Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

C4 Pathway and CAM01:27

C4 Pathway and CAM

Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Respiration Pathways01:26

Respiration Pathways

Cellular respiration is a fundamental metabolic process that enables organisms to generate energy from organic molecules. One of its central pathways is the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, which plays a crucial role in energy production and biosynthetic processes.Conversion of Pyruvate to Acetyl-CoAThe pyruvate generated from glycolysis undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex, producing acetyl-CoA, one molecule of NADH, and one...
The Citric Acid Cycle: Output01:28

The Citric Acid Cycle: Output

The citric acid cycle is termed an amphibolic pathway as it operates both anabolically and catabolically. The cyclic reactions balance the flux of the substrates to provide an optimal concentration of NADH and ATP to the cell.
Regulation of Citric Acid Cycle
The citric acid cycle is regulated in several ways, including feedback inhibition, regulation of enzyme activities, and associated anaplerotic or cataplerotic pathways.
The primary substrate of the TCA cycle—acetyl CoA—is produced by the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The transcriptional dynamics of TIFY/JAZ and BBX families in jasmonate signaling reveal SlBBX17 as a positive regulator of tomato defense.

Plant cell reports·2026
Same author

The MassBank contributions of the mFam collaboration.

Metabolomics : Official journal of the Metabolomic Society·2026
Same author

A sequential MAP kinase cascade regulates mechanical signalling.

Nature communications·2026
Same author

dSaCas9 enables enhanced transcriptional activation in Nicotiana benthamiana compared to its dSpCas9 ortholog.

BMC plant biology·2026
Same author

A synthetic expression system for orthogonal gene expression in Nicotiana benthamiana.

Plant molecular biology·2026
Same author

Decoding Plant Metabolism.

Plant physiology·2026

Related Experiment Video

Updated: May 13, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data.

Alex Van Moerkercke1, Michele Fabris, Jacob Pollier

  • 1Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium.

Plant & Cell Physiology
|March 16, 2013
PubMed
Summary

This study introduces CathaCyc, a metabolic pathway database for Madagascar periwinkle, built from RNA-Seq data. It aids in understanding plant metabolism and discovering new enzymes for medicinal compounds like vinblastine.

Keywords:
BioCycCatharanthus roseusDeep sequencingMadagascar periwinkleMetabolismTranscriptome

More Related Videos

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

Related Experiment Videos

Last Updated: May 13, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

Area of Science:

  • Plant Metabolism
  • Bioinformatics
  • Medicinal Chemistry

Background:

  • Madagascar periwinkle (Catharanthus roseus) produces valuable terpenoid indole alkaloids (TIAs) like vinblastine and vincristine.
  • Understanding complex metabolic networks is crucial for discovering new enzymes and engineering pathways.
  • Genome data is lacking for most medicinal plants, necessitating alternative approaches for pathway reconstruction.

Purpose of the Study:

  • To construct a comprehensive metabolic pathway database for Catharanthus roseus using RNA-Seq data.
  • To enable the discovery of missing enzymes and study metabolic pathway evolution.
  • To provide a resource for engineering medicinal plant metabolic pathways.

Main Methods:

  • Utilized RNA-Seq data from Catharanthus roseus to build the CathaCyc database.
  • Curated pathways involved in TIAs, triterpenoids, and jasmonate hormone synthesis.
  • Integrated publicly available RNA-Seq expression data for pathway analysis.

Main Results:

  • Developed CathaCyc (version 1.0) with 390 pathways and 1,347 enzymes, covering primary and secondary metabolism.
  • Demonstrated the suitability of RNA-Seq data for constructing pathway databases.
  • Identified distinct regulatory patterns in terpenoid and TIA pathways influenced by development and environment.

Conclusions:

  • CathaCyc is a valuable resource for studying and exploiting medicinal plant metabolism.
  • RNA-Seq data is effective for building metabolic pathway databases for non-model organisms.
  • This database facilitates research into the biosynthesis of important medicinal compounds.