Position-specific incorporation of biotinylated non-natural amino acids into a protein in a cell-free translation system

Biotinylation is useful for the detection, purification and immobilization of proteins. It is performed by chemical modification, although position-specific and quantitative biotinylation is rarely achieved. We developed a position-specific biotinylation method using biotinylated non-natural amino acids. We showed that biotinylated p-aminophenylalanine derivatives were incorporated into a protein more efficiently than biotinylated lysine derivatives in a cell-free translation system. In addition, the biotinylated p-aminophenylalanines overcame the serious position-dependency observed for biotinylated lysines. The present method will be useful for detection and purification of proteins along with comprehensive exploration of surface-exposed residues and oriented immobilization of proteins.     

Contribution of the Cell Wall Component Teichuronopeptide to pH Homeostasis and Alkaliphily in the Alkaliphile Bacillus lentus C-125

A teichuronopeptide (TUP) is one of major structural components of the cell wall of the facultative alkaliphilic strain Bacillus lentus C-125. A mutant defective in TUP synthesis grows slowly at alkaline pH. An upper limit of pH for growth of the mutant was 10.4, while that of the parental strain C-125 was 10.8. Gene tupA, directing synthesis of TUP, was cloned from C-125 chromosomal DNA. The primary translation product of this gene is likely a cytoplasmic protein (57. 3 kDa) consisting of 489 amino acid residues. Introduction of the tupA gene into the TUP-defective mutant complemented the mutation responsible for the pleiotropic phenotypes of the mutant, leading to simultaneous disappearance of the defect in TUP synthesis, the diminished ability for cytoplasmic pH homeostasis, and the low tolerance for alkaline conditions. These results demonstrate that the acidic polymer TUP in the cell wall plays a role in pH homeostasis in this alkaliphile.     

Effects of mutation of Asn694 in Aspergillus niger α-glucosidase on hydrolysis and transglucosylation

Aspergillus niger α-glucosidase (ANG), a member of glycoside hydrolase family 31, catalyzes hydrolysis of α-glucosidic linkages at the non-reducing end. In the presence of high concentrations of maltose, the enzyme also catalyzes the formation of α-(1→6)-glucosyl products by transglucosylation and it is used for production of the industrially useful panose and isomaltooligosaccharides. The initial transglucosylation by wild-type ANG in the presence of 100 mM maltose [Glc(α1–4)Glc] yields both α-(1→6)- and α-(1→4)-glucosidic linkages, the latter constituting ~25% of the total transfer reaction product. The maltotriose [Glc(α1–4)Glc(α1–4)Glc], α-(1→4)-glucosyl product disappears quickly, whereas the α-(1→6)-glucosyl products panose [Glc(α1–6)Glc(α1–4)Glc], isomaltose [Glc(α1–6)Glc], and isomaltotriose [Glc(α1–6)Glc(α1–6)Glc] accumulate. To modify the transglucosylation properties of ANG, residue Asn694, which was predicted to be involved in formation of the plus subsites of ANG, was replaced with Ala, Leu, Phe, and Trp. Except for N694A, the mutations enhanced the initial velocity of the α-(1→4)-transfer reaction to produce maltotriose, which was then degraded at a rate similar to that by wild-type ANG. With increasing reaction time, N694F and N694W mutations led to the accumulation of larger amounts of isomaltose and isomaltotriose than achieved with the wild-type enzyme. In the final stage of the reaction, the major product was panose (N694A and N694L) or isomaltose (N694F and N694W).

     

Photosynthetic characteristics and nitrogen allocation in the black locust (<Emphasis Type="Italic">Robinia pseudoacacia</Emphasis> L.) grown in a FACE system

Key message

The black locust is adapted to elevated [CO ₂ ] through changes in nitrogen allocation characteristics in leaves.

Abstract

The black locust (Robinia pseudoacacia L.) is an invasive woody legume within Japan. This prolific species has a high photosynthetic rate and growth rate, and undergoes symbiosis with N₂-fixing micro-organisms. To determine the effect of elevated CO₂ concentration [CO₂] on its photosynthetic characteristics, we studied the chlorophyll (Chl) and leaf nitrogen (N) content, and the leaf structure and N allocation patterns in the leaves and acetylene reduction activity after four growing seasons, in R. pseudoacacia. Our specimens were grown at ambient [CO₂] (370 μmol mol^?1) and at elevated [CO₂] (500 μmol mol^?1), using a free air CO₂ enrichment (FACE) system. Net photosynthetic rate at growth [CO₂] (A _growth) and acetylene reduction activity were significantly higher, but maximum carboxylation rate of RuBisCo (V _cmax), maximum rate of electron transport driving RUBP regeneration (J _max), net photosynthetic rate under enhanced CO₂ concentration and light saturation (A _max), the N concentration in leaf, and in leaf mass per unit area (LMA) and ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCo) content were significantly lower grown at elevated [CO₂] than at ambient [CO₂]. We also found that RuBisCo/N were less at elevated [CO₂], whereas Chl/N increased significantly. Allocation characteristics from N in leaves to photosynthetic proteins, N_L (Light-harvesting complex: LHC, photosystem I and II: PSI and PSII) and other proteins also changed. When R. pseudoacacia was grown at elevated [CO₂], the N allocation to RuBisCo (N_R) decreased to a greater extent but N_L and N remaining increased relative to specimens grown at ambient [CO₂]. We suggest that N remobilization from RuBisCo is more efficient than from proteins of electron transport (N_E), and from N_L. These physiological responses of the black locust are significant as being an adaptation strategy to global environmental changes.

     

The effect of molecular packing on the occurrence of spin crossover phenomena in one-dimensional Fe(II)-bis-Schiff base complexes

Two new one-dimensional Fe(II)-bis-Schiff base complexes, [Fe(L1)(pyz)] · CH₂Cl₂ (1) and [Fe(L2)(pyz)] · 2CH₂Cl₂ (2) (H₂L1 = bis(O-vanillin)-O-phenylenediimine, H₂L2 = bis(O-vanillin)-2,3-naphthalenediimine, pyz = pyrazine) are reported with their crystal structures and magnetic property. Compound 1 shows a two-step SCO behavior while 2 shows HS at all the temperature range measured. Although the extension of aromatic moiety from benzene (L1) to naphthalene (L2) was introduced for the purpose of strengthening the cooperativity, it leads to the absence of SCO, due to the unanticipated π–π interaction, which leads to the longer Fe–N bond lengths and a weak ligand field around Fe(II) ion.     

Primary Conformation Change in Bacteriorhodopsin on Photoexcitation

Ultrafast dynamics of bacteriorhodopsin (bR) has been extensively studied experimentally and theoretically. However, there are several contradictory results reported, indicating that its detailed dynamics and initial process have not yet been fully clarified. In this work, changes in the amplitude and phase of molecular vibration in the isomerization process of bR were real-time probed simultaneously at 128 different wavelengths through intensity modulation of the electronic transition. Systematic information on the transient change in continuous spectrum extending from 505 nm (2.45 eV) to 675 nm (1.84 eV) showed different dynamics in each spectral region reflecting the difference in the excited states and intermediates dominating the dynamics during the photoisomerization. Careful analysis of the transient spectral changes and spectrograms calculated from the vibrational real-time traces elucidated that the primary event just after photoexcitation is the deformation of the retinal configuration, which decays within 30 fs near the C=N bond in the protonated Schiff base. The intensity of C=N stretching mode starts to decrease before the initiation of the frequency modulation of the C=C stretching mode. The C=C stretching mode frequency was modulated by a coupled torsion around the C₁₃=C₁₄ bond, leading to the photoisomerization around the bond. This study clarified the dynamics of the C=N and C=C stretching modes working as key vibration modes in the photoisomerization of bR. Furthermore, we have elucidated the modulation and decay dynamics of the C=C stretching mode in the photoreaction starting from H (Franck-Condon excited state) followed by I (twisted excited), and J (first intermediate) states.     

Structural insight into human CK2α in complex with the potent inhibitor ellagic acid

We determined the 2.35-Å crystal structure of a human CK2 catalytic subunit (referred to as CK2α complexed with the ATP-competitive, potent CK2 inhibitor ellagic acid. The inhibitor binds to CK2α with a novel binding mode, including water-mediated hydrogen bonds. This structural information may support discovery of potent CK2 inhibitors.     

Automated system for high-throughput protein production using the dialysis cell-free method

High-throughput protein production systems have become an important issue, because protein production is one of the bottleneck steps in large-scale structural and functional analyses of proteins. We have developed a dialysis reactor and a fully automated system for protein production using the dialysis cell-free synthesis method, which we previously established to produce protein samples on a milligram scale in a high-throughput manner. The dialysis reactor was designed to be suitable for an automated system and has six dialysis cups attached to a flat dialysis membrane. The automated system is based on a Tecan Freedom EVO 200 workstation in a three-arm configuration, and is equipped with shaking incubators, a vacuum module, a robotic centrifuge, a plate heat sealer, and a custom-made tilting carrier for collection of reaction solutions from the flat-bottom cups with dialysis membranes. The consecutive process, from the dialysis cell-free protein synthesis to the partial purification by immobilized metal affinity chromatography on a 96-well filtration plate, was performed within ca. 14 h, including 8 h of cell-free protein synthesis. The proteins were eluted stepwise in a high concentration using EDTA by centrifugation, while the resin in the filtration plate was washed on the vacuum manifold. The system was validated to be able to simultaneously and automatically produce up to 96 proteins in yields of several milligrams with high well-to-well reliability, sufficient for structural and functional analyses of proteins. The protein samples produced by the automated system have been utilized for NMR screening to judge the protein foldedness and for structure determinations using heteronuclear multi-dimensional NMR spectroscopy. The automated high-throughput protein production system represents an important breakthrough in the structural and functional studies of proteins and has already contributed a massive amount of results in the structural genomics project at the RIKEN Structural Genomics/Proteomics Initiative (RSGI).