Using genome and transcriptome analysis to elucidate biosynthetic pathways

Wang, Ning; Huo, Yi-Xin

doi:10.1016/j.copbio.2022.102708

Cited by 16 publications

(9 citation statements)

References 48 publications

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“…128 Transcriptomics, on the other hand, studies the behavior of genes through techniques that allow the identification and quantification of RNA transcripts; the sum of all these transcripts is defined as transcriptome. 128,129 Both disciplines are of particular importance, as prior to the availability of its comprising techniques, the presence of MEL was only inferred by chemical analysis, 61,130 which makes the process slow from an industrial point of view.…”

Section: Genomics Transcriptomics and Metabolomics Of Mel Producersmentioning

confidence: 99%

Section: Genomicsmentioning

confidence: 99%

“…156 Transcriptome analysis allows a more profound and wholesome understanding of gene expression under a determined condition and is well suited for identifying functional genes in biosynthetic pathways. 129 Although knowing the function of the genes within the genome is ideal to monitor key informative genes under determined conditions; thus, decisive information can be extracted from analysis based on hybridization microarray approaches. Transcriptome profiling by RNA sequencing (RNA-Seq) based approaches can be implemented without a priori functional information not only to quantitate RNA molecules but to identify the coding regions in genomic sequences and aid in the prediction of genes in an annotation pipeline.…”

Section: Genomics Transcriptomics and Metabolomics Of Mel Producersmentioning

confidence: 99%

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Production of mannosylerythritol lipids: biosynthesis, multi-omics approaches, and commercial exploitation

Solano-González

Solano-Campos

2022

Mol. Omics

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Section: Genomics Transcriptomics and Metabolomics Of Mel Producersmentioning

confidence: 99%

Section: Genomicsmentioning

confidence: 99%

Section: Genomics Transcriptomics and Metabolomics Of Mel Producersmentioning

confidence: 99%

See 1 more Smart Citation

Production of mannosylerythritol lipids: biosynthesis, multi-omics approaches, and commercial exploitation

Solano-González

Solano-Campos

2022

Mol. Omics

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“…Transcriptome sequencing using high-throughput technologies is an e cient tool for elucidating the biosynthetic pathways and evaluating the candidate genes. It can create transcript information for speci c tissues quickly and accurately [7,10]. Several researchers have identi ed genes and proteins that regulate biomineralization in freshwater pear mussel Cristaria plicata [7], Hyriopsis cumingii [4,11], marine pearl Pinctada margaritifera [8], Pinctada maxima and Pinctada martensi [12].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of Indian freshwater pearl mussel Lamellidens marginalis to unravel the genes associated with biomineralization

Suman

Kumar

Saurabh

et al. 2023

Preprint

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Background:The freshwater pearl mussel Lamellidens marginalis is found throughout India and is culturing to produce freshwater pearls. Understanding the process of pearl biomineralization provides insight into the genes responsible for the secretion of the complex nacre. However, information on the transcriptome of L. marginalis pearl sac, mantle tissue and gonads are lacking. Methods and Results: The present study generated the transcriptome resources for L. marginalis and identified genes involved in the biomineralization process in the species. The Illumina paired-end sequencing generated 11.13 million raw reads, and the reads were assembled into 133,246 contigs and 26,373 unigenes. 21,033 out of 26,373 unigenes showed homology with previously reported molluscan proteins. Genes of several proteins associated with biomineralization, namely, pif, perlucin, calreticulin, calmodulin, chitin synthase, chitin dehydrogenase, carbonic anhydrase, tyrosinase, shell matrix protein, chitinase 3, chitinase domain-containing protein 1, chitinase-like protein PB1E7.04c, and putative chitinase-1 were identified in the study. Conclusion: This study's findings will help identify differentially expressed genes that govern the characteristics of the pearl and identify the type-I markers in the genes.

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“…Microbial synthesis is an attractive alternative for the production of triterpenoids, traditionally manufactured by extraction from plant materials. − Most triterpenoids are biosynthesized from 2,3-oxidosqualene, a linear 30-carbon compound, and a few triterpenoids are synthesized via squalene and lanosterol. In the past decade, Saccharomyces cerevisiae has become a successful chassis for the production of various triterpenoids as well as other terpenoids because it not only provides the precursors through its native mevalonate (MVA) pathway but also the ER membrane for expression of the enzymes involved in triterpenoid biosynthesis, such as cytochrome P450 monooxygenases (P450s) and cytochrome P450 reductases (CPRs). − …”

Section: Introductionmentioning

confidence: 99%

Engineering Critical Amino Acid Residues of Lanosterol Synthase to Improve the Production of Triterpenoids in Saccharomyces cerevisiae

et al. 2022

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Triterpenoids are a subgroup of terpenoids and have wide applications in the food, cosmetics, and pharmaceutical industries. The heterologous production of various triterpenoids in Saccharomyces cerevisiae, as well as other microbes, has been successfully implemented as these production hosts not only produce the precursor of triterpenoids 2,3-oxidosqualene by the mevalonate pathway but also allow simple expression of plant membrane-anchored enzymes. Nevertheless, 2,3oxidosqualene is natively converted to lanosterol catalyzed by the endogenous lanosterol synthase (Erg7p), causing low production of recombinant triterpenoids. While simple deletion of ERG7 was not effective, in this study, the critical amino acid residues of Erg7p were engineered to lower this critical enzyme activity. The engineered S. cerevisiae indeed accumulated 2,3-oxidosqualene up to 180 mg/L. Engineering triterpenoid synthesis into the ERG7-modified strain resulted in 7.3-and 3-fold increases in the titers of dammarane-type and lupane-type triterpenoids, respectively. This study presents an efficient inducer-free strategy for lowering Erg7p activity, thereby providing 2,3-oxidosqualene for the enhanced production of various triterpenoids.

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Using genome and transcriptome analysis to elucidate biosynthetic pathways

Cited by 16 publications

References 48 publications

Production of mannosylerythritol lipids: biosynthesis, multi-omics approaches, and commercial exploitation

Production of mannosylerythritol lipids: biosynthesis, multi-omics approaches, and commercial exploitation

Transcriptome analysis of Indian freshwater pearl mussel Lamellidens marginalis to unravel the genes associated with biomineralization

Engineering Critical Amino Acid Residues of Lanosterol Synthase to Improve the Production of Triterpenoids in Saccharomyces cerevisiae

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