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Xu Q, Ali S, Afzal M, Nizami AS, Han S, Dar MA, Zhu D. Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172967. [PMID: 38705297 DOI: 10.1016/j.scitotenv.2024.172967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/06/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.
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Affiliation(s)
- Qi Xu
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Shehbaz Ali
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Muhammad Afzal
- Soil & Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Abdul-Sattar Nizami
- Sustainable Development Study Centre, Government College University, Lahore 54000, Pakistan
| | - Song Han
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Mudasir A Dar
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Daochen Zhu
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China.
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Glenn SJ, Gentry-Lear Z, Shavlik M, Harms MJ, Asaki TJ, Baylink A. Bacterial vampirism mediated through taxis to serum. eLife 2024; 12:RP93178. [PMID: 38820052 PMCID: PMC11142651 DOI: 10.7554/elife.93178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024] Open
Abstract
Bacteria of the family Enterobacteriaceae are associated with gastrointestinal (GI) bleeding and bacteremia and are a leading cause of death, from sepsis, for individuals with inflammatory bowel diseases. The bacterial behaviors and mechanisms underlying why these bacteria are prone to bloodstream entry remain poorly understood. Herein, we report that clinical isolates of non-typhoidal Salmonella enterica serovars, Escherichia coli, and Citrobacter koseri are rapidly attracted toward sources of human serum. To simulate GI bleeding, we utilized an injection-based microfluidics device and found that femtoliter volumes of human serum are sufficient to induce bacterial attraction to the serum source. This response is orchestrated through chemotaxis and the chemoattractant L-serine, an amino acid abundant in serum that is recognized through direct binding by the chemoreceptor Tsr. We report the first crystal structures of Salmonella Typhimurium Tsr in complex with L-serine and identify a conserved amino acid recognition motif for L-serine shared among Tsr orthologues. We find Tsr to be widely conserved among Enterobacteriaceae and numerous World Health Organization priority pathogens associated with bloodstream infections. Lastly, we find that Enterobacteriaceae use human serum as a source of nutrients for growth and that chemotaxis and the chemoreceptor Tsr provide a competitive advantage for migration into enterohemorrhagic lesions. We define this bacterial behavior of taxis toward serum, colonization of hemorrhagic lesions, and the consumption of serum nutrients as 'bacterial vampirism', which may relate to the proclivity of Enterobacteriaceae for bloodstream infections.
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Affiliation(s)
- Siena J Glenn
- Washington State University, Department of Veterinary Microbiology and PathologyPullmanUnited States
| | | | - Michael Shavlik
- University of Oregon, Institute of Molecular BiologyEugeneUnited States
| | - Michael J Harms
- University of Oregon, Institute of Molecular BiologyEugeneUnited States
- University of Oregon, Department of Chemistry & BiochemistryEugeneUnited States
| | - Thomas J Asaki
- Washington State University, Department of Mathematics and StatisticsPullmanUnited States
| | - Arden Baylink
- Washington State University, Department of Veterinary Microbiology and PathologyPullmanUnited States
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3
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Zhao Q, Yao F, Li W, Liu S, Bi S. Identification of a dCache-type chemoreceptor in Campylobacter jejuni that specifically mediates chemotaxis towards methyl pyruvate. Front Microbiol 2024; 15:1400284. [PMID: 38784811 PMCID: PMC11111895 DOI: 10.3389/fmicb.2024.1400284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
The foodborne pathogenic bacterium Campylobacter jejuni utilizes chemotaxis to assist in the colonization of host niches. A key to revealing the relationship among chemotaxis and pathogenicity is the discovery of signaling molecules perceived by the chemoreceptors. The C. jejuni chemoreceptor Tlp11 is encoded by the highly infective C. jejuni strains. In the present study, we report that the dCache-type ligand-binding domain (LBD) of C. jejuni ATCC 33560 Tlp11 binds directly to novel ligands methyl pyruvate, toluene, and quinoline using the same pocket. Methyl pyruvate elicits a strong chemoattractant response, while toluene and quinoline function as the antagonists without triggering chemotaxis. The sensory LBD was used to control heterologous proteins by constructing chimeras, indicating that the signal induced by methyl pyruvate is transmitted across the membrane. In addition, bioinformatics and experiments revealed that the dCache domains with methyl pyruvate-binding sites and ability are widely distributed in the order Campylobacterales. This is the first report to identify the class of dCache chemoreceptors that bind to attractant methyl pyruvate and antagonists toluene and quinoline. Our research provides a foundation for understanding the chemotaxis and virulence of C. jejuni and lays a basis for the control of this foodborne pathogen.
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fulian Yao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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4
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Tikhomirova A, McNabb ER, Petterlin L, Bellamy GL, Lin KH, Santoso CA, Daye ES, Alhaddad FM, Lee KP, Roujeinikova A. Campylobacter jejuni virulence factors: update on emerging issues and trends. J Biomed Sci 2024; 31:45. [PMID: 38693534 PMCID: PMC11064354 DOI: 10.1186/s12929-024-01033-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
Campylobacter jejuni is a very common cause of gastroenteritis, and is frequently transmitted to humans through contaminated food products or water. Importantly, C. jejuni infections have a range of short- and long-term sequelae such as irritable bowel syndrome and Guillain Barre syndrome. C. jejuni triggers disease by employing a range of molecular strategies which enable it to colonise the gut, invade the epithelium, persist intracellularly and avoid detection by the host immune response. The objective of this review is to explore and summarise recent advances in the understanding of the C. jejuni molecular factors involved in colonisation, invasion of cells, collective quorum sensing-mediated behaviours and persistence. Understanding the mechanisms that underpin the pathogenicity of C. jejuni will enable future development of effective preventative approaches and vaccines against this pathogen.
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Affiliation(s)
- Alexandra Tikhomirova
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Emmylee R McNabb
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Luca Petterlin
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Georgia L Bellamy
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Kyaw H Lin
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christopher A Santoso
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Ella S Daye
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Fatimah M Alhaddad
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Kah Peng Lee
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Anna Roujeinikova
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.
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Fields JL, Zhang H, Bellis NF, Petersen HA, Halder SK, Rich-New ST, Wu H, Wang F. Structural diversity and clustering of bacterial flagellar outer domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585621. [PMID: 38562817 PMCID: PMC10983879 DOI: 10.1101/2024.03.18.585621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we elucidate atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyzed all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a previously unexplored cluster, indicating new opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.
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6
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Glenn SJ, Gentry-Lear Z, Shavlik M, Harms MJ, Asaki TJ, Baylink A. Bacterial vampirism mediated through taxis to serum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.07.548164. [PMID: 37461633 PMCID: PMC10350070 DOI: 10.1101/2023.07.07.548164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Bacteria of the family Enterobacteriaceae are associated with gastrointestinal (GI) bleeding and bacteremia and are a leading cause of death, from sepsis, for individuals with inflammatory bowel diseases. The bacterial behaviors and mechanisms underlying why these bacteria are prone to bloodstream entry remains poorly understood. Herein, we report that clinical isolates of non-typhoidal Salmonella enterica serovars, Escherichia coli, and Citrobacter koseri are rapidly attracted toward sources of human serum. To simulate GI bleeding, we utilized a custom injection-based microfluidics device and found that femtoliter volumes of human serum are sufficient to induce the bacterial population to swim toward and aggregate at the serum source. This response is orchestrated through chemotaxis, and a major chemical cue driving chemoattraction is L-serine, an amino acid abundant in serum that is recognized through direct binding by the chemoreceptor Tsr. We report the first crystal structures of Salmonella Typhimurium Tsr in complex with L-serine and identify a conserved amino acid recognition motif for L-serine shared among Tsr orthologues. By mapping the phylogenetic distribution of this chemoreceptor we found Tsr to be widely conserved among Enterobacteriaceae and numerous World Health Organization priority pathogens associated with bloodstream infections. Lastly, we find that Enterobacteriaceae use human serum as a source of nutrients for growth and that chemotaxis and the chemoreceptor Tsr provides a competitive advantage for migration into enterohaemorrhagic lesions. We term this bacterial behavior of taxis toward serum, colonization of hemorrhagic lesions, and the consumption of serum nutrients, as 'bacterial vampirism' which may relate to the proclivity of Enterobacteriaceae for bloodstream infections.
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7
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Gentry-Lear Z, Franco K, Shavlik M, Harms MJ, Baylink A. Navigating contradictions: Salmonella Typhimurium chemotactic responses to conflicting chemoeffector signals show parity with bacterial growth benefits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576330. [PMID: 38293242 PMCID: PMC10827161 DOI: 10.1101/2024.01.18.576330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Many bacteria that colonize the guts of animals use chemotaxis to direct swimming motility and select sites for colonization based on sources of effectors derived from the host, diet, and microbial competitors of the local environ. The complex ecosystem of the gastrointestinal tract contains mixtures of chemoattractants and chemorepellents, but it remains poorly understood how swimming bacteria navigate conflicting signals. The enteric pathogen Salmonella Typhimurium possesses Tsr, a chemoreceptor protein that directs both chemoattraction and chemorepulsion responses, which we employed as a model to study chemotaxis in the presence of conflicting effector stimuli. We investigated how S. Typhimurium responds to human fecal matter, an effector source in the enteric lumen that contains high concentrations of indole, a bacteriostatic chemorepellent produced by the native commensals of the microbiota, and also nutrients such as l-serine, a chemoattractant. The indole concentration in human feces is more than 12-fold the concentration required for half-maximal chemorepulsion, however, we find S. Typhimurium, and various clinical isolates of non-typhoidal S. enterica serovars, are strongly attracted to liquid fecal matter. We further investigated the chemotactic responses of S. Typhimurium to titrations of indole and l-serine and revealed that chemorepulsion to indole is overridden in the presence of excess l-serine. We capture the inversion of these two opposing taxis behaviors in a phenomenon we define as "chemohalation" in which the bacteria organize into a halo around the treatment source with an interior zone of avoidance, which represents a compromise between chemoattraction and chemorepulsion. Growth analyses reveal that the chemotactic responses to these opposing effectors align chemoattraction and chemorepulsion with the relative growth of the bacteria in culture. Hence, our study supports the view that evolution has finely tuned chemotaxis to assess environmental habitability by evaluating the tradeoffs in bacterial growth based on the local combination of effectors.
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Affiliation(s)
- Zealon Gentry-Lear
- University of Oregon, Department of Chemistry & Biochemistry, Eugene, OR, 97403
| | - Kailie Franco
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, WA 99164
| | - Michael Shavlik
- University of Oregon, Department of Chemistry & Biochemistry, Eugene, OR, 97403
| | - Michael J. Harms
- University of Oregon, Department of Chemistry & Biochemistry, Eugene, OR, 97403
- University of Oregon, Institute of Molecular Biology, Eugene, OR, 97403
| | - Arden Baylink
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, WA 99164
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8
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Phan TV, Mattingly HH, Vo L, Marvin JS, Looger LL, Emonet T. Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model. Proc Natl Acad Sci U S A 2024; 121:e2309251121. [PMID: 38194458 PMCID: PMC10801886 DOI: 10.1073/pnas.2309251121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.
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Affiliation(s)
- Trung V. Phan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | | | - Lam Vo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | - Jonathan S. Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA20147
| | - Loren L. Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA20147
- HHMI, University of California, San Diego, CA92093
- Department of Neurosciences, University of California, San Diego, CA92093
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Department of Physics, Yale University, New Haven, CT06511
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9
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Seymour JR, Brumley DR, Stocker R, Raina JB. Swimming towards each other: the role of chemotaxis in bacterial interactions. Trends Microbiol 2024:S0966-842X(23)00360-8. [PMID: 38212193 DOI: 10.1016/j.tim.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024]
Abstract
Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.
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Affiliation(s)
- Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
| | - Douglas R Brumley
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia.
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
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10
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Matilla MA, Krell T. Sensing the environment by bacterial plant pathogens: What do their numerous chemoreceptors recognize? Microb Biotechnol 2024; 17:e14368. [PMID: 37929806 PMCID: PMC10832524 DOI: 10.1111/1751-7915.14368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023] Open
Abstract
Bacteria have evolved multiple sensing strategies to efficiently adapt to their natural hosts and environments. In the context of plant pathology, chemotaxis allows phytopathogenic bacteria to direct their movement towards hosts through the detection of a landscape of plant-derived molecules, facilitating the initiation of the infective process. The importance of chemotaxis for the lifestyle of phytopathogens is also reflected in the fact that they have, on average, twice as many chemoreceptors as bacteria that do not interact with plants. Paradoxically, the knowledge about the function of plant pathogen chemoreceptors is scarce. Notably, many of these receptors seem to be specific to plant-interacting bacteria, suggesting that they may recognize plant-specific compounds. Here, we highlight the need to advance our knowledge of phytopathogen chemoreceptor function, which may serve as a base for the development of anti-infective therapies for the control of phytopathogens.
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Affiliation(s)
- Miguel A. Matilla
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
| | - Tino Krell
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
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Matilla MA, Krell T. Targeting motility and chemotaxis as a strategy to combat bacterial pathogens. Microb Biotechnol 2023; 16:2205-2211. [PMID: 37387327 PMCID: PMC10686171 DOI: 10.1111/1751-7915.14306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Affiliation(s)
- Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasGranadaSpain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasGranadaSpain
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12
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Zhou B, Garber JM, Vlach J, Azadi P, Ng KKS, Escalante-Semerena JC, Szymanski CM. Campylobacter jejuni uses energy taxis and a dehydrogenase enzyme for l-fucose chemotaxis. mBio 2023; 14:e0273223. [PMID: 38032212 PMCID: PMC10746189 DOI: 10.1128/mbio.02732-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE In this study, we identify a separate role for the Campylobacter jejuni l-fucose dehydrogenase in l-fucose chemotaxis and demonstrate that this mechanism is not only limited to C. jejuni but is also present in Burkholderia multivorans. We now hypothesize that l-fucose energy taxis may contribute to the reduction of l-fucose-metabolizing strains of C. jejuni from the gastrointestinal tract of breastfed infants, selecting for isolates with increased colonization potential.
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Affiliation(s)
- Bibi Zhou
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Jolene M. Garber
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Jiri Vlach
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | | | - Christine M. Szymanski
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
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13
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Matilla MA, Gavira JA, Krell T. Accessing nutrients as the primary benefit arising from chemotaxis. Curr Opin Microbiol 2023; 75:102358. [PMID: 37459734 DOI: 10.1016/j.mib.2023.102358] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 09/17/2023]
Abstract
About half of the known bacterial species perform chemotaxis that gains them access to sites that are optimal for growth and survival. The motility apparatus and chemotaxis signaling pathway impose a large energetic and metabolic burden on the cell. There is almost no limit to the type of chemoeffectors that are recognized by bacterial chemoreceptors. For example, they include hormones, neurotransmitters, quorum-sensing molecules, and inorganic ions. However, the vast majority of chemoeffectors appear to be of metabolic value. We review here the experimental evidence indicating that accessing nutrients is the main selective force that led to the evolution of chemotaxis.
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Affiliation(s)
- Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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14
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Isenberg RY, Holschbach CS, Gao J, Mandel MJ. Functional analysis of cyclic diguanylate-modulating proteins in Vibrio fischeri. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550417. [PMID: 37546929 PMCID: PMC10402110 DOI: 10.1101/2023.07.24.550417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
As bacterial symbionts transition from a motile free-living state to a sessile biofilm state, they must coordinate behavior changes suitable to each lifestyle. Cyclic diguanylate (c-di-GMP) is an intracellular signaling molecule that can regulate this transition, and it is synthesized by diguanylate cyclase (DGC) enzymes and degraded by phosphodiesterase (PDE) enzymes. Generally, c-di-GMP inhibits motility and promotes biofilm formation. While c-di-GMP and the enzymes that contribute to its metabolism have been well-studied in pathogens, considerably less focus has been placed on c-di-GMP regulation in beneficial symbionts. Vibrio fischeri is the sole beneficial symbiont of the Hawaiian bobtail squid (Euprymna scolopes) light organ, and the bacterium requires both motility and biofilm formation to efficiently colonize. C-di-GMP regulates swimming motility and cellulose exopolysaccharide production in V. fischeri. The genome encodes 50 DGCs and PDEs, and while a few of these proteins have been characterized, the majority have not undergone comprehensive characterization. In this study, we use protein overexpression to systematically characterize the functional potential of all 50 V. fischeri proteins. All 28 predicted DGCs and 14 predicted PDEs displayed at least one phenotype consistent with their predicted function, and a majority of each displayed multiple phenotypes. Finally, active site mutant analysis of proteins with the potential for both DGC and PDE activities revealed potential activities for these proteins. This work presents a systems-level functional analysis of a family of signaling proteins in a tractable animal symbiont and will inform future efforts to characterize the roles of individual proteins during lifestyle transitions.
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Affiliation(s)
- Ruth Y. Isenberg
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Chandler S. Holschbach
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
| | - Jing Gao
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mark J. Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
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15
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Phan TV, Mattingly HH, Vo L, Marvin JS, Looger LL, Emonet T. Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543315. [PMID: 37333331 PMCID: PMC10274659 DOI: 10.1101/2023.06.01.543315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.
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Affiliation(s)
- Trung V. Phan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | | | - Lam Vo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | | | - Loren L. Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
- Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
- Quantitative Biology Institute, Yale University, New Haven, CT
- Department of Physics, Yale University, New Haven, CT
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16
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Chen C, Chen K, Huang Z, Huang X, Wang Z, He F, Qin M, Long C, Tang B, Mo X, Liu J, Tang W. Identification of intestinal microbiome associated with lymph-vascular invasion in colorectal cancer patients and predictive label construction. Front Cell Infect Microbiol 2023; 13:1098310. [PMID: 37249979 PMCID: PMC10215531 DOI: 10.3389/fcimb.2023.1098310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/04/2023] [Indexed: 05/31/2023] Open
Abstract
Objective To identify differences between the composition, abundance, and biological function of the intestinal microbiome of patients with and without lymph-vascular invasion (LVI) colorectal cancer (CRC) and to construct predictive labels to support accurate assessment of LVI in CRC. Method 134 CRC patients were included, which were divided into two groups according to the presence or absence of LVI, and their intestinal microbiomes were sequenced by 16SrRNA and analyzed for differences. The transcriptome sequencing data of 9 CRC patients were transformed into immune cells abundance matrix by CIBERSORT algorithm, and the correlation among LVI-associated differential intestinal microbiomes, immune cells, immune-related genes and LVI-associated differential GO items and KEGG pathways were analyzed. A random forest (RF) and eXtreme Gradient Boosting (XGB) model were constructed to predict the LVI of CRC patients based on the differential microbiome. Result There was no significant difference in α-diversity and β-diversity of intestinal microbiome between CRC patients with and without LVI (P > 0.05). Linear discriminant analysis Effect Size (LEfSe) analysis showed 34 intestinal microbiomes enriched in CRC patients of the LVI group and 5 intestinal microbiomes were significantly enriched in CRC patients of the non-lymph-vascular invasion (NLVI) group. The RF and XGB prediction models constructed with the top 15% of the LVI-associated differential intestinal microbiomes ranked by feature significance had good efficacy. Conclusions There are 39 intestinal flora with significantly different species abundance between the LVI and NLVI groups. g:Alistipes.s:Alistipes_indistinctus is closely associated with colorectal cancer vascular invasion. LVI-associated differential intestinal flora may be involved in regulating the infiltration of immune cells in CRC and influencing the expression of immune-related genes. LVI-associated differential intestinal flora may influence the process of vascular invasion in CRC through a number of potential biological functions. RF prediction models and XGB prediction models constructed based on microbial markers of gut flora can be used to predict CRC-LVI conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xianwei Mo
- *Correspondence: Weizhong Tang, ; Jungang Liu, ; Xianwei Mo,
| | - Jungang Liu
- *Correspondence: Weizhong Tang, ; Jungang Liu, ; Xianwei Mo,
| | - Weizhong Tang
- *Correspondence: Weizhong Tang, ; Jungang Liu, ; Xianwei Mo,
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