Isolation and purification of a new 105 kDa protein kinase from rat liver nuclei

Quest for the Crypto-phosphoproteome

Protein phosphorylation is one of the most studied post-translational modifications (PTMs). Despite the remarkable advances in phosphoproteomics, a chemically less-stable subset of the phosphosites, which we call the crypto-phosphoproteome, has remained underexplored due to technological challenges. In this Viewpoint, we briefly summarize the current understanding of these elusive protein phosphorylations and identify the missing pieces for future studies.

Exceptionally versatile – arginine in bacterial post-translational protein modifications

Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.

Development of a stable phosphoarginine analog for producing phosphoarginine antibodies

pAIE is designed and synthesized as a stable analog and bioisostere of acid-labile pArg, to produce pArg specific antibodies, facilitating the detection of protein arginine phosphorylation.

Phosphohistidine phosphatase 1 (PHPT1) also dephosphorylates phospholysine of chemically phosphorylated histone H1 and polylysine

BACKGROUND

Phosphohistidine phosphatase 1 (PHPT1), also named protein histidine phosphatase (PHP), is a eukaryotic enzyme dephosphorylating proteins and peptides that are phosphorylated on a histidine residue. A preliminary finding that histone H1, which lacks histidine, was phosphorylated by phosphoramidate and dephosphorylated by PHPT1 prompted the present investigation.

METHODS

Histone H1 and polylysine were phosphorylated at a low concentration (3.9 mM) of phosphoramidate. Their dephosphorylation by recombinant human PHPT1 was investigated by using a DEAE-Sepharose spin column technique earlier developed by us for studies on basic phosphoproteins and phosphopeptides. Determination of protein-bound, acid-labile phosphate was performed by a malachite green method. Mass spectrometry (MS) was used to investigate the occurrence of N-ε-phospholysine residues in a phosphorylated histone H1.2 preparation, and to measure the activity of PHPT1 against free N-ω-phosphoarginine.

RESULTS

Histone H1.2, which lacks histidine, was phosphorylated by phosphoramidate on several lysine residues, as shown by MS. PHPT1 was shown to dephosphorylate phosphohistone H1 at a rate similar to that previously described for the dephosphorylation of phosphohistidine-containing peptides. In addition, phosphopolylysine was an equally good substrate for PHPT1. However, no dephosphorylation of free phosphoarginine by PHPT1 could be detected.

CONCLUSION

The finding that PHPT1 can dephosphorylate phospholysine in chemically phosphorylated histone H1 and polylysine demonstrates a broader specificity for this enzyme than known so far.

Phosphoproteomics--more than meets the eye

PTMs enable cells to adapt to internal and external stimuli in the milliseconds to seconds time regime. Protein phosphorylation is probably the most important of these modifications as it affects protein structure and interactions, critically influencing the life cycle of a cell. In the last 15 years, new insights into phosphorylation have been provided by highly sensitive MS-based approaches combined with specific phosphopeptide enrichment strategies. Although so far research has mainly focused on the discovery and characterization of O-phosphorylation, this review also briefly outlines the current knowledge about N-phosphorylation depicting its ubiquitous relevance. Further, common pitfalls in sample preparation, LC-MS analysis, and subsequent data analysis are discussed as well as issues regarding quality and comparability of studies on protein phosphorylation.

P-N bond protein phosphatases

The current work briefly reviews what is currently known about protein phosphorylation on arginine, lysine and histidine residues, where PN bonds are formed, and the protein kinases that catalyze these reactions. Relatively little is understood about protein arginine and lysine kinases and the role of phosphorylation of these residues in cellular systems. Protein histidine phosphorylation and the two-component histidine kinases play important roles in cellular signaling systems in bacteria, plants and fungi. Their roles in vertebrates are much less well researched and there are no protein kinases similar to the two-component histidine kinases. The main focus of the review however, is to present current knowledge of the characterization, mechanisms of action and biological roles of the phosphatases that catalyze the hydrolysis of these phosphoamino acids. Very little is known about protein phosphoarginine and phospholysine phosphatases, although their existence is well documented. Some of these phosphatases exhibit very broad specificity in terms of which phosphoamino acids are substrates, however there appear to be one or two quite specific protein phospholysine and phosphoarginine phosphatases. Similarly, there are phosphatases with broad substrate specificities that catalyze the hydrolysis of phosphohistidine in protein substrates, including the serine/threonine phosphatases 1, 2A and 2C. However there are two, more specific, protein phosphohistidine phosphatases that have been well characterized and for which structures are available, SixA is a phosphatase associated with two-component histidine kinase signaling in bacteria, and the other is found in a number of organisms, including mammals. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.

Electron capture dissociation mass spectrometric analysis of lysine-phosphorylated peptides

Phosphorylation of proteins is an essential signalling mechanism in eukaryotic and prokaryotic cells. Although N-phosphorylation of basic amino acid is known for its importance in biological systems, it is still poorly explored in terms of products and mechanisms. In the present study, two MS fragmentation methods, ECD (electron-capture dissociation) and CID (collision-induced dissociation), were tested as tools for analysis of N-phosphorylation of three model peptides, RKRSRAE, RKRARKE and PLSRTLSVAAKK. The peptides were phosphorylated by reaction with monopotassium phosphoramidate. The results were confirmed by ¹H NMR and ³¹P NMR studies. The ECD method was found useful for the localization of phosphorylation sites in unstable lysine-phosphorylated peptides. Its main advantage is a significant reduction of the neutral losses related to the phosphoramidate moiety. Moreover, the results indicate that the ECD–MS may be useful for analysis of regioselectivity of the N-phosphorylation reaction. Stabilities of the obtained lysine-phosphorylated peptides under various conditions were also tested.

Protein histidine phosphatase activity in rat liver and spinach leaves

Whole cell extracts from rat liver or spinach leaves contain divalent ion-independent protein histidine phosphatase activity due to phosphatases of the PP1/PP2A family. In the rat liver extract, almost all the activity was found in the PP1, PP2A1 and PP2A2 peaks. In the spinach leaf extract, four phosphorylase phosphatase activity peaks were resolved--three containing PP1 and one containing PP2A--and all showed histidine phosphatase activity. Thus, protein histidine phosphatase activity is expressed in the cytosolic forms of protein phosphatases of the PP1/PP2A family in mammalian and plant cells.

Protein kinases and phosphatases that act on histidine, lysine, or arginine residues in eukaryotic proteins: a possible regulator of the mitogen-activated protein kinase cascade

Phosphohistidine goes undetected in conventional studies of protein phosphorylation, although it may account for 6% of total protein phosphorylation in eukaryotes. Procedures for studying protein N- kinases are described. Genes whose products are putative protein histidine kinases occur in a yeast and a plant. In rat liver plasma membranes, activation of the small G-protein, Ras, causes protein histidine phosphorylation. Cellular phosphatases dephosphorylate phosphohistidine. One eukaryotic protein histidine kinase has been purified, and specific proteins phosphorylated on histidine have been observed. There is a protein arginine kinase in mouse and protein lysine kinases in rat. Protein phosphohistidine may regulate the mitogen-activated protein kinase cascade.

Characterization of N omega-phosphoarginine hydrolase from rat liver

N omega-Phosphoarginine hydrolase from rat liver hydrolyzed N omega-phosphoarginine into arginine and inorganic phosphate, whereas it did not release inorganic phosphate from 19 other phosphorylated compounds containing a N-P bond, an O-P bond or a C-P bond. In addition, it was not able to transfer the phosphoryl moiety from N omega-phosphoarginine to ADP. These results indicated that this enzyme was distinct from both phosphoamidase and arginine kinase. Its properties were as follows: thiol compounds were essential for its activity; it was stimulated by 1.5-2-fold in the presence of 0.001% Lubrol, Tween 20, poly(oxyethylene) 9-lauryl ether and Nonidet P-40, while 0.004% sodium lauryl sulfate inhibited the activity completely; concentrations of sodium molybdate and sodium vanadate necessary for 50% inhibition were 7 microM and 12 microM, respectively; some proteins stimulated the activity, while lysophosphatidic acid, lysophosphatidylinositol, and phosphatidic acid suppressed the activity even in the presence of poly(oxyethylene) 9-lauryl ether.

Calcium, cyclic AMP and protein kinase C--partners in mitogenesis

Evidence is steadily mounting that the proto-oncogenes, whose products organize and start the programs that drive normal eukaryotic cells through their chromosome replication/mitosis cycles, are transiently stimulated by sequential signals from a multi-purpose, receptor-operated mechanism (consisting of internal surges of Ca2+ and bursts of protein kinase C activity resulting from phosphatidylinositol 4,5-bisphosphate breakdown and the opening of membrane Ca2+ channels induced by receptor-associated tyrosine-protein kinase activity) and bursts of cyclic AMP-dependent kinase activity. The bypassing or subversion of the receptor-operated Ca2+/phospholipid breakdown/protein kinase C signalling mechanism is probably the basis of the freeing of cell proliferation from external controls that characterizes all neoplastic transformations.

A cyclic nucleotide and calcium-independent protein kinase of chick brain: activation by a heat-stable protein

A heat-stable trichloracetic acid-stable protein fraction stimulates protein kinase activity in chick brain cytosol. This protein kinase (tentatively referred to as protein kinase S) can be partially purified by chromatography on DEAE-cellulose and Sepharose G-100. The partially purified protein kinase has an absolute requirement for magnesium and the heat-stable protein for the phosphotransferase activity and is not influenced by cyclic nucleotides, calcium or ethylenediaminetetraacetic acid. The substrate specificity of protein kinase S indicates that it is not a casein kinase and prefers histones over the substrates tested. The specific activity of this protein kinase changes with chick brain development and the activity increased by two-fold by the second post-hatch week, suggesting a role of this protein kinase in chick brain development.

The effects of thyroparathyroidectomy and 1,25 dihydroxyvitamin D3 on changes in the activities of some cytoplasmic and nuclear protein kinases during liver regeneration

Partial hepatectomy (HPX), which proliferatively activates the remaining liver cells, triggered two transient prereplicative surges in the total activities of cytoplasmic types I and II cyclic AMP-dependent protein kinase holoenzymes, and of nuclear catalytic subunits from cyclic AMP-dependent protein kinases. It also induced a transient prereplicative increase in the activities of a nuclear Ca2+-calmodulin-stimulable, protamine-phosphorylating protein kinase, and a nuclear poly(L-lysine)-phosphorylating, 105 kDa protein kinase. Thyroparathyroidectomy (TPTX) delayed and reduced the first surge and completely eliminated the second surge of both of the cytoplasmic cyclic AMP-dependent protein kinases, reduced the rises in the activity of nuclear catalytic subunits, and completely eliminated the surge of the Ca2+-calmodulin-stimulable protein kinase, but did not affect the surge of the nuclear 105 kDa protein kinase. The impairment of the responses of the two cyclic AMP-dependent protein kinases to HPX in TPTX rats was not accompanied by a rise in the level of heat-stable inhibitor of cyclic AMP-dependent protein kinase activity. One intraperitoneal injection of 1,25-dihydroxyvitamin D1 into TPTX rats immediately after HPX completely restored the post-HPX surges in the activity of type I cyclic AMP-dependent protein kinase, but the hormone, even in high doses, had little or not effect on the type II isoenzyme or the nuclear Ca2+-calmodulin-stimulable, protamine-phosphorylating enzyme.