Cyanophycin granule polypeptide protease in a unicellular cyanobacterium

An assay was developed to measure the proteolysis of cyanophycin granule polypeptide in crude extracts of a unicellular cyanobacterium. The substrate was radioactively labeled cyanophycin granule polypeptide formed by an unicellular cyanobacterium grown in the presence of chloramphenicol. Substrate polypeptide displayed identical chemical properties with polypeptide isolated from non-chloramphenicol-treated cells. Solubilization of radioactivity as arginine indicated hydrolysis of polypeptide. Radioactively labeled aspartate and arginine from hydrolyzed polypeptide was related to nmol amino acid using a combination of paper chromatography, liquid scintillation analysis, and ninhydrin quantitation. Protease activity was found in extracts of nitrogen-limited cells harvested 16–24 h after a nitrogen source was added back. Optimal pH for protease activity was 8.0 and optimum temperature was 35°C. Protease activity in crude extracts followed Michaelis-Menten kinetics with a V _max of 92 nmol arginine per 15 min/mg protein and a K _m of 2.1×10³ nmol arginine. Protease activity was inhibited by arginine and by high concentrations of aspartate.     

Protein hydrolysates from Bluefin Tuna (Thunnus thynnus) heads as influenced by the extent of enzymatic hydrolysis

Functional properties and antioxidant activities of protein hydrolysates from tuna (Thunnus thynnus) heads (THPHs), with different degrees of hydrolysis, obtained by treatment with Bacillus mojavensis A21 alkaline proteases and Alcalase, were investigated. Protein content of all freeze-dried THPHs ranged from 73.74 ± 0.5 to 78.56 ± 1.2%. The THPHs had excellent solubility, compared to untreated tuna head proteins and possessed interfacial properties, which were governed by their concentrations. Similarly, at a degree of hydrolysis (DH) of 12 and 15%, > 90% nitrogen solubility was observed at all experimental pH values tested. The emulsifying activity index (EAI) and emulsion stability index (ESI) of both hydrolysates at different DHs decreased (p < 0.05) with increasing DH. At low DH (5%), hydrolysates exhibited strong emulsifying properties. All THPHs produced by the A21 proteases generally showed higher antioxidative activity than that of the Alcalase protein hydrolysates. The highest DPPH radical-scavenging activity (78 ± 2.1% at 3 mg/mL) was obtained with a DH of 15%. The IC₅₀ value for the β-carotene bleaching assay was 0.5 ± 0.03 mg/mL. Alcalase (DH = 12%) and A21 (DH = 15%) protein hydrolysates contained glutamic acid/glutamine and arginine as the major amino acids, followed by lysine, aspartic acid/ asparagine, histidine, valine, phenylalanine, and leucine. In addition, the THPHs had a high percentage of essential amino acids, which made up 50.52 and 50.47%, of the protein hydrolysates obtained by the Alcalase and A21 proteases, respectively. Therefore, THPHs can be used as a promising source of functional peptides with antioxidant properties.     

THE NATURE OF THE IONIZABLE GROUPS IN PROTEINS

Analysis of the experimental titration curves shows that gelatin contains acid groups with dissociation indices at pH 2.9 to 3.5 corresponding quantitatively with the content in dicarboxylic amino acids; and that the acidic group at pH 9.4 in egg albumin agrees with the amount of tyrosine. The amounts of histidine and lysine present in both these proteins agree quantitatively with basic groups at pH 6.1 and pH 10.4 to 10.6, respectively. However, the quantity of the arginine group (pH 8.1) in these proteins is considerably less than the amount of arginine found on hydrolysis. This deficiency is compensated (quantitatively with gelatin and approximately with egg albumin) by a basic group at pH 4.6. The structure of this "4.6 group" should be similar to aniline and cytosine in consisting of an amino group on a conjugated unsaturated (perhaps cyclic) system. It would appear that the 4.6 group is disrupted on hydrolysis, producing arginine, and may be referred to as "prearginine." The presence of prearginine in proteins, instead of the full amount of arginine, has an important effect on the properties. Otherwise the isoelectric point of gelatin would be 8.0 (instead of 4.7) and of egg albumin 6.6 (instead of 4.8), and the titration curves would be quite different in shape between pH 4 and 10. Deamination of gelatin produces no decrease in prearginine, arginine, or histidine groups, but removes nearly all of the lysine group.     

THE PREARGININE IN EDESTIN AND ITS RESISTANCE TO HYDROLYSIS

The titration data of edestin show that all the arginine found on hydrolysis exists in this protein as "prearginine." The extra ionizable groups of histidine, lysine and tyrosine are free in the quantities found on hydrolysis. Part of the extra carboxyl groups of aspartic and glutamic acids are bound as amides, and 50 per cent are bound in some other manner (perhaps anhydride) leaving only about 6 per cent of these groups free to ionize in edestin. The prearginine in edestin is not converted into arginine on hydrolysis with pepsin up to 18 per cent (of the total hydrolysis). In more highly hydrolyzed solutions it is not possible to detect such a conversion, due to high buffering. Complete hydrolysis however converts prearginine into arginine which can be isolated. Hydrolyzed edestin promotes the growth of sarcomatous fibroblasts about equally well whether 5, 14 or 18 per cent hydrolyzed.     

Characterization and determination of titratable groups of proteins by linearization of titration curves. II. Application to lysozyme

The potentiometric acid-base titration curve of fully protonated lysozyme at ionic strengths of 0.10 and 1.0 m has been performed. The stoichiometry and the pK_a values of each titratable group have been determined through the linearization of titration curves. Two types of carboxylic groups with pK_a values of 3.76 and 5.02, the imidazole group with pK_a 7.37 and the amine group with pK_a 9.63, have been identified at an ionic strength of 0.10 m at 25.0°C. The number of titratable groups found per mole of protein has been 5.12 and 5.60 for the two types of carboxylic groups, 1.13 for the imidazole group, and 3.19 for the amino groups. The endpoint of the titration of the protein obtained by this method accords quite well with the endpoint obtained by the use of Gran function applied to the excess of strong base.     

pH-dependent random coil 1H, 13C,and 15N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements

The pK _a values and charge states of ionizable residues in polypeptides and proteins are frequently determined via NMR-monitored pH titrations. To aid the interpretation of the resulting titration data, we have measured the pH-dependent chemical shifts of nearly all the ¹H, ¹³C, and ¹⁵N nuclei in the seven common ionizable amino acids (X = Asp, Glu, His, Cys, Tyr, Lys, and Arg) within the context of a blocked tripeptide, acetyl-Gly-X-Gly-amide. Alanine amide and N-acetyl alanine were used as models of the N- and C-termini, respectively. Together, this study provides an essentially complete set of pH-dependent intra-residue and nearest-neighbor reference chemical shifts to help guide protein pK _a measurements. These data should also facilitate pH-dependent corrections in algorithms used to predict the chemical shifts of random coil polypeptides. In parallel, deuterium isotope shifts for the side chain ¹⁵N nuclei of His, Lys, and Arg in their positively-charged and neutral states were also measured. Along with previously published results for Asp, Glu, Cys, and Tyr, these deuterium isotope shifts can provide complementary experimental evidence for defining the ionization states of protein residues.     

Identification and characterization of the ATP·Mg-dependent protein phosphatase activator (F A) as a microtubule protein kinase in the brain

The activating factor of ATP·Mg-dependent protein phosphatase (F _A) has been identified in brain microtubules. When using purified MAP-2 (microtubule associated protein 2) and tau proteins as substrates,F _A could phosphorylate MAP-2 to 16 moles of phosphates per mole of protein with aK _m value of 0.4 µM, and tau proteins to 4 moles of phosphates per mole of proteins with aK _m value of about 3 µM. When using microtubules as substrates,F _A could enhance many-fold the endogenous phosphorylation of many microtubule-associated proteins including MAP-2, tau proteins, and several low-molecular-weight MAPs. In contrast to other reported MAP kinases, such as cAMP-dependent protein kinase and Ca⁺²/phospholipid-dependent protein kinase, theF _A-catalyzed phosphorylation of tau proteins could cause an electrophoretic mobility shift on sodium dodecyl sulfate polyacrylamide gel electrophoresis, suggesting that a dramatic conformational change of tau proteins was produced byF _A. Peptide mapping analysis of the phosphopeptides derived from SV8 protease digestion revealed thatF _A could phosphorylate MAP-2 and tau proteins on at least four specific sites distinctly different from those phosphorylated by cAMP-dependent and Ca⁺²/phospholipid-dependent MAP kinases. Quantitative analysis further indicated that approximately 19% of the total endogenous kinase activity in brain microtubules was due toF _A. Taken together, the results provide initial evidence that the ATP·Mg-dependent protein phosphatase activating factor (F _A) is a potent and unique MAP kinase, and may represent one of the major factors involved in phosphorylation of brain microtubules.     

Properties of arginase from liver of Macaca fascicularis: Comparison of normals with red blood cell arginase deficient monkeys

Deficiency of arginase (E.C. 3.5.3.1), the fifth enzyme of the urea cycle, was found in the red blood cells (RBCs) of Macaca fascicularis monkeys (<0.2 µmol arginine cleaved/g Hb/min; normal =49.2). Liver biopsies were obtained from two of these monkeys and from one monkey with normal levels of RBC arginase activity. Arginase from both groups of animals required Mn²⁺ for maximal enzyme activity and demonstrated a pH optimum of 10.2 in vitro. The activity of arginase in the livers of all three monkeys was 1.1 mmol arginine cleaved/g protein/min. The apparent K _m for arginine of arginase in the livers of the RBC-deficient monkeys was 7.4 and 5.9mm and in the normal monkey was 6.9mm. Similar patterns of heat denaturation were seen at 69 C without Mn²⁺ present and 79 C in the presence of 20mm Mn²⁺. No difference in mobility on either acidic or basic polyacrylamide gels for liver arginase from either RBC-deficient or normal monkeys was found. In addition, liver arginase from all three monkeys reacted similarly with anti-human liver arginase antibody. Liver arginases in RBC-deficient and normal monkeys were identical by ten criteria. These studies do not distinguish among several hypotheses for the genetic determination of arginase in different organs of this species and of man.     

Binding interactions in a kinase active site modulate background ATP hydrolysis

Kinases play central roles in many cellular processes, transferring the terminal phosphate groups of nucleoside triphosphates (NTPs) onto substrates. In the absence of substrates, kinases can also hydrolyse NTPs producing NDPs and inorganic phosphate. Hydrolysis is usually much less efficient than the native phosphoryl transfer reaction. This may be related to the fact that NTP hydrolysis is metabolically unfavorable as it unproductively consumes the cell's energy stores. It has been suggested that substrate interactions could drive changes in NTP binding pocket, activating catalysis only when substrates are present. Structural data show substrate-induced conformational rearrangements, however there is a lack of corresponding functional information. To better understand this phenomenon, we developed a suite of isothermal titration calorimetry (ITC) kinetics methods to characterize ATP hydrolysis by the antibiotic resistance enzyme aminoglycoside-3′-phosphotransferase-IIIa (APH(3′)-IIIa). We measured K_m, k_cat, and product inhibition constants and single-turnover kinetics in the presence and absence of non-substrate aminoglycosides (nsAmgs) that are structurally similar to the native substrates. We found that the presence of an nsAmg increased the chemical step of cleaving the ATP γ-phosphate by at least 10- to 20-fold under single-turnover conditions, supporting the existence of interactions that link substrate binding to substantially enhanced catalytic rates. Our detailed kinetic data on the association and dissociation rates of nsAmgs and ADP shed light on the biophysical processes underlying the enzyme's Theorell-Chance reaction mechanism. Furthermore, they provide clues on how to design small-molecule effectors that could trigger efficient ATP hydrolysis and generate selective pressure against bacteria harboring the APH(3′)-IIIa.     

Composition of the cell wall and other fractions of the autolyzed yeast form of Histoplasma capsulatum

Comparison of two strains ofHistoplasma capsulatum yielded data differing only in quantification, and the constituents observed and identified were galactose, glucose, mannose, glucosamine and amino acids. A comparison of hydrochloric acid and formic acid hydrolyses ofH. capsulatum fractions indicated hydrochloric acid to be of more value than 88 per cent formic acid hydrolysis for composition analyses. The removal of formyl esters from formic acid hydrolysates was found necessary and was accomplished byN HCl hydrolysis for 30 min. Two derivative artifacts were observed with formic acid hydrolysis; D-1, which was refractory to subsequent HCl hydrolysis, and D-2, which disappeared after HCl hydrolysis. Another artifact, D-3, was observed with 6N HCl hydrolysis of histoplasma cell wall fractions. The following conditions of hydrolysis were found to be useful: (1) glucose release was measured after hydrolysis inN HCl for 4 hr; (2) glucosamine release was measured after hydrolysis in 6N HCl for 9 hr; (3) amino acid release was accomplished by 6N HCl hydrolysis for 18 hr; and (4), hexoses released were determined by gas liquid chromatography (GLC) after hydrolysis in bothN HCl and in 88 per cent formic acid for 24 hr, followed byN HCl for 30 min. Several different types of carbohydrate polymers have been reported in the parasitic yeast form ofH. capsulatum. There is general agreement on the occurrence of amino acids as protein (8, 12, 13), chitin (7, 19) and several hexoses, including glucose and glucosamine, which are found in cell wall polymers (7, 8, 11–16, 19, 20, 24). The presence of uronic acid was also reported (14, 15), but not confirmed, by Domer, Hamilton & Harkin (8), and mannose was not found by all investigators (12). We undertook a study of graded acid hydrolyses and of composition analysis of the autolysis products of the yeast form by various procedures in order to add further to the above information.     

The natural non-protein amino acid N-β-methylamino-l-alanine (BMAA) is incorporated into protein during synthesis

N-β-methylamino-l-alanine (BMAA) is an amino acid produced by cyanobacteria and accumulated through trophic levels in the environment and natural food webs. Human exposure to BMAA has been linked to progressive neurodegenerative diseases, potentially due to incorporation of BMAA into protein. The insertion of BMAA and other non-protein amino acids into proteins may trigger protein misfunction, misfolding and/or aggregation. However, the specific mechanism by which BMAA is associated with proteins remained unidentified. Such studies are challenging because of the complexity of biological systems and samples. A cell-free in vitro protein synthesis system offers an excellent approach for investigation of changing amino acid composition in protein. In this study, we report that BMAA incorporates into protein as an error in synthesis when a template DNA sequence is used. Bicinchoninic acid assay of total protein synthesis determined that BMAA effectively substituted for alanine and serine in protein product. LC–MS/MS confirmed that BMAA was selectively inserted into proteins in place of other amino acids, but isomers N-(2-aminoethyl)glycine (AEG) and 2,4-diaminobutyric acid (DAB) did not share this characteristic. Incorporation of BMAA into proteins was significantly higher when genomic DNA from post-mortem brain was the template. About half of BMAA in the synthetic proteins was released with denaturation with sodium dodecylsulfonate and dithiothreitol, but the remaining BMAA could only be released by acid hydrolysis. Together these data demonstrate that BMAA is incorporated into the amino acid backbone of proteins during synthesis and also associated with proteins through non-covalent bonding.     

A virus inhibitory protein isolated from Cyamopsis tetragonoloba (L.) Taub. upon induction of systemic antiviral resistance shares partial amino acid sequence homology with a lectin

Key message

Two virus inhibitory proteins were purified from Cyamopsis tetragonoloba , induced to resist virus infections by CIP-29, a systemic resistance inducing protein from Clerodendrum inerme , and characterized. One of them shared homology with a lectin.

Abstract

CIP-29, a known 29 kDa systemic antiviral resistance inducing protein isolated from Clerodendrum inerme, has been used to induce systemic resistance in Cyamopsis tetragonoloba against Sunn-hemp rosette virus (SRV). Paper reports the detection of virus inhibitory activity in induced-resistant leaf sap of C. tetragonoloba, and the purification of two virus inhibitory agents (VIAs) thereof. VIA activity was recorded as a reduction in lesion number of SRV, Tobacco mosaic virus, and Papaya ringspot virus, when they were incubated separately with resistant sap and inoculated onto susceptible C. tetragonoloba, Nicotiana tabacum cv. Xanthi-nc, and Chenopodium quinoa, respectively. The two VIAs were isolated from resistant C. tetragonoloba plant leaves using combinations of column chromatography. Both were basic proteins, and since their M _r was 32 and 62 kDa, these VIAs were called CT-VIA-32 and CT-VIA-62, respectively, on the basis of their molecular mass and the host. CT-VIA-62 displayed better activity, and was thus studied further. It tested positive for a glycoprotein, and was serologically detected only in leaf tissue post-induction. Tryptic peptides generated in-gel, post SDS-PAGE of CT-VIA-62, were sequenced through LC/MS/MS. All CT-VIA-62 peptides were found to share homologies with proteins from Medicago truncatula that possess a mannose-binding lectin domain.     

Photosystem II recovery in the presence and absence of chloroplast protein repair in the symbionts of corals exposed to bleaching conditions

Increased seawater temperature causes photoinhibition due to accumulation of photodamaged photosystem II (PSII) in symbiotic algae (genus Symbiodinium) within corals, and it is assumed to be associated with coral bleaching. To avoid photoinhibition, photosynthetic organisms repair the photodamaged PSII through replacing the PSII proteins, primarily the D1 protein, with newly synthesised proteins. However, in experiments using cultured Symbiodinium strains, the PSII repair of Symbiodinium has been suggested not to be related to the synthesis of the D1 protein. In this study, we examined the relationship between the recovery of PSII photochemical efficiency (F _V/F _M) and the content of D1 protein after high-light and high-temperature treatments using the bleaching-sensitive coral species, Pocillopora damicornis and Acropora millepora, and the bleaching-tolerant coral species, Montipora digitata and Pavona decussata. When corals were exposed to strong light (600 µmol photons m^?2 s^?1) at elevated temperature (32 °C) for 8 h, significant bleaching occurred in bleaching-sensitive coral species although an almost similar extent of reduced PSII function was found across all coral species tested. During a subsequent 15-h recovery under low light (10 µmol photons m^?2 s^?1) at optimal temperature (22 °C), the reduced F _V/F _M recovered close to initial levels in all coral species, but the reduced D1 content recovered only in one coral species (Pavona decussata). D1 content was therefore not strongly linked to chloroplast protein synthesis-dependent PSII repair. These results demonstrate that the recovery of photodamaged PSII does not always correspond with the recovery of D1 protein content in Symbiodinium within corals, suggesting that photodamaged PSII can be repaired by a unique mechanism in Symbiodinium within corals.     

Structural studies of a human hybrid immunoglobulin

The structure of an hypothesized hybrid or “Lepore-type” IgG contained in the serum of donor 2904 was investigated. Previous immunological studies suggested that this serum contained IgG with aγ3-γ1 hybrid heavy chain consisting of aγ3 Fd portion and aγ1 Fc. Structural studies have now shown that the carboxyl terminal end of the 2904 hybrid IgG, including much of the Fc fragment, isγ1 in character. However, the fingerprints of the Fc tryptic peptides at both pH 3.6 and pH 6.4 included a peptide, possibly from the hinge region, in peptide maps of Fc from aγG3 Gm (5) myeloma protein, but absent from maps of Fc peptides fromγG1 proteins. Gel filtration of the CNBr fragments of Fc from 2904 suggested that the hinge region isγ3-like. Papain cleavage experiments indicated an elevated level of resistant IgG, which agrees with immunological findings of an increasedγG2 subclass level. Our data confirm previous reports that theγ chain C-terminal octadecapeptides fromγG3 proteins have a subclass specific residue of arginine and indicate that within this subclass there is an allotypic variation related to the Gm type of the protein.     

Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Key message

We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species.

Abstract

Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F₅ recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene—a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.     

The protein sequence homology of γ-crystallins among major vertebrate classes and their DNA sequence homology to heat-shock protein genes

A systematic characterization of lens crystallins from five major classes of vertebrates was carried out by exclusion gel filtration, cation-exchange chromatography and N-terminal sequence determination. All crystallin fractions except that of γ-crystallin were found to be N-terminally blocked. γ-Crystallin is present in major classes of vertebrates except the bird, showing none, or decreased amounts, of this protein in chicken and duck lenses, respectively. N-Terminal sequence analysis of the purified γ-crystallin polypeptides showed extensive homology between different classes of vertebrates, supporting the close relatedness of this family of crystallin even from the evolutionarily distant species. Comparison of nucleotide sequences and their predicted amino acid sequences between γ-crystallins of carp and rat lenses and heat-shock proteins demonstrated partial sequence homology of the encoded polypeptides and striking homology at the gene level. The unexpected strong homology of complementary DNA (cDNA) lies in the regions coding for 40 N-terminal residues of carp γ-II, rat γ2-1, and the middle segments of 23,000- and 70,000-M _r heat-shock proteins. The optimal alignment of DNA sequences along these two segments shows about 50% homology. The percentage of protein sequence identity for the corresponding aligned segments is only 20%. The weak sequence homology at the protein level is also found between the invertebrate squid crystallin and rat γ-crystallin polypeptides. These results pointed to the possibility of unifying three major classes of vertebrate crystallins into one α/β/γ superfamily and corroborated the previous supposition that the existing crystallins in the animal kingdom are probably mutually interrelated, sharing a common ancestry.     

Potentiometric titration studies on globular proteins

A power series method was applied to solve the Poisson-Boltzmann equation for the spherical polyelectrolyte model and numerical calculation with an electronic computer was performed to obtain surface electric potential on rigid globular proteins. Deviation from the ideal linear relationship in Linderstrom-Lang's plot was found to become noticeable as the surface charge density and the radius of protein increases and ionic strength decreases. The calculated surface potential was compared with potentiometric titration data of several proteins whose radii have been analyzed. Assuming the radius of the counterions to be equal to about 1.0 Å, the data for phenolic groups in ribonuclease and for carboxyl groups in conalbumin were interpreted. Reversible intramolecular transformation was found for α-lactalbumin by comparing the present results with the potentiometric titration data for carboxyl groups. The molecular size of each protein was discussed.     

The localization of auxin transporters PIN3 and LAX3 during lateral root development in Arabidopsis thaliana

Fluorophore tagged proteins are used in Arabidopsis thaliana to understand their functional role in plant development. This requires the analysis of their spatial localization in planta. However, the localization analysis is often perturbed by a significant overlap of the fluorophores used to label proteins of interest and the optical filtering methods available on the confocal microscope. This problem can be addressed by the use of spectral imaging with linear unmixing the image data. We applied this method to help us identify double transgenic A. thaliana lines which expressed two fluorescently tagged auxin transporter proteins: the auxin efflux protein PIN-FORMED-3 (PIN3), tagged with green fluorescent protein (GFP), and the auxin influx protein LIKE-AUX1-3 (LAX3), tagged with yellow fluorescent protein (YFP). This method allows the reliable separation of overlapping GFP and YFP fluorescence signals and subsequent localization analysis highlighting the potential benefit of this methodology in studies of lateral root development.