Biology subjects

Schnetz, K.

Publications and source records attributed to Schnetz, K..

3 recordsLinked to original sources

bioRxiv2026

Context-dependent regulation of RpoS-dependent and RpoS-independent gene transcription by Crl during exponential growth in Escherichia coli

RpoS, an alternative sigma factor, directly regulates approximately 10% of gene transcription in E. coli. The small protein Crl functions as a partner that assists RpoS in exerting its regulatory role, particularly during the stationary phase. However, the coordinating role of Crl during the exponential phase remains unclear. In addition, whether Crl can regulate gene transcription independently of RpoS is still unknown. Therefore, in this study, we used the RpoS-dependent operon hdeAB and the RpoS-independent operon proVWX as model systems to investigate the transcriptional regulatory function of Crl using RT-qPCR and 3C-qPCR. Since the expression of both Crl and RpoS is modulated by environmental signals, we further examined the transcription of these operons under different pH and osmotic conditions. The results showed that Crl can regulate transcription independently of RpoS and exhibits environment-specific bidirectional regulation. Overall, this study improves our understanding of the regulatory mechanisms of Crl and highlights the complexity of transcriptional regulation.

microbiology↗

bioRxiv2026

Adaptive gene transcription in Escherichia coli under environmental stress

Escherichia coli is highly sensitive to acid and osmotic stress but adapts by modulating the expression of stress responsive genes. Nucleoid-associated proteins (NAPs) play key roles in DNA organization and sensing environmental changes. The histone-like nucleoid structuring protein H-NS is an NAP acting as a global regulator of stress genes. H-NS may alter local chromatin structure to modulate the expression of such genes in response to environmental stress. The H-NS homolog StpA co-regulates several target genes, but its precise role is poorly defined. To investigate the regulatory interplay between these two proteins, we examined transcription, DNA binding and chromatin structure at two regulated operons, hdeAB and proVWX, in E. coli following exposure to acid and salt shock. Our results show that H-NS senses pH and osmotic cues to remodel chromatin and relieve repression, while StpA compensates for H-NS loss, particularly at proVWX, highlighting a coordinated regulatory network.

microbiology↗

bioRxiv2022

High abundance of transcription regulators compacts the nucleoid in Escherichia coli

In enteric bacteria organization of the circular chromosomal DNA into a highly dynamic and toroidal shaped nucleoid involves various factors such as DNA supercoiling, nucleoid-associated proteins (NAPs), the structural maintenance of chromatin (SMC) complex, and macro-domain organizing proteins. Here we show that ectopic expression of transcription regulators at high levels leads to nucleoid compaction. This serendipitous result was obtained by fluorescence microscopy upon ectopic expression of the transcription regulator and phosphodiesterase PdeL of Escherichia coli of a strain expressing the mCherry-tagged HU- subunit (HupA) for nucleoid staining. Nucleoid compaction by PdeL depends on DNA-binding, but not on its enzymatic phosphodiesterase activity. Nucleoid compaction was also observed upon high-level ectopic expression of the transcription regulators LacI, RutR, RcsB, LeuO and Cra, which range from single target gene regulators to global regulators. In case of LacI its high-level expression in presence of the gratuitous inducer IPTG also led to nucleoid compaction indicating that compaction is caused by unspecific DNA-binding. In all cases nucleoid compaction correlated with misplacement of the FtsZ ring and loss of MukB foci, a subunit of the SMC complex. Thus, high levels of several transcription regulators cause nucleoid compaction with consequences on transcription, replication, and cell division. ImportanceThe bacterial nucleoid is a highly organized and dynamic structure for simultaneous, transcription, replication and segregation of the bacterial genome. Compaction of the nucleoid and disturbance of DNA segregation and cell division by artificially high levels of transcription regulators, as described here, reveals that an excess of DNA-binding protein disturbs nucleoid structuring. The results suggest that ectopic expression levels of DNA-binding proteins for genetic studies of their function but also for their purification should be carefully controlled and adjusted.

microbiology↗