InChI isotopologue and isotopomer specifications.

This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically-resolved chemical entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically-resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry. SCIENTIFIC CONTRIBUTION: This new extension to the InChI standard would enable improved annotation of analytical datasets characterizing chemical entities, supporting the FAIR (Findable, Accessible, Interoperable, and Reusable) guiding principles of data stewardship for chemical datasets, ultimately promoting Open Science in chemistry.

Publishing in the Open Access and Open Science era.

Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan.

DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata.

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.

Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.

Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions. Now, queries need to access not only the whole genomes of multiple pathogens but also make connections using robust contextual metadata to identify issues of public health relevance. Databases that over time developed a patchwork of submission formats and requirements need to be consistently organized and coordinated internationally to allow effective searches.To help resolve these issues, we propose a common pathogen data structure called the Pathogen Data Object Model (DOM) that will formalize the minimum pieces of sequence data and contextual data necessary for general public health uses, while recognizing that submitters will likely withhold a wide range of non-public contextual data. Further, we propose contributors use the Pathogen DOM for all pathogen submissions (bacterial, viral, fungal, and parasites), which will simplify data submissions and provide a consistent and transparent data structure for downstream data analyses. We also highlight how improved submission tools can support the Pathogen DOM, offering users additional easy-to-use methods to ensure this structure is followed.

SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan.

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum.

Hibiscus trionum, commonly known as the 'Flower of an Hour', is an easily cultivated plant in the Malvaceae family that is widespread in tropical and temperate regions, including drylands. The purple base part of its petal exhibits structural colour due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.

Genome Analysis Identifies a Novel Type III Secretion System (T3SS) Category in Vibrio Species.

The nanomachine referred to as the type III secretion system (T3SS) is used by many Gram-negative pathogens or symbionts to inject their effector proteins into host cells to promote their infections or symbioses. Among the genera possessing T3SS is Vibrio, which consists of diverse species of Gammaproteobacteria including human pathogenic species and inhabits aquatic environments. We describe the genetic overview of the T3SS gene clusters in Vibrio through a phylogenetic analysis from 48 bacterial strains and a gene order analysis of the two previously known categories in Vibrio (T3SS1 and T3SS2). Through this analysis we identified a new T3SS category (named T3SS3) that shares similar core and related proteins (effectors, translocons, and chaperones) with the Ssa-Esc family of T3SSs in Salmonella, Shewanella, and Sodalis. The high similarity between T3SS3 and the Ssa-Esc family suggests a possibility of genetic exchange among marine bacteria with similar habitats.

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species.

The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata, found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups, with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.

Bile Salt Hydrolase Degrades ß-Lactam Antibiotics and Confers Antibiotic Resistance on Lactobacillus paragasseri.

Bile salt hydrolase (BSH) is a well-characterized probiotic enzyme associated with bile detoxification and colonization of lactic acid bacteria in the human gastrointestinal tract. Here, we isolated a putative BSH (LpBSH) from the probiotic bacterium Lactobacillus paragasseri JCM 5343T and demonstrated its bifunctional activity that allows it to degrade not only bile salts but also the antibiotic (penicillin). Although antibiotic resistance and bile detoxification have been separately recognized as different microbial functions, our findings suggest that bifunctional BSHs simultaneously confer ecological advantages to host gut bacteria to improve their survival in the mammalian intestine by attaining a high resistance to bile salts and ß-lactams. Strain JCM 5343T showed resistance to both bile salts and ß-lactam antibiotics, suggesting that LpBSH may be involved in this multi-resistance of the strain. We further verified that such bifunctional enzymes were broadly distributed among the phylogeny, suggesting that the bifunctionality may be conserved in other BSHs of gut bacteria. This study revealed the physiological role and phylogenetic diversity of bifunctional enzymes degrading bile salts and ß-lactams in gut bacteria. Furthermore, our findings suggest that the hitherto-overlooked penicillin-degrading activity of penicillin acylase could be a potential new target for the probiotic function of gut bacteria.

Mitochondrial genome of Garcinia mangostana L. variety Mesta.

Fruits of Garcinia mangostana L. (mangosteen) are rich in nutrients with xanthones found in the pericarp having great pharmaceutical potential. Mangosteen variety Mesta is only found in Malaysia, which tastes sweeter than the common Manggis variety in Southeast Asia. In this study, we report the complete mitogenome of G. mangostana L. variety Mesta with a total sequence length of 371,235 bp of which 1.7% could be of plastid origin. The overall GC content of the mitogenome is 43.8%, comprising 29 protein-coding genes, 3 rRNA genes, and 21 tRNA genes. Repeat and tandem repeat sequences accounted for 5.8% and 0.15% of the Mesta mitogenome, respectively. There are 333 predicted RNA-editing sites in Mesta mitogenome. These include the RNA-editing events that generated the start codon of nad1 gene and the stop codon of ccmFC gene. Phylogenomic analysis using both maximum likelihood and Bayesian analysis methods showed that the mitogenome of mangosteen variety Mesta was grouped under Malpighiales order. This is the first complete mitogenome from the Garcinia genus for future evolutionary studies.

Comprehensive Metabolomic Comparison of Five Cereal Vinegars Using Non-Targeted and Chemical Isotope Labeling LC-MS Analysis.

Vinegar is used as an acidic condiment and preservative worldwide. In Asia, various black vinegars are made from different combinations of grains, such as Sichuan bran vinegar (SBV), Shanxi aged vinegar (SAV), Zhenjiang aromatic vinegar (ZAV), and Fujian Monascus vinegar (FMV) in China and Ehime black vinegar in Japan (JBV). Understanding the chemical compositions of different vinegars can provide information about nutritional values and the quality of the taste. This study investigated the vinegar metabolome using a combination of GC-MS, conventional LC-MS, and chemical isotope labeling LC-MS. Different types of vinegar contained different metabolites and concentrations. Amino acids and organic acids were found to be the main components. Tetrahydroharman-3-carboxylic acid and harmalan were identified first in vinegar. Various diketopiperazines and linear dipeptides contributing to different taste effects were also detected first in vinegar. Dipeptides, 3-phenyllactic acid, and tyrosine were found to be potential metabolic markers for differentiating vinegars. The differently expressed pathway between Chinese and Japanese vinegar was tryptophan metabolism, while the main difference within Chinese vinegars was aminoacyl-tRNA biosynthesis metabolism. These results not only give insights into the metabolites in famous types of cereal vinegar but also provide valuable knowledge for making vinegar with desirable health characteristics.

Isolation of a Highly Thermostable Bile Salt Hydrolase With Broad Substrate Specificity From Lactobacillus paragasseri.

Bile salt hydrolase (BSH) enzymes produced by intestinal Lactobacillus species have been recognized as major targets for probiotic studies owing to their weight-loss and cholesterol-lowering effects. In this study, we isolated a highly thermostable BSH with broad substrate specificity, designed as LapBSH (BSH from a probiotic bacterium, Lactobacillus paragasseri JCM 5343 T ). The recombinant LapBSH protein clearly hydrolyzed 12 different substrates, including primary/secondary, major/minor, and taurine/glycine-conjugated bile salts in mammalian digestive tracts. Intriguingly, LapBSH further displayed a highly thermostable ability among all characterized BSH enzymes. Indeed, this enzyme retained above 80% of its optimum BSH activity even after 6 h of incubation at 50-90°C. LapBSH also exerted a functionally stable activity and maintained above 85% of its original activity after pre-heating at 85°C for 2 h. Therefore, LapBSH is a very unique probiotic enzyme with broad substrate specificity and high thermostability. The strain itself, JCM 5343T, was also found to exhibit high heat-resistance ability and could form colonies even after exposure to 85°C for 2 h. As thermostable enzyme/bacterium offers industrial and biotechnological advantages in terms of its productivity and stability improvements, both thermostable LapBSH and thermotolerant L. paragasseri JCM 5343T could be promising candidates for future probiotic research.

Assessment of Greenhouse Tomato Anthesis Rate Through Metabolomics Using LASSO Regularized Linear Regression Model.

While the high year-round production of tomatoes has been facilitated by solar greenhouse cultivation, these yields readily fluctuate in response to changing environmental conditions. Mathematic modeling has been applied to forecast phenotypes of tomatoes using environmental measurements (e.g., temperature) as indirect parameters. In this study, metabolome data, as direct parameters reflecting plant internal status, were used to construct a predictive model of the anthesis rate of greenhouse tomatoes. Metabolome data were obtained from tomato leaves and used as variables for linear regression with the least absolute shrinkage and selection operator (LASSO) for prediction. The constructed model accurately predicted the anthesis rate, with an R2 value of 0.85. Twenty-nine of the 161 metabolites were selected as candidate markers. The selected metabolites were further validated for their association with anthesis rates using the different metabolome datasets. To assess the importance of the selected metabolites in cultivation, the relationships between the metabolites and cultivation conditions were analyzed via correspondence analysis. Trigonelline, whose content did not exhibit a diurnal rhythm, displayed major contributions to the cultivation, and is thus a potential metabolic marker for predicting the anthesis rate. This study demonstrates that machine learning can be applied to metabolome data to identify metabolites indicative of agricultural traits.

Development of RIKEN Plant Metabolome MetaDatabase.

The advancement of metabolomics in terms of techniques for measuring small molecules has enabled the rapid detection and quantification of numerous cellular metabolites. Metabolomic data provide new opportunities to gain a deeper understanding of plant metabolism that can improve the health of both plants and humans that consume them. Although major public repositories for general metabolomic data have been established, the community still has shortcomings related to data sharing, especially in terms of data reanalysis, reusability and reproducibility. To address these issues, we developed the RIKEN Plant Metabolome MetaDatabase (RIKEN PMM, http://metabobank.riken.jp/pmm/db/plantMetabolomics), which stores mass spectrometry-based (e.g. gas chromatography-MS-based) metabolite profiling data of plants together with their detailed, structured experimental metadata, including sampling and experimental procedures. Our metadata are described as Linked Open Data based on the Resource Description Framework using standardized and controlled vocabularies, such as the Metabolomics Standards Initiative Ontology, which are to be integrated with various life and biomedical science data using the World Wide Web. RIKEN PMM implements intuitive and interactive operations for plant metabolome data, including raw data (netCDF format), mass spectra (NIST MSP format) and metabolite annotations. The feature is suitable not only for biologists who are interested in metabolomic phenotypes, but also for researchers who would like to investigate life science in general through plant metabolomic approaches.

A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria.

In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.

Oligosaccharide Metabolism and Lipoteichoic Acid Production in Lactobacillus gasseri and Lactobacillus paragasseri.

Lactobacillus gasseri and Lactobacillus paragasseri are human commensal lactobacilli that are candidates for probiotic application. Knowledge of their oligosaccharide metabolic properties is valuable for synbiotic application. The present study characterized oligosaccharide metabolic systems and their impact on lipoteichoic acid (LTA) production in the two organisms, i.e., L. gasseri JCM 1131T and L. paragasseri JCM 11657. The two strains grew well in medium with glucose but poorly in medium with raffinose, and growth rates in medium with kestose differed between the strains. Oligosaccharide metabolism markedly influenced their LTA production, and apparent molecular size of LTA in electrophoresis recovered from cells cultured with glucose and kestose differed from that from cells cultured with raffinose in the strains. On the other hand, more than 15-fold more LTA was observed in the L. gasseri cells cultured with raffinose when compared with glucose or kestose after incubation for 15 h. Transcriptome analysis identified glycoside hydrolase family 32 enzyme as a potential kestose hydrolysis enzyme in the two strains. Transcriptomic levels of multiple genes in the dlt operon, involved in D-alanine substitution of LTA, were lower in cells cultured with raffinose than in those cultured with kestose or glucose. This suggested that the different sizes of LTA observed among the carbohydrates tested were partly due to different levels of alanylation of LTA. The present study indicates that available oligosaccharide has the impact on the LTA production of the industrially important lactobacilli, which might influence their probiotic properties.

α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae.

Papilio machaon hippocrates C. Felder et R. Felder, 1864 (Papilionidae) larvae are pests of plants of the family Apiaceae. It is unclear whether Apiaceae plants show induced defensive responses against P. machaon hippocrates larvae, and if so, how these responses are induced. Comparison of the fatty acid (FA) composition of the leaves of host plants and the regurgitant of P. machaon hippocrates larvae by LC-MS revealed a great increase in α-linolenic acid (α-LA) in the regurgitant compared with the FAs contained in the leaves. However, specific FA amino acid conjugates, known as elicitor compounds, such as volicitin, were not detected. Sterile host plants (Saposhnikovia divaricata (Turcz.) Schischk., Apiaceae) were treated with α-LA to mimic the damage made by P. machaon hippocrates larvae. After α-LA treatment to leaves, induced defensive reactions, i.e., release of volatile compounds such as α- and ß-pinene and camphene (possible induced indirect defense) and the accumulation of specialized metabolites such as (R)-falcarinol and bergapten (possible induced direct defense) were observed. These findings highlight the role of α-LA in the interaction between P. machaon hippocrates larvae and Apiaceae host plants.

Genetic Markers of Genome Rearrangements in Helicobacter pylori.

Helicobacter pylori exhibits a diverse genomic structure with high mutation and recombination rates. Various genetic elements function as drivers of this genomic diversity including genome rearrangements. Identifying the association of these elements with rearrangements can pave the way to understand its genome evolution. We analyzed the order of orthologous genes among 72 publicly available complete genomes to identify large genome rearrangements, and rearrangement breakpoints were compared with the positions of insertion sequences, genomic islands, and restriction modification genes. Comparison of the shared inversions revealed the conserved genomic elements across strains from different geographical locations. Some were region-specific and others were global, indicating that highly shared rearrangements and their markers were more ancestral than strain-or region-specific ones. The locations of genomic islands were an important factor for the occurrence of the rearrangements. Comparative genomics helps to evaluate the conservation of various elements contributing to the diversity across genomes.