Acetylation of conserved lysines fine‐tunes mitochondrial malate dehydrogenase activity in land plants

Abstract

SUMMARY Plants need to rapidly and flexibly adjust their metabolism to changes of their immediate environment. Since this necessity results from the sessile lifestyle of land plants, key mechanisms for orchestrating central metabolic acclimation are likely to have evolved early. Here, we explore the role of lysine acetylation as a post‐translational modification to directly modulate metabolic function. We generated a lysine acetylome of the moss Physcomitrium patens and identified 638 lysine acetylation sites, mostly found in mitochondrial and plastidial proteins. A comparison with available angiosperm data pinpointed lysine acetylation as a conserved regulatory strategy in land plants. Focusing on mitochondrial central metabolism, we functionally analyzed acetylation of mitochondrial malate dehydrogenase (mMDH), which acts as a hub of plant metabolic flexibility. In P. patens mMDH1, we detected a single acetylated lysine located next to one of the four acetylation sites detected in Arabidopsis thaliana mMDH1. We assessed the kinetic behavior of recombinant A. thaliana and P. patens mMDH1 with site‐specifically incorporated acetyl‐lysines. Acetylation of A. thaliana mMDH1 at K169, K170, and K334 decreases its oxaloacetate reduction activity, while acetylation of P. patens mMDH1 at K172 increases this activity. We found modulation of the malate oxidation activity only in A. thaliana mMDH1, where acetylation of K334 strongly activated it. Comparative homology modeling of MDH proteins revealed that evolutionarily conserved lysines serve as hotspots of acetylation. Our combined analyses indicate lysine acetylation as a common strategy to fine‐tune the activity of central metabolic enzymes with likely impact on plant acclimation capacity.

Advances in proteome-wide analysis of plant lysine acetylation

“…This indicates a possible evolutionarily conserved role of LysAc in regulating the functions and activities of mitochondrial proteins and maintaining the operation of the TCA cycle. Balparda et al. (2021 ) also pointed out that more protein LysAc events occurred in TCA cycle enzymes and pyruvate decarboxylase (PDC) in both P .…”

“…patens , LysAc at K172 of mitochondrial MDH1 (mMDH1) doubles its catalytic rate in the direction of oxaloacetate reduction compared with the unmodified protein and is considered to be a requirement under conditions of high NAD + demand. By contrast, LysAc of K172 has no effects on the enzymatic parameters of the malate oxidation reaction ( Balparda et al., 2021 ). In A .…”

“…In addition, LysAc of K170 can decrease catalytic efficiency in both directions. LysAc of a C-terminal lysine (K334) of mMDH1 increases the catalytic efficiency of malate oxidation and decreases that of oxaloacetate reduction ( Balparda et al., 2021 ). Similarly, LysAc of K99 and K140 in E .…”

“…coli and human, changes in catalytic efficiency are due to increased enzymatic activity caused by LysAc, whereas in A . thaliana , they are due to increased affinity for malate ( Venkat et al., 2017 ; Balparda et al., 2021 ). Therefore, the effects of LysAc on MDH vary across different organisms.…”

“…thaliana ( Finkemeier et al., 2011 ; Wu et al., 2011 ; Koenig et al., 2014 ; Hartl et al., 2017 ; Uhrig et al., 2017 ; Liu et al., 2018 ; Koskela et al., 2018 ; Bienvenut et al., 2020 ), Vitis vinifera ( Melo-Braga et al., 2012 ; Liu et al., 2019 ), Pisum sativum ( Smith-Hammond et al., 2014a ), Glycine max ( Smith-Hammond et al., 2014b ; Li et al., 2021a ), Oryza sativa ( Nallamilli et al., 2014 ; He et al., 2016 ; Xiong et al., 2016 ; Wang et al., 2017 ; Li et al., 2018a , 2018b ; Meng et al., 2018 ; Xue et al., 2018 ; Zhou et al., 2018 ), Fragaria ananassa ( Fang et al., 2015 ), Medicago truncatula ( Marx et al., 2016 ), Triticum aestivum ( Zhang et al., 2016 ; Zhu et al., 2018 ; Guo et al., 2020 ), Brachypodium distachyon ( Zhen et al., 2016 ), Picea asperata ( Xia et al., 2016 ), Camellia sinensis ( Xu et al., 2017 ; Jiang et al., 2018 ), Zea mays ( Walley et al., 2018 ; Yan et al., 2020 ), Kandelia candel ( Pan et al., 2018 ), Gossypium hirsutum ( Singh et al., 2020 ), Hibiscus cannabinus ( Chen et al., 2019 ), Paulownia tomentosa ( Cao et al., 2019 ), Petunia hybrida ( Zhao et al., 2020 ), Nicotiana benthamiana ( Yuan et al., 2021 ), Populus tremula × Populus alba ( Liao et al., 2021 ), Broussonetia papyrifera ( Li et al., 2021b ), and Phoebe zhennan ( Zhao et al., 2021 ) ( Table 1 ). By contrast, the Lys-acetylproteomes of lower plants are poorly studied and have been documented only in Phaeodactylum tricornutum ( Chen et al., 2018 ) and Physcomitrium patens ( Balparda et al., 2021 ). T...…”