Cloning of DNA oligo pools for in vitro expression

Current advancements in fungal engineering technologies for Sustainable Development Goals

Fungi are emerging as key organisms in tackling global challenges related to agricultural and food productivity, environmental sustainability, and climate change. This review delves into the transformative potential of fungal genomics and metabolic engineering, two forefront fields in modern biotechnology. Fungal genomics entails the thorough analysis and manipulation of fungal genetic material to enhance desirable traits, such as pest resistance, nutrient absorption, and stress tolerance. Metabolic engineering focuses on altering the biochemical pathways within fungi to optimize the production of valuable compounds, including biofuels, pharmaceuticals, and industrial enzymes. By artificial intelligence (AI)-driven integration of genetic and metabolic engineering techniques, we can harness the unique capabilities of both filamentous and mycorrhizal fungi to develop sustainable agricultural practices, enhance soil health, and promote ecosystem restoration. This review explores the current state of research, technological advancements, and practical applications, offering insights into scalability challenges on how integrative fungal genomics and metabolic engineering can deliver innovative solutions for a sustainable future.

Culture Wars: Empirically Determining the Best Approach for Plasmid Library Amplification

DNA libraries are critical components of many biological assays. These libraries are often kept in plasmids that are amplified in E. coli to generate sufficient material for an experiment. Library uniformity is critical for ensuring that every element in the library is tested similarly and is thought to be influenced by the culture approach used during library amplification. We tested five commonly used culturing methods for their ability to uniformly amplify plasmid libraries: liquid, semisolid agar, cell spreader-spread plates with high or low colony density, and bead-spread plates. Each approach was evaluated with two library types: a random 80-mer library, representing high complexity and low coverage of similar sequence lengths, and a human TF ORF library, representing low complexity and high coverage of diverse sequence lengths. We found that no method was better than liquid culture, which produced relatively uniform libraries regardless of library type. However, when libraries were transformed with high coverage, the culturing method had minimal impact on uniformity or amplification bias. Plating libraries was the worst approach by almost every measure for both library types and, counterintuitively, produced the strongest biases against long sequence representation. Semisolid agar amplified most elements of the library uniformly but also included outliers with orders of magnitude higher abundance. For amplifying DNA libraries, liquid culture, the simplest method, appears to be best.

Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids

BACKGROUND

N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability is driven by changes in genetic sequences ('cis') or cellular environments ('trans') and via which mechanisms.

RESULTS

Here we dissect the determinants governing RNA methylation via interspecies and intraspecies hybrids in yeast and mammalian systems, coupled with massively parallel reporter assays and m6A-QTL reanalysis. We find that m6A evolution and variability is driven primarily in 'cis', via two mechanisms: (1) variations altering m6A consensus motifs, and (2) variation impacting mRNA secondary structure. We establish that mutations impacting RNA structure - even when distant from an m6A consensus motif - causally dictate methylation propensity. Finally, we demonstrate that allele-specific differences in m6A levels lead to allele-specific changes in gene expression.

CONCLUSIONS

Our findings define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.

Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability

N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we propose that m6A deposition is not selective. Instead, it is exclusion based: m6A consensus motifs are methylated by default, unless they are within a window of ∼100 nt from a splice junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture, allows in silico recapitulation of experimentally measured m6A profiles. We provide evidence that exclusion from splice junctions is mediated by the exon junction complex (EJC), potentially via physical occlusion, and that previously observed associations between exon-intron architecture and mRNA decay are mechanistically mediated via m6A. Our findings establish a mechanism coupling nuclear mRNA splicing and packaging with the covalent installation of m6A, in turn controlling cytoplasmic decay.