have distinct conformations. Based on the structural architecture, we generated several mutant variants of Deg9, determined their structure and tested their proteolytic activity towards ARR4. The results of the structural and biochemical analyses allowed us to propose a model for a novel mechanism of substrate recognition and activity regulation of Deg9. In this model, protease activation of one tetramer is mediated by en-bloc reorientation of the protease domains to open an entrance for the substrate in the opposite (inactive) tetramer. This study provides the structural basis for understanding how the levels of nuclear signal components are regulated by a plant protease.

PDM4, a Pentatricopeptide Repeat Protein, Affects Chloroplast Gene Expression and Chloroplast Development in Arabidopsis thaliana

“…Derived from cyanobacterial ancestors, the chloroplasts belong to semi-autonomous organelles which possess their own genomes. Over the last billion years, the chloroplast genome has lost numerous genes in higher plants and generally remains about 120 genes which encode primary components of translation, transcription, and photosynthesis apparatus, as well as contains some critical biogenesis-related genes such as accD, clpP1, matK, ycf1, and ycf2 (Sato et al, 1999;Leister, 2003;Ouyang et al, 2017). Although the chloroplast genome is small and with limited coding information, the transcriptional process is much more complex than that of prokaryotes which are usually organized in polycistronic transcriptional units.…”

Proteome and Interactome Linked to Metabolism, Genetic In-Formation Processing and Abiotic Stress, in the Gametophyte of Two Woodferns

“…On the other hand, many proteins found are related to protein catabolism or degradation, being subunits of proteasomes, i.e., complexes characterized by their ability to degrade proteins or ubiquitination structures. Others such as AT1G09130; CLP PROTEASE PROTEOLYTIC SUBUNIT 2 (CLP2); CLP PROTEASE R SUBUNIT 4 (CLPR4); LON PRO-TEASE 1 (LON1); PRESEQUENCE PROTEASE 1 (PREP1), which degrades in mitochondria the pre-sequences of proteins that have entered after being cut, since the other option, export them to the cytoplasm, costs a lot of energy and has low efficiency (Stahl et al, 2002); and also DEGRADATION OF PERIPLASMIC PROTEINS 9 (DEG9), which degrades the A. thaliana response regulator 4 (ARR4), a regulator which participates in light and cytokinin signaling pathways by modulating the activity of phytochrome B (Ouyang et al, 2017). Plants have to deal with heat stress, and for this, the gametophytes of the study count with the aminopeptidases LEUCYL AMINOPEPTIDASE 1 and 3 (LAP1 and LAP3), probably involved in the processing and turnover of intracellular proteins, and function as molecular chaperones protecting them from heat-induced damage (Scranton et al, 2012).…”