Detection of ubiquityl-calmodulin conjugates with a novel high-molecular weight ubiquitylprotein-isopeptidase in rabbit tissues
European Journal of Medical Research volume 15, Article number: 428 (2010)
The selective degradation of many proteins in eukaryotic cells is carried out by the ubiquitin system. In this pathway, proteins are targeted for degradation by covalent ligation to ubiquitin, a highly conserved protein . Ubiquitylated proteins were degraded by the 26S protea-some in an ATP-depended manner. The degradation of ubiquitylated proteins were controlled by isopeptidase cleavage. A well characterised system of ubiquitylation and deubiquitylation is the calmodulin system in vitro . Detection of ubiquityl-calmodulin conjugtates in vivo have not been shown so far. In this article we discuss the detection of ubiquitin calmodulin conjugates in vivo by incubation with a novel high-molecular weight ubiquitylprotein-isopeptidase in rabbit tissues. Proteins with a molecular weight of ubiquityl-calmodulin conjugates could be detected in all organs tested. Incubation with ubiquitylprotein-isopeptidase showed clearly a decrease of ubiquitin calmodulin conjugates in vivo with an origination of unbounded ubiquitin. These results suggest that only few ubiquitin calmodulin conjugates exist in rabbit tissues.
A: absorption, optical density; BSA: bovine serum albumin; DTE: dithioerythriol; CaM: calmodulin; APFII: DEAE fraction II; SDS-Page: sodium dodecyl sulfate polyacrylamide electrophoresis; TCA: trichloracetic acid; w/v: weight in g per volume; uCam: ubiquityl-calmodulin (has two meanings:a. general name for all conjugates of calmodulin with ubiquitin: b. if specified designates the monoconjugate); uCam-Syn F1: uCam synthetase protein factor 1; uCaM-Syn F2: uCaM synthetase protein factor2.
ATP-dependent-26-S-protease (26S-proteasome, EC 3.4.99. -)
ATP-ubiquitin-dependent proteolytic pathway
(ubiquitin protein ligase + ATP-dependent-26-S-protease)
Multicatalytic endopeptidase complex (20S-proteasome, EC 126.96.36.199)
Ubiquitin-calmodulin ligase (ubiquityl-calmodulin synthetase, EC 188.8.131.52.);
Ubiquitin-calmodulin hydrolase, (ubiquityl-calmodulin isopeptidase, EC 3.4.99.-);
Ubiquitin-protein ligase, (E1, E2, E3; EC 184.108.40.206.); Ubiquitin thiolesterase (ubiquitin carboxyl-terminal esterase, EC 220.127.116.11).
Two forms of ubiquitin function have been described: (a) catabolic and (b) non-catabolic.
In the (a) catabolic pathway, protein ubiquitylation, which involves the covalent binding of multiple ubiquitin molecules with a specific ATP-dependent ligase system on substrates following ATP-dependent protein breakdown via 26S proteasome.
Examples of the catabolic protein ubiquitylation are:
Unassembled mutant type I collagen pro-alpha1 (I) chains , a-casein , growth hormone receptor  p53 , cyclin , nuclear oncoprotein , MHC class I heavy chains  and RNA-polymerase II .
The ubiquitin/proteasome system is a major pathway of selective protein degradation in eukaryotic cells. Ubiquitin-mediated degradation of proteins plays important roles in the control of numerous processes, including cell-cycle  cell division , stress response , extracellular modulators like NFκB [13–15], morphogenesis of neurons , modulation of cell receptors , ion channels  and DNA-repair [18, 19].
(b) non-catabolic protein ubiquitylation whitout terminating in degradation by the 26S proteasome. Examples of the non-catabolic protein ubiquitylation are:
The pathway for the protein breakdown contains an ubiquitin-protein-conjugating system, a protease and an isopeptidase. The ubiquitin-conjugating system is made of three different enzymatic components. E1 is the ubiquitin activating enzyme, E2 is the ubiquitin-conjugating enzyme and E3 is the ubiquitin-protein ligase. Ubiquitin is first of all adenylated by the conjugating enzyme (E1) and then transferred to a thiol group for covalent linkage. This is followed by a transesterfication to the conjugating enzyme (E2) which can either transfer ubiquitin directly to a target protein or together with the ubiquitin-protein ligase (E3).
A well characterised system for ubiquitylation and deubiquitylation is the calmodulin system in vitro. Ubiquitin-calmodulin ligase (ubiquityl-calmodulin synthetase, uCaM-synthetase, EC 18.104.22.168), covalently modifies vertebrate [20, 22–25], plant, fungus  and yeast  calmodulins with ubiquitin according to the following reaction (n = 1-5) :
Of major biological relevance is the dependence of this reaction on μM Ca2++ concentrations [23, 24] making calmodulin the first protein where ubiquitylation is regulated by second messenger. UCaM-synthetase has been detected in most tissues of the rabbit  and also in the simple eukaryote, yeast (S. cervisiae)  and leads to a calmodulin molecule multiubiquitylated (up to u3/4CaM and u5CaM) at a single lysine residue [25, 27]. UCaM-synthetase can be separated into two essentially inactive protein components  which have recently been purified [29, 30]. The first one (uCaM-Syn F1, 224 kDa) binds to ubiquitin-Sepharose and is the ubiquitin activating enzyme (E1). The second component (uCaM-Syn F2, 623 kDa) binds to calmodulin-Sepharose and bestows specificity to the reaction . Although the biological function of calmodulin ubiquitylation is not exactly known it has been suggested that this covalent modification suppresses the biological activity of cal modulin in the activation of phosphorylase kinase . In this connection the hypothesis emerged that ubiquitylation of calmodulin may be a physiologically reversible process similar to protein phosphorylation and dephosphorylation [2, 26] possibly catalyzed by a highly specific ubiquitylprotein-isopeptidase as described in detail in this paper. Andersen et al [31, 32] first reported the splitting of an N...-ubiquityl-protein bound in a natural ubiquitin conjugate. This isopeptidase was capable of splitting the protein A24 (histone 2A-ubiquitin conjugate) into histone 2A and ubiquitin. Matsui et al.  identified the reaction products in detailed analysis as intact ubiquitin and histone 2A.
This isopeptidase was shown to have a molecular mass of 38 kDa and to be present in the cytoplasm of most eukaryotes . Since no other natural ubiquitin conjugates were available putative isopeptidase activity in other work has been measured with more or less nonspecific substrates such as artificial ubiquitin-protein conjugates, amides or esters [34–37]. A first group of enzymes hydrolyzing small molecules conjugated to ubiquitin (e.g. residual peptides attached to ubiquitin) has been termed "ubiquitin carboxyl-terminal esterases/hydrolases" (EC 22.214.171.124) and appear not to have the ability to hydrolyze endogenous 12© I-ubiquityl-protein conjugates [37, 38]. These hydrolases usually have molecular masses in the range of 30 kDa [35, 37, 39–41]. A typical enzyme of this group is the ubiquitin carboxyl-terminal esterase L1 (UCH-L1) and ubiquitin carboxyl-terminal esterase L3 (UCH-L3) . This enzyme is found in nerve cells throughout the brain. Ubiquitin carboxyl-terminal esterase L1 is probably involved in the cell machinery that breaks down unwanted proteins. Although the exact function of ubiquitin carboxyl-terminal esterase L1 is not fully understood, it appears to have two enzyme activities. One activity, called hydrolase, removes and recycles ubiquitin molecules from degraded proteins. This recycling step is important to sustain the degradation process. The other enzyme activity, known as ligase, links together ubiquitin molecules for use in tagging proteins for disposal. An association between M. Alzheimer  and M. Parkinson , but also the Huntington  disease are discussed.
A second group of isopeptidases (ubiquityl-protein hydrolases) capable of splitting larger ubiquityl-protein conjugates has been estimated to be in a molecular mass range of 100-200 kDa . A third type of isopeptidase which cleaves free homooligomers and homopolymers of ubiquitin i.e. diubiquitin and multiubiquitin chains (ubiquityl-ubiquitin hydrolase) has been reported as a monomer with a native molecular mass of 100 kDa  An ATP-dependent C-terminal hydrolase  and ATP-dependent isopeptidase [47, 48] have also been reported which may be associated with the 26S proteasome [46, 48]. Recently enzymes containing both C-terminal hydrolase and isopeptidase activities have been reported [49, 50]. At the moment the biological function of these isopeptidases is unclear.
Against this background we tested the hypothesis that the incubation of rabbit muscle tissues with ubiquitylprotein-isopeptidase could detect ubiquityl-calmodulin conjugates in vivo.
Ubiquitin, Anti-Sheep IgG Peroxidase Conjugate Product No. A-3415 was purchased from Sigma (Munich). Nembutal® was obtained from Sanofi (Hannover). Leupeptine, iodacetamide and dithioerytol (DTE) were obtained from Biomol (Hamburg). For chromatographic application fractogel EMD-DEAE 650 (s) and TSK HW-65 (s) Merck (Darmstadt) were used. Problott‚-membrane (pit size of 0,025 μm) was purchased from Applied Biosystems (Weiterstadt). RPN ECL western blotting detection reagents and the hyperfilm were purchased by Amersham (Braunschweig). The western-blot equipment was obtained from Sartorius (Göttingen). Coomassie Brillant Blue R-250 (= Serva Blue R), methanol and BSA were obtained from Serva (Heidelberg). The molecular weight standards for SDS-PAGE bovine serum albumin (BSA) 66 kDa, ovalbumin 45 kDa, glyceraldehyde 3-phosphate dehydrogenase 36 kDa, carbonic anhydratase 29.2 kDa, trypsinogen 25 kDa, trypsin inhibitor 20.1 kDa and lactalbumin 14.2 kDa were obtained from Sigma (Munich).
The ubiquitin- antibody employed in this work was set up and featured by Gehrke and Jennissen . The affinity purification of ubiquitin-antibody was carried out by an unpublished method from G. Botzet and H.P. Jennissen on ubiquitin-sepharose.
All chemicals were of the highest available or analytical grade. Water was deionized, distilled and then passed through a Milli-Q-system (Millipore, Witten) before use.
Reticulocyte-rich blood (ca. 85%) was generated in rabbits (3-4 kg) by the phenylhydrazine method [51, 52]. In this procedure, 2.5% (w/v) phenylhydrazine in 0.9% NaCl, pH 7.4, is injected s.c. into the back of rabbits. On days 1-4 an amount of 0.13 ml/kg was injected. On day 8 rabbits were given a lethal overdose of 250 mg Evipan and bled for harvesting of reticulocyte by incision of the jugulars. Coagulation was inhibited by addition of 1 M sodium citrate, pH 7.4, to a final concentration of 10 mM into polyethylene beakers coated with silicone spray. All further work was performed with beakers and tubes siliconized in this way. The reticulocytes were washed twice at 5°C in a 10-fold volume of buffer containing 10 mM potassium phosphate, 0.15 M NaCl, pH 7.4
Preparation of reticulocytes without ATP depletion
To prevent reticulocytes from ATP depletion the procedure of red blood cell preparation described by Lew and Garcia-Sancho  was modified as follows.
Freshly drawn blood (anticoagulated by sodium citrate, pH 7.4 at final concentration of 10 mM) was centrifuged for 20 min. at 2200 g at room temperature and the pelleted cells were resuspended in 10 volumes of buffer supplemented with glucose and containing 145 mM NaCl, 5 mM KCl, 10 mM NaOH-neutralized HEPES, 10 mM glucose, 0.15 mM MgCl2, 0.1 mM EGTA, (pH 7.4). The wash was repeated three times, supernatant, buffy coat and topmost cell layer were removed after each centrifugation. An amount of 150 ml of resulted cell pellet was incubated for 60 min. at 37°C in 2 volumes of the same buffer supplemented with 1 mM Ca2+ and centrifuged again under the same conditions. Reticulocytes were then lysed with 2 volumes of lyses buffer containing 10 mM iodacetamide, 20 mM EGTA, and pH 7.0. Lysate was centrifuged at 100000 g for 90 min. at 4°C and supernatant was used for further preparations.
Rabbits were given a lethal dose of Nembutal® (see above) and immediately exsanguinated by decapitation and suspending from the hind legs. The excised tissues are: heart and white muscle (Musculus psoas minor). The tissues were extensively washed with water to remove residual blood. The excised tissue was cut into small pieces and immediately frozen in liquid nitrogen. The frozen tissue was then transferred to a -80°C freezer and stored. For the described experiments the tissues of five New Zealand rabbits (CHBBch) were pooled. The preparation of tissue extracts is based on the previously described procedure . According to this method 6 g of frozen (-80°C) rabbit tissue was homogenized in 3 mM K2HPO4/KH2PO4, 1 mM DTE, 5 μg/ml leupeptine, 15 mM iodacetamide, 5 mM EDTA, 5 mM EGTA, 5 × 10-5 M PMSF, pH 7.4 (buffer B) in a Bühler homogenizer (E.Bühler, Bodelshausen 10 ml vessel, diameter of the knife 1 cm) at full speed for 1 min at 4°C. This homogenate was centrifuged at 40 000 × g for 30 min in a Beckmann L-7/80 ultracentrifuge. The supernatant was given in a gauze filled measuring cylinder.
Cleaning of the chromatography glass column with chromosulfuric acid
The glass column (8.2 cm × 1.2 cm × 0.5 cm Merck, Darmstadt) was heated for one hour in chromosulfuric acid and then washed up with Millipore water as long as no chromosulfuric acid was externally visible. The glass column was finally treated in boiled Millipore water for one hour.
Lysate (250 mg) was applied (4 ml/h) by a peristaltic pump (Perpex, Guldner) to the column (8.2 cm × 1.2 cm × 0.5 cm Merck, Darmstadt) with 400 μl packed fractogel EMD-DEAE 650 (s). The fractogel cartridges were protected by a pre-column containing 250 μl packed underivatized fractogel TSK-HW 65 (S). The column was eluted in a single step with 4 ml/h 500 mM KCl, 20 mM Tris/HCl, 5 μg/ml leupeptine, 5 mM iodacetamide, pH 7.2. The elution pool was dialyzed on a rotating glass frame for 4 h against 6 l of 20 mM Tris/HCl, 1 mM DTE, 5 mM iodacetamide, pH 7.6. The eluate, the wash-fraction and the pass-through-fraction.
Ubiquitin was coupled to Sepharose 4B by the divinylsulfone method [51, 54]. Sepharose was first activated by divinylsulfone (= DVS-Sepharose) as described in . Ubiquitin coupling solution was made by adding 540 mg ubiquitin to 45 ml 0.2 M NaHCO2, pH 9.5. This solution was dialyzed in SpectraPor (cutoff 6-8 kDa) dialysis bags against 0.2 M NaHCO2, pH 9.5 for 3 hours with one buffer change after 1 hour. After dialysis the solution (45 ml) had a protein concentration of 6.3 mg/ml. The 45 ml of this ubiquitin coupling solution were added to 45 g "wet weight"  DVS-Sepharose 4B and incubated first for 6 hours at room temperature and then for another 21 hours at 5°C. After this time the gel was sucked dry on a small Büchner funnel and 45 ml stopping buffer containing 0.2 M NaHCO3 with 40 mg/ml glycine pH 9.5 was added. This stopping mixture was incubated for 4 hours at room temperature. The gel was then extensively washed with 20 mM Tris/HCl, pH 7.0 followed by washing at room temperature with 5-10 vol. each of H2O, 1% SDS, H2O, BSA
(5 mg/ml in H2O), H2O, 1 M NaCl, H2O, respectively. It was then stored at 5°C in H2O with 0.02% NaN3. The degree of substitution was measured by the depletion procedure (decrease of free ubiquitin in the bulk) employing the stainless steel grid method . The coupling efficiency was ca. 95% (not shown). For regeneration after several cycles of use ubiquitin-Sepharose was washed at room temperature with 5-10 vol. each of H2O, 1% SDS, H2O, BSA (5 mg/ml in H2O), H2O, 1 M NaCl, H2O respectively and then stored at 5°C in H2O with 0.02% NaN2.
For the preparative isolation of affinity-enriched isopeptidase activity fractogel-APF II was applied to ubiquitin-Sepharose (5.9 mg Ubiquitin/ml packed gel, 5 cm i.D. × 2.8 cm gel height, flow rate 25 ml/h, fraction vol. 2.5 ml) as described by . The gel was equilibrated with 50 mM Tris/HCl, 5 mM ATP, 10 mM MgCl2, pH 7.5 (buffer G). To a sample of fractogel-APF II (175 mg) 5 mM ATP, 10 mM MgCl2 (final concentration) were added and the mixture was applied to the column and then washed with 3 volumes of buffer G. The column was eluted with 5 volumes 50 mM Tris/HCl, 0,1 mM EDTA, 10 mM DTE, pH 9.0 (Buffer H). The eluate was pooled, concentrated in Centricon 30 tubes (Amicon, Witten) in a preparative Beckmann centrifuge (Rotor JA 20, 4000 × g, 4-5°C) and simultaneously dialyzed against 50 mM Tris/HCl, 0.5 mM DTE, 5 μg/ml leupeptine, pH 7.2 (buffer I)
Ubiquitin calmodulin conjugates
Reaction mixtures for the synthesis of preparative amounts of ubiquityl-calmodulin conjugates contained in a final volume of 10 ml: 50 mM Tris/HCl, 1 mM DTE, 5 mM MgCl2, 1 mM ATP, 10 mM phosphocreatine, 0.1 mM CaCl2, 0.1 mg/ml creatine kinase, 3.0 mg/ml ubiquitin, 0.5 mg/ml 125I-BH-calmodulin and 3.6 mg/ml. The reaction was stopped after 4 h at 37°C by adding 30 ml of 20 mM sodium
β-glycerophosphate, 1 mM CaCl2, pH 7.0 (buffer H) and heating to 96°C for 10 min. Subsequently the mixture was placed on ice for 5 min. Denatured proteins were spun down (20000 × g, 15 min, 4°C) and the supernatant (39 ml, 1.9 mg/ml) was applied at room temperature to a fluphenazine column (1.5 cm i.d. × 2.8 cm gel height; 5 ml packed gel) equilibrated with buffer H (flow rate 33 ml/h, fraction vol.). The column was washed with 10 ml buffer H followed by 80 - 100 ml 20 mM sodium β-glycerophosphate, 1 mM CaCl2, 300 mM NaCl, pH 7.0. In this way the unabsorbed ubiquitin was separated from the adsorbed conjugates and unconjugated free calmodulin. The ubiquityl-calmodulin conjugates and free calmodulin were eluted from the column with 4050 ml 20 mM sodium β-glycerophosphate, 10 mM EGTA, 500 mM NaCl, pH 7.0. This "EGTA-eluate" from the FP-Sepharose column was concentrated by TCA precipitation (5%), the resulting pellet was neutralized with 1 M sodium phosphate and resuspended in 2-4 ml 20 mM sodium phosphate, 1 M NaCl, pH 7.0 (buffer J).
The concentrated EGTA-eluate from the FP-Sepharose (1.8 ml; 3.5 mg/ml) was directly applied to a column of Chelating Sepharose Fast Flow (1.5 cm i.d. × 2.8 cm gel height, flow rate 14 ml/h, fraction vol. 5 ml) charged with Cu2+  and equilibrated with buffer J ("column procedure"). After application of the sample the column was washed with 20 ml buffer J (elution of free calmodulin). Elution of the ubiquityl-calmodulin conjugates was facilitated stepwise by a series of acetate buffers of different volumes adjusted to the different pH values as follows: 40 ml 0.1 M sodium acetate, 1 M NaCl, pH 6.0; 30 ml 0.1 M sodium acetate, 1 M NaCl, pH 5.5; 110 ml 0.1 M sodium acetate, 1 M NaCl, pH 5.0; 60 ml 0.1 M sodium acetate, 1 M NaCl, pH 4.75; 20 ml 0.1 M sodium acetate, 1 M NaCl, pH 4.5; 30 ml 0.1 M sodium acetate, 1 M NaCl, pH 3.2. The separation of ubiquityl-calmodulin conjugates from free calmodulin was monitored by 15% SDS-PAGE. Fractions containing ubiquityl-calmodulin devoid of free calmodulin were pooled, concentrated and dialyzed on Centricon 10 tubes against 10 mM sodium β-glycerophosphate, 0.1 mM CaCl2, pH 7.0. In the case that the different conjugate fractions were not separated all conjugates were eluted at pH 3.0 in one step. The conjugate yield in this procedure was ca. 1 mg.
Primary ubiquitin antibody
The ubiquitin antibody was prepared and characterized by Gehrke and Jennissen . The ubiquitin antibody was in subsequent purified by affinity chromatography on the ubiquitin-sepharose (unpublished data). The ubiquitin antibody was diluted 1:1000 in 10 mM Tris/HCl, 150 mM NaCl, 30 mg/ml BSA, pH 7.0 (buffer B).
SDS-PAGE was performed with 15% gels according to . 200 μg protein per lane were applicated. The molecular weight standards for SDS-PAGE and the ubiquitin-calmodulin standards are given under Materials.
The protein transfer of Problott®-membrane based on a method of Towbin et al. . The method was modified and optimized by M. Dietsch and H.P. Jennissen (unpublished data). Two graphite plates (Sartorius, Göttingen) were chosen as electrodes in a semidry-blotting system .
Blot-arrangement anode: 3 layers of Whatman®-filter paper (Nr. 3, Whatman®, Madestone, UK) in 300 mM Tris/HCl, 20% methanol, pH 10.4. 2 layers of What-man® filter paper in 25 mM Tris/HCl, 20% methanol, pH 10.4. 1 layer Problott®-membrane, 1 layer SDSPAGE. Blot-arrangement cathode: 2 layers of Whatman® filter paper in 25 mM Tris/HCl 20% methanol, pH 9.4. The blot was weighted with 2.5 kg and blotted with 40 mA for 31/2 h. After the transfer the Problott®-membrane was washed four times in 10 mM Tris, 150 mM NaCl, pH 7.0 (buffer A) and then air dried. The molecular standards (Serva Blue R) were stained with 0.1% amidoschwarz, 40% methanol and 1% acetic acid for 20-30 sec. Amidoschwarz was eliminated from the Problott®-membrane with millipore water. The destained Problott®-membrane was dried by air and then incubated for 1 h at 120°C under vacuum in a dessicator (Swerdlow et al., 1986). After the heat processing the Problott®-membrane was incubated for 10 min in methanol and washed for 10 min in 10 mM Tris, 150 mM NaCl, pH 7.0 and finally reblocked with 10 mM Tris/HCl, 150 mM NaCl, 30 mg/ml BSA, pH 7.0 for 90 min (buffer B). Both primary and secondary antibodies were diluted 1:1000 in buffer B. After 90 min incubation with primary antibody the Problott®-membrane was washed four times for 15 min in buffer A. The Problott®-membrane was reblocked 5 min in buffer B and in a further step incubated 30 min with secondary antibody (peroxidase labelled anti sheep antibody, Sigma) following by rinsing one time each 5 and 10 min and three times 15 min in buffer A. The Problott®-membrane was incubated 1 min in 1 vol. detection reagent 1 + 1 vol. detection reagent 2 (Amersham) and placed between two layers of thin plastic foil in the presence of enhancer foils (Cronex Lightning Plus, Dupont de Nemours) and were exposed to hyper-film (18 × 24 cm Amersham) for 2-5 min.
Competitive ubiquitin western blot
In the case of ubiquitin displacement blot, unconjugated ubiquitin were added in a concentration of 5 mg/ml to the primary antibody.
Splitting of ubiquitin-conjugates with ubiquitylprotein-isopeptidase
Before incubation of the rabbit tissues with the ubiquitylprotein-isopeptidase, the probes were dialyzed against 20 mM Tris/HCl, 20 mM β-mercaptoethanol, 5 × 10-5 PMSF, pH 8.0. to eliminate iodacetamide. Iodacetamide inhibits the ubiquitylprotein-isopeptidase irreversible.
The batches, incubated with ubiquitylprotein-isopeptidase had a final concentration of 50 mM Tris/HCl, 1 mM DTE, 50 μM PMSF und 5 μg/ml leupeptine, pH 8.0. After incubation at 37°C for a given time (60 min.) in a waterbath, the reaction were irreversible inhibited by a final concentration of 5 mM iodacetamide and 10% w/v TCA (final concentration 5% TCA, 20 min, 0°C). Each batch was incubated with 25 μg ubiquitylprotein-isopeptidase.
Ubiquityl-calmodulin isopeptidase test
Ubiquityl-calmodulin isopeptidase test was used for experimental verification of "true" ubiquityl-protein conjugates (as well as free branched multiubiquitin chains) in examined probes and its discrimination from linear polyubiquitin chains. Reaction mixtures for ubiquitylcalmodulin isopeptidase tests contained in a total volume of 230.8 μl 50 mM Tris/HCl, 5 mM Mg acetate, 8.5 μg ubiquityl-calmodulin conjugates or 100 μg of APF II fraction from non-ATP depleted reticulocytes and 50 μg enriched ubiquityl-calmodulin isopeptidase fraction. Incubation was stopped after 60 min. by adding of TCA at final concentration of 5%. The pellets were neutralized with 60 μl laemmli sample buffer, heated to 96°C for 10 min and then subjected for SDS-PAGE. Respective volumes of 50 mM Tris/HCl, 5 mM iodacetamide were added to control probes instead of the enzyme solution.
Amino acid analysis
Purified ubiquitin, calmodulin and monoubiquitination products of calmodulin were hydrolyzed in vacuum for 24 and 48 hours in 6 N HCl, 0.1% (w/v) phenol at 110°C. Amino acid analysis (OPA method) was done on a Spherisorb O.D.S. II column (Fa. Grom, Herrenberg) as described by [25, 61].
Splitting of internal rabbit muscle ubiquitin-conjugates with trypsin
The batches (200 μg protein) incubated with trypsin had a final concentration of 20 mM Trsi/HCl, 20 mM βmercaptoethanol, 5 × 10-5 PMSF, pH 8.0. After incubation at 37°C for a given time (30 min) in a water bath, the reaction was stopped irreversible with 10% w/v TCA (final concentration 5% TCA, 20 min, 0°C). Each bath was incubated with 65 μg Trypsin.
Protein was determined after TCA precipitation (5%), washing and resolubilization to the method of (Lowry) on an AutoAnalyzer (Technicon) employing BSA as standard.
Incubation of ubiquitin calmodulin conjugates with ubiquitylprotein-isopeptidase
After synthesis of in vitro purified first- and higher-order ubiquitin calmodulin conjugates we posed the question if these conjugates could serve as a substrate of the ubiquitylprotein-isopeptidase. Incubation of ubiquitin calmodulin conjugates (Figure 1) with different concentrations of Ubiquitylprotein-isopeptidase clearly showed that only a small concentration of Enzyme is needed to dissociate all ubiquitin calmodulin conjugates into unbound calmodulin and unconjugated ubiquitin. However, this experiment did not conclusively prove that the isopeptide bonds of ubiquitin calmodulin conjugates had been cleaved. The same results would be observed if ubiquitin were cleaved proteolytically at the Arg74-Gly75 peptide bond which would release ubiquitin-des-Gly-Gly which would be indistinguishable on SDS-PAGE from native ubiquitin. An endogenous tissue protease splitting at this position was reported by Haas et al. . Therefore it had to be demonstrated that ubiquitin as well as calmodulin were released from the conjugates in intact primary-structural form, before the conclusion of true isopeptidase activity could be drawn. Figure 1 showed clearly only two proteins of 17 kDa and 8.5 kDa are formed as products from first and second-order conjugates of calmodulin. No intermediate or low molecular mass species were detectable. The two protein products displayed the identical molecular mass of the intact calmodulin and intact ubiquitin. However, a limited proteolysis involving only a few amino acids could not be excluded.
The release of unbounded ubiquitin and calmodulin were therefore isolated from the incubation mixture and the amino acid composition was determined. The analysis of the regained products (Table 1 and 2) demonstrates that the amino acid composition of both ubiquitin and calmodulin correspond to that predicted by the sequence. The released ubiquitin contains 6 glycine residues and one methionine, demonstrating that both the N-terminal and C-terminal ends must have remained intact. Analogously the released calmodulin contains 11 alanine and 7 lysine residues (Table 2) demonstrating the presence of an intact N-terminal and C-terminal structure of this protein also. The 11 detected glycine residues exclude any additional glycines residues remaining from ubiquitin. Such additional glycines would be expected if a proteolytic cleavage of the Arg74-Gly75 site on ubiquitin in the conjugate had taken place. Since first- and second-order conjugates were employed in the experiment of Figure 1, the results strongly indicated that two types of bonds were split: (a) the N...-ubiquityl-ubiquitin isopeptide bond and (b) the N...-ubiquityl-calmodulin isopeptide linkage.
Characterisation of the blotting system
Competitive western blot
Competition of unconjugated ubiquitin with his hapten served as control for specificity of the affinity purified antibody. The more unconjugated ubiquitin were needed to displace the antibody from his binding site, the merrier specific is the primary antibody. Unconjugated monomeric ubiquitin (5 mg/ml) was added into the primary antibody solution. Addition of 5 mg/ml (final concentration) unconjugated ubiquitin led to complete disappearance of the ubiquitin-conjugate (lane 2 Figure 2). High ubiquitin concentrations (~ 1 mM) were necessary in order to prevent a reaction with the ubiquityl-calmodulin conjugates. This indicates the high affinity of our antibody to ubiquitin-conjugates. Incubation with 50 μg of ubiquitylproteinisopeptidase (see material) led to complete disappearance of the ubiquityl-calmodulin conjugates (Figure 2, lane 3) and unconjugated ubiquitin (free ubiquitin) originates.
Sensitivity of anti-ubiquitin antibodies against free ubiquitin
Titration experiments of increasing amounts of monomeric unconjugated ubiquitin (Figure 3 and 4) showed a linear dependence of signal intensity from ubiquitin amount. the lower detection limit of our primary ubiquitin-antibody is assigned to approximately 50 ng.
Western-blot analysis of organ tissues with ubiquitin-antibody
Detection of ubiquityl-calmodulin conjugates in reticulocyte APFII
The reticulocyte is a well characterised biological system . It was one of the first organ tissues in witch the ubiquitin-calmodulin ligase and the ubiquitylprotein-isopeptidase were characterized. Figure 5 shows a western blot of ubiquityl-calmodulin conjugates and reticulocytes APFII plus and minus ubiquitylprotein-isopeptidase. the ubiquitylprotein-isopeptidase incubation of 8.5 μg ubiquitin calmodulin conjugates showed a total degradation of the conjugates and unconjugated ubiquitin originates. However, the western blot of reticulocyte APFII with an affinity purified ubiquitin antibody showed proteins with a molecular weight between 30 kDa and 40 kDa, consistent with ubiquitin calmodulin conjugates (ucaM I and uCaM II). after incubation with ubiquitylprotein-isopeptidase, high molecular proteins (Lane 4, Figure 5) were almost cleaved by the isopeptidase and unconjugated ubiquitin originates. This finding supposed the existence of ubiquitin calmodulin conjugates in reticulocyte APFII in vivo.
Since, the calmodulin concentration in skeletal muscle is very high and the muscle degradation is controlled by the proteasome system [63–66] we hypothesized the existence of ubiquityl-calmodulin conjugates also in the skeletal muscle.
Western-blot analysis of heart muscle with ubiquitin-antibody
The western-blot with an affinity purified ubiquitin-antibody of the heart muscle showed protein bands in the range of 30 to 40 kDa, consistent with molecular weights of ubiquityl-calmodulin conjugates (uCaM I and II). After incubation with 12.5 μg ubiquitylproteinisopeptidase (Figure 6a, lane 2), the purified ubiquitylcalmodulin conjugates disappeared and unconjugated ubiquitin originated (see also Figure 1). However, we also proofed the incubation condition for ubiquitylprotein- isopeptidase in the rabbit tissue itself (Figure 6a). As a control, additional purified ubiquitin calmodulin conjugates were put into the pass through of the heart muscle. Under these conditions we could clearly show a cleavage of ubiquitin calmodulin conjugates in the mixture of heart muscle and added ubiquitin calmodulin conjugates. Furthermore, we tested the increasing effect of isopeptidase titration (lane 3 and 4 Figure 6a) in the heart muscle pass through. The increase of isopeptidase concentration in the incubation mixture had no additional effect of the cleavage ubiquityl-calmodulin conjugates in the organ tissue, so that for further experiments 25 μg ubiquitylprotein-isopeptidase were put into each incubation assay. In contrast, the addition of 5 mM iodacetamide (lane 6, Figure 6a), irreversible inhibited the ubiquitylprotein-isopeptidase and no cleavage of ubiquitin calmodulin conjugates could be observed (lane 6, Figure 6a).
For visualization and standardised analysis ubiquitylated proteins in the organ tissues, we objectify by evaluation of two criteria: molecular weight and pixel intensity. western blot data were reduced to the densitogram scan (Phoretix 1D, nonlinear Dynamics LTD). Figure 6b and 6c shows the reduction of the densitogram scan of ubiquityl-calmodulin conjugates before (Figure 6b) and after (Figure 6c) incubation with the ubiquitylprotein-isopeptidase. as a result, unconjugated ubiquitin originated.
Incubation of organ tissues with ubiquitylprotein-isopeptidase
The incubation of the heart muscle APFII (Figure 7a) with the ubiquitylprotein-isopeptidase showed only little effect. The extract (Figure 7a) showed only a small signal level reduction in the photometric curve. A two-fold higher peak area is obtained for unconjugated ubiquitin in the extract of the heart muscle than before enzyme incubation. The incubation of heart muscle-APFII (see Figure 7b) showed no signal level reduction, but a 20-fold higher unconjugated ubiquitin level. There is a discrepancy between signal level reduction and the arise of unconjugated ubiquitin. Ubiquityl-calmodulin conjugates from order I and II in the heart muscle extract and APFII could not be observed.
Incubation of the white muscle-extract and APFII with the ubiquitylprotein-isopeptidase
The signal level in the high-molecular field of the white muscle-extract (Figure 8a) decreases after ubiquitylprotein-isopeptidase incubation (lane 3 and 6). A 68-fold higher unconjugated ubiquitin level is obtained after enzyme incubation without identification of any co-reactant of the ubiquitylprotein-isopeptidase. Of note, only the protein peak with a molecular weight of 27 kDa (Figure 8b), consistent with the ubiquityl-calmodulin conjugate first order, could be identified as a co-reactant of the ubiquitylprotein-isopeptidase. The incubation of the white muscle APFII demonstrates the signal level reduction of three protein peaks (see Figure 8c). These proteins have a molecular weight of 43, 27 and 14 kDa. The amount of unconjugated ubiquitin is negligible. A 3.1fold higher unconjugated ubiquitin level is obtained after enzyme incubation.
In conclusion, ubiquityl-calmodulin conjugates could only be detected in the reticulocyte APFII and in the white muscle extract (uCaM I) and APFII (uCaM I and uCaM II).
However, the western blots with affinity purified antibody showed a multiplicity of ubiquitin conjugates. To exclude a cross reactivity of the affinity purified ubiquitin antibody and to verify these conjugates as in vivo ubiquitin conjugates we incubated the organ tissues with trypsin, because trypsin can split ubiquitin-conjugates . The trypsinated ubiquitin is termed des-Gly-Glyubiquitin or ubiquitin-T. The last two amino acid of the ubiquitin were separated, because trypsin in general splits between the two amino acids arg and gly. The ubiquitin T it self, is resistant against further trypsin splitting.
The loss of trypsin incubation experiments is the absence of facility to distinguish between the decomposition product of the "mother-protein" or the multiubiquitin chains. Ubiquitin-T arises during the splitting of ubiquitin-chains. Of note, the ubiquitin antibody detected the ubiquitin-T 10-12 fold worser than unconjugated ubiquitin (data not shown). However, the occurrence of ubiquitin-T after trypsin incubation strongly indicates the existence of ubiquitin-conjugates in the organ tissues.
Trypsin-incubation of the heart muscle
After trypsin-incubation of the heart muscle-extract (Figure 9a and 9b) protein peaks with a molecular weight of 43, 24 and 13 kDa, indicating weaker signal intensity as the control. the signal level in the extract is clearly decreased by incubation with trypsin and ubiquitin-T originated. a new protein band is detected by the ubiquitinantibody at 7 kDa initially not detectable in the control. Presumably a degradation product of the ubiquitin-conjugate occurs in this case. the APFII of the heart muscle (Figure 9c) shows a general signal reduction. In particular the protein peaks with a molecular weight of 38 and 24 kDa showed a decrease of signal strength. Ubiquitint and a protein peak with a molecular weight of 7 kDa arise. also the heart muscle-APFII shows a decreasing signal intensity of all protein peaks detected. In this case ubiquitin-T and the protein peak with 7 kDa can be obtained.
Trypsin-incubation of the white muscle
The white muscle-extract (Figure 10a and 10b) shows a similar picture, in regard to reduction of signal intensity. after trypsin-incubation only a middle and low molecular protein "smear" could be detected. Ubiquitin-t and a 7 kDa protein arise after enzyme incubation. The proteins with a molecular weight of 63, 47, 38 and 29 kDa showed after incubation only weak protein peaks. In addition, white muscle APFII showed also a signal intensity reduction after trypsin incubation. Ubiquitin-T and a 7 kDa protein arise. the peak area of the ubiquitin is 7-fold higher in the APFII (Figure 10c) after trypsinincubation than in the control. both extract and APFII of the white muscle indicate a clear shift of protein peaks from higher molecular weight to lower molecular weight.
In all employed rabbit organs the ubiquitylproteinisopeptidase incubation led to a signal reduction of high molecular weight proteins and/or unconjugated ubiquitin. we identified for the first time in vivo ubiquitylcalmodulin conjugates in the investigated organ tissues. substrates of the ubiquitylprotein-isopeptidase could be identified and had a molecular weight between 30 and 40 kDa, consistent with the molecular weight of ubiquityl-calmodulin conjugates (ucaM I and uCaM II). the splitting of ubiquitin-conjugates with the ubiquitylprotein-isopeptidase is a new highly specific method for the detection of endogenous ubiquitin calmodulin conjugates in organ tissues.
The specificity of the ubiquitylprotein-isopeptidase implies that only the isopeptide bond is splited, leaving all other peptide bonds of the conjugated proteins intact. since isopeptidases are endoproteinase type hydrolases it is essential therefore that all other possible cleavages of amide bonds in the substrate proteins involved are excluded. The first natural ubiquityl-protein conjugate for which such a specific cleavage of an isopeptide bond could be shown [31–33] was the chromosomal protein A24 (ubiquityl-H2A semihistone, uH2A [68, 69]) which was also the very first protein conjugate of ubiquitin discovered and it was concluded that the ubiquitylation of histone A2 is a reversible process not related to ubiquitin dependent proteolysis . In this paper we demonstrated that a novel isopeptidase exists which splits ubiquityl-calmodulins and releases intact ubiquitin and calmodulin according to the following reaction scheme (n = 1 - 5):
Polyubiquitylated calmodulin is split into the two components: free calmodulin and free ubiquitin. Both the molecular mass and the amino acid composition (Table 1) are identical in the reaction products and the native proteins calmodulin and ubiquitin proving that only the connecting isopeptide bonds are cleaved leaving the primary structures intact. The enzyme splits the N...-ubiquityl-calmodulin bond which has been shown to be located in the n-terminal portion (amino acids 1- 107) of calmodulin . The amino acid to which calmodulin is linked is a lysine residue since methylation of calmodulin by formaldehyde followed by reduction (unpublished) abolishes ubiquitylation.
In the case of the enzyme incubation in this work the isopeptidase should have a high specificity, because only few proteins were deubiquitylated by this enzyme. In contrast to the trypsin-incubation all high molecular ubiquitin positive protein peaks were cleaved by trypsin and ubiquitin-T arises. This indicates a high specificity of the employed isopeptidase and underlines the theory of selective cleavage of ubiquityl-calmodulin conjugates in vivo.
Ubiquityl-calmodulin conjugates (uCaM I and uCaM II) would serve as "internal-standards" with the isopeptidease-incubation. The calmodulin is bound at position Lys 21 with the ubiquitin by means of a particular enzyme system . The deubiquitylation of proteins was induced by specific isopeptidases. These enzymes catalyse the cleavage of isopeptide bound of ubiquitin and the targed protein. Consequently unconjugated ubiquitin arises.
Isopeptidases have an important physiological function. They adjust disassembly of ubiquitylated proteins and consequently regulate the degradation of proteins by the 26S proteasome . This mechanism can be adjusted by the isopeptidases and/or can be made reversible so that this step in the degradation of ubiquitylated proteins is a key position.
Another possibility for the regulation of ubiquitylated proteins is E4 . E4 regulates the length of ubiquitin chains and therefore the degradation over the 26S proteasome. In the case of the non-catabole ubiquitylation the biological function is adjusted by deubiquitylation.
Furthermore, the possibility exists via the binding of ubiquitin to multiubiquitin chains to adjust the disassembly of ubiquitylated proteins. Ubiquitin possess seven lysines. It is theoretical possible that ubiquitin chains originates from every lysine in vitro. In vivo ubiquitin chains were only linked at Lys 6, Lys 11, Lys 29, Lys 48 and Lys 63. Only Lys 48 serves as a signal for disassembly via the 26S proteasome [72, 73]. Lys 63 serves as a DNA repair signal and the lysines: Lys 6, Lys 11, Lys 29 presumable for the receptor internalisation . In contrast to the ubiquitin-system, ubiquitin-like proteins such as the sentrines have their own isopeptidases. The isopeptidase Ulp1  and SENP1-SENP 7  divides exclusively sentrine-conjugates and can not cleave ubiquitinconjugates. It is improbable that ubiquitin-isopeptidases also cleave ubiquitin-like proteins. The binding of the sentrine-conjugates occurs similar to the ubiquitin-conjugates. Via a particular enzyme system, the sentrines were coupled in an ATP-depending manner to their target protein.
Cross-reactivity with ubiquitin-like proteins can be excluded, because of the high specifity of the primary antibody used in this work. However, ubiquitin-like proteins have their own, very specific isopeptidases [76–81].
Although an affinity purified ubiquitin antibody was employed, we surprisingly detected a great number of internal ubiquitin-conjugates. One possible explanation for these findings is the occurrence of cross-reactions with other proteins containing a great amino acid sequence homology. Haas  et al. described 1991 a typ 1 inducible "ubiquitin cross-reactive protein" (UCRP or ISG15). UCRP has a great sequence homology to ubiquitin and has a molecular weight of 15 kDa (see Table 3).
Both ubiquitin and UCRP are recognized at equimolar amount of an affinity purified polyclonal ubiquitinantibody . In contrast, affinity purified polyclonal UCRP-antibody reacts considerably worse with ubiquitin than UCRP . In a numerous of different organ tissues , for example lymphoid cells, smooth and stripped muscle, in epithelial cells and neurons, the UCRP was detected and has similar function like ubiquitin. A further "ubiquitin like-protein" was described in 1997. It is a protein regarding to the group of sentrines (Sentrin-1, Sentrin-2 und Sentrin-3). They were also called SUMO-1, PIC-1, GMP-1, UBL1 und SMT3C [85–92] and are detectable in all investigated tissues . Sentrines have a molecular weight of 6, 14 and 90 kDa. Sentrine-1 has 101 amino acids and possesses a ubiquitin-like domain (amino acid 22-97) which is 18% identical and 48% homologous (Table 3) to human ubiquitin. Sentrine-2 has 95 amino acids which are 46% identical and 66% homologous (Table 3) to Sentrin-1. Sentrine-3 has 103 amino acids which are 97% (Table 3) identical to Sentrin-2. Further ubiquitin-like proteins were described in 1997 (NEDD8)  and 1998 (Apg12) . NEDD8 and Rub1 have a molecular weight of 6 kDa.
Only for the UCRP experimental data exist, that ubiquitin-antibody reacts equimolar, what is to be traced back to the high sequence homology (up to 66%). Therefore, it can not be excluded that UCRP-conjugates represent a part of the found protein peaks. The fact however, that in the analyzed organ tissues no protein peak with a molecular weight of 15 kDa was detectable, and UCRP ubiquitously in the organs occur, opens improbably the cross-reaction with our ubiquitin-antibody and therefore also cross-reaction with UCRP-conjugates. In the work of Hinchey , no cross-reaction with ubiquitin was described for the Sentrine SUMO-1-2 and the SUMO-3. The Sentrine family members have a sequence homology of 16% to ubiquitin. This makes a cross-reaction very improbable with ubiquitin-antibody and was also confirmed experimentally from Hinchey . These are convincing arguments against the cross-reaction of sentrines and their conjugates with ubiquitin-antibody. In literature cross-reactions of ubiquitin-like proteins with ubiquitin-antibody are described as improbable.
The muscles were presumably degraded by the 26S proteasome in the situation of denavation , fasting , azidosis , tumor illness  and burning . Furthermore, first results for disassembly of muscle proteins via the 26S proteasome may be arranged: actin (42 kDa), myosin (510 kDa), troponine (78 kDa) and tropomyosine (64 kDa) . The ubiquitylated proteins found in this work are in accordance with the literature. However, in this study additional ubiquitylated proteins were detected which have not been described in the literature mentioned above. A possible interpretation is the different extraction conditions of muscles in the experimental settings. In the study of G. Tiao  septic rats were investigated. Lecker et al.  employed streptozotocin induced rats which developed diabetes mellitus. All organs employed in this work were gained from sacrificed rabbits under Nembutal®-sedation without induction of any stress factors and without further preparatory treatment. Ubiquitin is a heat shock protein and therefore induced in stress situations. The extraction conditions are crucial for the ubiquitylation pattern in organ tissues. The different "ubiquitylated organ patterns" could consequently be explained through the different experimental setups and different animal models. Presumably there are differences in the ubiquitylated organ patterns between two species.
The trypsin-incubation of organ tissues is a procedure to prove the existence of "internal" ubiquitin-conjugates. Here, trypsin (see material and methods) cleaves the last two amino acids of the ubiquitin and/or of the ubiquitin-conjugates and ubiquitin-T (des Gly-Gly ubiquitin) results. The protein peaks not detectable after incubation with trypsin are ubiquitin-conjugates. After trypsin-incubation decomposition products can often be observed. These decomposition products are splitted ubiquitin-T from the ubiquitin chains or the targeted protein. In all employed organ tissues a signal reduction of ubiquitylated proteins could be observed. Various decomposition partners (11 and 13 kDa) were detectable. Both proteins were cleaved by the ubiquitylprotein-isopeptidase and were detected by a calmodulinantibody (data not shown). This indicates that these proteins could presumably be composition products of ubiquitin-calmodulin conjugates. Trypsin itself generated new protein peaks initially not detectable with the ubiquitin-antibody. The protein peak with a molecular weight of 6 kDa could be the Sentrin NEDD8 and/or RUB1 . Both proteins have a molecular weight of 6 kDa. As described before a cross reaction by sentrine with an ubiquitin-antibody is improbable. Presumably it is a degradation product of ubiquitin.
This work is the first attempt to detect ubiquitylcalmodulin conjugate in vivo via ubiquitylprotein isopeptidase incubation. Further experiments had to be done to go more in detail for this question.
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This work was supported by grants (Je 84/8-1, Je 84/9-1) from the Deutsche Forschungsgemeinschaft. The authors appreciate the excellent technical assistance of G. Botzet †.
A retraction note to this article can be found online at http://dx.doi.org/10.1186/2047-783X-16-10-II.
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Sixt, S., Jennissen, H., Winterhalter, M. et al. Detection of ubiquityl-calmodulin conjugates with a novel high-molecular weight ubiquitylprotein-isopeptidase in rabbit tissues. Eur J Med Res 15, 428 (2010). https://doi.org/10.1186/2047-783X-15-10-428
- protein degradation