Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum DOI Creative Commons
Tito Damiani, Joshua David Smith, Téo Hebra

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(5)

Published: March 1, 2025

Plant specialized metabolites play key roles in diverse physiological processes and ecological interactions. Identifying structurally novel metabolites, as well discovering known compounds new species, is often crucial for answering broader biological questions. The Piper genus (Piperaceae family) its special phytochemistry has been extensively studied over the past decades. Here, we investigated alkaloid diversity of fimbriulatum, a myrmecophytic plant native to Central America, using metabolomics workflow that combines untargeted LC-MS/MS analysis with range recently developed computational tools. Specifically, leverage open MS/MS spectral libraries data repositories metabolite annotation, guiding isolation efforts toward (i.e., dereplication). As result, identified several alkaloids belonging five different classes isolated one seco-benzylisoquinoline featuring linear quaternary amine moiety which named fimbriulatumine. Notably, many were never reported Piperaceae plants. Our findings expand this family demonstrate value revisiting well-studied families state-of-the-art workflows uncover previously overlooked chemodiversity. To contextualize our within context, employed automated mining literature reports scaffolds mapped results onto angiosperm tree life. By doing so, highlight remarkable provide framework generating hypotheses on biosynthetic evolution these metabolites. Many tools resources used study remain underutilized science community. This manuscript demonstrates their potential through practical application aims promote accessibility approaches.

Language: Английский

Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives DOI Creative Commons
Shuangqian Shen, Chuansong Zhan, Chenkun Yang

et al.

Molecular Plant, Journal Year: 2022, Volume and Issue: 16(1), P. 43 - 63

Published: Sept. 16, 2022

Language: Английский

Citations

151
Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking DOI Creative Commons
Zhiwei Zhou,

Mingdu Luo,

Haosong Zhang

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 4, 2022

Abstract Liquid chromatography - mass spectrometry (LC-MS) based untargeted metabolomics allows to measure both known and unknown metabolites in the metabolome. However, metabolite annotation is a major challenge metabolomics. Here, we develop an approach, namely, knowledge-guided multi-layer network (KGMN), enable global from knowns unknowns The KGMN approach integrates three-layer networks, including knowledge-based metabolic reaction network, MS/MS similarity peak correlation network. To demonstrate principle, apply vitro enzymatic system different biological samples, with ~100–300 putative annotated each data set. Among them, >80% are corroborated silico tools. Finally, validate 5 that absent common libraries through repository mining synthesis of chemical standards. Together, enables efficient annotations, substantially advances discovery recurrent for samples model organisms, towards deciphering dark matter

Language: Английский

Citations

142
Recent advances in proteomics and metabolomics in plants DOI Creative Commons
Shijuan Yan, Ruchika Bhawal, Zhibin Yin

et al.

Molecular Horticulture, Journal Year: 2022, Volume and Issue: 2(1)

Published: July 23, 2022

Over the past decade, systems biology and plant-omics have increasingly become main stream in plant research. New developments mass spectrometry bioinformatics tools, methodological schema to integrate multi-omics data leveraged recent advances proteomics metabolomics. These progresses are driving a rapid evolution field of research, greatly facilitating our understanding mechanistic aspects metabolisms interactions plants with their external environment. Here, we review MS-based metabolomics tools workflows special focus on applications research using several case studies related stress response, gene/protein function characterization, metabolic signaling pathways exploration, natural product discovery. We also present projection concerning future perspectives development including challenges for system biology. This is intended provide readers an overview how advanced MS technology, integrated application can be used advance

Language: Английский

Citations

72
A lipidome landscape of aging in mice DOI
Hiroshi Tsugawa, Tomoaki Ishihara,

Kota Ogasa

et al.

Nature Aging, Journal Year: 2024, Volume and Issue: 4(5), P. 709 - 726

Published: April 12, 2024

Language: Английский

Citations

21
Harnessing metabolomics for enhanced crop drought tolerance DOI Creative Commons
Ali Raza, Muhammad Anas, Savita Bhardwaj

et al.

The Crop Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

4
Integrative omics approaches for biosynthetic pathway discovery in plants DOI Creative Commons
Kumar Saurabh Singh, Justin J. J. van der Hooft, Saskia C. M. Van Wees

et al.

Natural Product Reports, Journal Year: 2022, Volume and Issue: 39(9), P. 1876 - 1896

Published: Jan. 1, 2022

This review discusses genomics-, transcriptomics- and metabolomics-based plant biosynthetic pathway discovery, highlights the potential for integrative omics approaches.

Language: Английский

Citations

48
Bioinformatics in bioscience and bioengineering: Recent advances, applications, and perspectives DOI Creative Commons

Kazuma Uesaka,

Hiroya Oka, Ryuji Kato

et al.

Journal of Bioscience and Bioengineering, Journal Year: 2022, Volume and Issue: 134(5), P. 363 - 373

Published: Sept. 17, 2022

Language: Английский

Citations

45
Plant and microbial sciences as key drivers in the development of metabolomics research DOI Creative Commons
Asaph Aharoni, Royston Goodacre, Alisdair R. Fernie

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(12)

Published: March 17, 2023

This year marks the 25th anniversary of coinage term metabolome [S. G. Oliver et al ., Trends Biotech. 16 , 373–378 (1998)]. As field rapidly advances, it is important to take stock progress which has been made best inform disciplines future. While a medical-centric perspective on metabolomics recently published [M. Giera Cell Metab. 34 21–34 (2022)], this largely ignores pioneering contributions by plant and microbial science communities. In perspective, we provide contemporary overview all fields in employed with particular emphasis both methodological application breakthroughs sciences that have shaped evolving research discipline from very early days its establishment. will not cover types assays currently but focus mainly those utilizing mass spectrometry–based measurements since they are far most prominent. Having established historical context metabolomics, address key challenges facing offer potential approaches these can be faced. Most salient among fact vast majority features as yet annotated high confidence; what may refer definitive identification. We discuss standard compound libraries artificial intelligence technologies challenge use natural variance–based such genome-wide association studies attempt assign specific functions myriad structurally similar complex specialized metabolites. conclude stating our contention epic need greater cooperative efforts biologists, chemists, computer scientists an interest kingdoms life than date. Ultimately, better linkage genome data likely also needed particularly considering Earth BioGenome Project.

Language: Английский

Citations

30
Capturing the microbial volatilome: an oft overlooked 'ome' DOI Creative Commons
Laura Meredith, Malak Tfaily

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 30(7), P. 622 - 631

Published: Jan. 14, 2022

Language: Английский

Citations

35
Recent Advances in Minimizing Cadmium Accumulation in Wheat DOI Creative Commons
Min Zhou, Zhengguo Li

Toxics, Journal Year: 2022, Volume and Issue: 10(4), P. 187 - 187

Published: April 12, 2022

Cadmium (Cd), a toxic heavy metal, affects the yield and quality of crops. Wheat (Triticum aestivum L.) can accumulate high Cd content in grain, which poses major worldwide hazard to human health. Advances our understanding toxicity for plants humans, different parameters influencing uptake accumulation, as well phytoremediation technologies relieve pollution wheat have been made very recently. In particular, molecular mechanisms under stress increasingly recognized. this review, we focus on recently described omics functional genes uncovering stress, mitigation strategies reduce wheat.

Language: Английский

Citations

30