Biology subjects

Jagadeesan, R.

Publications and source records attributed to Jagadeesan, R..

8 recordsLinked to original sources

bioRxiv2025

Thermal shifts can override the effects of Transcription-targeting Antibiotics

Bacteria traverse diverse stresses but rarely experience them in isolation. Thermal fluctuations and antibiotic exposure often coincide. Yet, how cells transduce these concurrent cues into gene regulatory programs remains unresolved. Here, we show that in Escherichia coli, cold and heat shocks exert dominance over antibiotic stresses across multiple levels of bacterial physiology. First, combined exposure to antibiotics and thermal shifts produced transcriptomes that consistently converged to temperature-defined transcriptomic states. This dominance emerges through the effects of thermal shifts on metabolism, nucleoid organization, engagement of antibiotic targets with DNA, over-expression of global transcription regulators, drug-target conformational plasticity, and regulatory induction of efflux pathways during combined exposure. Finally, cross-species simulations and phylogenetic analysis revealed that thermal disruption of antibiotic efficiency is conserved across evolutionary distant bacterial species. Together, these results identify temperature as a critical determinant of antibiotic efficacy.

microbiology↗

bioRxiv2025

Single-cell Analysis of Attenuation-Driven Transcription Reveals New Principles of Bacterial Gene Regulation

Transcription attenuation fine-tunes biosynthetic gene expression in bacteria via premature termination upon metabolic signals. In transcription initiation-controlled bacterial systems, promoter architecture and transcription factor binding sets the size of transcriptional bursts at {sigma}70 promoters, while distal enhancer elements and associated transcriptional activators modulate burst frequency at {sigma}54 promoters. Using the tryptophan biosynthesis operon as a model, we show that transcription attenuation, acting post-initiation and alongside transcriptional repression, simultaneously modulates both burst size and frequency from a {sigma}70 promoter. This challenges the view that frequency modulation requires distal enhancer input and reveals that post-initiation mechanisms can shape divergent transcriptional bursting. We also uncover that bacteria use cross-feeding as a previously unrecognised strategy for controlling cell-to-cell variation in gene expression, with implications for metabolic coordination among cells. These findings redefine transcription dynamics within cell populations and suggest new principles by which bacteria regulate gene expression to adapt to environmental change.

microbiology↗

bioRxiv2025

Mechanisms shaping the transcriptome of E. coli to non-lethal rifampicin stress

Rifampicin, by hampering transcription, perturbs bacteria even at non-lethal concentrations. In response, Escherichia coli adapts its phenotype to minimize mortality, which is followed by beneficial mutations. Most genome-wide transcriptional regulatory mechanisms controlling the adaptations remain unidentified. We studied the genome-wide, time-resolved, transcriptional program of susceptible E. coli cells under non-lethal rifampicin stress. Dynamically, the transcriptome widely diverged from the control, but later partially realigned. The mechanisms were changes in RNAP and Gyrase levels, promoter sequences, transcription factor network, intergenic distance, sensitivity to DNA supercoiling buildup, {sigma} factor specificity, (p)ppGpp, and a few global regulators. These results show that the genome-wide response dynamics to rifampicin is influenced by the structure of the gene regulatory network. Next, we compared the evolutionarily distant pathogen Mycobacterium tuberculosis. In both species, adjacent genes on the DNA exhibited similar response strengths. Also, the response strengths of orthologous genes were correlated, suggesting that both species implement similar (likely beneficial) phenotypic adaptations. In support, E. coli orthologs were enriched in the mechanisms identified as influential. Overall, E. coli, and likely other bacteria, have mechanisms influencing specific gene cohort responses to non-lethal rifampicin stress, which likely enhances survivability, thus facilitating the emergence of resistance.

systems biology↗

bioRxiv2024

Isolating the effect of beat salience on rhythmic auditory stimulation outcomes

Rhythmic auditory stimulation (RAS) is an intervention for gait-disordered populations that involves synchronizing footsteps to regular auditory cues. Previous research has shown that high-groove music (music that induces the desire to move or dance to it) improves gait relative to low-groove music, but how this effect occurs is unclear. Greater beat salience in high-groove music may improve gait because salient beats are easier to synchronize with. Here, we manipulated beat salience by embedding metronome tones to emphasize beat onsets in both high- and low-groove music. We expected that, if beat salience drives gait improvements to high-groove music, then embedding metronome in low-groove music would elicit similar gait improvements (e.g. increased stride velocity). Here, we quantified gait synchronization in terms of period-matching (overall step rate to the cue pace) and phase-matching (individual step onsets to beat onsets). We tested a sample of healthy younger and older adults, with auditory cues matched to 10% faster than baseline. Low-groove music with embedded metronome, compared to without, elicited better period-matching; there were no differences between metronome conditions in high-groove music. These findings suggest gait improvements to high-groove music could be due to its high beat salience. On the other hand, embedded metronome did not improve phase-matching accuracy, but high-groove music did. This suggests that beat salience may not improve gait via easing step-to-beat synchronization, but rather through an overall increase in movement vigor.

neuroscience↗

bioRxiv2023

Transcription attenuation in synthetic promoters in tandem formation

Closely spaced promoters are ubiquitous in prokaryotic and eukaryotic genomes. How their structure and dynamics relate remains unclear, particularly for tandem formations. To study their transcriptional interference, we engineered two pairs and one trio of synthetic promoters in non-overlapping, tandem formation, in single-copy plasmids. From in vivo measurements in E. coli cells, we found that promoters in tandem formation have attenuated transcription rates. The attenuation strength can be widely fine-tuned by the promoters positioning, natural regulatory mechanisms, and other factors, including the antibiotic rifampicin, which hampers RNAP promoter escape. From this, and supported by in silico models, we concluded that the attenuation emerges from premature terminations generated by collisions between RNAPs elongating from upstream promoters and RNAPs occupying downstream promoters. Moreover, we found that these collisions can cause one or both RNAPs to fall-off. The broad spectrum of possible, externally regulated, attenuation strengths in synthetic tandem promoters should make these structures valuable internal regulators of future synthetic circuits.

synthetic biology↗

bioRxiv2023

A library of reporters of the global regulators of gene expression of Escherichia coli

The topology of the transcription factor network (TFN) of E. coli is far from uniform, with 22 global regulator (GR) proteins controlling one-third of all genes. So far, their production rates cannot be tracked by comparable fluorescent proteins. We developed a library of fluorescent reporters for 16 GRs for this purpose. Each consists of a single-copy plasmid coding for GFP fused to the full-length copy of the native promoter. We tracked their activity in exponential and stationary growth, as well as under weak and strong stresses. We show that the reporters have high sensitivity and specificity to all stresses tested and detect single-cell variability in transcription rates. Given the influence of GRs on the TFN, we expect that the new library will contribute to dissecting global transcriptional stress-response programs of E. coli. Moreover, the library can be invaluable in bioindustrial applications that tune those programs to, instead of cell growth, favor productivity while reducing energy consumption. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/568972v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@15d7ef4org.highwire.dtl.DTLVardef@139d856org.highwire.dtl.DTLVardef@aa0517org.highwire.dtl.DTLVardef@344a2b_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2023

Dynamics of bacterial operons during genome-wide stresses

Bacterial gene networks have operons, each coordinating several genes under a primary promoter. Half of the operons in Escherichia coli have been reported to also contain internal promoters. We studied their role during genome-wide stresses targeting key transcription regulators, RNAP and gyrase. Our results suggest that operons responses are influenced by stress-related changes in premature elongation terminations and internal promoters activity. Globally, this causes the responses of genes in the same operon to differ with the distance between them in a wavelike pattern. Meanwhile, premature terminations are affected by positive supercoiling buildup, collisions between elongating and promoter-bound RNAPs, and local regulatory elements. We report similar findings in E. coli under other stresses and in evolutionarily distant bacteria Bacillus subtilis, Corynebacterium glutamicum, and Helicobacter pylori. Our results suggest that the strength, number, and positioning of operons internal promoters might have evolved to compensate for premature terminations, providing distal genes similar response strengths.

systems biology↗

bioRxiv2021

Positive supercoiling buildup is a trigger of E. coli's short-term response to cold shock

Adaptation to cold shock (CS) is a key survival skill of gut bacteria of warm-blooded animals. In E. coli, this skill emerges from a complex transcriptional program of multiple, timely-ordered shifts in gene expression. We identified short-term, cold shock repressed (CSR) genes by RNA-seq and provide evidence that their variability in evolutionary fitness is low and that their responsiveness to cold emanates from intrinsic features. Given that their single-cell variability in protein numbers increases after CS, we hypothesized that the responsiveness of a large portion of CSR genes is triggered by the high propensity for transcription locking due to positive supercoiling buildup (PSB). We then proposed a model of this phenomenon and, in support, show that nearly half of CSR genes are highly responsive to Gyrase inhibition. Also, their response strengths to CS and Gyrase inhibition correlate and most CSR genes increase their single-cell variability in protein numbers. Further, during CS, the cells nucleoid density increases (in agreement with increased numbers of positive supercoils), their energy levels become depleted (while the resolving of positive supercoils is ATP dependent), and the colocalization of Gyrases and the nucleoid increases (in agreement with increased time length for resolving supercoils). We conclude that high sensitivity to PSB is at the core of the short-term, cold shock responsive transcriptional program of E. coli and propose that this gene feature may be useful for providing temperature sensitivity to chromosome-integrated synthetic circuits.

systems biology↗