luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase.
bacterial luciferase
luminescence
phylogeny
small‐angle x‐ray scattering
x‐ray crystallography
Journal
Proteins
ISSN: 1097-0134
Titre abrégé: Proteins
Pays: United States
ID NLM: 8700181
Informations de publication
Date de publication:
22 Aug 2024
22 Aug 2024
Historique:
revised:
20
07
2024
received:
16
04
2024
accepted:
05
08
2024
medline:
22
8
2024
pubmed:
22
8
2024
entrez:
22
8
2024
Statut:
aheadofprint
Résumé
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)
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Russian Science Foundation
ID : 21-64-00018
Organisme : Ministry of Science and Higher Education of the Russian Federation
ID : 075-15-2021-1354
Organisme : Ministry of Science and Higher Education of the Russian Federation
ID : 075-03-2024-117
Informations de copyright
© 2024 Wiley Periodicals LLC.
Références
A. Fleiss and K. S. Sarkisyan, “A Brief Review of Bioluminescent Systems (2019),” Current Genetics 65 (2019): 877–882, https://doi.org/10.1007/s00294‐019‐00951‐5.
Z. M. Kaskova, A. S. Tsarkova, and I. V. Yampolsky, “1001 Lights: Luciferins, Luciferases, Their Mechanisms of Action and Applications in Chemical Analysis, Biology and Medicine,” Chemical Society Reviews 45 (2016): 6048–6077, https://doi.org/10.1039/C6CS00296J.
A. A. Kotlobay, K. S. Sarkisyan, Y. A. Mokrushina, et al., “Genetically Encodable Bioluminescent System From Fungi,” Proceedings of the National Academy of Sciences of the United States of America 115 (2018): 12728–12732, https://doi.org/10.1073/pnas.1803615115.
X. Zhou, S. Mehta, and J. Zhang, “Genetically Encodable Fluorescent and Bioluminescent Biosensors Light Up Signaling Networks,” Trends in Biochemical Sciences 45 (2020): 889–905, https://doi.org/10.1016/j.tibs.2020.06.001.
S. V. Bazhenov, U. S. Novoyatlova, E. S. Scheglova, et al., “Bacterial Lux‐Biosensors: Constructing, Applications, and Prospects,” Biosensors and Bioelectronics: X 13 (2023): 100323, https://doi.org/10.1016/j.biosx.2023.100323.
T. Mitiouchkina, A. S. Mishin, L. G. Somermeyer, et al., “Plants With Genetically Encoded Autoluminescence,” Nature Biotechnology 38 (2020): 944–946, https://doi.org/10.1038/s41587‐020‐0500‐9.
E. Brodl, A. Winkler, and P. Macheroux, “Molecular Mechanisms of Bacterial Bioluminescence,” Computational and Structural Biotechnology Journal 16 (2018): 551–564, https://doi.org/10.1016/j.csbj.2018.11.003.
P. Dunlap, “Biochemistry and Genetics of Bacterial Bioluminescence,” Advances in Biochemical Engineering/Biotechnology 144 (2014): 37–64, https://doi.org/10.1007/978‐3‐662‐43385‐0_2.
G. S. Timmins, S. K. Jackson, and H. M. Swartz, “The Evolution of Bioluminescent Oxygen Consumption as an Ancient Oxygen Detoxification Mechanism,” Journal of Molecular Evolution 52 (2001): 321–332, https://doi.org/10.1007/s002390010162.
O. E. Melkina, V. Y. Kotova, M. N. Konopleva, I. V. Manukhov, K. S. Pustovoit, and G. B. Zavilgelsky, “Photoreactivation of UV‐Exposed Escherichia coli K12 AB1886 uvrA6 via Luminescence of Photobacterium leiognathi Luciferase,” Molecular Biology 49 (2015): 928–932, https://doi.org/10.1134/S0026893315060175.
K. L. Visick and E. G. Ruby, “Vibrio fischeri and Its Host: It Takes Two to Tango,” Current Opinion in Microbiology 9 (2006): 632–638, https://doi.org/10.1016/j.mib.2006.10.001.
M. Zarubin, S. Belkin, M. Ionescu, and A. Genin, “Bacterial Bioluminescence as a Lure for Marine Zooplankton and Fish,” Proceedings of the National Academy of Sciences of the United States of America 109 (2012): 853–857, https://doi.org/10.1073/pnas.1116683109.
A. Phintha and P. Chaiyen, “Unifying and Versatile Features of Flavin‐Dependent Monooxygenases: Diverse Catalysis by a Common C4a‐(Hydro)peroxyflavin,” Journal of Biological Chemistry 299 (2023): 105413, https://doi.org/10.1016/j.jbc.2023.105413.
Q. Tian, J. Wu, H. Xu, Z. Hu, Y. Huo, and L. Wang, “Cryo‐EM Structure of the Fatty Acid Reductase LuxC–LuxE Complex Provides Insights Into Bacterial Bioluminescence,” Journal of Biological Chemistry 298 (2022): 102006, https://doi.org/10.1016/j.jbc.2022.102006.
C. R. Tabib, E. Brodl, and P. Macheroux, “Evidence for the Generation of Myristylated FMN by Bacterial Luciferase,” Molecular Microbiology 104 (2017): 1027–1036, https://doi.org/10.1111/mmi.13676.
E. Brodl, A. Csamay, C. Horn, J. Niederhauser, H. Weber, and P. Macheroux, “The Impact of LuxF on Light Intensity in Bacterial Bioluminescence,” Journal of Photochemistry and Photobiology B: Biology 207 (2020): 111881, https://doi.org/10.1016/j.jphotobiol.2020.111881.
Z. T. Campbell, A. Weichsel, W. R. Montfort, and T. O. Baldwin, “Crystal Structure of the Bacterial Luciferase/Flavin Complex Provides Insight Into the Function of the Beta Subunit,” Biochemistry 48 (2009): 6085–6094, https://doi.org/10.1021/bi900003t.
J. M. Sparks and T. O. Baldwin, “Functional Implications of the Unstructured Loop in the (Beta/Alpha)(8) Barrel Structure of the Bacterial Luciferase Alpha Subunit,” Biochemistry 40 (2001): 15436–15443, https://doi.org/10.1021/bi0111855.
Z. T. Campbell and T. O. Baldwin, “Two Lysine Residues in the Bacterial Luciferase Mobile Loop Stabilize Reaction Intermediates,” Journal of Biological Chemistry 284 (2009): 32827–32834, https://doi.org/10.1074/jbc.M109.031716.
N. Lawan, R. Tinikul, P. Surawatanawong, A. J. Mulholland, and P. Chaiyen, “QM/MM Molecular Modeling Reveals Mechanism Insights Into Flavin Peroxide Formation in Bacterial Luciferase,” Journal of Chemical Information and Modeling 62 (2022): 399–411, https://doi.org/10.1021/acs.jcim.1c01187.
J. F. Sinclair, J. J. Waddle, E. F. Waddill, and T. O. Baldwin, “Purified Native Subunits of Bacterial Luciferase Are Active in the Bioluminescence Reaction but Fail to Assemble Into the Alpha Beta Structure,” Biochemistry 32 (1993): 5036–5044, https://doi.org/10.1021/bi00070a010.
B. W. Noland, L. J. Dangott, and T. O. Baldwin, “Folding, Stability, and Physical Properties of the α Subunit of Bacterial Luciferase,” Biochemistry 38 (1999): 16136–16145, https://doi.org/10.1021/bi991449b.
H. Choi, C.‐K. Tang, and S.‐C. Tu, “Catalytically Active Forms of the Individual Subunits of Vibrio harveyi Luciferase and Their Kinetic and Binding Properties,” Journal of Biological Chemistry 270 (1995): 16813–16819, https://doi.org/10.1074/jbc.270.28.16813.
J. J. Tanner, M. D. Miller, K. S. Wilson, S.‐C. Tu, and K. L. Krause, “Structure of Bacterial Luciferase β2 Homodimer: Implications for Flavin Binding,” Biochemistry 36 (1997): 665–672, https://doi.org/10.1021/bi962511x.
J. B. Thoden, H. M. Holden, A. J. Fisher, et al., “Structure of the β2 Homodimer of Bacterial Luciferase From Vibrio harveyi: X‐Ray Analysis of a Kinetic Protein Folding Trap,” Protein Science 6 (1997): 13–23, https://doi.org/10.1002/pro.5560060103.
S. A. Moore and M. N. James, “Structural Refinement of the Non‐fluorescent Flavoprotein From Photobacterium leiognathi at 1.60 Å Resolution,” Journal of Molecular Biology 249 (1995): 195–214, https://doi.org/10.1006/jmbi.1995.0289.
A. Kita, S. Kasai, M. Miyata, and K. Miki, “Structure of Flavoprotein FP390 From a Luminescent Bacterium Photobacterium phosphoreum Refined at 2.7 Å Resolution,” Acta Crystallographica Section D 52 (1996): 77–86, https://doi.org/10.1107/S0907444995009796.
T. Bergner, C. R. Tabib, A. Winkler, et al., “Structural and Biochemical Properties of LuxF From Photobacterium leiognathi,” Biochimica et Biophysica Acta (BBA)—Proteins and Proteomics 1854 (2015): 1466–1475, https://doi.org/10.1016/j.bbapap.2015.07.008.
T. Xu, S. Ripp, G. S. Sayler, and D. M. Close, “Expression of a Humanized Viral 2A‐Mediated lux Operon Efficiently Generates Autonomous Bioluminescence in Human Cells,” PLoS One 9 (2014): e96347, https://doi.org/10.1371/journal.pone.0096347.
B. Cui, L. Zhang, Y. Song, et al., “Engineering an Enhanced, Thermostable, Monomeric Bacterial Luciferase Gene as a Reporter in Plant Protoplasts,” PLoS One 9 (2014): e107885, https://doi.org/10.1371/journal.pone.0107885.
T. Vannier, P. Hingamp, F. Turrel, L. Tanet, M. Lescot, and Y. Timsit, “Diversity and Evolution of Bacterial Bioluminescence Genes in the Global Ocean,” NAR Genomics and Bioinformatics 2 (2020): lqaa018, https://doi.org/10.1093/nargab/lqaa018.
S. El‐Gebali, J. Mistry, A. Bateman, et al., “The Pfam Protein Families Database in 2019,” Nucleic Acids Research 47 (2019): D427–D432, https://doi.org/10.1093/nar/gky995.
S. F. Altschul, T. L. Madden, A. A. Schäffer, et al., “Gapped BLAST and PSI‐BLAST: A New Generation of Protein Database Search Programs,” Nucleic Acids Research 25 (1997): 3389–3402, https://doi.org/10.1093/nar/25.17.3389.
R. C. Edgar, “Search and Clustering Orders of Magnitude Faster Than BLAST,” Bioinformatics 26 (2010): 2460–2461, https://doi.org/10.1093/bioinformatics/btq461.
K. Katoh and D. M. Standley, “MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability,” Molecular Biology and Evolution 30 (2013): 772–780, https://doi.org/10.1093/molbev/mst010.
K. Katoh, K. Misawa, K. Kuma, and T. Miyata, “MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform,” Nucleic Acids Research 30 (2002): 3059–3066, https://doi.org/10.1093/nar/gkf436.
S. Capella‐Gutiérrez, J. M. Silla‐Martínez, and T. Gabaldón, “trimAl: A Tool for Automated Alignment Trimming in Large‐Scale Phylogenetic Analyses,” Bioinformatics 25 (2009): 1972–1973, https://doi.org/10.1093/bioinformatics/btp348.
M. N. Price, P. S. Dehal, and A. P. Arkin, “FastTree 2—Approximately Maximum‐Likelihood Trees for Large Alignments,” PLoS One 5 (2010): e9490, https://doi.org/10.1371/journal.pone.0009490.
S. Q. Le and O. Gascuel, “An Improved General Amino Acid Replacement Matrix,” Molecular Biology and Evolution 25 (2008): 1307–1320, https://doi.org/10.1093/molbev/msn067.
A. Rambaut, “FigTree v1.4,” 2012, https://github.com/rambaut/figtree/releases.
F. W. Studier, “Protein Production by Auto‐Induction in High‐Density Shaking Cultures,” Protein Expression and Purification 41 (2005): 207–234, https://doi.org/10.1016/j.pep.2005.01.016.
V. V. Nazarenko, A. Remeeva, A. Yudenko, et al., “A Thermostable Flavin‐Based Fluorescent Protein From Chloroflexus aggregans: A Framework for Ultra‐High Resolution Structural Studies,” Photochemical & Photobiological Sciences 18 (2019): 1793–1805, https://doi.org/10.1039/c9pp00067d.
W. Kabsch, “XDS,” Acta Crystallographica, Section D: Biological Crystallography 66 (2010): 125–132, https://doi.org/10.1107/S0907444909047337.
P. Evans, “Scaling and Assessment of Data Quality,” Acta Crystallographica, Section D: Biological Crystallography 62 (2005): 72–82, https://doi.org/10.1107/S0907444905036693.
A. Vagin and A. Teplyakov, “Molecular Replacement With MOLREP,” Acta Crystallographica, Section D: Biological Crystallography 66 (2009): 22–25, https://doi.org/10.1107/S0907444909042589.
J. Jumper, R. Evans, A. Pritzel, et al., “Highly Accurate Protein Structure Prediction With AlphaFold,” Nature 596 (2021): 583–589, https://doi.org/10.1038/s41586‐021‐03819‐2.
P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, “Features and Development of Coot,” Acta Crystallographica, Section D: Biological Crystallography 66 (2010): 486–501, https://doi.org/10.1107/S0907444910007493.
G. N. Murshudov, P. Skubák, A. A. Lebedev, et al., “REFMAC5 for the Refinement of Macromolecular Crystal Structures,” Acta Crystallographica, Section D: Biological Crystallography 67 (2011): 355–367, https://doi.org/10.1107/S0907444911001314.
T. N. Murugova, O. I. Ivankov, Y. L. Ryzhykau, et al., “Mechanisms of Membrane Protein Crystallization in ‘Bicelles’,” Scientific Reports 12 (2022): 11109, https://doi.org/10.1038/s41598‐022‐13945‐0.
G. V. Tsoraev, E. A. Protasova, E. A. Klimanova, et al., “Anti‐Stokes Fluorescence Excitation Reveals Conformational Mobility of the C‐Phycocyanin Chromophores,” Structural Dynamics 9 (2022): 054701, https://doi.org/10.1063/4.0000164.
D. Svergun, C. Barberato, and M. H. J. Koch, “CRYSOL—A Program to Evaluate X‐Ray Solution Scattering of Biological Macromolecules From Atomic Coordinates,” Journal of Applied Crystallography 28 (1995): 768–773, https://doi.org/10.1107/S0021889895007047.
P. V. Konarev, V. V. Volkov, A. V. Sokolova, M. H. J. Koch, and D. I. Svergun, “PRIMUS: A Windows PC‐Based System for Small‐Angle Scattering Data Analysis,” Journal of Applied Crystallography 36 (2003): 1277–1282, https://doi.org/10.1107/S0021889803012779.
D. Franke, M. V. Petoukhov, P. V. Konarev, et al., “ATSAS 2.8: A Comprehensive Data Analysis Suite for Small‐Angle Scattering From Macromolecular Solutions,” Journal of Applied Crystallography 50 (2017): 1212–1225, https://doi.org/10.1107/S1600576717007786.
S. Mallik, D. S. Tawfik, and E. D. Levy, “How Gene Duplication Diversifies the Landscape of Protein Oligomeric State and Function,” Current Opinion in Genetics & Development 76 (2022): 101966, https://doi.org/10.1016/j.gde.2022.101966.
T. Iizuka, Y. Jojima, R. Fudou, M. Tokura, A. Hiraishi, and S. Yamanaka, “Enhygromyxa salina gen. nov., sp. nov., a Slightly Halophilic Myxobacterium Isolated From the Coastal Areas of Japan,” Systematic and Applied Microbiology 26 (2003): 189–196, https://doi.org/10.1078/072320203322346038.
J. K. Inlow and T. O. Baldwin, “Mutational Analysis of the Subunit Interface of Vibrio harveyi Bacterial Luciferase,” Biochemistry 41 (2002): 3906–3915, https://doi.org/10.1021/bi012113g.
J. W. Hastings, K. Weber, J. Friedland, A. Eberhard, G. Mitchell, and A. Gunsalus, “Structurally Distinct Bacterial Luciferases,” Biochemistry 8 (1969): 4681–4689, https://doi.org/10.1021/bi00840a004.
P. Colepicolo, K. W. Cho, G. O. Poinar, and J. W. Hastings, “Growth and Luminescence of the Bacterium Xenorhabdus luminescens From a Human Wound,” Applied and Environmental Microbiology 55 (1989): 2601–2606, https://doi.org/10.1128/aem.55.10.2601‐2606.1989.
P. Rogers and W. D. McElroy, “Enzymic Determination of Aldehyde Permeability in Luminous Bacteria. I. Effect of Chain Length on Light Emission and Penetration,” Archives of Biochemistry and Biophysics 75 (1958): 87–105, https://doi.org/10.1016/0003‐9861(58)90400‐4.
J. W. Hastings, “Biological Diversity, Chemical Mechanisms, and the Evolutionary Origins of Bioluminescent Systems,” Journal of Molecular Evolution 19 (1983): 309–321, https://doi.org/10.1007/BF02101634.
C. E. Paul, D. Eggerichs, A. H. Westphal, D. Tischler, and W. J. H. van Berkel, “Flavoprotein Monooxygenases: Versatile Biocatalysts,” Biotechnology Advances 51 (2021): 107712, https://doi.org/10.1016/j.biotechadv.2021.107712.
R. Tinikul, P. Chunthaboon, J. Phonbuppha, and T. Paladkong, “Bacterial Luciferase: Molecular Mechanisms and Applications,” Enzyme 47 (2020): 427–455, https://doi.org/10.1016/bs.enz.2020.06.001.
S. Bazhenov, U. Novoyatlova, E. Scheglova, et al., “Influence of the luxR Regulatory Gene Dosage and Expression Level on the Sensitivity of the Whole‐Cell Biosensor to Acyl‐Homoserine Lactone,” Biosensors 11 (2021): 166, https://doi.org/10.3390/bios11060166.
A. G. Kessenikh, U. S. Novoyatlova, S. V. Bazhenov, et al., “Constructing of Bacillus subtilis‐Based Lux‐Biosensors With the Use of Stress‐Inducible Promoters,” International Journal of Molecular Sciences 22 (2021): 9571, https://doi.org/10.3390/ijms22179571.
C. Gregor, K. C. Gwosch, S. J. Sahl, and S. W. Hell, “Strongly Enhanced Bacterial Bioluminescence With the Ilux Operon for Single‐Cell Imaging,” Proceedings of the National Academy of Sciences of the United States of America 115 (2018): 962–967, https://doi.org/10.1073/pnas.1715946115.
A. Gabdulkhakov, I. Gushchin, I. Kapranov, et al., “Russian BAG for Xtallography and BioSAXS,” 2021, https://doi.org/10.15151/ESRF‐ES‐573998198.
H. M. Berman, J. Westbrook, Z. Feng, et al., “The Protein Data Bank,” Nucleic Acids Research 28 (2000): 235–242.
A. G. Kikhney, C. R. Borges, D. S. Molodenskiy, C. M. Jeffries, and D. I. Svergun, “SASBDB: Towards an Automatically Curated and Validated Repository for Biological Scattering Data,” Protein Science 29 (2020): 66–75, https://doi.org/10.1002/pro.3731.