scholarly journals A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms

2020 ◽  
Author(s):  
Marianne Grognot ◽  
Katja M. Taute
Keyword(s):  
Escherichia Coli ◽  
Statistical Power ◽  
Caulobacter Crescentus ◽  
Climate Science ◽  
Chemotaxis Assay ◽  
Environmental Chemical ◽  
Chemical Gradients ◽  
Behavioral Mechanisms ◽  
Motility Behavior

AbstractHow bacteria navigate environmental chemical gradients has implications ranging from health to climate science. The underlying behavioral mechanisms are unknown for most species due to a lack in techniques bridging scales from individual 3D motility behavior to the statistical power required to assess the resulting performance. We present the first demonstration of such a multiscale 3D chemotaxis assay and reveal that Caulobacter crescentus chemotaxis breaks with the Escherichia coli paradigm.

scholarly journals A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms

2020 ◽  
Author(s):  
Marianne Grognot ◽  
Katja Taute
Keyword(s):  
Statistical Power ◽  
Caulobacter Crescentus ◽  
Bacterial Species ◽  
Climate Science ◽  
Population Level ◽  
Chemotaxis Assay ◽  
3D Navigation ◽  
Environmental Chemical ◽  
Chemical Gradients ◽  
Behavioral Mechanisms

Abstract How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, contrary to previous reports, Caulobacter crescentus breaks with the E. coli paradigm.

scholarly journals A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marianne Grognot ◽  
Katja M. Taute
Keyword(s):  
Statistical Power ◽  
Caulobacter Crescentus ◽  
Bacterial Species ◽  
Climate Science ◽  
Population Level ◽  
Chemotaxis Assay ◽  
3D Navigation ◽  
Environmental Chemical ◽  
Chemical Gradients ◽  
Behavioral Mechanisms

AbstractHow motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, contrary to previous reports, Caulobacter crescentus breaks with the E. coli paradigm.

Bacterial Multicellularity: The Biology of Escherichia coli Building Large-Scale Biofilm Communities

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Diego O. Serra ◽  
Regine Hengge
Keyword(s):  
Escherichia Coli ◽  
Large Scale ◽  
Second Messengers ◽  
Emergent Properties ◽  
Annual Review ◽  
Publication Date ◽  
Growth And Survival ◽  
Chemical Gradients ◽  
Life Itself ◽  
Scale Matrix

Biofilms are a widespread multicellular form of bacterial life. The spatial structure and emergent properties of these communities depend on a polymeric extracellular matrix architecture that is orders of magnitude larger than the cells that build it. Using as a model the wrinkly macrocolony biofilms of Escherichia coli, which contain amyloid curli fibers and phosphoethanolamine (pEtN)-modified cellulose as matrix components, we summarize here the structure, building, and function of this large-scale matrix architecture. Based on different sigma and other transcription factors as well as second messengers, the underlying regulatory network reflects the fundamental trade-off between growth and survival. It controls matrix production spatially in response to long-range chemical gradients, but it also generates distinct patterns of short-range matrix heterogeneity that are crucial for tissue-like elasticity and macroscopic morphogenesis. Overall, these biofilms confer protection and a potential for homeostasis, thereby reducing maintenance energy, which makes multicellularity an emergent property of life itself. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences

2020 ◽  
Vol 48 (18) ◽  
pp. 10034-10044 ◽  
Author(s):  
Clayton B Woodcock ◽  
John R Horton ◽  
Xing Zhang ◽  
Robert M Blumenthal ◽  
Xiaodong Cheng
Keyword(s):  
Escherichia Coli ◽  
Cell Cycle ◽  
Dna Methyltransferase ◽  
Caulobacter Crescentus ◽  
Substrate Recognition ◽  
Its Sequence ◽  
Amino Groups ◽  
Dna And Rna ◽  
Acid Type ◽  
Target Molecules

Abstract S-adenosyl-l-methionine dependent methyltransferases catalyze methyl transfers onto a wide variety of target molecules, including DNA and RNA. We discuss a family of methyltransferases, those that act on the amino groups of adenine or cytosine in DNA, have conserved motifs in a particular order in their amino acid sequence, and are referred to as class beta MTases. Members of this class include M.EcoGII and M.EcoP15I from Escherichia coli, Caulobacter crescentus cell cycle–regulated DNA methyltransferase (CcrM), the MTA1-MTA9 complex from the ciliate Oxytricha, and the mammalian MettL3-MettL14 complex. These methyltransferases all generate N6-methyladenine in DNA, with some members having activity on single-stranded DNA as well as RNA. The beta class of methyltransferases has a unique multimeric feature, forming either homo- or hetero-dimers, allowing the enzyme to use division of labor between two subunits in terms of substrate recognition and methylation. We suggest that M.EcoGII may represent an ancestral form of these enzymes, as its activity is independent of the nucleic acid type (RNA or DNA), its strandedness (single or double), and its sequence (aside from the target adenine).

scholarly journals Suppression of Amber Codons in Caulobacter crescentus by the Orthogonal Escherichia coli Histidyl-tRNA Synthetase/tRNAHis Pair

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e83630 ◽  
Author(s):  
Jae-hyeong Ko ◽  
Paula Montero Llopis ◽  
Jennifer Heinritz ◽  
Christine Jacobs-Wagner ◽  
Dieter Söll
Keyword(s):  
Escherichia Coli ◽  
Caulobacter Crescentus ◽  
Trna Synthetase

scholarly journals Conformational shifts in a chemoreceptor helical hairpin control kinase signaling in Escherichia coli

2019 ◽  
Vol 116 (31) ◽  
pp. 15651-15660
Author(s):  
Qun Gao ◽  
Anchun Cheng ◽  
John S. Parkinson
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Salt Bridge ◽  
Soft Agar ◽  
Side Chain ◽  
Wild Type ◽  
Chemical Gradients ◽  
Helical Hairpin ◽  
Mutant Receptors ◽  
Activity Dependent

Motile Escherichia coli cells use chemoreceptor signaling arrays to track chemical gradients with exquisite precision. Highly conserved residues in the cytoplasmic hairpin tip of chemoreceptor molecules promote assembly of trimer-based signaling complexes and modulate the activity of their CheA kinase partners. To explore hairpin tip output states in the serine receptor Tsr, we characterized the signaling consequences of amino acid replacements at the salt-bridge residue pair E385-R388. All mutant receptors assembled trimers and signaling complexes, but most failed to support serine chemotaxis in soft agar assays. Small side-chain replacements at either residue produced OFF- or ON-shifted outputs that responded to serine stimuli in wild-type fashion, suggesting that these receptors, like the wild-type, operate as two-state signaling devices. Larger aliphatic or aromatic side chains caused slow or partial kinase control responses that proved dependent on the connections between core signaling units that promote array cooperativity. In a mutant lacking one of two key adapter-kinase contacts (interface 2), those mutant receptors exhibited more wild-type behaviors. Lastly, mutant receptors with charged amino acid replacements assembled signaling complexes that were locked in kinase-ON (E385K|R) or kinase-OFF (R388D|E) output. The hairpin tips of mutant receptors with these more aberrant signaling properties probably have nonnative structures or dynamic behaviors. Our results suggest that chemoeffector stimuli and adaptational modifications influence the cooperative connections between core signaling units. This array remodeling process may involve activity-dependent changes in the relative strengths of interface 1 and 2 interactions between the CheW and CheA.P5 components of receptor core signaling complexes.

scholarly journals Nontraditional systems in aging research: an update

2020 ◽  
Author(s):  
Justyna Mikuła-Pietrasik ◽  
Martyna Pakuła ◽  
Małgorzata Markowska ◽  
Paweł Uruski ◽  
Ludwina Szczepaniak-Chicheł ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Drosophila Melanogaster ◽  
Caenorhabditis Elegans ◽  
Caulobacter Crescentus ◽  
Killer Whale ◽  
Somatic Cells ◽  
Greenland Shark ◽  
Arctica Islandica ◽  
Aging Research

Abstract Research on the evolutionary and mechanistic aspects of aging and longevity has a reductionist nature, as the majority of knowledge originates from experiments on a relatively small number of systems and species. Good examples are the studies on the cellular, molecular, and genetic attributes of aging (senescence) that are primarily based on a narrow group of somatic cells, especially fibroblasts. Research on aging and/or longevity at the organismal level is dominated, in turn, by experiments on Drosophila melanogaster, worms (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), and higher organisms such as mice and humans. Other systems of aging, though numerous, constitute the minority. In this review, we collected and discussed a plethora of up-to-date findings about studies of aging, longevity, and sometimes even immortality in several valuable but less frequently used systems, including bacteria (Caulobacter crescentus, Escherichia coli), invertebrates (Turritopsis dohrnii, Hydra sp., Arctica islandica), fishes (Nothobranchius sp., Greenland shark), reptiles (giant tortoise), mammals (blind mole rats, naked mole rats, bats, elephants, killer whale), and even 3D organoids, to prove that they offer biogerontologists as much as the more conventional tools. At the same time, the diversified knowledge gained owing to research on those species may help to reconsider aging from a broader perspective, which should translate into a better understanding of this tremendously complex and clearly system-specific phenomenon.

scholarly journals Responses of Escherichia coli Bacteria to Two Opposing Chemoattractant Gradients Depend on the Chemoreceptor Ratio

2010 ◽  
Vol 192 (7) ◽  
pp. 1796-1800 ◽  
Author(s):  
Yevgeniy Kalinin ◽  
Silke Neumann ◽  
Victor Sourjik ◽  
Mingming Wu
Keyword(s):  
Escherichia Coli ◽  
Growth Conditions ◽  
Growth Duration ◽  
E Coli ◽  
Chemical Gradients ◽  
Single Chemical ◽  
Decision Making Processes ◽  
Chemical Stimuli ◽  
Escherichia Coli Bacteria ◽  
Multiple Chemical

ABSTRACT Escherichia coli chemotaxis has long served as a simple model of environmental signal processing, and bacterial responses to single chemical gradients are relatively well understood. Less is known about the chemotactic behavior of E. coli in multiple chemical gradients. In their native environment, cells are often exposed to multiple chemical stimuli. Using a recently developed microfluidic chemotaxis device, we exposed E. coli cells to two opposing but equally potent gradients of major attractants, methyl-aspartate and serine. The responses of E. coli cells demonstrated that chemotactic decisions depended on the ratio of the respective receptor number of Tar/Tsr. In addition, the ratio of Tar to Tsr was found to vary with cells’ growth conditions, whereby it depended on the culture density but not on the growth duration. These results provide biological insights into the decision-making processes of chemotactic bacteria that are subjected to multiple chemical stimuli and demonstrate the importance of the cellular microenvironment in determining phenotypic behavior.

scholarly journals YhdJ, a Nonessential CcrM-Like DNA Methyltransferase of Escherichia coli and Salmonella enterica

2007 ◽  
Vol 189 (11) ◽  
pp. 4325-4327 ◽  
Author(s):  
Sarah E. Broadbent ◽  
Roberto Balbontin ◽  
Josep Casadesus ◽  
Martin G. Marinus ◽  
Marjan van der Woude
Keyword(s):  
Escherichia Coli ◽  
Salmonella Enterica ◽  
Dna Methyltransferase ◽  
Caulobacter Crescentus ◽  
Essential Gene ◽  
Gene Products ◽  
E Coli ◽  
Dna Adenine Methyltransferase

ABSTRACT The Caulobacter crescentus DNA adenine methyltransferase CcrM and its homologs in the α-Proteobacteria are essential for viability. CcrM is 34% identical to the yhdJ gene products of Escherichia coli and Salmonella enterica. This study provides evidence that the E. coli yhdJ gene encodes a DNA adenine methyltransferase. In contrast to an earlier report, however, we show that yhdJ is not an essential gene in either E. coli or S. enterica.

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