Reversible CO2 Fixation and Release by a Trinuclear Zn(II) Cryptate Complex and Operando Analysis of the Complex Structure.

Metal complexes inspired by carbonic anhydrase (CA), which is a metalloenzyme containing Zn(II), have been investigated as alternatives for CO2 fixation systems operating under ambient temperature and pressure conditions. In this study, we designed a trinuclear Zn(II) cryptate complex (Zn3 L) and demonstrated rapid CO2 fixation with carbonation of CO2 using Zn3 L. The CO2 fixation performance of Zn3 L surpassed that of a standard CO2 absorbent, KOH(aq) solution, under conditions of the same solute concentration. In addition, the reaction achieved operation without support addition of base, which has been often required in systems of CA-inspired complexes. Fixed CO2 was released by protonating polyazacryptate ligand (L) and breaking the complex structure, and deprotonation of L induced the reconstruction of Zn3 L, allowing it to refix CO2 . This reaction mechanism was proposed based on the analysis of operando extended X-ray absorption fine structure spectroscopy. Zn3 L also demonstrated the ability to capture dilute CO2 from air, and the volume of CO2 captured by Zn3 L was approximately 2.6 times that captured by the KOH(aq) solution. Our Zn3 L exhibited three valuable properties: rapid CO2 fixation without a base, reversibility, and ability to capture dilute CO2 ; thus Zn3 L is a promising candidate as CO2 fixatives.

Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy.

Three-dimensional (3D) reconstruction for cryogenic electron microscopy (cryo-EM) often falls into an ill-posed problem owing to several uncertainties in observations, including noise. To reduce excessive degree of freedom and avoid overfitting, the structural symmetry is often used as a powerful constraint. In the case of the helix, the entire 3D structure is determined by the subunit 3D structure and two helical parameters. There is no analytical method to simultaneously obtain both of the subunit structure and helical parameters. A common approach is to employ an iterative reconstruction in which the two optimizations are performed alternately. However, iterative reconstruction does not necessarily converge when a heuristic objective function is used for each optimization step. Also, the obtained 3D reconstruction highly depends on the initial guess of the 3D structure and the helical parameters. Herein, we propose a method for estimating the 3D structure and helical parameters that also performs an iterative optimization; however, the objective function for each step is derived from a single objective function to make the algorithm convergent and less sensitive to the initial guess. Finally, we evaluated the effectiveness of the proposed method by testing it on cryo-EM images, which were challenging to reconstruct using conventional methods.

Functional Analysis of Feedback Inhibition-Insensitive Variants of N-Acetyl Glutamate Kinase Found in Sake Yeast Mutants with Ornithine Overproduction.

In the yeast Saccharomyces cerevisiae, N-acetyl glutamate kinase (NAGK), which catalyzes the phosphorylation of N-acetyl glutamate to form N-acetyl glutamyl-5-phosphate, is one of the rate-limiting enzymes in the ornithine and arginine biosynthetic pathways. NAGK activity is strictly regulated via feedback inhibition by the end product, arginine. We previously reported that the Thr340Ile variant of NAGK was insensitive to arginine feedback inhibition and that the interaction between Lys336 and Thr340 in NAGK may be important for arginine recognition. In the present study, we demonstrated that amino acid changes of Thr340 to Ala, Leu, Arg, Glu, Ile, and Asn removed arginine feedback inhibition, although the Thr340Ser variant was subject to the feedback inhibition. Therefore, these results indicate that the arginine-binding cavity formed via the interaction between the carbonyl group in the main chain of Lys336 and the hydroxyl group in the side chain of the residue at position 340 is critical for arginine recognition of NAGK. In addition, we newly identified two mutations in the ARG5,6 gene encoding the Cys119Tyr or Val267Ala variant of NAGK of sake yeast mutants with intracellular ornithine accumulation. Although it is unlikely that Cys119 and Val267 are directly involved in arginine recognition, we found here that two variants of NAGK were insensitive to arginine feedback inhibition and contributed to high-level production of ornithine. Structural analysis of NAGK suggests that these two amino acid substitutions influence the sensitivity to Arg feedback inhibition through alterations in local conformation around each residue. IMPORTANCE Ornithine has a number of physiological benefits in humans. Thus, an Orn-rich alcoholic beverage is expected to relieve feelings of fatigue after drinking. In the yeast Saccharomyces cerevisiae, N-acetyl glutamate kinase (NAGK) encoded by the ARG5,6 gene catalyzes the second step in ornithine and arginine biosynthesis, and its activity is subjected to feedback inhibition by arginine. Here, we revealed a role of key residues in the formation of the arginine-binding cavity which is critical for arginine recognition of NAGK. In addition, we analyzed novel arginine feedback inhibition-insensitive variants of NAGK in sake yeast mutants with ornithine overproduction and proposed that the amino acid substitutions in the NAGK variants destabilize the arginine-binding cavity, leading to the lower sensitivity to arginine feedback inhibition of NAGK activity. These findings provide new insight into the allosteric regulation of NAGK activity and will help to construct superior industrial yeast strains for high-level production of ornithine.

Influence of mutation in the regulatory domain of α-isopropylmalate synthase from Saccharomyces cerevisiae on its activity and feedback inhibition.

Isoamyl alcohol (i-AmOH) is produced from α-ketoisocaproate in the l-leucine biosynthetic pathway in yeast and controlled by the negative feedback regulation of α-isopropylmalate synthase (IPMS), which senses the accumulation of l-leucine. It is known that i-AmOH production increases when mutations in the regulatory domain reduce the susceptibility to feedback inhibition. However, the impact of mutations in this domain on the IPMS activity has not been examined. In this study, we obtained 5 IPMS mutants, encoding the LEU4 gene, N515D/S520P/S542F/A551D/A551V, that are tolerant to 5,5,5-trifluoro-dl-leucine. All mutant proteins were purified and examined for both IPMS activity and negative feedback activity by in vitro experiments. The results showed that not only the negative-feedback regulation by l-leucine was almost lost in all mutants, but also the IPMS activity was greatly decreased and the difference in IPMS activity among Leu4 mutants in the presence of l-leucine was significantly correlated with i-AmOH production.

Evaluation of automated particle picking for cryogenic electron microscopy using high-precision transmission electron microscope simulation based on a multi-slice method.

This work describes the GRIPS automated particle-picking software for cryogenic electron microscopy and the evaluation of this software using elbis, a high-precision transmission electron microscope (TEM) image simulator. The goal was to develop a method that can pick particles under a small defocus condition where the particles are not clearly visible or under a condition where the particles are exhibiting preferred orientation. The proposed method handles these issues by repeatedly performing three processes, namely extraction, two-dimensional classification and positioning, and by introducing mask processing to exclude areas with particles that have already been picked. TEM images for evaluation were generated with a high-precision TEM image simulator. TEM images containing both particles and amorphous ice were simulated by randomly placing O atoms in the specimen. The experimental results indicate that the proposed method can be used to pick particles correctly under a relatively small defocus condition. Moreover, the results show that the mask processing introduced in the proposed method is valid for particles exhibiting preferred orientation. It is further shown that the proposed method is applicable to data collected from real samples.

Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast.

In the yeast Saccharomyces cerevisiae, the mitochondrial branched-chain amino acid (BCAA) aminotransferase Bat1 plays an important role in the synthesis of BCAAs (valine, leucine, and isoleucine). Our upcoming study (Large et al. bioRχiv. 10.1101/2020.06.26.166157, Large et al. 2020) will show that the heterozygous tetraploid beer yeast strain, Wyeast 1056, which natively has a variant causing one amino acid substitution of Ala234Asp in Bat1 on one of the four chromosomes, produced higher levels of BCAA-derived fusel alcohols in the brewer's wort medium than a derived strain lacking this mutation. Here, we investigated the physiological role of the A234D variant Bat1 in S. cerevisiae. Both bat1∆ and bat1A234D cells exhibited the same phenotypes relative to the wild-type Bat1 strain-namely, a repressive growth rate in the logarithmic phase; decreases in intracellular valine and leucine content in the logarithmic and stationary growth phases, respectively; an increase in fusel alcohol content in culture medium; and a decrease in the carbon dioxide productivity. These results indicate that amino acid change from Ala to Asp at position 234 led to a functional impairment of Bat1, although homology modeling suggests that Asp234 in the variant Bat1 did not inhibit enzymatic activity directly. KEY POINTS: • Yeast cells expressing Bat1A234D exhibited a slower growth phenotype. • The Val and Leu levels were decreased in yeast cells expressing Bat1A234D. • The A234D substitution causes a loss-of-function in Bat1. • The A234D substitution in Bat1 increased fusel alcohol production in yeast cells.

High-level production of ornithine by expression of the feedback inhibition-insensitive N-acetyl glutamate kinase in the sake yeast Saccharomyces cerevisiae.

We previously reported that intracellular proline (Pro) confers tolerance to ethanol on the yeast Saccharomyces cerevisiae. In this study, to improve the ethanol productivity of sake, a traditional Japanese alcoholic beverage, we successfully isolated several Pro-accumulating mutants derived from diploid sake yeast of S. cerevisiae by a conventional mutagenesis. Interestingly, one of them (strain A902-4) produced more than 10-fold greater amounts of ornithine (Orn) and Pro compared to the parent strain (K901). Orn is a non-proteinogenic amino acid and a precursor of both arginine (Arg) and Pro. It has some physiological functions, such as amelioration of negative states such as lassitude and improvement of sleep quality. We also identified a homo-allelic mutation in the ARG5,6 gene encoding the Thr340Ile variant N-acetylglutamate kinase (NAGK) in strain A902-4. The NAGK activity of the Thr340Ile variant was extremely insensitive to feedback inhibition by Arg, leading to intracellular Orn accumulation. This is the first report of the removal of feedback inhibition of NAGK activity in the industrial yeast, leading to high levels of intracellular Orn. Moreover, sake and sake cake brewed with strain A902-4 contained 4-5 times more Orn than those brewed with strain K901. The approach described here could be a practical method for the development of industrial yeast strains with overproduction of Orn.

Bayesian inference for three-dimensional helical reconstruction using a soft-body model.

Estimation of the three-dimensional (3D) structure of a protein using cryo transmission electron microscopy (cryo-TEM) is an inverse problem, which aims to estimate the parameters of a specific physical process from observations. In general, we need to model the observation process to estimate a structure. However, the inconsistency between the model and a real observation process decreases the estimation accuracy. In cryo-TEM, the flexibility of a soft protein, including the bending of a helix, can lead to inconsistencies between the observations because of the assumption that there is a consistent 3D structure behind each observed image. In this paper, we propose a 3D reconstruction algorithm for helical structures using a parametric soft-body model that can represent continuous deformation. We performed an approximate Bayesian inference for unobservable (hidden) variables, such as the deformation parameters, projection angle, and two-dimensional origin offset (shift) of each protein in the 3D structure estimation problem. Our principled approach is not only beneficial to deal with the uncertainties in the estimation, but also beneficial to make the optimization algorithm convergent and efficient. Reconstructions with artificial molecules validated the advantage of the proposed method, particularly, when deformed helices were imaged under a low signal-to-noise ratio condition. Moreover, we confirmed that the proposed method successfully reconstructed a 3D structure from cryo-TEM images of the tobacco mosaic virus.

Stable N-acetyltransferase Mpr1 improves ethanol productivity in the sake yeast Saccharomyces cerevisiae.

N-Acetyltransferase Mpr1 was originally discovered as an enzyme that detoxifies L-azetidine-2-carboxylate through its N-acetylation in the yeast Saccharomyces cerevisiae Σ1278b. Mpr1 protects yeast cells from oxidative stresses possibly by activating a novel L-arginine biosynthesis. We recently constructed a stable variant of Mpr1 (N203K) by a rational design based on the structure of the wild-type Mpr1 (WT). Here, we examined the effects of N203K on ethanol fermentation of the sake yeast S. cerevisiae strain lacking the MPR1 gene. When N203K was expressed in the diploid Japanese sake strain, its fermentation performance was improved compared to WT. In a laboratory-scale brewing, a sake strain expressing N203K produced more ethanol than WT. N203K also affected the contents of flavor compounds and organic acids. These results suggest that the stable Mpr1 variant contributes to the construction of new industrial yeast strains with improved fermentation ability and diversity of taste and flavor.

Ordered silica mineralization by regulating local reaction conditions.

Using cationic peptides with tetramethyl orthosilicate, a silica nano-film >100 µm in size with <100 nm thickness was constructed under physiological conditions. Control of silica nucleation speed and location was found to be the dominant factor affecting the ordered architecture. Our approach adds new insight into bottom-up nanomaterial construction and contributes to evaluating the silica mineralization system in living organisms.

Metabolic switching of sake yeast by kimoto lactic acid bacteria through the [GAR+] non-genetic element.

In traditional kimoto-type sake production, cells of Saccharomyces cerevisiae sake yeast are grown in a starter mash generated by lactate fermentation by lactic acid bacteria (LAB) such as Leuconostoc mesenteroides and Lactobacillus sakei. However, the microbial interactions between sake yeast and kimoto LAB have not been well analyzed. Since the formation of a prion-like element (designated [GAR+]) in yeast cells is promoted by bacteria, we here examined the associated phenotype (i.e., increased glucosamine resistance) in sake yeast strains K701 (a representative sake strain) and Km67 (a strain isolated from kimoto-type sake mash). Approximately 0.5% of K701 and Km67 cells, as well as 0.2% of laboratory strain X2180 cells, exhibited increased glucosamine resistance under pure culture conditions, and the frequency of this metabolic switching was further enhanced by coculture with kimoto LAB. The LAB-promoted emergence of the glucosamine-resistant cells was the most prominent in Km67, suggesting that this strain possesses an advanced mechanism for response to LAB. While the glucosamine-resistant clones of X2180 and K701 exhibited lower rates of alcoholic fermentation under high-glucose conditions than did the respective naive strains, glucosamine resistance did not severely affect alcoholic fermentation in Km67. The population of dead cells after alcoholic fermentation was decreased in the glucosamine-resistant clones of X2180, K701, and Km67. These results suggested that the formation of [GAR+] in Km67 may be beneficial in kimoto-type sake making, since [GAR+] may increase cell viability in the sake starter mash without impairing alcoholic fermentation performance.

The C-terminal region of the yeast monocarboxylate transporter Jen1 acts as a glucose signal-responding degron recognized by the α-arrestin Rod1.

In response to changes in nutrient conditions, cells rearrange the composition of plasma membrane (PM) transporters to optimize their metabolic flux. Not only transcriptional gene regulation, but also inactivation of specific transporters is important for fast rearrangement of the PM. In eukaryotic cells, endocytosis plays a role in transporter inactivation, which is triggered by ubiquitination of these transporters. The Nedd4 family E3 ubiquitin ligase is responsible for ubiquitination of the PM transporters and requires that a series of α-arrestin proteins are targeted to these transporters. The mechanism by which an α-arrestin recognizes its cognate transporters in response to environmental signals is of intense scientific interest. Excess substrates or signal transduction pathways are known to initiate recognition of transporters by α-arrestins. Here, we identified an endocytic-sorting signal in the monocarboxylate transporter Jen1 from yeast (Saccharomyces cerevisiae), whose endocytic degradation depends on the Snf1-glucose signaling pathway. We found that the C-terminal 20-amino acid-long region of Jen1 contains an amino acid sequence required for association of Jen1 to the α-arrestin Rod1, as well as lysine residues important for glucose-induced Jen1 ubiquitination. Notably, fusion of this region to the methionine permease, Mup1, whose endocytosis is normally induced by excess methionine, was sufficient for Mup1 to undergo glucose-induced, Rod1-mediated endocytosis. Taken together, our results demonstrate that the Jen1 C-terminal region acts as a glucose-responding degron for α-arrestin-mediated endocytic degradation of Jen1.

A Molecular and Serological Survey of Rickettsiales Bacteria in Wild Sika Deer (Cervus nippon nippon) in Shizuoka Prefecture, Japan: High Prevalence of Anaplasma Species.

We surveyed Rickettsiales bacteria, including Rickettsia, Ehrlichia, Anaplasma, and Neoehrlichia, in wild sika deer (Cervus nippon nippon) from Shizuoka prefecture, Japan. In spleen samples from 187 deer, Anaplasma phagocytophilum (deer type), A. bovis, and A. centrale were successfully detected by PCR assay targeting to 16S rDNA or p44/msp2, and their positive rates were 96.3% (180/187), 53.5% (100/187), and 78.1% (146/187), respectively. Additionally, 2 or 3 Anaplasma species could be detected from a single deer in 165 spleen samples (88.2%), indicating dual or triple infection. In contrast, A. phagocytophilum (human type) 16S rDNA, Rickettsia gltA, Ehrlichia p28/omp-1, and Neoehrlichia 16S rDNA could not be amplified. The serological test of 105 deer serum samples by immunofluorescence assay showed that the detection of antibodies against antigens of A. phagocytophilum HZ (US-human isolate) and Rickettsia japonica YH were 29.5% (31/105) and 75.2% (79/105), respectively. These findings suggest that A. phagocytophilum (deer type), A. centrale, and A. bovis are highly dominant and prevalent in wild sika deer from Shizuoka, a central region of Japan, and that the antibodies against some Rickettsiales bacteria have also been retained in deer blood.

Isolation and characterization of awamori yeast mutants with L-leucine accumulation that overproduce isoamyl alcohol.

Awamori shochu is a traditional distilled alcoholic beverage made from steamed rice in Okinawa, Japan. Although it has a unique aroma that is distinguishable from that of other types of shochu, no studies have been reported on the breeding of awamori yeasts. In yeast, isoamyl alcohol (i-AmOH), known as the key flavor of bread, is mainly produced from α-ketoisocaproate in the pathway of L-leucine biosynthesis, which is regulated by end-product inhibition of α-isopropylmalate synthase (IPMS). Here, we isolated mutants resistant to the L-leucine analog 5,5,5-trifluoro-DL-leucine (TFL) derived from diploid awamori yeast of Saccharomyces cerevisiae. Some of the mutants accumulated a greater amount of intracellular L-leucine, and among them, one mutant overproduced i-AmOH in awamori brewing. This mutant carried an allele of the LEU4 gene encoding the Ser542Phe/Ala551Val variant IPMS, which is less sensitive to feedback inhibition by L-leucine. Interestingly, we found that either of the constituent mutations (LEU4(S542F) and LEU4(A551V)) resulted in the TFL tolerance of yeast cells and desensitization to L-leucine feedback inhibition of IPMS, leading to intracellular L-leucine accumulation. Homology modeling also suggested that L-leucine binding was drastically inhibited in the Ser542Phe, Ala551Val, and Ser542Phe/Ala551Val variants due to steric hindrance in the cavity of IPMS. As we expected, awamori yeast cells expressing LEU4(S542F), LEU4(A551V), and LEU4(S542F/A551V) showed a prominent increase in extracellular i-AmOH production, compared with that of cells carrying the vector only. The approach described here could be a practical method for the breeding of novel awamori yeasts to expand the diversity of awamori taste and flavor.

Mechanochemical lithiation of layered polysilane.

Lithiated polysilane was synthesized by the mechanochemical reaction of layered polysilane with metallic lithium. The resulting dark green powder formed a Si-Li bond on the surface and demonstrated electroconductivity.

Light-harvesting photocatalysis for water oxidation using mesoporous organosilica.

An organic-based photocatalysis system for water oxidation, with visible-light harvesting antennae, was constructed using periodic mesoporous organosilica (PMO). PMO containing acridone groups in the framework (Acd-PMO), a visible-light harvesting antenna, was supported with [Ru(II)(bpy)3(2+)] complex (bpy = 2,2'-bipyridyl) coupled with iridium oxide (IrO(x)) particles in the mesochannels as photosensitizer and catalyst, respectively. Acd-PMO absorbed visible light and funneled the light energy into the Ru complex in the mesochannels through excitation energy transfer. The excited state of Ru complex is oxidatively quenched by a sacrificial oxidant (Na2S2O8) to form Ru(3+) species. The Ru(3+) species extracts an electron from IrO(x) to oxidize water for oxygen production. The reaction quantum yield was 0.34 %, which was improved to 0.68 or 1.2 % by the modifications of PMO. A unique sequence of reactions mimicking natural photosystem II, 1) light-harvesting, 2) charge separation, and 3) oxygen generation, were realized for the first time by using the light-harvesting PMO.

Detection and characterization of p44/msp2 transcript variants of Anaplasma phagocytophilum from naturally infected ticks and wild deer in Japan.

Anaplasma phagocytophilum is an obligate intracellular bacterium and causes a febrile illness in humans and livestock. In nature, this bacterium is sustained in a tick-mammal cycle. Several p44/msp2-related genes are expressed from a single expression locus by gene conversion. In this study, we obtained 119 cDNA sequences of p44/msp2 transcripts from A. phagocytophilum in 6 Haemaphysalis ticks and 3 wild sika deer (Cervus nippon) in Japan. These 119 sequences were classified into 36 different variant sequences based on their similarities. The 36 cDNA sequences were phylogenetically grouped into 2 major clusters--tick- and deer-associated. The tick-associated sequences were further classified into 4 distinct subclusters, suggesting that A. phagocytophilum in ticks seems to selectively express specific p44/msp2 transcripts, such as the transcripts in the 4 subclusters that were closely related to previously identified p44/msp2 genes. The deer-associated sequences were also grouped into 4 subclusters, but these transcripts were probably more diverse than the transcripts derived from ticks. This might be due to the relatively nonselective expression of p44/msp2 in deer or the strain differences in A. phagocytophilum from ticks and deer in separate geographic regions or both. Thus, this study may contribute to the understanding of A. phagocytophilum p44/msp2 expression in nature in Japan.

Novel synthesis of bifunctional catalysts with different microenvironments.

Acid-base bifunctional activity governed by -NH(2) group's microenvironment is evident from two different catalysts scrutinized by interchanging the location of -SO(3)H/NH(2) groups on periodic mesoporous ethylenesilica. The hydrophobic local environment plays a significant role in one-pot deacetalization/nitroaldol condensation.

Theoretical studies on Si-C bond cleavage in organosilane precursors during polycondensation to organosilica hybrids.

Molecular orbital theory calculations were carried out to predict the occurrence of Si-C bond cleavage in various organosilane precursors during polycondensation to organosilica hybrids under acidic and basic conditions. On the basis of proposed mechanisms for cleavage of the Si-C bonds, the proton affinity (PA) of the carbon atom at the ipso-position and the PA of the carbanion generated after Si-C cleavage were chosen as indices for Si-C bond stability under acidic and basic conditions, respectively. The indices were calculated using a density functional theory (DFT) method for model compounds of organosilane precursors (R-Si(OH)(3)) having organic groups (R) of benzene (Ph), biphenyl (Bp), terphenyl (Tph), naphthalene (Nph), N-methylcarbazole (MCz), and anthracene (Ant). The orders for the predicted stability of the Si-C bond were Ph > Nph > Bp > Ant > Tph > MCz for acidic conditions and Ph > MCz > Bp > Nph > Tph > Ant for basic conditions. These behaviors were primarily in agreement with experimental results where cleavage of the Si-C bonds occurred for Tph (both acidic and basic), MCz (acidic), and Ant (basic). The Si-C bond cleavage of organosilane precursors during polycondensation is qualitatively predicted from these indices based on our theoretical approach.

Enhanced photocatalysis of rhenium(I) complex by light-harvesting periodic mesoporous organosilica.

This paper describes a new conceptual design for enhancement of photocatalytic CO(2) reduction of a rhenium(I) complex by light harvesting of periodic mesoporous organosilica (PMO). Mesoporous biphenyl-silica (Bp-PMO) anchoring fac-[Re(I)(bpy)(CO)(3)(PPh(3))](+)(OTf)(-) (bpy =2,2'-bipyridine; OTf = CF(3)SO(3)) in the mesochannels was synthesized by co-condensation of two organosilane precursors, 4,4'-bis(triethoxysilyl)biphenyl and 4-[4-{3-(trimethoxysilyl)propylsulfanyl}butyl]-4'-methyl-2,2'-bipyridine in the presence of a template surfactant, followed by coordination of a rhenium precursor, [Re(I)(CO)(5)(PPh(3))](+)(OTf)(-) to the bipyridine ligand in the mesochannels. The 280 nm light was effectively absorbed by the biphenyl groups in Bp-PMO, and the excited energy was funneled into the Re complex by resonance energy transfer, which enhanced photocatalytic CO evolution from CO(2) by a factor of 4.4 compared with direct excitation of the Re complex. Bp-PMO had an additional merit to protect the Re complex against a decomposition by UV irradiation. These results demonstrate the potential of PMOs as a light-harvesting antenna for designing various photoreaction systems, mimicking the natural photosynthesis.