Classifying DNA assembly protocols for devising cellular architectures

Chlorophyll as key indicator to evaluate astaxanthin accumulation ability of Haematococcus pluvialis

Background

Natural astaxanthin is mainly derived from Haematococcus pluvialis. In the photoinduction phase, astaxanthin accumulation ability can be significantly affected by the characteristics of H. pluvialis cells in the proliferation phase. Based on sequential heterotrophy–dilution–photoinduction (SHDP) technology, the authors’ previous study showed that high astaxanthin accumulation ability is accompanied by high chlorophyll content of H. pluvialis heterotrophic cell; whereas the mechanism of this result remained largely obscure. Therefore, transcriptome analysis was conducted to explain this mechanism.

Results

RNA-seq analysis showed that the transcription level of chlorophyll synthesis-related genes was negatively correlated with genes related to astaxanthin synthesis. A metabolic network between chlorophyll synthesis and astaxanthin accumulation was proposed.

Conclusions

The relationship between chlorophyll synthesis and astaxanthin accumulation was clarified. Chlorophyll degradation products might be used for astaxanthin synthesis through certain pathways. This study enlightens on the mechanism for the transformation of pigment and is conducive to optimize culture process of H. pluvialis by improving the chlorophyll content of heterotrophic cell.

UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction

Overexpression of key genes is a basic strategy for overproducing target products via metabolic engineering. Traditionally, identifying those key genes/pathways largely relies on the knowledge of biochemistry and bioinformatics. In this study, a modeling tool named UP Finder was developed to facilitate the rapid identification of gene overexpression strategies. It was based on the COBRA toolbox under MATLAB environment. All the key gene/pathway targets are identified in one click after simply loading a Systems Biology Markup Language model and specifying a metabolite as the targeted product. The outputs are also quantitatively ranked to show the preference for determining overexpression strategies in pathway design. Analysis examples for overproducing lycopene precursor in Escherichia coli and fatty acyl-ACP in the cyanobacterium Synechocystis sp. PCC 6803 by the UP Finder showed high degree of agreement with the reported key genes in the literatures.

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A modeling interface is developed for identifying gene overexpression targets.

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It evaluates the yield contribution for each overexpression candidate.

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The outputs are ranked to show the preference for determining strategies.

DNA Assembly Tools and Strategies for the Generation of Plasmids

Since the discovery of restriction enzymes and the generation of the first recombinant DNA molecule over 40 years ago, molecular biology has evolved into a multidisciplinary field that has democratized the conversion of a digitized DNA sequence stored in a computer into its biological counterpart, usually as a plasmid, stored in a living cell. In this article, we summarize the most relevant tools that allow the swift assembly of DNA sequences into useful plasmids for biotechnological purposes. We cover the main components and stages in a typical DNA assembly workflow, namely in silico design, de novo gene synthesis, and in vitro and in vivo sequence assembly methodologies.

SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution

The de novo synthesis of genes is becoming increasingly common in synthetic biology studies. However, the inherent error rate (introduced by errors incurred during oligonucleotide synthesis) limits its use in synthesising protein libraries to only short genes. Here we introduce SpeedyGenes, a PCR-based method for the synthesis of diverse protein libraries that includes an error-correction procedure, enabling the efficient synthesis of large genes for use directly in functional screening. First, we demonstrate an accurate gene synthesis method by synthesising and directly screening (without pre-selection) a 747 bp gene for green fluorescent protein (yielding 85% fluorescent colonies) and a larger 1518 bp gene (a monoamine oxidase, producing 76% colonies with full catalytic activity, a 4-fold improvement over previous methods). Secondly, we show that SpeedyGenes can accommodate multiple and combinatorial variant sequences while maintaining efficient enzymatic error correction, which is particularly crucial for larger genes. In its first application for directed evolution, we demonstrate the use of SpeedyGenes in the synthesis and screening of large libraries of MAO-N variants. Using this method, libraries are synthesised, transformed and screened within 3 days. Importantly, as each mutation we introduce is controlled by the oligonucleotide sequence, SpeedyGenes enables the synthesis of large, diverse, yet controlled variant sequences for the purposes of directed evolution.