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Luo Y, Pi S, Liu YJ. Mechanistic Insights into the Bacterial Luciferase-based Bioluminescence Resonance Energy Transfer Luminescence: The Role of Protein Complex Dimer. Chemphyschem 2024; 25:e202300973. [PMID: 38345139 DOI: 10.1002/cphc.202300973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/11/2024] [Indexed: 02/29/2024]
Abstract
Bacterial bioluminescence holds significant potential in the realm of optical imaging due to the inherent advantages of bioluminescence and ease of operation. However, its practical utility is hindered by its low light intensity. The fusion of bacterial luciferase with a highly fluorescent protein has been demonstrated to significantly enhance autonomous luminescence. Nevertheless, the underlying mechanism behind this enhancement remains unclear, and there is a dearth of research investigating the mechanistic aspects of bioluminescence resonance energy transfer (BRET) luminescence, whether it occurs naturally or can be achieved through experimental means. In this study, we investigated the phenomenon of bacterial luciferase-based BRET luminescence employing a range of computational techniques, including structural modeling, molecular docking, molecular dynamics simulations, as well as combined quantum mechanics and molecular mechanics calculations. The theoretical findings suggest that the BRET luminescence occurs through resonance energy transfer between the excited bioluminophore and the ground chromophore within the protein complex dimer. The proposed mechanism of the protein complex dimer offers a microscopic understanding of the intriguing BRET phenomenon and has the potential to inspire further practical applications in the field of optical imaging.
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Affiliation(s)
- Yanling Luo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shuangqi Pi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai, China
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2
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Pi S, Luo Y, Liu YJ. Thorough Understanding of Bioluminophore Production in Bacterial Bioluminescence. J Phys Chem A 2022; 126:6604-6616. [DOI: 10.1021/acs.jpca.2c04311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuangqi Pi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yanling Luo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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3
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Yang J, Hu S, Wu M, Liao A, Liang S, Lin Y. Construction of luminescent Escherichia coli via expressing lux operons and their application on toxicity test. Appl Microbiol Biotechnol 2022; 106:6317-6333. [PMID: 36028635 DOI: 10.1007/s00253-022-12136-1] [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: 07/06/2022] [Revised: 08/08/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022]
Abstract
Recombinant luminescent Escherichia coli strains could be used to detect the toxicity of pure or mixed contaminants as a light-off sensor. In this work, the lux operon of Photobacterium phosphoreum T3 was identified for the first time. Recombinant luminescent E. coli strains were constructed via expressing the lux operons of P. phosphoreum T3 and Vibrio qinghaiensis Q67 in E. coli MG1655, and the optimal protectant containing 10% (w/v) trehalose and 4% sucrose was used to prepare the freeze-dried recombinant luminescent E. coli cells. Then, these freeze-dried E. coli cells were subjected to acute toxicity detection. The results showed that luminescent E. coli strains displayed sensitive toxic responses to BPA, nFe2O3, Cd, Pb, As, and Hg, for example, the EC50 values of BPA and nFe2O3 to luminescent E. coli strains ranged from 1.54 to 50.19 mg/l and 17.50 to 21.52 mg/l, respectively. Indeed, luminescent E. coli strains exhibited more sensitive responses to Cd, Pb, and Hg than the natural strain Q67. The results suggested that recombinant luminescent E. coli strains could be used for the detection of acute toxicity. Furthermore, the combined toxicities of BPA and nFe2O3, Hg, and Pb were measured, and the joint effects of these mixtures were evaluated with luminescent E. coli. The results indicated that the joint effects of BPA and nFe2O3 suggested to be synergistic or additive to luminescent E. coli, while the joint effects of heavy metals and nFe2O3 exhibited additivities. The cellular endocytosis for Fe2O3 nanoparticles was not observed, which could explain the additive instead of synergistic effects between heavy metals and nFe2O3. KEY POINTS: • Sequence of the lux operon from P. phosphoreum T3 was reported for the first time. • Recombinant luminescent E. coli was more sensitive to Cd, Pb, and Hg than Q67. • Joint effects of BPA and nFe2O3 were synergistic or additive to luminescent E. coli.
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Affiliation(s)
- Jun Yang
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shulin Hu
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Minhui Wu
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Anqi Liao
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shuli Liang
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China. .,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
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4
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Similarities and Differences in Quorum Sensing-Controlled Bioluminescence between Photobacterium phosphoreum T3 and Vibrio qinghaiensis sp.-Q67. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12042066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Quorum sensing is a density-dependent mechanism using chemical signal molecules termed autoinducers to regulate diverse biological processes in bacteria, including bioluminescence. However, the correlation between growth and light emission of two typical luminescent bacteria, Photobacterium phosphoreum T3 and Vibrio qinghaiensis sp.-Q67, is still unclear. This study investigates the variations of bioluminescence and the light-emission-involved gene expression of the above two strains, respectively, showing that bioluminescence is population density-dependent. Furthermore, the effect of crude extracts (175, 350, 700 and 1750 mg/L) from the bacterial culture that contains the potential autoinducers on the bioluminescence is explored. At the exponential and the early stationary growth phase, T3 did not exhibit an obvious light intensity and cell density change after adding crude extracts at 175 and 350 mg/L, while the light intensity decreased at 700 and 1750 mg/L, showing a luminescence inhibition. For Q67, the light intensity increased dramatically with crude extract concentration. These results suggest that the bioluminescence process of both T3 and Q67 is controlled by quorum sensing. Furthermore, the different response modes of these two strains to autoinducers imply that the two strains could be applied to different compounds for toxicity assesses.
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5
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Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:ijms222111311. [PMID: 34768741 PMCID: PMC8582858 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
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6
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Kaku T, Sugiura K, Entani T, Osabe K, Nagai T. Enhanced brightness of bacterial luciferase by bioluminescence resonance energy transfer. Sci Rep 2021; 11:14994. [PMID: 34294849 PMCID: PMC8298465 DOI: 10.1038/s41598-021-94551-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Using the lux operon (luxCDABE) of bacterial bioluminescence system as an autonomous luminous reporter has been demonstrated in bacteria, plant and mammalian cells. However, applications of bacterial bioluminescence-based imaging have been limited because of its low brightness. Here, we engineered the bacterial luciferase (heterodimer of luxA and luxB) by fusion with Venus, a bright variant of yellow fluorescent protein, to induce bioluminescence resonance energy transfer (BRET). By using decanal as an externally added substrate, color change and ten-times enhancement of brightness was achieved in Escherichia coli when circularly permuted Venus was fused to the C-terminus of luxB. Expression of the Venus-fused luciferase in human embryonic kidney cell lines (HEK293T) or in Nicotiana benthamiana leaves together with the substrate biosynthesis-related genes (luxC, luxD and luxE) enhanced the autonomous bioluminescence. We believe the improved luciferase will forge the way towards the potential development of autobioluminescent reporter system allowing spatiotemporal imaging in live cells.
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Affiliation(s)
- Tomomi Kaku
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kazunori Sugiura
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Tetsuyuki Entani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kenji Osabe
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Takeharu Nagai
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan.
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7
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Ramesh C, Mohanraju R. Isolation and characterization of marine bioluminescent bacteria for toxicity bioassays and biotechnological applications. Braz J Microbiol 2021; 52:1191-1199. [PMID: 34235704 DOI: 10.1007/s42770-021-00471-w] [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: 12/07/2020] [Accepted: 03/16/2021] [Indexed: 10/20/2022] Open
Abstract
Toxic heavy metals pollution posed severe health hazards to the environment and biodiversity. Therefore, the development of rapid and non-invasive bioassays is in the race to monitor toxic chemicals using novel approaches. This study isolated and characterized an intense blue luminescence-producing marine bacteria, Vibrio campbellii STF1, for biosensing applications. Species-level identification of this strain was confirmed based on various phenotypic tests and multilocus sequence approach using 16s rRNA, toxR, and luxA gene sequence analysis. Fatty acid methyl ester analysis revealed the presence of three predominant fatty acids C15:0 anteiso (21.73%), C17:0 anteiso (11.27%), and C19:0 anteiso (9.08%) in STF1. Luciferase enzyme from V. campbellii STF1 was extracted, partially purified, and molecular masses (alpha subunit 40 kDa and beta subunit 37 kDa) were determined by SDS-PAGE gel for in vivo assays. MALDI-TOF-MS analysis of V. campbellii cells' protein extracts showed distinct mass spectral peaks at m/z of 2615, 3948, and 4232 da. V. campbellii STF1 is resistant to heavy metal lead, while other metals such as cadmium, copper, and mercury inhibited its growth and luminescence. Crude ethyl acetate extraction of V. campbellii demonstrated antibacterial activity against Shigella dysenteriae type 5 with a maximum inhibition zone of 27.0±1.0 mm.
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Affiliation(s)
- Chatragadda Ramesh
- Biological Oceanography Division (BOD), CSIR-National Institute of Oceanography (CSIR-NIO), Dona Paula, Goa, 403004, India. .,Department of Ocean Studies and Marine Biology, Pondicherry Central University, Port Blair, Andaman and Nicobar Islands, 744112, India.
| | - Raju Mohanraju
- Department of Ocean Studies and Marine Biology, Pondicherry Central University, Port Blair, Andaman and Nicobar Islands, 744112, India
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8
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Burtseva O, Baulina O, Zaytseva A, Fedorenko T, Chekanov K, Lobakova E. In vitro Biofilm Formation by Bioluminescent Bacteria Isolated from the Marine Fish Gut. MICROBIAL ECOLOGY 2021; 81:932-940. [PMID: 33247364 DOI: 10.1007/s00248-020-01652-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The internal surface of the animal gastrointestinal tract is covered by microbial biofilms. They play an important role in the development and functioning of the host organism and protect it against pathogens. Microbial communities of gastrointestinal biofilms are less elucidated than luminal microbiota. Therefore, the studies of biofilm formation by gastrointestinal microorganisms are a topical issue. For the first time, we report the formation of a biofilm in vitro by the strains of bioluminescent bacteria isolated from the intestines of marine fish. These bacteria exhibit co-aggregation and tend to attach to solid surfaces. The attachment of cells is accompanied by appearance of the pili. Then, we observed the formation of microcolonies and the production of extracellular polymer substances (EPSs) connecting bacterial cells into an integrated system. The presence of acidic polysaccharides is shown in the EPS when using the ruthenium red staining. Acidic polysaccharides in this matrix is a biochemical evidence of microbial biofilms. On the fibers of the polymer matrix, these bacteria form the "mushroom body"-type structures. Matured biofilms exhibit a specific three-dimensional architecture with pores and channels formed by cells and EPS. We also demonstrated the formation of a biofilm by binary culture of the luminous enterobacterium Kosakonia cowanii and a Gram-positive Macrococcus sp. The data obtained help to understand the role of these bacteria in the intestines of fish. They lead to a new study in the field of investigation of the intestinal microbiome of fish.
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Affiliation(s)
- Olga Burtseva
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Baulina
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Zaytseva
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Fedorenko
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Chekanov
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
- National Research Nuclear University MEPhi, Centre for Humanities Research and Technology, Moscow, Russia.
| | - Elena Lobakova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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9
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Goodheart JA, Minsky G, Brynjegard-Bialik MN, Drummond MS, Munoz JD, Fallon TR, Schultz DT, Weng JK, Torres E, Oakley TH. Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence. Sci Rep 2020; 10:10443. [PMID: 32591605 PMCID: PMC7320024 DOI: 10.1038/s41598-020-67209-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 06/04/2020] [Indexed: 11/09/2022] Open
Abstract
Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Laboratory culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination of the biosynthetic pathways of the luciferins. Other groups, including terrestrial fireflies, do synthesize their own luciferin, but culturing them is difficult and the biosynthetic pathway for firefly luciferin remains unclear. An additional independent origin of endogenous bioluminescence is found within ostracods from the family Cypridinidae, which use their luminescence for defense and, in Caribbean species, for courtship displays. Here, we report the first complete life cycle of a luminous ostracod (Vargula tsujii Kornicker & Baker, 1977, the California Sea Firefly) in the laboratory. We also describe the late-stage embryogenesis of Vargula tsujii and discuss the size classes of instar development. We find embryogenesis in V. tsujii ranges from 25–38 days, and this species appears to have five instar stages, consistent with ontogeny in other cypridinid lineages. We estimate a complete life cycle at 3–4 months. We also present the first complete mitochondrial genome for Vargula tsujii. Bringing a luminous ostracod into laboratory culture sets the stage for many potential avenues of study, including learning the biosynthetic pathway of cypridinid luciferin and genomic manipulation of an autogenic bioluminescent system.
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Affiliation(s)
- Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Geetanjali Minsky
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Mira N Brynjegard-Bialik
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Michael S Drummond
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - J David Munoz
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032-8201, USA
| | - Timothy R Fallon
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Darrin T Schultz
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95060, USA.,Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, 96060, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Elizabeth Torres
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032-8201, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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10
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Vannier T, Hingamp P, Turrel F, Tanet L, Lescot M, Timsit Y. Diversity and evolution of bacterial bioluminescence genes in the global ocean. NAR Genom Bioinform 2020; 2:lqaa018. [PMID: 33575578 PMCID: PMC7671414 DOI: 10.1093/nargab/lqaa018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 12/19/2022] Open
Abstract
Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.
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Affiliation(s)
- Thomas Vannier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Pascal Hingamp
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Floriane Turrel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
| | - Lisa Tanet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
| | - Magali Lescot
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Youri Timsit
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
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11
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Hayek M, Baraquet C, Lami R, Blache Y, Molmeret M. The Marine Bacterium Shewanella woodyi Produces C 8-HSL to Regulate Bioluminescence. MICROBIAL ECOLOGY 2020; 79:865-881. [PMID: 31741007 DOI: 10.1007/s00248-019-01454-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Quorum sensing (QS), a cell-to-cell communication system involved in the synchronization of bacterial behavior in a cell-density-dependent manner has been shown to control phenotypes such as luminescence, virulence, and biofilm formation. The marine strain, Shewanella woodyi MS32 has been identified as a luminous bacterium. Very little information is known on this bacterium, in particular if its luminescence and biofilm formation are controlled by QS. In this study, we have demonstrated that S. woodyi MS32 emits luminescence in planktonic and sessile conditions. The putative QS regulatory genes homologous to luxI and luxR identified in the S. woodyi MS32 genome, named swoI and swoR, are divergently transcribed and are not genetically linked to the lux operon in contrast with its closest parent Shewanella hanedai and with Aliivibrio fischeri. Interestingly, the phylogenetic analysis based on the SwoI and SwoR sequences shows that a separate horizontal gene transfer (HGT) occurred for the regulatory genes and for the lux operon. Functional analyses demonstrate that the swoI and swoR mutants were non-luminescent. Expression of lux genes was impaired in the QS regulatory mutants. N-octanoyl-L-homoserine lactone (C8-HSL) identified using liquid chromatography mass spectrometry in the wild-type strain (but not in ΔswoI) can induce S. woodyi luminescence. No significant difference has been detected between the wild-type and mutants on adhesion and biofilm formation in the conditions tested. Therefore, we have demonstrated that the luxCDABEG genes of S. woodyi MS32 are involved in luminescence emission and that the swoR/swoI genes, originated from a separate HGT, regulate luminescence through C8-HSL production.
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Affiliation(s)
- Mahmoud Hayek
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France
| | - Claudine Baraquet
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France
| | - Raphaël Lami
- Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Yves Blache
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France
| | - Maëlle Molmeret
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France.
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12
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Iafrate M, Fruhwirth GO. How Non-invasive in vivo Cell Tracking Supports the Development and Translation of Cancer Immunotherapies. Front Physiol 2020; 11:154. [PMID: 32327996 PMCID: PMC7152671 DOI: 10.3389/fphys.2020.00154] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 12/26/2022] Open
Abstract
Immunotherapy is a relatively new treatment regimen for cancer, and it is based on the modulation of the immune system to battle cancer. Immunotherapies can be classified as either molecular or cell-based immunotherapies, and both types have demonstrated promising results in a growing number of cancers. Indeed, several immunotherapies representing both classes are already approved for clinical use in oncology. While spectacular treatment successes have been reported, particularly for so-called immune checkpoint inhibitors and certain cell-based immunotherapies, they have also been accompanied by a variety of severe, sometimes life-threatening side effects. Furthermore, not all patients respond to immunotherapy. Hence, there is the need for more research to render these promising therapeutics more efficacious, more widely applicable, and safer to use. Whole-body in vivo imaging technologies that can interrogate cancers and/or immunotherapies are highly beneficial tools for immunotherapy development and translation to the clinic. In this review, we explain how in vivo imaging can aid the development of molecular and cell-based anti-cancer immunotherapies. We describe the principles of imaging host T-cells and adoptively transferred therapeutic T-cells as well as the value of traceable cancer cell models in immunotherapy development. Our emphasis is on in vivo cell tracking methodology, including important aspects and caveats specific to immunotherapies. We discuss a variety of associated experimental design aspects including parameters such as cell type, observation times/intervals, and detection sensitivity. The focus is on non-invasive 3D cell tracking on the whole-body level including aspects relevant for both preclinical experimentation and clinical translatability of the underlying methodologies.
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Affiliation(s)
| | - Gilbert O. Fruhwirth
- Imaging Therapy and Cancer Group, Department of Imaging Chemistry and Biology, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
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13
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Gregor C, Pape JK, Gwosch KC, Gilat T, Sahl SJ, Hell SW. Autonomous bioluminescence imaging of single mammalian cells with the bacterial bioluminescence system. Proc Natl Acad Sci U S A 2019; 116:26491-26496. [PMID: 31792180 PMCID: PMC6936394 DOI: 10.1073/pnas.1913616116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Bioluminescence-based imaging of living cells has become an important tool in biological and medical research. However, many bioluminescence imaging applications are limited by the requirement of an externally provided luciferin substrate and the low bioluminescence signal which restricts the sensitivity and spatiotemporal resolution. The bacterial bioluminescence system is fully genetically encodable and hence produces autonomous bioluminescence without an external luciferin, but its brightness in cell types other than bacteria has, so far, not been sufficient for imaging single cells. We coexpressed codon-optimized forms of the bacterial luxCDABE and frp genes from multiple plasmids in different mammalian cell lines. Our approach produces high luminescence levels that are comparable to firefly luciferase, thus enabling autonomous bioluminescence microscopy of mammalian cells.
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Affiliation(s)
- Carola Gregor
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Jasmin K. Pape
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Klaus C. Gwosch
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Tanja Gilat
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Steffen J. Sahl
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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14
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Lee J, Müller F, Visser AJWG. The Sensitized Bioluminescence Mechanism of Bacterial Luciferase. Photochem Photobiol 2018; 95:679-704. [PMID: 30485901 DOI: 10.1111/php.13063] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/17/2018] [Indexed: 11/27/2022]
Abstract
After more than one-half century of investigations, the mechanism of bioluminescence from the FMNH2 assisted oxygen oxidation of an aliphatic aldehyde on bacterial luciferase continues to resist elucidation. There are many types of luciferase from species of bioluminescent bacteria originating from both marine and terrestrial habitats. The luciferases all have close sequence homology, and in vitro, a highly efficient light generation is obtained from these natural metabolites as substrates. Sufficient exothermicity equivalent to the energy of a blue photon is available in the chemical oxidation of the aldehyde to the corresponding carboxylic acid, and a luciferase-bound FMNH-OOH is a key player. A high energy species, the source of the exothermicity, is unknown except that it is not a luciferin cyclic peroxide, a dioxetanone, as identified in the pathway of the firefly and the marine bioluminescence systems. Besides these natural substrates, variable bioluminescence properties are found using other reactants such as flavin analogs or aldehydes, but results also depend on the luciferase type. Some rationalization of the mechanism has resulted from spatial structure determination, NMR of intermediates and dynamic optical spectroscopy. The overall light path appears to fall into the sensitized class of chemiluminescence mechanism, distinct from the dioxetanone types.
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Affiliation(s)
- John Lee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | | | - Antonie J W G Visser
- Laboratory of Biochemistry Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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15
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Volpe A, Kurtys E, Fruhwirth GO. Cousins at work: How combining medical with optical imaging enhances in vivo cell tracking. Int J Biochem Cell Biol 2018; 102:40-50. [PMID: 29960079 PMCID: PMC6593261 DOI: 10.1016/j.biocel.2018.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
Microscopy and medical imaging are related in their exploitation of electromagnetic waves, but were developed to satisfy differing needs, namely to observe small objects or to look inside subjects/objects, respectively. Together, these techniques can help elucidate complex biological processes and better understand health and disease. A current major challenge is to delineate mechanisms governing cell migration and tissue invasion in organismal development, the immune system and in human diseases such as cancer where the spatiotemporal tracking of small cell numbers in live animal models is extremely challenging. Multi-modal multi-scale in vivo cell tracking integrates medical and optical imaging. Fuelled by basic research in cancer biology and cell-based therapeutics, it has been enabled by technological advances providing enhanced resolution, sensitivity and multiplexing capabilities. Here, we review which imaging modalities have been successfully used for in vivo cell tracking and how this challenging task has benefitted from combining macroscopic with microscopic techniques.
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Affiliation(s)
- Alessia Volpe
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, SE1 7EH, London, UK
| | - Ewelina Kurtys
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, SE1 7EH, London, UK
| | - Gilbert O Fruhwirth
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, SE1 7EH, London, UK.
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16
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Magana M, Sereti C, Ioannidis A, Mitchell CA, Ball AR, Magiorkinis E, Chatzipanagiotou S, Hamblin MR, Hadjifrangiskou M, Tegos GP. Options and Limitations in Clinical Investigation of Bacterial Biofilms. Clin Microbiol Rev 2018; 31:e00084-16. [PMID: 29618576 PMCID: PMC6056845 DOI: 10.1128/cmr.00084-16] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria can form single- and multispecies biofilms exhibiting diverse features based upon the microbial composition of their community and microenvironment. The study of bacterial biofilm development has received great interest in the past 20 years and is motivated by the elegant complexity characteristic of these multicellular communities and their role in infectious diseases. Biofilms can thrive on virtually any surface and can be beneficial or detrimental based upon the community's interplay and the surface. Advances in the understanding of structural and functional variations and the roles that biofilms play in disease and host-pathogen interactions have been addressed through comprehensive literature searches. In this review article, a synopsis of the methodological landscape of biofilm analysis is provided, including an evaluation of the current trends in methodological research. We deem this worthwhile because a keyword-oriented bibliographical search reveals that less than 5% of the biofilm literature is devoted to methodology. In this report, we (i) summarize current methodologies for biofilm characterization, monitoring, and quantification; (ii) discuss advances in the discovery of effective imaging and sensing tools and modalities; (iii) provide an overview of tailored animal models that assess features of biofilm infections; and (iv) make recommendations defining the most appropriate methodological tools for clinical settings.
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Affiliation(s)
- Maria Magana
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
| | - Christina Sereti
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
- Department of Microbiology, Thriassio General Hospital, Attiki, Greece
| | - Anastasios Ioannidis
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta, Greece
| | - Courtney A Mitchell
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Anthony R Ball
- Gliese 623b, Mendon, Massachusetts, USA
- GAMA Therapeutics LLC, Pepperell, Massachusetts, USA
| | - Emmanouil Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens-Goudi, Greece
| | | | - Michael R Hamblin
- Harvard-MIT Division of Health Science and Technology, Cambridge, Massachusetts, USA
- Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - George P Tegos
- Gliese 623b, Mendon, Massachusetts, USA
- GAMA Therapeutics LLC, Pepperell, Massachusetts, USA
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17
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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18
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Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. Nutrients 2017; 10:nu10010014. [PMID: 29295502 PMCID: PMC5793242 DOI: 10.3390/nu10010014] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/24/2017] [Accepted: 12/19/2017] [Indexed: 02/06/2023] Open
Abstract
The human milk microbiota is a complex and diverse ecosystem that seems to play a relevant role in the mother-to-infant transmission of microorganisms during early life. Bacteria present in human milk may arise from different sources, and recent studies suggest that at least some of them may be originally present in the maternal digestive tract and may reach the mammary gland through an endogenous route during pregnancy and lactation. The objective of this work was to elucidate whether some lactic acid bacteria are able to translocate and colonize the mammary gland and milk. For this purpose, two lactic acid bacteria strains (Lactococcus lactis MG1614 and Lactobacillus salivarius PS2) were transformed with a plasmid containing the lux genes; subsequently, the transformed strains were orally administered to pregnant mice. The murine model allowed the visualization, isolation, and Polymerase Chain Reaction (PCR)-detection of the transformed bacteria in different body locations, including mammary tissue and milk, reinforcing the hypothesis that physiological translocation of maternal bacteria during pregnancy and lactation may contribute to the composition of the mammary and milk microbiota.
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19
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Side DD, Nassisi V, Pennetta C, Alifano P, Di Salvo M, Talà A, Chechkin A, Seno F, Trovato A. Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171586. [PMID: 29308273 PMCID: PMC5750040 DOI: 10.1098/rsos.171586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
We present an effective dynamical model for the onset of bacterial bioluminescence, one of the most studied quorum sensing-mediated traits. Our model is built upon simple equations that describe the growth of the bacterial colony, the production and accumulation of autoinducer signal molecules, their sensing within bacterial cells, and the ensuing quorum activation mechanism that triggers bioluminescent emission. The model is directly tested to quantitatively reproduce the experimental distributions of photon emission times, previously measured for bacterial colonies of Vibrio jasicida, a luminescent bacterium belonging to the Harveyi clade, growing in a highly drying environment. A distinctive and novel feature of the proposed model is bioluminescence 'quenching' after a given time elapsed from activation. Using an advanced fitting procedure based on the simulated annealing algorithm, we are able to infer from the experimental observations the biochemical parameters used in the model. Such parameters are in good agreement with the literature data. As a further result, we find that, at least in our experimental conditions, light emission in bioluminescent bacteria appears to originate from a subtle balance between colony growth and quorum activation due to autoinducers diffusion, with the two phenomena occurring on the same time scale. This finding is consistent with a negative feedback mechanism previously reported for Vibrio harveyi.
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Affiliation(s)
- Domenico Delle Side
- Dipartimento di Matematica e Fisica ‘Ennio De Giorgi’, Università del Salento, Lecce, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Lecce, Lecce, Italy
| | - Vincenzo Nassisi
- Dipartimento di Matematica e Fisica ‘Ennio De Giorgi’, Università del Salento, Lecce, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Lecce, Lecce, Italy
| | - Cecilia Pennetta
- Dipartimento di Matematica e Fisica ‘Ennio De Giorgi’, Università del Salento, Lecce, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Lecce, Lecce, Italy
| | - Pietro Alifano
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Marco Di Salvo
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Adelfia Talà
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Aleksei Chechkin
- Akhiezer Institute for Theoretical Physics, Kharkov Institute of Physics and Technology, Kharkov 61108, Ukraine
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
- Dipartimento di Fisica e Astronomia ‘Galileo Galilei’, Università di Padova, Padova, Italy
| | - Flavio Seno
- Dipartimento di Fisica e Astronomia ‘Galileo Galilei’, Università di Padova, Padova, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Padova, Padova, Italy
| | - Antonio Trovato
- Dipartimento di Fisica e Astronomia ‘Galileo Galilei’, Università di Padova, Padova, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Padova, Padova, Italy
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20
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Iqbal M, Doherty N, Page AML, Qazi SNA, Ajmera I, Lund PA, Kypraios T, Scott DJ, Hill PJ, Stekel DJ. Reconstructing promoter activity from Lux bioluminescent reporters. PLoS Comput Biol 2017; 13:e1005731. [PMID: 28922354 PMCID: PMC5619816 DOI: 10.1371/journal.pcbi.1005731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/28/2017] [Accepted: 08/19/2017] [Indexed: 11/19/2022] Open
Abstract
The bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has also been adapted for eukaryotic cells, and can be used for whole cell biosensors, or in real time with live animals without the need for euthanasia. However, correct interpretation of bioluminescent data is limited: the bioluminescence is different from gene expression because of nonlinear molecular and enzyme dynamics of the Lux system. We have developed a computational approach that, for the first time, allows users of Lux assays to infer gene transcription levels from the light output. This approach is based upon a new mathematical model for Lux activity, that includes the actions of LuxAB, LuxEC and Fre, with improved mechanisms for all reactions, as well as synthesis and turn-over of Lux proteins. The model is calibrated with new experimental data for the LuxAB and Fre reactions from Photorhabdus luminescens—the source of modern Lux reporters—while literature data has been used for LuxEC. Importantly, the data show clear evidence for previously unreported product inhibition for the LuxAB reaction. Model simulations show that predicted bioluminescent profiles can be very different from changes in gene expression, with transient peaks of light output, very similar to light output seen in some experimental data sets. By incorporating the calibrated model into a Bayesian inference scheme, we can reverse engineer promoter activity from the bioluminescence. We show examples where a decrease in bioluminescence would be better interpreted as a switching off of the promoter, or where an increase in bioluminescence would be better interpreted as a longer period of gene expression. This approach could benefit all users of Lux technology. Bioluminescent reporters are used in many areas of biology as fast, sensitive and non-destructive measures of gene expression. They have been developed for bacteria, adapted now for other kinds of organisms, and recently been used for whole cell biosensors, and for real-time live animal models for infection without the need for euthanasia. However, users of Lux technologies rely on the light output being similar to the gene expression they wish to measure. We show that this is not the case. Rather, there is a nonlinear relationship between the two: light output can be misleading and so limits the way that such data can be interpreted. We have developed a new computational method that, for the first time, allows users of Lux reporters to infer accurate gene transcription levels from bioluminescent data. We show examples where a small decrease in light would be better interpreted as promoter being switched off, or where an increase in light would be better interpreted as promoter activity for a longer time.
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Affiliation(s)
- Mudassar Iqbal
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Neil Doherty
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Anna M. L. Page
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Saara N. A. Qazi
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Ishan Ajmera
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Peter A. Lund
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Theodore Kypraios
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - David J. Scott
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Philip J. Hill
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Dov J. Stekel
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
- * E-mail:
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21
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Moi IM, Roslan NN, Leow ATC, Ali MSM, Rahman RNZRA, Rahimpour A, Sabri S. The biology and the importance of Photobacterium species. Appl Microbiol Biotechnol 2017; 101:4371-4385. [PMID: 28497204 DOI: 10.1007/s00253-017-8300-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
Photobacterium species are Gram-negative coccobacilli which are distributed in marine habitats worldwide. Some species are unique because of their capability to produce luminescence. Taxonomically, about 23 species and 2 subspecies are validated to date. Genomes from a few Photobacterium spp. have been sequenced and studied. They are considered a special group of bacteria because some species are capable of producing essential polyunsaturated fatty acids, antibacterial compounds, lipases, esterases and asparaginases. They are also used as biosensors in food and environmental monitoring and detectors of drown victim, as well as an important symbiont.
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Affiliation(s)
- Ibrahim Musa Moi
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Bauchi State University Gadau, P.M.B. O65, Bauchi, Bauchi State, Nigeria
| | - Noordiyanah Nadhirah Roslan
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Azam Rahimpour
- Department of Tissue Engineering and Regenerative Medicine, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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22
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Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade. Sci Rep 2017; 7:41394. [PMID: 28145490 PMCID: PMC5286417 DOI: 10.1038/srep41394] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 01/09/2023] Open
Abstract
The core of the Vibrio Harveyi clade contains V. harveyi, V. campbellii, V. owensii, V. jasicida, and V. rotiferianus. They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences and phenotypes. To better understand their evolutionary relationships and functional features, we sequenced a shrimp pathogen strain V. harveyi 1114GL, reclassified it as V. campbellii and compared this and 47 other sequenced Vibrio genomes in the Harveryi clade. A phylogeny based on 1,775 genes revealed that both V. owensii and V. jasicida were closer to V. campbellii than to V. harveyi and that V. campbellii strains can be divided into two distinct groups. Species-specific genes such as intimin and iron acquisition genes were identified in V. campbellii. In particular, the 1114GL strain contains two bacterial immunoglobulin-like genes for cell adhesion with 22 Big_2 domains that have been extensively reshuffled and are by far the most expanded among all species surveyed in this study. The 1114GL strain differed from ATCC BAA-1116 by ~9% at the synonymous sites, indicating high diversity within V. campbellii. Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity.
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23
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Luo Y, Liu YJ. Bioluminophore and Flavin Mononucleotide Fluorescence Quenching of Bacterial Bioluminescence-A Theoretical Study. Chemistry 2016; 22:16243-16249. [PMID: 27665749 DOI: 10.1002/chem.201603314] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 02/02/2023]
Abstract
Bacterial bioluminescence with continuous glow has been applied to the fields of environmental toxin monitoring, drug screening, and in vivo imaging. Nonetheless, the chemical form of the bacterial bioluminophore is still a bone of contention. Flavin mononucleotide (FMN), one of the light-emitting products, and 4a-hydroxy-5-hydro flavin mononucleotide (HFOH), an intermediate of the chemical reactions, have both been assumed candidates for the light emitter because they have similar molecular structures and fluorescence wavelengths. The latter is preferred in experiments and was assigned in our previous density functional study. HFOH displays weak fluorescence in solutions, but exhibits strong bioluminescence in the bacterial luciferase. FMN shows the opposite behavior; its fluorescence is quenched when it is bound to the luciferase. This is the first example of flavin fluorescence quenching observed in bioluminescent systems and is merely an observation, both the quenching mechanism and quencher are still unclear. Based on theoretical analysis of high-level quantum mechanics (QM), combined QM and molecular mechanics (QM/MM), and molecular dynamics (MD), this paper confirms that HFOH in its first singlet excited state is the bioluminophore of bacterial bioluminescence. More importantly, the computational results indicate that Tyr110 in the luciferase quenches the FMN fluorescence via an electron-transfer mechanism.
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Affiliation(s)
- Yanling Luo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China.
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24
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Long MC, Poganik JR, Aye Y. On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry. J Am Chem Soc 2016; 138:3610-22. [PMID: 26907082 PMCID: PMC4805449 DOI: 10.1021/jacs.5b12608] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/28/2022]
Abstract
Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is "tethering"-a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein-protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: "multifunctional scaffolding" versus "on-demand targeting". By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.
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Affiliation(s)
- Marcus
J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Jesse R. Poganik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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Dunn AK, Rader BA, Stabb EV, Mandel MJ. Regulation of Bioluminescence in Photobacterium leiognathi Strain KNH6. J Bacteriol 2015; 197:3676-85. [PMID: 26350139 PMCID: PMC4626902 DOI: 10.1128/jb.00524-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/03/2015] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Bacterial bioluminescence is taxonomically restricted to certain proteobacteria, many of which belong to the Vibrionaceae. In the most well-studied cases, pheromone signaling plays a key role in regulation of light production. However, previous reports have indicated that certain Photobacterium strains do not use this regulatory method for controlling luminescence. In this study, we combined genome sequencing with genetic approaches to characterize the regulation of luminescence in Photobacterium leiognathi strain KNH6, an extremely bright isolate. Using transposon mutagenesis and screening for decreased luminescence, we identified insertions in genes encoding components necessary for the luciferase reaction (lux, lum, and rib operons) as well as in nine other loci. These additional loci encode gene products predicted to be involved in the tricarboxylic acid (TCA) cycle, DNA and RNA metabolism, transcriptional regulation, and the synthesis of cytochrome c, peptidoglycan, and fatty acids. The mutagenesis screen did not identify any mutants with disruptions of predicted pheromone-related loci. Using targeted gene insertional disruptions, we demonstrate that under the growth conditions tested, luminescence levels do not appear to be controlled through canonical pheromone signaling systems in this strain. IMPORTANCE Despite the long-standing interest in luminous bacteria, outside a few model organisms, little is known about the regulation and function of luminescence. Light-producing marine bacteria are widely distributed and have diverse lifestyles, suggesting that the control and significance of luminescence may be similarly diverse. In this study, we apply genetic tools to the study of regulation of light production in the extremely bright isolate Photobacterium leiognathi KNH6. Our results suggest an unusual lack of canonical pheromone-mediated control of luminescence and contribute to a better understanding of alternative strategies for regulation of a key bacterial behavior. These experiments lay the groundwork for further study of the regulation and role of bioluminescence in P. leiognathi.
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Affiliation(s)
- Anne K Dunn
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Bethany A Rader
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Eric V Stabb
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Mark J Mandel
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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