Shulou(Shulou.com)11/24 Report--

Core hint

At present, there are three major pain points in plant metabolism research.

It is difficult to detect species-specific metabolites comprehensively and accurately by ⚫ traditional detection technology and public database.

⚫ KEGG contains limited metabolic pathways and cannot enrich species-specific secondary metabolic pathways.

⚫ KEGG contains limited metabolic pathways and is unable to screen genes related to specific metabolic pathways.

Where there is demand, Maiev's metabolism is there. Centering on these three major problems, Maiwei Metabolism "High Precision Secondary Metabolism Research team" adopted the whole stack self-developed technology layout strategy to develop a new generation of Xietong Road Map-MetMapTM, which has independent intellectual property rights and is far ahead.

User comments

Maiwei Metabolism, as a leading enterprise in the field of mass spectrometry, always adheres to technological innovation and "only innovation can lead". Along the way, there are too many hardships. "the sharp sword needs to be polished, and the fragrance of plum blossoms comes from the cold winter". User satisfaction is our greatest recognition, Maiwei Metabolism will strive to provide better products and services to researchers.

Professor Chen Wei, Huazhong Agricultural University

Our research group has been committed to the study of metabonomics of important food crops for a long time, hoping to provide new ideas and biochemical clues for genomics and promote people's in-depth understanding of the metabolic process of important food crops. further promote the genetic improvement of crops, especially the improvement of nutritional quality. In recent years, related research results have been published in Nature Genetics,Nature Communications, PNAS, Plant Cell and other journals.

Comments: "the summary information of metabolic pathways in KEGG plays a very important role in life science research and is widely used by everyone." However, plant secondary metabolite synthesis and metabolic pathways are relatively lacking. Maiwei Metabolism MetMap ™database creatively expands KEGG metabolic database, constructs the pathway of secondary metabolite synthesis, and integrates metabolic biosynthesis genes, which plays an important reference role for plant metabolism and biology researchers. "

Professor Liang Mei, College of Horticulture and Forestry, Huazhong Agricultural University

The research group used monkey face flower as the basic material to explore the formation mechanism and regulation methods of flower color of other ornamental plants (such as rose and lily) in China, and combined with mathematical simulation to realize the molecular design of flower color. The doctor graduated from the citrus team of Huazhong Agricultural University, studied under Academician Deng Xiuxin and Professor Chai Lijun, and conducted postdoctoral research in Professor Yuan Yaowu Laboratory of the University of Connecticut. Published as the first author in Science, Science Advances, Nature Plants and other international authoritative magazines.

Comments: "my research pays more attention to flavonoids and carotenoid pathways. Maiwei metabolizes MetMap ™in addition to KEGG substances and pathways, but also includes species-specific substances and pathways, which can better solve my scientific problems."

Zhu Feng, researcher, Huazhong Agricultural University

After graduating from Professor Cheng Yunjiang of Huazhong Agricultural University, he went to Professor Alisdair Fernie of Max Planck Institute of Molecular Plant Physiology in Germany to carry out postdoctoral work. At present, it is mainly engaged in the research on the biological basis and regulation mechanism of postharvest horticultural products. Fourteen papers have been published in Plant Cell, Trends in Plant Science, Autophagy and other journals as first author (including juxtaposition) and common newsletter.

Comments: "my research direction is the formation and postharvest maintenance of citrus fruit storage and transportation quality. Maiwei Metabolism has developed metabolic detection methods for different metabolites and established a complete metabolite characteristic fragment database, which can provide high-quality metabolic group and multi-group comprehensive analysis, which is recommended!"

Professor Hu Wei, Institute of Tropical Biotechnology, Chinese Academy of Tropical Agricultural Sciences

He is currently the director of the big data Center of Tropical Biomics of the Chinese Academy of Thermal Sciences and the deputy director of the key Laboratory of Tropical crop Biology and genetic data Utilization of the Agriculture and Village Department. Mainly engaged in tropical crop germplasm resources and genetics and breeding research, published 83 papers as the first author or correspondent author (including juxtaposition) in Nature Plants, Advanced Science, Molecular Plant, Genome Biology and other domestic and foreign academic journals.

Comments: "plants are very rich in compounds, with the development of mass spectrometry detection technology, we can detect more and more primary and secondary metabolites." However, there are a variety of plant-specific secondary metabolite modifications, and many pathway genes have not been reported, so the metabolic pathway is very complex. The construction of Maiwei metabolic MetMap ™provides an important basis for the study of plant metabolic group, the construction of metabolic pathway and the process of plant biology.

Associate Professor Gao Yanqiang, Northeast Forestry University

The research group mainly uses population genetic materials to comprehensively analyze the genetic variation and biochemical basis of crop metabolic groups by means of modern molecular biology techniques, and carries out basic research on the application of physiology, biochemistry and stress biology of berries with northeast characteristics. As the first author (including juxtaposition), many papers have been published in Nature Genetics,PNAS,Plant Cell,Plant and Cell Physiology and other journals.

Comments: "Maiwei Metabolism MetMap ™database integrates the specific metabolites of different plant species, and summarizes the synthetic genes of metabolic pathways based on the literature. The work is very careful and meticulous, which provides a good metabolic review and reference for plant metabolic group and genome research. Based on this database, the integration of metabonomics, genomes, transcriptome and proteome will help us to mine new metabolites and biology-related genes, while contributing to botany research. "

Detailed introduction

1. Metabolic group is the bridge between genome and phenotypic group.

In 2002, Plant Molecular Biology published an article entitled "Metabolomics-the link between genotypes and phenotypes" by Professor Oliver Fiehn online, which clarified that metabonomics is a bridge between genomics and phenotype, and this argument is also reflected in many literatures.

For example, in the study of rice grain size, the main substance involved in the study is trigonelline, and the key gene that controls grain size is the gene Os02g57760 annotated as N-methyltransferase.

[Chen, Wei, et al.Nature Communications 7 (2016): 12767]

In the study of the color of papaya, the main type of substance that determines the color is carotenoid. There are differences in gene synthesis pathways involved in the ripening process of peel and pulp of papaya. The α-branch of LCYE in the peel is normally synthesized into lutein, which is yellow at last, while β-carotene and other substances are mainly synthesized in the pulp, so it is orange-red.

[Shen et al. BMC Genomics 2019]

In addition to quality studies, there are similar cases in abiotic stress. Under salt stress, rice will synthesize more glycosides and flavonoids to resist antioxidation, and its key gene is annotated as the glycoside transferase gene GSA1.

[Dong, Nai Qian, et al. Nature Communications 11.1 (2020)]

There are numerous such studies, which also show that metabonomics can play an important role as a bridge between phenotype and gene in gene-related research.

two。 The main problems faced by plant metabonomics at present

2.1 Diversity and accuracy of identification of plant secondary metabolites

In 1891, H.Kossel clearly divided plant metabolism into primary metabolism and secondary metabolism. Primary metabolism is necessary to maintain cell life, and its metabolites exist in all plants, including sugars, lipids, amino acids and so on. On the other hand, there are differences in the specificity of species, organs, tissues and growth stages of secondary metabolism, and the secondary metabolites produced are also a kind of small molecular organic compounds that are not necessary for plant growth and development. at the same time, many secondary metabolites are involved in plant disease resistance, stress resistance or physiological activities, such as the accumulation of flavonoid glycoside metabolites in rice to resist ultraviolet radiation. The alkaloids accumulated in traditional Chinese medicine plants have anti-inflammatory and other physiological activities.

Schematic diagram of plant metabolic network

It is estimated that the number of metabolites produced by plants is 200000 ~ 1 million, of which only 8000 are primary metabolites, and the others are basically secondary metabolites. For such a large number of secondary metabolites, it is a challenge to detect all the metabolites in the samples and to identify them accurately.

Types and characteristics of plant secondary metabolites

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2.2 current status of KEGG pathway in plants

The construction of pathways is an unavoidable focus in the study of plant biology, but at present, the substances covered by KEGG pathways are limited, and the growth rate of material annotations and pathway annotations in KEGG database has been slow in the past two years. Compared with 2022, only 123 new substances were added to the pathways in 2023, and all the substances annotated to the pathways accounted for only 33.5% of the materials in KEGG database. The metabolites and gene annotations of map00941 and map00944, which are widely used in plants, have not changed in the past two years (Table 1), which can not meet the increasing number of [plant widely targeted ®metabolic group] data to carry out more in-depth analysis, but also seriously limited the in-depth study of genes.

Table 1.KEGG Database data comparison between 2022 and 2023

3. Far ahead of the new generation of plant metabolic pathway map-- MetMap

To sum up, building MetMap ™can directly solve these three problems:

3.1 how to measure matter

The qualitative determination of matter is the first important point.

Based on the widely targeted ®metabonomics detection method, the collection mode of high qualitative accuracy of high resolution mass spectrometer is used to detect the substance. At the same time, based on the material information collected when the local database is built, the material information in the sample is collected and matched under the same experimental conditions to determine the substance qualitatively, in order to achieve the most accurate identification results.

Mirror matching results of secondary mass spectra of substances

Substances should be thoroughly inspected.

In addition to qualitative accuracy, it is particularly important to detect as many substances in the sample as possible. Based on the limited availability of the public plant database, Maiwei built a local database of 30000 matching instruments, including 1800 + primary metabolites and 28000 + plant secondary metabolites, which can cover more plant secondary metabolites and achieve the goal of detecting new substances.

At present, plant widely targeted ®metabonomics technology is used to detect different species, and the detection can basically reach the level of 1000-2500, so that all substances in the samples should be detected.

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The qualitative determination of matter is the foundation of the article.

Since the launch of plant widely targeted metabolomics technology in 2015, we have worked with customers all over the country, and over the years, we have published a number of articles on the use of plant widely targeted ®metabonomics to solve biological problems. Some of the high-scoring articles are as follows:

3.2 how to enrich to get a new pathway

Based on the fact that the current path information on KEGG is limited, and the construction of new paths is time-consuming and laborious, in order to solve this problem, we independently constructed a new generation of road map MetMapTM. Starting from the basic KEGG pathway, the pathway expands into a new generation of pathways that contain more substances downstream.

For example, based on star channel Map00941 and Map00944, Maiwei's own road map MetMap ™105-Luteolin aglycones biosynthesis is extended. We use substances detected from lily, tea, tomato, Arabidopsis thaliana, rice, wheat, epimedium, corn and other species to carry out pathway annotation tests. the results show that the detected substances are not only annotated to KEGG pathway K00941 and K00944, but also on this new pathway. the number of material annotations in the new pathway can reach or even exceed the number of material annotations in KEGG pathway. This can make full use of the detected substances.

Table 2.MetMap ™105 access and actual project annotation test

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3.3 how to find the gene

All the biological problems are inseparable from the in-depth study of gene function, but the discovery of new genes is difficult, and MetMapTM can solve this problem. Combine metabolic group and transcriptome / genomics data analysis to annotate metabolites and genes / enzymes simultaneously, thus annotating new genes on the new pathway.

MetMap ™105-Luteolin aglycones biosynthesis

Note: the circle represents the metabolite and the box represents the enzyme (gene). Respect copyright, please do not use for other commercial purposes.

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Maiwei Metabolism is a new generation of pathway MetMap ™based on independent innovation of metabolism (Metabolic) and pathway (Map), which detects new substances, unlocks new pathways and discovers new genes.

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