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Rybina AA, Glushak RA, Bessonova TA, Dakhnovets AI, Rudenko AY, Ozhiganov RM, Kaznadzey AD, Tutukina MN, Gelfand MS. Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli. Sci Rep 2024; 14:7852. [PMID: 38570624 PMCID: PMC10991401 DOI: 10.1038/s41598-024-58492-y] [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: 08/11/2023] [Accepted: 03/29/2024] [Indexed: 04/05/2024] Open
Abstract
CsqR (YihW) is a local transcription factor that controls expression of yih genes involved in degradation of sulfoquinovose in Escherichia coli. We recently showed that expression of the respective gene cassette might be regulated by lactose. Here, we explore the phylogenetic and functional traits of CsqR. Phylogenetic analysis revealed that CsqR had a conserved Met25. Western blot demonstrated that CsqR was synthesized in the bacterial cell as two protein forms, 28.5 (CsqR-l) and 26 kDa (CsqR-s), the latter corresponding to start of translation at Met25. CsqR-s was dramatically activated during growth with sulfoquinovose as a sole carbon source, and displaced CsqR-l in the stationary phase during growth on rich medium. Molecular dynamic simulations revealed two possible states of the CsqR-s structure, with the interdomain linker being represented by either a disordered loop or an ɑ-helix. This helix allowed the hinge-like motion of the N-terminal domain resulting in a switch of CsqR-s between two conformational states, "open" and "compact". We then modeled the interaction of both CsqR forms with putative effectors sulfoquinovose, sulforhamnose, sulfoquinovosyl glycerol, and lactose, and revealed that they all preferred the same pocket in CsqR-l, while in CsqR-s there were two possible options dependent on the linker structure.
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Affiliation(s)
- Anna A Rybina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205.
| | - Roman A Glushak
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Tatiana A Bessonova
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
| | | | - Alexander Yu Rudenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Ratislav M Ozhiganov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Anna D Kaznadzey
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Maria N Tutukina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
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2
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Esteban-Torres M, Ruiz L, Rossini V, Nally K, van Sinderen D. Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait. Gut Microbes 2023; 15:2235067. [PMID: 37526383 PMCID: PMC10395257 DOI: 10.1080/19490976.2023.2235067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.
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Affiliation(s)
- Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Benefitial Microbes (MicroHealth Group), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Valerio Rossini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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3
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Duan Y, Liu S, Gao Y, Zhang P, Mao D, Luo Y. Macrolides mediate transcriptional activation of the msr(E)-mph(E) operon through histone-like nucleoid-structuring protein (HNS) and cAMP receptor protein (CRP). J Antimicrob Chemother 2021; 77:391-399. [PMID: 34747464 DOI: 10.1093/jac/dkab395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The msr(E)-mph(E) operon exists widely in diverse species of bacteria and msr(E) and mph(E) genes confer high resistance to macrolides. We aimed to explore whether macrolides regulate the transcription of the operon. METHODS Antibiotic resistance genes in clinical isolates of Klebsiella pneumoniae were analysed by WGS. The transcription of the msr(E)-mph(E) operon was investigated by quantitative PCR. Construction of enhanced green fluorescent protein (eGFP) reporter plasmids, gene knockout and complementation experiments were used to further explore the induction mechanism of macrolides for the operon. Sequence analysis was finally used to investigate whether the operon exists widely in diverse species of bacteria. RESULTS We originally found that the treatment of a pandrug-resistant isolate of K. pneumoniae (KP1517) with macrolides obviously up-regulated the msr(E)-mph(E) operon, which was further confirmed in another nine clinical isolates of K. pneumoniae. The induction mechanism of macrolides for the operon was partly elucidated. Macrolides could activate the operon promoter, and the J10/J35 regions (J10: 5'-AGTTATCAT-3'; J35: 5'-TTGTCT-3') of the promoter were determined. Histone-like nucleoid-structuring protein (HNS) and cAMP receptor protein (CRP) were involved in the erythromycin-mediated activation of the operon promoter. The 476 strains of bacteria carrying the msr(E)-mph(E) operon currently in the NCBI database are mainly Acinetobacter baumannii (158; 33%), K. pneumoniae (95; 20%), Escherichia coli (26; 5%) and Proteus mirabilis (25; 5%). They were mainly isolated from human clinical samples (287; 60%) and had a wide geographical distribution. CONCLUSIONS Macrolides could activate transcription of the msr(E)-mph(E) operon through HNS and CRP in K. pneumoniae and E. coli, and this might occur in diverse species of bacteria.
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Affiliation(s)
- Yitao Duan
- College of Environmental Science and Engineering, Nankai University, Tianjin, China.,Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuangqing Liu
- Department of Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuting Gao
- College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Peng Zhang
- College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Luo
- College of Environmental Science and Engineering, Nankai University, Tianjin, China.,State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
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Gao Y, Lim HG, Verkler H, Szubin R, Quach D, Rodionova I, Chen K, Yurkovich JT, Cho BK, Palsson BO. Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. Nucleic Acids Res 2021; 49:9696-9710. [PMID: 34428301 PMCID: PMC8464067 DOI: 10.1093/nar/gkab735] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 08/08/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, no TRN is fully characterized since the identity and activity of all the transcriptional regulators comprising a TRN are not known. Here, we experimentally evaluate 40 uncharacterized proteins in Escherichia coli K-12 MG1655, which were computationally predicted to be transcription factors (TFs). First, we used a multiplexed chromatin immunoprecipitation method combined with lambda exonuclease digestion (multiplexed ChIP-exo) assay to characterize binding sites for these candidate TFs; 34 of them were found to be DNA-binding proteins. We then compared the relative location between binding sites and RNA polymerase (RNAP). We found 48% (283/588) overlap between the TFs and RNAP. Finally, we used these data to infer potential functions for 10 of the 34 TFs with validated DNA binding sites and consensus binding motifs. Taken together, this study: (i) significantly expands the number of confirmed TFs to 276, close to the estimated total of about 280 TFs; (ii) provides putative functions for the newly discovered TFs and (iii) confirms the functions of four representative TFs through mutant phenotypes.
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Affiliation(s)
- Ye Gao
- Department of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Hans Verkler
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Daniel Quach
- Department of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Irina Rodionova
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ke Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - James T Yurkovich
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, 2800, Kongens Lyngby, Denmark
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5
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Glinski DA, Van Meter RJ, Purucker ST, Henderson WM. Route of exposure influences pesticide body burden and the hepatic metabolome in post-metamorphic leopard frogs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146358. [PMID: 33752009 PMCID: PMC8935488 DOI: 10.1016/j.scitotenv.2021.146358] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
Abstract
Pesticides are being applied at a greater extent than in the past. Once pesticides enter the ecosystem, many environmental factors can influence their residence time. These interactions can result in processes such as translocation, environmental degradation, and metabolic activation facilitating exposure to target and non-target species. Most anurans start off their life cycle in aquatic environments and then transition into terrestrial habitats. Their time in the aquatic environment is generally short; however, many important developmental stages occur during this tenure. Post-metamorphosis, most species spend many years on land but migrate back to the aquatic environment for breeding. Due to the importance of both the aquatic and terrestrial environments to the life stages of amphibians, we investigated how the route of exposure (i.e., uptake from contaminated soils vs. uptake from contaminated surface water) influences pesticide bioavailability and body burden for four pesticides (bifenthrin (BIF), chlorpyrifos (CPF), glyphosate (GLY), and trifloxystrobin (TFS)) as well as the impact on the hepatic metabolome of adult leopard frogs (Gosner stage 46 with 60-90 days post-metamorphosis). Body burden concentrations for amphibians exposed in water were significantly higher (ANOVA p < 0.0001) compared to amphibians exposed to contaminated soil across all pesticides studied. Out of 80 metabolites that were putatively identified, the majority expressed a higher abundance in amphibians that were exposed in pesticide contaminated water compared to soil. Ultimately, this research will help fill regulatory data gaps, aid in the creation of more accurate amphibian dermal uptake models and inform continued ecological risk assessment efforts.
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Affiliation(s)
- Donna A Glinski
- NRC Postdoctoral Research Fellow with the U.S. Environmental Protection Agency, Athens, GA 30605, USA.
| | - Robin J Van Meter
- Departments of Biology and Environmental Science & Studies, Washington College, Chestertown, MD 21620, USA
| | - S Thomas Purucker
- U.S. Environmental Protection Agency, ORD/CCTE, Research Triangle Park, NC 27709, USA
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Sokaribo AS, Perera SR, Sereggela Z, Krochak R, Balezantis LR, Xing X, Lam S, Deck W, Attah-Poku S, Abbott DW, Tamuly S, White AP. A GMMA-CPS-Based Vaccine for Non-Typhoidal Salmonella. Vaccines (Basel) 2021; 9:vaccines9020165. [PMID: 33671372 PMCID: PMC7922415 DOI: 10.3390/vaccines9020165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
Non-typhoidal Salmonella are a major cause of gastroenteritis worldwide, as well as causing bloodstream infections in sub-Saharan Africa with a high fatality rate. No vaccine is currently available for human use. Current vaccine development strategies are focused on capsular polysaccharides (CPS) present on the surface of non-typhoidal Salmonella. This study aimed to boost the amount of CPS purified from S. Typhimurium for immunization trials. Random mutagenesis with Tn10 transposon increased the production of CPS colanic acid, by 10-fold compared to wildtype. Immunization with colanic acid or colanic acid conjugated to truncated glycoprotein D or inactivated diphtheria toxin did not induce a protective immune response in mice. However, immunization with Generalized Modules for Membrane Antigens (GMMAs) isolated from colanic acid overproducing isolates reduced Salmonella colonization in mice. Our results support the development of a GMMA-CPS-based vaccine against non-typhoidal Salmonella.
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Affiliation(s)
- Akosiererem S. Sokaribo
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Sumudu R. Perera
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Zoe Sereggela
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Ryan Krochak
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Lindsay R. Balezantis
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Xiaohui Xing
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J4B1, Canada; (X.X.); (D.W.A.)
| | - Shirley Lam
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - William Deck
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - Sam Attah-Poku
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - Dennis Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J4B1, Canada; (X.X.); (D.W.A.)
| | - Shantanu Tamuly
- Department of Veterinary Biochemistry, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 781022, Assam, India;
| | - Aaron P. White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
- Correspondence: ; Tel.: +01-306-966-7485
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Shimada T, Yamamoto K, Nakano M, Watanabe H, Schleheck D, Ishihama A. Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12. MICROBIOLOGY-SGM 2018; 165:78-89. [PMID: 30372406 DOI: 10.1099/mic.0.000740] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The binding sites of YihW, an uncharacterized DeoR-family transcription factor (TF) of Escherichia coli K-12, were identified using Genomic SELEX screening at two closely located sites, one inside the spacer between the bidirectional transcription units comprising the yihUTS operon and the yihV gene, and another one upstream of the yihW gene itself. Recently the YihUTS and YihV proteins were identified as catalysing the catabolism of sulfoquinovose (SQ), a hydrolysis product of sulfoquinovosyl diacylglycerol (SQDG) derived from plants and other photosynthetic organisms. Gel shift assay in vitro and reporter assay in vivo indicated that YihW functions as a repressor for all three transcription units. De-repression of the yih operons was found to be under the control of SQ as inducer, but not of lactose, glucose or galactose. Furthermore, a mode of its cooperative DNA binding was suggested for YihW by atomic force microscopy. Hence, as a regulator of the catabolism of SQ, we renamed YihW as CsqR.
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Affiliation(s)
- Tomohiro Shimada
- 1Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Kaneyoshi Yamamoto
- 2Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan.,3Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo, Japan
| | - Masahiro Nakano
- 4Kyoto University, Institute for Frontier Life and Medical Sciences, Sakyo-ku, Kyoto, Japan
| | - Hiroki Watanabe
- 2Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - David Schleheck
- 5Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Akira Ishihama
- 3Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo, Japan
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