Programmed cell death is an event displayed by many different organisms along the evolutionary scale. In plants, programmed cell death is necessary for development and the hypersensitive response to stress or pathogenic infection. A common feature in programmed cell death across organisms is the translocation of cytochrome
c from mitochondria to the cytosol. To better understand the role of cytochrome
c in the onset of programmed cell death in plants, a proteomic approach was developed based on affinity chromatography and using
Arabidopsis thaliana cytochrome
c as bait. Using this approach, ten putative new cytochrome
c partners were identified. Of these putative partners and as indicated by bimolecular fluorescence complementation, nine of them bind the heme protein in plant protoplasts and human cells as a heterologous system. The
in vitro interaction between cytochrome
c and such soluble cytochrome
c-targets was further corroborated using surface plasmon resonance. Taken together, the results obtained in the study indicate that
Arabidopsis thaliana cytochrome
c interacts with several distinct proteins involved in protein folding, translational regulation, cell death, oxidative stress, DNA damage, energetic metabolism, and mRNA metabolism. Interestingly, some of these novel
Arabidopsis thaliana cytochrome
c-targets are closely related to those for
Homo sapiens cytochrome
c (Martínez-Fábregas
et al., unpublished). These results indicate that the evolutionarily well-conserved cytosolic cytochrome
c, appearing in organisms from plants to mammals, interacts with a wide range of targets on programmed cell death. The data have been deposited to the ProteomeXchange with identifier PXD000280.Programmed cell death (PCD)
1 is a fundamental event for the development of multicellular organisms and the homeostasis of their tissues. It is an evolutionarily conserved mechanism present in organisms ranging from yeast to mammals (
1–
3).In mammals, cytochrome
c (C
c) and dATP bind to apoptosis protease-activating factor-1 (Apaf-1) in the cytoplasm, a process leading to the formation of the Apaf-1/caspase-9 complex known as apoptosome. This apoptosome subsequently activates caspases-3 and -7 (
4,
5). In other organisms, such as
Caenorhabditis elegans or
Drosophila melanogaster, however, C
c is not essential for the assembly and activation of the apoptosome (
6) despite the presence of proteins homologous to Apaf-1—cell death abnormality-4 (CED-4) in
C. elegans and
Drosophila Apaf-1-related killer (Dark) in
D. melanogaster—which have been found to be essential for caspase cascade activation. Furthermore, other organisms such as
Arabidopsis thaliana lack Apaf-1 (
7). In fact, only highly distant caspase homologues (metacaspases) (
8,
9), serine proteases (saspases) (
10), phytaspases (
11) and VEIDases (
12–
14) with caspase-like activity have been detected in plants; however, their targets remain veiled and whether they are activated by C
c remains unclear.Intriguingly, the release of C
c from mitochondria into the cytoplasm during the onset of PCD is an evolutionarily conserved event found in organisms ranging from yeast (
15) and plants (
16) to flies (
17), and mammals (
18). However, understanding of the roles of this phenomenon in different species can be said to be uneven at best. In fact, the release of C
c from mitochondria has thus far been considered a random event in all organisms, save mammals. Thus, the participation of C
c in the onset and progression of PCD needs to be further elucidated.Even in the case of mammals, the role(s) of C
c in the cytoplasm during PCD remain(s) controversial. Recently, new putative functions of C
c, going beyond the already-established apoptosome assembly process, have been proposed in the nucleus (
19,
20) and the endoplasmic reticulum (
21–
23). Neither these newly proposed functions nor other arising functions, such as oxidative stress (
24), are as yet fully understood. This current state of affairs demands deeper exploration of the additional roles played by C
c in nonmammalian species.In this study, putative novel C
c-partners involved in plant PCD were identified. For this identification, a proteomic approach was employed based on affinity chromatography and using C
c as bait. The C
c-interacting proteins were identified using nano-liquid chromatography tandem mass spectrometry (NanoLC-MS/MS). These C
c-partners were then further confirmed
in vivo through bimolecular fluorescence complementation (BiFC) in
A. thaliana protoplasts and human HEK293T cells, as a heterologous system. Finally, the C
c-GLY2, C
c-NRP1 and C
c-TCL interactions were corroborated
in vitro using surface plasmon resonance (SPR).These results indicate that C
c is able to interact with targets in the plant cell cytoplasm during PCD. Moreover, they provide new ways of understanding why C
c release is an evolutionarily well-conserved event, and allow us to propose C
c as a signaling messenger, which somehow controls different essential events during PCD.
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