Proteases are associated with a minor fucoxanthin chlorophyll a/c-binding protein from the diatom,Chaetoceros gracilis

We previously showed that most subunits in the oxygen-evolving photosystem II (PSII) preparation from the diatom Chaetoceros gracilis are proteolytically unstable. Here, we focused on identifying the proteases that cleave PSII subunits in thylakoid membranes. Major PSII subunits and fucoxanthin chlorophyll (Chl) a/c‐binding proteins (FCPs) were specifically degraded in thylakoid membranes. The PSI subunits, PsaA and PsaB, were slowly degraded, and cytochrome f was barely degraded. Using zymography, proteolytic activities for three metalloproteases (116, 83, and 75 kDa) and one serine protease (156 kDa) were detected in thylakoid membranes. Two FCP fractions (FCP-A and FCP-B/C) and a photosystem fraction were separated by sucrose gradient centrifugation using dodecyl maltoside‐solubilized thylakoids. The FCP-A fraction featured enriched Chl c compared with the bulk of FCP-B/C. Zymography revealed that 116, 83, and 94 kDa metalloproteases were mostly in the FCP-A fraction along with the 156 kDa serine protease. When solubilized thylakoids were separated with clear-native PAGE, zymography detected only the 83 kDa metalloprotease in the FCP-A band. Because FCP-A is selectively associated with PSII, these FCP-A-associated metalloproteases and serine protease may be responsible for the proteolytic degradation of FCPs and PSII in thylakoid membranes.     

Promotion of Salvia miltiorrhiza hairy root growth and tanshinone production by polysaccharide–protein fractions of plant growth-promoting rhizobacterium Bacillus cereus

This study was to examine the effects of polysaccharides from a plant growth-promoting rhizobacterium (PGPR) Bacillus cereus on the growth and tanshinone production of Salvia miltiorrhiza hairy roots. A polysaccharide fraction designated BPS was isolated from the hot water extract of B. cereus cells by ethanol precipitation. BPS applied to the root culture at 100–400 mg l⁻¹ a few days before the stationary growth phase stimulated the tanshinone accumulation of roots by about 7-fold (1.59 mg g⁻¹ versus 0.19 mg g⁻¹) and also notably promoted the root growth (15% increase in biomass). BPS was a polysaccharide–protein complex containing about 27% protein, which is essential for root growth promotion. BPS was separated by ultrafiltration into two molecular weight (MW) fractions, of which the high MW fraction (∼35.8 kDa) with higher protein content (∼31%) promoted the root growth while the lower MW fraction with lower protein content (∼17%) suppressed the growth. The results suggest that the polysaccharide portion of BPS was responsible for stimulating the tanshinone accumulation while the protein portion was responsible for promoting the hairy root growth. Polysaccharides from PGPR are potential sources of active elicitors and growth-promoting agents for plant roots in culture.     

Hydroxyproline-O-glycosylated peptide tags enhance recombinant protein yields in tobacco transient expression

Plant transient expression provides a rapid production platform for recombinant proteins but is linked with low protein yields. To test if plant-specific hydroxyproline (Hyp)-O-glycosylated peptide tags attached to a target protein can improve overall yields of recombinant protein transiently expressed in Nicotiana benthamiana, enhanced green fluorescence protein (EGFP) was expressed as a fusion with 5 or 32 tandem repeats of a serine–proline motif, designated (SP)₅ or (SP)₃₂, which is known to direct extensive Hyp-O-glycosylation in plants. EGFP containing the (SP)_n motif showed enhanced yields in the order as follows: EGFP < EGFP-(SP)₅ ≪ (SP)₅-EGFP < (SP)₃₂-EGFP. The EGFP equivalent yield of (SP)₃₂-EGFP was up to 16-fold greater than that of the EGFP control. In addition, both fully glycosylated (SP)₃₂-EGFP (∼115 kDa) and partially glycosylated (SP)₃₂-EGFP (∼40 kDa) were detected in protein extracts of N. benthamiana. These two types of glycoforms were completely segregated between media and cells in tobacco BY-2 cell cultures.     

A novel angiotensin I-converting enzyme (ACE) inhibitory peptide from a marine Chlorella ellipsoidea and its antihypertensive effect in spontaneously hypertensive rats

Marine Chlorella ellipsoidea protein was hydrolyzed using Protamex, Kojizyme, Neutrase, Flavourzyme, Alcalase, trypsin, α-chymotrypsin, pepsin and papain. Alcalase-proteolytic hydrolysate exhibited the highest ACE inhibitory activity among them and was fractionated into three ranges of molecular weight (below 5 kDa, 5–10 kDa and above 10 kDa). The below 5 kDa fraction showed the highest ACE inhibitory activity and was used for subsequent purification steps. During consecutive purification, a potent ACE inhibitory peptide from marine C. ellipsoidea, which was composed of 4 amino acids, Val–Glu–Gly–Tyr (MW: 467.2 Da, IC₅₀ value: 128.4 μM), was isolated. Lineweaver–Burk plots suggest that the peptide purified acts as a competitive inhibitor against ACE and stable against gastrointestinal enzymes of pepsin, trypsin and α-chymotrypsin. Furthermore, antihypertensive effect in spontaneously hypertensive rats (SHRs) also revealed that oral administration of purified peptide can decrease systolic blood pressure significantly. The results suggest that marine C. ellipsoidea would be an attractive raw material for the manufacture of antihypertensive nutraceutical ingredients.     

Characterization of a highly efficient heterodimeric xylosidase from Humicola insolens

A heterodimeric xylosidase (E.C. 3.2.1.37) with robust activity is secreted among the plant cell wall degrading enzymes produced by the saprophytic fungus Humicola insolens. The xylosidase has been purified to homogeneity by gel filtration and cation exchange chromatography, and demonstrated to be composed of two protein subunits of 68 and 17 kDa with a molecular mass in solution of approximately 85 kDa based on a combination of SDS-PAGE, size exclusion chromatography and analytical ultracentrifugation. Peptide sequence identities from the subunits indicate the 68 kDa subunit contains a catalytic protein domain and the 17 kDa subunit a carbohydrate binding module. The xylosidase has wide biotechnological potential with maximum activity exhibited at 70 °C and kinetic constants with p-nitrophenol xylopyranoside substrate that suggest it has the highest catalytic efficiency recorded to date (Vmax 22.17 μmoles/min/mg, Km 1.74 mM and Kcat 6787/s).     

Dietary oils mediate cortisol kinetics and the hepatic mRNA expression profile of stress-responsive genes in gilthead sea bream (Sparus aurata) exposed to crowding stress. Implications on energy homeostasis and stress susceptibility

Juveniles of gilthead sea bream were fed with plant protein-based diets with fish oil (FO diet) or vegetable oils (66VO diet) as dietary lipid sources. No differences in growth performance were found between both groups, and fish with an average body mass of 65–70 g were crowded (90–100 kg/m³) to assess the stress response within the 72 h after the onset of stressor. The rise in plasma cortisol and glucose levels was higher in stressed fish of group 66VO (66VO-S) than in FO group (FO-S), but the former stressed group regained more quickly the cortisol resting values of the corresponding non-stressed diet group. The cell–tissue repair response represented by derlin-1, 75 kDa glucose-regulated protein and 170 kDa glucose-regulated protein was triggered at a lower level in 66VO-S than in FO-S fish. This occurred in concert with a long-lasting up-regulation of glucocorticoid receptors, antioxidant enzymes, enzyme subunits of the mitochondrial respiratory chain, and enzymes involved in tissue fatty acid uptake and β-oxidation. This gene expression pattern allows a metabolic phenotype that is prone to “high power” mitochondria, which would support the replacement of fish oil with vegetable oils when theoretical requirements in essential fatty acids for normal growth are met by diet.     

Differential protein expression for geothermal Agrostis scabra and turf-type Agrostis stolonifera differing in heat tolerance

Heat stress is a major factor limiting the growth of cool-season grasses in warm climatic regions by affecting many physiological processes, including protein metabolism. Protein degradation often occurs with increasing temperatures, but certain specific proteins such as heat shock proteins (HSPs) may be induced or enhanced in their expression under supraoptimal temperatures. The objectives of this study were to determine the critical temperature that causes protein induction or degradation in two Agrostis grass species differing in heat tolerance and to compare protein profiles between the two species under different temperature regimes. Plants of heat-tolerant Agrostis scabra and two cultivars of heat-sensitive Agrostis stolonifera (‘L-93’ and ‘Penncross’) were exposed to constant day/night temperatures of 20, 30, 35, 40, or 45 °C for 14 d. Leaf photochemical efficiency (Fv/Fm), chlorophyll and carotenoid contents, and soluble protein content declined with increasing temperatures. The decreases were the least severe for A. scabra, intermediate for ‘L-93’, and the most severe for ‘Penncross’, indicating interspecific and intraspecific variations in heat tolerance in Agrostis species. Protein degradation was observed at 30–45 °C in both cultivars of A. stolonifera, and at 40–45 °C in A. scabra.HSPs were induced or enhanced at 35–45 °C in ‘L-93’ and A. scabra, and at 40–45 °C in ‘Penncross’. Immunoblotting also revealed stronger expressions of HSP60 and HSP70 in A. scabra or ‘L-93’ than in ‘Penncross’ at 35–45 °C after 3 d. The results suggested the superior heat tolerance of Agrostis grass species and cultivars could be attributed to the early induction of HSPs, particularly small molecular weight (23 kDa), at a lower level of heat stress and the maintenance of protein thermostability, particularly high-molecular weight proteins (83 kDa and large units of Rubisco).     

Purification and characterization of recombinant Bacillus subtilis 168 catalase using a basic polypeptide from ribosomal protein L2

An efficient purification system for purifying recombinant Bacillus subtilis 168 catalase (KatA) expressed in Escherichia coli was developed. The basic region containing 252–273 amino acids derived from E. coli ribosomal protein L2 was used as an affinity tag while the small ubiquitin-like modifier (SUMO) was introduced as one specific protease cleavage site between the target protein and the purification tags. L2 (252–273)–SUMO fusion protein purification method can be effectively applied to purify the recombinant catalase using cation exchange resin. This purification procedure was used to purify the KatA and achieved a purification fold of 30.5, a specific activity of 48,227.2 U/mg and an activity recovery of 74.5%. The enzyme showed a Soret peak at 407 nm. The enzyme kept its activity between pH 5 and 10 and between 30 °C and 60 °C, with the highest activity at pH 8.0 and 37 °C. The enzyme displayed an apparent Km of 39.08 mM for hydrogen peroxide. These results agree well with the previous reports about B. subtilis catalase. L2 (252–273)–SUMO fusion protein purification technique provides a novel and effective fusion expression system for the production of recombinant proteins.     

Changes in protein quantities of phosphoenolpyruvate carboxylase and Rubisco activase in various wheat genotypes

In early seedlings of wheat genotypes two isoforms of Rubisco activase with molecular weights of 42 and 46 kDa are expressed. Amounts of both isoforms significantly increase in early seedlings of the durum wheat genotype Barakatli-95 exposed to salt stress. But at the beginning of the tillering stage, the changes in quantities of both RCA isoforms are different in durum and bread wheat genotypes subjected to a 3-day drought stress. In the leaves of the early seedlings of the studied wheat genotypes exposed to drought stress quantities of PEPC subunits increase compared to the control but they remain relatively stable in early roots and germinating seeds. However, quantities of its subunits decrease sharply in roots and germinating seeds of early seedlings under the influence of 100 mM NaCl. In flag leaves and ear elements of the Barakatli-95 genotype grown under normal water supply conditions protein quantities of PEPC subunits change differently depending on time. Changes in protein quantities of RCA, PEPC and Rubisco enzymes have been studied comparatively in ear elements and flag leaves after the fourth day of anthesis.     

Enzymatic degradation of amylouronate (α-(1 → 4)-linked glucuronan) by α-glucuronidase from Paenibacillus sp. TH501b

Enzymatic degradation of amylouronate (α-(1 → 4)-linked polyglucuronic acid sodium salt, α-(1 → 4)-linked glucuronan), which was prepared from water-soluble starch by 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated oxidation, was investigated. A bacterial strain TH501b capable of degrading amylouronate was isolated from soil samples collected in the natural environment. Molecular analysis of the 16S rRNA gene showed that TH501b belongs to the genus Paenibacillus. A hydrolytic enzyme responsible for the degradation of amylouronate, amylouronate hydrolase-I (AUH-I), was detected in the cell-free extract of TH501b. AUH-I was purified by four steps of column chromatography and some properties were characterized. The molecular mass of the native AUH-I was estimated to be approximately 115 kDa by size exclusion chromatography (SEC), whereas sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) showed two major bands at 80 kDa and 46 kDa, respectively. The enzyme was most active at pH 6.0–7.0 and 30 °C. The SEC analysis of reaction products revealed that AUH-I liberated glucuronate as a sole product from amylouronate, indicating that AUH-I hydrolyzed amylouronate exolytically, and thus, was classified as α-glucuronidase.     

The effect of limited hydrolysis with Neutrase and ultrafiltration on the anti-adipogenic activity of soy protein

Limited hydrolysis of isolated soy protein (ISP) with Neutrase for 4 h to obtain the hydrolysate (NH4h) revealed the ability to suppress glycerol-3-phosphate dehydrogenase (GPDH) activity and relative lipid accumulation (RLA) in 3T3-L1 cells during differentiation. Lower GPDH activity or RLA indicates higher anti-adipogenic activity. Sequentially fractionating NH4h with 30–1 kDa (kilo-daltons) molecular weight cut-off (MWCO) membranes to obtain the 1 kDa concentrate resulted in further enhancing its anti-adipogenic activity in the cells. The GPDH activity significantly decreased from 280 to 100 U/mg protein (p < 0.05). When comparing the high-performance size-exclusion chromatography (HPSEC) profiles, the most active peptide for the anti-adipogenic activity was primarily composed of peptides with molecular weight between 1300 and 2200 Da. The in vitro effect of gastrointestinal protease on the anti-adipogenic activity of 1 kDa concentrate was also investigated. The results suggested that gastrointestinal proteases have very little effect on anti-adipogenic activity of the concentrate. According to the Western immunoblot analysis, 1 kDa concentrate inhibits adipogenesis by affecting the expression of peroxisome proliferators-activated receptor γ (PPARγ) and the CCAAT/enhancer binding protein α (C/EBPα) during 3T3-L1 cells differentiation.     

Expression and purification of 15 kDa granulysin utilizing an insect cell secretion system

Granulysin is an antimicrobial and proinflammatory protein expressed in activated human T cells and natural killer cells. A single mRNA produces the 15 kDa isoform which is then cleaved at the amino and carboxy termini to produce the 9 kDa isoform. Recombinant 9 kDa granulysin has been studied in detail but little is known about the function of the 15 kDa isoform, and no protocol has been published describing expression and purification of this form. Two commercially available preparations of the recombinant 15 kDa granulysin contain tags that may affect function. Here we describe for the first time a method to produce 15 kDa granulysin as a secreted protein from insect cells. The 15 kDa granulysin is purified using a HiTrap Heparin column and a Resource S column. A typical a yield of purified 15 kDa granulysin is 0.6 mg/L of insect cell supernatant.     

Pre-analytical factors in clinical proteomics investigations: Impact of ex vivo protein modifications for multiple sclerosis biomarker discovery

Serum proteome investigations have raised an incredible interest in the research of novel molecular biomarker, nevertheless few of the proposed evidences have been translated to the clinical practice. One of the limiting factors has been the lack of generally accepted guidelines for clinical proteomics studies and the lack of a robust analytical and pre-analytical ground for the proposed classification models. Pre-analytical issues may results in a deep impact for biomarker discovery campaign. In this study we present a systematic evaluation of sample storage and sampling conditions for clinical proteomics investigations.We have developed and validated a linear MALDI-TOF-MS protein profiling method to explore the low protein molecular weight region (5–20 kDa) of serum samples. Data normalization and processing was performed using optimise peak detection routine (LIMPIC) able to describe each group under investigation. Data were acquired either from healthy volunteers and from multiple sclerosis patients in order to highlight ex vivo protein profile alteration related to different physio-pathological conditions. Our data showed critical conditions for serum protein profiles depending on storage times and temperatures: 23 °C, 4 °C, ? 20 °C and ? 80 °C. We demonstrated that upon a ? 20 °C short term storage, characteristic degradation profiles are associated with different clinical groups. Protein signals were further identified after preparative HPLC separation by peptide sequencing on a nanoLC-Q-TOF TANDEM mass spectrometer. Apolipoprotein A-IV and complement C3 protein fragments, transthyretin and the oxidized isoforms in different apolipoprotein species represent the major molecular features of such a degradation pattern.     

Influence of host plant nitrogen fertilization on hemolymph protein profiles of herbivore Spodoptera exigua and development of its endoparasitoid Cotesia marginiventris

Nitrogen has complex effects on plant–herbivore–parasitoid tritrophic interactions. The negative effects of low nitrogen fertilization in host plants on insect herbivores can be amplified to the higher trophic levels. In the present study, we examined the impact of varying nitrogen fertilization (42, 112, 196, and 280 ppm) of cotton plants (Gossypium hirsutum L.) on the interactions between the beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), and the hymenopteran endoparasitoid Cotesia marginiventris (Cresson) (Hymenoptera: Braconidae). We predicted that the development and fitness of C. marginiventris would be adversely affected by low host plant nitrogen fertilization through the herbivore S. exigua. The percentage of C. marginiventris offspring developing to emerge and spin a cocoon, and total mortality of parasitized S. exigua larvae were unaffected by nitrogen level. The developmental time of C. marginiventris larvae in S. exigua larvae feeding on low (42 ppm) nitrogen cotton plants was approximately 30% longer than that of those feeding on higher (112, 196, and 280 ppm) nitrogen plants. Parasitoid size (length of right metathoracic tibia), a proxy for fitness, of C. marginiventris males was positively affected by nitrogen level. Total amounts of S. exigua hemolymph proteins were not affected by nitrogen level, but were reduced by parasitism by C. marginiventris. Two proteins with molecular weights of ca. 84 and 170 kDa dominated the S. exigua larval hemolymph proteins. Concentrations of the 170 kDa hemolymph protein were unaffected by nitrogen treatment, but parasitism reduced concentrations of the 170 kDa protein. Concentrations of the 84 kDa protein, on the other hand, were interactively affected by parasitism and nitrogen treatment: higher nitrogen fertilization (112, 196, and 280 ppm) increased protein concentrations relative to the 42 ppm treatment for unparasitized S. exigua larvae, whereas nitrogen treatment had no effects on parasitized larvae. For S. exigua larvae feeding on 42 ppm nitrogen plants, parasitism increased concentration of the 84 kDa protein, while for those feeding on 112, 196, and 280 ppm nitrogen plants, parasitism decreased concentrations of the protein. Possible mechanisms and ecological consequences for the extended development of C. marginiventris on S. exigua hosts grown on low-nitrogen plants are discussed.     

The effects of age,energy and protein intake on protein turnover and the expression of proteolysis-related genes in the broiler breeder hen

A study was conducted to determine the changes that occur to proteolysis and related genes due to age, protein, and energy intake in high-yield broiler breeder hens (Gallus gallus). Cobb 700 broiler breeders were randomly assigned to one of six diets in a 2 × 3 factorial fashion. Two levels of energy (390 and 450 kcal/day) and three levels of protein (22, 24, and 26 g CP/day) were utilized. Protein turnover was determined in the left pectoralis at 22, 26, 31 and 44 weeks. Relative mRNA expression of calpain 2 (CAPN2), proteasome C2 subunit (PSMA1), and F box protein 32 (FBXO32) were determined via RT-PCR at 20, 25, and 44 weeks. Contrasts indicate fractional synthesis rate (FSR) and FBXO32 increase to a maximum at 25–26 weeks and a decrease thereafter. A significant drop in PSMA1 and FBXO32 was observed between 25 and 44 weeks and matched the decrease observed in FBR. No differences were detected in the levels of fractional synthesis and degradation, or the expression of CAPN2, PSMA1, and FBXO32, due to protein or energy intake. In summary, protein turnover was upregulated during the transition into sexual maturity and decreased thereafter. The observed changes in degradation appeared to be mediated by the ubiquitin–proteasome pathway.     

A mechanism based protein crosslinker for acyl carrier protein dehydratases

Recent advances in the structural study of fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic enzymes have illuminated our understanding of modular enzymes of the acetate pathway. However, one significant and persistent challenge in such analyses is resolution of the acyl carrier protein (ACP), a small (～9 kDa) protein to which biosynthetic intermediates are tethered throughout the biosynthetic cycle. Here we report a chemoenzymatic crosslinking strategy in which the installation of a historical suicide substrate scaffold upon the 4′-phosphopantetheine (PPant) arm of the ACP is used to capture the active site of acyl carrier protein dehydratase (DH) domains in FAS. Through the synthesis of a small panel of related probes we identify structural features essential for ACP–DH crosslinking, and apply gel-based assays to demonstrate the stability as well as purification strategies for isolation of the chemoenzymatically modified ACP. Applying these carrier protein crosslinking techniques to the structural analysis of FAS and PKS complexes has the potential to provide snapshots of these biosynthetic assembly lines at work.     

Role of the two ATPase domains of Escherichia coli UvrA in binding non-bulky DNA lesions and interaction with UvrB

The UvrA protein is the initial DNA damage-sensing protein in bacterial nucleotide excision repair and detects a wide variety of structurally unrelated lesions. After initial recognition of DNA damage, UvrA loads the UvrB protein onto the DNA. This protein then verifies the presence of a lesion, after which UvrA is released from the DNA.UvrA contains two ATPase domains, both belonging to the ABC ATPase superfamily. We have determined the activities of two mutants, in which a single domain was deactivated. Inactivation of either one ATPase domain in Escherichia coli UvrA results in a complete loss of ATPase activity, indicating that both domains function in a cooperative way. We could show that this ATPase activity is not required for the recognition of bulky lesions by UvrA, but it does promote the specific binding to the less distorting cyclobutane–pyrimidine dimer (CPD). The two ATPase mutants also show a difference in UvrB-loading, depending on the length of the DNA substrate. The ATPase domain I mutant was capable of loading UvrB on a lesion in a 50 bp fragment, but this loading was reduced on a longer substrate. For the ATPase domain II mutant the opposite was found: UvrB could not be loaded on a 50 bp substrate, but this loading was rescued when the length of the fragment was increased. This differential loading of UvrB by the two ATPase mutants could be related to different interactions between the UvrA and UvrB subunits.