Biology subjects

Häussler, S.

Publications and source records attributed to Häussler, S..

5 recordsLinked to original sources

bioRxiv2025

Cis non-coding genetic variation drives gene expression changes in the E. coli and P. aeruginosa pangenomes

Bacteria use gene regulation to dynamically adapt to changes in their environment, including resistance to stress and the occupation of new niches. Gene expression is known to vary within a species pangenome, but the extent to which these changes could be explained by genetic variants in cis non-coding regions has so far been poorly investigated. Statistical genetics offers a hypothesis-free approach to this problem, as opposed to mechanistic models, which can be used only for reference isolates that are not representative of the whole species. In this study, we assembled two genomic and transcriptomic datasets for Escherichia coli (N=117) and Pseudomonas aeruginosa (N=413) and identified associations between genetic variants in cis non-coding regions and recorded gene expression variation. We identified at least one associated variant in up to 39% of the tested genes in both species. We partly validated the associations in-silico and in-vitro for E. coli, reinforcing the difficulty of identifying a single mechanism generating gene expression diversity. We then investigated the relevance of non-coding variants in explaining the variability in antimicrobial resistance in both species using two additional publicly available datasets, identifying a large number of these variants across antimicrobial compounds. This work confirms the role of genetic variation in often overlooked regions of bacterial genomes in influencing molecular and clinically relevant phenotypes.

microbiology↗

bioRxiv2025

FlashFold: a standalone command-line tool for accelerated protein structure prediction

AlphaFold has revolutionized the decades-old issue of precisely predicting protein structures. However, its high accuracy relies on a computationally intensive step that involves searching vast databases for homologous sequences as the query protein of interest. Additionally, predicting the quaternary structure of protein complexes requires prior knowledge of subunit counts, a prerequisite rarely met. To address these limitations, we introduce FlashFold - a fast, user-friendly tool for protein structure prediction. It accelerates homology searches using a compact built-in database, enabling structure predictions up to 3-fold faster than AlphaFold3, with sacrificing little or no accuracy. Unlike others, FlashFold features adaptable built-in databases that allow users to easily incorporate their own privately sequenced data - an option that can positively influence the prediction accuracy. Moreover, it allows users to estimate stoichiometry of protein complexes directly from sequence information. To support high-throughput workflows and streamline downstream decision-making, it generates interactive and filterable summary reports, enabling users to efficiently visualize protein structures, and interpret large volumes of prediction results. FlashFold runs locally on Linux and Mac, eliminating reliance on third-party servers. FlashFold is available at https://github.com/chayan7/flashfold.

bioinformatics↗

bioRxiv2024

BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis

Bacterial single-cell RNA sequencing has the potential to elucidate within-population heterogeneity of prokaryotes, as well as their interaction with host systems. Despite conceptual similarities, the statistical properties of bacterial single-cell datasets are highly dependent on the protocol, making proper processing essential to tap their full potential. We present BacSC, a fully data-driven computational pipeline that processes bacterial single-cell data without requiring manual intervention. BacSC performs data-adaptive quality control and variance stabilization, selects suitable parameters for dimension reduction, neighborhood embedding, and clustering, and provides false discovery rate control in differential gene expression testing. We validated BacSC on a broad selection of bacterial single-cell datasets spanning multiple protocols and species. Here, BacSC detected subpopulations in Klebsiella pneumoniae, found matching structures of Pseudomonas aeruginosa under regular and low-iron conditions, and better represented subpopulation dynamics of Bacillus subtilis. BacSC thus simplifies statistical processing of bacterial single-cell data and reduces the danger of incorrect processing.

bioinformatics↗

bioRxiv2022

Transcriptome dynamics of Pseudomonas aeruginosa during transition from replication-uncoupled to -coupled growth

In bacteria, either chromosome duplication is coupled to cell division with only one replication round per cell cycle or DNA is replicated faster than the cells divide thus both processes are uncoupled. Here, we show that the opportunistic pathogen Pseudomonas aeruginosa switches from fast uncoupled to sustained coupled growth when cultivated under standard laboratory conditions. The transition was characterized by fast-paced, sequential changes in transcriptional activity along the ori-ter axis of the chromosome reflecting adaptation to the metabolic needs during both growth phases. Quorum sensing (QS) activity was highest at the onset of the coupled growth phase during which only a quarter of the cells keeps replicating. RNA sequencing of subpopulations of these cultures sorted based on their DNA content, revealed a strong gene dosage effect as well as specific expression patterns for replicating and non-replicating cells. Expression of flagella and mexE, involved in multi drug efflux was restricted to cells that did not replicate, while those that did showed a high activity of the cell division locus and recombination genes. A possible role of QS in the formation of these subpopulations upon switching to coupled growth could be a subject of further research. Significance statementThe coordination of gene expression with the cell cycle has so far been studied only in a handful of bacteria, the bottleneck being the need for synchronized cultures. Here, we determined replication-associated effects on transcription by comparing Pseudomonas aeruginosa cultures that differ in their growth mode and number of replicating chromosomes. We further show that cell cycle-specific gene regulation can be principally identified by RNA sequencing of subpopulations from cultures that replicate only once per cell division and that are sorted according to their DNA content. Our approach opens the possibility to study asynchronously growing bacteria from a wide phylogenetic range and thereby enhance our understanding of the evolution of cell-cycle control on the transcriptional level.

microbiology↗

bioRxiv2022

Constitutive production of flagellar proteins is required for proper flagellation in Shewanella putrefaciens

Flagella are multiprotein complexes whose assembly and positioning requires complex spatiotemporal control. Flagellar assembly is thought to be controlled by several transcriptional tiers, which is mediated through various master regulators. Here, we revisited the regulation of flagellar genes in polarly flagellated gammaproteobacteria by the regulators FlrA, RpoN ({sigma}54) and FliA ({sigma}28) in Shewanella putrefaciens CN-32 at the transcript and protein level. As expected, strict control at both levels occurred for for highly abundant flagellar proteins, including the building blocks for the outer rings, rod, hook and filament. In contrast, a number of regulatory and structural proteins were always present also in the absence of the main regulators. Initiation of flagella assembly and motor activation likely relies on the abundance control of only few structural key components required for formation of the MS- and C-ring and the flagellar type III secrection system. We identified {sigma}70-dependent promoters driving constitutive expression of some flagellar genes including the regulators of flagellar number and positioning, FlhF and FlhG. Reduction of the constitutive expression levels resulted in emergence of hyperflagellation. Thus, basal expression and presence of flagellar proteins is required for proper flagellation, which adds a deeper layer to the regulation of flagellar synthesis and assembly. SignificanceThe tier-based transcriptional regulation underlying bacterial flagella synthesis is - with certain variations - well-established in various species. Here we show that initiation and proceeding of flagellar synthesis can be simply based on the control of some key components and highly abundant building blocks. We further identified a 'tier zero, a set of constitutively produced flagellar regulators and building blocks, which is required, for example, to maintain the flagellar counter. We expect this not only to apply to our model species Shewanella, but also to other flagella regulation systems in bacteria.

microbiology↗