scholarly journals Comparative Transcriptomic Analysis Uncovers Genes Responsible for the DHA Enhancement in the Mutant Aurantiochytrium sp.

2020 ◽  
Vol 8 (4) ◽  
pp. 529
Author(s):  
Liangxu Liu ◽  
Zhangli Hu ◽  
Shuangfei Li ◽  
Hao Yang ◽  
Siting Li ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Mutant Strain ◽  
Uv Irradiation ◽  
Breeding Strategy ◽  
Transcriptomic Analysis ◽  
High Yield ◽  
Chain Polyunsaturated Fatty Acid ◽  
Wild Type ◽  
Promising Source ◽  
Comparative Transcriptomic Analysis

Docosahexaenoic acid (DHA), a n-3 long-chain polyunsaturated fatty acid, is critical for physiological activities of the human body. Marine eukaryote Aurantiochytrium sp. is considered a promising source for DHA production. Mutational studies have shown that ultraviolet (UV) irradiation (50 W, 30 s) could be utilized as a breeding strategy for obtaining high-yield DHA-producing Aurantiochytrium sp. After UV irradiation (50 W, 30 s), the mutant strain X2 which shows enhanced lipid (1.79-fold, 1417.37 mg/L) and DHA (1.90-fold, 624.93 mg/L) production, was selected from the wild Aurantiochytrium sp. Instead of eicosapentaenoic acid (EPA), 9.07% of docosapentaenoic acid (DPA) was observed in the mutant strain X2. The comparative transcriptomic analysis showed that in both wild type and mutant strain, the fatty acid synthesis (FAS) pathway was incomplete with key desaturases, but genes related to the polyketide synthase (PKS) pathway were observed. Results presented that mRNA expression levels of CoAT, AT, ER, DH, and MT down-regulated in wild type but up-regulated in mutant strain X2, corresponding to the increased intercellular DHA accumulation. These findings indicated that CoAT, AT, ER, DH, and MT can be exploited for high DHA yields in Aurantiochytrium.

scholarly journals Mechanism study on the enhanced DHA synthesis in the mutant Thraustochytriidae sp. through comparative transcriptomic analysis

2020 ◽  
Author(s):  
liangxu liu ◽  
Zhangli Hu ◽  
Shuangfei Li ◽  
Hao Yang ◽  
Siting Li ◽  
...  
Keyword(s):  
Transcriptomic Analysis ◽  
Omega 3 ◽  
Wild Type ◽  
Mechanism Study ◽  
Enoyl Reductase ◽  
Omega 3 Fatty Acid ◽  
Coa Transferase ◽  
Dha Enrichment ◽  
Promising Source ◽  
Comparative Transcriptomic Analysis

Abstract Background: Docosahexaenoic acid (DHA) is an essential omega-3 fatty acid for the human retina, skin, and cerebral cortex. Marine eukaryote Thraustochytriidae sp. was considered as a promising source for the n -3 LC-PUFAs production. However, the mechanism how the LC-PUFAs was synthesized in Thraustochytriidae sp. still remained unclarified. To explore the vital genes responsible for the DHA enrichment, the functional transcriptomic annotation was compared between the wild type and preeminent mutant of Thraustochytriidae sp. X2. Results: After the UV irradiation (50 W, 30 s), the mutant X2 showed enhanced lipid (78.88 % more) and DHA (23.77 % more) production compared with the wild type. Instead of EPA, 9.07 % of DPA was observed in the mutant X2. The comparative transcriptomic analysis showed that in both wild type and mutant strain, FAS was incomplete and lacked key desaturases, but genes related to the PKS pathway were observed. It was oberved that mRNA expression levels of CoA-transferase (CoAT) , acyltransferase (AT), enoyl reductase (ER) , dehydratase (DH) and methyltransferase (MT) down-regulated in wild type but up-regulated in mutant X2, corresponding to the increased intercellular DHA accumulation. Conclusion: These findings indicated the potential genes that can be exploited for high DHA yields in Thraustochytriidae sp..

scholarly journals Comparative Transcriptomic Analysis of Antimony Resistant and Susceptible Leishmania Infantum Lines

2020 ◽  
Author(s):  
Juvana Moreira Andrade ◽  
Leilane Oliveira Gonçalves ◽  
Daniel Barbosa Liarte ◽  
Davi Alvarenga Lima ◽  
Frederico Gonçalves Guimarães ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Transcriptomic Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
P Value ◽  
Resistant Line ◽  
Wild Type ◽  
Antimony Resistance ◽  
Comparative Transcriptomic Analysis

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to Gene Ontology database. The functional enrichment analysis for biological process showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanism of Leishmania, identifying several potential genes for resistance markers and drug targets against leishmaniasis.

scholarly journals Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

2020 ◽  
Author(s):  
Juvana Moreira Andrade ◽  
Leilane Oliveira Gonçalves ◽  
Daniel Barbosa Liarte ◽  
Davi Alvarenga Lima ◽  
Frederico Gonçalves Guimarães ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Transcriptomic Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
P Value ◽  
Resistant Line ◽  
Wild Type ◽  
Antimony Resistance ◽  
Comparative Transcriptomic Analysis

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the Gene Ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

scholarly journals Comparative Transcriptomic Analysis Reveals Diverse Expression Pattern Underlying Fatty Acid Composition among Different Beef Cuts

Foods ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 117
Author(s):  
Tianliu Zhang ◽  
Qunhao Niu ◽  
Tianzhen Wang ◽  
Xu Zheng ◽  
Haipeng Li ◽  
...  
Keyword(s):  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Candidate Genes ◽  
Acid Composition ◽  
Genetic Selection ◽  
Transcriptomic Analysis ◽  
Functional Enrichment ◽  
Ampk Signaling ◽  
Gene Network Analysis ◽  
Comparative Transcriptomic Analysis

Beef is an important dietary source of quality animal proteins and amino acids in human nutrition. The fatty acid composition is one of the indispensable indicators affecting nutritional value of beef. However, a comprehensive understanding of the expression changes underlying fatty acid composition in representative beef cuts is needed in cattle. This study aimed to characterize the dynamics of fatty acid composition using comparative transcriptomic analysis in five different type of beef cuts. We identified 7545 differentially expressed genes (DEGs) among 10 pair-wise comparisons. Co-expression gene network analysis identified two modules, which were significantly correlated with 2 and 20 fatty acid composition, respectively. We also identified 38 candidate genes, and functional enrichment showed that these genes were involved in fatty acid biosynthetic process and degradation, PPAR, and AMPK signaling pathway. Moreover, we observed a cluster of DEGs (e.g., SCD, LPL, FABP3, and PPARD) which were involved in the regulation of lipid metabolism and adipocyte differentiation. Our results provide some valuable insights into understanding the transcriptome regulation of candidate genes on fatty acid composition of beef cuts, and our findings may facilitate the designs of genetic selection program for beneficial fatty acid composition in beef cattle.

scholarly journals Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Juvana Moreira Andrade ◽  
Leilane Oliveira Gonçalves ◽  
Daniel Barbosa Liarte ◽  
Davi Alvarenga Lima ◽  
Frederico Gonçalves Guimarães ◽  
...  
Keyword(s):  
Leishmania Infantum ◽  
Ribosome Biogenesis ◽  
Transcriptomic Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Resistant Line ◽  
Wild Type ◽  
Antimony Resistance ◽  
Comparative Transcriptomic Analysis

Abstract Background One of the major challenges to leishmaniasis treatment is the emergence of parasites resistant to antimony. To study differentially expressed genes associated with drug resistance, we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing. Methods All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search. Results The analytical pipeline considering an adjusted p-value < 0.05 and fold change > 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the gene ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host–parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation. Conclusions The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with the antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

scholarly journals Effects of Methanol on Carotenoids as Well as Biomass and Fatty Acid Biosynthesis in Schizochytrium limacinum B4D1

2019 ◽  
Vol 85 (19) ◽  
Author(s):  
Huanmin Du ◽  
Xiaoping Liao ◽  
Zhengquan Gao ◽  
Yang Li ◽  
Yu Lei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acid ◽  
Cell Growth ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Expression Profiles ◽  
Total Sterol ◽  
Transcriptomic Analysis ◽  
Schizochytrium Limacinum ◽  
Promising Source

ABSTRACT Schizochytrium is a promising source for the production of docosahexaenoic acid and astaxanthin. The effects of different methanol concentrations on astaxanthin, biomass, and production of the lipids, squalene, and total sterol in Schizochytrium limacinum B4D1 were investigated. Astaxanthin began to accumulate when the methanol concentration reached 3.2% and peaked at 5.6% methanol, with a 2,000-fold increase over that in the control. However, under cultivation with 5.6% methanol, the biomass, lipids, squalene, and total sterol decreased to various degrees. Transcriptomic analysis was performed to explore the effects of different methanol concentrations (0%, 3.2%, and 5.6%) on the expression profile of B4D1. Three key signaling pathways were found to play important roles in regulating cell growth and metabolism under cultivation with methanol. Five central carbon metabolism-associated genes were significantly downregulated in response to 5.6% methanol and thus were expected to result in less ATP and NADPH being available for cell growth and synthesis. High methanol conditions significantly downregulated three genes involved in fatty acid and squalene/sterol precursor biosynthesis but significantly upregulated geranylgeranyl diphosphate synthase, lycopene β-cyclase, and β-carotene 3-hydroxylase, which are involved in astaxanthin synthesis, thus resulting in an increase in the levels of precursors and the final production of astaxanthin. Additionally, the transcriptional levels of three stress response genes were upregulated. This study investigates gene expression profiles in the astaxanthin producer Schizochytrium when grown under various methanol concentrations. These results broaden current knowledge regarding genetic expression and provide important information for promoting astaxanthin biosynthesis in Schizochytrium. IMPORTANCE Schizochytrium strains are usually studied as oil-producing strains, but they can also synthesize other secondary metabolites, such as astaxanthin. In this study, methanol was used as an inducer, and we explored its effects on the production of astaxanthin, a highly valuable substance in Schizochytrium. Methanol induced Schizochytrium to synthesize large amounts of astaxanthin. Transcriptomic analysis was used to investigate the regulation of signaling and metabolic pathways (mainly relative gene expression) in Schizochytrium grown in the presence of various concentrations of methanol. These results contribute to the understanding of the underlying molecular mechanisms and may aid in the future optimization of Schizochytrium for astaxanthin biosynthesis.

scholarly journals Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

2020 ◽  
Author(s):  
Juvana Moreira Andrade ◽  
Leilane Oliveira Gonçalves ◽  
Daniel Barbosa Liarte ◽  
Davi Alvarenga Lima ◽  
Frederico Gonçalves Guimarães ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Transcriptomic Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
P Value ◽  
Resistant Line ◽  
Wild Type ◽  
Antimony Resistance ◽  
Comparative Transcriptomic Analysis

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the Gene Ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

scholarly journals Comprehensive study of the lipid from whelk (Chlorostoma rusticum and Neverita didyma) with emphasis on characterization of phospholipid molecular species by shot-gun strategy

2019 ◽  
Vol 8 ◽  
Author(s):  
Zhong-Yuan Liu ◽  
Kai-Qi Gang ◽  
Fa-Wen Yin ◽  
Hong-Kai Xie ◽  
Liang Song ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Molecular Species ◽  
Chain Polyunsaturated Fatty Acid ◽  
Total Lipids ◽  
Phospholipid Molecular Species ◽  
Promising Source ◽  
Long Chain ◽  
Fatty Acid Compositions ◽  
Comprehensive Study

In the present study, an effective shot-gun lipidomic methodology was established to determine the glycerophospholipid (GP) molecular species of two species of edible marine whelks (Chlorostoma rusticum and Neverita didyma). Simultaneously, the lipid content, lipid classes, phospholipid (PL) subclasses and fatty acid compositions were also investigated. Over 210 molecular species of GP including glycerophosphocholine, lysoglycerophosphocholine, glycerophosphoethanolamine, lysoglycerophosphoethanolamine, glycerophosphoserine, lysoglycerophosphoserine, glycerophosphoinositol and lysoglycerophosphoinositol were characterized in the two abovementioned whelk species. The predominant GP molecular species contained n-3 long chain polyunsaturated fatty acid (n-3 LC-PUFA), especially docosahexaenoic acid and eicosapentaenoic acid. Meanwhile, PL (57.70-58.86% of total lipids) and PUFA (21.69-37.68% of total FA) take large proportions in whelk lipids. Among PL, phosphatidylcholine (50.58-52.41 mol%) and phosphatidylethanolamine (27.67-32.73 mol%) were dominant. Therefore, marine whelks turn out to be promising source of n-3 LC-PUFA existed in PL form and thus directly contribute to the health benefits of consumer.

scholarly journals Comparative transcriptomic analysis of silkwormBmovo-1 and wild type silkworm ovary

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Renyu Xue ◽  
Xiaolong Hu ◽  
Liyuan Zhu ◽  
Guangli Cao ◽  
Moli Huang ◽  
...  
Keyword(s):  
Transcriptomic Analysis ◽  
Wild Type ◽  
Comparative Transcriptomic Analysis
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