scholarly journals Metabolism of Non-growing Cells and Their Application in Biotransformation

2020 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Metabolic Pathways ◽  
Metabolic Flux ◽  
Resting Cells ◽  
Rna Seq ◽  
Research Gaps ◽  
Alternative Mode ◽  
Proteomics Technology ◽  
Mode Of Operation ◽  
Carbon Substrates ◽  
Typical Mode

Growing cells is the typical mode of operation in many aspects of biotechnology and metabolic engineering. This comes about due to cell growth processes creating a driving force that pull metabolic flux along different metabolic pathways, that indirectly help move substrate to product. But, there is an alternative mode of operation that uses resting (non-growing) cells to achieve similar or even higher productivities. In general, resting cells are provided with carbon substrates for biocatalytic reactions but starved of nitrogen or phosphorus. Such resting cells have been usefully employed in many forms of biocatalysis and biotransformation, with or without cofactor regeneration. However, much remains unknown about the transcriptome and metabolome of resting cells in biotransformation settings. This short writeup provides the backdrop of resting cells in biocatalysis, documents their use in biotransformation with application examples, and identifies research gaps that could be filled with contemporary RNA-seq and mass spectrometry proteomics technology. Overall, utility of resting cells in biocatalysis and the extant knowledge gap in their fundamental physiology are highlighted in this resource.

scholarly journals Transcriptome Analysis of Oleaginous Fungus Mucor circinelloides WJ11 in Response to Exogenous Soybean Oil as Carbon Source

2021 ◽  
Vol 16 (6) ◽  
pp. 1934578X2110233
Author(s):  
Caili Sun ◽  
Aabid Manzoor Shah ◽  
Junhuan Yang ◽  
Zongmin Wang ◽  
Lanlan Zhu ◽  
...  
Keyword(s):  
Carbon Source ◽  
Soybean Oil ◽  
Lipid Content ◽  
Metabolic Pathways ◽  
Mucor Circinelloides ◽  
Lipid Biosynthesis ◽  
Rna Seq ◽  
Plant Oil ◽  
Carbon Substrates ◽  
Oleaginous Fungus

Mucor circinelloides is an oleaginous fungus that utilizes a wide variety of carbon substrates for its growth. The different sources of carbon strongly influence the total lipid content of the fungus. These different carbon substrates are assimilated and dissimilated through different metabolic pathways before entering into the TAG synthesis pathway. In the present study, we attempted to explore the mechanism of ex-novo lipid biosynthesis in M. circinelloides WJ11 in response to exogenous plant oil as a carbon source through transcriptomic analysis. The lipid content of WJ11 grown in a media containing mixed soybean oil with glucose as a carbon source was up to 43.8%, an increase of 13.9% as compared to glucose alone as the carbon source. RNA-Seq analysis was performed to investigate global gene expression patterns in the oil-treated WJ11. Based on RNA-seq analysis, among the 4646 differentially expressed genes (DEGs), 2379 were up-regulated and 2267 down-regulated. The expression of acetyl-CoA synthetase, 6-phosphofructokinase, alcohol dehydrogenase (NADP+), fructose-bisphosphate aldolase, and pyruvate kinase was down-regulated while genes related to triglyceride synthesis were up-regulated. The majority of genes and pathways related to lipid biosynthesis were up-regulated indicating a diversion of metabolic pathways towards lipid biosynthesis. The data generated advance the genomic resources and provide insights into the mechanisms of ex-novo lipid accumulation in fungi that use exogenous oil as a carbon source.

scholarly journals A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3924
Author(s):  
Maria Leonor Santos ◽  
Mariaelena D’Ambrosio ◽  
Ana P. Rodrigo ◽  
A. Jorge Parola ◽  
Pedro M. Costa
Keyword(s):  
Metabolic Pathways ◽  
Molecular Networks ◽  
Bile Pigments ◽  
Rna Seq ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Organ Specific ◽  
Bright Green ◽  
Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

scholarly journals Drought tolerance molecular responses of two cultivated varieties Jerusalem artichoke (Helianthus tuberosus L.) as revealed by RNA-Seq

2020 ◽  
Author(s):  
Shipeng Yang ◽  
Lihui Wang ◽  
Qiwen Zhong ◽  
Guangnan Zhang ◽  
Haiwang Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Metabolic Pathways ◽  
Jerusalem Artichoke ◽  
Tibet Plateau ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Concentration Gradients ◽  
Light Reaction ◽  
Metabolic Activities

Abstract Background Jerusalem artichoke (Helianthus tuberosus L.) is a highly stress-resistant crop, especially it grows normally in the desertified land of Qinghai-Tibet Plateau in the past two years, and has become a crop with agricultural, industrial and ecological functions. However, there are few studies on drought resistance of Jerusalem artichoke at present, and studies on the mechanisms of stress resistance of Jerusalem artichoke breeding and fructan are seriously lagging behind. In this study, we selected two differentially resistant cultivars for drought stress experiments with different concentration gradients, the aim was finding DEGs and metabolic pathways associated with drought stress. Results Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. It was suggested that flavonoids could help Jerusalem artichoke to resist drought stress and maintain normal metabolic activities. In addition, the gene analysis of the abscisic acid (ABA) key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1, but QY1 had more genes in response to drought stress as a whole. By combining RNA-Seq and WGCNA, a weighted gene co-expression network was constructed and divided into modules. By analyzing specifically the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase had the highest significance in these pathways. Conclusions These findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the excavation of related genes.

scholarly journals Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Anika Küken ◽  
Frederik Sommer ◽  
Liliya Yaneva-Roder ◽  
Luke CM Mackinder ◽  
Melanie Höhne ◽  
...  
Keyword(s):  
Experimental Data ◽  
Chlamydomonas Reinhardtii ◽  
Metabolic Pathways ◽  
Metabolic Flux ◽  
Flux Distribution ◽  
Photosynthetic Performance ◽  
Computational Approach ◽  
Cellular Processes ◽  
Diffusional Barrier ◽  
Computational Strategy

Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms.

scholarly journals Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis

2019 ◽  
Vol 48 (2) ◽  
pp. 996-1009 ◽  
Author(s):  
Yaokang Wu ◽  
Taichi Chen ◽  
Yanfeng Liu ◽  
Rongzhen Tian ◽  
Xueqin Lv ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Metabolic Pathways ◽  
Metabolic Flux ◽  
Target Genes ◽  
Fine Tuning ◽  
Dual Control ◽  
Genetic Circuits ◽  
Dynamic Regulation ◽  
Batch Bioreactor ◽  
Acetoin Production

Abstract Dynamic regulation is an effective strategy for fine-tuning metabolic pathways in order to maximize target product synthesis. However, achieving dynamic and autonomous up- and down-regulation of the metabolic modules of interest simultaneously, still remains a great challenge. In this work, we created an autonomous dual-control (ADC) system, by combining CRISPRi-based NOT gates with novel biosensors of a key metabolite in the pathway of interest. By sensing the levels of the intermediate glucosamine-6-phosphate (GlcN6P) and self-adjusting the expression levels of the target genes accordingly with the GlcN6P biosensor and ADC system enabled feedback circuits, the metabolic flux towards the production of the high value nutraceutical N-acetylglucosamine (GlcNAc) could be balanced and optimized in Bacillus subtilis. As a result, the GlcNAc titer in a 15-l fed-batch bioreactor increased from 59.9 g/l to 97.1 g/l with acetoin production and 81.7 g/l to 131.6 g/l without acetoin production, indicating the robustness and stability of the synthetic circuits in a large bioreactor system. Remarkably, this self-regulatory methodology does not require any external level of control such as the use of inducer molecules or switching fermentation/environmental conditions. Moreover, the proposed programmable genetic circuits may be expanded to engineer other microbial cells and metabolic pathways.

scholarly journals Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 380 ◽  
Author(s):  
Zhaoxu Gao ◽  
Biying Dong ◽  
Hongyan Cao ◽  
Hang He ◽  
Qing Yang ◽  
...  
Keyword(s):  
Time Series ◽  
Metabolic Pathways ◽  
Expression Patterns ◽  
Plant Stress ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Aluminum Stress ◽  
Biological Regulation ◽  
Al Stress ◽  
The Impact

Pigeonpea is an important economic crop in the world and is mainly distributed in tropical and subtropical regions. In order to further expand the scope of planting, one of the problems that must be solved is the impact of soil acidity on plants in these areas. Based on our previous work, we constructed a time series RNA sequencing (RNA-seq) analysis under aluminum (Al) stress in pigeonpea. Through a comparison analysis, 11,425 genes were found to be differentially expressed among all the time points. After clustering these genes by their expression patterns, 12 clusters were generated. Many important functional pathways were identified by gene ontology (GO) analysis, such as biological regulation, localization, response to stimulus, metabolic process, detoxification, and so on. Further analysis showed that metabolic pathways played an important role in the response of Al stress. Thirteen out of the 23 selected genes related to flavonoids and phenols were downregulated in response to Al stress. In addition, we verified these key genes of flavonoid- and phenol-related metabolism pathways by qRT-PCR. Collectively, our findings not only revealed the regulation mechanism of pigeonpea under Al stress but also provided methodological support for further exploration of plant stress regulation mechanisms.

scholarly journals A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1070 ◽  
Author(s):  
Puzhi Xu ◽  
Ping Liu ◽  
Changming Zhou ◽  
Yan Shi ◽  
Qingpeng Wu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Infectious Bronchitis Virus ◽  
Metabolic Pathways ◽  
Host Responses ◽  
Integrated Analysis ◽  
Specific Gene ◽  
Rna Seq ◽  
Infectious Bronchitis ◽  
Infection Processes

Chicken gout resulting from nephropathogenic infectious bronchitis virus (NIBV) has become a serious kidney disease problem in chicken worldwide with alterations of the metabolic phenotypes in multiple metabolic pathways. To investigate the mechanisms in chicken responding to NIBV infection, we examined the global transcriptomic and metabolomic profiles of the chicken’s kidney using RNA-seq and GC–TOF/MS, respectively. Furthermore, we analyzed the alterations in cecal microorganism composition in chickens using 16S rRNA-seq. Integrated analysis of these three phenotypic datasets further managed to create correlations between the altered kidney transcriptomes and metabolome, and between kidney metabolome and gut microbiome. We found that 2868 genes and 160 metabolites were deferentially expressed or accumulated in the kidney during NIBV infection processes. These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. In addition, the comprehensive correlations between the kidney metabolome and cecal microbial community showed contributions of gut microbiota in the progression of NIBV-infection. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout.

RNA-Seq data analysis to identify enriched metabolic pathways and a prognostic signature in squamous cell lung cancer.

2018 ◽  
Vol 36 (15_suppl) ◽  
pp. e24288-e24288
Author(s):  
Jhajaira M Araujo ◽  
Claudio J. Flores ◽  
I. Tirado-Hurtado ◽  
Christian Diego Rolfo ◽  
Luis E. Raez ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Data Analysis ◽  
Squamous Cell ◽  
Cell Lung Cancer ◽  
Metabolic Pathways ◽  
Squamous Cell Lung Cancer ◽  
Rna Seq ◽  
Prognostic Signature

Molecular approaches to the manipulation of carbon allocation in plants

1993 ◽  
Vol 71 (6) ◽  
pp. 765-778 ◽  
Author(s):  
S. D. Blakeley ◽  
D. T. Dennis
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Metabolic Pathways ◽  
Carbon Allocation ◽  
Genetic Manipulation ◽  
Biosynthetic Pathways ◽  
Molecular Approaches ◽  
Carbon Substrates ◽  
Storage Organs ◽  
Storage Products

In plants, sucrose is the end product of photosynthesis and is converted to a wide variety of storage compounds in tissues such as seeds and tubers. The allocation of carbon from sucrose to the various metabolic pathways leading to these products will determine the quantity of each synthesized in the respective storage organs. If the level of the enzymes involved in the allocation of carbon could be changed by genetic manipulation, it is probable that the relative yields of the various storage products can also be altered. The initial breakdown of sucrose occurs in the cytosol of the cell. Many biosynthetic pathways, however, including those involved in the synthesis of storage products such as fatty acids, starch, and amino acids, occur in the plastid. The distribution of carbon substrates for these processes will be determined, to a large extent, by the flux of carbon through the glycolytic pathways found in both the cytosolic and plastid compartments. This article will discuss the importance and consequences of compartmentation, review the extent of our understanding of glycolysis and other enzymes and pathways regulating carbon allocation, and will speculate on the potential for the genetic manipulation of these pathways. Key words: genetic manipulation, carbon allocation, metabolism, glycolysis.

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