TY - JOUR

T1 - Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

AU - Fuchs, Philippe

AU - Rugen, Nils

AU - Carrie, Chris

AU - Elsässer, Marlene

AU - Finkemeier, Iris

AU - Giese, Jonas

AU - Hildebrandt, Tatjana M.

AU - Kühn, Kristina

AU - Maurino, Veronica G.

AU - Ruberti, Cristina

AU - Schallenberg-Rüdinger, Mareike

AU - Steinbeck, Janina

AU - Braun, Hans Peter

AU - Eubel, Holger

AU - Meyer, Etienne H.

AU - Müller-Schüssele, Stefanie J.

AU - Schwarzländer, Markus

N1 - Funding Information: We thank Michael Senkler (Hannover) for excellent bioinformatics support. We further thank Ian Max Møller (Aarhus) and José Gualberto (Strasbourg), as well as both anonymous reviewers for critical reading and very helpful comments that have strengthened this manuscript. This work was enabled through the collaborative DFG research grant PAK918 (EU54/4‐1, IF1655/3‐1, MA2379/14‐1, MU4137/1‐1, SCHA1953/3‐1, SCHW1719/5‐1) as part of the ‘Plant Mitochondria in New Light’ initiative.

PY - 2020/1/17

Y1 - 2020/1/17

N2 - Mitochondria host vital cellular functions, including oxidative phosphorylation and co-factor biosynthesis, which are reflected in their proteome. At the cellular level plant mitochondria are organized into hundreds of discrete functional entities, which undergo dynamic fission and fusion. It is the individual organelle that operates in the living cell, yet biochemical and physiological assessments have exclusively focused on the characteristics of large populations of mitochondria. Here, we explore the protein composition of an individual average plant mitochondrion to deduce principles of functional and structural organisation. We perform proteomics on purified mitochondria from cultured heterotrophic Arabidopsis cells with intensity-based absolute quantification and scale the dataset to the single organelle based on criteria that are justified by experimental evidence and theoretical considerations. We estimate that a total of 1.4 million protein molecules make up a single Arabidopsis mitochondrion on average. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40 000 for Voltage-Dependent Anion Channel 1 to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat proteins that modify mitochondrial transcripts. For our analysis, we consider the physical and chemical constraints of the single organelle and discuss prominent features of mitochondrial architecture, protein biogenesis, oxidative phosphorylation, metabolism, antioxidant defence, genome maintenance, gene expression, and dynamics. While assessing the limitations of our considerations, we exemplify how our understanding of biochemical function and structural organization of plant mitochondria can be connected in order to obtain global and specific insights into how organelles work.

AB - Mitochondria host vital cellular functions, including oxidative phosphorylation and co-factor biosynthesis, which are reflected in their proteome. At the cellular level plant mitochondria are organized into hundreds of discrete functional entities, which undergo dynamic fission and fusion. It is the individual organelle that operates in the living cell, yet biochemical and physiological assessments have exclusively focused on the characteristics of large populations of mitochondria. Here, we explore the protein composition of an individual average plant mitochondrion to deduce principles of functional and structural organisation. We perform proteomics on purified mitochondria from cultured heterotrophic Arabidopsis cells with intensity-based absolute quantification and scale the dataset to the single organelle based on criteria that are justified by experimental evidence and theoretical considerations. We estimate that a total of 1.4 million protein molecules make up a single Arabidopsis mitochondrion on average. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40 000 for Voltage-Dependent Anion Channel 1 to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat proteins that modify mitochondrial transcripts. For our analysis, we consider the physical and chemical constraints of the single organelle and discuss prominent features of mitochondrial architecture, protein biogenesis, oxidative phosphorylation, metabolism, antioxidant defence, genome maintenance, gene expression, and dynamics. While assessing the limitations of our considerations, we exemplify how our understanding of biochemical function and structural organization of plant mitochondria can be connected in order to obtain global and specific insights into how organelles work.

KW - antioxidant defence

KW - Arabidopsis thaliana

KW - cofactor synthesis

KW - intensity-based absolute quantification

KW - mitochondrial fission

KW - mitochondrial genome

KW - oxidative phosphorylation

KW - plant mitochondrion

KW - proteomics

KW - RNA editing

KW - single organelle

KW - TCA cycle

UR - http://www.scopus.com/inward/record.url?scp=85074860583&partnerID=8YFLogxK

U2 - 10.1111/tpj.14534

DO - 10.1111/tpj.14534

M3 - Article

C2 - 31520498

AN - SCOPUS:85074860583

VL - 101

SP - 420

EP - 441

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

IS - 2

ER -