Convenient synthesis and delivery of a megabase-scale designer accessory chromosome empower biosynthetic capacity.

Synthetic biology confers new functions to hosts by introducing exogenous genetic elements, yet rebuilding complex traits that are based on large-scale genetic information remains challenging. Here, we developed a CRISPR/Cas9-mediated haploidization method that bypasses the natural process of meiosis. Based on the programmed haploidization in yeast, we further developed an easy-to-use method designated HAnDy (Haploidization-based DNA Assembly and Delivery in yeast) that enables efficient assembly and delivery of large DNA, with no need for any fussy in vitro manipulations. Using HAnDy, a de novo designed 1.024 Mb synthetic accessory chromosome (synAC) encoding 542 exogenous genes was parallelly assembled and then directly transferred to six phylogenetically diverse yeasts. The synAC significantly promotes hosts' adaptations and increases the scope of the metabolic network, which allows the emergence of valuable compounds. Our approach should facilitate the assembly and delivery of large-scale DNA for expanding and deciphering complex biological functions.

Design and deep learning of synthetic B-cell-specific promoters.

Synthetic biology and deep learning synergistically revolutionize our ability for decoding and recoding DNA regulatory grammar. The B-cell-specific transcriptional regulation is intricate, and unlock the potential of B-cell-specific promoters as synthetic elements is important for B-cell engineering. Here, we designed and pooled synthesized 23 640 B-cell-specific promoters that exhibit larger sequence space, B-cell-specific expression, and enable diverse transcriptional patterns in B-cells. By MPRA (Massively parallel reporter assays), we deciphered the sequence features that regulate promoter transcriptional, including motifs and motif syntax (their combination and distance). Finally, we built and trained a deep learning model capable of predicting the transcriptional strength of the immunoglobulin V gene promoter directly from sequence. Prediction of thousands of promoter variants identified in the global human population shows that polymorphisms in promoters influence the transcription of immunoglobulin V genes, which may contribute to individual differences in adaptive humoral immune responses. Our work helps to decipher the transcription mechanism in immunoglobulin genes and offers thousands of non-similar promoters for B-cell engineering.

A DNA Inversion System in Eukaryotes Established via Laboratory Evolution.

DNA inversion is a type of site-specific recombination system that plays an important role in the generation of genetic diversity and phenotypic adaptation by programmed rearrangements in bacteria. However, no such inversion system exhibiting a strong directionality bias has been identified or developed in eukaryotes yet. Here, using directed evolution of Rci recombinase, a tyrosine recombinase from a bacterial DNA inversion system, we identified a mutant Rci8 with a ratio of inversion/deletion up to ∼4320 in yeast. Based on Rci8 recombinase and sfxa101 sites, we have established a DNA inversion system in yeast and mammalian cells, enabling specificity for DNA inversions between inverted sites over deletions between directly repeated sites. Our results validated that the reversible DNA inversion system can act as an on/off transcriptional switch. Moreover, we demonstrate that the inversion system can also work on linear chromosomes. The eukaryotic DNA inversion system would provide a new tool for fields of genetic circuits, cellular barcoding, and synthetic genomes.

Characterization and phenol adsorption performance of activated carbon prepared from tea residue by NaOH activation.

The preparation of activated carbon (AC) using tea residue was addressed in this work. The preparation process incorporated two-step pyrolysis and activation using NaOH. The influence of activation temperature between 500°C and 700°C on the properties of the AC sample was investigated. The physicochemical properties of the AC sample were characterized. The results show that the optimum temperature for the activation process is 700°C, which generates the AC sample with higher specific surface area and total pore volume, respectively, of 819 m2 g-1 and 0.443 cm3 g-1. The oxygen-containing functional groups evolve on the AC sample during the activation process. The phenol adsorption test was performed to evaluate the adsorption performance of the AC sample. The adsorption data confirm that phenol adsorption on the AC sample obtained at 700°C follows the pseudo-second-order kinetics model. Hereby, the electron donor-acceptor interaction mechanism can describe the adsorption process. The AC sample obtained at 700°C performs superior phenol adsorption performance. The maximum phenol adsorption capacity is 320 mg g-1, which is higher than that of several AC samples reported previously. Thus, the tea residue acts as a good precursor for the AC with promising adsorption capacity by the NaOH chemical activation method.