Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production.

The concerted effort for bioproduction of higher alcohols and other commodity chemicals has yielded a consortium of metabolic engineering techniques to identify targets to enhance performance of engineered microbial strains. Here, we demonstrate the use of metabolomics as a tool to systematically identify targets for improved production phenotypes in Escherichia coli. Gas chromatography/mass spectrometry (GC/MS) and ion-pair LC-MS/MS were performed to investigate metabolic perturbations in various 1-propanol producing strains. Two initial strains were compared that differ in the expression of the citramalate and threonine pathways, which hold a synergistic relationship to maximize production yields. While this results in increased productivity, no change in titer was observed when the threonine pathway was overexpressed beyond native levels. Metabolomics revealed accumulation of upstream byproducts, norvaline and 2-aminobutyrate, both of which are derived from 2-ketobutyrate (2KB). Eliminating the competing pathway by gene knockouts or improving flux through overexpression of glycolysis gene effectively increased the intracellular 2KB pool. However, the increase in 2KB intracellular concentration yielded decreased production titers, indicating toxicity caused by 2KB and an insufficient turnover rate of 2KB to 1-propanol. Optimization of alcohol dehydrogenase YqhD activity using an ribosome binding site (RBS) library improved 1-propanol titer (g/L) and yield (g/g of glucose) by 38 and 29% in 72 h compared to the base strain, respectively. This study demonstrates the use of metabolomics as a powerful tool to aid systematic strain improvement for metabolically engineered organisms.

The genus Psilotreta Banks (Trichoptera, Odontoceridae) in Japan.

The Japanese species of Psilotreta Banks (Trichoptera, Odontoceridae) are reviewed. Five described species and three new species are recognized: P. japonica (Banks 1906), P. kisoensis Iwata 1928, P. voluta Kawase 2021, P. moritai Kawase 2021, P. flavida Kawase 2021, P. spatulata sp. nov., P. atrocaudata sp. nov., and P. bitubercula sp. nov. Adults of the three new species are described and those of P. japonica and P. kisoensis are redescribed. Illustrations of male and female genitalia of the remaining three species are provided for comparison. The larva of P. spatulata sp. nov. is described and those of P. japonica and P. kisoensis are redescribed. The larva of P. voluta is indistinguishable from that of P. spatulata sp. nov.

Description of three new species of Psilotreta (Trichoptera: Odontoceridae) from Japan.

Three new species of the caddisfly genus Psilotreta (Trichoptera: Odontoceridae) from Japan are described: P. voluta sp. nov., P. moritai sp. nov., and P. flavida sp. nov. These three species are easily distinguishable by the male genitalia from previously known Japanese species, P. japonica (Banks 1906) and P. kisoensis Iwata 1928. The three new species are similar to P. vertebrata Yuan et al. 2008, P. cuboides Yuan et al. 2008, and P. excavata Yuan et al. 2008 from the Chinese mainland, and P. clyssan Malicky 2014 from Taiwan, in the shapes of the lateral processes and intermediate appendages of segment X of the male genitalia, but can be distinguished from these species and each other. All Japanese species of Psilotreta listed above belong to the P. chinensis Species Group.

Elucidation of the whole carotenoid biosynthetic pathway of aphids at the gene level and arthropodal food chain involving aphids and the red dragonfly.

BACKGROUND: Aphids can be positioned as robust pest insects in farming and as ones of the model organisms for arthropods in molecular biology. Carotenoids are pigments that protect organisms from photooxidative damage caused by excessive light. Aphids were shown to possess genes of fungal origin for carotenoid biosynthesis, whereas a little knowledge was available about the functions of the genes and the biosynthetic pathway. Even carotenoid species contained in aphids were not enough understood. Main purpose of this study is to clarify these insufficient findings. RESULTS: The whole carotenoid biosynthetic pathway of the pea aphid (Acyrthosiphon pisum) was elucidated at the gene level, through comprehensive functional analysis of its carotenogenic genes, using Escherichia coli that synthesized carotenoid substrates, along with structural and quantitative analysis of carotenoids from various aphid species. Four genes were needed to synthesize all carotenoids accumulated in aphids from geranylgeranyl diphosphate. The tor gene mediated desaturation reaction from phytoene to 3,4-didehydrolycopene. It was revealed that a gene designated ApCrtYB3, which was considered to have functionally evolved in aphids, can convert lycopene into uncommon carotenoids with the γ-ring such as (6'S)-ß,γ-carotene and γ,γ-carotene. We further demonstrated that the atypical carotenoids work as ecological indicators for estimating the food chain from aphids to predatory arthropods, and showed that aphids contributed with significant levels to the food chain from insect herbivores to several predatory arthropods, i.e., the red dragonfly (Sympetrum frequens; adults), seven-spotted ladybird (Coccinella septempunctata), and two spiders, Oxyopes sertatus and Nephila clavata. Gut microflora of the dragonfly (mature adults) was also found to include endosymbiotic bacteria such as Serratia symbiotica specific to the black bean aphid (Aphis fabae). CONCLUSIONS: We revealed the whole carotenoid biosynthetic pathway of aphids, including functional identification of the corresponding genes. Subsequently, we showed that arthropodal food chain can be estimated using the uncommon carotenoids of aphids as ecological indicators. This result indicated that aphids made significant contributions to the food chain of several predatory arthropods including the red-dragonfly adults. Aphids are likely to be positioned as an important "phytochemicals" source for some predatory insects and arachnids, which are often active under bright sunlight.

Mesenchymal stem cell-induced 3D displacement field of cell-adhesion matrices with differing elasticities.

Cells maintain homeostasis and perform various functions by interacting mechanically with a cell-adhesive matrix. Regarding cellular differentiation, it has been found that matrix elasticity can determine the differentiation lineage of mesenchymal stem cells (MSCs). Direct quantitative measurements of the mechanical interaction between MSCs and matrix for differentiation, however, have yet to be reported. Herein, the displacement field of the cell-adhesive matrix was observed quantitatively using a digital volume correlation (DVC) method. Maximum displacement and cellular traction stress were analyzed when the MSC differentiated into a neuron-like cell or an osteoblast-like cell on a soft or hard elastic matrix, respectively. The function of non-muscle myosin II (NMM II), which plays an important role in intracellular cytoskeletal dynamics, was investigated during cellular differentiation. The mechanical interaction (maximum displacement and subjected area of the matrix) between the cell and matrix was dependent on matrix elasticity. It has also been shown that the mechanical interaction between the intracellular cytoskeleton and cell-adhesion matrix is indispensable for cellular differentiation. This work provides the first quantitative visualization of the mechanical interaction between MSCs and the cell-adhesion matrix for differentiation.

Different-batch metabolome analysis of Saccharomyces cerevisiae based on gas chromatography/mass spectrometry.

Each experimental step in metabolomics based on mass spectrometry for microorganisms, such as cultivation, sampling, extraction of metabolites, analysis, and data processing includes different systematic errors. Even if the same protocol is used, it is difficult to compare the data from different cultivation days or different analysis days. To obtain reliable quantitative data, it is necessary to develop an analytical workflow that can reduce errors from different batch of cultivation and analysis days. We compared metabolomics methods for Saccharomyces cerevisiae in terms of reproducibility to optimize the analytical workflow, particularly quenching and data processing. Our data also showed that reproducible data could be obtained with high signal to noise ratio. Therefore, we optimized a time segmented selective ion monitoring (SIM) method for high sensitive analysis with low-risk of false positives. The optimized workflow was applied to metabolome analysis of single transcription factor deletion mutants. As a result, we obtained clusters that were independent of cultivation day and analysis day but were strain-dependent. This study can help to implement large-scale or long-term studies, in which samples are divided among several laboratories because of the high number of samples.