Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective 15N-labelling and production of perdeuterated proteins in H2O

Selectively isotope labelled protein samples can be prepared in vivo or in vitro from selectively labelled amino acids but, in many cases, metabolic conversions between different amino acids result in isotope scrambling. The best results are obtained by cell-free protein synthesis, where metabolic enzymes are generally less active, but isotope scrambling can never be suppressed completely. We show that reduction of E. coli S30 extracts with NaBH₄ presents a simple and inexpensive way to achieve cleaner selective isotope labelling in cell-free protein synthesis reactions. The purpose of the NaBH₄ is to inactivate all pyridoxal-phosphate (PLP) dependent enzymes by irreversible reduction of the Schiff bases formed between PLP and lysine side chains of the enzymes or amino groups of free amino acids. The reduced S30 extracts retain their activity of protein synthesis, can be stored as well as conventional S30 extracts and effectively suppress conversions between different amino acids. In addition, inactivation of PLP-dependent enzymes greatly stabilizes hydrogens bound to α-carbons against exchange with water, minimizing the loss of α-deuterons during cell-free production of proteins from perdeuterated amino acids in H₂O solution. This allows the production of highly perdeuterated proteins that contain protons at all exchangeable positions, without having to back-exchange labile deuterons for protons as required for proteins that have been synthesized in D₂O.     

Production and Analysis of Perdeuterated Lipids from Pichia pastoris Cells

Probing molecules using perdeuteration (i.e deuteration in which all hydrogen atoms are replaced by deuterium) is extremely useful in a wide range of biophysical techniques. In the case of lipids, the synthesis of the biologically relevant unsaturated perdeuterated lipids is challenging and not usually pursued. In this work, perdeuterated phospholipids and sterols from the yeast Pichia pastoris grown in deuterated medium are extracted and analyzed as derivatives by gas chromatography and mass spectrometry respectively. When yeast cells are grown in a deuterated environment, the phospholipid homeostasis is maintained but the fatty acid unsaturation level is modified while the ergosterol synthesis is not affected by the deuterated culture medium. Our results confirm that the production of well defined natural unsaturated perdeuterated lipids is possible and gives also new insights about the process of desaturase enzymes.     

Deuterated detergents for structural and functional studies of membrane proteins: Properties,chemical synthesis and applications

Abstract

Detergents are amphiphilic compounds that have crucial roles in the extraction, purification and stabilization of integral membrane proteins and in experimental studies of their structure and function. One technique that is highly dependent on detergents for solubilization of membrane proteins is solution-state NMR spectroscopy, where detergent micelles often serve as the best membrane mimetic for achieving particle sizes that tumble fast enough to produce high-resolution and high-sensitivity spectra, although not necessarily the best mimetic for a biomembrane. For achieving the best quality NMR spectra, detergents with partial or complete deuteration can be used, which eliminate interfering proton signals coming from the detergent itself and also eliminate potential proton relaxation pathways and strong dipole-dipole interactions that contribute line broadening effects. Deuterated detergents have also been used to solubilize membrane proteins for other experimental techniques including small angle neutron scattering and single-crystal neutron diffraction and for studying membrane proteins immobilized on gold electrodes. This is a review of the properties, chemical synthesis and applications of detergents that are currently commercially available and/or that have been synthesized with partial or complete deuteration. Specifically, the detergents are sodium dodecyl sulphate (SDS), lauryldimethylamine-oxide (LDAO), n-octyl-β-D-glucoside (β-OG), n-dodecyl-β-D-maltoside (DDM) and fos-cholines including dodecylphosphocholine (DPC). The review also considers effects of deuteration, detergent screening and guidelines for detergent selection. Although deuterated detergents are relatively expensive and not always commercially available due to challenges associated with their chemical synthesis, they will continue to play important roles in structural and functional studies of membrane proteins, especially using solution-state NMR.     

The Synthesis of Deuterionucleosides

Abstract

The synthesis of deuterionucleosides for site-specific incorporation into oligo-DNA or -RNA is herein reviewed for NMR or biological studies. The review covers the following aspects: (i) deuteration of the aglycone; (ii) single-site chemical deuteration of the sugar residues; (iii) multiple-site chemical deuteration of the sugar residues; (iv) enzymatic synthesis of deuterated nucleosides or nucleotides; and (v) synthesis of labelled nucleosides with multiple isotopes.     

Backbone assignment of perdeuterated proteins using long-range H/C-dipolar transfers

For micro-crystalline proteins, solid-state nuclear magnetic resonance spectroscopy of perdeuterated samples can provide spectra of unprecedented quality. Apart from allowing to detect sparsely introduced protons and thereby increasing the effective resolution for a series of sophisticated techniques, deuteration can provide extraordinary coherence lifetimes—obtainable for all involved nuclei virtually without decoupling and enabling the use of scalar magnetization transfers. Unfortunately, for fibrillar or membrane-embedded proteins, significantly shorter transverse relaxation times have been encountered as compared to micro-crystalline proteins despite an identical sample preparation, calling for alternative strategies for resonance assignment. In this work we propose an approach towards sequential assignment of perdeuterated proteins based on long-range ¹H/¹³C Cross Polarization transfers. This strategy gives rise to H/N-separated correlations involving C^α, C^β, and CO chemical shifts of both, intra- and interresidual contacts, and thus connecting adjacent residues independent of transverse relaxation times.     

Efficient condensed-phase production of perdeuterated soluble and membrane proteins

Protein perdeuteration approaches have tremendous value in protein NMR studies, but are limited by the high cost of perdeuterated media. Here, we demonstrate that E. coli cultures expressing proteins using either the condensed single protein production method (cSPP), or conventional pET expression plasmids, can be condensed prior to protein expression, thereby providing high-quality ²H, ¹³C, ¹⁵N-enriched protein samples at 2.5–10% the cost of traditional methods. As an example of the value of such inexpensively-produced perdeuterated proteins, we produced ²H, ¹³C, ¹⁵N-enriched E. coli cold shock protein A (CspA) and EnvZb in 40× condensed phase media, and obtained NMR spectra suitable for 3D structure determination. The cSPP system was also used to produce ²H, ¹³C, ¹⁵N-enriched E. coli plasma membrane protein YaiZ and outer membrane protein X (OmpX) in condensed phase. NMR spectra can be obtained for these membrane proteins produced in the cSPP system following simple detergent extraction, without extensive purification or reconstitution. This allows a membrane protein’s structural and functional properties to be characterized prior to reconstitution, or as a probe of the effects of subsequent purification steps on the structural integrity of membrane proteins. We also provide a standardized protocol for production of perdeuterated proteins using the cSPP system. The 10–40 fold reduction in costs of fermentation media provided by using a condensed culture system opens the door to many new applications for perdeuterated proteins in spectroscopic and crystallographic studies.     

Expression of deuterium-isotope-labelled protein in the yeast Pichia pastoris for NMR studies

Deuterium isotope labelling is important for NMR studies of large proteins and complexes. Many eukaryotic proteins are difficult to express in bacteria, but can be efficiently produced in the methylotrophic yeast Pichia pastoris. In order to facilitate NMR studies of the malaria parasite merozoite surface protein-1 (MSP1) complex and its interactions with antibodies, we have investigated production of the MSP1-19 protein in P. pastoris grown in deuterated media. The resulting deuteration patterns were analyzed by NMR and mass spectrometry. We have compared growth characteristics and levels of heterologous protein expression in cells adapted to growth in deuterated media (95% D₂O), compared with expression in non-adapted cells. We have also compared the relative deuteration levels and the distribution pattern of residual protiation in protein from cells grown either in 95% D₂O medium with protiated methanol as carbon source, or in 95% D₂O medium containing deuterated methanol. A high level of uniform C deuteration was demonstrated, and the consequent reduction of backbone amide signal linewidths in [¹H/¹⁵N]-correlation experiments was measured. Residual protiation at different positions in various amino acid residues, including the distribution of methyl isotopomers, was also investigated. The deuteration procedures examined here should facilitate economical expression of ²H/¹³C/¹⁵N-labelled protein samples for NMR studies of the structure and interactions of large proteins and protein complexes.     

Optimum levels of exchangeable protons in perdeuterated proteins for proton detection in MAS solid-state NMR spectroscopy

We present a systematic study of the effect of the level of exchangeable protons on the observed amide proton linewidth obtained in perdeuterated proteins. Decreasing the amount of D₂O employed in the crystallization buffer from 90 to 0%, we observe a fourfold increase in linewidth for both ¹H and ¹⁵N resonances. At the same time, we find a gradual increase in the signal-to-noise ratio (SNR) for ¹H–¹⁵N correlations in dipolar coupling based experiments for H₂O concentrations of up to 40%. Beyond 40%, a significant reduction in SNR is observed. Scalar-coupling based ¹H–¹⁵N correlation experiments yield a nearly constant SNR for samples prepared with ≤30% H₂O. Samples in which more H₂O is employed for crystallization show a significantly reduced NMR intensity. Calculation of the SNR by taking into account the reduction in ¹H T ₁ in samples containing more protons (SNR per unit time), yields a maximum SNR for samples crystallized using 30 and 40% H₂O for scalar and dipolar coupling based experiments, respectively. A sensitivity gain of 3.8 is obtained by increasing the H₂O concentration from 10 to 40% in the CP based experiment, whereas the linewidth only becomes 1.5 times broader. In general, we find that CP is more favorable compared to INEPT based transfer when the number of possible ¹H,¹H interactions increases. At low levels of deuteration (≥60% H₂O in the crystallization buffer), resonances from rigid residues are broadened beyond detection. All experiments are carried out at MAS frequency of 24 kHz employing perdeuterated samples of the chicken α-spectrin SH3 domain.     

Induction of heat shock proteins during initiation of solvent formation inClostridium acetobutylicum

Summary The response to stresses produced by changes in the fermentation conditions ofClostridium acetobutylicum in continuous culture was determined under acid- and solvent-producing conditions. Using a phosphate-limited chemostat it was found that specificheatshockproteins (hsp 73, hsp 72 [Dnak], hsp 67 [GroEL], hsp 17 and hsp 14) were synthesized at elevated levels during the shift from acid to solvent formation. The induction of these stress proteins was observed before acetone and butanol were detected in the medium and was therefore not a response to these solvents present in the medium. Simultaneously with the induction of hsps, changes in the synthesis rates of other cellular proteins were observed. Synthesis of proteins associated with the acid production phase decreased and of proteins correlated with the solvent production phase increased. Some hsps, including the DnaK- and GroEL-similar proteins, hsp 73 and hsp 21, were also induced by a change in the growth rate and/or the pH. The analysis of the general regulation of the heat shock response inC. acetobutylicum revealed that the induction of at least 15 hsps after a temperature up-shift was transient and that two temporal classes of hsps could be distinguished. The synthesis of one group of hsps reached a maximum after 6 min and another around 11 min after the temperature upshift and returned to steady-state levels 30 to 40 min after the shock.     

A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe,Tyr and Trp

A novel biosynthetic strategy is described for the preparation of deuterated proteins containing protons at the ring carbons of Phe, Tyr and Trp, using the aromatic amino acid precursor shikimic acid. Specific protonation at aromatic side chains, with complete deuteration at C^/positions was achieved in proteins overexpressed in bacteria grown in shikimate-supplemented D₂O medium. Co-expression of a shikimate transporter in prototrophic bacteria resulted in protonation levels of 62–79%, whereas complete labeling was accomplished using shikimate auxotrophic bacteria. Our labeling protocol permits the measurement of important aromatic side chain derived distance restraints in perdeuterated proteins that could be utilized to enhance the accuracy of NMR structures calculated using low densities of NOEs from methyl selectively protonated samples.     

Side-chain to backbone correlations from solid-state NMR of perdeuterated proteins through combined excitation and long-range magnetization transfers

Proteins with excessive deuteration give access to proton detected solid-state NMR spectra of extraordinary resolution and sensitivity. The high spectral quality achieved after partial proton back-exchange has been shown to start a new era for backbone assignment, protein structure elucidation, characterization of protein dynamics, and access to protein parts undergoing motion. The large absence of protons at non-exchangeable sites, however, poses a serious hurdle for characterization of side chains, which play an important role especially for structural understanding of the protein core and the investigation of protein–protein and protein–ligand interactions, e.g. This has caused the perdeuteration approach to almost exclusively be amenable to backbone characterization only. In this work it is shown that a combination of isotropic ¹³C mixing with long-range ¹H/¹³C magnetization transfers can be used effectively to also access complete sets of side-chain chemical shifts in perdeuterated proteins and correlate these with the protein backbone with high unambiguity and resolution. COmbined POlarization from long-Range transfers And Direct Excitation (COPORADE) allows this strategy to yield complete sets of aliphatic amino acid resonances with reasonable sensitivity.     

探索大肠杆菌细胞膜合成过程中脂肪酸的掺入模式

【目的】探索大肠杆菌生长分裂过程中,脂肪酸作为底物在细胞膜合成过程中的掺入模式。【方法】本研究解析了以乙酰CoA为底物,合成中间产物长链脂酰-ACP,随后合成磷脂酰乙醇胺(phosphatidylethanolamine,PE)的途径,并将合成途径中的10个关键酶与绿色荧光蛋白(enhanced green fluorescent protein,EGFP)或红色荧光蛋白(monmer Cherry,mCherry)进行融合,在大肠杆菌内表达这些融合蛋白,用激光共聚焦荧光显微镜成像的方式来获得这些融合蛋白的定位信息。【结果】宽场荧光显微镜成像结果显示,磷脂酰乙醇胺合成途径中的10个酶在不同表达水平下出现不同的定位模式。在大肠杆菌中高水平表达融合蛋白EGFP-FabA、EGFP-FabB、EGFP-FabI、EGFP-FabG、EGFP-PlsB和EGFP-PssA时,细胞两极和中部有大量蛋白聚集的现象。EGFP-FabD、EGFP-FabF、EGFP-CdsA、EGFP-PSD在不同表达水平下,均匀分散在细胞质或细胞膜上。缩时影像(Time-lapse)结果显示,合成途径中的一个关键蛋白EGFP-Pls B在细胞分裂前随着细胞膜的内陷聚集到细胞隔膜,随着细胞分裂,母细胞的隔膜成为新细胞的两极。【结论】本研究通过获取磷脂酰乙醇胺合成相关蛋白酶在大肠杆菌中的定位结果,推测脂肪酸分子是在细胞分裂隔膜和两极掺入,被催化合成PE后被运送到细胞膜其他位置。     

Heterologous expression of a deuterated membrane-integrated receptor and partial deuteration in methylotrophic yeasts

Methylotrophic yeast has previously been shown to be an excellent system for the cost-effective production of perdeuterated biomass and for the heterologous expression of membrane receptors. A protocol for the expression of 85% deuterated, functional human -opiate receptor was established. For partially deuterated biomass, deuteration level and distribution were determined for fatty acids, amino acids and carbohydrates. It was shown that prior to biosynthesis of lipids and amino acids (and of carbohydrates, to a lower extent), exchange occurs between water and methanol hydrogen atoms, so that 80%–90% randomly deuterated biomass and over-expressed proteins may be obtained using only deuterated water.     

Production of highly active fungal milk-clotting enzyme by solid-state fermentation

Abstract

Cheese production is projected to reach 20 million metric tons by 2020, of which 33% is being produced using calf rennet (EC 3.4.23.4). There is shortage of calf rennet, and use of plant and microbial rennets, hydrolyze milk proteins non-specifically resulting in low curd yields. This study reports fungal enzymes obtained from cost effective medium, with minimal down streaming, whose activity is comparable with calf and Mucor rennet. Of the fifteen fungi that were screened, Mucor thermohyalospora (MTCC 1384) and Rhizopus azygosporus (MTCC 10195) exhibited the highest milk-clotting activity (MCA) of 18,383?±?486?U/ml and 16,373?± 558?U/ml, respectively. Optimization exhibited a 33% increase in enzyme production (30?g wheat bran containing 6% defatted soy meal at 30?°C, pH 7) for M. thermohyalospora. The enzyme was active from pH 5–10 and temperature 45–55?°C. Rhizopus azygosporus exhibited 31% increase in enzyme production (30?g wheat bran containing 4% defatted soy meal at 30?°C, pH 6) and the enzyme was active from pH 6–9 at 50?°C. Curd yields prepared from fungal enzyme extract decreased (5–9%), when compared with calf rennet and Mucor rennet. This study describes the potential of fungal enzymes, hitherto unreported, as a viable alternative to calf rennet     

Properties ofEscherichia coli grown in deuterated media

The effects on a number of parameters of transferringEscherichia coli between protonated and deuterated media were studied; these included growth, oxygen consumption and the synthesis of DNA, RNA, total protein, and β-galactosidase. Similar measurements were made on cells fully adapted to growth on deuterated media. The amino acid compositions of deuterated and protonated cellular protein were similar, but in deuterated cells the ratio protein: DNA was doubled. Deutero- and protio-β-galactosidase had similarK _M values and turnover numbers in D₂O and H₂O. The kinetics of β-galactosidase synthesis were not changed by deuteration, but it was found that lower concentrations of inducer were required to achieve particular levels of induction. Brief exposure to inducer in one medium, followed by removal of inducer and expression of enzyme-forming-potential in either D₂O or H₂O, showed that mRNA synthesized by deuterated cells was translated equally well in both media. mRNA synthesized by protonated cells was translated about twice as efficiently in H₂O. Inducible strains (but not a regulator constitutive) lost the capacity to synthesize enzymically active β-galactosidase after more than 100 generations in D₂O-acetate. The defect persisted when such cells were grown in H₂O-acetate, but enzyme activity was restored by growth in H₂O-glycerol. The failure to produce active enzyme was not due to a failure of the induction mechanism; gel electrophoresis revealed the presence of an inactive protein species. The nature of adaptation to deuteration is discussed.     

An Early Stage of Cold Acclimation with Four Phases of Protein Synthesis in Crowns of Winter Wheat

During an early stage of cold acclimation, prominent changes in protein-synthetic activities were found to occur in the crown, which is the part where the stem joins the root of winter wheat (Triticum aestivum L. cv. Horoshirikomugi). This stage was complete within a week of cold treatment, and from the protein-synthetic activities, this stage of cold acclimation could be divided into four phases. First, when the plant seedlings were placed at 0°C, there was a lag period of 1d and no newly inducible proteins were formed during this time. During the second phase (1 to 2d), as the first response to cold, 16 new proteins were synthesized and the active synthesis of 6 preexisting proteins was reinitiated, while syntheses of at least 5 preexisting proteins were depressed. During the third phase (2 to 5d), the levels of most of the cold-inducible proteins reached a maximum, but synthesis of at least 6 preexisting proteins started to decrease. During the fourth phase (after 5d), the synthetic activities of the 6 proteins returned to the original levels and synthesis of another set of 3 new proteins started. During this phase, the synthesis of both protein fractions, the cold-inducible and the preexisting proteins, reached a steady state. After this period, no major changes in the protein profile could be detected. During the third phase, the most active synthesis of the cold-inducible proteins, in particular, proteins designated C10 (M_r 53k), C12a (M_r 46k), and C12b (M_r 46k), occurred, concurrent with the abrupt and transient decrease in the synthetic activities of a set of 6 preexisting proteins. These results suggest that, in addition to the induction of a set of new proteins, the preferential or selective synthesis of proteins required for accommodation to the cold environment takes place at an early stage of acclimation.     

产肌醇毕赤酵母细胞工厂的优化

【背景】肌醇是一种B族维生素,广泛应用于食品、医药、饲料等领域。微生物发酵法是最具前景的肌醇生产方法,但使用大肠杆菌生产的肌醇在食品及医药领域中的使用受到限制。毕赤酵母作为生物安全菌株是工业上生产异源蛋白的良好宿主,其本身含有天然的肌醇合成途径,具有被改造成为高效生产肌醇细胞工厂的潜力。【目的】通过代谢工程改造毕赤酵母工程菌株,降低副产物的生成并提高肌醇的产量。【方法】以实验室前期构建的产肌醇毕赤酵母工程菌株为出发菌株,确定副产物阿拉伯糖醇、核糖醇和甘露糖合成相关基因。通过关键基因敲除、发酵液中葡萄糖浓度控制降低副产物的产量。通过过表达甘油转运蛋白、甘油激酶和甘油-3-磷酸脱氢酶基因实现产肌醇毕赤酵母对甘油和葡萄糖的共利用,得到重组菌Z10。经过发酵条件优化,进一步提高Z10的肌醇产量。【结果】在最优条件下,重组菌Z10的肌醇产量达到36.7 g/L,是目前酵母类细胞工厂生产肌醇的最高值,副产物总产量与出发菌株相比降低了63.1%。【结论】在毕赤酵母中建立了降低阿拉伯糖醇、核糖醇和甘露糖合成的有效策略,并通过甘油、葡萄糖共利用及相对应的发酵条件优化提高了肌醇产量,为肌醇及其他高价值生物...     

Exploiting Leishmania tarentolae cell-free extracts for the synthesis of human solute carriers

Abstract

Cell-free protein production offers a versatile alternative to complement in vivo expression systems. However, usage of prokaryotic cell-free systems often leads to non-functional proteins. We modified a previously designed cell-free system based on the protozoan Leishmania tarentolae, a parasite of the Moorish gecko Tarentola mauritanica, together with a species-independent translational sequences-based plasmid to produce human membrane proteins in 2 hours reaction time. We successfully established all four commonly used expression modes for cell-free synthesis of membrane proteins with a human organic anion transporter, SLC17A3, as a model membrane protein: (i) As precipitates without the addition of any hydrophobic environment, (ii) in the presence of detergents, (iii) with the addition of liposomes, and (iv) supplemented with nanodiscs. We utilized this adapted system to synthesize 22 human solute carriers from 20 different families. Our results demonstrate the capability of the Leishmania tarentolae cell-free system for the production of a huge variety of human solute carriers in the precipitate mode. Furthermore, purified SLC17A3 shows the formation of an oligomeric state.     

Cotton CSLD3 restores cell elongation and cell wall integrity mainly by enhancing primary cellulose production in the Arabidopsis cesa6 mutant

Key message

Overexpression of cotton cellulose synthase like D3 (GhCSLD3) gene partially rescued growth defect of atcesa6 mutant with restored cell elongation and cell wall integrity mainly by enhancing primary cellulose production.

Abstract

Among cellulose synthase like (CSL) family proteins, CSLDs share the highest sequence similarity to cellulose synthase (CESA) proteins. Although CSLD proteins have been implicated to participate in the synthesis of carbohydrate-based polymers (cellulose, pectins and hemicelluloses), and therefore plant cell wall formation, the exact biochemical function of CSLD proteins remains controversial and the function of the remaining CSLD genes in other species have not been determined. In this study, we attempted to illustrate the function of CSLD proteins by overexpressing Arabidopsis AtCSLD2, -3, -5 and cotton GhCSLD3 genes in the atcesa6 mutant, which has a background that is defective for primary cell wall cellulose synthesis in Arabidopsis. We found that GhCSLD3 overexpression partially rescued the growth defect of the atcesa6 mutant during early vegetative growth. Despite the atceas6 mutant having significantly reduced cellulose contents, the defected cell walls and lower dry mass, GhCSLD3 overexpression largely restored cell wall integrity (CWI) and improved the biomass yield. Our result suggests that overexpression of the GhCSLD protein enhances primary cell wall synthesis and compensates for the loss of CESAs, which is required for cellulose production, therefore rescuing defects in cell elongation and CWI.

     

Prospects for an HIV Vaccine: Conventional Approaches and DNA Immunization

Abstract

Microbial transglutaminase is an important enzyme in food processing for improving protein properties by catalyzing the cross-linking of proteins. Recently, this enzyme has been shown to exhibit wider potential application in tissue engineering, textiles and leather processing, site-specific protein conjugation and wheat gluten allergy reduction. The production of microbial transglutaminase has been significantly improved thanks to advances in bioprocess engineering and genetic engineering during the last three decades. More recently, studies on the biological mechanism of transglutaminase synthesis have further contributed towards the understanding of microbial transglutaminase production by Streptomyces. This will further facilitate improving the production of recombinant microbial transglutaminase. In this paper, we will review the progress in bioprocess engineering and genetic engineering in microbial transglutaminase production. We will highlight our understanding of the biological mechanisms of microbial transglutaminase synthesis, including biotechnological approaches used based on these biological mechanisms as a way of improving transglutaminase production.We address in addition the future research needs for microbial transglutaminase production.