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Yudenko A, Bazhenov SV, Aleksenko VA, Goncharov IM, Semenov O, Remeeva A, Nazarenko VV, Kuznetsova E, Fomin VV, Konopleva MN, Al Ebrahim R, Sluchanko NN, Ryzhykau Y, Semenov YS, Kuklin A, Manukhov IV, Gushchin I. luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase. Proteins 2024. [PMID: 39171358 DOI: 10.1002/prot.26739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/20/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Several clades of luminescent bacteria are known currently. They all contain similar lux operons, which include the genes luxA and luxB encoding a heterodimeric luciferase. The aldehyde oxygenation reaction is presumed to be catalyzed primarily by the subunit LuxA, whereas LuxB is required for efficiency and stability of the complex. Recently, genomic analysis identified a subset of bacterial species with rearranged lux operons lacking luxB. Here, we show that the product of the luxA gene from the reduced luxACDE operon of Enhygromyxa salina is luminescent upon addition of aldehydes both in vivo in Escherichia coli and in vitro. Overall, EsLuxA is much less bright compared with luciferases from Aliivibrio fischeri (AfLuxAB) and Photorhabdus luminescens (PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure of EsLuxA determined at the resolution of 2.71 Å reveals a (β/α)8 TIM-barrel fold, characteristic for other bacterial luciferases, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil in Vibrio harveyi LuxA, form α-helices in EsLuxA. Phylogenetic analysis shows EsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of the luxA gene and its speciation to luxA and luxB in the previously described luminescent bacteria. Our work paves the way for the development of new bacterial luciferases that have an advantage of being encoded by a single gene.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey V Bazhenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vladimir A Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vadim V Fomin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maria N Konopleva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Rahaf Al Ebrahim
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Yury Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Yury S Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ilya V Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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Brodl E, Csamay A, Horn C, Niederhauser J, Weber H, Macheroux P. The impact of LuxF on light intensity in bacterial bioluminescence. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2020; 207:111881. [PMID: 32325406 DOI: 10.1016/j.jphotobiol.2020.111881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 10/24/2022]
Abstract
The enzymes involved in bacterial bioluminescence are encoded in the lux operon with a conserved gene order of luxCDABEG. Some photobacterial strains carry an additional gene, termed luxF, which produces the LuxF protein, whose function and influence on bacterial bioluminescence is still uncertain. The LuxF protein binds the flavin derivative 6-(3'-(R)-myristyl)-flavin mononucleotide (myrFMN), which is generated as a side product in the luciferase-catalyzed reaction. This study utilized an Escherichia coli (E. coli) based lux operon expression system where the lux operons of Photobacterium leiognathi subsp. mandapamensis 27561 or of Photobacterium leiognathi subsp. leiognathi 25521, namely luxCDAB(F)EG, were cloned into a single expression vector. Exclusion of luxF gene from the lux operon enabled novel insights into the role of LuxF protein in light emission. E. coli cultures harboring and expressing the genes of the lux operon including luxF gene emit more light than without luxF gene. Furthermore, isolation of the tightly bound flavin derivative revealed the presence of at least three different flavin derivatives. Analysis by UV/Vis absorption and NMR spectroscopy as well as mass spectrometry showed that the flavin derivatives bear fatty acids of various chain lengths. This distribution of FMN derivatives is vastly different to what was found in bioluminescent bacteria and indicates that the luciferase is supplied with a range of aldehyde substrates in E. coli.
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Affiliation(s)
- Eveline Brodl
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12/2, 8010 Graz, Austria
| | - Alexandra Csamay
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12/2, 8010 Graz, Austria
| | - Christina Horn
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12/2, 8010 Graz, Austria
| | - Johannes Niederhauser
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12/2, 8010 Graz, Austria
| | - Hansjörg Weber
- Graz University of Technology, Institute of Organic Chemistry, Stremayrgasse 9, 8010 Graz, Austria
| | - Peter Macheroux
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12/2, 8010 Graz, Austria.
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Brodl E, Niederhauser J, Macheroux P. In Situ Measurement and Correlation of Cell Density and Light Emission of Bioluminescent Bacteria. J Vis Exp 2018:57881. [PMID: 30010658 PMCID: PMC6102015 DOI: 10.3791/57881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
There is a considerable number of bacterial species capable of emitting light. All of them share the same gene cluster, namely the lux operon. Despite this similarity, these bacteria show extreme variations in characteristics like growth behavior, intensity of light emission or regulation of bioluminescence. The method presented here is a newly developed assay that combines recording of cell growth and bioluminescent light emission intensity over time utilizing a plate reader. The resulting growth and light emission characteristics can be linked to important features of the respective bacterial strain, such as quorum sensing regulation. The cultivation of a range of bioluminescent bacteria requires a specific medium (e.g., artificial sea water medium) and defined temperatures. The easy to handle, non-bioluminescent standard-research bacterium Escherichia coli (E. coli), on the other hand, can be cultivated inexpensively in high quantities in laboratory scale. Exploiting E. coli by introducing a plasmid containing the whole lux operon can simplify experimental conditions and additionally opens up many possibilities for future applications. The expression of all lux genes utilizing an E. coli expression strain was achieved by construction of an expression plasmid via Gibson cloning and insertion of four fragments containing seven lux genes and three rib genes of the lux-rib operon into a pET28a vector. E. coli based lux gene expression can be induced and controlled via Isopropyl-β-D-thiogalactopyranosid (IPTG) addition resulting in bioluminescent E. coli cells. The advantages of this system are to avoid quorum sensing regulation restrictions and complex medium compositions along with non-standard growth conditions, such as defined temperatures. This system enables analysis of lux genes and their interplay, by the exclusion of the respective gene from the lux operon, or even addition of novel genes, exchanging the luxAB genes from one bacterial strain by another, or analyzing protein complexes, such as luxCDE.
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Affiliation(s)
- Eveline Brodl
- Institute of Biochemistry, Graz University of Technology
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Kelley LA, Sternberg MJE. Partial protein domains: evolutionary insights and bioinformatics challenges. Genome Biol 2015; 16:100. [PMID: 25986583 PMCID: PMC4436111 DOI: 10.1186/s13059-015-0663-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.
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Affiliation(s)
- Lawrence A Kelley
- Structural Bioinformatics Group, Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Michael J E Sternberg
- Structural Bioinformatics Group, Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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Prakash A, Bateman A. Domain atrophy creates rare cases of functional partial protein domains. Genome Biol 2015; 16:88. [PMID: 25924720 PMCID: PMC4432964 DOI: 10.1186/s13059-015-0655-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/15/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain atrophy, where protein domains lose a significant number of core structural elements. RESULTS Here, we implement a new pipeline to systematically identify new cases of domain atrophy across all known protein sequences. The output of this pipeline was carefully checked by hand, which filtered out partial domain instances that were unlikely to represent true domain atrophy due to misannotations or un-annotated sequence fragments. We identify 75 cases of domain atrophy, of which eight cases are found in a three-dimensional protein structure and 67 cases have been inferred based on mapping to a known homologous structure. Domains with structural variations include ancient folds such as the TIM-barrel and Rossmann folds. Most of these domains are observed to show structural loss that does not affect their functional sites. CONCLUSION Our analysis has significantly increased the known cases of domain atrophy. We discuss specific instances of domain atrophy and see that there has often been a compensatory mechanism that helps to maintain the stability of the partial domain. Our study indicates that although domain atrophy is an extremely rare phenomenon, protein domains under certain circumstances can tolerate extreme mutations giving rise to partial, but functional, domains.
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Affiliation(s)
- Ananth Prakash
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
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Kasai S. Freshwater bioluminescence in Vibrio albensis (Vibrio cholerae biovar albensis) NCIMB 41 is caused by a two-nucleotide deletion in luxO. J Biochem 2007; 139:471-82. [PMID: 16567412 DOI: 10.1093/jb/mvj048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We previously proposed that the function of the lux operon is to produce a halotolerant flavodoxin, FP390 or P-flavin binding protein, and not to produce light. A crucial basis of this hypothesis is that almost all species of luminous bacteria emit light in culture media containing over 2% NaCl. However, Vibrio albensis (Vibrio cholerae biovar albensis) NCIMB 41 emits light in freshwater and this appears to be in direct conflict with our hypothesis. To determine why this exceptional freshwater bioluminescence is emitted, we studied the lux operon and the regulatory system of the operon in this strain, and found that expression of the operon is regulated by a system involving a derivative of 4,5-dihydroxy 2,3-pentanedione, DPD, as an inducer, and the repressor gene for the lux operon, luxO, is damaged by deletion of two nucleotides. Furthermore, to study the effect of damage to the luxO gene, pUC18 derivatives containing the damaged and repaired luxO sequences were prepared. Cells transfected with the damaged luxO sequence emitted light like the parental strain, whereas ones transfected with the repaired one did so only sparingly. Here we show that the light emission in freshwater by this strain is not in conflict with our hypothesis.
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Affiliation(s)
- Sabu Kasai
- Department of Applied Chemistry and Bioapplied Chemistry, Graduate School of Engineering, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka 558-8585.
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