Biology subjects

Erhardt, M.

Publications and source records attributed to Erhardt, M..

At least 19 recordsLinked to original sources

bioRxiv2026

The cost-benefit trade-off of peritrichous flagellation in bacteria

Many bacteria assemble multiple flagella, although building flagella imposes a substantial biosynthetic and energetic cost. We used the peritrichously flagellated model organism Salmonella enterica to quantify how flagellar abundance affects bacterial growth, proteome allocation, and motility. For this, we generated genetically modified strains with inducible or constitutive expression of the flagellar master regulator flhDC, resulting in a panel of strains ranging from nearly non-flagellated to hyperflagellated cells. We found that higher flagellar investment reduced growth rate and redirected proteome allocation, with an expansion of the flagellar sector occurring largely at the expense of the ribosomal sector. Growth analyses of flagellar assembly mutants, combined with cost modeling, suggested that flagellin biosynthesis dominated the energetic burden, whereas motor rotation contributed a smaller additional cost. Despite the associated cost, increased flagellation improved soft-agar spreading, single-cell swimming speed, effective diffusivity, and competitive fitness in spatially structured environments. A coarse-grained proteome-allocation model parametrized from these data reproduced the observed growth penalties, while simulations of navigation in dynamic chemical gradients predicted that motility benefits saturate near a flagellar investment of 3% of proteome mass. Beyond this point, rising biosynthetic costs outweigh diminishing motility gains. In summary, these results support a quantitative cost-benefit model in which heterogeneous, spatially structured environments favor an intermediate number of flagella by balancing motility benefits against the biosynthetic costs of building and operating multiple flagella.

microbiology↗

bioRxiv2026

BactoMate: an integrated platform for reproducible bacterial microscopy analysis

Quantitative microscopy of microorganisms increasingly produces large, multidimensional datasets, yet their analysis often depends on fragmented workflows spanning file conversion, segmentation, quality control, fluorescence quantification, tracking, and visualization. Here, we present BactoMate, an open-source, cross-platform graphical user interface that integrates these steps into a unified workflow for microbial image analysis. BactoMate incorporates established segmentation methods and supports both single-file and batch processing. Its modules enable image preprocessing, cell segmentation, morphology-based quality control, fluorescence and foci quantification, single-cell tracking, lineage reconstruction, structured data export, and generation of quality-control and visualization outputs. We demonstrate the applicability of BactoMate across multichannel fluorescence imaging, bacterial swimming assays, microcolony lineage analysis, phage infection assay and a microfluidic time series. All user-configurable parameters are exposed through the interface, are recorded alongside structured outputs and can be loaded for reproducible image analyses across experiments to reduce introduction of bias. By reducing workflow handoffs while preserving parameter control and exportable results, BactoMate enables accessible, reproducible, and scalable quantitative analysis of microbial microscopy data.

microbiology↗

bioRxiv2026

SigA forms amyloid fibrils and supports the competition of Shigella with the microbiota

Shigella sonnei is an enteropathogen that causes bacillary dysentery. During the first step of its virulence cycle, it must outcompete the resident microbiota to establish its own niche. Here we report that SigA, the sole SPATE (Serine Protease Autotransporter of Enterobacteriaceae) family member in S. sonnei, plays an indirect but central role in this process. A genome-wide analysis showed that the SPATE family includes SigA, Pic, SepA, and Sat. We demonstrated that SigA self-assembles into amyloid fibrils (F-SigA) independently of its protease activity. F-SigA remains associated with the S. sonnei surface in vitro and in vivo. Purified F-SigA fibrils have a diameter of 17.7 {+/-} 3.2 nm, and their amyloid organization was confirmed using specific markers and biochemical methods. F-SigA is secreted into the lumen in vivo and localizes to the surface of the colonic epithelium. We found that colicin E1 (ColE1) interacts with F-SigA amyloid fibrils, and that F-SigA-ColE1 complexes display antimicrobial activity that promotes S. sonnei competition with other bacteria. Because Pic, another Shigella SPATE, also forms amyloid fibrils, we anticipate that this virulence mechanism may be relevant across a wide range of Shigella strains and enterobacteria and may serve additional roles during the Shigella virulence cycle.

microbiology↗

bioRxiv2026

Regulatory memory and growth-coupled inheritance shape nutrient-dependent flagella number variation in Salmonella

Bacteria must balance the advantage of movement against the cost of building flagella, yet how nutrient availability shapes variation in flagellar number across single cells remains unclear. Here, we combine time-resolved basal-body measurements in Salmonella enterica with a mechanistically constrained stochastic model of flagellar remodeling. The model separates two routes from nutrient availability to flagellar number: an RflP-dependent regulatory memory that sets a synthesis target via a latent sensing-memory variable, and a physical inheritance process in which synthesis, binomial partitioning, and division reshape the flagellar-number distribution. Coarse-graining this process yields leaky-integrator dynamics in which the mean flagellar number tracks a regulatory target, while the latent correlation follows acquisition-decay dynamics. In wild-type cells, nutrient-dependent acquisition raises the target and increases flagellar investment; in {Delta}rflP cells, loss of acquisition produces a transient overshoot that isolates the intrinsic decay (memory) timescale of the regulatory state. The fitted model predicts a held-out nutrient condition and reveals which parameter combinations are identifiable from the data. Analysis of the fitted dynamics suggests that precision is tuned primarily by sensing-dependent signal amplitude, rather than integration time, with an apparent [~]1.7-fold increase in effective wild-type noise amplitude after mean normalization, consistent with a precision cost of active regulation relative to the mutant. A model-free, information-geometric (Cramer-Rao) speed limit further shows that active remodeling approaches the statistical speed allowed by the observed distributional variability. Together, these results reveal how Salmonella cells couple regulatory memory with growth-dependent inheritance to record recent nutrient history in their flagellar number.

systems biology↗

bioRxiv2026

Human-restricted Salmonella exploit preassembled flagella for intracellular motility and vacuolar escape

Human-restricted typhoidal Salmonella enterica serovars cause systemic infections known as enteric fever, whereas most non-typhoidal serovars cause self-limiting gastroenteritis. Both groups rely on flagella-mediated motility during intestinal colonization and invasion, yet their intracellular flagellar programs appear to diverge after host cell entry. Non-typhoidal Salmonella are thought to rapidly silence flagellar expression intracellularly, whereas human-restricted S. Paratyphi A maintains flagellar gene expression and uses motility to evade xenophagy. However, the fate and function of flagella assembled before invasion have remained unclear. Here, we used fluorescence microscopy to follow preassembled flagella during epithelial cell invasion across typhoidal and non-typhoidal Salmonella. We show that intracellular bacteria remain flagellated during invasion across epithelial cell lines, serovars, and invasion conditions, indicating that Salmonella do not universally shed or lose preassembled flagella upon host cell entry. We demonstrate that internalized flagella are disassembled within Salmonella-containing vacuoles, whereas cytosolic flagella are targeted by autophagy. We further show that S. Paratyphi A uses flagella assembled before invasion to power intracellular motility and promote escape from the Salmonella-containing vacuole, and that intracellular motility is a phenotype shared by typhoidal Salmonella. Together, these findings reveal that human-restricted Salmonella can exploit preassembled flagella inside host cells as part of an intracellular pathogenic strategy. We propose that intracellular motility represents an adaptation to the human epithelial environment that may promote vacuolar escape and host restriction. ImportanceFlagella are best known for driving bacterial motility before host cell invasion, but their fate and function after intracellular entry remain poorly understood. This study shows that Salmonella do not universally lose their flagella during epithelial cells invasion. Instead, both typhoidal and non-typhoidal Salmonella serovars enter host cells with intact preassembled flagella, but only human-restricted typhoidal serovars use them for intracellular motility. This distinction separates flagellar presence from flagellar function and identifies intracellular motility as a serovar-specific behavior associated with human-restricted systemic disease. The findings suggest that typhoidal Salmonella have adapted to the human epithelial intracellular environment by maintaining a motile state that may promote escape from the Salmonella-containing vacuole and favor cytosolic lifestyle. More broadly, this work reframes flagella not only as extracellular colonization factors but also as intracellular determinants of pathogen behavior, host adaptation, and disease outcome.

microbiology↗

bioRxiv2026

The last bacterial common ancestor encoded a complex flagellum

Bacterial flagella are rotary nanomachines that enable motility in diverse environments. Although more than 40 genes are required to assemble, operate, and regulate a functional flagellum in model organisms, only 24 flagellar genes have previously been inferred to be conserved across bacteria. This discrepancy raises a fundamental question: did the last bacterial common ancestor encode a simpler, partial flagellum that was elaborated later in a lineage-specific manner, or does the apparent absence of conserved components reflect limitations in detecting highly diverged homologs? Here we combine large-scale profile- and sequence-based searches across a comprehensive bacterial genome set with conserved sequence signatures, gene-tree clustering and flagellar gene-neighborhood evidence to reconstruct the ancestral complexity of bacterial flagellar systems. We identify 28 additional flagellar gene families whose distributions and evolutionary histories support an origin before major bacterial diversification, yielding a 52-gene ancestral flagellum. The ancestral flagellum included all proteins of the secretion/export apparatus, basal body, axial components, motor-force generators and regulatory checkpoints required to build and operate a functional, contemporary flagellum. These findings revise models of early bacterial evolution and overturn the notion that the ancestral flagellum was genetically minimal. Instead, they suggest that the last bacterial common ancestor possessed a highly complex flagellar system comprising more components than are typically found in extant bacteria, many of whose flagella appear to have been shaped by lineage-specific gene loss.

microbiology↗

bioRxiv2026

Molecular basis of the Druantia anti-phage defense system

Eukaryotes and prokaryotes have evolved diverse antiviral immune systems, many containing helicase modules central to defense. Druantia are widespread bacterial anti-phage defense systems, each built around a large helicase domain-containing protein, DruE, paired with variable subunits. Here, we investigate the molecular basis of a minimal two-protein module Druantia system, DruH-E. We demonstrate that DruH-E is sufficient to confer robust anti-phage defense. DruE exists in equilibrium between a monomer and an asymmetric dimer, with dimerization required for in vivo immunity. Cryo-EM structures define DruE asymmetric dimer assembly and its dsDNA unwinding mechanism, revealing a topologically closed architecture that is specifically activated by dsDNA substrates with a 3' overhang. We further identify DruH as an ssDNA-binding protein regulated by a metabolic switch, where its activity is inhibited by ATP at physiological concentrations through direct competition with ssDNA. Supported by mass spectrometry and single-cell microscopy data, we establish key determinants of the Druantia defense system and reveal how it mediates a direct antiviral immune mechanism.

microbiology↗

bioRxiv2026

A compact Druantia defense clears phage infections via single-stranded DNA recognition and directional duplex unwinding

Bacteria encode diverse anti-phage defense systems triggered by invader-specific molecular cues. Here, we report that the compact type III-A Druantia system recognizes exposed single-stranded DNA to drive phage clearance. Using representative systems from Escherichia coli, we show that the two encoded proteins, DruE and DruH, together clear restriction-sensitive or recombination-prone phages without affecting cell growth or viability. DruE dimerizes and engages DNA at exposed single-stranded regions to unwind DNA with 3'-to-5' directionality, resorting to unique molecular lock, wedge, and clamp elements that aid strand separation and processive translocation. DruH is a monomer in isolation and indirectly interacts with DruE and other host proteins under uninfected conditions, with an infection resulting in the dissociation of the complex. Taken together, our results reveal that exposed single-stranded DNA can trigger bacterial immunity through the directional helicase activity of type III-A Druantia. HighlightsO_LIThe E. coli Druantia III-A defense, comprising DruE and DruH, clears infecting phages C_LIO_LIDruE dimers bind exposed single-stranded DNA and unwind the upstream DNA duplex C_LIO_LI3'-to-5' DNA unwinding is aided by molecular lock, wedge, and clamp elements C_LIO_LIDruE interacts with DruH and host proteins, which are displaced upon infection C_LI

microbiology↗

bioRxiv2026

Crystal structure of E. coli Nissle 1917 flagellin reveals novel features that modulate bacterial motility but not TLR5 recognition

The probiotic E. coli Nissle 1917 (EcN) strain is known to promote intestinal homeostasis via flagellin, the protomer of its motility apparatus, the flagellum. The flagellin of EcN shows atypical features, namely a hypervariable region (HVR), whose structure and significance have remained elusive. We therefore determined the crystal structure of the E. coli Nissle 1917 flagellin FliC at a resolution of 1.2 [A] which revealed an unusual domain architecture: the canonical D1 domain was found connected by an extended linker to an extensive HVR whose D2, D3 and D4 domains form an outer domain (OD) which surrounds the filament core comprised of conserved domains D0-D1. Using both recombinant proteins and gene-edited EcN strains expressing mutant flagellins, the functional requirement for these unique features was subsequently studied for effects on immune recognition on intestinal epithelial and immune cells, as well as on flagellar protein expression, assembly and bacterial motility. While human and mouse TLR5 immune recognition of flagellar proteins or intact bacteria was only moderately affected by removal of linker or D4, especially linker removal reduced protein stability and bacterial motility in both soft agar and liquid media swimming assays. Interestingly, depending on the environment, D4 or HVR removal had different effects on motility and surface structure. Finally, a site-directed mutagenesis approach highlighted that loss of TLR5 recognition strictly entails loss of motility but not vice versa. Our data indicate that specific HVRs/OD might be relevant for motility of E. coli Nissle 1917 in specialized environments, but not for immune recognition. Moreover, we find mutational tolerance is greater for immune recognition than for motility, providing new insights into bacterial adaptation to the host environment.

microbiology↗

bioRxiv2026

The CUTIN SYNTHASE enzyme family was a key driver of cuticle emergence in land plants

The plant cuticle is a key adaptation acquired during the colonization of land. It forms a hydrophobic barrier at the interface with the environment, fulfilling essential protective and developmental functions. Despite its evolutionary significance and central role in land plant biology, the determinants that drove the emergence of the cuticle remain poorly understood. Here, we show that the CUTIN SYNTHASE (CUS) enzyme family, which synthesises the lipidic polyester that forms the structural framework of the cuticle in flowering plants, originated in a common ancestor of land plants, concomitant with terrestrialization. Using the moss Physcomitrium patens, we further demonstrate that CUS function is conserved among land plants. Inactivation of CUS genes disrupts gametophore development, the first tissue forming a cuticle during the moss life cycle, and compromises cuticle integrity. We also show that P. patens CUS enzymes localize to the apoplast, where they mediate the formation of a 10,16-dihydroxyhexadecanoic acid polyester using 2-mono-(10,16-dihydroxyhexadecanoyl)glycerol as substrate. Overall, our results reveal the conservation of CUS catalytic and physiological functions over 500 million years and support a pivotal role for this enzyme family in the emergence of the cuticle in an ancestral land plant during terrestrialization. SIGNIFICANCEThe cuticle is a hallmark of land plants that fulfills essential roles, ranging from protection to development. Elucidating the mechanisms underlying its emergence and formation therefore has the potential to reveal fundamental aspects of land plant evolution and biology. Here, we show that the CUTIN SYNTHASE (CUS) enzyme family, which catalyzes the formation of the cuticle framework in flowering plants, arose in an ancestor of land plants during terrestrialization. Using the moss Physcomitrium patens, we further demonstrate that CUS function has been conserved for 500 million years across bryophytes and tracheophytes. We propose that the emergence of the CUS family was a key event in establishing the plant cuticle during terrestrialization.

plant biology↗

bioRxiv2025

The FliI ATPase couples ATP hydrolysis to substrate switching in bacterial flagellar type-III secretion

Bacterial flagella are assembled by a specialized type III secretion system that exports structural subunits in a defined order. While the ATPase FliI is known to couple ATP hydrolysis to substrate translocation, its role in the transition between early and late secretion stages has remained unclear. Here, we systematically analyzed Salmonella enterica strains with defined FliI point mutations and found that FliI activity is dispensable for early substrate export and hook-basal body formation but is important for triggering the substrate specificity switch and promoting late substrate export. Mutant strains showed delayed gene expression from class 3 promoters, prolonged early secretion, and impaired flagellar filament assembly, despite normal FliI localization and oligomerization. These findings support the involvement of FliI in controlling the temporal dynamics of flagellar assembly. We propose that FliI contributes to substrate switching, ensuring robust and orderly fT3SS function. This study highlights the multifaceted role of the fT3SS ATPase in optimizing the efficiency and robustness of flagellum assembly. SignificanceThe ordered export of substrates by bacterial type III secretion systems is essential for the assembly of complex surface structures such as the flagellum, yet the mechanisms that control the timing of substrate switching remain poorly understood. The bacterial flagellar ATPase FliI is best known for being involved in energizing the flagellar type III secretion system. Here, we show that FliI contributes to the transition from early to late substrate export during flagellar biogenesis. Using targeted FliI mutants in Salmonella, we show that ATPase activity is dispensable for early export but important for proper substrate switching and late-stage flagellar assembly. These findings highlight the multifaceted roles of FliI during flagellar assembly beyond activating the flagellar type III secretion system.

microbiology↗

bioRxiv2025

Structure of a novel contractile injection system in subsp.

Extracellular contractile injection systems (eCISs) are phage-derived nanomachines used by bacteria to deliver effectors into target cells. Well-studied examples include the Photorhabdus asymbiotica virulence cassettes and the antifeeding prophage from Serratia entomophila, which have been engineered for heterologous cargo delivery. Recent genomic analyses identified previously uncharacterized eCIS gene clusters in the opportunistic human pathogen Salmonella enterica subspecies salamae, but their structure, function, and biotechnological potential remain unexplored. Here, we report a high-resolution cryo-electron microscopy structure of the S. enterica eCIS. Our atomic models reveal a unique sheath architecture, an expansive cage-like shell around a central spike, and an associated transmembrane hydrolase. We identify a putative effector encoded within the operon exhibiting periplasmic toxicity and provide evidence that the S. enterica eCIS deviates from canonical eCISs by interacting with the inner membrane. Guided by these structural features, we uncover a previously unannotated cluster of contractile injection systems (CISs). Together, our findings expand the known diversity of CISs structures and functions and lay the groundwork for engineering customizable protein delivery platforms.

microbiology↗

bioRxiv2025

FliO is an evolutionarily conserved yet diversified core component of the bacterial flagellar type III secretion system

The bacterial flagellum is a complex nanomachine essential for motility, environmental sensing, and host colonization. While many of its core components have been well characterized, the relevance of proteins such as FliO, which are inconsistently annotated and poorly conserved at the sequence level, has remained ambiguous in their evolutionary and functional status. Here, we present a comprehensive phylogenomic and structural analysis of FliO across >30,000 representative genomes spanning >100 bacterial phyla. Additionally, during this analysis, we found that approximately 40% of bacterial genomes contain flagellar genes - significantly fewer than previously reported. Using a custom pipeline combining low-threshold HMM searches, operon context analysis, and structural information, we demonstrate that FliO is present in [~]95% of genomes encoding the core flagellar components FliP, FliQ, and FliR. This suggests that FliO is a nearly ubiquitous and ancestral core component of the flagellar type III secretion system (fT3SS). FliO exhibits considerable structural diversity, including lineage-specific acquisitions of LysM and AMIN domains. We identify FliO homologs not only in canonical flagellar systems but also in some virulence-associated T3SS and even some non-flagellated organisms, suggesting functional repurposing and highlighting its functional plasticity. Functional studies in Campylobacter jejuni reveal that FliO and its AMIN domain are critical for efficient bipolar flagellation, membrane stability of the export gate component FlhB, and colonization of the host. These findings establish FliO as a core, yet evolutionarily dynamic, component of flagella and provide new insights into the evolution and diversification of bacterial secretion systems.

microbiology↗

bioRxiv2024

Structure of the complete extracellular bacterial flagellum reveals mechanism for flagellin incorporation

The bacterial flagellum is essential for motility, adhesion, and colonization in pathogens like Salmonella enterica and Campylobacter jejuni. Its extracellular structure comprises the hook, hook-filament junction, filament, and filament cap. The native structures of the hook-filament junction and the cap remain elusive, leaving the molecular details of cap-mediated filament assembly largely uncharacterized. Here, we report the structure of the complete extracellular flagellum, encompassing the hook, hook-filament junction, filament, and cap. This structure reveals intermediates of filament assembly, providing a molecular blueprint for flagellin folding and insertion at the filament tip. Mutagenesis and functional assays demonstrate the crucial roles of the caps terminal regions in flagellin incorporation, and of the structural integrity of the hook-filament junction. Finally, the structure of the cap and hook-filament junction prior to filament assembly reveals the structural basis for the initiation of filament assembly. Collectively, this study provides comprehensive insights into flagellum assembly and how flagellin incorporation is coupled with its secretion.

microbiology↗

bioRxiv2024

Bacterial motility depends on a critical flagellum length and energy-optimised assembly

The flagellum is the most complex macromolecular structure known in bacteria and comprised of around two dozen distinct proteins. The main building block of the long, external flagellar filament, flagellin, is secreted through the flagellar type-III secretion system at a remarkable rate of several tens of thousands amino acids per second, significantly surpassing the rates achieved by other pore-based protein secretion systems. The evolutionary implications and potential benefits of this high secretion rate for flagellum assembly and function, however, have remained elusive. In this study, we provide both experimental and theoretical evidence that the flagellar secretion rate has been evolutionarily optimized to facilitate rapid and efficient construction of a functional flagellum. By synchronizing flagellar assembly, we found that a minimal filament length of 2.5 {micro}m was required for swimming motility. Biophysical modelling revealed that this minimal filament length threshold resulted from an elasto-hydrodynamic instability of the whole swimming cell, dependent on the filament length. Furthermore, we developed a stepwise filament labeling method combined with electron microscopy visualization to validate predicted flagellin secretion rates of up to 10,000 amino acids per second. A biophysical model of flagellum growth demonstrates that the observed high flagellin secretion rate efficiently balances filament elongation and energy consumption, thereby enabling motility in the shortest amount of time. Taken together, these insights underscore the evolutionary pressures that have shaped the development and optimization of the flagellum and type-III secretion system, illuminating the intricate interplay between functionality and efficiency in assembly of large macromolecular structures. Significance statementOur study demonstrates how protein secretion of the bacterial flagellum is finely tuned to optimize filament assembly rate and flagellum function while minimizing energy consumption. By measuring flagellar filament lengths and bacterial swimming after initiation of flag-ellum assembly, we were able to establish the minimal filament length necessary for swimming motility, which we rationalized physically as resulting from an elasto-hydrodynamic instability of the swimming cell. Our bio-physical model of flagellum growth further illustrates how the physiological flagellin secretion rate is optimized to maximize filament elongation while conserving energy. These findings illuminate the evolutionary pressures that have shaped the function of the bacterial flagellum and type-III secretion system, driving improvements in bacterial motility and overall fitness.

microbiology↗

bioRxiv2024

Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage

AbstractRNA viruses co-opt the host endomembrane system and organelles to build replication complexes for infection. How the host responds to these membrane perturbations is poorly understood. Here, we explore the autophagic response of Arabidopsis thaliana to three viruses that hijack different cellular compartments. Autophagy is significantly induced within systemically infected tissues, its disruption rendering plants highly sensitive to infection. Contrary to being an antiviral defense mechanism as previously suggested, quantitative analyses of the viral loads established autophagy as a tolerance pathway. Further analysis of one of these viruses, the Turnip Crinkle Virus (TCV) that hijack mitochondria, showed that despite perturbing mitochondrial integrity, TCV does not trigger a typical mitophagy response. Instead, TCV and Turnip yellow mosaic virus (TYMV) infection activates a distinct selective autophagy mechanism, where oligomeric metabolic enzymes moonlight as selective autophagy receptors and degrade key executors of defense and cell death such as EDS1. Altogether, our study reveals an autophagy-regulated metabolic rheostat that gauges cellular integrity during viral infection and degrades cell death executors to avoid catastrophic amplification of immune signaling.

plant biology↗

bioRxiv2024

FlhE functions as a chaperone to prevent formation of periplasmic flagella in Gram-negative bacteria

The bacterial flagellum is an organelle utilized by many Gram-negative bacteria to facilitate motility. The flagellum is composed of a several {micro}m long, extracellular filament that is connected to a cytoplasmic rotor-stator complex via a periplasmic rod. Composed of [~]20 structural proteins, ranging from a few subunits to several thousand building blocks, the flagellum is a paradigm of a complex macromolecular structure that utilizes a highly regulated assembly process. This process is governed by multiple checkpoints that ensure an ordered gene expression pattern coupled to the assembly of the various flagellar building blocks in order to produce a functional flagellum. Using epifluorescence, super-resolution STED and transmission electron microscopy, we discovered that in Salmonella, the absence of one periplasmic protein, FlhE, prevents proper flagellar morphogenesis and results in the formation of periplasmic flagella. The periplasmic flagella disrupt cell wall synthesis, leading to a loss of the standard cell morphology resulting in cell lysis. We propose a model where FlhE functions as a periplasmic chaperone to control assembly of the periplasmic rod to prevent formation of periplasmic flagella. Our results highlight that bacteria evolved sophisticated regulatory mechanisms to control proper flagellar assembly and minor deviations from this highly regulated process can cause dramatic physiological consequences.

microbiology↗

bioRxiv2024

Fluorescent tools for the standardized work in Gram-negative bacteria

Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 16 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using super-resolution microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in gram- negative bacteria and beyond.

microbiology↗