Biology subjects

Sigrist, R.

Publications and source records attributed to Sigrist, R..

3 recordsLinked to original sources

bioRxiv2024

Maramycin, a cytotoxic isoquinolinequinone terpenoid produced through heterologous expression of a bifunctional indole prenyltransferase /tryptophan indole-lyase in S. albidoflavus

Isoquinolinequinones represent an important family of natural alkaloids with profound biological activities. Heterologous expression of a rare bifunctional indole prenyltransferase /tryptophan indole-lyase enzyme from Streptomyces mirabilis P8-A2 in S. albidoflavus J1074 led to the activation of a putative isoquinolinequinone biosynthetic gene cluster and production of a novel isoquinolinequinone alkaloid, named maramycin (1). The structure of maramycin was determined by analysis of spectroscopic (1D/2D NMR) and MS spectrometric data. The prevalence of this bifunctional biosynthetic enzyme was explored and found to be a recent evolutionary event with only a few representatives in Nature. Maramycin exhibited moderate cytotoxicity against human prostate cancer cell lines, LNCaP and C4-2B. The discovery of maramycin (1) enriched the chemical diversity of natural isoquinolinequinones and also provided new insights into crosstalk between the host biosynthetic genes and the heterologous biosynthetic genes in generating new chemical scaffolds.

bioengineering↗

bioRxiv2024

Machine Learning Uncovers the Transcriptional Regulatory Network for the Production Host Streptomyces albidoflavus J1074

Streptomyces albidoflavus is a popular and genetically tractable platform strain used for natural product discovery and production via the expression of heterologous biosynthetic gene clusters (BGCs). However, its transcriptional regulatory network (TRN) and its impact on secondary metabolism is poorly understood. Here we characterized its TRN by applying an independent component analysis to a compendium of 218 high quality RNA-seq transcriptomes from both in-house and public sources spanning 88 unique growth conditions. We obtained 78 independently modulated sets of genes (iModulons) that quantitatively describe the TRN and its activity state across diverse conditions. Through analyses of condition-dependent TRN activity states, we (i) describe how the TRN adapts to different growth conditions, (ii) conduct a cross-species iModulon comparison, uncovering shared features and unique characteristics of the TRN across lineages, (iii) detail the transcriptional activation of several endogenous BGCs, including surugamide, minimycin and paulomycin, and (iv) infer potential functions of 40% of the uncharacterized genes in the S. albidoflavus genome. Our findings provide a comprehensive and quantitative understanding of the TRN of S. albidoflavus, providing a knowledge base for further exploration and experimental validation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/574332v3_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1a7d0aorg.highwire.dtl.DTLVardef@10750eborg.highwire.dtl.DTLVardef@1518644org.highwire.dtl.DTLVardef@145f5b4_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

CASCADE-Cas3 Enables Highly Efficient Genome Engineering in Streptomyces Species

Type I CRISPR systems are widespread in bacteria and archaea. The main differences compared to more widely applied type II systems are multi-effector CASCADE needed for crRNA processing and target recognition, as well as the processive nature of the hallmark nuclease Cas3. Given the widespread nature of type I systems, the processive nature of Cas3, as well as the recombinogenic overhangs created by Cas3, we hypothesized that Cas3 would be uniquely positioned to enable efficient genome engineering in streptomycetes. Here, we report a new type I based CRISPR genome engineering tool for streptomycetes. The plasmid system, called pCRISPR-Cas3, utilizes a compact type I-C CRISPR system and enables highly efficient genome engineering. pCRISPR-Cas3, outperforms pCRISPR-Cas9 and facilitates targeted and random sized deletions, as well as substitutions of large genomic regions such as biosynthetic gene clusters. Without additional modifications, pCRISPR-Cas3 enabled genome engineering in several Streptomyces species at high efficiencies.

synthetic biology↗