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Robertson JM, Garza EA, Stubbusch AKM, Dupont CL, Hwa T, Held NA. Marine bacteria Alteromonas spp. require UDP-glucose-4-epimerase for aggregation and production of sticky exopolymer. mBio 2024:e0003824. [PMID: 38958440 DOI: 10.1128/mbio.00038-24] [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: 01/06/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
The physiology and ecology of particle-associated marine bacteria are of growing interest, but our knowledge of their aggregation behavior and mechanisms controlling their association with particles remains limited. We have found that a particle-associated isolate, Alteromonas sp. ALT199 strain 4B03, and the related type-strain A. macleodii 27126 both form large (>500 μm) aggregates while growing in rich medium. A non-clumping variant (NCV) of 4B03 spontaneously arose in the lab, and whole-genome sequencing revealed a partial deletion in the gene encoding UDP-glucose-4-epimerase (galEΔ308-324). In 27126, a knock-out of galE (ΔgalE::kmr) resulted in a loss of aggregation, mimicking the NCV. Microscopic analysis shows that both 4B03 and 27126 rapidly form large aggregates, whereas their respective galE mutants remain primarily as single planktonic cells or clusters of a few cells. Strains 4B03 and 27126 also form aggregates with chitin particles, but their galE mutants do not. Alcian Blue staining shows that 4B03 and 27126 produce large transparent exopolymer particles (TEP), but their galE mutants are deficient in this regard. This study demonstrates the capabilities of cell-cell aggregation, aggregation of chitin particles, and production of TEP in strains of Alteromonas, a widespread particle-associated genus of heterotrophic marine bacteria. A genetic requirement for galE is evident for each of the above capabilities, expanding the known breadth of requirement for this gene in biofilm-related processes. IMPORTANCE Heterotrophic marine bacteria have a central role in the global carbon cycle. Well-known for releasing CO2 by decomposition and respiration, they may also contribute to particulate organic matter (POM) aggregation, which can promote CO2 sequestration via the formation of marine snow. We find that two members of the prevalent particle-associated genus Alteromonas can form aggregates comprising cells alone or cells and chitin particles, indicating their ability to drive POM aggregation. In line with their multivalent aggregation capability, both strains produce TEP, an excreted polysaccharide central to POM aggregation in the ocean. We demonstrate a genetic requirement for galE in aggregation and large TEP formation, building our mechanistic understanding of these aggregative capabilities. These findings point toward a role for heterotrophic bacteria in POM aggregation in the ocean and support broader efforts to understand bacterial controls on the global carbon cycle based on microbial activities, community structure, and meta-omic profiling.
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Affiliation(s)
- Jacob M Robertson
- Division of Biological Sciences, UC San Diego, La Jolla, California, USA
| | - Erin A Garza
- Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, California, USA
| | - Astrid K M Stubbusch
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Earth Sciences, Geological Institute, ETH Zurich, Zurich, Switzerland
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, California, USA
| | - Terence Hwa
- Division of Biological Sciences, UC San Diego, La Jolla, California, USA
- Department of Physics, UC San Diego, La Jolla, California, USA
| | - Noelle A Held
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, California, USA
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2
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Spencer-Williams I, Meyer M, DePas W, Elliott E, Haig SJ. Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:20360-20369. [PMID: 37970641 DOI: 10.1021/acs.est.3c05272] [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: 11/17/2023]
Abstract
Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.
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Affiliation(s)
- Isaiah Spencer-Williams
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Mitchell Meyer
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - William DePas
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - Emily Elliott
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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3
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Greenwich JL, Fleming D, Banin E, Häussler S, Kjellerup BV, Sauer K, Visick KL, Fuqua C. The biofilm community resurfaces: new findings and post-pandemic progress. J Bacteriol 2023; 205:e0016623. [PMID: 37756166 PMCID: PMC10601713 DOI: 10.1128/jb.00166-23] [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] [Indexed: 09/29/2023] Open
Abstract
The ninth American Society for Microbiology Conference on Biofilms was convened in-person on 13-17 November 2022 in Charlotte, NC. As the first of these conferences since prior to the start of the COVID-19 pandemic, the energy among the participants of the conference was clear, and the meeting was a tremendous success. The mixture of >330 oral and poster presentations resoundingly embodied the vitality of biofilm research across a wide range of topics and multiple scientific disciplines. Special activities, including a pre-conference symposium for early career researchers, further enhanced the attendee experience. As a general theme, the conference was deliberately structured to provide high levels of participation and engagement among early career scientists.
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Affiliation(s)
| | - Derek Fleming
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Birthe V. Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
| | - Karin Sauer
- Department of Biological Sciences, University of Binghamton, Binghamton, New York, USA
| | - Karen L. Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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4
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Dayton H, Kiss J, Wei M, Chauhan S, LaMarre E, Cornell WC, Morgan CJ, Janakiraman A, Min W, Tomer R, Price-Whelan A, Nirody JA, Dietrich LE. Cell arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.20.545666. [PMID: 37645902 PMCID: PMC10462148 DOI: 10.1101/2023.06.20.545666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm's depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.
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Affiliation(s)
- Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Julie Kiss
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Shradha Chauhan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Emily LaMarre
- Program in Biology, The Graduate Center, City University of New York, New York, NY 10016
| | | | - Chase J. Morgan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Anuradha Janakiraman
- Program in Biology, The Graduate Center, City University of New York, New York, NY 10016
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Jasmine A Nirody
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois 60637
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10025
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5
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Lee SH, Secchi E, Kang PK. Rapid formation of bioaggregates and morphology transition to biofilm streamers induced by pore-throat flows. Proc Natl Acad Sci U S A 2023; 120:e2204466120. [PMID: 36989304 PMCID: PMC10083537 DOI: 10.1073/pnas.2204466120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Bioaggregates are condensed porous materials comprising microbes, organic and inorganic matters, and water. They are commonly found in natural and engineered porous media and often cause clogging. Despite their importance, the formation mechanism of bioaggregates in porous media systems is largely unknown. Through microfluidic experiments and direct numerical simulations of fluid flow, we show that the rapid bioaggregation is driven by the interplay of the viscoelastic nature of biomass and hydrodynamic conditions at pore throats. At an early stage, unique flow structures around a pore throat promote the biomass attachment at the throat. Then, the attached biomass fluidizes when the shear stress at the partially clogged pore throat reaches a critical value. After the fluidization, the biomass is displaced and accumulated in the expansion region of throats forming bioaggregates. We further find that such criticality in shear stress triggers morphological changes in bioaggregates from rounded- to streamer-like shapes. This knowledge was used to control the clogging of throats by tuning the flow conditions: When the shear stress at the throat exceeded the critical value, clogging was prevented. The bioaggregation process did not depend on the detailed pore-throat geometry, as we reproduced the same dynamics in various pore-throat geometries. This study demonstrates that pore-throat structures, which are ubiquitous in porous media systems, induce bioaggregation and can lead to abrupt disruptions in flow.
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Affiliation(s)
- Sang Hyun Lee
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN55455
| | - Eleonora Secchi
- Institute of Environmental Engineering, ETH Zürich, Zürich8093, Switzerland
| | - Peter K. Kang
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN55455
- Saint Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN55455
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6
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Inactivation kinetics of 280 nm UV-LEDs against Mycobacterium abscessus in water. Sci Rep 2023; 13:2186. [PMID: 36750678 PMCID: PMC9905057 DOI: 10.1038/s41598-023-29338-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic premise plumbing pathogens (OPPPs) that cause a burdensome waterborne respiratory disease. Due to their resistance to chemical disinfectants and regrowth in biofilms in drinking water distribution systems, treatment can be better performed using small ultraviolet disinfection units at the point-of-use (POU), such as at a tap or showerhead. Ultraviolet light-emitting diodes (UV-LEDs) are well suited for such applications, but fluence-response data are not available for one of the most important NTM, Mycobacterium abscessus. In this study, a bench-scale 280 nm UV-LED apparatus was used to irradiate M. abscessus in a water matrix. The fluence-response profile was sigmoidal, exhibiting both shoulder and tailing phenomena. Simple linear regression and the Geeraerd's inactivation kinetics model yielded k values of 0.36 and 0.37 cm2/mJ, respectively, revealing that M. abscessus is more resistant to UV than Pseudomonas aeruginosa and Legionella pneumophila, which suggests that NTM are among the most UV-resistant OPPPs. Results of this study suggest that 280 nm UV-LED irradiation can be an effective and practical option to inactivate M. abscessus at the POU. Disinfection units that can deliver a fluence of 10 mJ/cm2 are expected to achieve nearly 2 log (99%) inactivation of M. abscessus.
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7
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Boopathi S, Ramasamy S, Haridevamuthu B, Murugan R, Veerabadhran M, Jia AQ, Arockiaraj J. Intercellular communication and social behaviors in mycobacteria. Front Microbiol 2022; 13:943278. [PMID: 36177463 PMCID: PMC9514802 DOI: 10.3389/fmicb.2022.943278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell communication is a fundamental process of bacteria to exert communal behaviors. Sputum samples of patients with cystic fibrosis have often been observed with extensive mycobacterial genetic diversity. The emergence of heterogenic mycobacterial populations is observed due to subtle changes in their morphology, gene expression level, and distributive conjugal transfer (DCT). Since each subgroup of mycobacteria has different hetero-resistance, they are refractory against several antibiotics. Such genetically diverse mycobacteria have to communicate with each other to subvert the host immune system. However, it is still a mystery how such heterogeneous strains exhibit synchronous behaviors for the production of quorum sensing (QS) traits, such as biofilms, siderophores, and virulence proteins. Mycobacteria are characterized by division of labor, where distinct sub-clonal populations contribute to the production of QS traits while exchanging complimentary products at the community level. Thus, active mycobacterial cells ensure the persistence of other heterogenic clonal populations through cooperative behaviors. Additionally, mycobacteria are likely to establish communication with neighboring cells in a contact-independent manner through QS signals. Hence, this review is intended to discuss our current knowledge of mycobacterial communication. Understanding mycobacterial communication could provide a promising opportunity to develop drugs to target key pathways of mycobacteria.
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Affiliation(s)
- Seenivasan Boopathi
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Subbiah Ramasamy
- Department of Biochemistry, Cardiac Metabolic Disease Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Raghul Murugan
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Maruthanayagam Veerabadhran
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Ai-Qun Jia
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- *Correspondence: Ai-Qun Jia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
- Jesu Arockiaraj ;
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8
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Glby, Encoded by MAB_3167c, Is Required for In Vivo Growth of Mycobacteroides abscessus and Exhibits Mild β-Lactamase Activity. J Bacteriol 2022; 204:e0004622. [PMID: 35380462 PMCID: PMC9112878 DOI: 10.1128/jb.00046-22] [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: 11/24/2022] Open
Abstract
Mycobacteroides abscessus (Mab; also known as Mycobacterium abscessus) is an emerging opportunistic pathogen. Patients with structural lung conditions such as bronchiectasis, cystic fibrosis, and chronic obstructive pulmonary disease are at high risk of developing pulmonary Mab disease. This disease is often chronic as the current treatment regimens are sub-efficacious. Here, we characterize the phenotype of a Mab strain lacking the MAB_3167c locus, which encodes a protein hereafter referred to as Glby. We demonstrate that the loss of Glby impairs normal planktonic growth in liquid broth, results in longer average cell length, and a melding of surfaces between cells. Glby also exhibits a mild β-lactamase activity. We also present evidence that amino acid substitutions that potentially alter Glby function are not favored. Lastly, we demonstrate that, in a mouse model of pulmonary Mab infection, the mutant lacking Glby was unable to proliferate, gradually cleared, and was undetectable after 3 weeks. These data suggest that an agent that inhibits Glby in vivo may be an efficacious treatment against Mab disease. IMPORTANCEMycobacteroides abscessus can cause chronic pulmonary infections requiring administration of multiple antibiotics, still resulting in a low cure rate. The incidence of M. abscessus disease is increasing in the United States and the developed regions of the world. We show for the first time that a protein, Glby, affects growth of this bacterium. Using a mouse model of lung M. abscessus disease, we demonstrate that Glby is required for this bacterium to cause disease.
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9
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Pfister CA, Light SH, Bohannan B, Schmidt T, Martiny A, Hynson NA, Devkota S, David L, Whiteson K. Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes. mSystems 2022; 7:e0137421. [PMID: 35014872 PMCID: PMC8751383 DOI: 10.1128/msystems.01374-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/26/2022] Open
Abstract
Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The "environment first" research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common "microbe first" research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function.
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Affiliation(s)
- Catherine A. Pfister
- Department of Ecology & Evolution and The Microbiome Center, University of Chicago, Chicago, Illinois, USA
| | - Samuel H. Light
- Department of Microbiology & Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Brendan Bohannan
- Environmental Studies and Biology, University of Oregon, Eugene, Oregon, USA
| | - Thomas Schmidt
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam Martiny
- Earth System Science & Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Nicole A. Hynson
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Suzanne Devkota
- Microbiome Research, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lawrence David
- Molecular Genetics & Microbiology, Duke University, Durham, North Carolina, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
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10
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Ivshina IB, Tyumina EA, Bazhutin GA, Vikhareva EV. Response of Rhodococcus cerastii IEGM 1278 to toxic effects of ibuprofen. PLoS One 2021; 16:e0260032. [PMID: 34793540 PMCID: PMC8601567 DOI: 10.1371/journal.pone.0260032] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022] Open
Abstract
The article expands our knowledge on the variety of biodegraders of ibuprofen, one of the most frequently detected non-steroidal anti-inflammatory drugs in the environment. We studied the dynamics of ibuprofen decomposition and its relationship with the physiological status of bacteria and with additional carbon and energy sources. The involvement of cytoplasmic enzymes in ibuprofen biodegradation was confirmed. Within the tested actinobacteria, Rhodococcus cerastii IEGM 1278 was capable of complete oxidation of 100 μg/L and 100 mg/L of ibuprofen in 30 h and 144 h, respectively, in the presence of an alternative carbon source (n-hexadecane). Besides, the presence of ibuprofen induced a transition of rhodococci from single- to multicellular lifeforms, a shift to more negative zeta potential values, and a decrease in the membrane permeability. The initial steps of ibuprofen biotransformation by R. cerastii IEGM 1278 involved the formation of hydroxylated and decarboxylated derivatives with higher phytotoxicity than the parent compound (ibuprofen). The data obtained indicate potential threats of this pharmaceutical pollutant and its metabolites to biota and natural ecosystems.
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Affiliation(s)
- Irina B. Ivshina
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
- * E-mail:
| | - Elena A. Tyumina
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
| | - Grigory A. Bazhutin
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
| | - Elena V. Vikhareva
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
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11
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Belardinelli JM, Li W, Avanzi C, Angala SK, Lian E, Wiersma CJ, Palčeková Z, Martin KH, Angala B, de Moura VCN, Kerns C, Jones V, Gonzalez-Juarrero M, Davidson RM, Nick JA, Borlee BR, Jackson M. Unique Features of Mycobacterium abscessus Biofilms Formed in Synthetic Cystic Fibrosis Medium. Front Microbiol 2021; 12:743126. [PMID: 34777289 PMCID: PMC8586431 DOI: 10.3389/fmicb.2021.743126] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/28/2021] [Indexed: 12/04/2022] Open
Abstract
Characterizing Mycobacterium abscessus complex (MABSC) biofilms under host-relevant conditions is essential to the design of informed therapeutic strategies targeted to this persistent, drug-tolerant, population of extracellular bacilli. Using synthetic cystic fibrosis medium (SCFM) which we previously reported to closely mimic the conditions encountered by MABSC in actual cystic fibrosis (CF) sputum and a new model of biofilm formation, we show that MABSC biofilms formed under these conditions are substantially different from previously reported biofilms grown in standard laboratory media in terms of their composition, gene expression profile and stress response. Extracellular DNA (eDNA), mannose-and glucose-containing glycans and phospholipids, rather than proteins and mycolic acids, were revealed as key extracellular matrix (ECM) constituents holding clusters of bacilli together. None of the environmental cues previously reported to impact biofilm development had any significant effect on SCFM-grown biofilms, most likely reflecting the fact that SCFM is a nutrient-rich environment in which MABSC finds a variety of ways of coping with stresses. Finally, molecular determinants were identified that may represent attractive new targets for the development of adjunct therapeutics targeting MABSC biofilms in persons with CF.
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Affiliation(s)
- Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Shiva K Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Elena Lian
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Crystal J Wiersma
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Zuzana Palčeková
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Kevin H Martin
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Bhanupriya Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Vinicius C N de Moura
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Callan Kerns
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Victoria Jones
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, United States.,Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Bradley R Borlee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
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12
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Improved production of the non-native cofactor F 420 in Escherichia coli. Sci Rep 2021; 11:21774. [PMID: 34741069 PMCID: PMC8571402 DOI: 10.1038/s41598-021-01224-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
The deazaflavin cofactor F420 is a low-potential, two-electron redox cofactor produced by some Archaea and Eubacteria that is involved in methanogenesis and methanotrophy, antibiotic biosynthesis, and xenobiotic metabolism. However, it is not produced by bacterial strains commonly used for industrial biocatalysis or recombinant protein production, such as Escherichia coli, limiting our ability to exploit it as an enzymatic cofactor and produce it in high yield. Here we have utilized a genome-scale metabolic model of E. coli and constraint-based metabolic modelling of cofactor F420 biosynthesis to optimize F420 production in E. coli. This analysis identified phospho-enol pyruvate (PEP) as a limiting precursor for F420 biosynthesis, explaining carbon source-dependent differences in productivity. PEP availability was improved by using gluconeogenic carbon sources and overexpression of PEP synthase. By improving PEP availability, we were able to achieve a ~ 40-fold increase in the space–time yield of F420 compared with the widely used recombinant Mycobacterium smegmatis expression system. This study establishes E. coli as an industrial F420-production system and will allow the recombinant in vivo use of F420-dependent enzymes for biocatalysis and protein engineering applications.
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Kumari B, Kaur J. Correlation of over-expression of rv1900c with enhanced survival of M. smegmatis under stress conditions: Modulation of cell surface properties. Gene 2021; 791:145720. [PMID: 34019937 DOI: 10.1016/j.gene.2021.145720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/21/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
Mycobacterium tuberculosis has distinct cell wall composition that helps in intracellular survival of bacteria. Rv1900c, a two domain protein, has been grouped in lip gene family. The expression of rv1900c was upregulated under acidic, nutritive and iron stress conditions in M. tuberculosis H37Ra. To investigate the biological effect of Rv1900c in mycobacterium physiology, rv1900c gene was cloned in M. smegmatis, a surrogate host. Its counterpart MSMEG_4477 in M. smegmatis demonstrated 38% protein similarity with Rv1900c. MSMEG_4477 gene was knocked out in M. smegmatis by homologous recombination. rv1900c and MSMEG_4477 genes, cloned in pVV16, were expressed in the M. smegmatis knockout strain (M. smegmatis ΔMSMEG_4477). Gene knockout significantly altered colony morphology and growth kinetics of M. smegmatis. M. smegmatis ΔMSMEG_1900 (pVV16::rv1900c) colonies were less wrinkled and had smooth surface as compared to M. smegmatis ΔMSMEG_4477. The changes were reverted back to normal upon expression of MSMEG_4477 in knockout strain M. smegmatis ΔMSMEG_4477 (pVV16::MSMEG_4477). The expression of rv1900c enhanced the biofilm formation and survival of bacteria under various in vitro stresses like acidic, nutritive stress, including lysozyme, SDS and multiple antibiotics treatment in comparison to control. On the other hand the expression of rv1900c decreased the cell wall permeability. The resistance provided by M. smegmatis ΔMSMEG_4477 (pVV16::MSMEG_4477) was comparable to M. smegmatis having vector alone (MS_vec). The lipid content of M. smegmatis ΔMSMEG_1900 (pVV16::rv1900c) was observed to be different from M. smegmatis ΔMSMEG_4477 (pVV16::MSMEG_4477). M. smegmatis ΔMSMEG_1900 (pVV16::rv1900c) was more tolerant to stress conditions in comparison to M. smegmatis ΔMSMEG_4477 (pVV16::MSMEG_4477). Expression of rv1900c enhanced the intracellular survival of mycobacteria. Therefore, the present study suggested an association of Rv1900c to the stress tolerance by cell wall modification that might have resulted in enhanced intracellular survival of the mycobacteria.
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Affiliation(s)
- Bandana Kumari
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh, India
| | - Jagdeep Kaur
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh 160014, India.
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Niño-Padilla EI, Velazquez C, Garibay-Escobar A. Mycobacterial biofilms as players in human infections: a review. BIOFOULING 2021; 37:410-432. [PMID: 34024206 DOI: 10.1080/08927014.2021.1925886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/18/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
The role of biofilms in pathogenicity and treatment strategies is often neglected in mycobacterial infections. In recent years, the emergence of nontuberculous mycobacterial infections has necessitated the development of novel prophylactic strategies and elucidation of the mechanisms underlying the establishment of chronic infections. More importantly, the question arises whether members of the Mycobacterium tuberculosis complex can form biofilms and contribute to latent tuberculosis and drug resistance because of the long-lasting and recalcitrant nature of its infections. This review discusses some of the molecular mechanisms by which biofilms could play a role in infection or pathological events in humans.
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Affiliation(s)
| | - Carlos Velazquez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
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Bharti S, Maurya RK, Venugopal U, Singh R, Akhtar MS, Krishnan MY. Rv1717 Is a Cell Wall - Associated β-Galactosidase of Mycobacterium tuberculosis That Is Involved in Biofilm Dispersion. Front Microbiol 2021; 11:611122. [PMID: 33584576 PMCID: PMC7873859 DOI: 10.3389/fmicb.2020.611122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/16/2020] [Indexed: 01/12/2023] Open
Abstract
Understanding the function of conserved hypothetical protein (CHP)s expressed by a pathogen in the infected host can lead to better understanding of its pathogenesis. The present work describes the functional characterization of a CHP, Rv1717 of Mycobacterium tuberculosis (Mtb). Rv1717 has been previously reported to be upregulated in TB patient lungs. Rv1717 belongs to the cupin superfamily of functionally diverse proteins, several of them being carbohydrate handling proteins. Bioinformatic analysis of the amino acid sequence revealed similarity to glycosyl hydrolases. Enzymatic studies with recombinant Rv1717 purified from Escherichia coli showed that the protein is a β-D-galactosidase specific for pyranose form rather than the furanose form. We expressed the protein in Mycobacterium smegmatis (Msm), which lacks its ortholog. In MsmRv1717, the protein was found to localize to the cell wall (CW) with a preference to the poles. MsmRv1717 showed significant changes in colony morphology and cell surface properties. Most striking observation was its unusual Congo red colony morphotype, reduced ability to form biofilms, pellicles and autoagglutinate. Exogenous Rv1717 not only prevented biofilm formation in Msm, but also degraded preformed biofilms, suggesting that its substrate likely exists in the exopolysaccharides of the biofilm matrix. Presence of galactose in the extracellular polymeric substance (EPS) has not been reported before and hence we used the galactose-specific Wisteria floribunda lectin (WFL) to test the same. The lectin extensively bound to Msm and Mtb EPS, but not the bacterium per se. Purified Rv1717 also hydrolyzed exopolysaccharides extracted from Msm biofilm. Eventually, to decipher its role in Mtb, we downregulated its expression and demonstrate that the strain is unable to disperse from in vitro biofilms, unlike the wild type. Biofilms exposed to carbon starvation showed a sudden upregulation of Rv1717 transcripts supporting the potential role of Rv1717 in Mtb dispersing from a deteriorating biofilm.
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Affiliation(s)
- Suman Bharti
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Rahul Kumar Maurya
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | | | - Radhika Singh
- Toxicology and Health Risk Assessment Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Md Sohail Akhtar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
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Qu Q, Wang J, Cui W, Zhou Y, Xing X, Che R, Liu X, Chen X, Bello-Onaghise G, Dong C, Li Z, Li X, Li Y. In vitro activity and In vivo efficacy of Isoliquiritigenin against Staphylococcus xylosus ATCC 700404 by IGPD target. PLoS One 2019; 14:e0226260. [PMID: 31860659 PMCID: PMC6924684 DOI: 10.1371/journal.pone.0226260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
Staphylococcus xylosus (S. xylosus) is a type of coagulase-negative Staphylococcus, which was previously considered as non-pathogenic. However, recent studies have linked it with cases of mastitis in cows. Isoliquiritigenin (ISL) is a bioactive compound with pharmacological functions including antibacterial activity. In this study, we evaluated the effect of ISL on S. xylosus in vitro and in vivo. The MIC of ISL against S. xylosus was 80 μg/mL. It was observed that sub-MICs of ISL (1/2MIC, 1/4MIC, 1/8MIC) significantly inhibited the formation of S. xylosus biofilm in vitro. Previous studies have observed that inhibiting imidazole glycerol phosphate dehydratase (IGPD) concomitantly inhibited biofilm formation in S. xylosus. So, we designed experiments to target the formation of IGPD or inhibits its activities in S. xylosus ATCC 700404. The results indicated that the activity of IGPD and its histidine content decreased significantly under 1/2 MIC (40 μg/mL) ISL, and the expression of IGPD gene (hisB) and IGPD protein was significantly down-regulated. Furthermore, Bio-layer interferometry experiments showed that ISL directly interacted with IGPD protein (with strong affinity; KD = 234 μM). In addition, molecular docking was used to predict the binding mode of ISL and IGPD. In vivo tests revealed that, ISL significantly reduced TNF-α and IL-6 levels, mitigated the destruction of the mammary glands and reversed the production of inflammatory cells in mice. The results of the study suggest that, ISL may inhibit S. xylosus growth by acting on IGPD, which can be used as a target protein to treat infections caused by S. xylosus.
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Affiliation(s)
- Qianwei Qu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Jinpeng Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Wenqiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Yonghui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xiaoxu Xing
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Ruixiang Che
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xin Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xueying Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - God’spower Bello-Onaghise
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Chunliu Dong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Zhengze Li
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, P. R. China
| | - Xiubo Li
- Feed Research Institute Chinese Academy of Agricultural Science, Harbin, Heilongjiang, P. R. China
| | - Yanhua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
- * E-mail:
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