Phosphoproteomic Analysis of Spiroplasma eriocheiris and Crosstalk with Acetylome Reveals the Role of Post-Translational Modifications in Metabolism

Background: Post-translational modifications (PTMs) such as phosphorylation are an essential regulatory mechanism of protein function and associated with a range of biological processes beyond genome and transcriptome. Spiroplasma eriocheiris, a wall-less helical bacterium, is one of the smallest known self-replicating bacteria and a novel pathogen of freshwater crustacean. Methods: To study the physiological characteristics and regulatory mechanism of S. eriocheiris, the protein phosphorylation in the bacterium were systematically investigated by iTRAQ analyzed by LC-MS/MS. Data are available via ProteomeXchange with identifier PXD015055. Results: We identified 465 phosphorylation sites in 246 proteins involved in a broad spectrum of fundamental biological process ranging from regulation of metabolic pathways to protein synthesis. Notably, most proteins in glycolysis and all proteins in the arginine deiminase system were phosphorylated. Meanwhile, the cytoskeleton proteins (Fibril, Mrebs and ET-Tu) were all phosphorylated suggest that the phosphorylation also may play a crucial role in cell skeleton formation. We have got a lot of highly conserved proteins and phosphorylation sites by analysis, and those proteins or phosphorylation sites were mainly participated in glucose metabolism and protein synthesis. Crosstalk analysis with protein-protein interaction networks in relation to phosphorylated proteins and acetylated proteins found that the two PTMs are required for playing crucial roles in many physiological processes in S. eriocheiris. By comparing the relative positions of acetylation versus phosphorylation, we found that the two modifications often found close to proximity on the same protein. Conclusions: The results imply that there is previously unreported hidden role of phosphorylation that define the functional state of Spiroplasma.

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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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Peptidomics analysis of potato protein hydrolysates: post-translational modifications and peptide hydrophobicity

10.26434/chemrxiv.5664853 ◽

2017 ◽

Author(s):

Shixiang Yao ◽

Chibuike Udenigwe

Keyword(s):

Protein Function ◽

Structural Changes ◽

Protein Hydrolysates ◽

Proteolytic Processing ◽

Methionine Oxidation ◽

Potato Protein ◽

Post Translational Modifications ◽

Peptide Hydrophobicity ◽

Proteins And Peptides

Post-translational modifications (PTMs) often <a></a><a>occur in proteins</a> and play a regulatory role in protein function. However, the role of PTMs in food-derived peptides remains largely unknown. The shotgun peptidomics strategy was employed to identify PTMs in peptides from potato protein hydrolysates. Various hydrophobicity-inducing PTMs were found to be located in different potato peptides, <i>e.g</i>. acetylation of lysine, N-terminal of proteins and peptides, C-terminal amidation, asparagine/glutamine deamidaiton, methylation and trimethylation, methionine oxidation, and N-terminal pyro-glutamate formation. Some of the PTMs are likely formed by chemical reactions that occur during isolation and proteolytic processing of potato proteins. The PTMs enhance peptide hydrophobicity, which can improve bioactivity, decrease solubility and increase the bitterness of peptides. This is the first report that food-derived peptides are widely modified by various PTMs associated with hydrophobicity-inducing structural changes. This finding will enhance understanding of the behaviour of bioactive peptides in biological matrices.

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A structural view of PA2G4 isoforms with opposing functions in cancer

Journal of Biological Chemistry ◽

10.1074/jbc.rev120.014293 ◽

2020 ◽

Vol 295 (47) ◽

pp. 16100-16112

Author(s):

Brendan W. Stevenson ◽

Michael A. Gorman ◽

Jessica Koach ◽

Belamy B. Cheung ◽

Glenn M. Marshall ◽

...

Keyword(s):

Structural Features ◽

Cellular Growth ◽

Structure Based Drug Design ◽

Post Translational Modifications ◽

Protein Protein Interaction ◽

Interaction Sites ◽

Structure Relationship ◽

Relationship Of ◽

Functional Components

The role of proliferation-associated protein 2G4 (PA2G4), alternatively known as ErbB3-binding protein 1 (EBP1), in cancer has become apparent over the past 20 years. PA2G4 expression levels are correlated with prognosis in a range of human cancers, including neuroblastoma, cervical, brain, breast, prostate, pancreatic, hepatocellular, and other tumors. There are two PA2G4 isoforms, PA2G4-p42 and PA2G4-p48, and although both isoforms of PA2G4 regulate cellular growth and differentiation, these isoforms often have opposing roles depending on the context. Therefore, PA2G4 can function either as a contextual tumor suppressor or as an oncogene, depending on the tissue being studied. However, it is unclear how distinct structural features of the two PA2G4 isoforms translate into different functional outcomes. In this review, we examine published structures to identify important structural and functional components of PA2G4 and consider how they may explain its crucial role in the malignant phenotype. We will highlight the lysine-rich regions, protein-protein interaction sites, and post-translational modifications of the two PA2G4 isoforms and relate these to the functional cellular role of PA2G4. These data will enable a better understanding of the function and structure relationship of the two PA2G4 isoforms and highlight the care that will need to be undertaken for those who wish to conduct isoform-specific structure-based drug design campaigns.

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Determination of the Role of Microcystis aeruginosa in Toxin Generation Based on Phosphoproteomic Profiles

Toxins ◽

10.3390/toxins10070304 ◽

2018 ◽

Vol 10 (7) ◽

pp. 304 ◽

Cited By ~ 9

Author(s):

Jiangqi Qu ◽

Liping Shen ◽

Meng Zhao ◽

Wentong Li ◽

Chengxia Jia ◽

...

Keyword(s):

Microcystis Aeruginosa ◽

Physiological Activity ◽

Redox Homeostasis ◽

Common Species ◽

Cyanobacterial Blooms ◽

Phosphorylation Sites ◽

Protein Protein Interaction ◽

Toxin Protein

Microcystis aeruginosa is the most common species responsible for toxic cyanobacterial blooms and is considered a significant contributor to the production of cyanotoxins, particularly the potent liver toxins called microcystins. Numerous studies investigating Microcystis spp. blooms have revealed their deleterious effects in freshwater environments. However, the available knowledge regarding the global phosphoproteomics of M. aeruginosa and their regulatory roles in toxin generation is limited. In this study, we conducted comparative phosphoproteomic profiling of non-toxic and toxin-producing strains of M. aeruginosa. We identified 59 phosphorylation sites in 37 proteins in a non-toxic strain and 26 phosphorylation sites in 18 proteins in a toxin-producing strain. The analysis of protein phosphorylation abundances and functions in redox homeostasis, energy metabolism, light absorption and photosynthesis showed marked differences between the non-toxic and toxin-producing strains of M. aeruginosa, indicating that these processes are strongly related to toxin generation. Moreover, the protein-protein interaction results indicated that BJ0JVG8 can directly interact with the PemK-like toxin protein B0JQN8. Thus, the phosphorylation of B0JQN8 appears to be associated with the regulatory roles of toxins in physiological activity.

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Turning the Knobs: The Impact of Post-translational Modifications on Carbon Metabolism

Frontiers in Plant Science ◽

10.3389/fpls.2021.781508 ◽

2022 ◽

Vol 12 ◽

Author(s):

Cleverson C. Matiolli ◽

Rafael Cavém Soares ◽

Hugo L. S. Alves ◽

Isabel A. Abreu

Keyword(s):

Carbon Metabolism ◽

Biotic And Abiotic Stresses ◽

Holistic View ◽

Post Translational Modifications ◽

Adverse Conditions ◽

Protein Protein Interaction ◽

Physiological Processes ◽

Protein Properties ◽

The Impact

Plants rely on the carbon fixed by photosynthesis into sugars to grow and reproduce. However, plants often face non-ideal conditions caused by biotic and abiotic stresses. These constraints impose challenges to managing sugars, the most valuable plant asset. Hence, the precise management of sugars is crucial to avoid starvation under adverse conditions and sustain growth. This review explores the role of post-translational modifications (PTMs) in the modulation of carbon metabolism. PTMs consist of chemical modifications of proteins that change protein properties, including protein-protein interaction preferences, enzymatic activity, stability, and subcellular localization. We provide a holistic view of how PTMs tune resource distribution among different physiological processes to optimize plant fitness.

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PROTEIN DYNAMICS IN PHOSPHORYLATION-MEDIATED ALLOSTERY PROBED BY AMIDE EXCHANGE MASS SPECTROMETRY

COSMOS ◽

10.1142/s0219607713300014 ◽

2013 ◽

Vol 09 (01) ◽

pp. 19-27

Author(s):

MADHUBRATA GHOSH ◽

GANESH S. ANAND

Keyword(s):

Mass Spectrometry ◽

Protein Dynamics ◽

Protein Function ◽

Post Translational Modifications ◽

Exchange Mass Spectrometry ◽

Amide Exchange ◽

Hydrogen Deuterium ◽

Deuterium Exchange Mass Spectrometry ◽

And Function

A major goal of molecular biology is to correlate molecular structure with function. Since most enzymes and biological catalysts are proteins, the focus for correlating 'form' with 'function' has been entirely on protein macromolecular structure. It is obvious that any understanding of protein function must come through an understanding protein dynamics. Furthermore, all of the regulatory reactions are through changes in dynamics brought about by post-translational modifications, the most important of which is phosphorylation. This review highlights the important role of covalent phosphorylation and noncovalent phosphates in regulating allosteric effects and function through a study of protein dynamics. Mass spectrometry is a relatively new and increasingly important tool for describing protein dynamics. All examples described in this review have been studied by amide hydrogen/deuterium exchange mass spectrometry.

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Unstructured Conformations Are a Substrate Requirement for the Sir2 Family of NAD-dependent Protein Deacetylases

Journal of Biological Chemistry ◽

10.1074/jbc.m508247200 ◽

2005 ◽

Vol 280 (43) ◽

pp. 36073-36078 ◽

Cited By ~ 36

Author(s):

Ahlia N. Khan ◽

Peter N. Lewis

Keyword(s):

Protein Function ◽

Cellular Localization ◽

Substrate Recognition ◽

Histone Deacetylation ◽

Sequence Specificity ◽

Post Translational Modifications ◽

Protein Substrates ◽

Dependent Protein

The regulation of protein function is often achieved through post-translational modifications including phosphorylation, methylation, ubiquitination, and acetylation. The role of acetylation has been most extensively studied in the context of histones, but it is becoming increasingly evident that this modification now includes other proteins. The Sir2 family of NAD-dependent deacetylases was initially recognized as mediating gene silencing through histone deacetylation, but several family members display non-nuclear sub-cellular localization and deacetylate non-histone protein substrates. Although many structural and enzymatic studies of Sir2 proteins have been reported, how substrate recognition is achieved by this family of enzymes is unknown. Here we use in vitro deacetylase assays and a variety of potential substrates to examine the substrate specificity of yeast homologue Hst2. We show that Hst2 is specific for acetyl-lysine within proteins; it does not deacetylate small polycations such as acetyl-spermine or acetylated amino ter-mini of proteins. Furthermore we have found that Hst2 displays conformational rather than sequence specificity, preferentially deacetylating acetyl-lysine within unstructured regions of proteins. Our results suggest that this conformational requirement may be a general feature for substrate recognition in the Sir2 family.

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Peptidomics analysis of potato protein hydrolysates: post-translational modifications and peptide hydrophobicity

10.26434/chemrxiv.5664853.v1 ◽

2017 ◽

Author(s):

Shixiang Yao ◽

Chibuike Udenigwe

Keyword(s):

Protein Function ◽

Structural Changes ◽

Protein Hydrolysates ◽

Proteolytic Processing ◽

Methionine Oxidation ◽

Potato Protein ◽

Post Translational Modifications ◽

Peptide Hydrophobicity ◽

Proteins And Peptides

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Quantitative Proteomics and Phosphoproteomics Supports a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis

10.1101/2020.02.14.950030 ◽

2020 ◽

Author(s):

Margaret E. Wilson ◽

Shin-Cheng Tzeng ◽

Megan M. Augustin ◽

Matthew Meyer ◽

Xiaoyue Jiang ◽

...

Keyword(s):

Stress Responses ◽

Protein Function ◽

Response Factors ◽

Post Translational Modifications ◽

Dna Damaging Agents ◽

Metabolism Enzymes ◽

Damage Response ◽

Increased Sensitivity ◽

Work Supports

Summary/AbstractProtein phosphorylation is one of the most prevalent post-translational modifications found in eukaryotic systems. It serves as a key molecular mechanism that regulates protein function in response to environmental stimuli. The Mut9-Like Kinases (MLKs) are a plant-specific family of Ser/Thr kinases linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. Proteins involved in light, circadian, and hormone signaling, as well as several chromatin-modifying enzymes and DNA damage response factors, were found to have altered phosphorylation profiles in the absence of MLK family kinases. In addition to altered phosphorylation levels, mlk mutant seedlings have an increase in glucosinolate metabolism enzymes. Subsequently, we show that a functional consequence of the changes to the proteome and phosphoproteome in mlk mutant plants is elevated glucosinolate accumulation, and increased sensitivity to DNA damaging agents. Combined with previous reports, this work supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs serve as key regulators linking environmental inputs to developmental outputs.

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POPDC proteins and cardiac function

Biochemical Society Transactions ◽

10.1042/bst20190249 ◽

2019 ◽

Vol 47 (5) ◽

pp. 1393-1404 ◽

Cited By ~ 4

Author(s):

Thomas Brand

Keyword(s):

Potential Role ◽

Striated Muscle ◽

Short Review ◽

Effector Proteins ◽

Muscle Disease ◽

Disease Genes ◽

Protein Protein Interaction ◽

Interaction Partners ◽

And Function

Abstract The Popeye domain-containing gene family encodes a novel class of cAMP effector proteins in striated muscle tissue. In this short review, we first introduce the protein family and discuss their structure and function with an emphasis on their role in cyclic AMP signalling. Another focus of this review is the recently discovered role of POPDC genes as striated muscle disease genes, which have been associated with cardiac arrhythmia and muscular dystrophy. The pathological phenotypes observed in patients will be compared with phenotypes present in null and knockin mutations in zebrafish and mouse. A number of protein–protein interaction partners have been discovered and the potential role of POPDC proteins to control the subcellular localization and function of these interacting proteins will be discussed. Finally, we outline several areas, where research is urgently needed.

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