The new world of inorganic polyphosphates

2016 ◽  
Vol 44 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Cristina Azevedo ◽  
Adolfo Saiardi
Keyword(s):  
Protein Modification ◽  
Biochemical Characterization ◽  
Covalent Attachment ◽  
Detection Methods ◽  
Inorganic Polyphosphate ◽  
Post Translational Modifications ◽  
Topoisomerase 1 ◽  
Lysine Residues ◽  
Acidic Conditions

Post-translational modifications (PTMs) add regulatory features to proteins that help establish the complex functional networks that make up higher organisms. Advances in analytical detection methods have led to the identification of more than 200 types of PTMs. However, some modifications are unstable under the present detection methods, anticipating the existence of further modifications and a much more complex map of PTMs. An example is the recently discovered protein modification polyphosphorylation. Polyphosphorylation is mediated by inorganic polyphosphate (polyP) and represents the covalent attachment of this linear polymer of orthophosphate to lysine residues in target proteins. This modification has eluded MS analysis as both polyP itself and the phosphoramidate bonds created upon its reaction with lysine residues are highly unstable in acidic conditions. Polyphosphorylation detection was only possible through extensive biochemical characterization. Two targets have been identified: nuclear signal recognition 1 (Nsr1) and its interacting partner, topoisomerase 1 (Top1). Polyphosphorylation occurs within a conserved N-terminal polyacidic serine (S) and lysine (K) rich (PASK) cluster. It negatively regulates Nsr1–Top1 interaction and impairs Top1 enzymatic activity, namely relaxing supercoiled DNA. Modulation of cellular levels of polyP regulates Top1 activity by modifying its polyphosphorylation status. Here we discuss the significance of the recently identified new role of inorganic polyP.

scholarly journals Development of a yeast model to study the contribution of vacuolar polyphosphate metabolism to lysine polyphosphorylation

2019 ◽  
Vol 295 (6) ◽  
pp. 1439-1451 ◽  
Author(s):  
Cristina Azevedo ◽  
Yann Desfougères ◽  
Yannasittha Jiramongkol ◽  
Hamish Partington ◽  
Sasanan Trakansuebkul ◽  
...  
Keyword(s):  
Cell Lysis ◽  
Covalent Attachment ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Target Domain ◽  
Inorganic Polyphosphate ◽  
Topoisomerase 1 ◽  
Lysine Residues ◽  
Polyphosphate Metabolism ◽  
Nuclear Targets

A recently-discovered protein post-translational modification, lysine polyphosphorylation (K-PPn), consists of the covalent attachment of inorganic polyphosphate (polyP) to lysine residues. The nonenzymatic nature of K-PPn means that the degree of this modification depends on both polyP abundance and the amino acids surrounding the modified lysine. K-PPn was originally discovered in budding yeast (Saccharomyces cerevisiae), in which polyP anabolism and catabolism are well-characterized. However, yeast vacuoles accumulate large amounts of polyP, and upon cell lysis, the release of the vacuolar polyP could nonphysiologically cause K-PPn of nuclear and cytosolic targets. Moreover, yeast vacuoles possess two very active endopolyphosphatases, Ppn1 and Ppn2, that could have opposing effects on the extent of K-PPn. Here, we characterized the contribution of vacuolar polyP metabolism to K-PPn of two yeast proteins, Top1 (DNA topoisomerase 1) and Nsr1 (nuclear signal recognition 1). We discovered that whereas Top1-targeting K-PPn is only marginally affected by vacuolar polyP metabolism, Nsr1-targeting K-PPn is highly sensitive to the release of polyP and of endopolyphosphatases from the vacuole. Therefore, to better study K-PPn of cytosolic and nuclear targets, we constructed a yeast strain devoid of vacuolar polyP by targeting the exopolyphosphatase Ppx1 to the vacuole and concomitantly depleting the two endopolyphosphatases (ppn1Δppn2Δ, vt-Ppx1). This strain enabled us to study K-PPn of cytosolic and nuclear targets without the interfering effects of cell lysis on vacuole polyP and of endopolyphosphatases. Furthermore, we also define the fundamental nature of the acidic amino acid residues to the K-PPn target domain.

scholarly journals Role of UBC9 in the Regulation of the Adipogenic Program in 3T3-L1 Adipocytes

Endocrinology ◽  
2010 ◽  
Vol 151 (11) ◽  
pp. 5255-5266 ◽  
Author(s):  
Angelo Cignarelli ◽  
Mariangela Melchiorre ◽  
Alessandro Peschechera ◽  
Antonella Conserva ◽  
Lucia Adelaide Renna ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Small Interfering Rna ◽  
Protein Modification ◽  
Covalent Attachment ◽  
Mrna Levels ◽  
Protein Levels ◽  
Mrna Induction ◽  
Induction Of Differentiation ◽  
Interfering Rna

The small ubiquitin-like modifier-conjugating enzyme UBC9, involved in protein modification through covalent attachment of small ubiquitin-like modifier and other less defined mechanisms, has emerged as a key regulator of cell proliferation and differentiation. To explore the role of UBC9 in adipocyte differentiation, the UBC9 protein levels were examined in differentiating 3T3-L1 cells. UBC9 mRNA and protein levels were increased 2.5-fold at d 2 and then gradually declined to basal levels at d 8 of differentiation. In addition, UBC9 was expressed predominantly in the nucleus of preadipocytes but shifted to cytoplasmic compartments after d 4, after induction of differentiation. UBC9 knockdown was then achieved in differentiating 3T3-L1 preadipocytes using a specific small interfering RNA. Oil-Red-O staining demonstrated accumulation of large triglyceride droplets in approximately 90% of control cells, whereas lipid droplets were smaller and evident in only 30% of cells treated with the UBC9-specific small interfering RNA. CCAAT/enhancer-binding protein (C/EBP)-δ, peroxisome proliferator-activated receptor-γ, and C/EBPα mRNA levels were increased severalfold 2–6 d after induction of differentiation in control cells, whereas the expression of these transcription factors was significantly lower in the presence of UBC9 gene silencing. Adenovirus-mediated overexpression of a catalytically inactive mutant UBC9 protein in 3T3-L1 cells resulted in no changes in expression of adipogenic transcription factors and conversion to mature adipocytes as compared with control. In conclusion, UBC9 appears to play an important role in adipogenesis. The temporal profile of UBC9 induction and its ability to affect C/EBPδ mRNA induction support a role for this protein during early adipogenesis.

scholarly journals Glucose autoxidation and protein modification. The potential role of ‘autoxidative glycosylation’ in diabetes

1987 ◽  
Vol 245 (1) ◽  
pp. 243-250 ◽  
Author(s):  
S P Wolff ◽  
R T Dean
Keyword(s):  
Protein Modification ◽  
Potential Role ◽  
Chelating Agent ◽  
Tryptophan Fluorescence ◽  
Protein Glycosylation ◽  
Covalent Attachment ◽  
Amino Groups ◽  
Tryptophan Fluorescence Quenching

Monosaccharide autoxidation (a transition metal-catalysed process that generates H2O2 and ketoaldehydes) appears to contribute to protein modification by glucose in vitro. The metal-chelating agent diethylenetriaminepenta-acetic acid (DETAPAC), which inhibits glucose autoxidation, also reduces the covalent attachment of glucose to bovine serum albumin. A maximal 45% inhibition of covalent attachment was observed, but this varied with glucose and DETAPAC concentrations in a complex fashion, suggesting at least two modes of attachment. The extent of inhibition of the metal-catalysed pathway correlated with the extent of inhibition of glycosylation-associated chromo- and fluorophore development. DETAPAC also inhibited tryptophan fluorescence quenching associated with glycosylation. Conversely, ketoaldehydes analogous to those produced by glucose autoxidation, but generated by 60Co irradiation, bound avidly to albumin and accelerated browning reactions. It is therefore suggested that a component of protein glycosylation is dependent upon glucose autoxidation and subsequent covalent attachment of ketoaldehydes. The process of glucose autoxidation, or ketoaldehydes derived therefrom, appear to be important in chromophoric and fluorophoric alterations. It is noted, consistent with these observations, that the chemical evidence for the currently accepted ‘Amadori’ product derived from the reaction of glucose with protein amino groups is consistent also with the structure expected for the attachment of a glucose-derived ketoaldehyde to protein. The concept of ‘autoxidative glycosylation’ is briefly discussed in relation to oxidative stress in diabetes mellitus.

SUMO: getting it on

2007 ◽  
Vol 35 (6) ◽  
pp. 1409-1413 ◽  
Author(s):  
J. Anckar ◽  
L. Sistonen
Keyword(s):  
Biological Processes ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Sumo Conjugation ◽  
Lysine Residues ◽  
Ubiquitin Conjugating Enzyme ◽  
Specificity Determinants ◽  
Conjugating Enzyme

Post-translational modification of cellular proteins by the SUMO (small ubiquitin-related modifier) is involved in numerous modes of regulation in widely different biological processes. In contrast with ubiquitination, SUMO conjugation is highly specific in terms of target lysine residues, but many aspects of substrate and lysine selection by the SUMO conjugating machinery are still poorly understood. SUMOylation events usually occur on the ΨKXE SUMO consensus motifs, which mediate binding to Ubc9 (ubiquitin-conjugating enzyme 9), the SUMO E2 conjugating enzyme. Although most, if not all, SUMO conjugations are catalysed by Ubc9, far from all ΨKXE tetrapeptides are modified, demonstrating a need for additional specificity determinants in SUMOylation. Recent results intimately link regulation of SUMOylation to other post-translational modifications, including phosphorylation and acetylation and reveal that certain lysine residues are marked for SUMOylation by negatively charged amino acid residues or phosphorylation events immediately downstream of the consensus site. In the present review, we explore the intriguing role of extended motifs in the regulation of SUMO conjugation.

Post-translational modifications of lysine in DNA-damage repair

2012 ◽  
Vol 52 ◽  
pp. 93-111 ◽  
Author(s):  
Snehajyoti Chatterjee ◽  
Parijat Senapati ◽  
Tapas K. Kundu
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Post Translational Modifications ◽  
Dna Repair Mechanisms ◽  
The Past ◽  
Damage Repair ◽  
Lysine Residues ◽  
Repair Mechanisms ◽  
Genotoxic Insult

DNA damage in cells is often the result of constant genotoxic insult. Nevertheless, efficient DNA repair pathways are able to maintain genomic integrity. Over the past decade it has been revealed that it is not only kinase signalling pathways which play a central role in this process, but also the different post-translational modifications at lysine residues of histone (chromatin) and non-histone proteins. These lysine modifications include acetylation, methylation, ubiquitination and SUMOylation. Genomic instability is often the major cause of different diseases, especially cancer, where lysine modifications are altered and thereby have an impact on the various DNA repair mechanisms. This chapter will discuss the recent advances in our understanding of the role of different lysine modifications in DNA repair and its physiological consequences.

scholarly journals The PPIP5K Family Member Asp1 Controls Inorganic Polyphosphate Metabolism in S. pombe

2021 ◽  
Vol 7 (8) ◽  
pp. 626
Author(s):  
Marina Pascual-Ortiz ◽  
Eva Walla ◽  
Ursula Fleig ◽  
Adolfo Saiardi
Keyword(s):  
Family Member ◽  
Protein Modification ◽  
Cell Cycle Control ◽  
Specific Class ◽  
Inorganic Polyphosphate ◽  
Yeast Saccharomyces Cerevisiae ◽  
Evolutionarily Conserved ◽  
Inositol Pyrophosphates ◽  
Polyphosphate Metabolism

Inorganic polyphosphate (polyP) which is ubiquitously present in both prokaryotic and eukaryotic cells, consists of up to hundreds of orthophosphate residues linked by phosphoanhydride bonds. The biological role of this polymer is manifold and diverse and in fungi ranges from cell cycle control, phosphate homeostasis and virulence to post-translational protein modification. Control of polyP metabolism has been studied extensively in the budding yeast Saccharomyces cerevisiae. In this yeast, a specific class of inositol pyrophosphates (IPPs), named IP7, made by the IP6K family member Kcs1 regulate polyP synthesis by associating with the SPX domains of the vacuolar transporter chaperone (VTC) complex. To assess if this type of regulation was evolutionarily conserved, we determined the elements regulating polyP generation in the distantly related fission yeast Schizosaccharomyces pombe. Here, the VTC machinery is also essential for polyP generation. However, and in contrast to S. cerevisiae, a different IPP class generated by the bifunctional PPIP5K family member Asp1 control polyP metabolism. The analysis of Asp1 variant S. pombe strains revealed that cellular polyP levels directly correlate with Asp1-made IP8 levels, demonstrating a dose-dependent regulation. Thus, while the mechanism of polyP synthesis in yeasts is conserved, the IPP player regulating polyP metabolism is diverse.

scholarly journals The development of a molecular toolbox to examine the role of protein O-mannosylation in actinobacteria

2021 ◽  
Author(s):  
Nakita Buenbrazo
Keyword(s):  
Functional Role ◽  
Protein Modification ◽  
Cell Function ◽  
Protein Glycosylation ◽  
Covalent Attachment ◽  
Cell Defense ◽  
Domains Of Life ◽  
Cell Processes

Protein glycosylation is the most abundant and diverse protein modification that occurs in all domains of life. It is defined as the covalent attachment of a carbohydrate moiety to a specific amino acid on a target protein. The functional role of this attachment is implicated in and spans various cell processes from cell signaling, cell defense, and pathogenesis – to name a few. A specific type of protein glycosylation, called protein O-mannosylation (POM) is a process found to be conserved from bacteria to man. In humans, POM is required for healthy cell function, and the absence of POM can cause fatal diseases. Certain prokaryotic species possess a related POM system, but it is poorly understood. It is our hypothesis that the analysis of the POM system in simpler organisms can aid in the characterization of this process and the functional role of the mannosylated proteins that are produced. However, the protocols to prove this theory do not yet exist. This thesis establishes a collection of developed protocols that can be used to characterize the POM systems from gram-positive species Corynebacterium glutamicum and Cellulomonas fimi. In addition the first ever evidence of a C. fimi glycoprotein being glycosylated by the endogenous C. glutamicum POM system is provided.

scholarly journals Post-translational modifications by SIRT3 de-2-hydroxyisobutyrylase activity regulate glycolysis and enable nephrogenesis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luca Perico ◽  
Marina Morigi ◽  
Anna Pezzotta ◽  
Daniela Corna ◽  
Valerio Brizi ◽  
...  
Keyword(s):  
Kidney Development ◽  
Renal Diseases ◽  
Nephron Number ◽  
Self Renewal ◽  
Post Translational Modifications ◽  
Nephron Endowment ◽  
Nephron Progenitors ◽  
Lysine Residues ◽  
Epigenetic Processes

AbstractAbnormal kidney development leads to lower nephron number, predisposing to renal diseases in adulthood. In embryonic kidneys, nephron endowment is dictated by the availability of nephron progenitors, whose self-renewal and differentiation require a relatively repressed chromatin state. More recently, NAD+-dependent deacetylase sirtuins (SIRTs) have emerged as possible regulators that link epigenetic processes to the metabolism. Here, we discovered a novel role for the NAD+-dependent deacylase SIRT3 in kidney development. In the embryonic kidney, SIRT3 was highly expressed only as a short isoform, with nuclear and extra-nuclear localisation. The nuclear SIRT3 did not act as deacetylase but exerted de-2-hydroxyisobutyrylase activity on lysine residues of histone proteins. Extra-nuclear SIRT3 regulated lysine 2-hydroxyisobutyrylation (Khib) levels of phosphofructokinase (PFK) and Sirt3 deficiency increased PFK Khib levels, inducing a glycolysis boost. This altered Khib landscape in Sirt3−/− metanephroi was associated with decreased nephron progenitors, impaired nephrogenesis and a reduced number of nephrons. These data describe an unprecedented role of SIRT3 in controlling early renal development through the regulation of epigenetics and metabolic processes.

scholarly journals Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3728 ◽  
Author(s):  
Sarah M. Engle ◽  
Justin J. Crowder ◽  
Sheldon G. Watts ◽  
Christopher J. Indovina ◽  
Samuel Z. Coffey ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Ubiquitin Ligase ◽  
Apolipoprotein B ◽  
Major Protein ◽  
Sequence Motifs ◽  
Complete Understanding ◽  
Post Translational Modifications ◽  
Lysine Residues ◽  
Associated Proteins

Conserved homologues of the Hrd1 ubiquitin ligase target for degradation proteins that persistently or aberrantly engage the endoplasmic reticulum translocon, including mammalian apolipoprotein B (apoB; the major protein component of low-density lipoproteins) and the artificial yeast protein Deg1-Sec62. A complete understanding of the molecular mechanism by which translocon-associated proteins are recognized and degraded may inform the development of therapeutic strategies for cholesterol-related pathologies. Both apoB and Deg1-Sec62 are extensively post-translationally modified. Mass spectrometry of a variant of Deg1-Sec62 revealed that the protein is acetylated at the N-terminal methionine and two internal lysine residues. N-terminal and internal acetylation regulates the degradation of a variety of unstable proteins. However, preventing N-terminal and internal acetylation had no detectable consequence for Hrd1-mediated proteolysis of Deg1-Sec62. Our data highlight the importance of empirically validating the role of post-translational modifications and sequence motifs on protein degradation, even when such elements have previously been demonstrated sufficient to destine other proteins for destruction.

Metabolic ink lactate modulates epigenomic landscape: A concerted role of pro-tumor microenvironment and macroenvironment during carcinogenesis

2020 ◽  
Vol 20 ◽  
Author(s):  
Nilesh Kumar Sharma ◽  
Jayanta K. Pal
Keyword(s):  
Tumor Microenvironment ◽  
Tumor Heterogeneity ◽  
Environmental Pressures ◽  
Post Translational Modifications ◽  
Histone Lysine ◽  
Lysine Residues ◽  
New Form ◽  
Epigenomic Regulation ◽  
Epigenomic Reprogramming

: Tumor heterogeneity is influenced by various factors including genetic, epigenetic and axis of metabolic-epigenomic regulation. In recent, metabolic-epigenomic reprogramming is considered as one of many tumor hallmarks and it appears to be driven by both microenvironment and macroenvironment factors including diet, microbiotas and environmental pressures. Epigenetically, histone lysine residues are altered by various post-translational modifications (PTMs) such as acetylation, acylation, methylation and lactylation. Furthermore, lactylation is suggested as a new form of PTM that uses lactate substrate as a metabolic ink for epigenetic writer enzyme that remodel histone proteins. Therefore, preclinical and clinical attempts are warranted to disrupt pathway of metabolic-epigenomic reprogramming that will turn pro-tumor microenvironment into antitumor microenvironment. This paper highlights the metabolic-epigenomic regulation events including lactylation and its metabolic substrate lactate in tumor microenvironment.

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