Splitsville: structural and functional insights into the dynamic bacterial Z ring

The juxtamembrane domain of StkP is phosphorylated and influences cell division in Streptococcus pneumoniae

Eukaryotic-like membrane Ser/Thr protein kinases play a pivotal role in different aspects of bacterial physiology. In contrast to the diversity of their extracellular domains, their cytoplasmic catalytic domains are highly conserved. However, the function of a long juxtamembrane domain (JMD), which connects the catalytic domain to the transmembrane helix, remains elusive. In this study, we investigated the function of the JMD of the Ser/Thr protein kinase StkP in the cell division of Streptococcus pneumoniae. We observed that the deletion of the JMD affected the ability of StkP to phosphorylate some of its endogenous substrates, thereby resulting in significant cell morphogenesis defects. Furthermore, multiple threonine residues were identified as being phosphorylated in the JMD. To investigate the functional significance of these phosphorylation sites, we conducted an integrative analysis, combining structural biology, proteomics, and bacterial cell imaging. Our results revealed that the phosphorylation of the JMD did not perturb the phosphorylation of StkP substrates. However, we observed that it modulated the timing of StkP localization to the division septum and the dynamics of cell constriction. We further demonstrated that phosphorylation of the JMD facilitated the recruitment of several cell division proteins, suggesting that it is required to assemble the division machinery at the division septum. In conclusion, this study demonstrates that the function of the JMD of StkP is modulated by phosphorylation and is critical for the cell division of S. pneumoniae. These observations may serve as a model for understanding the regulatory function of other bacterial Ser/Thr protein kinases.IMPORTANCEHow bacterial serine/threonine protein kinases are activated remains highly debated. In particular, models rely on the observations made with their eukaryotic counterparts, and only a few studies have investigated the molecular activation mechanism of bacterial serine/threonine protein kinases. This is particularly the case with regard to the juxtamembrane domain (JMD), which is proposed to contribute to kinase activation in numerous eukaryotic kinases. This study demonstrates that the juxtamembrane domain is likely not essential for the activation of the serine/threonine protein kinase StkP of S. pneumoniae. Rather, our findings reveal that it is required for cell division, where its phosphorylation affects the assembly of the division machinery at the division septum. These observations allow us to assign a function to the JMD in StkP-mediated regulation of pneumococcal cell division, thereby providing a new avenue for understanding the contribution of membrane serine/threonine protein kinases in the physiology of other bacteria.

Combining live fluorescence imaging with in situ cryoelectron tomography sheds light on the septation process in Deinococcus radiodurans

Cell division is a fundamental biological process that allows a single mother cell to produce two daughter cells. In walled bacteria, different modes of cell division have been reported that are notably associated with distinctive cell shapes. In all cases, division involves a step of septation, corresponding to the growth of a new dividing cell wall, followed by splitting of the two daughter cells. The radiation-resistant Deinococcus radiodurans is a spherical bacterium protected by a thick and unusual cell envelope. It has been reported to divide using a distinctive mode of septation in which two septa originating from opposite sides of the cell progress with a flat leading edge until meeting and fusing at mid-cell. In the present study, we have combined conventional and superresolution fluorescence microscopy of live bacteria with in situ cryogenic electron tomography of bacterial lamellae to investigate the septation process in D. radiodurans. This work provides important insight into i) the complex architecture and multilayered composition of the cell envelope of this bacterium, ii) the unusual "sliding doors" septation process and iii) the sequence of events and molecular mechanisms underlying septal closure, including the synthesis of a FtsZ-dependent peptidoglycan layer that rigidifies and straightens the growing septa.

Bacterial extracellular vesicles target different bacterial species, impairing cell division and diminishing their pathogenicity

Extracellular vesicles (EVs) produced by bacteria contain many bacterial-derived molecules, which play an important role in host interactions and as mediators of bacterial communication. However, the role of EVs in interspecies interactions and their physiological and ecological significance are not well understood. In this study, we found that Escherichia coli EVs inhibit the growth of group A Streptococcus (GAS; Streptococcus pyogenes) by inducing defective cell division via the following processes. E. coli EVs first attach to the cell surface of GAS. In EV-attached GAS cells, multiple septa and Z-rings form in close proximity, which clearly differs from the typical cell division process. This is due to inhibition of peptidoglycan (PG) remodeling in the process after septum formation, in which the next cell division is initiated without completion of peripheral PG synthesis. Therefore, cell division proceeds while inducing cell elongation and cell separation failure, leading to growth inhibition. Furthermore, EV alters the expression of approximately 10% of all genes encoded on the GAS genome, and the diverse functions of these gene sets, which include replication, division, and metabolism, suggest that EVs have a variety of biological effects on the targeted bacterial cells. Notably, E. coli EVs significantly decreased the expression of genes involved in representative GAS virulence, such as slo, nga, and hasA, and also markedly attenuated the pathogenicity of GAS in mice. Our findings provide insight into the competitive functions of EVs between different bacterial species, expanding current knowledge on EV-mediated interspecies interactions.

Antibacterial Effect and Mechanism of Chelerythrine on Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) is a biotrophic bacterial pathogen, which causes devastating bacterial blight disease worldwide. In this study, we thoroughly investigated the antimicrobial effect of the plant-derived extract chelerythrine against Xanthomonas oryzae pv. oryzae (Xoo) and elucidated its mechanism. Chelerythrine is a quaternary ammonium alkaloid with a 2,3,7,8-tetrasubstituted phenanthridine structure, extracted from plants, such as the whole plant of Chelidonium majus, and the roots, stems, and leaves of Macleaya cordata. We found that chelerythrine significantly inhibited the growth of Xoo at a concentration of 1.25 μg/mL. Further experiments revealed that chelerythrine interfered with the division and reproduction of the bacterium, leading to its filamentous growth. Additionally, it increased the permeability of Xoo cell membranes and effectively decreased the pathogenicity of Xoo, including the inhibition of extracellular polysaccharide production, cellulase secretion, and biofilm formation. Chelerythrine induced the accumulation of reactive oxygen species in the bacterium, triggering oxidative stress. The result showed that chelerythrine inhibited the formation of the Z-ring of Xoo, interfered with the synthesis of pyrimidine and purine nucleotides, inhibited DNA damage repair, and inhibited the formation of peptidoglycan and lipid-like A, thus interfering with cell membrane permeability, inhibiting carbohydrate metabolism and phosphorylation of sugars, reducing pathogenicity, and ultimately inhibiting bacterial growth and leading to the destruction or lysis of bacterial cells. Altogether, our results suggest that the antimicrobial effect of chelerythrine on Xoo exhibits multi-target properties. Additionally, its effective inhibitory concentration is low. These findings provide a crucial theoretical basis and guidance for the development of novel and efficient plant-derived antimicrobial compounds.

Study of the antimicrobial activity of carvacrol and its mechanism of action against drug-resistant bacteria

Drug-resistant bacterial infections have been one of the critical health issues encountered worldwide currently because most conventional antibiotics are losing their effectiveness in clinical treatments. It is thus urgently to identify new antibiotics or alternatives against drug-resistant bacteria. For this purpose, we attempted to seek active compounds from commercially available natural products, which may be one of the fast-tracks to address the drug-resistant bacterial infections. In the present study, we investigated the antibacterial activity, antibacterial mechanism and synergistic effects of carvacrol against a panel of drug-resistant bacteria, including some clinical isolates. The results show that carvacrol (cymophenol), a monoterpenoid phenol, has excellent antibacterial activity. The MIC values against the bacteria examined are found to be 4-16 μg/mL. Our results also suggested that carvacrol might not likely to induce drug-resistance. More importantly, when carvacrol combined with first-line antibiotics, it exhibited good synergistic effects against drug-resistant bacteria. Moreover, in morphological studies, carvacrol could cause B. subtilis 168 elongation and S. aureus BAA-41 enlargement, which may suggest an antibacterial mechanism possibly correlated with the inhibition of bacterial cell division. We further demonstrated that carvacrol facilitated the polymerization of FtsZ that is a critically important protein for regulating bacterial cell division. Furthermore, molecular modeling predicted that carvacrol could interact with T7-loop of FtsZ. The findings of this study suggest that carvacrol may be a potential inhibitor of FtsZ and it could be utilized to combat drug-resistant bacteria in combination with existing antibiotics.

MdfA is a novel ClpC adaptor protein that functions in the developing Bacillus subtilis spore

Bacterial protein degradation machinery consists of chaperone-protease complexes that play vital roles in bacterial growth and development and have sparked interest as novel antimicrobial targets. ClpC-ClpP (ClpCP) is one such chaperone-protease complex, recruited by adaptors to specific functions in the model bacterium Bacillus subtilis and other Gram-positive bacteria, including the pathogens Staphylococcus aureus and Mycobacterium tuberculosis Here we have identified a new ClpCP adaptor protein, MdfA (metabolic differentiation factor A; formerly YjbA), in a genetic screen for factors that help drive B. subtilis toward metabolic dormancy during spore formation. A knockout of mdfA stimulates gene expression in the developing spore, while aberrant expression of mdfA during vegetative growth is toxic. MdfA binds directly to ClpC to induce its oligomerization and ATPase activity, and this interaction is required for the in vivo effects of mdfA Finally, a cocrystal structure reveals that MdfA binds to the ClpC N-terminal domain at a location analogous to that on the M. tuberculosis ClpC1 protein where bactericidal cyclic peptides bind. Altogether, our data and that of an accompanying study by Riley and colleagues support a model in which MdfA induces ClpCP-mediated degradation of metabolic enzymes in the developing spore, helping drive it toward metabolic dormancy.

Microscopic origin of the spatial and temporal precision in biological systems

All living systems display remarkable spatial and temporal precision, despite operating in intrinsically fluctuating environments. It is even more surprising given that biological phenomena are regulated by multiple chemical reactions that are also random. Although the underlying molecular mechanisms of surprisingly high precision in biology remain not well understood, a novel theoretical picture that relies on the coupling of relevant stochastic processes has recently been proposed and applied to explain different phenomena. To illustrate this approach, in this review, we discuss two systems that exhibit precision control: spatial regulation in bacterial cell size and temporal regulation in the timing of cell lysis by λ bacteriophage. In cell-size regulation, it is argued that a balance between stochastic cell growth and cell division processes leads to a narrow distribution of cell sizes. In cell lysis, it is shown that precise timing is due to the coupling of holin protein accumulation and the breakage of the cellular membrane. The stochastic coupling framework also allows us to explicitly evaluate dynamic properties for both biological systems, eliminating the need to utilize the phenomenological concept of thresholds. Excellent agreement with experimental observations is observed, supporting the proposed theoretical ideas. These observations also suggest that the stochastic coupling method captures the important aspects of molecular mechanisms of precise cellular regulation, providing a powerful new tool for more advanced investigations of complex biological phenomena.

Bacteriophage P1 protein Icd inhibits bacterial division by targeting FtsZ

The study of bacteriophage (phage) gene products and their effects on the host helps to better understand the phage-host relationship and provides clues for the development of new antimicrobial proteins. In this study, we focused on a small protein named Icd with 73 amino acids from phage P1. It inhibits the growth of Escherichia coli and rapidly blocks the formation of Z-ring. The results of bacterial two-hybrid and pull-down experiments showed that Icd directly targets FtsZ, a key protein in bacterial division. Furthermore, we identified the core region of Icd as amino acids 12-51; this 40-amino acid protein had similar antibacterial activity to the full-length Icd, inhibiting bacterial growth and division.

Multiscale modelling of active hydrogel elasticity driven by living polymers: softening by bacterial motor protein FtsZ

We present a neo-Hookean elasticity theory for hybrid mechano-active hydrogels, integrating motor proteins into polymer meshes to create composite materials with active softening due to modulable chain overlaps. Focusing on polyacrylamide (PA) hydrogels embedded with FtsZ, a bacterial cytokinetic protein powered by GTP, we develop a multiscale model using microscopic Flory theory of rubbery meshes through mesoscopic De Gennes' scaling concepts for meshwork dynamics and phenomenological Landau's formalism for second-order phase transitions. Our theoretical multiscale model explains the active softening observed in hybrid FtsZ-PA hydrogels by incorporating modulable meshwork dynamics, such as overlapping functionality and reptation dynamics, into an active mean-field of unbinding interactions. The novel FtsZ-based metamaterial and companion multiscale theory offer insights for designing, predicting, and controlling complex active hydrogels, with potential applications in technology and biomedicine.

Targeting Bacterial Cell Division with Benzodioxane-Benzamide FtsZ Inhibitors as a Novel Strategy to Fight Gram-Positive Ovococcal Pathogens

The widespread emergence of antimicrobial resistance (AMR) is a serious threat to global public health and among Gram-positive cocci, Streptococcus pneumoniae constitutes a priority in the list of AMR-threatening pathogens. To counteract this fundamental problem, the bacterial cell division cycle and the crucial proteins involved in this process emerged as novel attractive targets. FtsZ is an essential cell division protein, and FtsZ inhibitors, especially the benzamide derivatives, have been exploited in the last decade. In this work, we identified, for the first time, some benzodioxane-benzamide inhibitors capable of targeting FtsZ in Streptococcus pneumoniae, in addition to their previously demonstrated activity against other bacteria. These promising benzamides, with minimal inhibitory concentrations (MICs) ranging from 25 to 80 µg/mL, demonstrated bactericidal activity against S. pneumoniae. This was evidenced by their ability to dramatically affect growth and viability, further supported by the morphological changes observed through microscopy. Moreover, the compounds were characterized in vitro, combining turbidity measurements and confocal imaging, and significant alteration of a GTP-induced FtsZ assembly was found, in line with our previous data from other microorganisms.

GpsB interacts with FtsZ in multiple species and may serve as an accessory Z-ring anchor

Bacterial cytokinesis commences when a tubulin-like GTPase, FtsZ, forms a Z-ring to mark the division site. Synchronized movement of Z-ring filaments and peptidoglycan synthesis along the axis of division generates a division septum to separate the daughter cells. Thus, FtsZ needs to be linked to the peptidoglycan synthesis machinery. GpsB is a highly conserved protein among species of the Firmicutes phylum known to regulate peptidoglycan synthesis. Previously, we showed that Staphylococcus aureus GpsB directly binds to FtsZ by recognizing a signature sequence in its C-terminal tail (CTT) region. As the GpsB recognition sequence is also present in Bacillus subtilis, we speculated that GpsB may interact with FtsZ in this organism. Earlier reports revealed that disruption of gpsB and ftsA or gpsB and ezrA is deleterious. Given that both FtsA and EzrA also target the CTT of FtsZ for interaction, we hypothesized that in the absence of other FtsZ partners, GpsB-FtsZ interaction may become apparent. Our data confirm that is the case, and reveal that GpsB interacts with FtsZ in multiple species and stimulates the GTPase activity of the latter. Moreover, it appears that GpsB may serve as an accessory Z-ring anchor such as when FtsA, one of the main anchors, is absent.

Tubules, Rods, and Spirals: Diverse Modes of SepF-FtsZ Assembling

Z-ring formation by FtsZ, the master assembler of the divisome, is a key step in bacterial cell division. Membrane anchoring of the Z-ring requires the assistance of dedicated Z-ring binding proteins, such as SepF and FtsA. SepF participates in bundling and membrane anchoring of FtsZ in gram-positive bacteria. We report in vitro biophysical studies of the interactions between FtsZ and a cytoplasmic component of cognate SepF from three different bacteria: Mycobacterium tuberculosis, Staphylococcus aureus, and Enterococcus gallinarum. While the cytosolic domain of SepF from M. tuberculosis is primarily a dimer, those from S. aureus and E. gallinarum polymerize to form ring-like structures. Mycobacterial SepF helps in the bundling of FtsZ filaments to form thick filaments and large spirals. On the other hand, ring-forming SepF from the Firmicutes bundle FtsZ into tubules. Our results suggest that the oligomeric form of SepF directs how it bundles FtsZ filaments.

Spatio-temporal organization of the E. coli chromosome from base to cellular length scales

Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.

Determining the rate-limiting processes for cell division in Escherichia coli

A critical cell cycle checkpoint for most bacteria is the onset of constriction when the septal peptidoglycan synthesis starts. According to the current understanding, the arrival of FtsN to midcell triggers this checkpoint in Escherichia coli. Recent structural and in vitro data suggests that recruitment of FtsN to the Z-ring leads to a conformational switch in actin-like FtsA, which links FtsZ protofilaments to the cell membrane and acts as a hub for the late divisome proteins. Here, we investigate this putative pathway using in vivo measurements and stochastic cell cycle modeling at moderately fast growth rates. Quantitatively upregulating protein concentrations and determining the resulting division timings shows that FtsN and FtsA numbers are not rate-limiting for the division in E. coli. However, at higher overexpression levels, they affect divisions: FtsN by accelerating and FtsA by inhibiting them. At the same time, we find that the FtsZ numbers in the cell are one of the rate-limiting factors for cell divisions in E. coli. Altogether, these findings suggest that instead of FtsN, accumulation of FtsZ in the Z-ring is one of the main drivers of the onset of constriction in E. coli at faster growth rates.

A unique cell division protein critical for the assembly of the bacterial divisome

Identification of unique essential bacterial genes is important for not only the understanding of their cell biology but also the development of new antimicrobials. Here, we report a previously unrecognized core component of the Acinetobacter baumannii divisome. Our results reveal that the protein, termed Aeg1 interacts with multiple cell division proteins, including FtsN, which is required for components of the divisome to localize to the midcell. We demonstrate that the FtsAE202K and FtsBE65A mutants effectively bypassed the need of Aeg1 by A. baumannii, as did the activation variants FtsWM254I and FtsWS274G. Our results suggest that Aeg1 is a cell division protein that arrives at the division site to initiate cell division by recruiting FtsN, which activates FtsQLB and FtsA to induce the septal peptidoglycan synthase FtsWI. The discovery of the new essential cell division protein has provided a new target for the development of antibacterial agents.

Disruption of salt bridge interactions in the inter-domain cleft of the tubulin-like protein FtsZ of Escherichia coli makes cells sensitive to the cell division inhibitor PC190723

FtsZ forms a ring-like assembly at the site of division in bacteria. It is the first protein involved in the formation of the divisome complex to split the cell into two halves, indicating its importance in bacterial cell division. FtsZ is an attractive target for developing new anti-microbial drugs to overcome the challenges of antibiotic resistance. The most potent inhibitor against FtsZ is PC190723, which is effective against all strains and species of Staphylococcus, including the methicillin- and multi-drug-resistant Staphylococcus aureus and strains of Bacillus. However, FtsZs from bacteria such as E. coli, Streptococcus, and Enterococcus were shown to be resistant to this inhibitor. In this study, we provide further evidence that the three pairwise bridging interactions, between residues S227 and G191, R307 and E198 and D299 and R202, between S7, S9, S10 β-strands and the H7 helix occlude the inhibitor from binding to E. coli FtsZ. We generated single, double and triple mutations to disrupt those bridges and tested the effectiveness of PC190723 directly on Z-ring assembly in vivo. Our results show that the disruption of S227-G191 and R307-E198 bridges render EcFtsZ highly sensitive to PC190723 for Z-ring assembly. Ectopic expression of the double mutants, FtsZ S227I R307V results in hypersensitivity of the susceptible E. coli imp4213 strain to PC190723. Our studies could further predict the effectiveness of PC190723 or its derivatives towards FtsZs of other bacterial genera.

Architectural underpinnings of stochastic intergenerational homeostasis

Living systems are naturally complex and adaptive and offer unique insights into the strategies for achieving and sustaining stochastic homeostasis in different conditions. Here we focus on homeostasis in the context of stochastic growth and division of individual bacterial cells. We take advantage of high-precision long-term dynamical data that have recently been used to extract emergent simplicities and to articulate empirical intra- and intergenerational scaling laws governing these stochastic dynamics. From these data, we identify the core motif in the mechanistic coupling between division and growth, which naturally yields these precise rules, thus also bridging the intra- and intergenerational phenomenologies. By developing and utilizing techniques for solving a broad class of first-passage processes, we derive the exact analytic necessary and sufficient condition for sustaining stochastic intergenerational cell-size homeostasis within this framework. Furthermore, we provide predictions for the precision kinematics of cell-size homeostasis and the shape of the interdivision time distribution, which are compellingly borne out by the high-precision data. Taken together, these results provide insights into the functional architecture of control systems that yield robust yet flexible stochastic homeostasis.

Bacterial cell volume regulation and the importance of cyclic di-AMP

SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.

Inhibitor of Chromosome Segregation in Pseudomonas aeruginosa from Fungal Extracts

Chromosome segregation is an essential cellular process that has the potential to yield numerous targets for drug development. This pathway is presently underutilized partially due to the difficulties in the development of robust reporter assays suitable for high throughput screening. In bacteria, chromosome segregation is mediated by two partially redundant systems, condensins and ParABS. Based on the synthetic lethality of the two systems, we developed an assay suitable for screening and then screened a library of fungal extracts for potential inhibitors of the ParABS pathway, as judged by their enhanced activity on condensin-deficient cells. We found such activity in extracts of Humicola sp. Fractionation of the extract led to the discovery of four new analogues of sterigmatocystin, one of which, 4-hydroxy-sterigmatocystin (4HS), displayed antibacterial activity. 4HS induced the phenotype typical for parAB mutants including defects in chromosome segregation and cell division. Specifically, bacteria exposed to 4HS produced anucleate cells and were impaired in the assembly of the FtsZ ring. Moreover, 4HS binds to purified ParB in a ParS-modulated manner and inhibits its ParS-dependent CTPase activity. The data describe a small molecule inhibitor of ParB and expand the known spectrum of activities of sterigmatocystin to include bacterial chromosome segregation.

Antibacterial insights into alternariol and its derivative alternariol monomethyl ether produced by a marine fungus

Alternaria alternata FB1 is a marine fungus identified as a candidate for plastic degradation in our previous study. This fungus has been recently shown to produce secondary metabolites with significant antimicrobial activity against various pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and the notorious aquaculture pathogen Vibrio anguillarum. The antibacterial compounds were purified and identified as alternariol (AOH) and its derivative, alternariol monomethyl ether (AME). We found that AOH and AME primarily inhibited pathogenic bacteria (MRSA or V. anguillarum) by disordering cell division and some other key physiological and biochemical processes. We further demonstrated that AOH could effectively inhibit the unwinding activity of MRSA topoisomerases, which are closely related to cell division and are the potential action target of AOH. The antibacterial activities of AOH and AME were verified by using zebrafish as the in vivo model. Notably, AOH and AME did not significantly affect the viability of normal human liver cells at concentrations that effectively inhibited MRSA or V. anguillarum. Finally, we developed the genetic operation system of A. alternata FB1 and blocked the biosynthesis of AME by knocking out omtI (encoding an O-methyl transferase), which facilitated A. alternata FB1 to only produce AOH. The development of this system in the marine fungus will accelerate the discovery of novel natural products and further bioactivity study.IMPORTANCEMore and more scientific reports indicate that alternariol (AOH) and its derivative alternariol monomethyl ether (AME) exhibit antibacterial activities. However, limited exploration of their detailed antibacterial mechanisms has been performed. In the present study, the antibacterial mechanisms of AOH and AME produced by the marine fungus Alternaria alternata FB1 were disclosed in vitro and in vivo. Given their low toxicity on the normal human liver cell line under the concentrations exhibiting significant antibacterial activity against different pathogens, AOH and AME are proposed to be good candidates for developing promising antibiotics against methicillin-resistant Staphylococcus aureus and Vibrio anguillarum. We also succeeded in blocking the biosynthesis of AME, which facilitated us to easily obtain pure AOH. Moreover, based on our previous results, A. alternata FB1 was shown to enable polyethylene degradation.

Adaptive evolution of chloroplast division mechanisms during plant terrestrialization

Despite extensive research, the origin and evolution of the chloroplast division machinery remain unclear. Here, we employ recently sequenced genomes and transcriptomes of Archaeplastida clades to identify the core components of chloroplast division and reconstruct their evolutionary histories, respectively. Our findings show that complete division ring structures emerged in Charophytes. We find that Glaucophytes experienced strong selection pressure, generating diverse variants adapted to the changing terrestrial environments. By integrating the functions of chloroplast division genes (CDGs) annotated in a workflow developed using large-scale multi-omics data, we further show that dispersed duplications acquire more species-specific functions under stronger selection pressures. Notably, PARC6, a dispersed duplicate CDG, regulates leaf color and plant growth in Solanum lycopersicum, demonstrating neofunctionalization. Our findings provide an integrated perspective on the functional evolution of chloroplast division machinery and highlight the potential of dispersed duplicate genes as the primary source of adaptive evolution of chloroplast division.

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.

SulA does not sequester FtsZ in Escherichia coli cells during the SOS response

In Escherichia coli, the SulA protein is synthesized during the SOS response to arrest cell division. Two possible models of SulA action were proposed: the sequestration and the capping. In current paper, to clarify which model better reflects the SulA effect on cell division upon the SOS response, the FtsZ/SulA ratio was estimated inside cells based on fusion of both FtsZ and SulA to fluorescent protein mNeonGreen. This allowed to quantify this ratio by fluorescence microscopy as well as western blotting; moreover, the effect of SulA on FtsZ distribution patterns in cells was analyzed based on fluorescence microscopy images. The SulA concentration in cells under the SOS response was shown to be several times (about 10) lower than that of FtsZ. The effect of SulA was unequal to corresponding decrease in FtsZ concentration. These results are supported by uneven FtsZ distribution in cells under the SOS response. Together the results of current work indicate that the division arrest by SulA protein in E. coli cells could not be explained by the sequestration model.

Direct evidence of the ability of Pseudomonas aeruginosa and E. coli SulA to dimerize

The SulA protein of Escherichia coli and related bacteria interacts directly with FtsZ, blocking cell division by disrupting Z-ring formation, yet the precise mechanism remains not fully understood. Previous demonstrations of Pseudomonas aeruginosa SulA's dimerization capability were confined to X-ray crystallography and lacked confirmation under in vivo conditions. Additionally, uncertainty persisted regarding the dimerization potential of E. coli's SulA protein. This paper employs a bacterial two-hybrid system to establish that both P. aeruginosa and E. coli SulA proteins indeed possess the capacity for dimerization.

Studying Macromolecular Interactions of Cellular Machines by the Combined Use of Analytical Ultracentrifugation, Light Scattering, and Fluorescence Spectroscopy Methods

Cellular machines formed by the interaction and assembly of macromolecules are essential in many processes of the living cell. These assemblies involve homo- and hetero-associations, including protein-protein, protein-DNA, protein-RNA, and protein-polysaccharide associations, most of which are reversible. This chapter describes the use of analytical ultracentrifugation, light scattering, and fluorescence-based methods, well-established biophysical techniques, to characterize interactions leading to the formation of macromolecular complexes and their modulation in response to specific or unspecific factors. We also illustrate, with several examples taken from studies on bacterial processes, the advantages of the combined use of subsets of these techniques as orthogonal analytical methods to analyze protein oligomerization and polymerization, interactions with ligands, hetero-associations involving membrane proteins, and protein-nucleic acid complexes.

A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging

The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.

The ClpX chaperone and a hypermorphic FtsA variant with impaired self-interaction are mutually compensatory for coordinating Staphylococcus aureus cell division

Bacterial cell division requires the coordinated assembly and disassembly of a large protein complex called the divisome; however, the exact role of molecular chaperones in this critical process remains unclear. We here provide genetic evidence that ClpX unfoldase activity is a determinant for proper coordination of bacterial cell division by showing the growth defect of a Staphylococcus aureus clpX mutant is rescued by a spontaneously acquired G325V substitution in the ATP-binding domain of the essential FtsA cell division protein. The polymerization state of FtsA is thought to control initiation of bacterial septum synthesis and, while restoring the aberrant FtsA dynamics in clpX cells, the FtsAG325V variant displayed reduced ability to interact with itself and other cell division proteins. In wild-type cells, the ftsAG325V allele shared phenotypes with Escherichia coli superfission ftsA mutants and accelerated the cell cycle, increased the risk of daughter cell lysis, and conferred sensitivity to heat and antibiotics inhibiting cell wall synthesis. Strikingly, lethality was mitigated by spontaneous mutations that inactivate ClpX. Taken together, our results suggest that ClpX promotes septum synthesis by antagonizing FtsA interactions and illuminates the critical role of a protein unfoldase in coordinating bacterial cell division.

Benzodioxane-benzamides as promising inhibitors of Escherichia coli FtsZ

The conserved process of cell division in bacteria has been a long-standing target for antimicrobials, although there are few examples of potent broad-spectrum compounds that inhibit this process. Most currently available compounds acting on division are directed towards the FtsZ protein, a self-assembling GTPase that is a central element of the division machinery in most bacteria. Benzodioxane-benzamides are promising candidates, but poorly explored in Gram-negatives. We have tested a number of these compounds on E. coli FtsZ and found that many of them significantly stabilized the polymers against disassembly and reduced the GTPase activity. Reconstitution in crowded cell-like conditions showed that FtsZ bundles were also susceptible to these compounds, including some compounds that were inactive on protofilaments in dilute conditions. They efficiently killed E. coli cells defective in the AcrAB efflux pump. The activity of the compounds on cell growth and division generally showed a good correlation with their effect in vitro, and our experiments are consistent with FtsZ being the target in vivo. Our results uncover the detrimental effects of benzodioxane-benzamides on permeable E. coli cells via its central division protein, implying that lead compounds may be found within this class for the development of antibiotics against Gram-negative bacteria.

Salactin, a dynamically unstable actin homolog in Haloarchaea

IMPORTANCE

Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.

Benzodioxane-Benzamides as FtsZ Inhibitors: Effects of Linker's Functionalization on Gram-Positive Antimicrobial Activity

FtsZ is an essential bacterial protein abundantly studied as a novel and promising target for antimicrobials. FtsZ is highly conserved among bacteria and mycobacteria, and it is crucial for the correct outcome of the cell division process, as it is responsible for the division of the parent bacterial cell into two daughter cells. In recent years, the benzodioxane-benzamide class has emerged as very promising and capable of targeting both Gram-positive and Gram-negative FtsZs. In this study, we explored the effect of including a substituent on the ethylenic linker between the two main moieties on the antimicrobial activity and pharmacokinetic properties. This substitution, in turn, led to the generation of a second stereogenic center, with both erythro and threo isomers isolated, characterized, and evaluated. With this work, we discovered how the hydroxy group slightly affects the antimicrobial activity, while being an important anchor for the exploitation and development of prodrugs, probes, and further derivatives.

The C-terminal domain of MinC, a cell division regulation protein, is sufficient to form a copolymer with MinD

Assembly of cell division protein FtsZ into the Z-ring at the division site is a key step in bacterial cell division. The Min proteins can restrict the Z-ring to the middle of the cell. MinC is the main protein that obstructs Z-ring formation by inhibiting FtsZ assembly. Its N-terminal domain (MinCN ) regulates the localization of the Z-ring by inhibiting FtsZ polymerization, while its C-terminal domain (MinCC ) binds to MinD as well as to FtsZ. Previous studies have shown that MinC and MinD form copolymers in vitro. This copolymer may greatly enhance the binding of MinC to FtsZ, and/or prevent FtsZ filaments from diffusing to the ends of the cell. Here, we investigated the assembly properties of MinCC -MinD of Pseudomonas aeruginosa. We found that MinCC is sufficient to form the copolymers. Although MinCC -MinD assembles into larger bundles, most likely because MinCC is spatially more readily bound to MinD, its copolymerization has similar dynamic properties: the concentration of MinD dominates their copolymerization. The critical concentration of MinD is around 3 μm and when MinD concentration is high enough, a low concentration MinCC could still be copolymerized. We also found that MinCC -MinD can still rapidly bind to FtsZ protofilaments, providing direct evidence that MinCC also interacts directly with FtsZ. However, although the presence of minCC can slightly improve the division defect of minC-knockout strains and shorten the cell length from an average of 12.2 ± 6.7 to 6.6 ± 3.6 μm, it is still insufficient for the normal growth and division of bacteria.

Bacterial cell-size changes resulting from altering the relative expression of Min proteins

The timing of cell division, and thus cell size in bacteria, is determined in part by the accumulation dynamics of the protein FtsZ, which forms the septal ring. FtsZ localization depends on membrane-associated Min proteins, which inhibit FtsZ binding to the cell pole membrane. Changes in the relative concentrations of Min proteins can disrupt FtsZ binding to the membrane, which in turn can delay cell division until a certain cell size is reached, in which the dynamics of Min proteins frees the cell membrane long enough to allow FtsZ ring formation. Here, we study the effect of Min proteins relative expression on the dynamics of FtsZ ring formation and cell size in individual Escherichia coli bacteria. Upon inducing overexpression of minE, cell size increases gradually to a new steady-state value. Concurrently, the time required to initiate FtsZ ring formation grows as the size approaches the new steady-state, at which point the ring formation initiates as early as before induction. These results highlight the contribution of Min proteins to cell size control, which may be partially responsible for the size fluctuations observed in bacterial populations, and may clarify how the size difference acquired during asymmetric cell division is offset.

Structures of a FtsZ single protofilament and a double-helical tube in complex with a monobody

FtsZ polymerizes into protofilaments to form the Z-ring that acts as a scaffold for accessory proteins during cell division. Structures of FtsZ have been previously solved, but detailed mechanistic insights are lacking. Here, we determine the cryoEM structure of a single protofilament of FtsZ from Klebsiella pneumoniae (KpFtsZ) in a polymerization-preferred conformation. We also develop a monobody (Mb) that binds to KpFtsZ and FtsZ from Escherichia coli without affecting their GTPase activity. Crystal structures of the FtsZ-Mb complexes reveal the Mb binding mode, while addition of Mb in vivo inhibits cell division. A cryoEM structure of a double-helical tube of KpFtsZ-Mb at 2.7 Å resolution shows two parallel protofilaments. Our present study highlights the physiological roles of the conformational changes of FtsZ in treadmilling that regulate cell division.

Inhibitory activity of flavonoids fraction from Astragalus membranaceus Fisch. ex Bunge stems and leaves on Bacillus cereus and its separation and purification

Introduction: Astragalus membranaceus Fisch. ex Bunge is a traditional botanical drug with antibacterial, antioxidant, antiviral, and other biological activities. In the process of industrialization of A. membranaceus, most of the aboveground stems and leaves are discarded without resource utilization except for a small amount of low-value applications such as composting. This study explored the antibacterial activity of A. membranaceus stem and leaf extracts to evaluate its potential as a feed antibiotic substitute. Materials and methods: The antibacterial activity of the flavonoid, saponin, and polysaccharide fractions in A. membranaceus stems and leaves was evaluated by the disk diffusion method. The inhibitory activity of the flavonoid fraction from A. membranaceus stems and leaves on B. cereus was explored from the aspects of the growth curve, cell wall, cell membrane, biofilm, bacterial protein, and virulence factors. On this basis, the flavonoid fraction in A. membranaceus stems and leaves were isolated and purified by column chromatography to determine the main antibacterial components. Results: The flavonoid fraction in A. membranaceus stems and leaves had significant inhibitory activity against B. cereus, and the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were 1.5625 and 6.25 mg/mL, respectively. A. membranaceus stem and leaf flavonoid fraction can induce death of B. cereus in many ways, such as inhibiting growth, destroying cell wall and cell membrane integrity, inhibiting biofilm formation, inhibiting bacterial protein synthesis, and downregulating virulence factor expression. In addition, it was clear that the main flavonoid with antibacterial activity in A. membranaceus stems and leaves was isoliquiritigenin. Molecular docking showed that isoliquiritigenin could form a hydrogen bonding force with FtsZ. Conclusion: A. membranaceus stem and leaf flavonoid fractions had significant inhibitory activity against B. cereus, and the main chemical composition was isoliquiritigenin.

Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring in Escherichia coli

Understanding where proteins are localized in a bacterial cell is essential for understanding their function and regulation. This is particularly important for proteins that are involved in cell division, which localize at the division septum and assemble into highly regulated complexes. Current knowledge of these complexes has been greatly facilitated by super-resolution imaging using fluorescent protein fusions. Herein, we demonstrate with FtsZ that single-molecule PALM images can be obtained in-vivo using a genetically fused nanotag (ALFA), and a corresponding nanobody fused to mEos3.2. The methodology presented is applicable to other bacterial proteins.

Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY

We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.

Filamentous temperature sensitive mutant Z: a putative target to combat antibacterial resistance

In the pre-antibiotic era, common bacterial infections accounted for high mortality and morbidity. Moreover, the discovery of penicillin in 1928 marked the beginning of an antibiotic revolution, and this antibiotic era witnessed the discovery of many novel antibiotics, a golden era. However, the misuse or overuse of these antibiotics, natural resistance that existed even before the antibiotics were discovered, genetic variations in bacteria, natural selection, and acquisition of resistance from one species to another consistently increased the resistance to the existing antibacterial targets. Antibacterial resistance (ABR) is now becoming an ever-increasing concern jeopardizing global health. Henceforth, there is an urgent unmet need to discover novel compounds to combat ABR, which act through untapped pathways/mechanisms. Filamentous Temperature Sensitive mutant Z (FtsZ) is one such unique target, a tubulin homolog involved in developing a cytoskeletal framework for the cytokinetic ring. Additionally, its pivotal role in bacterial cell division and the lack of homologous structural protein in mammals makes it a potential antibacterial target for developing novel molecules. Approximately 2176 X-crystal structures of FtsZ were available, which initiated the research efforts to develop novel antibacterial agents. The literature has reported several natural, semisynthetic, peptides, and synthetic molecules as FtsZ inhibitors. This review provides valuable insights into the basic crystal structure of FtsZ, its inhibitors, and their inhibitory activities. This review also describes the available in vitro detection and quantification methods of FtsZ-drug complexes and the various approaches for determining drugs targeting FtsZ polymerization.

The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations

The FtsQBL is an essential molecular complex sitting midway through bacterial divisome assembly. To visualize and understand its structure, and the consequences of its membrane anchorage, we produced a model of the E. coli complex using the deep-learning prediction utility, AlphaFold 2. The heterotrimeric model was inserted into a 3-lipid model membrane and subjected to a 500-ns atomistic molecular dynamics simulation. The model is superb in quality and captures most experimentally derived structural features, at both the secondary structure and the side-chain levels. The model consists of a uniquely interlocking module contributed by the C-terminal regions of all three proteins. The functionally important constriction control domain residues of FtsB and FtsL are located at a fixed vertical position of ∼43-49 Å from the membrane surface. While the periplasmic domains of all three proteins are well-defined and rigid, the single transmembrane helices of each are flexible and their collective twisting and bending contribute to most structural variations, according to principal component analysis. Considering FtsQ only, the protein is more flexible in its free state relative to its complexed state-with the biggest structural changes located at the elbow between the transmembrane helix and the α-domain. The disordered N-terminal domains of FtsQ and FtsL associate with the cytoplasmic surface of the inner membrane instead of freely venturing into the solvent. Contact network analysis highlighted the formation of the interlocking trimeric module in FtsQBL as playing a central role in mediating the overall structure of the complex.

Widespread PRC barrel proteins play critical roles in archaeal cell division

Cell division is fundamental to all cellular life. Most of the archaea employ one of two alternative division machineries, one centered around the prokaryotic tubulin homolog FtsZ and the other around the endosomal sorting complex required for transport (ESCRT). However, neither of these mechanisms has been thoroughly characterized in archaea. Here, we show that three of the four PRC (Photosynthetic Reaction Center) barrel domain proteins of Haloferax volcanii (renamed Cell division proteins B1/2/3 (CdpB1/2/3)), play important roles in division. CdpB1 interacts directly with the FtsZ membrane anchor SepF and is essential for division, whereas deletion of cdpB2 and cdpB3 causes a major and a minor division defect, respectively. Orthologs of CdpB proteins are also involved in cell division in other haloarchaea. Phylogenetic analysis shows that PRC barrel proteins are widely distributed among archaea, including the highly conserved CdvA protein of the crenarchaeal ESCRT-based division system. Thus, diverse PRC barrel proteins appear to be central to cell division in most if not all archaea. Further study of these proteins is expected to elucidate the division mechanisms in archaea and their evolution.

Using conditional independence tests to elucidate causal links in cell cycle regulation in Escherichia coli

How cells regulate their cell cycles is a central question for cell biology. Models of cell size homeostasis have been proposed for bacteria, archaea, yeast, plant, and mammalian cells. New experiments bring forth high volumes of data suitable for testing existing models of cell size regulation and proposing new mechanisms. In this paper, we use conditional independence tests in conjunction with data of cell size at key cell cycle events (birth, initiation of DNA replication, and constriction) in the model bacterium Escherichia coli to select between the competing cell cycle models. We find that in all growth conditions that we study, the division event is controlled by the onset of constriction at midcell. In slow growth, we corroborate a model where replication-related processes control the onset of constriction at midcell. In faster growth, we find that the onset of constriction is affected by additional cues beyond DNA replication. Finally, we also find evidence for the presence of additional cues triggering initiations of DNA replication apart from the conventional notion where the mother cells solely determine the initiation event in the daughter cells via an adder per origin model. The use of conditional independence tests is a different approach in the context of understanding cell cycle regulation and it can be used in future studies to further explore the causal links between cell events.

Bacterial division ring stabilizing ZapA versus destabilizing SlmA modulate FtsZ switching between biomolecular condensates and polymers

Cytokinesis is a fundamental process for bacterial survival and proliferation, involving the formation of a ring by filaments of the GTPase FtsZ, spatio-temporally regulated through the coordinated action of several factors. The mechanisms of this regulation remain largely unsolved, but the inhibition of FtsZ polymerization by the nucleoid occlusion factor SlmA and filament stabilization by the widely conserved cross-linking protein ZapA are known to play key roles. It was recently described that FtsZ, SlmA and its target DNA sequences (SlmA-binding sequence (SBS)) form phase-separated biomolecular condensates, a type of structure associated with cellular compartmentalization and resistance to stress. Using biochemical reconstitution and orthogonal biophysical approaches, we show that FtsZ-SlmA-SBS condensates captured ZapA in crowding conditions and when encapsulated inside cell-like microfluidics microdroplets. We found that, through non-competitive binding, the nucleotide-dependent FtsZ condensate/polymer interconversion was regulated by the ZapA/SlmA ratio. This suggests a highly concentration-responsive tuning of the interconversion that favours FtsZ polymer stabilization by ZapA under conditions mimicking intracellular crowding. These results highlight the importance of biomolecular condensates as concentration hubs for bacterial division factors, which can provide clues to their role in cell function and bacterial survival of stress conditions, such as those generated by antibiotic treatment.

Models versus pathogens: how conserved is the FtsZ in bacteria?

Combating anti-microbial resistance by developing alternative strategies is the need of the hour. Cell division, particularly FtsZ, is being extensively studied for its potential as an alternative target for anti-bacterial therapy. Bacillus subtilis and Escherichia coli are the two well-studied models for research on FtsZ, the leader protein of the cell division machinery. As representatives of gram-positive and gram-negative bacteria, respectively, these organisms have provided an extensive outlook into the process of cell division in rod-shaped bacteria. However, research on other shapes of bacteria, like cocci and ovococci, lags behind that of model rods. Even though most regions of FtsZ show sequence and structural conservation throughout bacteria, the differences in FtsZ functioning and interacting partners establish several different modes of division in different bacteria. In this review, we compare the features of FtsZ and cell division in the model rods B. subtilis and E. coli and the four pathogens: Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis, and Pseudomonas aeruginosa. Reviewing several recent articles on these pathogenic bacteria, we have highlighted the functioning of FtsZ, the unique roles of FtsZ-associated proteins, and the cell division processes in them. Further, we provide a detailed look at the anti-FtsZ compounds discovered and their target bacteria, emphasizing the need for elucidation of the anti-FtsZ mechanism of action in different bacteria. Current challenges and opportunities in the ongoing journey of identifying potent anti-FtsZ drugs have also been described.

Importance of the 2,6-Difluorobenzamide Motif for FtsZ Allosteric Inhibition: Insights from Conformational Analysis, Molecular Docking and Structural Modifications

A conformational analysis and molecular docking study comparing 2,6-difluoro-3-methoxybenzamide (DFMBA) with 3-methoxybenzamide (3-MBA) has been undertaken for investigating the known increase of FtsZ inhibition related anti S. aureus activity due to fluorination. For the isolated molecules, the calculations reveal that the presence of the fluorine atoms in DFMBA is responsible for its non-planarity, with a dihedral angle of -27° between the carboxamide and the aromatic ring. When interacting with the protein, the fluorinated ligand can thus more easily adopt the non-planar conformation found in reported co-crystallized complexes with FtsZ, than the non-fluorinated one. Molecular docking studies of the favored non-planar conformation of 2,6-difluoro-3-methoxybenzamide highlights the strong hydrophobic interactions between the difluoroaromatic ring and several key residues of the allosteric pocket, precisely between the 2-fluoro substituent and residues Val203 and Val297 and between the 6-fluoro group and the residues Asn263. The docking simulation in the allosteric binding site also confirms the critical importance of the hydrogen bonds between the carboxamide group with the residues Val207, Leu209 and Asn263. Changing the carboxamide functional group of 3-alkyloxybenzamide and 3-alkyloxy-2,6-difluorobenzamide to a benzohydroxamic acid or benzohydrazide led to inactive compounds, confirming the importance of the carboxamide group.

Interaction of the bacterial division regulator MinE with lipid bicelles studied by NMR spectroscopy

The bacterial MinE and MinD division regulatory proteins form a standing wave enabling MinC, which binds MinD, to inhibit FtsZ polymerization everywhere except at the midcell, thereby assuring correct positioning of the cytokinetic septum and even distribution of contents to daughter cells. The MinE dimer undergoes major structural rearrangements between a resting six-stranded state present in the cytoplasm, a membrane-bound state, and a four-stranded active state bound to MinD on the membrane, but it is unclear which MinE motifs interact with the membrane in these different states. Using NMR, we probe the structure and global dynamics of MinE bound to disc-shaped lipid bicelles. In the bicelle-bound state, helix α1 no longer sits on top of the six-stranded β-sheet, losing any contact with the protein core, but interacts directly with the bicelle surface; the structure of the protein core remains unperturbed and also interacts with the bicelle surface via helix α2. Binding may involve a previously identified excited state of free MinE in which helix α1 is disordered, thereby allowing it to target the membrane surface. Helix α1 and the protein core undergo nanosecond rigid body motions of differing amplitudes in the plane of the bicelle surface. Global dynamics on the sub-millisecond time scale between a ground state and a sparsely populated excited state are also observed and may represent a very early intermediate on the transition path between the resting six-stranded and active four-stranded conformations. In summary, our results provide insights into MinE structural rearrangements important during bacterial cell division.

Identification of anti-Mycobacterium tuberculosis agents targeting the interaction of bacterial division proteins FtsZ and SepF

Tuberculosis (TB) is one of the deadly diseases caused by Mycobacterium tuberculosis (Mtb), which presents a significant public health challenge. Treatment of TB relies on the combination of several anti-TB drugs to create shorter and safer regimens. Therefore, new anti-TB agents working by different mechanisms are urgently needed. FtsZ, a tubulin-like protein with GTPase activity, forms a dynamic Z-ring in cell division. Most of FtsZ inhibitors are designed to inhibit GTPase activity. In Mtb, the function of Z-ring is modulated by SepF, a FtsZ binding protein. The FtsZ/SepF interaction is essential for FtsZ bundling and localization at the site of division. Here, we established a yeast two-hybrid based screening system to identify inhibitors of FtsZ/SepF interaction in M. tuberculosis. Using this system, we found compound T0349 showing strong anti-Mtb activity but with low toxicity to other bacteria strains and mice. Moreover, we have demonstrated that T0349 binds specifically to SepF to block FtsZ/SepF interaction by GST pull-down, fluorescence polarization (FP), surface plasmon resonance (SPR) and CRISPRi knockdown assays. Furthermore, T0349 can inhibit bacterial cell division by inducing filamentation and abnormal septum. Our data demonstrated that FtsZ/SepF interaction is a promising anti-TB drug target for identifying agents with novel mechanisms.

Obtainment of Threo and Erythro Isomers of the 6-Fluoro-3-(2,3,6,7,8,9-hexahydronaphtho[2,3-b][1,4]dioxin-2-yl)-2,3-dihydrobenzo[b][1,4]dioxine-5-carboxamide

2,6-difluorobenzamides have been deeply investigated as antibacterial drugs in the last few decades. Several 3-substituted-2,6-difluorobenzamides have proved their ability to interfere with the bacterial cell division cycle by inhibiting the protein FtsZ, the key player of the whole process. Recently, we developed a novel family of 1,4-tetrahydronaphthodioxane benzamides, having an ethoxy linker, which reached sub-micromolar MICs towards Gram-positive Staphylococcus aureus and Bacillus subtilis. A further investigation of their mechanism of action should require the development of a fluorescent probe, and the consequent definition of a synthetic pathway for its obtainment. In the present work, we report the obtainment of an unexpected bicyclic side product, 6-fluoro-3-(2,3,6,7,8,9-hexahydronaphtho[2,3-b][1,4]dioxin-2-yl)-2,3-dihydrobenzo[b][1,4]dioxine-5-carboxamide, coming from the substitution of one aromatic fluorine by the in situ formed alkoxy group, in the final opening of an epoxide intermediate. This side product was similarly achieved, in good yields, by opening the ring of both erythro and threo epoxides, and the two compounds were fully characterized using HRMS, 1H-NMR, 13C-NMR, HPLC and DSC.

Dynamics of the Synechococcus elongatus cytoskeletal GTPase FtsZ yields mechanistic and evolutionary insight into cyanobacterial and chloroplast FtsZs

The division of cyanobacteria and their chloroplast descendants is orchestrated by filamenting temperature-sensitive Z (FtsZ), a cytoskeletal GTPase that polymerizes into protofilaments that form a "Z ring" at the division site. The Z ring has both a scaffolding function for division-complex assembly and a GTPase-dependent contractile function that drives cell or organelle constriction. A single FtsZ performs these functions in bacteria, whereas in chloroplasts, they are performed by two copolymerizing FtsZs, called AtFtsZ2 and AtFtsZ1 in Arabidopsis thaliana, which promote protofilament stability and dynamics, respectively. To probe the differences between cyanobacterial and chloroplast FtsZs, we used light scattering to characterize the in vitro protofilament dynamics of FtsZ from the cyanobacterium Synechococcus elongatus PCC 7942 (SeFtsZ) and investigate how coassembly of AtFtsZ2 or AtFtsZ1 with SeFtsZ influences overall dynamics. SeFtsZ protofilaments assembled rapidly and began disassembling before GTP depletion, whereas AtFtsZ2 protofilaments were far more stable, persisting beyond GTP depletion. Coassembled SeFtsZ-AtFtsZ2 protofilaments began disassembling before GTP depletion, similar to SeFtsZ. In contrast, AtFtsZ1 did not alter disassembly onset when coassembled with SeFtsZ, but fluorescence recovery after photobleaching analysis showed it increased the turnover of SeFtsZ subunits from SeFtsZ-AtFtsZ1 protofilaments, mirroring its effect upon coassembly with AtFtsZ2. Comparisons of our findings with previous work revealed consistent differences between cyanobacterial and chloroplast FtsZ dynamics and suggest that the scaffolding and dynamics-promoting functions were partially separated during evolution of two chloroplast FtsZs from their cyanobacterial predecessor. They also suggest that chloroplasts may have evolved a mechanism distinct from that in cyanobacteria for promoting FtsZ protofilament dynamics.

Diversity and Potential Multifunctionality of Archaeal CetZ Tubulin-like Cytoskeletal Proteins

Tubulin superfamily (TSF) proteins are widespread, and are known for their multifaceted roles as cytoskeletal proteins underpinning many basic cellular functions, including morphogenesis, division, and motility. In eukaryotes, tubulin assembles into microtubules, a major component of the dynamic cytoskeletal network of fibres, whereas the bacterial homolog FtsZ assembles the division ring at midcell. The functions of the lesser-known archaeal TSF proteins are beginning to be identified and show surprising diversity, including homologs of tubulin and FtsZ as well as a third archaea-specific family, CetZ, implicated in the regulation of cell shape and possibly other unknown functions. In this study, we define sequence and structural characteristics of the CetZ family and CetZ1 and CetZ2 subfamilies, identify CetZ groups and diversity amongst archaea, and identify potential functional relationships through analysis of the genomic neighbourhoods of cetZ genes. We identified at least three subfamilies of orthologous CetZ proteins in the archaeal class Halobacteria, including CetZ1 and CetZ2 as well as a novel uncharacterized subfamily. CetZ1 and CetZ2 were correlated to one another as well as to cell shape and motility phenotypes across diverse Halobacteria. Among other known CetZ clusters in orders Archaeoglobales, Methanomicrobiales, Methanosarcinales, and Thermococcales, an additional uncharacterized group from Archaeoglobales and Methanomicrobiales is affiliated strongly with Halobacteria CetZs, suggesting that they originated via horizontal transfer. Subgroups of Halobacteria CetZ2 and Thermococcales CetZ genes were found adjacent to different type IV pili regulons, suggesting potential utilization of CetZs by type IV systems. More broadly conserved cetZ gene neighbourhoods include nucleotide and cofactor biosynthesis (e.g., F420) and predicted cell surface sugar epimerase genes. These findings imply that CetZ subfamilies are involved in multiple functions linked to the cell surface, biosynthesis, and motility.

FtsZ phosphorylation brings about growth arrest upon DNA damage in Deinococcus radiodurans

The polymerization/depolymerization dynamics of FtsZ play a pivotal role in cell division in the majority of the bacteria. Deinococcus radiodurans, a radiation-resistant bacterium, shows an arrest of growth in response to DNA damage with no change in the level of FtsZ. This bacterium does not deploy LexA/RecA type of DNA damage response and cell cycle regulation, and its genome does not encode SulA homologues of Escherichia coli, which attenuate FtsZ functions in response to DNA damage in other bacteria. A radiation-responsive Ser/Thr quinoprotein kinase (RqkA), characterized for its role in radiation resistance in this bacterium, could phosphorylate several cognate proteins, including FtsZ (drFtsZ) at Serine 235 (S235) and Serine 335 (S335) residues. Here, we reported the detailed characterization of S235 and S335 phosphorylation effects in the regulation of drFtsZ functions and demonstrated that the phospho-mimetic replacements of these residues in drFtsZ had grossly affected its functions that could result in cell cycle arrest in response to DNA damage in D. radiodurans. Interestingly, the phospho-ablative replacements were found to be nearly similar to drFtsZ, whereas the phospho-mimetic mutant lost the wild-type protein's signature characteristics, including its dynamics under normal conditions. The kinetics of post-bleaching recovery for drFtsZ and phospho-mimetic mutant were nearly similar at 2 h post-irradiation recovery but were found to be different under normal conditions. These results highlighted the role of S/T phosphorylation in the regulation of drFtsZ functions and cell cycle arrest in response to DNA damage, which is demonstrated for the first time, in any bacteria.

Lipid Surfaces and Glutamate Anions Enhance Formation of Dynamic Biomolecular Condensates Containing Bacterial Cell Division Protein FtsZ and Its DNA-Bound Regulator SlmA

Dynamic biomolecular condensates formed by liquid-liquid phase separation can regulate the spatial and temporal organization of proteins, thus modulating their functional activity in cells. Previous studies showed that the cell division protein FtsZ from Escherichia coli formed dynamic phase-separated condensates with nucleoprotein complexes containing the FtsZ spatial regulator SlmA under crowding conditions, with potential implications for condensate-mediated spatiotemporal control of FtsZ activity in cell division. In the present study, we assessed formation of these condensates in the presence of lipid surfaces and glutamate ions to better approximate the E. coli intracellular environment. We found that potassium glutamate substantially promoted the formation of FtsZ-containing condensates when compared to potassium chloride in crowded solutions. These condensates accumulated on supported lipid bilayers and eventually fused, resulting in a time-dependent increase in the droplet size. Moreover, the accumulated condensates were dynamic, capturing protein from the external phase. FtsZ partitioned into the condensates at the lipid surface only in its guanosine diphosphate (GDP) form, regardless of whether it came from FtsZ polymer disassembly upon guanosine triphosphate (GTP) exhaustion. These results provide insights into the behavior of these GTP-responsive condensates in minimal membrane systems, which suggest how these membraneless assemblies may tune critical bacterial division events during the cell cycle.