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Yan Y, Cao M, Ma J, Suo J, Bai X, Ge W, Lv X, Zhang Q, Chen J, Cui S, Yang B. Use of proteomics to elucidate characteristics of Cronobacter sakazakii under mild heat stress. Int J Food Microbiol 2024; 425:110885. [PMID: 39178661 DOI: 10.1016/j.ijfoodmicro.2024.110885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 08/13/2024] [Accepted: 08/17/2024] [Indexed: 08/26/2024]
Abstract
Cronobacter sakazakii is an opportunistic pathogen known for causing severe diseases. Mild heat treatment is commonly used in food processing, however, the pathogenic characteristics and underlying mechanisms of Cronobacter sakazakii strains remain poorly understood. In this study, we found that mild heat stress (MHS) at 52 °C can induce several deleterious effects in Cronobacter sakazakii, including damage to the cell wall, genomic DNA breakage, and misfolding of cytoplasmic proteins. These conditions lead to a decreased survival ability under acid, desiccation, and osmotic stress; a reduction in biofilm formation; and diminished motility. Notably, surviving C. sakazakii cells retain their pathogenicity, causing significant intestinal damage in newborn mice. This damage is characterized by epithelial sloughing and disruption of the intestinal structure. Tandem mass tag (TMT)-based proteomics identified 736 proteins with differential abundance across C. sakazakii strains subjected to mild heat stress, highlighting adaptations in biofilm formation, motility, and stress tolerance. Key regulatory changes were observed in phospholipid metabolism and protein synthesis, which underpin this complex stress response. This data illustrates a sophisticated balance between environmental adaptability and pathogenic potential. The metabolic and pathogenic responses of C. sakazakii to mild heat stress are closely linked to its phospholipid metabolism and the production of secretory proteins, both crucial for its virulence and reliant on membrane transport. This complex interplay emphasizes the need to understand these mechanisms to develop effective control strategies.
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Affiliation(s)
- Yanfei Yan
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Mengyuan Cao
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Jiaqi Ma
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Jia Suo
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Xiaobao Bai
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Wupeng Ge
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, Yangling, Shaanxi 712100, China
| | - Xin Lv
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, Yangling, Shaanxi 712100, China
| | - Qiang Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, Yangling, Shaanxi 712100, China.
| | - Jia Chen
- College of Chemical Technology, Shijiazhuang University, Shijiazhuang 050035, China.
| | - Shenghui Cui
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, Yangling, Shaanxi 712100, China.
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2
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Peterson E, Söderström B, Prins N, Le GHB, Hartley-Tassell LE, Evenhuis C, Grønnemose RB, Andersen TE, Møller-Jensen J, Iosifidis G, Duggin IG, Saunders B, Harry EJ, Bottomley AL. The role of bacterial size, shape and surface in macrophage engulfment of uropathogenic E. coli cells. PLoS Pathog 2024; 20:e1012458. [PMID: 39241059 DOI: 10.1371/journal.ppat.1012458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/26/2024] [Indexed: 09/08/2024] Open
Abstract
Uropathogenic Escherichia coli (UPEC) can undergo extensive filamentation in the host during acute urinary tract infections (UTIs). It has been hypothesised that this morphological plasticity allows bacteria to avoid host immune responses such as macrophage engulfment. However, it is still unclear what properties of filaments are important in macrophage-bacteria interactions. The aim of this work was to investigate the contribution of bacterial biophysical parameters, such as cell size and shape, and physiological parameters, such as cell surface and the environment, to macrophage engulfment efficiency. Viable, reversible filaments of known lengths and volumes were produced in the UPEC strain UTI89 using a variety of methods, including exposure to cell-wall targeting antibiotics, genetic manipulation and isolation from an in vitro human bladder cell model. Quantification of the engulfment ability of macrophages using gentamicin-protection assays and fluorescence microscopy demonstrated that the ability of filaments to avoid macrophage engulfment is dependent on a combination of size (length and volume), shape, cell surface and external environmental factors. UTI89 filamentation and macrophage engulfment efficiency was also found to occur independently of the SOS-inducible filamentation genes, sulA and ymfM in both in vivo and in vitro models of infection. Compared to filaments formed via antibiotic inhibition of division, the infection-derived filaments were preferentially targeted by macrophages. With several strains of UPEC now resistant to current antibiotics, our work identifies the importance of bacterial physiological and morphological states during infection.
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Affiliation(s)
- Elizabeth Peterson
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Australia
| | - Bill Söderström
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Australia
| | - Nienke Prins
- Janssen Vaccines and Prevention, Leiden, The Netherlands
| | - Giang H B Le
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | | | - Chris Evenhuis
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Australia
| | - Rasmus Birkholm Grønnemose
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Thomas Emil Andersen
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Gregory Iosifidis
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Australia
| | - Iain G Duggin
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Australia
| | | | - Elizabeth J Harry
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Australia
| | - Amy L Bottomley
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Australia
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3
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Welikala MU, Butterworth LJ, Behrmann MS, Trakselis MA. Tau mediated coupling between Pol III synthesis and DnaB helicase unwinding helps maintain genomic stability. J Biol Chem 2024:107726. [PMID: 39214305 DOI: 10.1016/j.jbc.2024.107726] [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: 04/10/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
The τ-subunit of the clamp loader complex (CLC) physically interacts with both the DnaB helicase and the polymerase III (Pol III) core α-subunit through Domains IV and V, respectively. This interaction is proposed to help maintain rapid and efficient DNA synthesis rates with high genomic fidelity and plasticity, facilitating enzymatic coupling within the replisome. To test this hypothesis, CRISPR-Cas9 editing was used to create site-directed genomic mutations within the dnaX gene at the C-terminus of τ predicted to interact with the α-subunit of Pol III. Perturbation of the α-τ binding interaction in vivo resulted in cellular and genomic stress markers that included reduced growth rates, fitness, and viabilities. Specifically, dnaX:mut strains showed increased cell filamentation, mutagenesis frequencies, and activated SOS. In situ fluorescence flow cytometry and microscopy quantified large increases in the amount of single-stranded DNA (ssDNA) gaps present. Removal of the C-terminus of τ (I618X) still maintained its interactions with DnaB and stimulated unwinding but lost its interaction with Pol III, resulting in significantly reduced rolling circle DNA synthesis. Intriguingly, dnaX:L635P/D636G had the largest induction of SOS, high mutagenesis, and the most prominent ssDNA gaps, which can be explained by an impaired ability to regulate the unwinding speed of DnaB resulting in a faster rate of in vitro rolling circle DNA replication, inducing replisome decoupling. Therefore, τ stimulated DnaB unwinding and physical coupling with Pol III acts to enforce replisome plasticity to maintain an efficient rate of synthesis and prevent genomic instability.
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Affiliation(s)
- Malisha U Welikala
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA
| | - Lauren J Butterworth
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA
| | - Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA.
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Afreen S, Singh N, Kaur M, Chaudhary N, Kumar A, Pahil S, Mohan B, Taneja N. Phenotypic and genomic characterization of a small colony variant of Klebsiella pneumoniae isolated from urine of a prostate cancer case. Indian J Med Microbiol 2024; 51:100664. [PMID: 38977132 DOI: 10.1016/j.ijmmb.2024.100664] [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: 02/10/2024] [Revised: 06/12/2024] [Accepted: 07/06/2024] [Indexed: 07/10/2024]
Abstract
Small colony variants (SCVs) in Klebsiella pneumoniae are rare and understudied. We report an SCV of Klebsiella pneumoniae isolated from the urine of a prostate cancer patient undergoing prolonged radiotherapy. The strain was non-lactose fermenting, non-mucoid, slow-growing, multi-drug resistant, and showed atypical biochemical reactions and biofilm formation. On whole genome sequencing, it showed low-level virulence, sequence type 231 and gene CTX-M-15. Three major porins OmpK35, OmpK36 and OmpK37 were found. SCVs pose challenges like difficulties in identification, altered metabolism, and increased biofilm formation, which contribute to persistent infections. Radiotherapy and chemotherapy may have led to the formation of the SCV phenotype.
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Affiliation(s)
- Sana Afreen
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
| | | | | | | | - Ajay Kumar
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
| | - Sapna Pahil
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
| | - Balvinder Mohan
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
| | - Neelam Taneja
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
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5
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Laanet PR, Bragina O, Jõul P, Vaher M. Plantago major and Plantago lanceolata Exhibit Antioxidant and Borrelia burgdorferi Inhibiting Activities. Int J Mol Sci 2024; 25:7112. [PMID: 39000214 PMCID: PMC11240987 DOI: 10.3390/ijms25137112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/15/2024] [Accepted: 06/20/2024] [Indexed: 07/16/2024] Open
Abstract
Lyme disease, caused by Borrelia burgdorferi sensu lato infection, is the most widespread vector-borne illness in the Northern Hemisphere. Unfortunately, using targeted antibiotic therapy is often an ineffective cure. The antibiotic resistance and recurring symptoms of Lyme disease are associated with the formation of biofilm-like aggregates of B. burgdorferi. Plant extracts could provide an effective alternative solution as many of them exhibit antibacterial or biofilm inhibiting activities. This study demonstrates the therapeutic potential of Plantago major and Plantago lanceolata as B. burgdorferi inhibitors. Hydroalcoholic extracts from three different samples of each plant were first characterised based on their total concentrations of polyphenolics, flavonoids, iridoids, and antioxidant capacity. Both plants contained substantial amounts of named phytochemicals and showed considerable antioxidant properties. The major non-volatile constituents were then quantified using HPLC-DAD-MS analyses, and volatile constituents were quantified using HS-SPME-GC-MS. The most prevalent non-volatiles were found to be plantamajoside and acteoside, and the most prevalent volatiles were β-caryophyllene, D-limonene, and α-caryophyllene. The B. burgdorferi inhibiting activity of the extracts was tested on stationary-phase B. burgdorferi culture and its biofilm fraction. All extracts showed antibacterial activity, with the most effective lowering the residual bacterial viability down to 15%. Moreover, the extracts prepared from the leaves of each plant additionally demonstrated biofilm inhibiting properties, reducing its formation by 30%.
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Affiliation(s)
- Pille-Riin Laanet
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Olga Bragina
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Piia Jõul
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Merike Vaher
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
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6
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Chong TN, Shapiro L. Bacterial cell differentiation enables population level survival strategies. mBio 2024; 15:e0075824. [PMID: 38771034 PMCID: PMC11237816 DOI: 10.1128/mbio.00758-24] [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: 05/22/2024] Open
Abstract
Clonal reproduction of unicellular organisms ensures the stable inheritance of genetic information. However, this means of reproduction lacks an intrinsic basis for genetic variation, other than spontaneous mutation and horizontal gene transfer. To make up for this lack of genetic variation, many unicellular organisms undergo the process of cell differentiation to achieve phenotypic heterogeneity within isogenic populations. Cell differentiation is either an inducible or obligate program. Induced cell differentiation can occur as a response to a stimulus, such as starvation or host cell invasion, or it can be a stochastic process. In contrast, obligate cell differentiation is hardwired into the organism's life cycle. Whether induced or obligate, bacterial cell differentiation requires the activation of a signal transduction pathway that initiates a global change in gene expression and ultimately results in a morphological change. While cell differentiation is considered a hallmark in the development of multicellular organisms, many unicellular bacteria utilize this process to implement survival strategies. In this review, we describe well-characterized cell differentiation programs to highlight three main survival strategies used by bacteria capable of differentiation: (i) environmental adaptation, (ii) division of labor, and (iii) bet-hedging.
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Affiliation(s)
- Trisha N Chong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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7
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Kiørboe T. Organismal trade-offs and the pace of planktonic life. Biol Rev Camb Philos Soc 2024. [PMID: 38855937 DOI: 10.1111/brv.13108] [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: 12/20/2023] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024]
Abstract
No one is perfect, and organisms that perform well in some habitat or with respect to some tasks, do so at the cost of performance in others: there are inescapable trade-offs. Organismal trade-offs govern the structure and function of ecosystems and attempts to demonstrate and quantify trade-offs have therefore been an important goal for ecologists. In addition, trade-offs are a key component in trait-based ecosystem models. Here, I synthesise evidence of trade-offs in plankton organisms, from bacteria to zooplankton, and show how a slow-fast gradient in life histories emerges. I focus on trade-offs related to the main components of an organism's Darwinian fitness, that is resource acquisition, survival, and propagation. All consumers need to balance the need to eat without being eaten, and diurnal vertical migration, where zooplankton hide at depth during the day to avoid visual predators but at the cost of missed feeding opportunities in the productive surface layer, is probably the best documented result of this trade-off. However, there are many other more subtle but equally important behaviours that similarly are the result of an optimisation of these trade-offs. Most plankton groups have also developed more explicit defence mechanisms, such as toxin production or evasive behaviours that are harnessed in the presence of their predators; the costs of these have often proved difficult to quantify or even demonstrate, partly because they only materialise under natural conditions. Finally, all multicellular organisms must allocate time and resources among growth, reproduction, and maintenance (e.g. protein turnover and DNA repair), and mate finding may compromise both survival and feeding. The combined effects of all these trade-offs is the emergence of a slow-fast gradient in the pace-of-life, likely the most fundamental principle for the organisation of organismal life histories. This crystallisation of trade-offs may offer a path to further simplification of trait-based models of marine ecosystems.
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Affiliation(s)
- Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, 2800 Kgs, Kemitorvet, Kgs. Lyngby, Denmark
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8
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Kohram M, Sanderson AE, Loui A, Thompson PV, Vashistha H, Shomar A, Oltvai ZN, Salman H. Nonlethal deleterious mutation-induced stress accelerates bacterial aging. Proc Natl Acad Sci U S A 2024; 121:e2316271121. [PMID: 38709929 PMCID: PMC11098108 DOI: 10.1073/pnas.2316271121] [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: 09/28/2023] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
Random mutagenesis, including when it leads to loss of gene function, is a key mechanism enabling microorganisms' long-term adaptation to new environments. However, loss-of-function mutations are often deleterious, triggering, in turn, cellular stress and complex homeostatic stress responses, called "allostasis," to promote cell survival. Here, we characterize the differential impacts of 65 nonlethal, deleterious single-gene deletions on Escherichia coli growth in three different growth environments. Further assessments of select mutants, namely, those bearing single adenosine triphosphate (ATP) synthase subunit deletions, reveal that mutants display reorganized transcriptome profiles that reflect both the environment and the specific gene deletion. We also find that ATP synthase α-subunit deleted (ΔatpA) cells exhibit elevated metabolic rates while having slower growth compared to wild-type (wt) E. coli cells. At the single-cell level, compared to wt cells, individual ΔatpA cells display near normal proliferation profiles but enter a postreplicative state earlier and exhibit a distinct senescence phenotype. These results highlight the complex interplay between genomic diversity, adaptation, and stress response and uncover an "aging cost" to individual bacterial cells for maintaining population-level resilience to environmental and genetic stress; they also suggest potential bacteriostatic antibiotic targets and -as select human genetic diseases display highly similar phenotypes, - a bacterial origin of some human diseases.
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Affiliation(s)
- Maryam Kohram
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Amy E. Sanderson
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Alicia Loui
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | | | - Harsh Vashistha
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Aseel Shomar
- Department of Chemical Engineering, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Zoltán N. Oltvai
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA15260
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA15260
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY14627
| | - Hanna Salman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.31.565030. [PMID: 37961685 PMCID: PMC10635034 DOI: 10.1101/2023.10.31.565030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions - Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueEs secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of one gene, one enzyme, one function, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. PLoS Genet 2024; 20:e1011287. [PMID: 38768229 PMCID: PMC11142719 DOI: 10.1371/journal.pgen.1011287] [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: 12/06/2023] [Revised: 05/31/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint residues in QueE that contribute distinctly to each of its functions-Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE's secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of "one gene, one enzyme, one function", which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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Affiliation(s)
- Samuel A. Adeleye
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
| | - Srujana S. Yadavalli
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
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11
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Ayibieke A, Wajima T, Kano S, Chatterjee NS, Hamabata T. The colonization factor CS6 of enterotoxigenic Escherichia coli contributes to host cell invasion. Microb Pathog 2024; 190:106636. [PMID: 38556103 DOI: 10.1016/j.micpath.2024.106636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/11/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Enterotoxigenic Escherichia coli (ETEC) is one of the main causes of diarrhea in children and travelers in low-income regions. The virulence of ETEC is attributed to its heat-labile and heat-stable enterotoxins, as well as its colonization factors (CFs). CFs are essential for ETEC adherence to the intestinal epithelium. However, its invasive capability remains unelucidated. In this study, we demonstrated that the CS6-positive ETEC strain 4266 can invade mammalian epithelial cells. The invasive capability was reduced in the 4266 ΔCS6 mutant but reintroduction of CS6 into this mutant restored the invasiveness. Additionally, the laboratory E. coli strain Top 10, which lacks the invasive capability, was able to invade Caco-2 cells after gaining the CS6-expressing plasmid pCS6. Cytochalasin D inhibited cell invasion in both 4266 and Top10 pCS6 cells, and F-actin accumulation was observed near the bacteria on the cell membrane, indicating that CS6-positive bacteria were internalized via actin polymerization. Other cell signal transduction inhibitors, such as genistein, wortmannin, LY294002, PP1, and Ro 32-0432, inhibited the CS6-mediated invasion of Caco-2 cells. The internalized bacteria of both 4266 and Top10 pCS6 strains were able to survive for up to 48 h, and 4266 cells were able to replicate within Caco-2 cells. Immunofluorescence microscopy revealed that the internalized 4266 cells were present in bacteria-containing vacuoles, which underwent a maturation process indicated by the recruitment of the early endosomal marker EEA-1 and late endosomal marker LAMP-1 throughout the infection process. The autophagy marker LC3 was also observed near these vacuoles, indicating the initiation of LC-3-associated phagocytosis (LAP). However, intracellular bacteria continued to replicate, even after the initiation of LAP. Moreover, intracellular filamentation was observed in 4266 cells at 24 h after infection. Overall, this study shows that CS6, in addition to being a major CF, mediates cell invasion. This demonstrates that once internalized, CS6-positive ETEC is capable of surviving and replicating within host cells. This capability may be a key factor in the extended and recurrent nature of ETEC infections in humans, thus highlighting the critical role of CS6.
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Affiliation(s)
- Alafate Ayibieke
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takeaki Wajima
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shigeyuki Kano
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Takashi Hamabata
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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12
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Snoeck S, Guidi C, De Mey M. "Metabolic burden" explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli. Microb Cell Fact 2024; 23:96. [PMID: 38555441 PMCID: PMC10981312 DOI: 10.1186/s12934-024-02370-9] [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: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Engineering bacterial strains to redirect the metabolism towards the production of a specific product has enabled the development of industrial biotechnology. However, rewiring the metabolism can have severe implications for a microorganism, rendering cells with stress symptoms such as a decreased growth rate, impaired protein synthesis, genetic instability and an aberrant cell size. On an industrial scale, this is reflected in processes that are not economically viable. MAIN TEXT In literature, most stress symptoms are attributed to "metabolic burden", however the actual triggers and stress mechanisms involved are poorly understood. Therefore, in this literature review, we aimed to get a better insight in how metabolic engineering affects Escherichia coli and link the observed stress symptoms to its cause. Understanding the possible implications that chosen engineering strategies have, will help to guide the reader towards optimising the envisioned process more efficiently. CONCLUSION This review addresses the gap in literature and discusses the triggers and effects of stress mechanisms that can be activated when (over)expressing (heterologous) proteins in Escherichia coli. It uncovers that the activation of the different stress mechanisms is complex and that many are interconnected. The reader is shown that care has to be taken when (over)expressing (heterologous) proteins as the cell's metabolism is tightly regulated.
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Affiliation(s)
- Sofie Snoeck
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Chiara Guidi
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Marjan De Mey
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium.
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13
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Bing J, Guan Z, Zheng T, Ennis CL, Nobile CJ, Chen C, Chu H, Huang G. Rapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection. Nat Commun 2024; 15:2381. [PMID: 38493178 PMCID: PMC10944540 DOI: 10.1038/s41467-024-46786-8] [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: 10/30/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Candida auris has become a serious threat to public health. The mechanisms of how this fungal pathogen adapts to the mammalian host are poorly understood. Here we report the rapid evolution of an adaptive C. auris multicellular aggregative morphology in the murine host during systemic infection. C. auris aggregative cells accumulate in the brain and exhibit obvious advantages over the single-celled yeast-form cells during systemic infection. Genetic mutations, specifically de novo point mutations in genes associated with cell division or budding processes, underlie the rapid evolution of this aggregative phenotype. Most mutated C. auris genes are associated with the regulation of cell wall integrity, cytokinesis, cytoskeletal properties, and cellular polarization. Moreover, the multicellular aggregates are notably more recalcitrant to the host antimicrobial peptides LL-37 and PACAP relative to the single-celled yeast-form cells. Overall, to survive in the host, C. auris can rapidly evolve a multicellular aggregative morphology via genetic mutations.
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Affiliation(s)
- Jian Bing
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Zhangyue Guan
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Tianhong Zheng
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Craig L Ennis
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, 95343, USA
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95343, USA
- Health Sciences Research Institute, University of California, Merced, Merced, CA, 95343, USA
| | - Changbin Chen
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China.
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China.
| | - Guanghua Huang
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China.
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14
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Pranjic M, Spät P, Semanjski Curkovic M, Macek B, Gruic-Sovulj I, Mocibob M. Resilience and proteome response of Escherichia coli to high levels of isoleucine mistranslation. Int J Biol Macromol 2024; 262:130068. [PMID: 38340920 DOI: 10.1016/j.ijbiomac.2024.130068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Accurate pairing of amino acids and tRNAs is a prerequisite for faithful translation of genetic information during protein biosynthesis. Here we present the effects of proteome-wide mistranslation of isoleucine (Ile) by canonical valine (Val) or non-proteinogenic norvaline (Nva) in a genetically engineered Escherichia coli strain with an editing-defective isoleucyl-tRNA synthetase (IleRS). Editing-defective IleRS efficiently mischarges both Val and Nva to tRNAIle and impairs the translational accuracy of Ile decoding. When mistranslation was induced by the addition of Val or Nva to the growth medium, an Ile-to-Val or Ile-to-Nva substitution of up to 20 % was measured by high-resolution mass spectrometry. This mistranslation level impaired bacterial growth, promoted the SOS response and filamentation during stationary phase, caused global proteome dysregulation and upregulation of the cellular apparatus for maintaining proteostasis, including the major chaperones (GroES/EL, DnaK/DnaJ/GrpE and HtpG), the disaggregase ClpB and the proteases (Lon, HslV/HslU, ClpA, ClpS). The most important consequence of mistranslation appears to be non-specific protein aggregation, which is effectively counteracted by the disaggregase ClpB. Our data show that E. coli can sustain high isoleucine mistranslation levels and remain viable despite excessive protein aggregation and severely impaired translational fidelity. However, we show that inaccurate translation lowers bacterial resilience to heat stress and decreases bacterial survival at elevated temperatures.
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Affiliation(s)
- Marija Pranjic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Philipp Spät
- Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Maja Semanjski Curkovic
- Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Boris Macek
- Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia.
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia.
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15
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Santos MNM, Pintor KL, Hsieh PY, Cheung YW, Sung LK, Shih YL, Lai EM. Agrobacteria deploy two classes of His-Me finger superfamily nuclease effectors exerting different antibacterial capacities against specific bacterial competitors. Front Microbiol 2024; 15:1351590. [PMID: 38426053 PMCID: PMC10902643 DOI: 10.3389/fmicb.2024.1351590] [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: 12/06/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024] Open
Abstract
The type VI secretion system (T6SS) assembles into a contractile nanomachine to inject effectors across bacterial membranes for secretion. The Agrobacterium tumefaciens species complex is a group of soil inhabitants and phytopathogens that deploys T6SS as an antibacterial weapon against bacterial competitors at both inter-species and intra-species levels. The A. tumefaciens strain 1D1609 genome encodes one main T6SS gene cluster and four vrgG genes (i.e., vgrGa-d), each encoding a spike protein as an effector carrier. A previous study reported that vgrGa-associated gene 2, named v2a, encodes a His-Me finger nuclease toxin (also named HNH/ENDO VII nuclease), contributing to DNase-mediated antibacterial activity. However, the functions and roles of other putative effectors remain unknown. In this study, we identified vgrGc-associated gene 2 (v2c) that encodes another His-Me finger nuclease but with a distinct Serine Histidine Histidine (SHH) motif that differs from the AHH motif of V2a. We demonstrated that the ectopic expression of V2c caused growth inhibition, plasmid DNA degradation, and cell elongation in Escherichia coli using DNAse activity assay and fluorescence microscopy. The cognate immunity protein, V3c, neutralizes the DNase activity and rescues the phenotypes of growth inhibition and cell elongation. Ectopic expression of V2c DNase-inactive variants retains the cell elongation phenotype, while V2a induces cell elongation in a DNase-mediated manner. We also showed that the amino acids of conserved SHH and HNH motifs are responsible for the V2c DNase activity in vivo and in vitro. Notably, V2c also mediated the DNA degradation and cell elongation of the target cell in the context of interbacterial competition. Importantly, V2a and V2c exhibit different capacities against different bacterial species and function synergistically to exert stronger antibacterial activity against the soft rot phytopathogen, Dickeya dadantii.
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Affiliation(s)
- Mary Nia M. Santos
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Aquaculture Research and Development Division, Department of Agriculture-National Fisheries Research and Development Institute (DA-NFRDI), Manila, Philippines
| | | | - Pei-Yu Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yee-Wai Cheung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Li-Kang Sung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
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16
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Kidner RQ, Goldstone EB, Laidemitt MR, Sanchez MC, Gerdt C, Brokaw LP, Ros-Rocher N, Morris J, Davidson WS, Gerdt JP. Host lipids regulate multicellular behavior of a predator of a human pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578218. [PMID: 38352462 PMCID: PMC10862850 DOI: 10.1101/2024.01.31.578218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
As symbionts of animals, microbial eukaryotes benefit and harm their hosts in myriad ways. A model microeukaryote (Capsaspora owczarzaki) is a symbiont of Biomphalaria glabrata snails and may prevent transmission of parasitic schistosomes from snails to humans. However, it is unclear which host factors determine Capsaspora's ability to colonize snails. Here, we discovered that Capsaspora forms multicellular aggregates when exposed to snail hemolymph. We identified a molecular cue for aggregation: a hemolymph-derived phosphatidylcholine, which becomes elevated in schistosome-infected snails. Therefore, Capsaspora aggregation may be a response to the physiological state of its host, and it may determine its ability to colonize snails and exclude parasitic schistosomes. Furthermore, Capsaspora is an evolutionary model organism whose aggregation may be ancestral to animals. This discovery, that a prevalent lipid induces Capsaspora multicellularity, suggests that this aggregation phenotype may be ancient. Additionally, the specific lipid will be a useful tool for further aggregation studies.
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Affiliation(s)
- Ria Q Kidner
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Martina R Laidemitt
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Melissa C Sanchez
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Catherine Gerdt
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Lorin P Brokaw
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Núria Ros-Rocher
- Department of Functional Genomics and Evolution, Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
- Department of Cell Biology and Infection and Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Jamie Morris
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati OH 45237, USA
| | - W Sean Davidson
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati OH 45237, USA
| | - Joseph P Gerdt
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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17
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Delik E, Eroğlu B, Tefon-Öztürk BE. Evaluation of the in vitro effects of concentrations of antibiotics on three Enterobacteriaceae isolates. World J Microbiol Biotechnol 2024; 40:73. [PMID: 38240926 PMCID: PMC10799096 DOI: 10.1007/s11274-023-03877-w] [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: 11/21/2023] [Accepted: 12/17/2023] [Indexed: 01/22/2024]
Abstract
Due to the misuse and overuse of antibiotics, bacteria are now exposed to sub-minimum inhibitory concentrations (sub-MICs) of antibiotics in various environments. In recent years, exposure of bacteria to sub-MICs of antibiotics has led to the widespread emergence of antibiotic-resistant bacteria. In this study, three bacterial species from the Enterobacteriaceae family (Raoultella ornithinolytica, Pantoea agglomerans and Klebsiella quasivariicola) were isolated from water. The antibiotic susceptibility of these bacteria to 16 antibiotics was then investigated. The effects of sub-MICs of four selected antibiotics (kanamycin, chloramphenicol, meropenem, and ciprofloxacin) on the growth, biofilm formation, surface polysaccharide production, siderophore production, morphology, and expression of the translational/transcriptional regulatory transformer gene rfaH of these bacteria were analysed. The MICs of kanamycin, chloramphenicol, meropenem, and ciprofloxacin were determined to be 1, 2, 0.03 and 0.03 µg/mL for R. ornithinolytica; 0.6, 6, 0.03 and 0.05 µg/mL for P. agglomerans; and 2, 5, 0.04 and 0.2 µg/mL for K. quasivariicola. The growth kinetics and biofilm formation ability decreased for all three isolates at sub-MICs. The surface polysaccharides of R. ornithinolytica and P. agglomerans increased at sub-MICs. There was no significant change in the siderophore activities of the bacterial isolates, with the exception of MIC/2 meropenem in R. ornithinolytica and MIC/2 kanamycin in K. quasivariicola. It was observed that the sub-MICs of meropenem and ciprofloxacin caused significant changes in bacterial morphology. In addition, the expression of rfaH in R. ornithinolytica and K. quasivariicola increased with the sub-MICs of the selected antibiotics.
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Affiliation(s)
- Eda Delik
- Biology Department, Faculty of Science, Akdeniz University, 07070, Antalya, Turkey
| | - Berfin Eroğlu
- Biology Department, Faculty of Science, Akdeniz University, 07070, Antalya, Turkey
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18
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Kiørboe T. Predation in a Microbial World: Mechanisms and Trade-Offs of Flagellate Foraging. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:361-381. [PMID: 37368955 DOI: 10.1146/annurev-marine-020123-102001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Heterotrophic nanoflagellates are the main consumers of bacteria and picophytoplankton in the ocean and thus play a key role in ocean biogeochemistry. They are found in all major branches of the eukaryotic tree of life but are united by all being equipped with one or a few flagella that they use to generate a feeding current. These microbial predators are faced with the challenges that viscosity at this small scale impedes predator-prey contact and that their foraging activity disturbs the ambient water and thus attracts their own flow-sensing predators. Here, I describe some of the diverse adaptations of the flagellum to produce sufficient force to overcome viscosity and of the flagellar arrangement to minimize fluid disturbances, and thus of the various solutions to optimize the foraging-predation risk trade-off. I demonstrate how insights into this trade-off can be used to develop robust trait-based models of microbial food webs.
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Affiliation(s)
- Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kongens Lyngby, Denmark;
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19
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Rahi P, Mühle E, Scandola C, Touak G, Clermont D. Genome sequence-based identification of Enterobacter strains and description of Enterobacter pasteurii sp. nov. Microbiol Spectr 2024; 12:e0315023. [PMID: 38099614 PMCID: PMC10783019 DOI: 10.1128/spectrum.03150-23] [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: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Accurate taxonomy is essential for microbial biological resource centers, since the microbial resources are often used to support new discoveries and subsequent research. Here, we used genome sequence data, alongside matrix-assisted laser desorption/ionization time-of-flight mass spectrometer biotyper-based protein profiling, to accurately identify six Enterobacter cloacae complex strains. This approach effectively identified distinct species within the E. cloacae complex, including Enterobacter asburiae, "Enterobacter xiangfangensis," and Enterobacter quasihormaechei. Moreover, the study revealed the existence of a novel species within the Enterobacter genus, for which we proposed the name Enterobacter pasteurii sp. nov. In summary, this study demonstrates the significance of adopting a genome sequence-driven taxonomy approach for the precise identification of bacterial strains in a biological resource center and expands our understanding of the E. cloacae complex.
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Affiliation(s)
- Praveen Rahi
- Collection of Institut Pasteur (CIP), Institut Pasteur, Université Paris Cité, Paris, France
| | - Estelle Mühle
- Collection of Institut Pasteur (CIP), Institut Pasteur, Université Paris Cité, Paris, France
| | - Cyril Scandola
- Ultrastructural Bioimaging Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Gerald Touak
- Collection of Institut Pasteur (CIP), Institut Pasteur, Université Paris Cité, Paris, France
| | - Dominique Clermont
- Collection of Institut Pasteur (CIP), Institut Pasteur, Université Paris Cité, Paris, France
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20
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Salas-Orozco MF, Lorenzo-Leal AC, de Alba Montero I, Marín NP, Santana MAC, Bach H. Mechanism of escape from the antibacterial activity of metal-based nanoparticles in clinically relevant bacteria: A systematic review. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 55:102715. [PMID: 37907198 DOI: 10.1016/j.nano.2023.102715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/05/2023] [Accepted: 10/05/2023] [Indexed: 11/02/2023]
Abstract
The emergency of antibiotic-resistant bacteria in severe infections is increasing, especially in nosocomial environments. The ESKAPE group is of special importance in the groups of multi-resistant bacteria due to its high capacity to generate resistance to antibiotics and bactericides. Therefore, metal-based nanomaterials are an attractive alternative to combat them because they have been demonstrated to damage biomolecules in the bacterial cells. However, there is a concern about bacteria developing resistance to NPs and their harmful effects due to environmental accumulation. Therefore, this systematic review aims to report the clinically relevant bacteria that have developed resistance to the NPs. According to the results of this systematic review, various mechanisms to counteract the antimicrobial activity of various NP types have been proposed. These mechanisms can be grouped into the following categories: production of extracellular compounds, metal efflux pumps, ROS response, genetic changes, DNA repair, adaptative morphogenesis, and changes in the plasma membrane.
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Affiliation(s)
- Marco Felipe Salas-Orozco
- Facultad de Estomatología, Doctorado en Ciencias Odontológicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
| | - Ana Cecilia Lorenzo-Leal
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Nuria Patiño Marín
- Facultad de Estomatología, Laboratorio de Investigación Clinica, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Miguel Angel Casillas Santana
- Maestría en Estomatología con Opcion Terminal en Ortodoncia, Facultad de Estomatología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Horacio Bach
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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21
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Peoples LM, Dore JE, Bilbrey EM, Vick-Majors TJ, Ranieri JR, Evans KA, Ross AM, Devlin SP, Church MJ. Oxic methane production from methylphosphonate in a large oligotrophic lake: limitation by substrate and organic carbon supply. Appl Environ Microbiol 2023; 89:e0109723. [PMID: 38032216 PMCID: PMC10734540 DOI: 10.1128/aem.01097-23] [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: 06/28/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Methane is an important greenhouse gas that is typically produced under anoxic conditions. We show that methane is supersaturated in a large oligotrophic lake despite the presence of oxygen. Metagenomic sequencing indicates that diverse, widespread microorganisms may contribute to the oxic production of methane through the cleavage of methylphosphonate. We experimentally demonstrate that these organisms, especially members of the genus Acidovorax, can produce methane through this process. However, appreciable rates of methane production only occurred when both methylphosphonate and labile sources of carbon were added, indicating that this process may be limited to specific niches and may not be completely responsible for methane concentrations in Flathead Lake. This work adds to our understanding of methane dynamics by describing the organisms and the rates at which they can produce methane through an oxic pathway in a representative oligotrophic lake.
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Affiliation(s)
- Logan M. Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E. Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Evan M. Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Trista J. Vick-Majors
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - John R. Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A. Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Abigail M. Ross
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Shawn P. Devlin
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J. Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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22
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Zhao X, Ruelens P, Farr AD, de Visser JAGM, Baraban L. Population dynamics of cross-protection against β-lactam antibiotics in droplet microreactors. Front Microbiol 2023; 14:1294790. [PMID: 38192289 PMCID: PMC10773670 DOI: 10.3389/fmicb.2023.1294790] [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: 09/15/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Bacterial strains that are resistant to antibiotics may protect not only themselves, but also sensitive bacteria nearby if resistance involves antibiotic degradation. Such cross-protection poses a challenge to effective antibiotic therapy by enhancing the long-term survival of bacterial infections, however, the current understanding is limited. Methods In this study, we utilize an automated nanoliter droplet analyzer to study the interactions between Escherichia coli strains expressing a β-lactamase (resistant) and those not expressing it (sensitive) when exposed to the β-lactam antibiotic cefotaxime (CTX), with the aim to define criteria contributing to cross-protection. Results We observed a cross-protection window of CTX concentrations for the sensitive strain, extending up to approximately 100 times its minimal inhibitory concentration (MIC). Through both microscopy and enzyme activity analyses, we demonstrate that bacterial filaments, triggered by antibiotic stress, contribute to cross-protection. Discussion The antibiotic concentration window for cross-protection depends on the difference in β-lactamase activity between co-cultured strains: larger differences shift the 'cross-protection window' toward higher CTX concentrations. Our findings highlight the dependence of opportunities for cross-protection on the relative resistance levels of the strains involved and suggest a possible specific role for filamentation.
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Affiliation(s)
- Xinne Zhao
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
| | - Philip Ruelens
- Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands
| | - Andrew D. Farr
- Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
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23
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Gangar T, Patra S. Antibiotic persistence and its impact on the environment. 3 Biotech 2023; 13:401. [PMID: 37982084 PMCID: PMC10654327 DOI: 10.1007/s13205-023-03806-6] [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: 05/23/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
From boon molecules to molecules contributing to rising concern has been the sojourn of antibiotics. The problem of antibiotic contamination has gotten worse due to antibiotics' pervasive use in every aspect of the environment. One such consequence of pollution is the increase in infections with antibiotic resistance. All known antimicrobials being used for human benefit lead to their repetitive and routine release into the environment. The misuse of antibiotics has aggravated the situation to a level that we are short of antibiotics to treat infections as organisms have developed resistance against them. Overconsumption is not just limited to human health care, but also occurs in other areas such as aquaculture, livestock, and veterinary applications for the purpose of improving feed and meat products. Due to their harmful effects on non-target species, the trace level of antibiotics in the aquatic ecosystem presents a significant problem. Since the introduction of antibiotics into the environment is more than their removal, they have been given the status of persistent pollutants. The buildup of antibiotics in the environment threatens aquatic life and may lead to bacterial strains developing resistance. As newer organisms are becoming resistant, there exists a shortage of antibiotics to treat infections. This has presented a very critical problem for the health-care community. Another rising concern is that the development of newer drug molecules as antibiotics is minimal. This review article critically explains the cause and nature of the pollution and the effects of this emerging trend. Also, in the latter sections, why we need newer antibiotics is questioned and discussed.
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Affiliation(s)
- Tarun Gangar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039 India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039 India
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24
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Creutz CE. Expression of bovine annexin A4 in E. coli rescues cytokinesis blocked by beta-lactam antibiotics. Biochem Biophys Rep 2023; 36:101553. [PMID: 37840691 PMCID: PMC10569963 DOI: 10.1016/j.bbrep.2023.101553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023] Open
Abstract
Treatment of bacteria with beta-lactam antibiotics can impair the process of cytokinesis, the final step in cell division, leading to the formation of a filamentous form of the bacteria. The expression of a mammalian calcium-dependent, membrane-binding protein, bovine annexin A4, in E. coli was found to reverse the inhibitory effects on cytokinesis of the beta-lactam antibiotics ampicillin, piperacillin, and cephalexin. This novel activity of the annexin was blocked by mutation of calcium binding sites in the annexin, indicating roles for calcium binding to the annexin and the binding of the annexin to membranes in restoring cytokinesis. The filamentous form of the bacteria has been reported to be more resistant to phagocytosis by cells of the immune system in eukaryotic hosts. Therefore, expression of annexins in pathogenic bacteria, by promoting the breakdown of the bacterial filaments, might serve as an adjuvant to enhance the efficacy of beta-lactam antibiotics.
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Affiliation(s)
- Carl E. Creutz
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
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25
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Lovegrove JT, Kent B, Förster S, Garvey CJ, Stenzel MH. The flow of anisotropic nanoparticles in solution and in blood. EXPLORATION (BEIJING, CHINA) 2023; 3:20220075. [PMID: 38264690 PMCID: PMC10742203 DOI: 10.1002/exp.20220075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/01/2023] [Indexed: 01/25/2024]
Abstract
The alignment of anisotropic nanoparticles in flow has been used for a range of applications such as the preparation of strong fibres and the assembly of in-plane aligned 1D-nanoobjects that are used for electronic devices, sensors, energy and biological application. Important is also the flow behaviour of nanoparticles that were designed for nanomedical applications such as drug delivery. It is widely observed that non-spherical nanoparticles have longer circulation times and a more favourable biodistribution. To be able to understand this behaviour, researchers have turned to analyzing the flow of non-spherical nanoparticles in the blood stream. In this review, an overview of microfluidic techniques that are used to monitor the alignment of anisotropic nanoparticles in solution will be provided, which includes analysis by small angle X-ray scattering (SAXS) and polarized light microscopy. The flow of these nanoparticles in blood is then discussed as the presence of red blood cells causes margination of some nanoparticles. Using fluorescence microscopy, the extent of margination can be identified, which coincides with the ability of nanoparticles to adhere to the cells grown along the wall. While these studies are mainly carried out in vitro using blood, initial investigations in vivo were able to confirm the unusual flow of anisotropic nanoparticles.
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Affiliation(s)
- Jordan Thomas Lovegrove
- Centre for Advanced Macromolecular DesignSchool of ChemistryThe University of New South WalesSydneyNew South WalesAustralia
| | - Ben Kent
- Centre for Advanced Macromolecular DesignSchool of ChemistryThe University of New South WalesSydneyNew South WalesAustralia
| | | | - Christopher J. Garvey
- Forschungsneutronenquelle Heinz Maier‐Leibnitz FRM II and Physik Department E13Technische Universität MünchenGarchingGermany
| | - Martina H. Stenzel
- Centre for Advanced Macromolecular DesignSchool of ChemistryThe University of New South WalesSydneyNew South WalesAustralia
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26
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van Gestel J, Wagner A, Ackermann M. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol 2023; 21:e3002338. [PMID: 37844064 PMCID: PMC10578586 DOI: 10.1371/journal.pbio.3002338] [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: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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27
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Son Y, Min J, Shin Y, Park W. Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress. Sci Rep 2023; 13:14970. [PMID: 37697016 PMCID: PMC10495460 DOI: 10.1038/s41598-023-42179-x] [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: 05/18/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Both culture-independent and culture-dependent analyses using Nanopore-based 16S rRNA sequencing showed that short-term exposure of Antarctic soils to low temperature increased biomass with lower bacterial diversity and maintained high numbers of the phylum Proteobacteria, Firmicute, and Actinobacteria including Pseudarthrobacter species. The psychrophilic Pseudarthrobacter psychrotolerans YJ56 had superior growth at 13 °C, but could not grow at 30 °C, compared to other bacteria isolated from the same Antarctic soil. Unlike a single rod-shaped cell at 13 °C, strain YJ56 at 25 °C was morphologically shifted into a filamentous bacterium with several branches. Comparative genomics of strain YJ56 with other genera in the phylum Actinobacteria indicate remarkable copy numbers of rimJ genes that are possibly involved in dual functions, acetylation of ribosomal proteins, and stabilization of ribosomes by direct binding. Our proteomic data suggested that Actinobacteria cells experienced physiological stresses at 25 °C, showing the upregulation of chaperone proteins, GroEL and catalase, KatE. Level of proteins involved in the assembly of 50S ribosomal proteins and L29 in 50S ribosomal proteins increased at 13 °C, which suggested distinct roles of many ribosomal proteins under different conditions. Taken together, our data highlights the cellular filamentation and protein homeostasis of a psychrophilic YJ56 strain in coping with high-temperature stress.
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Affiliation(s)
- Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Yoonjae Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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28
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Zhang D, Yin F, Qin Q, Qiao L. Molecular responses during bacterial filamentation reveal inhibition methods of drug-resistant bacteria. Proc Natl Acad Sci U S A 2023; 120:e2301170120. [PMID: 37364094 PMCID: PMC10318954 DOI: 10.1073/pnas.2301170120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Bacterial antimicrobial resistance (AMR) is among the most significant challenges to current human society. Exposing bacteria to antibiotics can activate their self-saving responses, e.g., filamentation, leading to the development of bacterial AMR. Understanding the molecular changes during the self-saving responses can reveal new inhibition methods of drug-resistant bacteria. Herein, we used an online microfluidics mass spectrometry system for real-time characterization of metabolic changes of bacteria during filamentation under the stimulus of antibiotics. Significant pathways, e.g., nucleotide metabolism and coenzyme A biosynthesis, correlated to the filamentation of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) were identified. A cyclic dinucleotide, c-di-GMP, which is derived from nucleotide metabolism and reported closely related to bacterial resistance and tolerance, was observed significantly up-regulated during the bacterial filamentation. By using a chemical inhibitor, ebselen, to inhibit diguanylate cyclases which catalyzes the synthesis of c-di-GMP, the minimum inhibitory concentration of ceftriaxone against ESBL-E. coli was significantly decreased. This inhibitory effect was also verified with other ESBL-E. coli strains and other beta-lactam antibiotics, i.e., ampicillin. A mutant strain of ESBL-E. coli by knocking out the dgcM gene was used to demonstrate that the inhibition of the antibiotic resistance to beta-lactams by ebselen was mediated through the inhibition of the diguanylate cyclase DgcM and the modulation of c-di-GMP levels. Our study uncovers the molecular changes during bacterial filamentation and proposes a method to inhibit antibiotic-resistant bacteria by combining traditional antibiotics and chemical inhibitors against the enzymes involved in bacterial self-saving responses.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
| | - Fan Yin
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
| | - Qin Qin
- Changhai Hospital, The Naval Military Medical University, Shanghai200433, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
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29
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Ramasamy KP, Brugel S, Eriksson K, Andersson A. Pseudomonas ability to utilize different carbon substrates and adaptation influenced by protozoan grazing. ENVIRONMENTAL RESEARCH 2023:116419. [PMID: 37321339 DOI: 10.1016/j.envres.2023.116419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
Bacteria are major utilizers of dissolved organic matter in aquatic systems. In coastal areas bacteria are supplied with a mixture of food sources, spanning from refractive terrestrial dissolved organic matter to labile marine autochthonous organic matter. Modelling scenarios indicate that in northern coastal areas, the inflow of terrestrial organic matter will increase, and autochthonous production will decrease, thus bacteria will experience a change in the food source composition. How bacteria will cope with such changes is not known. Here, we tested the ability of an isolated bacterium from the northern Baltic Sea coast, Pseudomonas sp., to adapt to varying substrates. We performed a 7-months chemostat experiment, where three different substrates were provided: glucose, representing labile autochthonous organic carbon, sodium benzoate representing refractive organic matter, and acetate - a labile but low energy food source. Growth rate has been pointed out as a key factor for fast adaptation, and since protozoan grazers speed-up the growth rate we added a ciliate to half of the incubations. The results show that the isolated Pseudomonas is adapted to utilize both labile and ring-structured refractive substrates. The growth rate was the highest on the benzoate substrate, and the production increased over time indicating that adaptation did occur. Further, our findings indicate that predation can cause Pseudomonas to change their phenotype to resist and promote survival in various carbon substrates. Genome sequencing reveals different mutations in the genome of adapted populations compared to the native populations, suggesting the adaptation of Pseudomonas sp. To changing environment.
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Affiliation(s)
- Kesava Priyan Ramasamy
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden.
| | - Sonia Brugel
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Karolina Eriksson
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
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30
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Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. Empowering drug off-target discovery with metabolic and structural analysis. Nat Commun 2023; 14:3390. [PMID: 37296102 PMCID: PMC10256842 DOI: 10.1038/s41467-023-38859-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/15/2023] [Indexed: 06/12/2023] Open
Abstract
Elucidating intracellular drug targets is a difficult problem. While machine learning analysis of omics data has been a promising approach, going from large-scale trends to specific targets remains a challenge. Here, we develop a hierarchic workflow to focus on specific targets based on analysis of metabolomics data and growth rescue experiments. We deploy this framework to understand the intracellular molecular interactions of the multi-valent dihydrofolate reductase-targeting antibiotic compound CD15-3. We analyse global metabolomics data utilizing machine learning, metabolic modelling, and protein structural similarity to prioritize candidate drug targets. Overexpression and in vitro activity assays confirm one of the predicted candidates, HPPK (folK), as a CD15-3 off-target. This study demonstrates how established machine learning methods can be combined with mechanistic analyses to improve the resolution of drug target finding workflows for discovering off-targets of a metabolic inhibitor.
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Affiliation(s)
- Sourav Chowdhury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Joao V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens Lyngby, Denmark
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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31
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Ehrhardt K, Becker AL, Grassl GA. Determinants of persistent Salmonella infections. Curr Opin Immunol 2023; 82:102306. [PMID: 36989589 DOI: 10.1016/j.coi.2023.102306] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Persistent bacterial infections constitute an enormous challenge for public health. Amongst infections with other bacteria, infections with typhoidal and nontyphoidal Salmonella enterica serovars can result in long-term infections of the human and animal host. Persistent infections that are asymptomatic are difficult to identify and thus can serve as a silent reservoir for transmission. Symptomatic persistent infections are often difficult to treat as they harbor a combination of antibiotic-tolerant and antibiotic-resistant bacteria and boost the spread of genetic antibiotic resistance. In the last couple of years, the field has made some major progress in understanding the role of persisters, their reservoirs as well as their interplay with host factors in persistent Salmonella infections.
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32
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Kim K, Wang T, Ma HR, Şimşek E, Li B, Andreani V, You L. Mapping single‐cell responses to population‐level dynamics during antibiotic treatment. Mol Syst Biol 2023; 19:e11475. [PMCID: PMC10333910 DOI: 10.15252/msb.202211475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 12/08/2023] Open
Abstract
Treatment of sensitive bacteria with beta‐lactam antibiotics often leads to two salient population‐level features: a transient increase in total population biomass before a subsequent decline, and a linear correlation between growth and killing rates. However, it remains unclear how these population‐level responses emerge from collective single‐cell responses. During beta‐lactam treatment, it is well‐recognized that individual cells often exhibit varying degrees of filamentation before lysis. We show that the cumulative probability of cell lysis increases sigmoidally with the extent of filamentation and that this dependence is characterized by unique parameters that are specific to bacterial strain, antibiotic dose, and growth condition. Modeling demonstrates how the single‐cell lysis probabilities can give rise to population‐level biomass dynamics, which were experimentally validated. This mapping provides insights into how the population biomass time‐kill curve emerges from single cells and allows the representation of both single‐ and population‐level responses with universal parameters.
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Affiliation(s)
- Kyeri Kim
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
- Center for Quantitative BiodesignDuke UniversityDurhamNCUSA
| | - Teng Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
- Center for Quantitative BiodesignDuke UniversityDurhamNCUSA
| | - Helena R Ma
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
- Center for Quantitative BiodesignDuke UniversityDurhamNCUSA
| | - Emrah Şimşek
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
- Center for Quantitative BiodesignDuke UniversityDurhamNCUSA
| | - Boyan Li
- Integrated Science Program, Yuanpei CollegePeking UniversityBeijingChina
| | - Virgile Andreani
- Biomedical Engineering DepartmentBoston UniversityBostonMAUSA
- Biological Design CenterBoston UniversityBostonMAUSA
| | - Lingchong You
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
- Center for Quantitative BiodesignDuke UniversityDurhamNCUSA
- Center for Genomic and Computational BiologyDuke UniversityDurhamNCUSA
- Department of Molecular Genetics and MicrobiologyDuke University School of MedicineDurhamNCUSA
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33
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Li CX, Qi Y, Chen Y, Zhang Y, Li B, Feng J, Zhang XZ. Tuning Bacterial Morphology to Enhance Anticancer Vaccination. ACS NANO 2023; 17:8815-8828. [PMID: 37093563 DOI: 10.1021/acsnano.3c02373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Morphology tuning is a potent strategy to modulate physiological effects of synthetic biomaterials, but it is rarely explored in microbe-based biochemicals due to the lack of artificial adjustability. Inspired by the interesting phenomenon of microbial transformation, Escherichia coli is rationally adjusted into filamentous morphology-adjusted bacteria (MABac) via chemical stimulation to prepare a bacteria-based vaccine adjuvant/carrier. Inactivated MABac display stronger immunogenicity and special delivery patterns (phagosome escape and cytoplasmic retention) that are sharply distinct from the short rod-shaped bacteria parent (Bac). Transcriptomic study further offers solid evidence for deeply understanding the in vivo activity of MABac-based vaccine, which more effectively motivates multiple cytosolic immune pathways (such as NOD-like receptors and STING) and induces pleiotropic immune responses in comparison with Bac. Harnessing the special functions caused by morphology tuning, the MABac-based adjuvant/carrier significantly improves the immunogenicity and delivery profile of cancer antigens in vivo, thus boosting cancer-specific immunity against the melanoma challenge. This study validates the feasibility of tuning bacterial morphology to improve their biological effects, establishing a facile engineering strategy that upgrades bacterial properties and functions without complex procedures like gene editing.
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Affiliation(s)
- Chu-Xin Li
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yongdan Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yingge Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yu Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Bin Li
- School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, PR China
| | - Jun Feng
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, PR China
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Pereira MMR, de Oliveira FM, da Costa AC, Junqueira-Kipnis AP, Kipnis A. Ferritin from Mycobacterium abscessus is involved in resistance to antibiotics and oxidative stress. Appl Microbiol Biotechnol 2023; 107:2577-2595. [PMID: 36862179 DOI: 10.1007/s00253-023-12420-8] [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: 11/02/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 03/03/2023]
Abstract
Mycobacterium abscessus subsp. massiliense (Mycma) is a rapidly growing Mycobacterium belonging to the M. abscessus complex that is often associated with lung and soft tissue infection outbreaks. Mycma is resistant to many antimicrobials, including those used for treating tuberculosis. Therefore, Mycma infections are difficult to treat and may lead to high infectious complication rates. Iron is essential for bacterial growth and establishment of infection. During infection, the host reduces iron concentrations as a defense mechanism. To counteract the host-induced iron deficiency, Mycma produces siderophores to capture iron. Mycma has two ferritins (encoded by mycma_0076 and mycma_0077) modulated by different iron concentrations, which allow the survival of this pathogen during iron scarcity. In this study, we constructed knockout (Mycma 0076KO) and complemented (Mycma 0076KOc) gene strains for mycma_0076 to understand the function of 0076 ferritin. Deletion of mycma_0076 in Mycma led to the transition in colony morphology from smooth to rough, alteration of the glycopeptidolipids spectra, increased permeability of the envelope, reduction in biofilm formation, increased susceptibility to antimicrobials and hydrogen peroxide-induced oxidative stress, and decreased internalization by macrophages. This study shows that Mycma_0076 ferritin in Mycma is involved in resistance to oxidative stress and antimicrobials, and alteration of cell envelope architecture. KEY POINTS: • Deletion of the mycma_0076 gene altered colony morphology to rough; • Mycma 0076KO changed GPL profile; • Absence of Mycma_0076 ferritin results in increased susceptibility to antimicrobials and oxidative stress in Mycma. Legend: a In wild-type M. abscessus subsp. massiliense strain, iron is captured from the environment by carboxymycobactins and mycobactins (1). Iron-dependent regulator (IdeR) proteins bind to ferrous iron (Fe+2) in the bacterial cytoplasm leading to the activation of the IdeR-Fe+2 complex (2). The activated complex binds to the promoter regions of iron-dependent genes, called iron box, which in turn help in the recruitment of RNA polymerase to promote transcription of genes such as mycma_0076 and mycma_0077 ferritin genes (3). Mycma_0076 and Mycma_0077 ferritins bind to excess iron in the medium and promote Fe2+ oxidation into ferric iron (Fe3+) and store iron molecules to be released under iron scarcity conditions. (4) Genes related to biosynthesis and transport of glycopeptidolipids (GPL) are expressed normally and the cell envelope is composed of different GPL species (colored squares represented on the cell surface (GPLs). Consequently, WT Mycma present smooth colony phenotype (5). b In Mycma 0076KO strain, the lack of ferritin 0076 causes overexpression of mycma_0077 (6), but does not restore wild-type iron homeostasis and thus may result in free intracellular iron, even in the presence of miniferritins (MaDps). The excess iron potentiates oxidative stress (7) by generating hydroxyl radicals through Fenton Reaction. During this process, through an unknown mechanism, that could involve Lsr2 (8), the expression of GPL synthesis locus is regulated positively and/or negatively, resulting in alteration of GPL composition in the membrane (as represented by different colors of squares on the cell surface), resulting in a rough colony phenotype (9). The changes of GPL can increase cell wall permeability, contributing to antimicrobial susceptibility (10).
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Affiliation(s)
- Maria Micaella Rodrigues Pereira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
| | - Fábio Muniz de Oliveira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
- Indiana Center for Regenerative Medicine and Engineering, School of Medicine, Indiana University, Indianapolis, IN, USA
| | | | | | - André Kipnis
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil.
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35
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Cayron J, Dedieu-Berne A, Lesterlin C. Bacterial filaments recover by successive and accelerated asymmetric divisions that allow rapid post-stress cell proliferation. Mol Microbiol 2023; 119:237-251. [PMID: 36527185 DOI: 10.1111/mmi.15016] [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: 07/19/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Filamentation is a reversible morphological change triggered in response to various stresses that bacteria might encounter in the environment, during host infection or antibiotic treatments. Here we re-visit the dynamics of filament formation and recovery using a consistent framework based on live-cells microscopy. We compare the fate of filamentous Escherichia coli induced by cephalexin that inhibits cell division or by UV-induced DNA-damage that additionally perturbs chromosome segregation. We show that both filament types recover by successive and accelerated rounds of divisions that preferentially occur at the filaments' tip, thus resulting in the rapid production of multiple daughter cells with tightly regulated size. The DNA content, viability and further division of the daughter cells essentially depends on the coordination between chromosome segregation and division within the mother filament. Septum positioning at the filaments' tip depends on the Min system, while the nucleoid occlusion protein SlmA regulates the timing of division to prevent septum closure on unsegregated chromosomes. Our results not only recapitulate earlier conclusions but provide a higher level of detail regarding filaments division and the fate of the daughter cells. Together with previous reports, this work uncovers how filamentation recovery allows for a rapid cell proliferation after stress treatment.
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Affiliation(s)
- Julien Cayron
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
| | - Annick Dedieu-Berne
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
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36
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Grézal G, Spohn R, Méhi O, Dunai A, Lázár V, Bálint B, Nagy I, Pál C, Papp B. Plasticity and Stereotypic Rewiring of the Transcriptome Upon Bacterial Evolution of Antibiotic Resistance. Mol Biol Evol 2023; 40:7013728. [PMID: 36718533 PMCID: PMC9927579 DOI: 10.1093/molbev/msad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 12/01/2022] [Accepted: 01/04/2023] [Indexed: 02/01/2023] Open
Abstract
Bacterial evolution of antibiotic resistance frequently has deleterious side effects on microbial growth, virulence, and susceptibility to other antimicrobial agents. However, it is unclear how these trade-offs could be utilized for manipulating antibiotic resistance in the clinic, not least because the underlying molecular mechanisms are poorly understood. Using laboratory evolution, we demonstrate that clinically relevant resistance mutations in Escherichia coli constitutively rewire a large fraction of the transcriptome in a repeatable and stereotypic manner. Strikingly, lineages adapted to functionally distinct antibiotics and having no resistance mutations in common show a wide range of parallel gene expression changes that alter oxidative stress response, iron homeostasis, and the composition of the bacterial outer membrane and cell surface. These common physiological alterations are associated with changes in cell morphology and enhanced sensitivity to antimicrobial peptides. Finally, the constitutive transcriptomic changes induced by resistance mutations are largely distinct from those induced by antibiotic stresses in the wild type. This indicates a limited role for genetic assimilation of the induced antibiotic stress response during resistance evolution. Our work suggests that diverse resistance mutations converge on similar global transcriptomic states that shape genetic susceptibility to antimicrobial compounds.
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Affiliation(s)
- Gábor Grézal
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary,Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Réka Spohn
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,HCEMM-BRC Translational Microbiology Research Lab, Szeged, Hungary
| | - Anett Dunai
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,HCEMM-BRC Pharmacodynamic Drug Interaction Research Group, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,SeqOmics Biotechnology Ltd., Mórahalom, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary,Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,National Laboratory of Biotechnology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
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Pashapour S, Seneca S, Schröter M, Frischknecht F, Platzman I, Spatz J. Design and Development of Extracellular Matrix Protein-Based Microcapsules as Tools for Bacteria Investigation. Adv Healthc Mater 2023; 12:e2202789. [PMID: 36599129 DOI: 10.1002/adhm.202202789] [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: 10/29/2022] [Revised: 12/19/2022] [Indexed: 01/06/2023]
Abstract
The extracellular matrix (ECM) plays an immense role in the homeostasis of tissues and organs, can function as a barrier for infectious agents, but is also exploited by pathogens during infection. Therefore, the development of well-defined 3D ECM models in the form of microcapsules to elucidate the interactions between ECM components and pathogens in confinement and study disease infectivity is important, albeit challenging. Current limitations are mainly attributed to the lack of biocompatible methods for the production of protein-based microcapsules. Herein, hollow ECM-based microcapsules from laminin-111 or laminin-111/collagen IV are generated to investigate the behavior of organisms within confined 3D extracellular matrices. Microcapsules are created using water-in-oil emulsion droplets stabilized by block copolymer surfactants as templates for the charge-mediated attraction of laminin or laminin-collagen proteins to the droplets' inner periphery, allowing for the formation of modular ECM-based microcapsules with tunable biophysical and biochemical properties and organism encapsulation. The release of E. coli-laden ECM-based protein microcapsules into a physiological environment revealed differences in the dynamic behavior of E. coli depending on the constitution of the surrounding ECM protein matrix. The developed ECM-based protein microcapsules have the potential to be implemented in several biomedical applications, including the design of in vitro infection models.
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Affiliation(s)
- Sadaf Pashapour
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120, Heidelberg, Germany.,Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, D-69120, Heidelberg, Germany
| | - Senne Seneca
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120, Heidelberg, Germany.,Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, D-69120, Heidelberg, Germany
| | - Martin Schröter
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120, Heidelberg, Germany.,Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, D-69120, Heidelberg, Germany.,Department of Chemistry and Earth Sciences, Heidelberg University, Im Neuenheimer Feld 225, D-69120, Heidelberg, Germany
| | - Friedrich Frischknecht
- Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 344, D-69120, Heidelberg, Germany.,German Center for Infection Research, DZIF, partner site Heidelberg, Im Neuenheimer Feld 344, D-69120, Heidelberg, Germany
| | - Ilia Platzman
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120, Heidelberg, Germany.,Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, D-69120, Heidelberg, Germany
| | - Joachim Spatz
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120, Heidelberg, Germany.,Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, D-69120, Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120, Heidelberg, Germany
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Däullary T, Imdahl F, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba AE, Zdzieblo D. A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection. Gut Microbes 2023; 15:2186109. [PMID: 36939013 PMCID: PMC10038062 DOI: 10.1080/19490976.2023.2186109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Infection research largely relies on classical cell culture or mouse models. Despite having delivered invaluable insights into host-pathogen interactions, both have limitations in translating mechanistic principles to human pathologies. Alternatives can be derived from modern Tissue Engineering approaches, allowing the reconstruction of functional tissue models in vitro. Here, we combined a biological extracellular matrix with primary tissue-derived enteroids to establish an in vitro model of the human small intestinal epithelium exhibiting in vivo-like characteristics. Using the foodborne pathogen Salmonella enterica serovar Typhimurium, we demonstrated the applicability of our model to enteric infection research in the human context. Infection assays coupled to spatio-temporal readouts recapitulated the established key steps of epithelial infection by this pathogen in our model. Besides, we detected the upregulation of olfactomedin 4 in infected cells, a hitherto unrecognized aspect of the host response to Salmonella infection. Together, this primary human small intestinal tissue model fills the gap between simplistic cell culture and animal models of infection, and shall prove valuable in uncovering human-specific features of host-pathogen interplay.
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Affiliation(s)
- Thomas Däullary
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Faculty of Biology, Biocenter, Chair of Microbiology, Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany
| | - Fabian Imdahl
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Oliver Dietrich
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Laura Hepp
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
| | - Tobias Krammer
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Christina Fey
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
| | - Winfried Neuhaus
- Austrian Institute of Technology (AIT), Vienna, Austria
- Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University (DPU), Krems, Austria
| | - Marco Metzger
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
- Fraunhofer Institute for Silicate Research, Project Center for Stem Cell Process Engineering, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Daniela Zdzieblo
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
- Fraunhofer Institute for Silicate Research, Project Center for Stem Cell Process Engineering, Würzburg, Germany
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Thapa M, Sadhukhan R, Mukherjee A, Biswas PK. Effects of nZnS vs. nZnO and ZnCl 2 on mungbean [Vigna radiata (L.) R. Wilczek] plant and Bradyrhizobium symbiosis: A life cycle study. NANOIMPACT 2023; 29:100440. [PMID: 36442836 DOI: 10.1016/j.impact.2022.100440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Scarce of knowledge of using Zinc (Zn) nanoparticles (NPs) to augment plant growth, Zn availability to plants and its potential toxicity warrants more NPs-plant life cycle studies. The main objectives of this study were to compare nano zinc sulphide (nZnS) with nano zinc oxide (nZnO) and ionic Zn i.e., ZnCl2, as a source of Zn, as well as to establish physiological impact of NPs on growth, yield and symbiosis of mungbean [Vigna radiata (L.) R. Wilczek] plants at different concentrations (0, 0.01, 0.1, 1 and 10 mg kg-1 of soil). In this study, mungbean plants were grown for 60 days (life cycle study) in natural soil infested with Bradyrhizobium. Effects of Zn compounds (nZnS, nZnO and ZnCl2) on plant height, dry biomass, number of nodules per plant, yield and fruit agronomical parameters along with micronutrient assessment were determined. Impact of Zn compounds on Bradyrhizobium-mungbean symbiosis was also unravelled. Results showed that both the NPs, (nZnS and nZnO) were more effective than ZnCl2 in promoting growth and yield up to a critical concentration and above which phytotoxic effects were observed. Both the NPs were more effective than ZnCl2 at increasing fruit Zn content also. Whereas, nZnS treatment was found to be better than nZnO in improving overall plant growth. Bradyrhizobium-mungbean symbiosis was not affected at lower NPs concentrations, while higher concentration revealed toxicity by damaging bacterial morphology and nodule formation. There was no nano specific toxicity found while, ZnCl2 showed relatively more toxicity than both the NPs. The present investigation demonstrated the concept of nano-micronutrient as well as NPs phytotoxicity by understanding NPs-plant interactions in the soil environment.
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Affiliation(s)
- Mala Thapa
- Food Technology and Biochemical Engineering, Jadavpur University, 188 Raja S.C. Mallick Road, Kolkata 700032, West Bengal, India; Biological Science Division, Agricultural and Ecological Research Unit (AERU), Indian Statistical Institute, Giridih 815301, Jharkhand, India.
| | - Raghunath Sadhukhan
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur 741252, West Bengal, India
| | - Abhishek Mukherjee
- Biological Science Division, Agricultural and Ecological Research Unit (AERU), Indian Statistical Institute, Giridih 815301, Jharkhand, India
| | - Prasanta Kumar Biswas
- Food Technology and Biochemical Engineering, Jadavpur University, 188 Raja S.C. Mallick Road, Kolkata 700032, West Bengal, India
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40
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Frirdich E, Vermeulen J, Biboy J, Vollmer W, Gaynor EC. Multiple Campylobacter jejuni proteins affecting the peptidoglycan structure and the degree of helical cell curvature. Front Microbiol 2023; 14:1162806. [PMID: 37143542 PMCID: PMC10151779 DOI: 10.3389/fmicb.2023.1162806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/10/2023] [Indexed: 05/06/2023] Open
Abstract
Campylobacter jejuni is a Gram-negative helical bacterium. Its helical morphology, maintained by the peptidoglycan (PG) layer, plays a key role in its transmission in the environment, colonization, and pathogenic properties. The previously characterized PG hydrolases Pgp1 and Pgp2 are important for generating C. jejuni helical morphology, with deletion mutants being rod-shaped and showing alterations in their PG muropeptide profiles in comparison to the wild type. Homology searches and bioinformatics were used to identify additional gene products involved in C. jejuni morphogenesis: the putative bactofilin 1104 and the M23 peptidase domain-containing proteins 0166, 1105, and 1228. Deletions in the corresponding genes resulted in varying curved rod morphologies with changes in their PG muropeptide profiles. All changes in the mutants complemented except 1104. Overexpression of 1104 and 1105 also resulted in changes in the morphology and in the muropeptide profiles, suggesting that the dose of these two gene products influences these characteristics. The related helical ε-Proteobacterium Helicobacter pylori has characterized homologs of C. jejuni 1104, 1105, and 1228 proteins, yet deletion of the homologous genes in H. pylori had differing effects on H. pylori PG muropeptide profiles and/or morphology compared to the C. jejuni deletion mutants. It is therefore apparent that even related organisms with similar morphologies and homologous proteins can have diverse PG biosynthetic pathways, highlighting the importance of studying PG biosynthesis in related organisms.
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Affiliation(s)
- Emilisa Frirdich
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Emilisa Frirdich,
| | - Jenny Vermeulen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Jacob Biboy
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Erin C. Gaynor
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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41
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Yu Z, Goodall ECA, Henderson IR, Guo J. Plasmids Can Shift Bacterial Morphological Response against Antibiotic Stress. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203260. [PMID: 36424175 PMCID: PMC9839882 DOI: 10.1002/advs.202203260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Bacterial cell filamentation is a morphological change wherein cell division is blocked, which can improve bacterial survival under unfavorable conditions (e.g., antibiotic stress that causes DNA damage). As an extrachromosomal DNA molecule, plasmids can confer additionally advantageous traits including antibiotic resistance on the host. However, little is known about whether plasmids could shift bacterial morphological responses to antibiotic stress. Here, it is reported that plasmid-free cells, rather than plasmid-bearing cells, exhibit filamentation and asymmetrical cell division under exposure to sub-inhibitory concentrations of antibiotics (ciprofloxacin and cephalexin). The underlying mechanism is revealed by investigating DNA damage, cell division inhibitor sulA, the SOS response, toxin-antitoxin module (parDE) located on plasmids, and efflux pumps. Significantly higher expression of sulA is observed in plasmid-free cells, compared to plasmid-bearing cells. Plasmid carriage enables the hosts to suffer less DNA damage, exhibit stronger efflux pump activities, and thus have a higher antibiotic tolerance. These benefits are attributed to the parDE module that mediates stress responses from plasmid-bearing cells and mainly contributes to cell morphological changes. Collectively, the findings demonstrate that plasmids can confer additional innate defenses on the host to antibiotics, thus advancing the understanding of how plasmids affect bacterial evolution in hostile environments.
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Affiliation(s)
- Zhigang Yu
- Australian Centre for Water and Environmental BiotechnologyThe University of QueenslandSt. LuciaBrisbaneQueensland4072Australia
| | - Emily C. A. Goodall
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaBrisbaneQueensland4072Australia
| | - Ian R. Henderson
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaBrisbaneQueensland4072Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental BiotechnologyThe University of QueenslandSt. LuciaBrisbaneQueensland4072Australia
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42
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YihE is a novel binding partner of Rho and regulates Rho-dependent transcription termination in the Cpx stress response. iScience 2022; 25:105483. [DOI: 10.1016/j.isci.2022.105483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/21/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
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Similarities and Differences among Species Closely Related to Candida albicans: C. tropicalis, C. dubliniensis, and C. auris. Cell Microbiol 2022. [DOI: 10.1155/2022/2599136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although Candida species are widespread commensals of the microflora of healthy individuals, they are also among the most important human fungal pathogens that under certain conditions can cause diseases (candidiases) of varying severity ranging from mild superficial infections of the mucous membranes to life-threatening systemic infections. So far, the vast majority of research aimed at understanding the molecular basis of pathogenesis has been focused on the most common species—Candida albicans. Meanwhile, other closely related species belonging to the CTG clade, namely, Candida tropicalis and Candida dubliniensis, are becoming more important in clinical practice, as well as a relatively newly identified species, Candida auris. Despite the close relationship of these microorganisms, it seems that in the course of evolution, they have developed distinct biochemical, metabolic, and physiological adaptations, which they use to fit to commensal niches and achieve full virulence. Therefore, in this review, we describe the current knowledge on C. tropicalis, C. dubliniensis, and C. auris virulence factors, the formation of a mixed species biofilm and mutual communication, the environmental stress response and related changes in fungal cell metabolism, and the effect of pathogens on host defense response and susceptibility to antifungal agents used, highlighting differences with respect to C. albicans. Special attention is paid to common diagnostic problems resulting from similarities between these species and the emergence of drug resistance mechanisms. Understanding the different strategies to achieve virulence, used by important opportunistic pathogens of the genus Candida, is essential for proper diagnosis and treatment.
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Csibra E, Stan GB. Absolute protein quantification using fluorescence measurements with FPCountR. Nat Commun 2022; 13:6600. [PMID: 36329019 PMCID: PMC9633595 DOI: 10.1038/s41467-022-34232-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
This paper presents a generalisable method for the calibration of fluorescence readings on microplate readers, in order to convert arbitrary fluorescence units into absolute units. FPCountR relies on the generation of bespoke fluorescent protein (FP) calibrants, assays to determine protein concentration and activity, and a corresponding analytical workflow. We systematically characterise the assay protocols for accuracy, sensitivity and simplicity, and describe an 'ECmax' assay that outperforms the others and even enables accurate calibration without requiring the purification of FPs. To obtain cellular protein concentrations, we consider methods for the conversion of optical density to either cell counts or alternatively to cell volumes, as well as examining how cells can interfere with protein counting via fluorescence quenching, which we quantify and correct for the first time. Calibration across different instruments, disparate filter sets and mismatched gains is demonstrated to yield equivalent results. It also reveals that mCherry absorption at 600 nm does not confound cell density measurements unless expressed to over 100,000 proteins per cell. FPCountR is presented as pair of open access tools (protocol and R package) to enable the community to use this method, and ultimately to facilitate the quantitative characterisation of synthetic microbial circuits.
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Affiliation(s)
- Eszter Csibra
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
| | - Guy-Bart Stan
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
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López‐Escarpa D, Castanheira S, García‐del Portillo F. OmpR and Prc contribute to switch the Salmonella morphogenetic program in response to phagosome cues. Mol Microbiol 2022; 118:477-493. [PMID: 36115022 PMCID: PMC9827838 DOI: 10.1111/mmi.14982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023]
Abstract
Salmonella enterica serovar Typhimurium infects eukaryotic cells residing within membrane-bound phagosomes. In this compartment, the pathogen replaces the morphogenetic penicillin-binding proteins 2 and 3 (PBP2/PBP3) with PBP2SAL /PBP3SAL , two proteins absent in Escherichia coli. The basis for this switch is unknown. Here, we show that PBP3 protein levels drop drastically when S. Typhimurium senses acidity, high osmolarity and nutrient scarcity, cues that activate virulence functions required for intra-phagosomal survival and proliferation. The protease Prc and the transcriptional regulator OmpR contribute to lower PBP3 levels whereas OmpR stimulates PBP2SAL /PBP3SAL production. Surprisingly, despite being essential for division in E. coli, PBP3 levels also drop in non-pathogenic and pathogenic E. coli exposed to phagosome cues. Such exposure alters E. coli morphology resulting in very long bent and twisted filaments indicative of failure in the cell division and elongation machineries. None of these aberrant shapes are detected in S. Typhimurium. Expression of PBP3SAL restores cell division in E. coli exposed to phagosome cues although the cells retain elongation defects in the longitudinal axis. By switching the morphogenetic program, OmpR and Prc allow S. Typhimurium to properly divide and elongate inside acidic phagosomes maintaining its cellular dimensions and the rod shape.
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Affiliation(s)
- David López‐Escarpa
- Laboratory of Intracellular Bacterial PathogensNational Centre for Biotechnology (CNB‐CSIC)MadridSpain
| | - Sónia Castanheira
- Laboratory of Intracellular Bacterial PathogensNational Centre for Biotechnology (CNB‐CSIC)MadridSpain
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Abstract
Escherichia coli arbitrarily encompasses facultative anaerobic, rod-shaped bacteria with defined respiratory and fermentative types of metabolism. The species diversification has been further advanced by atypical strains whose features deviate from the essential species-specific morphological and metabolic cutoff. The morphological cutoff is exemplified by bacterial filamentation. E. coli filamentation has been studied from two different perspectives: the first considers filamentation as a result of adaptive strategies and response to stress, while the second is based on findings from the cell division of E. coli's conditional mutants. Another cutoff is represented by E. coli's inability to use citrate as a sole carbon and energy source. In this study, we compared two atypical E. coli strains that belong to the same neuroinvasive ecovar but exhibit either of the two phenotypes that deviate from the species' features. While E. coli RS218 exists in the form of filaments incapable of growth on citrate, strain IHE3034 is represented as normal-sized bacteria able to ferment citrate under oxic conditions in the presence of glucose; in this paper, we show that these two phenotypes result from a bona fide trade-off. With the help of comparative proteomics and metabolomics, we discovered the proteome required for the upkeep of these phenotypes. The metabolic profiles of both strains reveal that under aerobic conditions, RS218 undergoes oxidative metabolism, while IHE3034 undergoes anaerobic respiration. Finally, we show that the use of citrate and filament formation are both linked in a trade-off occurring via a c-di-GMP-dependent phase variation event. IMPORTANCE Aerobic use of citrate and filamentous growth are arbitrary cutoffs for the Escherichia coli species. The strains that exhibit them as stable phenotypes are called atypical. In this study, we compare two atypical neuroinvasive E. coli strains, which alternatively display either of these phenotypes. We present the proteome and metabolome required for the maintenance of filamentous growth and show that anaerobic nitrate respiration is the main requirement for the use of citrate. The fact that the two phenotypes are differentially expressed by each strain prompted us to check if they are part of a trade-off. Indeed, these atypical characters are reversible and result from a c-di-GMP phase variation event. Thus, we revealed hidden links between stable morphological and metabolic phenotypes and provided information about alternative evolutionary pathways for the survival of E. coli strains in various host niches.
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The Transcriptional Regulator SpxA1 Influences the Morphology and Virulence of Listeria monocytogenes. Infect Immun 2022; 90:e0021122. [PMID: 36102657 PMCID: PMC9584327 DOI: 10.1128/iai.00211-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Listeria monocytogenes is a Gram-positive facultative anaerobe and an excellent model pathogen for investigating regulatory changes that occur during infection of a mammalian host. SpxA1 is a widely conserved transcriptional regulator that induces expression of peroxide-detoxifying genes in L. monocytogenes and is thus required for aerobic growth. SpxA1 is also required for L. monocytogenes virulence, although the SpxA1-dependent genes important in this context remain to be identified. Here, we sought to investigate the role of SpxA1 in a tissue culture model of infection and made the surprising discovery that ΔspxA1 cells are dramatically elongated during growth in the host cytosol. Quantitative microscopy revealed that ΔspxA1 cells also form elongated filaments extracellularly during early exponential phase in rich medium. Scanning and transmission electron microscopy analysis found that the likely cause of this morphological phenotype is aberrantly placed division septa localized outside cell midpoints. Quantitative mass spectrometry of whole-cell lysates identified SpxA1-dependent changes in protein abundance, including a significant number of motility and flagellar proteins that were depleted in the ΔspxA1 mutant. Accordingly, we found that both the filamentation and the lack of motility contributed to decreased phagocytosis of ΔspxA1 cells by macrophages. Overall, we identify a novel role for SpxA1 in regulating cell elongation and motility, both of which impact L. monocytogenes virulence.
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48
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Zhang D, Qin Q, Qiao L. Mass spectrometry profiling of single bacterial cells reveals metabolic regulation during antibiotics induced bacterial filamentation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Baines R, Patiballa SK, Booth J, Ramirez L, Sipple T, Garcia A, Fish F, Kramer-Bottiglio R. Multi-environment robotic transitions through adaptive morphogenesis. Nature 2022; 610:283-289. [PMID: 36224418 DOI: 10.1038/s41586-022-05188-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/03/2022] [Indexed: 11/09/2022]
Abstract
The current proliferation of mobile robots spans ecological monitoring, warehouse management and extreme environment exploration, to an individual consumer's home1-4. This expanding frontier of applications requires robots to transit multiple environments, a substantial challenge that traditional robot design strategies have not effectively addressed5,6. For example, biomimetic design-copying an animal's morphology, propulsion mechanism and gait-constitutes one approach, but it loses the benefits of engineered materials and mechanisms that can be exploited to surpass animal performance7,8. Other approaches add a unique propulsive mechanism for each environment to the same robot body, which can result in energy-inefficient designs9-11. Overall, predominant robot design strategies favour immutable structures and behaviours, resulting in systems incapable of specializing across environments12,13. Here, to achieve specialized multi-environment locomotion through terrestrial, aquatic and the in-between transition zones, we implemented 'adaptive morphogenesis', a design strategy in which adaptive robot morphology and behaviours are realized through unified structural and actuation systems. Taking inspiration from terrestrial and aquatic turtles, we built a robot that fuses traditional rigid components and soft materials to radically augment the shape of its limbs and shift its gaits for multi-environment locomotion. The interplay of gait, limb shape and the environmental medium revealed vital parameters that govern the robot's cost of transport. The results attest that adaptive morphogenesis is a powerful method to enhance the efficiency of mobile robots encountering unstructured, changing environments.
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Affiliation(s)
- Robert Baines
- School of Engineering and Applied Science, Yale University, New Haven, CT, USA
| | - Sree Kalyan Patiballa
- School of Engineering and Applied Science, Yale University, New Haven, CT, USA.,Department of Mechanical Engineering, The University of Alabama, Tuscaloosa, AL, USA
| | - Joran Booth
- School of Engineering and Applied Science, Yale University, New Haven, CT, USA
| | - Luis Ramirez
- School of Engineering and Applied Science, Yale University, New Haven, CT, USA
| | - Thomas Sipple
- School of Engineering and Applied Science, Yale University, New Haven, CT, USA
| | - Andonny Garcia
- School of Engineering and Applied Science, Yale University, New Haven, CT, USA
| | - Frank Fish
- Department of Biology, West Chester University, West Chester, PA, USA
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Fortuna MA. The phenotypic plasticity of an evolving digital organism. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220852. [PMID: 36117864 PMCID: PMC9470259 DOI: 10.1098/rsos.220852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Climate change will fundamentally reshape life on Earth in the coming decades. Therefore, understanding the extent to which species will cope with rising temperatures is of paramount importance. Phenotypic plasticity is the ability of an organism to change the morphological and functional traits encoded by its genome in response to the environment. I show here that plasticity pervades not only natural but also artificial systems that mimic the developmental process of biological organisms, such as self-replicating and evolving computer programs-digital organisms. Specifically, the environment can modify the sequence of instructions executed from a digital organism's genome (i.e. its transcriptome), which results in changes in its phenotype (i.e. the ability of the digital organism to perform Boolean logic operations). This genetic-based pathway for plasticity comes at a fitness cost to an organism's viability and generation time: the longer the transcriptome (higher fitness cost), the more chances for the environment to modify the genetic execution flow control, and the higher the likelihood for the genome to encode novel phenotypes. By studying to what extent a digital organism's phenotype is influenced by both its genome and the environment, I make a parallelism between natural and artificial evolving systems on how natural selection might slide trait regulation anywhere along a continuum from total environmental control to total genomic control, which harbours lessons not only for designing evolvable artificial systems, but also for synthetic biology.
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Affiliation(s)
- Miguel A. Fortuna
- Computational Biology Lab, Estación Biológica de Doñana (EBD), Spanish National Research Council (CSIC), Seville, Spain
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