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: Auxin is metabolized through kynurenine in Hypericum perforatum L

doi: 10.64898/2026.05.18.726114

Figure Lengend Snippet: (A) Schematic representation of major tryptophan (Trp)-derived metabolic pathways, including the kynurenine pathway (center), the indole-3-pyruvic acid (IPA)–indole-3-acetic acid (IAA) pathway, and the tryptamine– serotonin–melatonin branch (top). Solid, dashed, and double boxes indicate metabolites reported in animals, plants, or both, respectively. Enzymes are indicated at each step: IDO1/IDO2 (indoleamine 2,3-dioxygenase), TDO (tryptophan 2,3-dioxygenase), AFMID (arylformamidase), KAT (kynurenine aminotransferase), TDC (tryptophan decarboxylase), TAA1/TAR (tryptophan aminotransferase), KYNU (kynureninase), KMO (kynurenine 3-monooxygenase), HAAO (3-hydroxyanthranilate 3,4-dioxygenase), ACMSD (α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase), and QPRT (quinolinate phosphoribosyltransferase). Inhibitor targets are indicated at the corresponding steps: JM6 and RO 61-8048 inhibit KMO, and PF-04859989 inhibits KAT. (B) Chemical structures of the kynurenine pathway metabolites quantified in this study: kynurenine, kynurenic acid (KYNA), and 3-hydroxyanthranilic acid (3-HAA). (C) Chemical structures of the inhibitors used in this study. Core structural differences between JM6 and RO 61-8048 are highlighted in red.

Article Snippet: The compound (R)-3-amino-1-hydroxy-3,4-dihydroquinolin-2(1H)-one (PF-04859989) was identified by a high-throughput screen of the Pfizer compound library as a high-affinity inhibitor of human kynurenine aminotransferase (KAT; ).

Techniques: Derivative Assay

Journal: bioRxiv

Article Title: Auxin is metabolized through kynurenine in Hypericum perforatum L

doi: 10.64898/2026.05.18.726114

Figure Lengend Snippet: ( A) Representative images of explants cultured on MSO (control), kynurenine (KYN), indole-3-acetic acid (IAA), and IAA combined with inhibitors (IAA + JM6, IAA + PF-04859989 [PF], and IAA + RO 61-8048 [RO]). Scale bar = 1 cm (B) Rooting frequency, (C) internodal length (cm per node), (D) root number, and (E) maximum root length (cm) of explants under each treatment. For rooting frequency (B), bars represent mean proportion rooted ± SE. For (C–E), boxplots represent median (center line), interquartile range (box), and range (whiskers). Differences relative to the MSO control were evaluated using Dunnett-adjusted contrasts (p < 0.05; n = 12–18 per treatment).

Article Snippet: The compound (R)-3-amino-1-hydroxy-3,4-dihydroquinolin-2(1H)-one (PF-04859989) was identified by a high-throughput screen of the Pfizer compound library as a high-affinity inhibitor of human kynurenine aminotransferase (KAT; ).

Techniques: Cell Culture, Control

Journal: bioRxiv

Article Title: Auxin is metabolized through kynurenine in Hypericum perforatum L

doi: 10.64898/2026.05.18.726114

Figure Lengend Snippet: (A–C) Representative extracted ion chromatograms (EICs) of PF-04859989 (A), RO 61-8048 (B), and JM6 (KMO inhibitor II) (C) detected in plant tissue by LC–HRMS. Each panel shows the precursor ion trace at the expected m/z and retention time. (D–F) Relative abundance of PF (D), RO (E), and JM6 (F) in roots and shoots following treatment with MSO (control), inhibitor alone, or IAA + inhibitor. Peak areas are shown as log□□-transformed values. Boxplots represent median (center line), interquartile range (box), and range (whiskers). Signals corresponding to each inhibitor were observed in treated tissues and were not detected in MSO controls. Detection was also observed in IAA co-application treatments.

Article Snippet: The compound (R)-3-amino-1-hydroxy-3,4-dihydroquinolin-2(1H)-one (PF-04859989) was identified by a high-throughput screen of the Pfizer compound library as a high-affinity inhibitor of human kynurenine aminotransferase (KAT; ).

Techniques: Control, Transformation Assay

Journal: bioRxiv

Article Title: Auxin is metabolized through kynurenine in Hypericum perforatum L

doi: 10.64898/2026.05.18.726114

Figure Lengend Snippet: Concentrations of (A, D) kynurenic acid (KYNA), (B, E) kynurenine (KYN), and (C, F) 3-hydroxyanthranilic acid (3-HAA) in shoots (A–C) and roots (D–F) of explants cultured on MSO (control), IAA, or IAA combined with kynurenine pathway inhibitors (IAA + JM6, IAA + PF-04859989, and IAA + RO 61-8048). Concentrations are shown as log□□ (ng g −1 FW). Boxplots represent median (center line), interquartile range (box), and range (whiskers). For shoots (A–C), different letters indicate significant differences among treatments (one-way ANOVA followed by Tukey’s HSD, p < 0.05; n = 3). For roots (D–F), differences relative to the MSO control were evaluated using Dunnett-adjusted contrasts (p < 0.05; n = 3).

Article Snippet: The compound (R)-3-amino-1-hydroxy-3,4-dihydroquinolin-2(1H)-one (PF-04859989) was identified by a high-throughput screen of the Pfizer compound library as a high-affinity inhibitor of human kynurenine aminotransferase (KAT; ).

Techniques: Cell Culture, Control

Journal: bioRxiv

Article Title: Auxin is metabolized through kynurenine in Hypericum perforatum L

doi: 10.64898/2026.05.18.726114

Figure Lengend Snippet: Indole-3-acetic acid (IAA) is primarily synthesized from tryptophan through the indole-3-pyruvate (IPyA) pathway via tryptophan aminotransferase (TAA) and YUCCA flavin monooxygenase (YUC). Free IAA may be regulated through conjugation, catabolism, oxidative transformation and through feedback effects on tryptophan-derived metabolism. Kynurenine pathway metabolism proceeds through N-formyl-kynurenine and kynurenine, which occupies a central branch point between kynurenic acid formation via kynurenine aminotransferase (KAT) and downstream oxidative metabolism toward 3-hydroxyanthranilic acid (3-HAA) via kynurenine monooxygenase (KMO). Reactive oxygen species (ROS), temperature, drought, iron, and Fe 2+ are shown as potential stress and redox inputs that may influence auxin and kynurenine-associated metabolism. The pharmacological inhibitors used in this study are shown at their proposed targets: PF-04859989 at KAT, and RO-61-8048 and JM6 at kynurenine monooxygenase (KMO). Dashed arrows indicate proposed interactions linking auxin catabolism or oxidative transformation with kynurenine-associated metabolite accumulation and potential feedback on tryptophan-dependent auxin biosynthesis.

Article Snippet: The compound (R)-3-amino-1-hydroxy-3,4-dihydroquinolin-2(1H)-one (PF-04859989) was identified by a high-throughput screen of the Pfizer compound library as a high-affinity inhibitor of human kynurenine aminotransferase (KAT; ).

Techniques: Synthesized, Conjugation Assay, Transformation Assay, Derivative Assay