51
|
Alvarado A, Behrens W, Josenhans C. Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility. Front Microbiol 2020; 10:3055. [PMID: 32010106 PMCID: PMC6978683 DOI: 10.3389/fmicb.2019.03055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved complex sensing and signaling systems to react to their changing environments, most of which are present in all domains of life. Canonical bacterial sensing and signaling modules, such as membrane-bound ligand-binding receptors and kinases, are very well described. However, there are distinct sensing mechanisms in bacteria that are less studied. For instance, the sensing of internal or external cues can also be mediated by changes in protein conformation, which can either be implicated in enzymatic reactions, transport channel formation or other important cellular functions. These activities can then feed into pathways of characterized kinases, which translocate the information to the DNA or other response units. This type of bacterial sensory activity has previously been termed protein activity sensing. In this review, we highlight the recent findings about this non-canonical sensory mechanism, as well as its involvement in metabolic functions and bacterial motility. Additionally, we explore some of the specific proteins and protein-protein interactions that mediate protein activity sensing and their downstream effects. The complex sensory activities covered in this review are important for bacterial navigation and gene regulation in their dynamic environment, be it host-associated, in microbial communities or free-living.
Collapse
Affiliation(s)
- Alejandra Alvarado
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany
| | - Wiebke Behrens
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Christine Josenhans
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| |
Collapse
|
52
|
Suchanek VM, Esteban-López M, Colin R, Besharova O, Fritz K, Sourjik V. Chemotaxis and cyclic-di-GMP signalling control surface attachment of Escherichia coli. Mol Microbiol 2019; 113:728-739. [PMID: 31793092 DOI: 10.1111/mmi.14438] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/28/2019] [Indexed: 12/18/2022]
Abstract
Attachment to surfaces is an important early step during bacterial infection and during formation of submerged biofilms. Although flagella-mediated motility is known to be important for attachment of Escherichia coli and other bacteria, implications of motility regulation by cellular signalling remain to be understood. Here, we show that motility largely promotes attachment of E. coli, including that mediated by type 1 fimbriae, by allowing cells to reach, get hydrodynamically trapped at and explore the surface. Inactivation or inhibition of the chemotaxis signalling pathway improves attachment by suppressing cell reorientations and thereby increasing surface residence times. The attachment is further enhanced by deletion of genes encoding the cyclic diguanosine monophosphate (c-di-GMP)-dependent flagellar brake YcgR or the diguanylate cyclase DgcE. Such increased attachment in absence of c-di-GMP signalling is in contrast to its commonly accepted function as a positive regulator of the sessile state. It is apparently due to the increased swimming speed of E. coli in absence of YcgR-mediated motor control, which strengthens adhesion mediated by the type 1 fimbriae. Thus, both signalling networks that regulate motility of E. coli also control its engagement with both biotic and abiotic surfaces, which has likely implications for infection and biofilm formation.
Collapse
Affiliation(s)
- Verena Maria Suchanek
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - María Esteban-López
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Rémy Colin
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Olga Besharova
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Kirstin Fritz
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| |
Collapse
|
53
|
Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J 2019; 118:492-504. [PMID: 31839263 DOI: 10.1016/j.bpj.2019.11.3382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
The attractant chemotaxis response of Escherichia coli to norepinephrine requires that it be converted to 3,4-dihydroxymandelic acid (DHMA) by the monoamine oxidase TynA and the aromatic aldehyde dehydrogenase FeaB. DHMA is sensed by the serine chemoreceptor Tsr, and the attractant response requires that at least one subunit of the periplasmic domain of the Tsr homodimer (pTsr) has an intact serine-binding site. DHMA that is generated in vivo by E. coli is expected to be a racemic mixture of the (R) and (S) enantiomers, so it has been unclear whether one or both chiral forms are active. Here, we used a combination of state-of-the-art tools in molecular docking and simulations, including an in-house simulation-based docking protocol, to investigate the binding properties of (R)-DHMA and (S)-DHMA to E. coli pTsr. Our studies computationally predicted that (R)-DHMA should promote a stronger attractant response than (S)-DHMA because of a consistently greater-magnitude piston-like pushdown of the pTsr α-helix 4 toward the membrane upon binding of (R)-DHMA than upon binding of (S)-DHMA. This displacement is caused primarily by interaction of DHMA with Tsr residue Thr156, which has been shown by genetic studies to be critical for the attractant response to L-serine and DHMA. These findings led us to separate the two chiral species and test their effectiveness as chemoattractants. Both the tethered cell and motility migration coefficient assays validated the prediction that (R)-DHMA is a stronger attractant than (S)-DHMA. Our study demonstrates that refined computational docking and simulation studies combined with experiments can be used to investigate situations in which subtle differences between ligands may lead to diverse chemotactic responses.
Collapse
Affiliation(s)
- Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Jingyun Yang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Nitesh Sule
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Kenneth G Hull
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Mingzhao Zhu
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Daniel Romo
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Michael D Manson
- Department of Biology, Texas A&M University, College Station, Texas.
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.
| |
Collapse
|
54
|
Rebolleda-Gómez M, Wood CW. Unclear Intentions: Eavesdropping in Microbial and Plant Systems. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00385] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
55
|
Abstract
Prokaryotic organisms occupy the most diverse set of environments and conditions on our planet. Their ability to sense and respond to a broad range of external cues remain key research areas in modern microbiology, central to behaviors that underlie beneficial and pathogenic interactions of bacteria with multicellular organisms and within complex ecosystems. Advances in our understanding of the one- and two-component signal transduction systems that underlie these sensing pathways have been driven by advances in imaging the behavior of many individual bacterial cells, as well as visualizing individual proteins and protein arrays within living cells. Cryo-electron tomography continues to provide new insights into the structure and function of chemosensory receptors and flagellar motors, while advances in protein labeling and tracking are applied to understand information flow between receptor and motor. Sophisticated microfluidics allow simultaneous analysis of the behavior of thousands of individual cells, increasing our understanding of how variance between individuals is generated, regulated and employed to maximize fitness of a population. In vitro experiments have been complemented by the study of signal transduction and motility in complex in vivo models, allowing investigators to directly address the contribution of motility, chemotaxis and aggregation/adhesion on virulence during infection. Finally, systems biology approaches have demonstrated previously uncharted areas of protein space in which novel two-component signal transduction pathways can be designed and constructed de novo These exciting experimental advances were just some of the many novel findings presented at the 15th Bacterial Locomotion and Signal Transduction conference (BLAST XV) in January 2019.
Collapse
|
56
|
Bo TB, Zhang XY, Wen J, Deng K, Qin XW, Wang DH. The microbiota-gut-brain interaction in regulating host metabolic adaptation to cold in male Brandt's voles (Lasiopodomys brandtii). ISME JOURNAL 2019; 13:3037-3053. [PMID: 31455805 DOI: 10.1038/s41396-019-0492-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/20/2019] [Accepted: 07/24/2019] [Indexed: 12/25/2022]
Abstract
Gut microbiota play a critical role in orchestrating metabolic homeostasis of the host. However, the crosstalk between host and microbial symbionts in small mammals are rarely illustrated. We used male Brandt's voles (Lasiopodomys brandtii) to test the hypothesis that gut microbiota and host neurotransmitters, such as norepinephrine (NE), interact to regulate energetics and thermogenesis during cold acclimation. We found that increases in food intake and thermogenesis were associated with increased monoamine neurotransmitters, ghrelin, short-chain fatty acids, and altered cecal microbiota during cold acclimation. Further, our pair-fed study showed that cold temperature can alter the cecal microbiota independently of overfeeding. Using cecal microbiota transplant along with β3-adrenoceptor antagonism and PKA inhibition, we confirmed that transplant of cold-acclimated microbiota increased thermogenesis through activation of cAMP-PKA-pCREB signaling. In addition, NE manipulation induced a long-term alteration in gut microbiota structure. These data demonstrate that gut microbiota-NE crosstalk via cAMP signaling regulates energetics and thermogenesis during cold acclimation in male Brandt's voles.
Collapse
Affiliation(s)
- Ting-Bei Bo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xue-Ying Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Jing Wen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ke Deng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.,Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, Sichuan, China
| | - Xiao-Wei Qin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - De-Hua Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| |
Collapse
|
57
|
Mobeen F, Sharma V, Prakash T. Functional signature analysis of extreme Prakriti endophenotypes in gut microbiome of western Indian rural population. Bioinformation 2019; 15:490-505. [PMID: 31485135 PMCID: PMC6704335 DOI: 10.6026/97320630015490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/30/2019] [Indexed: 12/27/2022] Open
Abstract
Ayurveda is practiced in India from ancient times and stratifies the individuals based on their Prakriti constitution. Advancements in modern science have led to the association of Prakriti with molecular, biochemical, genomic and other entities. We have recently explored the gut microbiome composition and microbial signatures in healthy extreme Prakriti endo-phenotypes. However, their functional potentials are still lacking. The present study includes 63 females (29 Vata, 11 Pitta, and 23 Kapha) and 50 males (13 Vata, 18 Pitta, and 19 Kapha) samples. The predictive functional profiling and organism level functional traits of the human gut microbiome have been carried out in Prakriti groups using imputed metagenomic approach. A higher functional level redundancy is found than the taxonomy across the Prakriti groups, however the dominant taxa contributing to the functional profiles are found to be different. A high number of functional signatures specific to the Prakriti groups were identified in female datasets. Some of the functional signatures were found to be gender specific. For example, a higher abundance of microbes contributing potential pathogenic and stress tolerance related functions was found in Kapha in female and Pitta in male. The functional signatures correlated well with phenotypes and disease predisposition of Prakriti groups.
Collapse
Affiliation(s)
- Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| |
Collapse
|
58
|
Zou D, Meng X, Wang B, Dai Y, Yang R, Suo Y, Wu Y, Yang W, Lin R. Analysis of pharmacological mechanisms and targets mining of Wuzi-Yanzong-Wan for treating non-obstructive oligoasthenospermia. Biomed Pharmacother 2019; 115:108898. [DOI: 10.1016/j.biopha.2019.108898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/10/2019] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
|
59
|
Lamb E, Trimble MJ, McCarter LL. Cell-cell communication, chemotaxis and recruitment in Vibrio parahaemolyticus. Mol Microbiol 2019; 112:99-113. [PMID: 30938898 DOI: 10.1111/mmi.14256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2019] [Indexed: 01/16/2023]
Abstract
Motile bacteria are proficient at finding optimal environments for colonization. Often, they use chemotaxis to sense nutrient availability and dangerous concentrations of toxic chemicals. For many bacteria, the repertoire of chemoreceptors is large, suggesting they possess a broad palate with respect to sensing. However, knowledge of the molecules detected by chemotaxis signal transduction systems is limited. Some bacteria, like Vibrio parahaemolyticus, are social and swarm in groups on surfaces. This marine bacterium and human pathogen secretes the S signal autoinducer, which cues degradation of intracellular c-di-GMP leading to transcription of the swarming program. Here, we report that the S signal also directs motility at a behavioral level by serving as a chemoattractant. The data demonstrate that V. parahaemolyticus senses the S signal using SscL and SscS, homologous methyl-accepting chemotaxis proteins. SscL is required by planktonic bacteria for S signal chemotaxis. SscS plays a role during swarming, and mutants lacking this chemoreceptor swarm faster and produce colonies with more deeply branched swarming fronts than the wild type or the sscL mutant. Other Vibrio species can swim toward the S signal, suggesting a recruitment role for this cell-cell communication molecule in the context of polymicrobial marine communities.
Collapse
Affiliation(s)
- Evan Lamb
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael J Trimble
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Linda L McCarter
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| |
Collapse
|
60
|
Tovaglieri A, Sontheimer-Phelps A, Geirnaert A, Prantil-Baun R, Camacho DM, Chou DB, Jalili-Firoozinezhad S, de Wouters T, Kasendra M, Super M, Cartwright MJ, Richmond CA, Breault DT, Lacroix C, Ingber DE. Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites. MICROBIOME 2019; 7:43. [PMID: 30890187 PMCID: PMC6425591 DOI: 10.1186/s40168-019-0650-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/21/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Species-specific differences in tolerance to infection are exemplified by the high susceptibility of humans to enterohemorrhagic Escherichia coli (EHEC) infection, whereas mice are relatively resistant to this pathogen. This intrinsic species-specific difference in EHEC infection limits the translation of murine research to human. Furthermore, studying the mechanisms underlying this differential susceptibility is a difficult problem due to complex in vivo interactions between the host, pathogen, and disparate commensal microbial communities. RESULTS We utilize organ-on-a-chip (Organ Chip) microfluidic culture technology to model damage of the human colonic epithelium induced by EHEC infection, and show that epithelial injury is greater when exposed to metabolites derived from the human gut microbiome compared to mouse. Using a multi-omics approach, we discovered four human microbiome metabolites-4-methyl benzoic acid, 3,4-dimethylbenzoic acid, hexanoic acid, and heptanoic acid-that are sufficient to mediate this effect. The active human microbiome metabolites preferentially induce expression of flagellin, a bacterial protein associated with motility of EHEC and increased epithelial injury. Thus, the decreased tolerance to infection observed in humans versus other species may be due in part to the presence of compounds produced by the human intestinal microbiome that actively promote bacterial pathogenicity. CONCLUSION Organ-on-chip technology allowed the identification of specific human microbiome metabolites modulating EHEC pathogenesis. These identified metabolites are sufficient to increase susceptibility to EHEC in our human Colon Chip model and they contribute to species-specific tolerance. This work suggests that higher concentrations of these metabolites could be the reason for higher susceptibility to EHEC infection in certain human populations, such as children. Furthermore, this research lays the foundation for therapeutic-modulation of microbe products in order to prevent and treat human bacterial infection.
Collapse
Affiliation(s)
- Alessio Tovaglieri
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Alexandra Sontheimer-Phelps
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Biology, University of Freiburg, 79085, Freiburg, Germany
| | - Annelies Geirnaert
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Rachelle Prantil-Baun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Diogo M Camacho
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - David B Chou
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02115, USA
| | - Sasan Jalili-Firoozinezhad
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Bioengineering and iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1649-004, Lisbon, Portugal
| | - Tomás de Wouters
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Magdalena Kasendra
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Present Address: Emulate Inc., 27 Drydock Avenue, Boston, MA, 02210, USA
| | - Michael Super
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Mark J Cartwright
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Camilla A Richmond
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, 02139, USA
| | - David T Breault
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, 02139, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Christophe Lacroix
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, 02139, USA.
| |
Collapse
|