Article
Biotechnology & Applied Microbiology
Jan H. Nagel, Michael J. Wingfield, Bernard Slippers
Summary: The genomes of Botryosphaeriaceae fungi are rich in carbohydrate-active enzymes, proteases, lipases, and secondary metabolic biosynthetic gene clusters compared to other Dothideomycete genomes. These genomes also have moderate to high GC contents and low levels of repetitive DNA. The abundance of secreted hydrolytic enzymes and secondary metabolite biosynthetic gene clusters in the genomes of Botryosphaeria, Macrophomina, Lasiodiplodia, and Neofusicoccum suggest similarities to necrotrophic plant pathogens and endophytes of woody plants.
Article
Mycology
E. Kuhnert, J. C. Navarro-Munoz, K. Becker, M. Stadler, J. Collemare, R. J. Cox
Summary: This study analyzed the genetic background of Hypoxylaceae family, revealing a diversity of biosynthetic pathways in these organisms with majority arranged in biosynthetic gene clusters. Speciation was found to be accompanied by changes in secondary metabolism among these fungi, with potential for discovery of new biosynthetic pathways encoding useful compounds as more genomes become available.
STUDIES IN MYCOLOGY
(2021)
Review
Plant Sciences
Lorena I. Rangel, Melvin D. Bolton
Summary: Plants have various responses to counter disease, while plant pathogens orchestrate a finely tuned repertoire of virulence mechanisms. Secondary metabolite effectors (SMEs) play important roles in plant disease, including self-resistance and manipulation of the microbial community.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Microbiology
Drago Haas, Antje M. Thamm, Jiayi Sun, Lili Huang, Lijie Sun, Guillaume A. W. Beaudoin, Kim S. Wise, Claudia Lerma-Ortiz, Steven D. Bruner, Marian Breuer, Zaida Luthey-Schulten, Jiusheng Lin, Mark A. Wilson, Greg Brown, Alexander F. Yakunin, Inna Kurilyak, Jacob Folz, Oliver Fiehn, John I. Glass, Andrew D. Hanson, Christopher S. Henry, Valerie de Crecy-Lagard
Summary: Metabolite damage and repair mechanisms are vital for the survival of Mycoplasma JCVI-Syn3A, with key genes identified to play essential roles in these processes. The study also revealed a novel proofreading function in NAD synthesis and the potential dual role of a YqeK hydrolase domain as a sanitizing enzyme for the nucleotide pool. Additionally, the extension of the metabolic map showed the existence of metabolite damage control systems that are yet to be fully characterized.
Article
Agronomy
Luigi Formisano, Begona Miras-Moreno, Michele Ciriello, Christophe El-Nakhel, Giandomenico Corrado, Luigi Lucini, Giuseppe Colla, Youssef Rouphael
Summary: The study showed that treatments with Trichoderma and phosphite had positive effects on the growth and metabolism of zucchini squash plants, especially with the Trichoderma treatment leading to significant improvements in physiological performance and biomass production. Both treatments induced broad metabolic reprogramming in leaves, with common responses such as triggering ROS-mediated signaling processes and the accumulation of certain metabolites.
Review
Biology
Janani Manochkumar, Aswani Kumar Cherukuri, Raju Suresh Kumar, Abdulrahman I. Almansour, Siva Ramamoorthy, Thomas Efferth
Summary: This review provides a comprehensive overview of the -omics and multi-omics approaches used for characterizing marine metabolites, along with the need for data integration and machine learning algorithms. It also discusses the challenges and recommendations for conducting multi-omics studies.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Hazem S. S. Elshafie, Ippolito Camele, Amira A. A. Mohamed
Summary: Natural products, including primary metabolites (PMs) and secondary metabolites (SMs), play crucial roles in plant growth, reproduction, defense, and adaptation. SMs, including terpenoids, phenolics, and nitrogen-containing compounds, possess various biological activities and can be used as flavoring agents, food additives, and plant-disease control. This review focuses on the significance, biosynthesis, classification, biochemical characterization, and medical/pharmaceutical uses of plant SMs. Additionally, the potential of SMs as eco-friendly substitutes for synthetic pesticides and their role in enhancing plant resistance are discussed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Agriculture, Multidisciplinary
Muzaffer Barut, Muhammad Azhar Nadeem, Ozlem Akgur, Leyla Sezen Tansi, Muhammad Aasim, Muhammad Tanveer Altaf, Faheem Shehzad Baloch
Summary: This article discusses the relationship between plants and humans, as well as the role of plants in medicine synthesis. It introduces the developments in the plant omics era and related techniques such as gene sequencing and characterization. The article explores the research progress and potential in molecular breeding of medicinal and aromatic plants.
TURKISH JOURNAL OF AGRICULTURE AND FORESTRY
(2022)
Article
Microbiology
Bin Wei, Ao-Qi Du, Zhen-Yi Zhou, Cong Lai, Wen-Chao Yu, Jin-Biao Yu, Yan-Lei Yu, Jian-Wei Chen, Hua-Wei Zhang, Xue-Wei Xu, Hong Wang
Summary: The study systematically investigates the diversity and genetic variability of bacterial secondary metabolite biosynthetic gene clusters (BGCs) in 10121 prokaryotic genomes. It identifies certain bacterial genera as potential important sources of natural products, suggesting the need for individual evaluation of secondary metabolism potential. Comparative analysis within these genera reveals great diversity and novelty of BGCs, providing key information for targeted discovery of novel natural products.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Review
Plant Sciences
Umer Mahmood, Xiaodong Li, Yonghai Fan, Wei Chang, Yue Niu, Jiana Li, Cunmin Qu, Kun Lu
Summary: Crop production is facing challenges from increasing food demand and climate change. Advances in omics techniques and machine learning algorithms can accelerate crop breeding to cope with these challenges. Plant breeding and genetic engineering can develop nutrient sufficient and climate-resilient crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Maryke Wijma, Carolina Gimiliani Lembke, Augusto Lima Diniz, Luciane Santini, Leonardo Zambotti-Villela, Pio Colepicolo, Monalisa Sampaio Carneiro, Glaucia Mendes Souza
Summary: In order to reduce the environmental impacts caused by fossil fuels, it is important to increase the use of renewable energy sources globally. One promising source is sugarcane for biomass and bioenergy production. Studying the development of sugarcane in different planting seasons can aid in cultivation under global climate change scenarios. The research found differences in physiological, morphological, agrotechnological, transcriptomics, and metabolomics levels among different tissues of sugarcane, highlighting important metabolic categories across tissues.
Review
Plant Sciences
Panchsheela Nogia, Pratap Kumar Pati
Summary: The study focuses on the important roles of secondary metabolites (SMs) in plant growth, defense, development, and survival, as well as explores the transport mechanisms of SMs and the potential of engineering transporters to enhance metabolite production.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Jhon Venegas-Molina, Francisco J. Molina-Hidalgo, Elke Clicque, Alain Goossens
Summary: The interaction between metabolites and proteins plays a crucial role in cellular regulatory processes within and between organisms. Recent studies have shown that plant metabolites have diverse biological activities beyond their traditional roles, and technologies to study metabolite-protein interactions are being reviewed. This discussion provides insights from both plant and human perspectives, contributing to a better understanding of plant metabolic networks and facilitating agrochemical and drug discoveries.
TRENDS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Yangyang Li, Wei Zhu, Qingyuan Xiang, Jeongim Kim, Craig Dufresne, Yufeng Liu, Tianlai Li, Sixue Chen
Summary: Large-scale high throughput metabolomic technologies are crucial for systems biology, but the lack of a plant metabolite spectral library hinders metabolite identification in plant metabolomic studies. In this study, a plant metabolite spectral library was created using 544 authentic standards, enhancing the efficiency of identification in untargeted metabolomic studies. The process of creating the spectral library was described, and the mzVault library was deposited in a public repository for free download. A pseudo-targeted method was also developed based on the spectral library and applied to a proof-of-concept study of Arabidopsis leaf extracts. As more authentic standards become available, the spectral library can be expanded to improve the mzVault package.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Patricia M. B. Saint-Vincent, Anna Furches, Stephanie Galanie, Erica Teixeira Prates, Jessa L. L. Aldridge, Audrey Labbe, Nan Zhao, Madhavi Z. Z. Martin, Priya Ranjan, Piet Jones, David Kainer, Udaya C. C. Kalluri, Jin-Gui Chen, Wellington Muchero, Daniel A. A. Jacobson, Timothy J. J. Tschaplinski
Summary: Metabolite genome-wide association studies (mGWASs) are important in plant genetics and metabolomics, but there is a lack of experimental validation. This study presents a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships. Through high-throughput enzyme activity testing and metabolite screening, the study provides evidence for the role of UGTs in P. trichocarpa and identifies potential implications for sustainable biomass crop production.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lalida Sangpong, Gholamreza Khaksar, Pinnapat Pinsorn, Akira Oikawa, Ryosuke Sasaki, Alexander Erban, Mutsumi Watanabe, Karan Wangpaiboon, Takayuki Tohge, Joachim Kopka, Rainer Hoefgen, Kazuki Saito, Supaart Sirikantaramas
Summary: The study found that sucrose content increased during the ripening process of durian, while aspartate decreased. Changes in raffinose-family oligosaccharides were reported for the first time, and most amino acids increased. By transcriptomic analysis, key candidate genes can be identified for further research.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Medicinal
Taketo Okada, Takao Namiki, Takayuki Tohge, Shigehiko Kanaya
Summary: Kampo is a traditional Japanese medicine system validated over millennia in Asia, focusing on preventing and treating disease holistically based on specific diagnosis Sho. This complex medication system can be explained using chemometrics and informatic approaches.
JOURNAL OF NATURAL MEDICINES
(2022)
Article
Plant Sciences
Martine Lemaire-Chamley, Claude Koutouan, Joana Jorly, Julien Assali, Takuya Yoshida, Marilise Nogueira, Takayuki Tohge, Carine Ferrand, Lazaro E. P. Peres, Erika Asamizu, Hiroshi Ezura, Paul D. Fraser, Mohammad-Reza Hajirezaei, Alisdair R. Fernie, Christophe Rothan
Summary: The bZIP transcription factor SlTGA2.2 plays an important role in the growth and maturation of tomato fruits. By targeting the expression of a chimeric repressor, the study found that the repressor affects fruit development and metabolism, prolongs the time to reach maturity, and slows down fruit ripening. This research provides a useful tool for studying the molecular bases of tomato fruit transition to ripening.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Silvio Candido-Sobrinho, Valeria Lima, Francisco Freire, Leonardo de Souza, Jorge Gago, Alisdair R. Fernie, Danilo M. Daloso
Summary: Recent research suggests that metabolism-mediated stomatal closure mechanisms play a crucial role in regulating the differences in stomatal speediness between ferns and angiosperms. Ferns showed a lack of response to ABA and slower stomatal responses to sucrose and mannitol compared to angiosperms. Metabolomics analysis revealed that ferns accumulate more secondary metabolites than primary metabolites throughout the diel course, presenting a potential mechanism for the slower stomatal closure and differences in response to exogenous substances between ferns and angiosperms.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Yuting Liu, Alisdair R. Fernie, Takayuki Tohge
Summary: The O-methylation of specialized metabolites in plants is a unique decoration that provides structural and functional diversity. The O-methylation of flavonoids promotes antimicrobial activities and liposolubility. Characterizing the physiology roles of methoxylated flavonoids with flavonoid O-methyltransferases is useful for crop improvement and metabolic engineering.
Article
Plant Sciences
Jay C. Delfin, Yuri Kanno, Mitsunori Seo, Naoki Kitaoka, Hideyuki Matsuura, Takayuki Tohge, Takafumi Shimizu
Summary: AtGH3.10 plays a role in flower development and the wound stress response in Arabidopsis, partially overlapping with AtJAR1.
Article
Plant Sciences
Matteo Chialva, Davide Lucien Patono, Leonardo Perez de Souza, Mara Novero, Sara Vercellino, Moez Maghrebi, Michele Morgante, Claudio Lovisolo, Gianpiero Vigani, Alisdair Fernie, Valentina Fiorilli, Luisa Lanfranco, Paola Bonfante
Summary: Coffee, being one of the most traded commodities globally, exhibits a strong interaction with arbuscular mycorrhizal (AM) fungi. This study explored the mycorrhizal phenotype of two important coffee cultivars under phosphorus limitation and found that fungal colonization significantly increased biomass, photosynthetic efficiency, and plant nutrition. This interaction also led to reorganization of major metabolic pathways.
Article
Plant Sciences
Leonardo Perez de Souza, Elena Bitocchi, Roberto Papa, Takayuki Tohge, Alisdair R. Fernie
Summary: The process of crop domestication leads to a reduction in gene expression associated with metabolic diversity, particularly in genes involved in specialized metabolism. The reduction in diversity at the metabolite level has been assumed but never adequately assessed and quantified. This study used high coverage metabolomics to investigate metabolic diversity in common bean and found a shift towards lower diversity and specialization in domesticated bean accessions. Molecular networking analysis enabled a broader annotation of metabolites and revealed a metabolic shift from specialized metabolism to central metabolism upon domestication of this crop.
Review
Plant Sciences
Mutsumi Watanabe, Takayuki Tohge
Summary: Functional genomics approaches have successfully detected key metabolic polymorphisms in plant specialized metabolism through comparative omics analyses of wild-accessions and cultivars/wild species, as well as comparative genomic analyses in plant species focusing on gene clusters. In recent decades, intra-species specific metabolic polymorphisms, new functionalization of tandem duplicated genes, and metabolic gene clusters have been found as the main factors creating metabolic diversity of specialized metabolites in plants. However, strategic approaches depending on the target metabolic pathways are required for gene identification in plant specialized metabolism. The increasing availability of plant genome sequences and transcriptome data has facilitated inter-specific comparative analyses, including genomic analysis and gene co-expression network analysis. Here, we introduce functional genomics approaches with the integration of inter-/intra-species comparative metabolomics, their key roles in providing genomic signatures of metabolic evolution, and discuss future prospects of functional genomics on plant specialized metabolism.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Plant Sciences
Yue Jing, Mutsumi Watanabe, Fayezeh Aarabi, Alisdair R. Fernie, Monica Borghi, Takayuki Tohge
Summary: This study comprehensively analyzed the responses of four Brassicaceae species to UV-B radiation, revealing a reprogramming of the central metabolic pathway and the production of specific classes of flavonoids with increased protection against UV-B radiation. The activation of the phenylpropanoid-acetate pathway and the increase in phenylacylated-flavonoid glucosides were also observed across species. Interestingly, the expression of acyltransferase genes of the SCPLs protein class was constitutive but downregulated in response to UV-B radiation, possibly independent of the HY5 signaling pathway.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Thomas Naake, Feng Zhu, Saleh Alseekh, Federico Scossa, Leonardo Perez de Souza, Monica Borghi, Yariv Brotman, Tetsuya Mori, Ryo Nakabayashi, Takayuki Tohge, Alisdair R. Fernie
Summary: Plants synthesize specialized metabolites to interact with the environment. This study used genome-wide association studies and quantitative trait locus mapping to identify genetic loci controlling specialized metabolites in Arabidopsis seeds, including glucosinolates, flavonoids, and unknown sulfur-containing compounds.
Article
Plant Sciences
Monica Borghi, Leonardo Perez de Souza, Takayuki Tohge, Jianing Mi, Giovanni Melandri, Sebastian Proost, Marina C. M. Martins, Salim Al-Babili, Harro J. Bouwmeester, Alisdair R. Fernie
Summary: Anthesis is characterized by intense metabolic changes, including high-energy-level metabolism and transport of carbohydrates and amino acids. These changes play a crucial role in flower opening and may promote pollination in crops.
Article
Plant Sciences
Feng Zhu, Sagar Sudam Jadhav, Takayuki Tohge, Mohamed A. Salem, Je Min Li, James J. Giovannoni, Yunjiang Cheng, Saleh Alseekh, Alisdair R. Fernie
Summary: A reliable approach combining comparative transcriptomics and expression QTLs was used to identify 16 candidate genes involved in tomato fruit ripening. One potential ripening regulator, SlWD40, was validated and found to strongly co-express with master regulators and vital TFs. Overexpression and RNAi analysis of SlWD40 confirmed its role as an important ripening regulator. These findings contribute to our understanding of the gene regulatory networks involved in tomato ripening and demonstrate the effectiveness of comparative genomics and transcriptomics in identifying causal genes.
Article
Plant Sciences
Thomas Naake, Hiroshi A. Maeda, Sebastian Proost, Takayuki Tohge, Alisdair R. Fernie
Summary: This study investigated the deep evolutionary history of the type III polyketide synthases (PKSs) by conducting phylogenomic synteny network and phylogenetic analyses. The results revealed that CHS and LAP5/6 homologs evolved early by segmental duplication prior to the divergence of Bryophytes and Tracheophytes. The macroevolution of the PKS superfamily was suggested to be governed by whole-genome duplications and triplications, with recent functional divergence captured by gene sequence alterations.
