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Acquisition of bioluminescent trait by non-luminous organisms from luminous organisms through various origins. Photochem Photobiol Sci 2021; 20:1547-1562. [PMID: 34714534 DOI: 10.1007/s43630-021-00124-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/20/2021] [Indexed: 12/20/2022]
Abstract
Bioluminescence is a natural light emitting phenomenon that occurs due to a chemical reaction between luciferin and luciferase. It is primarily an innate and inherited trait in most terrestrial luminous organisms. However, most luminous organisms produce light in the ocean by acquiring luminous symbionts, luciferin (substrate), and/or luciferase (enzyme) through various transmission pathways. For instance, coelenterazine, a well-known luciferin, is obtained by cnidarians, crustaceans, and deep-sea fish through multi-level dietary linkages from coelenterazine producers such as ctenophores, decapods, and copepods. In contrast, some non-luminous Vibrio bacteria became bioluminescent by obtaining lux genes from luminous Vibrio species by horizontal gene transfer. Various examples detailed in this review show how non-luminescent organisms became luminescent by acquiring symbionts, dietary luciferins and luciferases, and genes. This review highlights three modes (symbiosis, ingestion, and horizontal gene transfer) that allow organisms lacking genes for autonomous bioluminescent systems to obtain the ability to produce light. In addition to bioluminescence, this manuscript discusses the acquisition of other traits such as pigments, fluorescence, toxins, and others, to infer the potential processes of acquisition.
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Simpson CA, Petersen BD, Haas NW, Geyman LJ, Lee AH, Podicheti R, Pepin R, Brown LC, Rusch DB, Manzella MP, Papenfort K, van Kessel JC. The quorum-sensing systems of Vibrio campbellii DS40M4 and BB120 are genetically and functionally distinct. Environ Microbiol 2021; 23:5412-5432. [PMID: 33998118 PMCID: PMC8458232 DOI: 10.1111/1462-2920.15602] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 05/13/2021] [Indexed: 11/28/2022]
Abstract
Vibrio campbellii BB120 (previously classified as Vibrio harveyi) is a fundamental model strain for studying quorum sensing in vibrios. A phylogenetic evaluation of sequenced Vibrio strains in Genbank revealed that BB120 is closely related to the environmental isolate V. campbellii DS40M4. We exploited DS40M4's competence for exogenous DNA uptake to rapidly generate greater than 30 isogenic strains with deletions of genes encoding BB120 quorum-sensing system homologues. Our results show that the quorum-sensing circuit of DS40M4 is distinct from BB120 in three ways: (i) DS40M4 does not produce an acyl homoserine lactone autoinducer but encodes an active orphan LuxN receptor, (ii) the quorum regulatory small RNAs (Qrrs) are not solely regulated by autoinducer signalling through the response regulator LuxO and (iii) the DS40M4 quorum-sensing regulon is much smaller than BB120 (~100 genes vs. ~400 genes, respectively). Using comparative genomics to expand our understanding of quorum-sensing circuit diversity, we observe that conservation of LuxM/LuxN proteins differs widely both between and within Vibrio species. These strains are also phenotypically distinct: DS40M4 exhibits stronger interbacterial cell killing, whereas BB120 forms more robust biofilms and is bioluminescent. These results underscore the need to examine wild isolates for a broader view of bacterial diversity in the marine ecosystem.
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Affiliation(s)
| | | | - Nicholas W Haas
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Logan J Geyman
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Aimee H Lee
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Ram Podicheti
- Centre for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
| | - Robert Pepin
- Mass Spectrometry Facility, Indiana University, Bloomington, IN, USA
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Laura C Brown
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Douglas B Rusch
- Centre for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
| | | | - Kai Papenfort
- Friedrich Schiller University, Institute of Microbiology, Jena, Germany
- Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
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Wang D, Wang S, Bai L, Nasir MS, Li S, Yan W. Mathematical Modeling Approaches for Assessing the Joint Toxicity of Chemical Mixtures Based on Luminescent Bacteria: A Systematic Review. Front Microbiol 2020; 11:1651. [PMID: 32849340 PMCID: PMC7412757 DOI: 10.3389/fmicb.2020.01651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/25/2020] [Indexed: 01/14/2023] Open
Abstract
Developments in industrial applications inevitably accelerate the discharge of enormous substances into the environment, whereas multi-component mixtures commonly cause joint toxicity which is distinct from the simple sum of independent effect. Thus, ecotoxicological assessment, by luminescent bioassays has recently brought increasing attention to overcome the environmental risks. Based on the above viewpoint, this review included a brief introduction to the occurrence and characteristics of toxic bioassay based on the luminescent bacteria. In order to assess the environmental risk of mixtures, a series of models for the prediction of the joint effect of multi-component mixtures have been summarized and discussed in-depth. Among them, Quantitative Structure-Activity Relationship (QSAR) method which was widely applied in silico has been described in detail. Furthermore, the reported potential mechanisms of joint toxicity on the luminescent bacteria were also overviewed, including the Trojan-horse type mechanism, funnel hypothesis, and fishing hypothesis. The future perspectives toward the development and application of toxicity assessment based on luminescent bacteria were proposed.
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Affiliation(s)
- Dan Wang
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Shaanxi, China
| | - Shan Wang
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Shaanxi, China
| | - Linming Bai
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Shaanxi, China
| | - Muhammad Salman Nasir
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Shaanxi, China.,Department of Structures and Environmental Engineering, University of Agriculture, Faisalabad, Pakistan
| | - Shanshan Li
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Shaanxi, China
| | - Wei Yan
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Shaanxi, China
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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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Deeva AA, Zykova EA, Nemtseva EV, Kratasyuk VA. Functional divergence between evolutionary‐related LuxG and Fre oxidoreductases of luminous bacteria. Proteins 2019; 87:723-729. [DOI: 10.1002/prot.25696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/28/2019] [Accepted: 04/12/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Anna A. Deeva
- Laboratory of Bioluminescent BiotechnologiesSiberian Federal University Krasnoyarsk Russian Federation
| | - Evgenia A. Zykova
- Mechanism of Cell Genome Functioning LaboratoryInstitute of Cell Biophysics RAS Pushchino Moscow Region Russian Federation
- Department of applied research informatizationState Institute of Information Technologies and Telecommunications (SIITandT “Informika”) Moscow Russian Federation
| | - Elena V. Nemtseva
- Laboratory of Bioluminescent BiotechnologiesSiberian Federal University Krasnoyarsk Russian Federation
- Laboratory of PhotobiologyInstitute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS” Krasnoyarsk Russian Federation
| | - Valentina A. Kratasyuk
- Laboratory of Bioluminescent BiotechnologiesSiberian Federal University Krasnoyarsk Russian Federation
- Laboratory of PhotobiologyInstitute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS” Krasnoyarsk Russian Federation
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Xuan G, Xiao Q, Wang J, Lin H, Pavase T. Expression of genes encoding the luciferase from Photobacterium leiognathi in Escherichia coli Rosetta (DE3) and its application in NADH detection. LUMINESCENCE 2018; 33:1010-1018. [PMID: 29920921 DOI: 10.1002/bio.3501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 02/01/2023]
Abstract
Cloning of genes encoding the luciferase from Photobacterium leiognathi YL in Escherichia coli Rosetta (DE3) was performed successfully and the expressed forms of lux AB were purified to homogeneity. Experimental measurements revealed that luciferase from Photobacterium leiognathi YL has good thermal stability and a high residual activity at extreme pH values, which are extremely important for its various ecological, industrial and medical applications. Furthermore, we made a first attempt for quantitative detection of NADH by recombinant E. coli Rosetta (DE3) coupled enzyme system. A good linear relationship between luminescence intensity and NADH with low (1-12 nmol/L) and high (10-500 nmol/L) concentration was observed, whose standard curve was y = 772.97× + 4041.1, R2 = 0.9884 and y = 1710× + 4.99 × 105 , R2 = 0.9727, respectively. Our results demonstrate a high sensitivity of recombinant E. coli coupled enzyme system to NADH on the basis of high soluble expression of recombinant luciferase and continuous and stable expression of some NAD(P)H-dependent flavin mononucleotide (FMN) reductases.
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Affiliation(s)
- Guanhua Xuan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Qilin Xiao
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Jingxue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Hong Lin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Tushar Pavase
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
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Bacterial Quorum Sensing Stabilizes Cooperation by Optimizing Growth Strategies. Appl Environ Microbiol 2016; 82:6498-6506. [PMID: 27565619 DOI: 10.1128/aem.01945-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/18/2016] [Indexed: 01/04/2023] Open
Abstract
Communication has been suggested as a mechanism to stabilize cooperation. In bacteria, chemical communication, termed quorum sensing (QS), has been hypothesized to fill this role, and extracellular public goods are often induced by QS at high cell densities. Here we show, with the bacterium Vibrio harveyi, that QS provides strong resistance against invasion of a QS defector strain by maximizing the cellular growth rate at low cell densities while achieving maximum productivity through protease upregulation at high cell densities. In contrast, QS mutants that act as defectors or unconditional cooperators maximize either the growth rate or the growth yield, respectively, and thus are less fit than the wild-type QS strain. Our findings provide experimental evidence that regulation mediated by microbial communication can optimize growth strategies and stabilize cooperative phenotypes by preventing defector invasion, even under well-mixed conditions. This effect is due to a combination of responsiveness to environmental conditions provided by QS, lowering of competitive costs when QS is not induced, and pleiotropic constraints imposed on defectors that do not perform QS. IMPORTANCE Cooperation is a fundamental problem for evolutionary biology to explain. Conditional participation through phenotypic plasticity driven by communication is a potential solution to this dilemma. Thus, among bacteria, QS has been proposed to be a proximate stabilizing mechanism for cooperative behaviors. Here, we empirically demonstrate that QS in V. harveyi prevents cheating and subsequent invasion by nonproducing defectors by maximizing the growth rate at low cell densities and the growth yield at high cell densities, whereas an unconditional cooperator is rapidly driven to extinction by defectors. Our findings provide experimental evidence that QS regulation prevents the invasion of cooperative populations by QS defectors even under unstructured conditions, and they strongly support the role of communication in bacteria as a mechanism that stabilizes cooperative traits.
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Dunlap P. Biochemistry and Genetics of Bacterial Bioluminescence. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 144:37-64. [DOI: 10.1007/978-3-662-43385-0_2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Urbanczyk H, Furukawa T, Yamamoto Y, Dunlap PV. Natural replacement of vertically inherited lux-rib genes of Photobacterium aquimaris by horizontally acquired homologues. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:412-416. [PMID: 23760826 DOI: 10.1111/j.1758-2229.2012.00355.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We report here the first instance of a complete replacement of vertically inherited luminescence genes by horizontally acquired homologues. Different strains of Photobacterium aquimaris contain homologues of the lux-rib genes that have a different evolutionary history. Strain BS1 from the Black Sea contains a vertically inherited lux-rib operon, which presumably arose in the ancestor of this species, whereas the type strain NBRC 104633(T) , from Sagami Bay, lacks the vertically inherited lux-rib operon and instead carries a complete and functional lux-rib operon acquired horizontally from a bacterium related to Photobacterium mandapamensis. The results indicate that the horizontal acquisition of the lux genes expanded the pan-genome of P. aquimaris, but it did not influence the phylogenetic divergence of this species.
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Affiliation(s)
- Henryk Urbanczyk
- Interdisciplinary Research Organization Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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Abstract
The bioluminescence emitted by the marine bacterium Vibrio fischeri is a particularly striking result of individual microbial cells co-ordinating a group behaviour. The genes responsible for light production are principally regulated by the LuxR-LuxI quorum-sensing system. In addition to LuxR-LuxI, numerous other genetic elements and environmental conditions control bioluminescence production. Efforts to mathematically model the LuxR-LuxI system are providing insight into the dynamics of this autoinduction behaviour. The Hawaiian squid Euprymna scolopes forms a natural symbiosis with V. fischeri, and utilizes the symbiont-derived bioluminescence for certain nocturnal behaviours, such as counterillumination. Recent work suggests that the tissue with which V. fischeri associates not only can detect bioluminescence but may also use this light to monitor the V. fischeri population.
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Affiliation(s)
- Tim Miyashiro
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706-1521, USA.
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Wollenberg M, Preheim S, Polz M, Ruby EG. Polyphyly of non-bioluminescent Vibrio fischeri sharing a lux-locus deletion. Environ Microbiol 2012; 14:655-68. [PMID: 21980988 PMCID: PMC3655796 DOI: 10.1111/j.1462-2920.2011.02608.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports the first description and molecular characterization of naturally occurring, non-bioluminescent strains of Vibrio fischeri. These 'dark' V. fischeri strains remained non-bioluminescent even after treatment with both autoinducer and aldehyde, substrate additions that typically maximize light production in dim strains of luminous bacteria. Surprisingly, the entire lux locus (eight genes) was absent in over 97% of these dark V. fischeri strains. Although these strains were all collected from a Massachusetts (USA) estuary in 2007, phylogenetic reconstructions allowed us to reject the hypothesis that these newly described non-bioluminescent strains exhibit monophyly within the V. fischeri clade. These dark strains exhibited a competitive disadvantage against native bioluminescent strains when colonizing the light organ of the model V. fischeri host, the Hawaiian bobtail squid Euprymna scolopes. Significantly, we believe that the data collected in this study may suggest the first observation of a functional, parallel locus-deletion event among independent lineages of a non-pathogenic bacterial species.
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Affiliation(s)
- M.S. Wollenberg
- Department of Medical Microbiology and Immunology, University of Wisconsin, 1550 Linden Drive, Room 5245, Madison, WI 53706-1521, USA
| | - S.P. Preheim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street, Bldg 48-417, Cambridge, MA 02139, USA
| | - M.F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street, Bldg 48-417, Cambridge, MA 02139, USA
| | - E. G. Ruby
- Department of Medical Microbiology and Immunology, University of Wisconsin, 1550 Linden Drive, Room 5245, Madison, WI 53706-1521, USA
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Contribution of rapid evolution of the luxR-luxI intergenic region to the diverse bioluminescence outputs of Vibrio fischeri strains isolated from different environments. Appl Environ Microbiol 2011; 77:2445-57. [PMID: 21317265 DOI: 10.1128/aem.02643-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio fischeri serves as a valuable model of bacterial bioluminescence, its regulation, and its functional significance. Light output varies more than 10,000-fold in wild-type isolates from different environments, yet dim and bright strains have similar organization of the light-producing lux genes, with the activator-encoding luxR divergently transcribed from luxICDABEG. By comparing the genomes of bright strain MJ11 and the dimmer ES114, we found that the lux region has diverged more than most shared orthologs, including those flanking lux. Divergence was particularly high in the intergenic sequence between luxR and luxI. Analysis of the intergenic lux region from 18 V. fischeri strains revealed that, with one exception, sequence divergence essentially mirrored strain phylogeny but with relatively high substitution rates. The bases conserved among intergenic luxR-luxI sequences included binding sites for known regulators, such as LuxR and ArcA, and bases of unknown significance, including a striking palindromic repeat. By using this collection of diverse luxR-luxI regions, we found that expression of P(luxI)-lacZ but not P(luxR)-lacZ transcriptional reporters correlated with the luminescence output of the strains from which the promoters originated. We also found that exchange of a small stretch of the luxI-luxR intergenic region between two strains largely reversed their relative brightness. Our results show that the luxR-luxI intergenic region contributes significantly to the variable luminescence output among V. fischeri strains isolated from different environments, although other elements of strain backgrounds also contribute. Moreover, the lux system appears to have evolved relatively rapidly, suggesting unknown environment-specific selective pressures.
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