Unveiling the underlying molecular basis of astaxanthin accumulation in Haematococcus through integrative metabolomic-transcriptomic analysis

Hoys, Cristina; Romero–Losada, Ana B.; Río, Esperanza Del; Guerrero, Miguel G.; Romero–Campero, Francisco J.; García-González, Mercedes

doi:10.1016/j.biortech.2021.125150

Cited by 25 publications

(7 citation statements)

References 49 publications

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“…The bHLH family TFs are reported to be carotenogenesis suppressors in plants [ 67 ]. In consistent with these findings, nitrogen limitation in the presence of high light can induce high level of astaxanthin accumulation in H. pluvialis , which was accompanied with downregulation of the TFs from bHLH family [ 68 ]. On the other hand, C3H, MYB, Nin-like, MTB_related and ERF TFs were highly expressed TF families under the effects of salicylic acid in the presence of high light [ 68 , 69 ].…”

Section: Astaxanthin Biosynthesis: Pathways Regulations and Distributionmentioning

confidence: 53%

“…In consistent with these findings, nitrogen limitation in the presence of high light can induce high level of astaxanthin accumulation in H. pluvialis , which was accompanied with downregulation of the TFs from bHLH family [ 68 ]. On the other hand, C3H, MYB, Nin-like, MTB_related and ERF TFs were highly expressed TF families under the effects of salicylic acid in the presence of high light [ 68 , 69 ]. In addition to TFs, some miRNAs also have been identified as responding miRNAs to sodium acetate and high light stress [ 70 ].…”

Section: Astaxanthin Biosynthesis: Pathways Regulations and Distributionmentioning

confidence: 53%

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Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies

Basiony

Ouyang

Wang

et al. 2022

Synthetic and Systems Biotechnology

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Section: Astaxanthin Biosynthesis: Pathways Regulations and Distributionmentioning

confidence: 53%

Section: Astaxanthin Biosynthesis: Pathways Regulations and Distributionmentioning

confidence: 53%

Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies

Basiony

Ouyang

Wang

et al. 2022

Synthetic and Systems Biotechnology

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“…Analysis combining the different functionalities implemented in our tools will allow researchers to extract relevant information in the form of functional annotation enrichment analysis over gene sets and genomic loci starting from raw high-throughput sequencing data. ALGAEFUN with MARACAS has been applied recently to determine the molecular systems underpinning astaxanthin accumulation in the microalgae of industrial interest Haematococcus lacustris [21].…”

Section: Resultsmentioning

confidence: 99%

“…In order to facilitate the progress in the characterization of the molecular systems regulating microalgae physiology, high throughput sequencing technologies have been recently applied to obtain the genome of a wide range of microalgae [7][8][9][10][11][12][13][14][15][16][17][18][19]. This has promoted the use of different omics, particularly transcriptomics based on RNA-seq data [20][21][22] and cistromics based on ChIPseq data [23,24], to initiate molecular systems biology studies in microalgae. Nonetheless, the impact of this type of studies on microalgae are hampered by the lack of freely available and easy to use online tools to analyze, extract relevant information and integrate omics data.…”

mentioning

confidence: 99%

ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS

Romero–Losada

Arvanitidou

Reyes

et al. 2021

Preprint

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Background: Microalgae are emerging as promising sustainable sources for biofuels, biostimulants in agriculture, soil bioremediation, feed and human nutrients. Nonetheless, the molecular mechanisms underpinning microalgae physiology and the biosynthesis of compounds of biotechnological interest are largely uncharacterized. This hinders the development of microalgae full potential as cell-factories. The recent application of omics technologies into microalgae research aims at unraveling these systems. Nevertheless, the lack of specific tools for analysing omics raw data generated from microalgae to provide biological meaningful information are hampering the impact of these technologies. The purpose of ALGAEFUN with MARACAS consists in providing researchers in microalgae with an enabling tool that will allow them to exploit transcriptomic and cistromic high-throughput sequencing data. Results: ALGAEFUN with MARACAS consists of two different tools. First, MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS) implements a fully automatic computational pipeline receiving as input RNA-seq (RNA sequencing) or ChIP-seq (chromatin immunoprecipitation sequencing) raw data from microalgae studies. MARACAS generates sets of differentially expressed genes or lists of genomic loci for RNA-seq and ChIP-seq analysis respectively. Second, ALGAEFUN (microALGAE FUNctional enrichment tool) is a web-based application where gene sets generated from RNA-seq analysis as well as lists of genomic loci from ChIP-seq analysis can be used as input. On the one hand, it can be used to perform Gene Ontology and biological pathways enrichment analysis over gene sets. On the other hand, using the results of ChIP-seq data analysis, it identifies a set of potential target genes and analyses the distribution of the loci over gene features. Graphical representation of the results as well as tables with gene annotations are generated and can be downloaded for further analysis. Conclusions: ALGAEFUN with MARACAS provides an integrated environment for the microalgae research community that facilitates the process of obtaining relevant biological information from raw RNA-seq and ChIP-seq data. These applications are designed to assist researchers in the interpretation of gene lists and genomic loci based on functional enrichment analysis. ALGAEFUN with MARACAS is publicly available on https://greennetwork.us.es/AlgaeFUN/ .

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“…However, despite their potential, many of these applications remain economically unfeasible at the industrial level 9,10 . Hence, optimizing culture systems and production methods is imperative, necessitating the application of artificial intelligence and machine learning tools 11 , along with further characterization of the molecular mechanisms underpinning microalgae physiology using systems and synthetic biology techniques [12][13][14][15] .…”

Section: Introductionmentioning

confidence: 99%

Multiomics responses to seasonal variations in diel cycles in the marine phytoplanktonic picoeukaryoteOstreococcus tauri

Romero–Losada

Arvanitidou

Garcia-Gómez

et al. 2023

Preprint

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Earth tilted rotation and translation around the Sun produce one of the most pervasive periodic environmental signals on our planet giving rise to seasonal variations in diel cycles. Although marine phytoplankton plays a key role on ecosystems and present promising biotechnological applications, multiomics integrative analysis of their response to these rhythms remains largely unexplored. We have chosen the marine picoeukaryoteOstreococcus taurias model organism grown under summer long days, winter short days, constant light and constant dark conditions to characterize these responses in marine phytoplankton. Although 80% of the transcriptome present diel rhythmicity under both seasonal conditions less than 5% maintained oscillations under all constant conditions. A drastic reduction in protein abundance rhythmicity was observed with 55% of the proteome oscillating. Seasonally specific rhythms were found in key physiological processes such as cell cycle progression, photosynthetic efficiency, carotenoid content, starch accumulation and nitrogen assimilation. A global orchestration between transcriptome, proteome and physiological dynamics was observed with specific seasonal temporal offsets between transcript, protein and physiological peaks.

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Unveiling the underlying molecular basis of astaxanthin accumulation in Haematococcus through integrative metabolomic-transcriptomic analysis

Cited by 25 publications

References 49 publications

Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies

Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies

ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS

Multiomics responses to seasonal variations in diel cycles in the marine phytoplanktonic picoeukaryoteOstreococcus tauri

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