Wiring the powerhouse: Systems‐to‐structure approaches for defining mitochondrial protein function

Introduction: The increasing global burden of ischemic heart disease demands a closer examination of the mechanisms by which myocardial reperfusion produces injury to initiate long-term heart failure. Reactive oxygen species (ROS) generated after ischemia reperfusion (IR), in conjunction with the dysfunction of mitochondrial metabolic enzymes, have been identified as a primary mediator of cardiac reperfusion injury. The acetylation of mitochondrial proteins, regulated by opposing actions of NAD + -dependent sirtuin deacetylases and the recently identified mitochondrial acetyltransferase GCN5L1, has emerged as a key point of intersection between nutrient status and mitochondrial protein function in cardiomyoctyes. This makes the association between acetylation and ROS production an important topic of investigation. Intriguingly, global protein acetylation was recently reported to be upregulated in the hearts of human patients with ischemic heart failure. Despite this, it remains unknown whether GCN5L1 acetyltransferase activity plays a role in the regulation of metabolic proteins during IR injury. Hypothesis: Cardiac deletion of the acetyltransferase GCN5L1 reduces the acetylation of mitochondrial proteins during IR, reducing aberrant activity and preventing ROS production. Methods: Isolated work-performing hearts from cardiac-specific inducible GCN5L1 knockout mice were subjected to global ischemia and reperfusion. Contractility (+/- dP/dT) of the left ventricle was measured throughout as an index of post IR functional recovery. Tissue damage was assessed by measuring the release of lactate dehydrogenase and post-reperfusion staining of viable tissue with triphenyltetrazolium chloride. Acetylation levels of mitochondrial proteins were measured during IR using immunoblotting of homogenized hearts, which were also used to evaluate ROS production. Results and Conclusions: Mitochondrial acetylation was decreased in GCN5L1 hearts compared to WT, coinciding with improved post-IR recovery. We therefore conclude that acetylation of mitochondrial proteins by the acetyltransferase GCN5L1 is an important regulatory mechanism of IR-induced, ROS-mediated damage.

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Tissue-specific effects of leptin administration on the abundance of mitochondrial proteins during neonatal development

Journal of Endocrinology ◽

10.1677/joe.1.06251 ◽

2005 ◽

Vol 187 (1) ◽

pp. 81-88 ◽

Cited By ~ 4

Author(s):

M G Gnanalingham ◽

A Mostyn ◽

J Wang ◽

R Webb ◽

D H Keisler ◽

...

Keyword(s):

Protein Function ◽

Uncoupling Protein ◽

Mitochondrial Protein ◽

Anion Channel ◽

Later Life ◽

Mitochondrial Proteins ◽

Control Mechanisms ◽

Voltage Dependent Anion Channel ◽

Tissue Specific ◽

The Brain

Many tissues undergo a rapid transition after birth, accompanied by dramatic changes in mitochondrial protein function. In particular, uncoupling protein (UCP) abundance increases at birth in the lung and adipose tissue, to then gradually decline, an adaptation that is important in enabling normal tissue function. Leptin potentially mediates some of these changes and is known to promote the loss of UCP1 from brown fat but its effects on UCP2 and related mitochondrial proteins (i.e. voltage-dependent anion channel (VDAC) and cytochrome c) in other tissues are unknown. We therefore determined the effects of once-daily jugular venous administration of ovine recombinant leptin on mitochondrial protein abundance as determined by immunoblotting in tissues that do (i.e. the brain and pancreas) and do not (i.e. liver and skeletal muscle) express UCP2. Eight pairs of 1-day-old lambs received either 100 μg leptin or vehicle daily for 6 days, before tissue sampling on day 7. Administration of leptin diminished UCP2 abundance in the pancreas, but not the brain. Leptin administration had no affect on the abundance of VDAC or cytochrome c in any tissue examined. In leptin-administered animals, but not controls, UCP2 abundance in the pancreas was positively correlated with VDAC and cytochrome c content, and UCP2 abundance in the brain with colonic temperature. In conclusion, leptin administration to neonatal lambs causes a tissue-specific loss of UCP2 from the pancreas. These effects may be important in the regulation of neonatal tissue development and potentially for optimising metabolic control mechanisms in later life.

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Systems Biochemistry Approaches to Defining Mitochondrial Protein Function

Cell Metabolism ◽

10.1016/j.cmet.2020.03.011 ◽

2020 ◽

Vol 31 (4) ◽

pp. 669-678

Author(s):

Andrew Y. Sung ◽

Brendan J. Floyd ◽

David J. Pagliarini

Keyword(s):

Protein Function ◽

Mitochondrial Protein

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Absence of Cardiolipin From the Outer Leaflet of a Mitochondrial Inner Membrane Mimic Restricts Opa1-Mediated Fusion

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.769135 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yifan Ge ◽

Sivakumar Boopathy ◽

Tran H. Nguyen ◽

Camila Makhlouta Lugo ◽

Luke H. Chao

Keyword(s):

Membrane Fusion ◽

Lipid Bilayers ◽

Protein Function ◽

Short Form ◽

Mitochondrial Protein ◽

Membrane Properties ◽

Inner Membrane ◽

Outer Leaflet ◽

Mitochondrial Inner Membrane

Cardiolipin is a tetra-acylated di-phosphatidylglycerol lipid enriched in the matrix-facing (inner) leaflet of the mitochondrial inner membrane. Cardiolipin plays an important role in regulating mitochondria function and dynamics. Yet, the mechanisms connecting cardiolipin distribution and mitochondrial protein function remain indirect. In our previous work, we established an in vitro system reconstituting mitochondrial inner membrane fusion mediated by Opa1. We found that the long form of Opa1 (l-Opa1) works together with the proteolytically processed short form (s-Opa1) to mediate fast and efficient membrane fusion. Here, we extend our reconstitution system to generate supported lipid bilayers with asymmetric cardiolipin distribution. Using this system, we find the presence of cardiolipin on the inter-membrane space-facing (outer) leaflet is important for membrane tethering and fusion. We discuss how the presence of cardiolipin in this leaflet may influence protein and membrane properties, and future applications for this approach.

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Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

Biochemical Journal ◽

10.1042/bcj20200084 ◽

2020 ◽

Vol 477 (7) ◽

pp. 1219-1225 ◽

Cited By ~ 4

Author(s):

Nikolai N. Sluchanko

Keyword(s):

Protein Function ◽

Intrinsically Disordered Protein ◽

Structural Basis ◽

Major Protein ◽

Post Translational Modifications ◽

Protein Protein Interaction ◽

Intrinsically Disordered ◽

Biochemical Journal ◽

Multiple Binding ◽

And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

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The challenge of detecting modifications on proteins

Essays in Biochemistry ◽

10.1042/ebc20190055 ◽

2020 ◽

Vol 64 (1) ◽

pp. 135-153 ◽

Cited By ~ 1

Author(s):

Lauren Elizabeth Smith ◽

Adelina Rogowska-Wrzesinska

Keyword(s):

Mass Spectrometry ◽

Protein Function ◽

Chemical Properties ◽

Lysine Acetylation ◽

Mass Determination ◽

Post Translational Modifications ◽

Site Specific ◽

The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

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