m-AAA Complexes Are Not Crucial for the Survival of Arabidopsis Under Optimal Growth Conditions Despite Their Importance for Mitochondrial Translation

The biogenesis and regulation of the plant oxidative phosphorylation system

Mitochondria are central organelles for respiration in plants. At the heart of this process is oxidative phosphorylation (OXPHOS) system, which generates ATP required for cellular energetic needs. OXPHOS complexes comprise of multiple subunits that originated from both mitochondrial and nuclear genome, which requires careful orchestration of expression, translation, import, and assembly. Constant exposure to reactive oxygen species due to redox activity also renders OXPHOS subunits to be more prone to oxidative damage, which requires coordination of disassembly and degradation. In this review, we highlight the composition, assembly, and activity of OXPHOS complexes in plants based on recent biochemical and structural studies. We also discuss how plants regulate the biogenesis and turnover of OXPHOS subunits and the importance of OXPHOS in overall plant respiration. Further studies in determining the regulation of biogenesis and activity of OXPHOS will advances the field, especially in understanding plant respiration and its role to plant growth and development.

Foliar Phenotypic Plasticity Reflects Adaptation to Environmental Variability

Arabidopsis thaliana ecotypes adapted to native habitats with different daylengths, temperatures, and precipitation were grown experimentally under seven combinations of light intensity and leaf temperature to assess their acclimatory phenotypic plasticity in foliar structure and function. There were no differences among ecotypes when plants developed under moderate conditions of 400 µmol photons m-2 s-1 and 25 °C. However, in response to more extreme light or temperature regimes, ecotypes that evolved in habitats with pronounced differences in either the magnitude of changes in daylength or temperature or in precipitation level exhibited pronounced adjustments in photosynthesis and transpiration, as well as anatomical traits supporting these functions. Specifically, when grown under extremes of light intensity (100 versus 1000 µmol photons m-2 s-1) or temperature (8 °C versus 35 °C), ecotypes from sites with the greatest range of daylengths and temperature over the growing season exhibited the greatest differences in functional and structural features related to photosynthesis (light- and CO2-saturated capacity of oxygen evolution, leaf dry mass per area or thickness, phloem cells per minor vein, and water-use efficiency of CO2 uptake). On the other hand, the ecotype from the habitat with the lowest precipitation showed the greatest plasticity in features related to water transport and loss (vein density, ratio of water to sugar conduits in foliar minor veins, and transpiration rate). Despite these differences, common structure-function relationships existed across all ecotypes and growth conditions, with significant positive, linear correlations (i) between photosynthetic capacity (ranging from 10 to 110 µmol O2 m-2 s-1) and leaf dry mass per area (from 10 to 75 g m-2), leaf thickness (from 170 to 500 µm), and carbohydrate-export infrastructure (from 6 to 14 sieve elements per minor vein, from 2.5 to 8 µm2 cross-sectional area per sieve element, and from 16 to 82 µm2 cross-sectional area of sieve elements per minor vein); (ii) between transpiration rate (from 1 to 17 mmol H2O m-2 s-1) and water-transport infrastructure (from 3.5 to 8 tracheary elements per minor vein, from 13.5 to 28 µm2 cross-sectional area per tracheary element, and from 55 to 200 µm2 cross-sectional area of tracheary elements per minor vein); (iii) between the ratio of transpirational water loss to CO2 fixation (from 0.2 to 0.7 mol H2O to mmol-1 CO2) and the ratio of water to sugar conduits in minor veins (from 0.4 to 1.1 tracheary to sieve elements, from 4 to 6 µm2 cross-sectional area of tracheary to sieve elements, and from 2 to 6 µm2 cross-sectional area of tracheary elements to sieve elements per minor vein); (iv) between sugar conduits and sugar-loading cells; and (v) between water conducting and sugar conducting cells. Additionally, the proportion of water conduits to sugar conduits was greater for all ecotypes grown experimentally under warm-to-hot versus cold temperature. Thus, developmental acclimation to the growth environment included ecotype-dependent foliar structural and functional adjustments resulting in multiple common structural and functional relationships.

Proteolytic regulation of mitochondrial oxidative phosphorylation components in plants

Mitochondrial function relies on the homeostasis and quality control of their proteome, including components of the oxidative phosphorylation (OXPHOS) pathway that generates energy in form of ATP. OXPHOS subunits are under constant exposure to reactive oxygen species due to their oxidation-reduction activities, which consequently make them prone to oxidative damage, misfolding, and aggregation. As a result, quality control mechanisms through turnover and degradation are required for maintaining mitochondrial activity. Degradation of OXPHOS subunits can be achieved through proteomic turnover or modular degradation. In this review, we present multiple protein degradation pathways in plant mitochondria. Specifically, we focus on the intricate turnover of OXPHOS subunits, prior to protein import via cytosolic proteasomal degradation and post import and assembly via intra-mitochondrial proteolysis involving multiple AAA+ proteases. Together, these proteolytic pathways maintain the activity and homeostasis of OXPHOS components.

Assessment of Protein Synthesis in Mitochondria Isolated from Rosette Leaves and Liquid Culture Seedlings of Arabidopsis

Mitochondria are subcellular organelles with their own genome and expression system, including translation machinery to make proteins. Several independent studies have shown that translation is an essential regulatory step in expression of the plant mitochondrial genome. Thus, the study of mitochondrial translation seems to be crucial for the comprehension of plant mitochondrial biogenesis and maintenance. In organello protein synthesis in isolated mitochondria is a direct method to visualize the translational products of this organellar genetic system. In this method, highly purified, functional mitochondria synthesize proteins in the presence of radiolabeled amino acids, such as methionine, and an energy regeneration system. The labeled, newly synthesized polypeptides are separated by SDS-polyacrylamide gel electrophoresis and are detected by autoradiography. Here we describe the detailed protocol for in organello labeling of translation products that was optimized for mitochondria isolated from rosette leaves and liquid culture seedlings of Arabidopsis thaliana plants.

Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases

The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.

Protein Processing in Plant Mitochondria Compared to Yeast and Mammals

Limited proteolysis, called protein processing, is an essential post-translational mechanism that controls protein localization, activity, and in consequence, function. This process is prevalent for mitochondrial proteins, mainly synthesized as precursor proteins with N-terminal sequences (presequences) that act as targeting signals and are removed upon import into the organelle. Mitochondria have a distinct and highly conserved proteolytic system that includes proteases with sole function in presequence processing and proteases, which show diverse mitochondrial functions with limited proteolysis as an additional one. In virtually all mitochondria, the primary processing of N-terminal signals is catalyzed by the well-characterized mitochondrial processing peptidase (MPP). Subsequently, a second proteolytic cleavage occurs, leading to more stabilized residues at the newly formed N-terminus. Lately, mitochondrial proteases, intermediate cleavage peptidase 55 (ICP55) and octapeptidyl protease 1 (OCT1), involved in proteolytic cleavage after MPP and their substrates have been described in the plant, yeast, and mammalian mitochondria. Mitochondrial proteins can also be processed by removing a peptide from their N- or C-terminus as a maturation step during insertion into the membrane or as a regulatory mechanism in maintaining their function. This type of limited proteolysis is characteristic for processing proteases, such as IMP and rhomboid proteases, or the general mitochondrial quality control proteases ATP23, m-AAA, i-AAA, and OMA1. Identification of processing protease substrates and defining their consensus cleavage motifs is now possible with the help of large-scale quantitative mass spectrometry-based N-terminomics, such as combined fractional diagonal chromatography (COFRADIC), charge-based fractional diagonal chromatography (ChaFRADIC), or terminal amine isotopic labeling of substrates (TAILS). This review summarizes the current knowledge on the characterization of mitochondrial processing peptidases and selected N-terminomics techniques used to uncover protease substrates in the plant, yeast, and mammalian mitochondria.

The FtsHi Enzymes of Arabidopsis thaliana: Pseudo-Proteases with an Important Function

FtsH metalloproteases found in eubacteria, animals, and plants are well-known for their vital role in the maintenance and proteolysis of membrane proteins. Their location is restricted to organelles of endosymbiotic origin, the chloroplasts, and mitochondria. In the model organism Arabidopsis thaliana, there are 17 membrane-bound FtsH proteases containing an AAA+ (ATPase associated with various cellular activities) and a Zn2+ metalloprotease domain. However, in five of those, the zinc-binding motif HEXXH is either mutated (FtsHi1, 2, 4, 5) or completely missing (FtsHi3), rendering these enzymes presumably inactive in proteolysis. Still, homozygous null mutants of the pseudo-proteases FtsHi1, 2, 4, 5 are embryo-lethal. Homozygous ftshi3 or a weak point mutant in FTSHi1 are affected in overall plant growth and development. This review will focus on the findings concerning the FtsHi pseudo-proteases and their involvement in protein import, leading to consequences in embryogenesis, seed growth, chloroplast, and leaf development and oxidative stress management.

The mitochondrial AAA protease FTSH3 regulates Complex I abundance by promoting its disassembly

ATP is generated in mitochondria by oxidative phosphorylation. Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) is the first multisubunit protein complex of this pathway, oxidizing NADH and transferring electrons to the ubiquinone pool. Typically, Complex I mutants display a slow growth rate compared to wild-type plants. Here, using a forward genetic screen approach for restored growth of a Complex I mutant, we have identified the mitochondrial ATP-dependent metalloprotease, Filamentous Temperature Sensitive H 3 (FTSH3), as a factor that is required for the disassembly of Complex I. An ethyl methanesulfonate-induced mutation in FTSH3, named as rmb1 (restoration of mitochondrial biogenesis 1), restored Complex I abundance and plant growth. Complementation could be achieved with FTSH3 lacking proteolytic activity, suggesting the unfoldase function of FTSH3 has a role in Complex I disassembly. The introduction of the rmb1 to an additional, independent, and extensively characterized Complex I mutant, ndufs4, resulted in similar increases to Complex I abundance and a partial restoration of growth. These results show that disassembly or degradation of Complex I plays a role in determining its steady-state abundance and thus turnover may vary under different conditions.

Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver

Eucommia ulmoides (Tu-chung) is an economically and ecologically important tree species which has attracted worldwide attention due to its application in pharmacology, landscaping, wind sheltering and sand fixation. Molecular marker technologies can elucidate the genetic mechanism and substantially improve the breeding efficiency of E. ulmoides. The current research updated the original linkage map, and quantitative trait loci (QTL) analysis was performed on tree growth traits measured over 10 consecutive years in an E. ulmoides F1 population (“Xiaoye” × “Qinzhong No.1”). In total, 452 polymorphic markers were scored from 365 simple sequence repeat (SSR) primers, with an average of 1.24 polymorphic markers per primer combination. The integrated map was 1913.29 cM (centimorgan) long, covering 94.10% of the estimated genome and with an average marker density of 2.20 cM. A total of 869 markers were mapped into 19 major independent linkage groups. Growth-related traits measured over 10 consecutive years showed a significant correlation, and 89 hypothetical QTLs were forecasted and divided into 27 distinct loci. Three traits for tree height, ground diameter and crown diameter detected 25 QTLs (13 loci), 32 QTLs (17 loci) and 15 QTLs (10 loci), respectively. Based on BLASTX search results in the NCBI database, six candidate genes were obtained. It is important to explore the growth-related genetic mechanism and lay the foundation for the genetic improvement of E. ulmoides at the molecular level.

NEEDLE1 encodes a mitochondria localized ATP-dependent metalloprotease required for thermotolerant maize growth

Meristems are highly regulated structures ultimately responsible for the formation of branches, lateral organs, and stems, and thus directly affect plant architecture and crop yield. In meristems, genetic networks, hormones, and signaling molecules are tightly integrated to establish robust systems that can adapt growth to continuous inputs from the environment. Here we characterized needle1 (ndl1), a temperature-sensitive maize mutant that displays severe reproductive defects and strong genetic interactions with known mutants affected in the regulation of the plant hormone auxin. NDL1 encodes a mitochondria-localized ATP-dependent metalloprotease belonging to the FILAMENTATION TEMPERATURE-SENSITIVE H (FTSH) family. Together with the hyperaccumulation of reactive oxygen species (ROS), ndl1 inflorescences show up-regulation of a plethora of stress-response genes. We provide evidence that these conditions alter endogenous auxin levels and disrupt primordia initiation in meristems. These findings connect meristem redox status and auxin in the control of maize growth.

Complexome Profiling Reveals Association of PPR Proteins with Ribosomes in the Mitochondria of Plants

Mitochondrial transcripts are subject to a wealth of processing mechanisms including cis- and trans-splicing events, as well as base modifications (RNA editing). Hundreds of proteins are required for these processes in plant mitochondria, many of which belong to the pentatricopeptide repeat (PPR) protein superfamily. The structure, localization, and function of these proteins is only poorly understood. Here we present evidence that several PPR proteins are bound to mitoribosomes in plants. A novel complexome profiling strategy in combination with chemical crosslinking has been employed to systematically define the protein constituents of the large and the small ribosomal subunits in the mitochondria of plants. We identified more than 80 ribosomal proteins, which include several PPR proteins and other non-conventional ribosomal proteins. These findings reveal a potential coupling of transcriptional and translational events in the mitochondria of plants. Furthermore, the data indicate an extremely high molecular mass of the "small" subunit, even exceeding that of the "large" subunit.

AAA Proteases: Guardians of Mitochondrial Function and Homeostasis

Mitochondria are dynamic, semi-autonomous organelles that execute numerous life-sustaining tasks in eukaryotic cells. Functioning of mitochondria depends on the adequate action of versatile proteinaceous machineries. Fine-tuning of mitochondrial activity in response to cellular needs involves continuous remodeling of organellar proteome. This process not only includes modulation of various biogenetic pathways, but also the removal of superfluous proteins by adenosine triphosphate (ATP)-driven proteolytic machineries. Accordingly, all mitochondrial sub-compartments are under persistent surveillance of ATP-dependent proteases. Particularly important are highly conserved two inner mitochondrial membrane-bound metalloproteases known as m-AAA and i-AAA (ATPases associated with diverse cellular activities), whose mis-functioning may lead to impaired organellar function and consequently to development of severe diseases. Herein, we discuss the current knowledge of yeast, mammalian, and plant AAA proteases and their implications in mitochondrial function and homeostasis maintenance.