Secretory signal sequence non-optimal codons are required for expression and export of beta-lactamase

In this study we altered the codon usage in the signal sequence of the bla gene, encoding β-lactamase in Escherichia coli. Changing all of the thirteen non-optimal codons to optimal lowered expression 4-fold as measured by minimum inhibitory concentration (MIC) to the β-lactam antibiotic ampicillin. The difference in ampicillin resistance was reduced at 28 °C compared to expression at 37 °C, suggesting that the optimised bla allele is misfolded and degraded by heat-shock regulated proteases. A screen was carried out, designed specifically to identify revertants with changes in codon usage resulting in higher MIC to ampicillin. The nine revertants revealed by this method all had optimal to non-optimal codon changes in the signal sequence. These results, and those of our previous study with maltose binding protein model system, confirm that non-optimal codons are important for expression and export of secretory proteins via both the SecB-dependent and -independent pathways.     

Experimental confirmation of a key role for non-optimal codons in protein export

Non-optimal codons are defined by low usage and low abundance of corresponding tRNA, and have an established role in translational pausing to allow the correct folding of proteins. Our previous work reported a striking abundance of non-optimal codons in the signal sequences of secretory proteins exported via the sec-dependent pathway in Escherichia coli. In the current study the signal sequence of maltose-binding protein (MBP) was altered so that non-optimal codons were substituted with the most optimal codon from their synonymous codon family. The expression of MBP from the optimized allele (malE-opt) was significantly less than wild-type malE. Expression of MBP from malE-opt was partially restored in a range of cytoplasmic and periplasmic protease deficient strains, confirming that reduced expression of MBP in malE-opt was due to its preferential degradation by cytoplasmic and periplasmic proteases. These data confirm a novel role for non-optimal codon usage in secretion by slowing the rate of translation across the N-terminal signal sequence to facilitate proper folding of the secreted protein.     

Directed evolution of efficient secretion in the SRP-dependent export of TolB

Signal sequence non-optimal codons have been shown to be important for the folding and efficient export of maltose binding protein (MBP), a SecB dependent protein. In this study, we analysed the importance of signal sequence non-optimal codons of TolB, a signal recognition particle (SRP) dependent exported protein. The protein production levels of wild type TolB (TolB-wt) and a mutant allele of TolB in which all signal sequence non-optimal codons were changed to a synonymous optimal codon (TolB-opt), revealed that TolB-opt production was 12-fold lower than TolB-wt. This difference could not be explained by changes in mRNA levels, or plasmid copy number, which was the same in both strains. A directed evolution genetic screen was used to select for mutants in the TolB-opt signal sequence that resulted in higher levels of TolB production. Analysis of the 46 independent TolB mutants that reverted to wild type levels of expression revealed that at least four signal sequence non-optimal codons were required. These results suggest that non-optimal codons may be required for the folding and efficient export of all proteins exported via the Sec system, regardless of whether they are dependent on SecB or SRP for delivery to the inner membrane.     

Influence of dietary protein levels and water temperature on growth,body composition and nutrient utilization of Cirrhinus mrigala (Hamilton, 1822) fry

The experiment was conducted to determine the protein requirement of Cirrhinus mrigala fry at three different water temperatures, 28, 30 and 32 °C, and to investigate the influence of dietary protein levels and water temperatures on weight gain, body composition, food and nutrient utilization. The 36% protein concentration in the diet yielded highest weight gain at all temperatures from 28 to 32 °C. However, daily protein intake was lower at 28 °C than at 30 and 32 °C. The diet with 36% dietary protein and 32.17% carbohydrate produced the best weight gain and gross conversion efficiency (GCE) at 30 °C. The protein-sparing effect was observed at temperatures 30 and 32 °C in diets 1 and 2, having carbohydrate levels 37.36–44.91%. Highest protein efficiency ratio (PER) was recorded at 28% dietary protein level, while it was lowest at 40% dietary protein level in all three temperatures. Lipid in the body of fishes increased at the end of the experiment in comparison to the initial body lipid. The body protein was found to be related to daily protein intake at 30 and 32 °C. Significant difference (P<0.05) was also noted between temperatures, the hepatosomatic index (HSI) and viscerosomatic index (VSI). The diet with 36% dietary protein and 32.17% carbohydrate was observed to be the best diet for C. mrigala fry at 28–32 °C.     

Thermal stability properties of an antifreeze protein from the desert beetle Microdera punctipennis

An insect antifreeze protein gene Mpafp698 was cloned by the RT-PCR approach from the desert beetle Microdera punctipennis. The gene was constructed and heterogeneously expressed in Escherichia coli as fusion proteins, His-MpAFP698, glutathione S-transferase (GST)-MpAFP698, and maltose-binding protein (MBP)-MpAFP698. The thermostability and thermal hysteresis activity of these proteins were determined, with the aim of elucidating the biological characteristics of this protein. The approximate thermal hysteresis (TH) value of the purified His-MpAFP698 was 0.37 °C at 0.84 mg/ml, and maintained approximately 95.7% of the TH activity at 100 °C for 5 min. Furthermore, heat incubation showed that MBP-MpAFP698 was 10 °C more thermostable than MBP protein, indicating that MpAFP698 could, to some extent, improve the thermal stability of the fused partner MBP protein. This study suggests that MpAFP698 has a high thermal stability and could be used to improve the thermal stability of the less stable proteins by producing fusion proteins, which could be used for biotechnological purposes.     

Evidence for aluminum-binding erythropoietin by size-exclusion chromatography coupled to electrothermal absorption atomic spectrometry

Erythropoietin (EPO) is a glycoprotein that stimulates erythropoiesis and is clinically used for treating anemia during chronic renal failure and for anemia in preterm infants. EPO formulations usually have elevated rates of contamination due to aluminum (Al), which is toxic to both types of patients. Size-exclusion chromatography (SEC) coupled with graphite furnace atomic absorption spectrometry (GF AAS) was employed to separate proteins and to quantify the amount of aluminum present in the elution volume corresponding to EPO and, therefore, to evaluate possible binding. Because EPO formulations contain human serum albumin (HSA), a chromatographic method was optimized for the separation of these proteins. Subsequent to the chromatographic separation, 1-mL fractions of the column effluent were collected, and the Al content in these aliquots was measured by GF AAS. EPO and HSA samples were incubated with Al for 4 h at 4 °C and 37 °C as well as for 16 h at 4 °C and 37 °C. Afterwards, they were injected into the chromatographic system. These samples were also submitted to ultrafiltration (10 and 50 kDa membranes), and Al was measured in the ultrafiltrates. The results showed that Al was present in the eluent volume corresponding to the EPO peak but not in the HSA peak in the chromatograms. Temperature strengthened the interaction because the Al present in the EPO fraction was 3 times higher at 37 °C compared to 4 °C. Thirty-eight percent of the Al present in a 2.4 μg/mL EPO standard solution, and approximately 50% of the Al in formulation samples containing approximately 11 μg/mL EPO and either citrate or phosphate, were non-ultrafiltrable, which suggests that EPO is an effective Al acceptor in vitro.     

Effects of temperature on the foraging and growth rate of juvenile common carp, Cyprinus carpio

Temperature had a significant and positive effect on the foraging and growth of juvenile common carp Cyprinus carpio (90-105 mm) between 16 and 28 °C. Metrics measured were feeding rate (items s⁻¹), functional response (feeding rate as a function of food density), specific growth rate and incremental fork lengths. Experiments that were conducted at 16, 20, 24 and 28 °C and used two food types revealed a strong thermal influence on foraging, with the highest feeding rates achieved at 24 °C. Functional responses also revealed optimal feeding rates in relation to food density occurred at temperatures >20 °C. Specific growth rate and incremental fork lengths were depressed at 16 and 28 °C when compared to those achieved at 20 and 24 °C. These outputs suggest an increase in foraging and growth of C. carpio according to a thermal gradient that were maximal between 24 and 28 °C.     

Effect of water temperature on dietary protein requirement,growth and body composition of Asian catfish, Clarias batrachus fry

This study aimed to evaluate the protein requirement of Clarias batrachus fry, were estimated at two different water temperatures, 28 and 32 °C. The influence of dietary protein level and water temperature on body composition, weight gain, food and nutrient utilization were estimated. The Asian catfish, C. batrachus fry were fed four diets containing 28% (diet 1), 32% (diet 2), 36% (diet 3) and 40% (diet 4) protein levels and reared at two water temperatures 28 and 32 °C for 60 days. Fry fed with diet 3 containing 36% protein showed the highest mean final body weight at 32 °C. Final body weight was significantly (P<0.05) affected by dietary treatments and temperatures. Clarias batrachus fry raised at 28 °C had higher feed efficiency (93.20%) than the fry reared at 32 °C (87.58%) with 28% dietary protein level. Further, feed efficiency decreased with increase in dietary protein level. Higher daily protein retention (0.089%) observed at lower (0.0217 g) daily protein intake at 28 °C than 0.0283 g at 32 °C. While, optimal (0.0282 g) daily protein intake showed higher daily weight gain at 32 °C. Productive protein value (% PPV) was maximum (1.76%) at 32 °C than at 28 °C (0.76%). Final body lipid recorded higher value than initial body lipid at both the temperatures. Hepatosomatic index (HSI) observed to have been influenced (P<0.05) by diets and temperatures, while viscerosomatic index (VSI) affected (P<0.05) by only diets and not (P>0.05) by temperatures. The study concluded that the diet 3 containing 36% protein was optimal for growth of C. batrachus fry at both the temperatures.     

Combined effects of temperature and cadmium exposure on haemocyte apoptosis and cadmium accumulation in the eastern oyster Crassostrea virginica (Gmelin)

Combined effects of acclimation temperature (12, 20 and 28 °C) and exposure to a toxic metal cadmium (Cd, 50 μg L⁻¹) on haemolymph parameters related to immune defense and metal transport were studied in a model marine bivalve, Crassostrea virginica. Acclimation to elevated temperatures resulted in higher plasma protein concentrations and increased Cd levels in oyster haemolymph plasma and haemocytes. Cd accumulation in haemocytes was linear over the 45 days of Cd exposure and accumulation rates were 0.10, 0.53 and 0.56 μg Cd g⁻¹ dry mass at 12, 20 and 28 °C, respectively. Percentage of blood Cd burden associated with haemocytes increased with increasing temperatures from 13–20% at 12 °C to 26–47% at 20 and 28 °C suggesting a higher role for cellular Cd transport at elevated temperatures. Cd levels in gills and hepatopancreas were positively correlated with Cd concentration in haemocytes, but accumulation rates were considerably faster, so that after 45 days of exposure Cd levels in gills and hepatopancreas were >10–20 times higher than in haemocytes. As a result of slow Cd accumulation possibly reflecting fast haemocyte turnover rates and/or exocytosis of Cd-containing granules, haemocytes in Cd-exposed oysters did not reach threshold Cd burdens required to trigger apoptosis. This suggests that haemocyte viability is not likely to contribute to immunosuppression in the environmentally relevant Cd range. In contrast, elevated temperature (28 °C) resulted in a significant increase in the percentage of apoptotic haemocytes compared to 12 or 20 °C supporting the notion that 28 °C is physiologically stressful for C. virginica. Overall, our study demonstrates strong effects of environmental temperature on haemocyte viability and other important blood parameters such as plasma protein content and metal transport capability which may mask potential Cd effects at environmentally relevant exposure levels.     

An efficient method to eliminate the protease activity contaminating commercial bovine pancreatic DNase I

A method was developed to eliminate the proteases contaminating commercial DNase I, which can cause degradation of target protein during the purification process. Bio Basic DNase stock solution (in Tris–HCl buffer [pH 8.0] containing 5 mM CaCl₂) was first incubated at 50 °C to generate autolysis of proteases and zymogens, leading to a significant reduction in protease activity while preserving DNase activity. The residual protease activity was completely inhibited by further incubation with 2 mM PMSF (phenylmethylsulfonyl fluoride) or 2× S8830 inhibitor cocktail. This approach could be readily applicable to eliminate the protease activity in any DNase products or during the preparation of commercial DNase.     

Effect of signal peptide on the stability and folding kinetics of maltose binding protein

While the role of the signal sequence in targeting proteins to specific subcellular compartments is well characterized, there are fewer studies that characterize its effects on the stability and folding kinetics of the protein. We report a detailed characterization of the folding kinetics and thermodynamic stabilities of maltose binding protein (MBP) and its precursor form, preMBP. Isothermal GdmCl and urea denaturation as a function of temperature and thermal denaturation studies have been carried out to compare stabilities of the two proteins. preMBP was found to be destabilized by about 2-6 kcal/mol (20-40%) with respect to MBP. Rapid cleavage of the signal peptide by various proteases shows that the signal peptide is accessible in the native form of preMBP. The observed rate constant of the major slow phase in folding was decreased 5-fold in preMBP relative to MBP. The rate constants of unfolding were similar at 25 degrees C, but preMBP also exhibited a large burst phase change in unfolding that was absent in MBP. At 10 degrees C, preMBP exhibited a higher unfolding rate than MBP as well as a large burst phase. The appreciable destabilization of MBP by signal peptide is functionally relevant, because it enhances the likelihood of finding the protein in an unfolded translocation-competent form and may influence the interactions of the protein with the translocation machinery. Destabilization is likely to result from favorable interactions between the hydrophobic signal peptide and other hydrophobic regions that are exposed in the unfolded state.     

The biological activity of Humanin analogs correlates with structure stabilities in solution

A single mutation has resulted in large differences in neuroprotective activity of a 24 amino acid Humanin (HN). A mutation of Ser7Ala (S7A-HN) resulted in loss of activity, while a mutation of Ser14Gly (S14G-HN) resulted in about 1000-fold increase. The mechanism of the effects conferred by these mutations have been totally unclear, although our recent structure analysis suggested a possibility of the effect of mutation on the structure stability. Here, we have studied the effects of buffer and temperature on the structure of these three HN peptides. These peptides showed a similar disordered structure at 10 °C in 10 mM phosphate, pH 6.0. They were also similar in phosphate-buffered saline (PBS) as long as the temperature was kept low at 10 °C. However, a large difference was observed in both phosphate buffer and PBS between the peptides, when the temperature was raised to a physiological temperature of 37 °C. While S14G-HN showed small changes in both solutions at 37 °C, the less active HN and inactive S7A-HN showed much larger changes under the identical conditions. In addition, it appeared that structure change at 37 °C was faster for S7A-HN than HN. These results show that the structure stability at 37 °C increases in the order of S7A-HN, HN and S14G-HN, in correlation with their neuroprotective activities.     

Thermostable single domain antibody–maltose binding protein fusion for Bacillus anthracis spore protein BclA detection

We constructed a genetic fusion of a single domain antibody (sdAb) with the thermal stable maltose binding protein from the thermophile Pyrococcus furiosus (PfuMBP). Produced in the Escherichia coli cytoplasm with high yield, it proved to be a rugged and effective immunoreagent. The sdAb–A5 binds BclA, a Bacillus anthracis spore protein, with high affinity (K_D ∼ 50 pM). MBPs, including the thermostable PfuMBP, have been demonstrated to be excellent folding chaperones, improving production of many recombinant proteins. A three-step purification of E. coli shake flask cultures of PfuMBP–sdAb gave a yield of approximately 100 mg/L highly purified product. The PfuMBP remained stable up to 120 °C, whereas the sdAb–A5 portion unfolded at approximately 68 to 70 °C but could refold to regain activity. This fusion construct was stable to heating at 1 mg/ml for 1 h at 70 °C, retaining nearly 100% of its binding activity; nearly one-quarter (24%) activity remained after 1 h at 90 °C. The PfuMBP–sdAb construct also provides a stable and effective method to coat gold nanoparticles. Most important, the construct was found to provide enhanced detection of B. anthracis Sterne strain (34F2) spores relative to the sdAb–A5 both as a capture reagent and as a detection reagent.     

Enhanced resistance to peroxide stress in Escherichia coli grown outside their niche temperatures

Extended exposure of Escherichia coli to temperatures above and below their growth optimum led to significant changes in oxidant production and antioxidant defense. At 20 °C an increase in the intracellular H₂O₂ concentration and oxidized glutathione (GSSG) level was observed against a background of low levels of reduced glutathione (GSH) and decreased catalase and glutathione reductase (GOR) activities. The intracellular H₂O₂ and GSSG concentrations had minimal values at 30 and 37 °C, but rose again at 42 °C, suggesting that oxidative processes were intensified at high temperatures. An increase in temperature from 20 to 42 °C led to an elevation in the oxygen respiration rate and superoxide production; a 5-fold increase in the intracellular GSH concentration and in the GSH:GSSG ratio occurred simultaneously. Catalase HPI and GOR activities were elevated 4.4- and 1.5-fold, respectively. Prolonged exposure to sublethal temperatures facilitated an adaptation to subsequent oxidative stress produced by the addition of H₂O₂.     

Mycosporine-like amino acids in azooxanthellate and zooxanthellate early developmental stages of the soft coral Heteroxenia fuscescens

The ontogenetic changes of MAAs in the soft coral Heteroxenia fuscescens was studied in relation to their symbiotic state (azooxanthellate vs. zooxanthellate) under different temperature conditions in the Gulf of Eilat, northern Red Sea. The HPLC chromatograms for extracts of the planulae, azoo- and zooxanthellate primary polyps of H. fuscescens from all dates of collection yielded a single peak at 320 nm that has been identified as the compound palythine. Concentration of palythine in planulae at 23 °C was 7.57 ± 1 nmol mg^− 1 protein and at 28 °C reached 17.29 ± 1 nmol × mg^− 1 protein. Concentration of palythine in azooxanthellate primary polyps was 16.4 ± 3 nmol × mg^− 1 protein and 28.37 ± 2.8 nmol × mg^− 1 protein at 23 °C and 28 °C respectively. The palythine concentration for zooxanthellate primary polyps at 23 °C was 13 ± 3 nmol × mg^− 1 protein and at 28 °C 32.7 ± 2 nmol mg^− 1 protein. Palythine concentrations were significantly higher at 28 °C in the different animal groups and correlated linearly with the ambient collection temperature. This study shows for the first time that UVR and temperature act synergistically and affect the MAA levels of early life-history stages of soft corals.     

Comparative analysis of enzymatic stability and amino acid sequences of thermostable alkaline proteases from two haloalkaliphilic bacteria isolated from Coastal region of Gujarat, India

Thermostable alkaline proteases from two haloalkaliphilic bacteria, Oceanobacillus iheyensis O.M.A₁8 (EU680961) and Haloalkaliphilic bacterium O.M.E₁2 (EU680960) were studied for enzymatic properties and amino acid sequences in comparative manner. The bacteria were isolated from salt enriched soil located in Okha, Coastal Gujarat, India. The unique aspect of the study was that alkaline protease from Haloalkaliphilic bacterium O.M.A₁8 optimally catalyzed the reaction over a wide range of temperature, 50-90 °C, with a half-life of 36 h at 90 °C. The molecular weights of O.M.A₁8 and O.M.E₁2 were 35 kDa and 25 kDa, respectively. The enzyme secretion was over the broader range of pH 8-11, with an optimum at 11. The alkaline proteases from the two haloalkaliphilic strains isolated from the same site reflected quite different characteristics features. To the best of our knowledge, we have not come across with any such report on the thermal stability of alkaline proteases from haloalkaliphiles. Amino acid sequences for both enzymes were deduced from the nucleotide sequences of their corresponding genes followed by the analysis of physico-chemical properties of the enzymes.     

Quantitative gene expression analysis in a brain slice model: influence of temperature and incubation media

We describe the RNA integrity (28S/18S ratio) and the messenger RNA (mRNA) expression of genes encoding glyceraldehyde 3-phosphate dehydrogenase (GAPDH), microtubule-associated serine/threonine kinase 2 (Mast2), and β-actin in cortical brain slices incubated for up to 24 h in Ringer’s solution and Dulbecco’s modified Eagle’s medium (DMEM) at 25 and 37 °C. Our data reveal an optimal temporal working window between 1 and 6 h when slices are incubated in Ringer’s solution at 25 °C that allows experiments related to gene expression dynamics to be performed more suitably than those carried out at 37 °C. In addition, we show that reference gene expression may be modified in dynamic experiments and may compromise studies of gene expression.     

Rapid thermal responses and thermal tolerance in adult codling moth Cydia pomonella (Lepidoptera: Tortricidae)

In order to preserve key activities or improve survival, insects facing variable and unfavourable thermal environments may employ physiological adjustments on a daily basis. Here, we investigate the survival of laboratory-reared adult Cydia pomonella at high or low temperatures and their responses to pre-treatments at sub-lethal temperatures over short time-scales. We also determined critical thermal limits (CTLs) of activity of C. pomonella and the effect of different rates of cooling or heating on CTLs to complement the survival assays. Temperature and duration of exposure significantly affected adult C. pomonella survival with more extreme temperatures and/or longer durations proving to be more lethal. Lethal temperatures, explored between −20 °C to −5 °C and 32 °C to 47 °C over 0.5, 1, 2, 3 and 4 h exposures, for 50% of the population of adult C. pomonella were −12 °C for 2 h and 44 °C for 2 h. Investigation of rapid thermal responses (i.e. hardening) found limited low temperature responses but more pronounced high temperature responses. For example, C. pomonella pre-treated for 2 h at 5 °C improved survival at −9 °C for 2 h from 50% to 90% (p < 0.001). At high temperatures, pre-treatment at 37 °C for 1 h markedly improved survival at 43 °C for 2 h from 20% to 90% (p < 0.0001). We also examined cross-tolerance of thermal stressors. Here, low temperature pre-treatments did not improve high temperature survival, while high temperature pre-treatment (37 °C for 1 h) significantly improved low temperature survival (−9 °C for 2 h). Inducible cross-tolerance implicates a heat shock protein response. Critical thermal minima (CTmin) were not significantly affected by cooling at rates of 0.06, 0.12 and 0.25 °C min⁻¹ (CTmin range: 0.3-1.3 °C). By contrast, critical thermal maxima (CTmax) were significantly affected by heating at these rates and ranged from 42.5 to 44.9 °C. In sum, these results suggest pronounced plasticity of acute high temperature tolerance in adult C. pomonella, but limited acute low temperature responses. We discuss these results in the context of local agroecosystem microclimate recordings. These responses are significant to pest control programmes presently underway and have implications for understanding the evolution of thermal tolerance in these and other insects.     

Low temperature induces the delivery of mature and immature CFTR to the plasma membrane

Deletion of phenylalanine 508 (ΔF508) is the most prevalent disease-causing mutation resulting in retention of the immature CFTR in the endoplasmic reticulum. The most common strategy to induce the delivery of ΔF508-CFTR to the surface of cells is by reducing the incubation temperature (≈28 °C). Cell surface biotinylation of HEK293T cells grown at 37 °C for 48 h, confirmed the presence of mature wild-type CFTR, but not ΔF508-CFTR at the cell surface. On the other hand, cells incubated at 28 °C for 16 h showed both mature and immature ΔF508-CFTR at their surface. The trafficking of immature ΔF508-CFTR, but not mature ΔF508-CFTR, to the cell surface occurred at low temperature even upon addition of BFA, suggesting the involvement of a Golgi-independent pathway. These results suggest that low temperature induces the appearance of a mix population of mature and immature CFTR molecules at the plasma membrane through distinct pathways.