Efficient de novo assembly and modification of large DNA fragments

Bioremediation of complex organic pollutants by engineered Vibrio natriegens

Industrial wastewater, petroleum pollution and plastic contamination are significant threats to global marine biosecurity because of their toxic, mutagenic and persistent nature1. The use of microorganisms in bioremediation has been constrained by the complexity of organic pollutants and limited tolerance to saline stress2. In this study, we used synthetic biology to engineer Vibrio natriegens into a strain capable of bioremediating complex organic pollutants in saline wastewater and soils. The competence master regulator gene tfoX was inserted into chromosome 1 of the V. natriegens strain Vmax and overexpressed to enhance DNA uptake and integration. Degradation gene clusters were chemically synthesized and assembled in yeast. We developed a genome engineering method (iterative natural transformation based on Vmax with amplified tfoX effect) to transfer five gene clusters (43 kb total) into Vmax. The engineered strain has the ability to bioremediate five organic pollutants (biphenyl, phenol, naphthalene, dibenzofuran and toluene) covering a broad substrate range, from monocyclic to multicyclic compounds, in industrial wastewater samples from a chlor-alkali plant and a petroleum refinery.

Efficient De Novo Assembly of 100 kb-Scale Human Functional Immunoglobulin Heavy Variable (IGHV) Gene Fragments In Vitro

Synthetic biology provides a powerful approach to functional studies of viral and microbial genomes. However, in vitro, efficient and scarless DNA manipulation on large and complex human genomes remains an inevitable challenge. Here, we de novo design and successfully assemble human functional immunoglobulin heavy variable (IGHV) gene fragments up to hundred-kilobase (kb)-sized, using an iterative in vitro assembly via Escherichia coli (E. coli) based on Gibson isothermal assembly. We describe an efficient method for "scarless" (without leaving any non-native sequences) engineering of the assembled ordered functional IGHV gene fragments, which contain complex and highly repetitive regions. Our method provides a suitable way to construct bacterial artificial chromosomes (BACs) (30-100 kb) with common materials, easy manipulations, and low cost. The construction of ordered functional IGHV gene BACs expands the synthetic biologist's chassis repertoire. It is essential for the adaptive immune response and constructing immunity humanized animal models.

Optimization of PCA Error Correction Conditions to Improve Efficiency of Virus Genome De Novo Synthesis

In recent years, there have been frequent global outbreaks of viral epidemics such as Zika, COVID-19, and monkeypox, which have had a huge impact on human health and society and have also spurred innovation in virus engineering technology. The rise of synthetic virus genome technology has provided researchers with a new platform to accelerate vaccine and drug development. Although DNA synthesis technology has made significant progress, the current virus genome synthesis technology still requires the assembly of short oligonucleotides of around 60 bp into kb-level lengths when constructing long segments, a process in which the commonly used polymerase chain reaction assembly (PCA) technology has high error rates and is cumbersome to operate. This study optimized the error correction conditions after PCA assembly, increasing the accuracy of synthesizing 1 kb DNA fragments from 4.2 ± 2.1% before error correction to 31.3 ± 3.1% after two rounds of correction, an improvement of over 6 times. This study provides a more efficient operational process for synthesizing virus genomes from scratch, indicating greater potential for virus engineering in epidemic prevention and control and the field of biomedicine.

Plant synthetic genomics: Big lessons from the little yeast

Yeast has been extensively studied and engineered due to its genetic amenability. Projects like Sc2.0 and Sc3.0 have demonstrated the feasibility of constructing synthetic yeast genomes, yielding promising results in both research and industrial applications. In contrast, plant synthetic genomics has faced challenges due to the complexity of plant genomes. However, recent advancements of the project SynMoss, utilizing the model moss plant Physcomitrium patens, offer opportunities for plant synthetic genomics. The shared characteristics between P. patens and yeast, such as high homologous recombination rates and dominant haploid life cycle, enable researchers to manipulate P. patens genomes similarly, opening promising avenues for research and application in plant synthetic biology. In conclusion, harnessing insights from yeast synthetic genomics and applying them to plants, with P. patens as a breakthrough, shows great potential for revolutionizing plant synthetic genomics.

Insights into a functional synthetic plant genome

Synthetic genomics involves the design, assembly, and transfer of artificially synthesized DNA fragments into target hosts to replace the native genome and construct viable forms of life. With advances in DNA synthesis and assembly techniques, the application of synthetic genomics in viruses, bacteria, and yeast has improved our knowledge of genome organization and function. Multicellular eukaryotic organisms are characterized by larger genomes, more complex epigenetic regulation, and widespread transposable elements, making genome synthesis challenging. Recently, the first synthetic multicellular eukaryotic organism was generated in the model plant Physcomitrium patens with a partially synthetic chromosome arm. Here, we introduce the design and assembly principles of moss genome synthesis. We also discuss the remaining technical barriers in the application of synthetic genomics in seed plants.

Crucial amino acids identified in Δ12 fatty acid desaturases related to linoleic acid production in Perilla frutescens

Perilla oil from the medicinal crop Perilla frutescens possess a wide range of biological activities and is generally used as an edible oil in many countries. The molecular basis for its formation is of particular relevance to perilla and its breeders. Here in the present study, four PfFAD2 genes were identified in different perilla cultivars, PF40 and PF70, with distinct oil content levels, respectively. Their function was characterized in engineered yeast strain, and among them, PfFAD2-1PF40, PfFAD2-1PF70 had no LA biosynthesis ability, while PfFAD2-2PF40 in cultivar with high oil content levels possessed higher catalytic activity than PfFAD2-2PF70. Key amino acid residues responsible for the enhanced catalytic activity of PfFAD2-2PF40 was identified as residue R221 through sequence alignment, molecular docking, and site-directed mutation studies. Moreover, another four amino acid residues influencing PfFAD2 catalytic activity were discovered through random mutation analysis. This study lays a theoretical foundation for the genetic improvement of high-oil-content perilla cultivars and the biosynthesis of LA and its derivatives.

A seven-sex species recognizes self and non-self mating-type via a novel protein complex

Although most species have two sexes, multisexual (or multi-mating type) species are also widespread. However, it is unclear how mating-type recognition is achieved at the molecular level in multisexual species. The unicellular ciliate Tetrahymena thermophila has seven mating types, which are determined by the MTA and MTB proteins. In this study, we found that both proteins are essential for cells to send or receive complete mating-type information, and transmission of the mating-type signal requires both proteins to be expressed in the same cell. We found that MTA and MTB form a mating-type recognition complex that localizes to the plasma membrane, but not to the cilia. Stimulation experiments showed that the mating-type-specific regions of MTA and MTB mediate both self- and non-self-recognition, indicating that T. thermophila uses a dual approach to achieve mating-type recognition. Our results suggest that MTA and MTB form an elaborate multifunctional protein complex that can identify cells of both self and non-self mating types in order to inhibit or activate mating, respectively.

A designer synthetic chromosome fragment functions in moss

Rapid advances in DNA synthesis techniques have enabled the assembly and engineering of viral and microbial genomes, presenting new opportunities for synthetic genomics in multicellular eukaryotic organisms. These organisms, characterized by larger genomes, abundant transposons and extensive epigenetic regulation, pose unique challenges. Here we report the in vivo assembly of chromosomal fragments in the moss Physcomitrium patens, producing phenotypically virtually wild-type lines in which one-third of the coding region of a chromosomal arm is replaced by redesigned, chemically synthesized fragments. By eliminating 55.8% of a 155 kb endogenous chromosomal region, we substantially simplified the genome without discernible phenotypic effects, implying that many transposable elements may minimally impact growth. We also introduced other sequence modifications, such as PCRTag incorporation, gene locus swapping and stop codon substitution. Despite these substantial changes, the complex epigenetic landscape was normally established, albeit with some three-dimensional conformation alterations. The synthesis of a partial multicellular eukaryotic chromosome arm lays the foundation for the synthetic moss genome project (SynMoss) and paves the way for genome synthesis in multicellular organisms.

Towards Plant Synthetic Genomics

Rapid advances in DNA synthesis techniques have allowed the assembly and engineering of viral and microbial genomes. Multicellular eukaryotic organisms, with their larger genomes, abundant transposons, and prevalent epigenetic regulation, present a new frontier to synthetic genomics. Plant synthetic genomics have long been proposed, and exciting progress has been made using the top-down approach. In this perspective, we propose applying bottom-up genome synthesis in multicellular plants, starting from the model moss Physcomitrium patens, in which homologous recombination, DNA delivery, and regeneration are possible, although further optimizations are necessary. We then discuss technical barriers, including genome assembly and plant transformation, associated with synthetic genomics in seed plants.

Enabling technology and core theory of synthetic biology

Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.

Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

Naturally occurring structural variations (SVs) are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes. Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched. In this study, an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) technology with two synthetic chromosomes, namely synV and synX. The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries. Our findings showed that complex SVs, including a pericentric inversion and a trans-chromosome translocation between synV and synX, resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin. Also, genetic targets were mapped, which resulted in a higher astaxanthin yield, thus demonstrating the SVs' ability to reorganize genetic information along the chromosomes. The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena. Collectively, this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.