Journal: Synthetic and Systems Biotechnology

Article Title: Metabolic engineering and adaptive laboratory evolution enhance squalene production in Yarrowia lipolytica

doi: 10.1016/j.synbio.2026.01.017

Figure Lengend Snippet: Schematic of constructing engineered Y. lipolytica strain for squalene production. I indicate lipid droplet engineering to modulate triacylglycerols synthesis and increase squalene storage capacity. II indicates modulation of the MVA pathway to promote squalene synthesis flux. III indicates enzyme fusion engineering to promote catalytic efficiency between ERG20 and SQS. IV indicates iterative copy numbering of the ScHMG1 gene. V indicates adaptive evolutionary engineering strategies. Red font represents endogenous genes, and blue font represents heterologous genes. DGA1, Diacylglycerol acyltransferase; LRO1, Phospholipid: diacylglycerol acyltransferase; ERG10, Acetyl-CoA acetyltransferase; ERG13, HMG-CoA synthase; ScHMG1, 3-hydroxy-3-methyl glutaryl coenzyme A reductase of S. cerevisiae origin; ERG20, farnesyl diphosphate synthase; SQS, squalene synthase.

Article Snippet: The 3-hydroxy-3-methylglutaryl-CoA reductase encoding gene ScHMG1 (GenBank ID: 854900) from S. cerevisiae was codon-optimized and synthesized (Genewiz, Suzhou, China).

Techniques:

Journal: Synthetic and Systems Biotechnology

Article Title: Metabolic engineering and adaptive laboratory evolution enhance squalene production in Yarrowia lipolytica

doi: 10.1016/j.synbio.2026.01.017

Figure Lengend Snippet: Enhancing the expression of ScHMG1 to boost squalene synthesis . (A) Schematic design of overexpressing ScHMG1 at the IntC locus. (B) Effects of enhanced ScHMG1 expression on squalene and lipid synthesis in the engineered Y. lipolytica strain. (C) The pH, biomass, and glucose consumption of the engineered strains after 72 h of fermentation.

Article Snippet: The 3-hydroxy-3-methylglutaryl-CoA reductase encoding gene ScHMG1 (GenBank ID: 854900) from S. cerevisiae was codon-optimized and synthesized (Genewiz, Suzhou, China).

Techniques: Expressing

Journal: bioRxiv

Article Title: The phenotypic landscape of the model firmicute Bacillus subtilis

doi: 10.64898/2026.05.13.724699

Figure Lengend Snippet: A-B. RFs are reproducible across conditions. RF of all sgRNAs plotted pairwise from each experimental replicate of every condition (done in triplicate): 11,566 sgRNAs x 149 conditions ≈ 1.7 million RF values per replicate. Pearson’s r for all comparisons > 0.95. Condition replicates with severely abnormal median sgRNA behavior and/or outlier correlation values to the other triplicates generally indicate bottlenecking from read depth and were excluded during preprocessing prior to this analysis (Methods). 100,000 randomly chosen data points are displayed (out of approximately 1.7 million). C. RF of sgRNAs shared between our library and previous work are consistent. sgRNAs were selected from ref . Lower minimum RF in ref reflects a higher sequencing depth in that study. Pearson’s r = 0.88. D. RF of fully-complementary sgRNAs targeting genes designated as “nonessential”, “impaired” or “essential” based on their single gene deletion phenotypes in KanR or ErmR libraries from ref . Box bounds: first and third quartile, midline: median, whiskers: most extreme datapoints. sgRNAs targeting nonessential genes with RF < 0.9 may reflect polar knockdown effects on essential operon partners.

Article Snippet: Oligos encoding sgRNAs included ∼100bp homology with the pJSHa77b backbone were ordered from Twist Biosciences and amplified for 14 cycles.

Techniques: Sequencing, Knockdown

Journal: bioRxiv

Article Title: The phenotypic landscape of the model firmicute Bacillus subtilis

doi: 10.64898/2026.05.13.724699

Figure Lengend Snippet: A. Gene-chemical S-Scores of genes involved in the elongasome or divisome against the cell-wall drug cefaclor and the FAS inhibitors cerulenin and triclosan. As expected, knockdown of genes comprising both the elongasome and divisiome (the PG synthesis machineries) are sensitized to the β-lactam cefaclor. In contrast, inhibition of FAS by triclosan or cerulenin generally had a protective effect on knockdown of elongasome genes, but a sensitizing effect on knockdown of divisome genes. Drug concentrations with strongest S-scores are displayed. For genes targeted by multiple knockdown bins, only the most responsive bin (greatest sum of absolute S-scores across the drug concentrations used) is shown. B. RF values of mntR knockdown and sufD knockdown across all conditions. For sufD , the average RF of the two fully-complementary sgRNAs is plotted. Blue = dipyridyl (iron chelator), Green = excess manganese, Purple = minimal and glucose complete media, Red = mupirocin.

Article Snippet: Oligos encoding sgRNAs included ∼100bp homology with the pJSHa77b backbone were ordered from Twist Biosciences and amplified for 14 cycles.

Techniques: Knockdown, Inhibition

Journal: bioRxiv

Article Title: The phenotypic landscape of the model firmicute Bacillus subtilis

doi: 10.64898/2026.05.13.724699

Figure Lengend Snippet: A. Growth of B. subtilis mutant strains grown as single colonies of knockouts on minimal media agar plates (x-axis, ) or in pooled liquid minimal media culture growth of this knockdown library (y-axis) (all genes present in both libraries; n = 3774 genes). For single colonies, WT growth is signified as a RF of 1.0. For growth in liquid culture, WT growth is signified as a RF of 1.0. Error bars signify standard deviation of RF values in minimal media of the two targeting sgRNAs in pooled culture. Auxotrophs are highlighted in red (defined in ref ). Cross-feeding behavior of a strain would manifest as a RF of 0 as single colonies and a RF of 1.0 in pooled culture (upper left quadrant). B. Growth of E. coli knockout strains grown as single colonies on minimal media agar plates (x-axis, ) or in pooled liquid minimal media culture growth (y-axis, ) (all genes present in both screens; n = 3410 genes). For single colonies, WT growth is signified as an S-score of 0. For growth in liquid culture, WT growth is signified as a L2FC of 0. Error bars signify standard deviation of two separate measurements of growth in pooled culture. Auxotrophs are highlighted in red (defined in ref ). Cross-feeding behavior of a strain would manifest as a negative S-score (i.e. S-score < -5) as single colonies and a L2FC of 0 in pooled culture (upper left quadrant).

Article Snippet: Oligos encoding sgRNAs included ∼100bp homology with the pJSHa77b backbone were ordered from Twist Biosciences and amplified for 14 cycles.

Techniques: Mutagenesis, Knockdown, Standard Deviation, Knock-Out