Biology subjects

Krell, T.

Publications and source records attributed to Krell, T..

10 recordsLinked to original sources

bioRxiv2026

Environmental sensing capacity predicts bacterial ecological strategies and environmental preferences

The ability to sense environmental variation is a prerequisite for ecological success. Sensor domains enable bacteria to detect nutrients, neighboring organisms, and physicochemical conditions, but whether variation in these sensing systems reflects ecological specialization remains unresolved. Here, we analyzed sensor domains across 51,343 bacterial genomes and 255 soil metagenomes spanning a climatic gradient to determine whether sensory repertoires encode bacterial ecological strategies and environmental preferences. Sensory repertoires exhibited strong phylogenetic conservatism and revealed signatures of genome streamlining, indicating that environmental sensing reflects trade-offs associated with maintaining sensory complexity. Taxa occupying environmentally heterogeneous habitats, particularly free-living aerobic generalists, encoded the largest sensory repertoires, consistent with selection for expanded environmental information processing. To link sensory function with ecological adaptation, we mapped experimentally-characterized ligand-binding motifs (LBMs) across genomes and metagenomes. Distinct LBM profiles discriminated host-associated and free-living taxa, aerobic and anaerobic lineages, and generalists and non-generalists, revealing a tight coupling between sensory capacity and ecological strategy. Across soil communities, motifs associated with osmoprotection and oxygen sensing were consistently enriched under increasing aridity, linking sensory function to environmental filtering in natural ecosystems. These findings identify environmental sensing as an important organizational axis of bacterial trait-based ecology that integrates evolutionary history, ecological lifestyle, and adaptation to local conditions. Environmental sensing should be considered for predicting microbial niches and responses to environmental change.

ecology↗

bioRxiv2025

Phosphorylated CheV interacts with a subset of chemoreceptors

Chemotaxis pathways are among the most complex signaling systems in bacteria. A central feature of these pathways is the ternary complex formed by chemoreceptors, the autokinase CheA, and the coupling proteins CheW and CheV. Whereas CheW is present in all chemotaxis pathways, CheV is primarily found in bacteria that contain many chemoreceptors. CheV is a fusion of a CheW-like domain to a phosphorylatable receiver domain. The roles of CheV and its phosphorylation are currently uncertain. Pseudomonas aeruginosa contains many chemoreceptors for which the cognate signals have been identified. Quantitative capillary chemotaxis assays of a cheV mutant revealed that responses to certain chemoeffectors, such as nitrate and -ketoglutarate, were drastically reduced, while responses to others, such as amino acids and inorganic phosphate, were comparable to the wild type, indicating that CheV selectively acts on specific chemoreceptors. To study the mechanism of CheV action, we conducted protein-protein interaction experiments using isothermal titration calorimetry. These studies showed that unphosphorylated CheV fails to bind to cytosolic fragments of the McpN and PctA chemoreceptors, which mediate responses to nitrate and amino acids, respectively. In contrast, the phosphorylation-mimic CheV D238E bound with very high affinity (KD = 8 nM) to McpN but failed to interact with PctA. Thus, CheV in P. aeruginosa binds to some chemoreceptors but not to others in a phosphorylation-dependent manner. These results suggest that CheV is a regulatory protein that modulates signaling through specific chemoreceptors. CheV may thus facilitate the coordination of chemotaxis responses in complex, multi-chemoreceptor systems. ImportanceOf all chemosensory signaling proteins, CheV is perhaps the least understood. Our demonstration that CheV interacts only with certain chemoreceptors offers fundamental new insights. These findings, combined with the observation that CheV is present in bacteria with numerous chemoreceptors, suggest that CheV plays a role in coordinating chemotactic outputs in complex chemosensory systems. Understanding the mechanisms by which chemotactic responses are defined in bacteria with a high number of chemoreceptors is a major research priority in the field of chemotaxis. While previous studies, including this one, show that the ability to be phosphorylated is crucial for CheV function, the molecular consequences of CheV phosphorylation have remained unclear. Our discovery that phosphorylation is essential for CheV binding to certain chemoreceptors fills in this critical gap in understanding the molecular mechanism of CheV. This study is likely to inspire further research into CheV function in other bacteria using similar approaches.

microbiology↗

bioRxiv2024

Chemoreceptor family in plant-associated bacteria responds preferentially to the plant signal molecule glycerol 3-phosphate

Plant pathogens and plant-associated bacteria contain about twice as many chemoreceptors as the bacterial average, indicating that chemotaxis is particularly important for bacteria-plant interactions. However, information on the corresponding chemoreceptors is limited. In this study, we identified the chemoreceptor PacP from the phytopathogen Pectobacterium atrosepticum, which exclusively recognized C3 phosphorylated compounds at its sCache ligand binding domain, mediating chemoattraction. Using a motif of PacP amino acid residues involved in ligand binding, we identified a chemoreceptor family, termed sCache_PC3, that was specific for C3 phosphorylated compounds. Isothermal titration calorimetry studies revealed that family members preferentially bound glycerol 3-phosphate, a key plant signaling molecule. Additionally, family members recognized glycerol 2-phosphate and glycolysis intermediates glyceraldehyde 3-phosphate, dihydroxyacetone phosphate and 3-phosphoglycerate. This study presents the first evidence of chemoreceptors that bind phosphorylated compounds. We show that the sCache_PC3 family has evolved from an ancestral sCache domain that respond primarily to Krebs cycle intermediates. Members of the sCache_PC3 family were mainly found in bacteria that interact with plants, including many important plant pathogens such as Brenneria, Dickeya, Musicola, Pectobacterium, and Herbaspirillum. Glycerol 3-phosphate is a signal molecule that is excreted by plants in response to stress and infection. Chemotaxis towards this molecule may thus be a means for bacteria to localize stressed plants and move to infection sites. This study lays the groundwork for investigating the functional importance of chemotaxis to phosphorylated C3 compounds in plant-bacteria interactions and virulence. Significance statementThe bacterial lifestyle has shaped the evolution of signal transduction systems, and the number and type of chemoreceptors varies greatly between bacteria occupying various ecological niches. Our understanding of the relationship between lifestyle and chemoreceptor function is limited and the discovery of a chemoreceptor family in plant-associated bacteria that primarily responds to an important plant signal molecule is a significant advancement, allowing for further studies to determine its physiological relevance. The lack of knowledge about signals recognized by bacterial receptors is currently a major challenge in microbiology. This study illustrates the potential of combining experimental ligand screening with computational ligand prediction to identify signals recognized by uncharacterized receptors.

microbiology↗

bioRxiv2024

Pseudomonas aeruginosa performs chemotaxis to serotonin, dopamine, epinephrine, and norepinephrine

Bacteria use chemotaxis to move to favorable ecological niches. For many pathogenic bacteria, chemotaxis is required for full virulence, particularly for the initiation of host colonization. There do not appear to be limits to the type of compounds that attract bacteria, and we are just beginning to understand how chemotaxis adapts them to their lifestyles. Quantitative capillary assays for chemotaxis show that P. aeruginosa is strongly attracted to serotonin, dopamine, epinephrine, and norepinephrine. Chemotaxis to these compounds is greatly decreased in a mutant lacking the TlpQ chemoreceptor, and complementation of this mutant with a plasmid harboring the tlpQ gene restores wild-type-like chemotaxis. Microcalorimetric titrations of the TlpQ sensor domain with these four compounds indicate that they bind directly to TlpQ. All four compounds are hormones and neurotransmitters that control a variety of processes and are also important signal molecules involved in the virulence of P. aeruginosa. They modulate motility, biofilm formation, the production of virulence factors and serve as siderophores that chelate iron. Therefore, chemotaxis to these four compounds is likely to alter P. aeruginosa virulence. Additionally, we believe that this is the first report of bacterial chemotaxis to serotonin and dopamine. This study provides an incentive for research to define the contribution of chemotaxis to these host signaling molecules to the virulence of P. aeruginosa.

microbiology↗

bioRxiv2024

Bacterial sensor evolved by decreasing complexity

Bacterial receptors feed into multiple signal transduction pathways that regulate a variety of cellular processes including gene expression, second messenger levels and motility. Receptors are typically activated by signal binding to ligand binding domains (LBD). Cache domains are omnipresent LBDs found in bacteria, archaea, and eukaryotes, including humans. They form the predominant family of extracytosolic bacterial LBDs and were identified in all major receptor types. Cache domains are composed of either a single (sCache) or a double (dCache) structural module. The functional relevance of bimodular LBDs remains poorly understood. Here, we identify the PacF chemoreceptor in the phytopathogen Pectobacterium atrosepticum that recognizes formate at the membrane distal module of its dCache domain, triggering chemoattraction. We further demonstrate that a family of formate-specific sCache domains has evolved from a dCache domain, exemplified by PacF, by losing the membrane proximal module. By solving high-resolution structures of two family members in complex with formate, we show that the molecular basis for formate binding at sCache and dCache domains is highly similar, despite their low sequence identity. The apparent loss of the membrane proximal module may be related to the observation that dCache domains bind ligands typically at the membrane distal module, whereas the membrane proximal module is not involved in signal sensing. This work advances our understanding of signal sensing in bacterial receptors and suggests that evolution by reducing complexity may be a common trend shaping their diversity. SignificanceMany bacterial receptors contain multi-modular sensing domains indicative of complex sensory processes. The presence of more than one sensing module likely permits the integration of multiple signals, although, the molecular detail and functional relevance for these complex sensors remain poorly understood. Bimodular sensory domains are likely to have arisen from the fusion or duplication of monomodular domains. Evolution by increasing complexity is generally believed to be a dominant force. Here we reveal the opposite - how a monomodular sensing domain has evolved from a bimodular one. Our findings will thus motivate research to establish whether evolution by decreasing complexity is typical of other sensory domains.

microbiology↗

bioRxiv2024

Differential CheR affinity for chemoreceptor C-terminal pentapeptides biases chemotactic responses

The capacity of chemotaxis pathways to respond to signal gradients relies on adaptation mediated by the coordinated action of CheR methyltransferases and CheB methylesterases. Many chemoreceptors contain a C-terminal pentapeptide at the end of a linker. In Escherichia coli, this pentapeptide forms a high-affinity binding site for CheR and phosphorylated CheB, and its removal interferes with adaptation. The analysis of all available chemoreceptor sequences showed that pentapeptide sequences vary greatly, and bacteria often possess multiple chemoreceptors that differ in their pentapeptide sequences. Using the phytopathogen Pectobacterium atrosepticum SCRI1043, we assessed whether this sequence variation alters CheR affinity and chemotaxis. SCRI1043 has 36 chemoreceptors, of which 19 possess a C-terminal pentapeptide. Using isothermal titration calorimetry, we show that the affinity of CheR for the different pentapeptides varies up to 11-fold (KD of 90 nM to 1 {micro}M). The pentapeptides with the highest and lowest affinities differed only in a single amino acid. Deletion of the cheR gene abolishes chemotaxis. PacC is the sole chemoreceptor for L-Asp in SCRI1043, and the replacement of its pentapeptide with those having the highest and lowest affinities significantly interfered with L-Asp chemotaxis. Variable pentapeptide sequences thus provide a mechanism to bias the responses mediated by chemoreceptors.

microbiology↗

bioRxiv2023

Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria

Purines and their derivatives are key molecules for controlling intracellular energy homeostasis and nucleotide synthesis. In eukaryotes, including humans, purines also act as signaling molecules that mediate extracellular communication and control key cellular processes, such as proliferation, migration, differentiation, and apoptosis. However, the signaling role of purines in bacteria is largely unknown. Here, by combining structural and sequence information, we define a purine-binding motif, which is present in sensor domains of thousands of bacterial receptors that modulate motility, gene expression, metabolism and second messenger turnover. The screening of compound libraries and microcalorimetric titrations of selected sensor domains validated their ability to specifically bind purine derivatives. The physiological relevance of purine sensing was demonstrated in a second messenger signaling system that modulates c-di-GMP levels.

microbiology↗

bioRxiv2023

Systematic mapping of chemoreceptor specificities for Pseudomonas aeruginosa

The chemotaxis network, one of the most prominent prokaryotic sensory systems, is present in most motile bacteria and archaea. Although the conserved signaling core of the network is well characterized, ligand specificities of a large majority of diverse chemoreceptors encoded in bacterial genomes remain unknown. Here we performed a systematic identification and characterization of new chemoeffectors for the opportunistic pathogen Pseudomonas aeruginosa, which has 26 chemoreceptors possessing most of the common types of ligand binding domains. By performing capillary chemotaxis assays for a library of growth-promoting compounds, we first identified a number of novel chemoattractants of varying strength. We subsequently mapped specificities of these ligands by performing Forster resonance energy transfer (FRET) and microfluidic measurements for hybrids containing ligand binding domains of P. aeruginosa chemoreceptors and the signaling domain of the Escherichia coli Tar receptor. Direct binding of ligands to chemoreceptors was further confirmed in vitro using thermal shift assay and microcalorimetry. Altogether, the combination of methods enabled us to assign several new attractants, including methyl 4-aminobutyrate, 5-aminovalerate, L-ornithine, 2-phenylethylamine and tyramine, to previously characterized chemoreceptors and to annotate a novel purine-specific receptor PctP. Our screening strategy could be applied for the systematic characterization of unknown sensory domains in a wide range of bacterial species. ImportanceChemotaxis of motile bacteria has multiple physiological functions. It enables bacteria to locate optimal ecological niches, mediates collective behaviors, and can play an important role in infection. These multiple functions largely depend on ligand specificities of chemoreceptors, and the number and identities of chemoreceptors show high diversity between organisms. Similar diversity is observed for the spectra of chemoeffectors, which include not only chemicals of high metabolic value but also bacterial, plant and animal signaling molecules. However, the systematic identification of chemoeffectors and their mapping to specific chemoreceptors remains a challenge. Here, we combined several in vivo and in vitro approaches to establish a systematic screening strategy for the identification of receptor ligands, and we applied it to identify a number of new physiologically relevant chemoeffectors for the important opportunistic human pathogen P. aeruginosa. This strategy can be equally applicable to map specificities of sensory domains from a wide variety of receptor types and bacteria.

microbiology↗

bioRxiv2023

Amine recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor

Bacteria contain many different receptor families that sense different signals permitting an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Due to a significant sequence divergence, the signal recognized by sensor domains is only poorly reflected in overall sequence identity. Biogenic amines are of central physiological relevance for microorganisms and serve for example as substrates for aerobic and anaerobic growth, neurotransmitters or osmoprotectants. Based on protein structural information and sequence analysis, we report here the identification of a sequence motif that is specific for amine-sensing dCache sensor domains (dCache_1AM). These domains were identified in more than 13,000 proteins from 8,000 bacterial and archaeal species. dCache_1AM containing receptors were identified in all major receptor families including sensor kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases. The screening of compound libraries and microcalorimetric titrations of selected dCache_1AM domains confirmed their capacity to specifically bind amines. Mutants in the amine binding motif or domains that contain a single mismatch in the binding motif, had either no or a largely reduced affinity for amines, illustrating the specificity of this motif. We demonstrate that the dCache_1AM domain has evolved from the universal amino acid sensing domain, providing novel insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and thus holds a strong promise to address an important bottleneck in microbiology: the identification of signals that stimulate numerous receptors.

microbiology↗

bioRxiv2021

Amino acid sensor conserved from bacteria to humans

Amino acids are recognized as signals by various receptors in bacteria, archaea, and eukaryotes. However, no common mechanism for amino acid recognition is currently known. Here we show that a subclass of a ubiquitous extracellular domain dCache_1 contains a simple amino acid recognition motif, and it is found throughout the Tree of Life. In bacteria, this motif exclusively binds amino acids, including GABA, and it is present in all major receptor types. In humans, this motif is found in 2{delta} subunits of voltage-gated calcium channels that are implicated in neuropathic pain and neurodevelopmental disorders. Our findings suggest that GABA-derived drugs bind to the same motif in human 2{delta} subunits that binds natural GABA ligands in bacterial chemoreceptors.

evolutionary biology↗