Biology subjects

Gockel, P.

Publications and source records attributed to Gockel, P..

3 recordsLinked to original sources

bioRxiv2025

Expanding the iModulon Knowledgebase for Bacillus subtilis: Updated Transcriptome Decomposition Reveals Novel Regulatory Mechanisms

1.The Gram-positive bacterium Bacillus subtilis is widely used as a model organism for studying cell differentiation, microbial physiology and gene regulation. Its genetic accessibility and strong protein secretion machinery make it an excellent host for industrial protein production. Transcriptomics has become an essential tool in understanding these traits and the organisms response to environmental stimuli. Recent advantages in transcriptomics have enabled genome-wide analysis of gene expression patterns under various environmental conditions and genetic perturbations, interpreting such data, however, remains challenging. Independent Component Analysis (ICA) has emerged as a powerful method to decompose bacterial transcriptomes into sets of co-regulated genes - so-called iModulons. In this study, we present an updated iModulon decomposition of Bacillus subtilis transcriptomes, generated from a compendium of 782 high-quality RNAseq samples. This dataset includes a wide range of environmental and genetic conditions. ICA decomposition revealed 142 iModulons, that captured 80% of the expression variance. We compare our version of the modularized B. subtilis transcriptome with previous decompositions and show that the updated composition enhances our understanding of B. subtilis gene regulation and enables novel insights into the organisms regulon structure and gene memberships of the WalR regulon.

systems biology↗

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↗

bioRxiv2020

Bacillus subtilis spore surface display of photodecarboxylase for the transformation of lipids to hydrocarbons

The display of enzymes on the surface of spores allows the rapid and very simple biotechnological production of immobilized enzymes. Here we describe the development of a Bacillus subtilis spore display platform and its application to produce hydrocarbons from lipids obtained from the oleaginous yeasts Yarrowia lipolytica, Cutaneotrichosporon oleaginosus as well as olive oil. Lipid hydrolysis was examined in a bienzymatic one-pot cascade using a commercially immobilized lipase (RO lipase) as well as spores with and without additional heterologous lipase expression. Decarboxylation of the released fatty acids was achieved displaying a photodecarboxylase (CvFAP) on the spore surface. Differences in composition of the formed hydrocarbons were observed depending on the lipids source. Using 3D printed lighting equipment titers of up to 64.0 {+/-} 5.6 mg/L hydrocarbons were produced.

bioengineering↗