Ct shift: A novel and accurate real-time PCR quantification model for direct comparison of different nucleic acid sequences and its application for transposon quantifications

Intron RPS25Ai, a Novel DNA Element, Has Global Effects on Synthetic Pathway Engineering by Empowering Protein Synthesis

Classical genetic components in synthetic biology encompass essential elements of promoters, transcription factors, protein-coding genes, and terminators while both academic and industrial needs require novel engineering tools. Our study explores the potential of introns as versatile, novel biological DNA elements. Using intron RPS25Ai from Saccharomyces cerevisiae, the expression of mCherry was enhanced by 18.4-fold, demonstrating spatiotemporal regulatory patterns at both transcriptional and translational levels. A molecular mechanism study shows that this distinctive fine-tuning control relies on correct splicing events and extends to post-transcriptional processes. Intron RPS25Ai was applied to a heterologous metabolic pathway in engineered yeast, increasing β-carotene production by 4.29-fold. RPS25Ai functioned as a multilevel regulatory genetic element, enabling the increase in the expression of crtYB both at the pre-mRNA (99%) and mature RNA level (64%), with a splicing efficiency of 82%. Furthermore, the intron-engineered strain achieved a genome-scale regulation, upregulating 67% of "intron-containing" genes, with an average expression increase of 27%, compared with the upregulation of only 37% of "no-intron" genes. In addition, RPS25Ai induced a comprehensive rearrangement of ribosomal components, with the expression of 89% of ribosomal genes being upregulated, further empowering protein synthesis in the β-carotene-producing yeast cell factory.

Functional indications for transposase domestications - Characterization of the human piggyBac transposase derived (PGBD) activities

Transposable elements are widespread in all living organisms. In addition to self-reproduction, they are a major source of genetic variation that drives genome evolution but our knowledge of the functions of human genes derived from transposases is limited. There are examples of transposon-derived, domesticated human genes that lost (SETMAR) or retained (THAP9) their transposase activity, however, several remnants in the human genome have not been thoroughly investigated yet. These include the five human piggyBac-derived sequences (PGBD1-5) which share ancestry with the Trichoplusia ni originated piggyBac (PB) transposase. Since PB is widely used in gene delivery applications, the potential activities of endogenous PGBDs are important to address. However, previous data is controversial, especially with the claimed transposition activity of PGBD5, it awaits further investigations. Here, we aimed to systematically analyze all five human PGBD proteins from several aspects, including phylogenetic conservation, potential transposase activity, expression pattern and their regulation in different stress conditions. Among PGBDs, PGBD5 is under the highest purifying selection, and exhibits the most cell type specific expression pattern. In a two-component vector system, none of the human PGBDs could mobilize either the insect PB transposon or the endogenous human PB-like MER75 and MER85 elements with intact terminal sequences. When cells were exposed to various stress conditions, including hypoxia, oxidative or UV stress, the expression profiles of all PGBDs showed different, often cell type specific responses; however, the pattern of PGBD5 in most cases had the opposite tendency than that of the other piggyBac-derived elements. Taken together, our results indicate that human PGBD elements did not retain their mobilizing activity, but their cell type specific, and cellular stress related expression profiles point toward distinct domesticated functions that require further characterization.

Identification of Essential Genes Associated With Prodigiosin Production in Serratia marcescens FZSF02

Prodigiosin is a promising secondary metabolite produced mainly by Serratia strains. To study the global regulatory mechanism of prodigiosin biosynthesis, a mutagenesis library containing 23,000 mutant clones was constructed with the EZ-Tn5 transposon, and 114 clones in the library showed altered prodigiosin production ability. For 37 of the 114 clones, transposon insertion occurred on the prodigiosin biosynthetic cluster genes; transposon inserted genes of the 77 clones belonged to 33 different outside prodigiosin biosynthetic cluster genes. These 33 genes can be divided into transcription-regulating genes, membrane protein-encoding genes, and metabolism enzyme-encoding genes. Most of the genes were newly reported to be involved in prodigiosin production. Transcriptional levels of the pigA gene were significantly downregulated in 22 mutants with different inserted genes, which was in accordance with the phenotype of decreased prodigiosin production. Functional confirmation of the mutant genes involved in the pyrimidine nucleotide biosynthesis pathway was carried out by adding orotate and uridylate (UMP) into the medium. Gene complementation confirmed the regulatory function of the EnvZ/OmpR two-component regulatory system genes envZ and ompR in prodigiosin production.

Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells

Setmar is a gene specific to simian genomes. The function(s) of its isoforms are poorly understood and their existence in healthy tissues remains to be validated. Here we profiled SETMAR expression and its genome-wide binding landscape in colon tissue. We found isoforms V3 and V6 in healthy and tumour colon tissues as well as incell lines. In two colorectal cell lines SETMAR binds to several thousand Hsmar1 and MADE1 terminal ends, transposons mostly located in non-genic regions of active chromatin including in enhancers. It also binds to a 12-bp motifs similar to an inner motif in Hsmar1 and MADE1 terminal ends. This motif is interspersed throughout the genome and is enriched in GC-rich regions as well as in CpG islands that contain constitutive replication origins. It is also found in enhancers other than those associated with Hsmar1 and MADE1. The role of SETMAR in the expression of genes, DNA replication and in DNA repair are discussed.

Antisense Oligonucleotides for Splice Modulation: Assessing Splice Switching Efficacy

Today, there are emerging numbers of oligonucleotide therapies being approved by the governmental authorities. These types of therapies present a different mode of action when compared to the traditional small molecules, acting at the RNA level instead of the protein level. In drug development, drug potency is defined by the drug affinity to the target biomolecule (target engagement), together with the ability to initiate a response at the molecular, cellular, tissue, or system level (efficacy). In oligonucleotide therapies, affinity and efficacy can be both easily evaluated by gene expression analysis. Although more advanced techniques can be used, this chapter presents a protocol to evaluate splice switching oligonucleotide efficacy that can be easily applied in a molecular biology laboratory without the need of advanced equipment. It describes all steps from sample preparation to data analysis.

Plasmid-normalized quantification of relative mitochondrial DNA copy number

Alterations of mitochondrial DNA (mtDNA) copy number have been associated with a wide variety of phenotypes and diseases. Unfortunately, the literature provides scarce methodical information about duplex targeting of nuclear and mtDNA that meets the quality criteria for qPCR. Therefore, we established a method for mtDNA copy number quantification using a quantitative PCR assay that allows for simultaneous targeting of a single copy nuclear gene (beta-2-microglobulin) and the t-RNA^Leu gene on the mtDNA. We include a plasmid containing both targets in order to normalize against differences in emission intensities of the fluorescent dyes Yakima Yellow and FAM. Applying the plasmid calibrator on an internal control reduced the intra-assay variability from 21% (uncorrected) to 7% (plasmid-corrected). Moreover, we noted that DNA samples isolated with different methods revealed different numbers of mtDNA copies, thus highlighting an important influence of the pre-analytical procedures. In summary, we developed a precise assay for mitochondrial copy number detection relative to nuclear DNA. Our method is applicable to comparative mitochondrial DNA copy number studies since the use of the dual insert plasmid allows correcting for the unequal emission intensities of the different fluorescent labels of the two targets.

Efficient CRISPR-Cas9 mediated multiplex genome editing in yeasts

BACKGROUND

The thermotolerant methylotrophic yeast Ogataea polymorpha has been regarded as an important organism for basic research and biotechnological applications. It is generally recognized as an efficient and safe cell factory in fermentative productions of chemicals, biofuels and other bio-products. However, it is difficult to genetically engineer for the deficiency of an efficient and versatile genome editing technology.

RESULTS

In this study, we developed a CRISPR-Cas9-assisted multiplex genome editing (CMGE) approach including multiplex genes knock-outs, multi-locus (ML) and multi-copy (MC) integration methods in yeasts. Based on CMGE, various genome modifications, including gene deletion, integration, and precise point mutation, were performed in O. polymorpha. Using the CMGE-ML integration method, three genes TAL from Herpetosiphon aurantiacus, 4CL from Arabidopsis thaliana and STS from Vitis vinifera of resveratrol biosynthetic pathway were simultaneously integrated at three different loci, firstly achieving the biosynthesis of resveratrol in O. polymorpha. Using the CMGE-MC method, ∼ 10 copies of the fusion expression cassette P _ScTEF1 -TAL-P _ScTPI1 -4CL-P _ScTEF2 -STS were integrated into the genome. Resveratrol production was increased ~ 20 fold compared to the one copy integrant and reached 97.23 ± 4.84 mg/L. Moreover, the biosynthesis of human serum albumin and cadaverine were achieved in O. polymorpha using CMGE-MC to integrate genes HSA and cadA, respectively. In addition, the CMGE-MC method was successfully developed in Saccharomyces cerevisiae.

CONCLUSIONS

An efficient and versatile multiplex genome editing method was developed in yeasts. The method would provide an efficient toolkit for genetic engineering and synthetic biology researches of O. polymorpha and other yeast species.