On the Detection and Functional Significance of the Protein-Protein Interactions of Mitochondrial Transport Proteins

MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks

Mitochondrial carriers (MCs) are essential proteins that transport metabolites across mitochondrial membranes and play a critical role in cellular metabolism. ADP/ATP (adenosine diphosphate/adenosine triphosphate) is one of the most important carriers as it contributes to cellular energy production and is susceptible to the powerful toxin bongkrekic acid. This toxin has claimed several lives; for example, a recent foodborne outbreak in Taipei, Taiwan, has caused four deaths and sickened 30 people. The issue of bongkrekic acid poisoning has been a long-standing problem in Indonesia, with reports as early as 1895 detailing numerous deaths from contaminated coconut fermented cakes. In bioinformatics, significant advances have been made in understanding biological processes through computational methods; however, no established computational method has been developed for identifying mitochondrial carriers. We propose a computational bioinformatics approach for predicting MCs from a broader class of secondary active transporters with a focus on the ADP/ATP carrier and its interaction with bongkrekic acid. The proposed model combines protein language models (PLMs) with multiwindow scanning convolutional neural networks (mCNNs). While PLM embeddings capture contextual information within proteins, mCNN scans multiple windows to identify potential binding sites and extract local features. Our results show 96.66% sensitivity, 95.76% specificity, 96.12% accuracy, 91.83% Matthews correlation coefficient (MCC), 94.63% F1-Score, and 98.55% area under the curve (AUC). The results demonstrate the effectiveness of the proposed approach in predicting MCs and elucidating their functions, particularly in the context of bongkrekic acid toxicity. This study presents a valuable approach for identifying novel mitochondrial complexes, characterizing their functional roles, and understanding mitochondrial toxicology mechanisms. Our findings, that utilize computational methods to improve our understanding of cellular processes and drug-target interactions, contribute to the development of therapeutic strategies for mitochondrial disorders, reducing the devastating effects of bongkrekic acid poisoning.

The conditional mitochondrial protein complexome in the Arabidopsis thaliana root and shoot

Protein complexes are important for almost all biological processes. Hence, to fully understand how cells work, it is also necessary to characterize protein complexes and their dynamics in response to various cellular cues. Moreover, the dynamics of protein interaction play crucial roles in regulating the (dis)association of protein complexes and, in turn, regulating biological processes such as metabolism. Here, mitochondrial protein complexes were investigated by blue native PAGE and size-exclusion chromatography under conditions of oxidative stress in order to monitor their dynamic (dis)associations. Rearrangements of enzyme interactions and changes in protein complex abundance were observed in response to oxidative stress induced by menadione treatment. These included changes in enzymatic protein complexes involving γ-amino butyric acid transaminase (GABA-T), Δ-ornithine aminotransferase (Δ-OAT), or proline dehydrogenase 1 (POX1) that are expected to affect proline metabolism. Menadione treatment also affected interactions between several enzymes of the tricarboxylic acid (TCA) cycle and the abundance of complexes of the oxidative phosphorylation pathway. In addition, we compared the mitochondrial complexes of roots and shoots. Considerable differences between the two tissues were observed in the mitochondrial import/export apparatus, the formation of super-complexes in the oxidative phosphorylation pathway, and specific interactions between enzymes of the TCA cycle that we postulate may be related to the metabolic/energetic requirements of roots and shoots.

The Role of TCA Cycle Enzymes in Plants

As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their function in vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.

The formation and function of plant metabolons

Metabolons are temporary structural-functional complexes of sequential enzymes of a metabolic pathway that are distinct from stable multi-enzyme complexes. Here we provide a brief history of the study of enzyme-enzyme assemblies with a particular focus on those that mediate substrate channeling in plants. Large numbers of protein complexes have been proposed for both primary and secondary metabolic pathways in plants. However, to date only four substrate channels have been demonstrated. We provide an overview of current knowledge concerning these four metabolons and explain the methodologies that are currently being applied to unravel their functions. Although the assembly of metabolons has been documented to arise through diverse mechanisms, the physical interaction within the characterized plant metabolons all appear to be driven by interaction with structural elements of the cell. We therefore pose the question as to what methodologies could be brought to bear to enhance our knowledge of plant metabolons that assemble via different mechanisms? In addressing this question, we review recent findings in non-plant systems concerning liquid droplet phase separation and enzyme chemotaxis and propose strategies via which such metabolons could be identified in plants. We additionally discuss the possibilities that could be opened up by novel approaches based on: (i) subcellular-level mass spectral imaging, (ii) proteomics, and (iii) emergent methods in structural and computational biology.

Metabolic evidence for distinct pyruvate pools inside plant mitochondria

The majority of the pyruvate inside plant mitochondria is either transported into the matrix from the cytosol via the mitochondria pyruvate carrier (MPC) or synthesized in the matrix by alanine aminotransferase (AlaAT) or NAD-malic enzyme (NAD-ME). Pyruvate from these origins could mix into a single pool in the matrix and contribute indistinguishably to respiration via the pyruvate dehydrogenase complex (PDC), or these molecules could maintain a degree of independence in metabolic regulation. Here we demonstrate that feeding isolated mitochondria with uniformly labelled ¹³C-pyruvate and unlabelled malate enables the assessment of pyruvate contribution from different sources to intermediate production in the tricarboxylic acid cycle. Imported pyruvate was the preferred source for citrate production even when the synthesis of NAD-ME-derived pyruvate was optimized. Genetic or pharmacological elimination of MPC activity removed this preference and allowed an equivalent amount of citrate to be generated from the pyruvate produced by NAD-ME. Increasing the mitochondrial pyruvate pool size by exogenous addition affected only metabolites from pyruvate transported by MPC, whereas depleting the pyruvate pool size by transamination to alanine affected only metabolic products derived from NAD-ME. PDC was more membrane-associated than AlaAT and NAD-ME, suggesting that the physical organization of metabolic machinery may influence metabolic rates. Together, these data reveal that the respiratory substrate supply in plants involves distinct pyruvate pools inside the matrix that can be flexibly mixed on the basis of the rate of pyruvate transport from the cytosol. These pools are independently regulated and contribute differentially to organic acid export from plant mitochondria.

Structures of Tetrahymena's respiratory chain reveal the diversity of eukaryotic core metabolism

Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate Tetrahymena thermophila (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt complex I (Tt-CI) and Tt-CIII2 (Tt-SC I+III2) and a structure of Tt-CIV2. Tt-SC I+III2 (~2.3 megadaltons) is a curved assembly with structural and functional symmetry breaking. Tt-CIV2 is a ~2.7-megadalton dimer with more than 50 subunits per protomer, including mitochondrial carriers and a TIM83-TIM133-like domain. Our structural and functional study of the T. thermophila respiratory chain reveals divergence in key components of eukaryotic respiration, thereby expanding our understanding of core metabolism.

Biology of PEST‐Containing Nuclear Protein: A Potential Molecular Target for Cancer Research

PEST-containing nuclear protein (PCNP), a novel nuclear protein, is involved in vital cellular processes like cell proliferation and mediates tumorigenesis. PCNP is a short-living, small nuclear protein of only 178 amino acids with two remarkable PEST sequences that are rich in proline (P), glutamic acid (E), serine (S), and threonine (T). The current understanding of PCNP reveals that PCNP has the ability to interact with cell cycle regulatory proteins; tumor suppressors (p53 and pRB), and promoters (cyclin E and cyclin D) to determine the fate of tissues to facilitate the process of either apoptosis or cell proliferation. In many preclinical studies, it has been evaluated that PCNP expression has associations with the development and progression of various cancers like neuroblastoma, lung adenocarcinoma, and ovarian cancer. Based on these depicted novel roles of PCNP in cell cycleregulation and of PCNP in tumorigenesis, it is logical to consider PCNP as a potential molecular target for cancer research. The aim of the current communication is to present an update on PCNP research and discussion on the potential role of PCNP in cancer development with challenges and opportunities perspectives. Considering the available evidence as a baseline for our statement, we anticipate that in the future, new research insights will strengthen the aim to develop PCNP-based diagnostic and therapeutic approaches that will move the PCNP from the laboratory to the cancer clinic.

From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants

The study of protein–protein interactions (PPIs) is fundamental in understanding the unique role of proteins within cells and their contribution to complex biological systems. While the toolkit to study PPIs has grown immensely in mammalian and unicellular eukaryote systems over recent years, application of these techniques in plants remains under-utilized. Affinity purification coupled to mass spectrometry (AP-MS) and proximity labeling coupled to mass spectrometry (PL-MS) are two powerful techniques that have significantly enhanced our understanding of PPIs. Relying on the specific binding properties of a protein to an immobilized ligand, AP is a fast, sensitive and targeted approach used to detect interactions between bait (protein of interest) and prey (interacting partners) under near-physiological conditions. Similarly, PL, which utilizes the close proximity of proteins to identify potential interacting partners, has the ability to detect transient or hydrophobic interactions under native conditions. Combined, these techniques have the potential to reveal an unprecedented spatial and temporal protein interaction network that better understands biological processes relevant to many fields of interest. In this review, we summarize the advantages and disadvantages of two increasingly common PPI determination techniques: AP-MS and PL-MS and discuss their important application to plant systems.