共检索到108条,权限内显示50条;
[学术文献 ] Targeting lignocellulolytic gene clusters in novel Trichoderma atroviride and Trichoderma harzianum strains through bacterial artificial chromosome–guided analysis 进入全文
Mycologia
Lignocellulosic biomass is a complex carbon source with recalcitrant properties whose degradation via industrial enzymatic hydrolysis is challenging, directly affecting the cost of reliable energy production. In nature, filamentous fungi, including Trichoderma species, degrade lignocellulose via an arsenal of hydrolytic and oxidative enzymes that act synergistically to process it into soluble sugar monomers. This work explored the genomic content of Trichoderma atroviride and Trichoderma harzianum strains with hydrolytic abilities by identifying regions possessing degradative enzyme–encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions and explore their genetic organization, proximal gene context, and gene expression under degradative conditions. With this tool, it was possible to inspect the linear structure and expression profile of target hydrolytic-rich genomic regions. The present work offers a perspective on the organization of genome regions related to carbohydrate metabolism. This study revealed novel genes and genome regions that are positively regulated during cellulose degradation, contributing to elucidating differences in gene organization that potentially impact hydrolysis among Trichoderma species.
[学术文献 ] Machine learning-guided engineering of T7 RNA polymerase and mRNA capping enzymes for enhanced gene expression in eukaryotic systems 进入全文
Chemical Engineering Journal
The integration of synthetic biology tools into eukaryotic systems offers both significant opportunities and challenges, particularly in optimizing transcriptional and post-transcriptional processes. T7 RNA polymerase (T7 RNAP) and mRNA capping enzymes (CEs) have been fused to enable eukaryotic mRNA production within a single construct. However, the activity of the fusion construct between the African Swine Fever Virus capping enzyme (ASFVCE) and T7 RNAP was relatively low. To address this, we fused the Brazilian Marseillevirus capping enzyme (BMCE) to T7 RNAP and developed a machine learning (ML) pipeline to engineer greatly improved fusion variants. This approach enabled the additive integration of nine predicted single substitutions that improved gene expression in yeast, thereby generating fusion polymerases that exhibited over 10-fold improvements in gene expression efficiency relative to the original fusion enzyme. Not only were ML substitutions additive for gene expression, they could be further combined with variants identified via directed evolution for even higher activities. By allowing ML predictions to guide validations we could rapidly explore the sequence landscape for enzyme optimization, achieving superior results even when compared to directed evolution. The improved enzymes have potential impact for numerous synthetic biology applications, including metabolic engineering, mRNA therapeutics, and cell free systems.
[学术文献 ] Reprogramming yeast metabolism to Alter fatty acid profiles from even-chain to odd-chain Configuration 进入全文
Bioresource Technology
Odd-chain fatty acids have significant applications in biofuels and pharmaceutical industries. In this study, a yeast cell factory was engineered to produce odd-chain fatty acids and their derivatives. The threonine biosynthesis pathway was initially engineered to enable the de novo synthesis of odd-chain fatty acids, resulting in odd-chain fatty acids accounting for 24.7 % of the total fatty acids. Subsequently, silencing the native fatty acid synthase and introducing a fatty acid synthase from Rhodotorula toruloides, which exhibits higher affinity for propionyl-CoA than the native enzyme, increased the proportion of odd-chain fatty acids to 51.9 %. Further modifications to the lipid metabolism enabled the production of odd-chain free fatty acids (184.1 mg/L) and odd-chain triglycerides (75.2 mg/g). This study successfully shifted the metabolism of Saccharomyces cerevisiae from traditional even-chain fatty acids to a strain dominant in odd-chain fatty acids, demonstrating the potential to develop a novel platform strain for producing specific odd-chain fatty acids derivatives.
[学术文献 ] Exploring multiobjective evolutionary algorithms for designing Ribonucleic Acid sequences: An experimental analysis 进入全文
Engineering Applications of Artificial Intelligence
"Evolutionary algorithms have proven effective in addressing the Ribonucleic Acid (RNA) inverse folding problem, a critical challenge in Biomedical Engineering. This problem, involving the discovery of a nucleotide RNA sequence that folds into a desired secondary structure, is formulated as a Multiobjective Optimization Problem. In this study, we introduce an approach incorporating three objective functions (Partition Function, Ensemble Diversity, and Nucleotides Composition) and a constraint (Similarity), utilizing a real-valued chromosome encoding. The primary focus is on analyzing and comparing the performance of four multiobjective evolutionary algorithms. We explore various crossover (Simulated Binary, Differential Evolution, One-Point, Two-Point, K-Point, and Exponential) and selection (Random and Tournament) operators, coupled with a fixed mutation operator (Polynomial). Our investigation involves 48 distinct algorithm-operator combinations, with the aim of solving a well-known benchmark set. This research makes a significant contribution to the field of Artificial Intelligence by addressing a complex problem through the lens of Multiobjective Optimization. The proposed framework not only advances our understanding of RNA inverse folding but also demonstrates the versatility of evolutionary algorithms in tackling real-world challenges in Biomedical Engineering. Our findings provide valuable insights into the behavior of different algorithmic elements and combinations, identifying optimal and suboptimal performers for future research and practical applications."
[学术文献 ] Transcriptomic profiles reveal hormonal regulation of sugar-induced stolon initiation in potato 进入全文
nature
Potato (Solanum tuberosum L.) is one of the world’s most important non-cereal food crops, with stolon development playing a crucial role in determining tuber yield. While some studies have examined the effects of sugars on potato stolon growth, their influence—particularly that of sucrose—on early stolon development remains unclear. Furthermore, the regulatory role of plant hormones in this process has yet to be established. Using a combination of in vitro culture, transcriptomics, gene expression analysis, and biochemical approaches, we investigated the contribution of sucrose (3% or 8%) on potato seedling stem nodes and stolon initials through phenotypic observation, RNA sequencing (RNA-seq), comparison of expression patterns, and hormone quantification. Firstly, compared to other types of sugars, we found that high concentrations of sucrose were the most effective in inducing stolon initial formation in potato seedlings. Furthermore, RNA-seq data showed that high sucrose levels significantly up-regulated the expression of genes involved in sugar metabolism and plant hormone metabolism. Additionally, the development of stem nodes and stolon initials under high sucrose conditions was also closely linked to hormone metabolism. Notably, high sucrose concentrations contributed to stem node and stolon initial development by modulating the IAA, CK, and GA signaling pathways. Based on the endogenous hormone measurement, and exogenous hormone application, together with heterologous overexpression of a potato Auxin response factor 9 (StARF9), we concluded that the early development of potato stolons was regulated by plant hormones, particularly auxin. In summary, this study elucidates the hormonal regulation of stolon initiation under high sucrose concentrations, offering a theoretical foundation and potential targets for in vitro culture and genetic improvement of potato.
[学术文献 ] A genomic variation map provides insights into potato evolution and key agronomic traits 进入全文
Cell
Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop, which requires a deep understanding of potato domestication and differentiation. In the present study, we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants. Using the variome map, we discovered the reshaping of tuber transcriptome during potato domestication, characterized genome-wide differentiation between landrace groups Stenotomum and Phureja. We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional steroidal glycoalkaloids (SGAs), and a Dehydration Responsive Element Binding (DREB) transcription factor conferring increased average tuber weight. In addition, genome similarity and group-specific SNP analyses indicated that tetraploid potatoes originated from the diploid Solanum tuberosum group Stenotomum. These findings shed light on the evolutionary trajectory of potato domestication and improvement, providing a solid foundation for advancing hybrid potato-breeding practices.
