Search bioRxivSearch

Biology subjects

Hua, N.

Publications and source records attributed to Hua, N..

2 recordsLinked to original sources

Clustering enzymes using E.coli inner cell membrane as scaffold in metabolic pathway

Clustering enzymes in the same metabolism pathway is a natural strategy to enhance the productivity. Several systems have been designed to artificially cluster desired enzymes in the cell, such as synthetic protein scaffold and nucleic acid scaffold. However, these scaffolds require complicated construction process and have limited slots for target enzymes. Following this direction, we designed a scaffold system based on natural cell membrane. Target enzymes (FabZ, FabG, FabI and TesA in fatty acid synthesis II pathway) are anchored on the E.coli inner membrane, showing the enhanced metabolism flux without the requirement of the further artificial interactions to force the clustering. Furthermore, anchoring the enzymes on the membrane enhances the products exportation, which further increases the productivity. Together, the proposed system has potential applications in producing valuable biomaterials.

synthetic biology

PGS: a dynamic and automated population-based genome structure software

Hi-C technologies are widely used to investigate the spatial organization of genomes. However, the structural variability of the genome is a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range/interchromosomal interactions. We pioneered a probabilistic approach for generating a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genomes organization in space and time. We provide a user-friendly software package, called PGS, that runs on local machines and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and also provides tools to extract and analyze the 3D coordinates of specific domains.

bioinformatics