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Esposito A, Rossi A, Stabile M, Pinto G, De Fino I, Melessike M, Tamanini A, Cabrini G, Lippi G, Aureli M, Loberto N, Renda M, Galietta LJV, Amoresano A, Dechecchi MC, De Gregorio E, Bragonzi A, Guaragna A. Assessing the Potential of N-Butyl-l-deoxynojirimycin (l-NBDNJ) in Models of Cystic Fibrosis as a Promising Antibacterial Agent. ACS Pharmacol Transl Sci 2024; 7:1807-1822. [PMID: 38898954 PMCID: PMC11184606 DOI: 10.1021/acsptsci.4c00044] [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: 01/26/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
Over the past few years, l-iminosugars have revealed attractive pharmacological properties for managing rare diseases including Cystic Fibrosis (CF). The iminosugar N-butyl-l-deoxynojirimycin (l-NBDNJ, ent-1), prepared by a carbohydrate-based route, was herein evaluated for its anti-inflammatory and anti-infective potential in models of CF lung disease infection. A significant decrease in the bacterial load in the airways was observed in the murine model of Pseudomonas aeruginosa chronic infection in the presence of l-NBDNJ, also accompanied by a modest reduction of inflammatory cells. Mechanistic insights into the observed activity revealed that l-NBDNJ interferes with the expression of proteins regulating cytoskeleton assembly and organization of the host cell, downregulates the main virulence factors of P. aeruginosa involved in the host response, and affects pathogen adhesion to human cells. These findings along with the observation of the absence of an in vitro bacteriostatic/bactericidal action of l-NBDNJ suggest the potential use of this glycomimetic as an antivirulence agent in the management of CF lung disease.
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Affiliation(s)
- Anna Esposito
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples I-80125, Italy
| | - Alice Rossi
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Maria Stabile
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples I-80131, Italy
| | - Gabriella Pinto
- Department
of Chemical Sciences, University of Naples
Federico II, Naples I-80126, Italy
| | - Ida De Fino
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Medede Melessike
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Anna Tamanini
- Section
of Clinical Biochemistry, Department of Engineering for Innovation
Medicine, University of Verona, Verona I-37134, Italy
| | - Giulio Cabrini
- Center on
Innovative Therapies for Cystic Fibrosis, Department of Life Sciences
and Biotechnology, University of Ferrara, Ferrara I-40121, Italy
| | - Giuseppe Lippi
- Section
of Clinical Biochemistry, Department of Engineering for Innovation
Medicine, University of Verona, Verona I-37134, Italy
| | - Massimo Aureli
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Milan I-20054, Italy
| | - Nicoletta Loberto
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Milan I-20054, Italy
| | - Mario Renda
- Telethon
Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples I-80078, Italy
| | - Luis J. V. Galietta
- Telethon
Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples I-80078, Italy
- Department
of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples I-80131, Italy
| | - Angela Amoresano
- Department
of Chemical Sciences, University of Naples
Federico II, Naples I-80126, Italy
- Istituto
Nazionale Biostrutture e Biosistemi, Consorzio Interuniversitario, Rome I-00136, Italy
| | - Maria Cristina Dechecchi
- Section
of Clinical Biochemistry, Department of Engineering for Innovation
Medicine, University of Verona, Verona I-37134, Italy
| | - Eliana De Gregorio
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples I-80131, Italy
| | - Alessandra Bragonzi
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Annalisa Guaragna
- Department
of Chemical Sciences, University of Naples
Federico II, Naples I-80126, Italy
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Stabile M, Esposito A, Iula VD, Guaragna A, De Gregorio E. PYED-1 Overcomes Colistin Resistance in Acinetobacter baumannii. Pathogens 2023; 12:1323. [PMID: 38003788 PMCID: PMC10674209 DOI: 10.3390/pathogens12111323] [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: 10/06/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Antibiotic resistance has become more and more widespread over the recent decades, becoming a major global health problem and causing colistin to be increasingly used as an antibiotic of last resort. Acinetobacter baumannii, an opportunistic pathogen that has rapidly evolved into a superbug exhibiting multidrug-resistant phenotypes, is responsible for a large number of hospital infection outbreaks. With the intensive use of colistin, A. baumannii resistance to colistin has been found to increase significantly. In previous work, we identified a deflazacort derivative, PYED-1 (pregnadiene-11-hydroxy-16,17-epoxy-3,20-dione-1), which exhibits either direct-acting or synergistic activity against Gram-positive and Gram-negative species and Candida spp., including A. baumannii. The aim of this study was to evaluate the antibacterial activity of PYED-1 in combination with colistin against both A. baumannii planktonic and sessile cells. Furthermore, the cytotoxicity of PYED-1 with and without colistin was assessed. Our results show that PYED-1 and colistin can act synergistically to produce a strong antimicrobial effect against multidrug-resistant populations of A. baumannii. Interestingly, our data reveal that PYED-1 is able to restore the efficacy of colistin against all colistin-resistant A. baumannii isolates. This drug combination could achieve a much stronger antimicrobial effect than colistin while using a much smaller dosage of the drugs, additionally eliminating the toxicity and resistance issues associated with the use of colistin.
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Affiliation(s)
- Maria Stabile
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy; (M.S.); (A.G.)
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Anna Esposito
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy;
| | - Vita Dora Iula
- Department of Laboratory Medicine, U.O.C Patologia Clinica, Ospedale del Mare—ASL Napoli1 Centro, 80145 Naples, Italy;
| | - Annalisa Guaragna
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy; (M.S.); (A.G.)
| | - Eliana De Gregorio
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
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Shi X, Li J, Wang X, Zhang X, Tang L. Effect of the gradual increase of Na 2SO 4 on performance and microbial diversity of aerobic granular sludge. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112696. [PMID: 33984643 DOI: 10.1016/j.jenvman.2021.112696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Aerobic granular sludge (AGS) is a promising technology in treating saline wastewater. The effects of sodium sulfate on contaminant removal performance and sludge characteristics of AGS were studied. The results showed that under the stress of sodium sulfate, AGS kept good removal performance of ammonia nitrogen (NH+ 4-N), chemical oxygen demand (COD), and total nitrogen (TN), with removal efficiency reaching 98.7%, 91.5% and 62.7%, respectively. When sodium sulfate reached 14700 mg/L, nitrite oxidizing bacteria (NOB) were inhibited and nitrite accumulation occurred, but it had little impact on total phosphorus (TP) removal. Under the stress of sodium sulfate, compactness and settling performance of AGS was enhanced. The microbial community greatly varied and the microbial diversity of aerobic granular sludge has decreased under the stress of sodium sulfate. The study reveals that AGS has great potential in application on treating saline wastewater.
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Affiliation(s)
- Xianbin Shi
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, Shenzhen, 518055, China
| | - Ji Li
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, Shenzhen, 518055, China
| | - Xiaochun Wang
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, Shenzhen, 518055, China
| | - Xiaolei Zhang
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, Shenzhen, 518055, China.
| | - Liaofan Tang
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, Shenzhen, 518055, China
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Esposito A, Vollaro A, Esposito EP, D’Alonzo D, Guaragna A, Zarrilli R, De Gregorio E. Antibacterial and Antivirulence Activity of Glucocorticoid PYED-1 against Stenotrophomonas maltophilia. Antibiotics (Basel) 2020; 9:E105. [PMID: 32131413 PMCID: PMC7148523 DOI: 10.3390/antibiotics9030105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022] Open
Abstract
Stenotrophomonas maltophilia, an environmental Gram-negative bacterium, is an emerging nosocomial opportunistic pathogen that causes life-threatening infections in immunocompromised patients and chronic pulmonary infections in cystic fibrosis patients. Due to increasing resistance to multiple classes of antibiotics, S. maltophilia infections are difficult to treat successfully. This makes the search for new antimicrobial strategies mandatory. In this study, the antibacterial activity of the heterocyclic corticosteroid deflazacort and several of its synthetic precursors was tested against S. maltophilia. All compounds were not active against standard strain S. maltophilia K279a. The compound PYED-1 (pregnadiene-11-hydroxy-16α,17α-epoxy-3,20-dione-1) showed a weak effect against some S. maltophilia clinical isolates, but exhibited a synergistic effect with aminoglycosides. PYED-1 at sub-inhibitory concentrations decreased S. maltophilia biofilm formation. Quantitative real-time polymerase chain reaction (RT-qPCR) analysis demonstrated that the expression of biofilm- and virulence- associated genes (StmPr1, StmPr3, sphB, smeZ, bfmA, fsnR) was significantly suppressed after PYED-1 treatment. Interestingly, PYED-1 also repressed the expression of the genes aph (3´)-IIc, aac (6´)-Iz, and smeZ, involved in the resistance to aminoglycosides.
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Affiliation(s)
- Anna Esposito
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy; (A.E.); (A.G.)
| | - Adriana Vollaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Eliana Pia Esposito
- Department of Public Health, University of Naples “Federico II”, Via S. Pansini 5, 80131 Naples, Italy; (E.P.E.); (R.Z.)
| | - Daniele D’Alonzo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy; (A.E.); (A.G.)
| | - Annalisa Guaragna
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy; (A.E.); (A.G.)
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples “Federico II”, Via S. Pansini 5, 80131 Naples, Italy; (E.P.E.); (R.Z.)
| | - Eliana De Gregorio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy;
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Quentin Y, Siguier P, Chandler M, Fichant G. Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases. BMC Genomics 2018; 19:475. [PMID: 29914351 PMCID: PMC6006769 DOI: 10.1186/s12864-018-4836-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022] Open
Abstract
Background Some mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-stranded circular DNA intermediates for excision and insertion and encode a transposase, TnpAIS200, which recognizes subterminal secondary structures at the insertion sequence ends. Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes. TnpAIS200-related proteins, TnpAREP, have been identified and could be responsible for REP sequence proliferation. These proteins share a conserved HuH/Tyrosine core domain responsible for catalysis and are involved in processes of ssDNA cleavage and ligation. Our goal is to characterize the diversity of these proteins collectively referred as the TnpAY1 family. Results A genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles. Conclusions We established a detailed classification of TnpAY1 proteins, consolidated by the analysis of the conserved core domains and the characterization of additional domains. The data obtained illustrate the unexpected diversity of the TnpAY1 family and provide a strong framework for future evolutionary and functional studies. By their potential function in ssDNA editing, they may confer adaptive responses to host cell physiology and metabolism. Electronic supplementary material The online version of this article (10.1186/s12864-018-4836-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yves Quentin
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
| | - Mick Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
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Wachter S, Raghavan R, Wachter J, Minnick MF. Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution. BMC Genomics 2018; 19:247. [PMID: 29642859 PMCID: PMC5896051 DOI: 10.1186/s12864-018-4608-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/16/2018] [Indexed: 01/05/2023] Open
Abstract
Background Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited. Results We describe two MITE families discovered during research on small non-coding RNAs (sRNAs) of C. burnetii. Two sRNAs, Cbsr3 and Cbsr13, were found to originate from a novel MITE family, termed QMITE1. Another sRNA, CbsR16, was found to originate from a separate and novel MITE family, termed QMITE2. Members of each family occur ~ 50 times within the strains evaluated. QMITE1 is a typical MITE of 300-400 bp with short (2-3 nt) direct repeats (DRs) of variable sequence and is often found overlapping annotated open reading frames (ORFs). Additionally, QMITE1 elements possess sigma-70 promoters and are transcriptionally active at several loci, potentially influencing expression of nearby genes. QMITE2 is smaller (150-190 bps), but has longer (7-11 nt) DRs of variable sequences and is mainly found in the 3′ untranslated region of annotated ORFs and intergenic regions. QMITE2 contains a GTAG repetitive extragenic palindrome (REP) that serves as a target for IS1111 TE insertion. Both QMITE1 and QMITE2 display inter-strain linkage and sequence conservation, suggesting that they are adaptive and existed before divergence of C. burnetii strains. Conclusions We have discovered two novel MITE families of C. burnetii. Our finding that MITEs serve as a source for sRNAs is novel. QMITE2 has a unique structure and occurs in large or small versions with unique DRs that display linkage and sequence conservation between strains, allowing for tracking of genomic rearrangements. QMITE1 and QMITE2 copies are hypothesized to influence expression of neighboring genes involved in DNA repair and virulence through transcriptional interference and ribonuclease processing. Electronic supplementary material The online version of this article (10.1186/s12864-018-4608-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shaun Wachter
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Rahul Raghavan
- Biology Department and Center for Life in Extreme Environments, Portland State University, Portland, OR, USA
| | - Jenny Wachter
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th St, Hamilton, MT, USA
| | - Michael F Minnick
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA.
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Wu D, Zhang Z, Yu Z, Zhu L. Optimization of F/M ratio for stability of aerobic granular process via quantitative sludge discharge. BIORESOURCE TECHNOLOGY 2018; 252:150-156. [PMID: 29316501 DOI: 10.1016/j.biortech.2017.12.094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
Food to microorganisms (F/M) ratio is one of the most important factors affecting microbial growth and pollutant removal in biological wastewater treatment system. For stability of aerobic granular process, optimal range of F/M ratio and a maneuverable F/M ratio control method via quantitative sludge discharge were investigated in this study. Results showed that stable aerobic granules were achieved with good settleability, high pollutant removal efficiency and microbial diversity when F/M ratio was controlled at 0.4-0.5 gCOD/gSS d. In addition, a maneuverable F/M ratio control method via quantitative sludge discharge was developed to verify the feasibility for optimization of F/M ratio. By this method, aerobic granules cultivated with the F/M ratio of 0.4 ± 0.02 gCOD/gSS d had better pollutant removal performance and stable structure with higher protein-like components in EPS. This study further revealed the importance of F/M ratio in the stability of aerobic granular sludge process.
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Affiliation(s)
- Di Wu
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Zhiming Zhang
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Zhuodong Yu
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Liang Zhu
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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Charnavets T, Nunvar J, Nečasová I, Völker J, Breslauer KJ, Schneider B. Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases. Biopolymers 2016; 103:585-96. [PMID: 25951997 PMCID: PMC4690160 DOI: 10.1002/bip.22666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/05/2015] [Indexed: 01/19/2023]
Abstract
Repetitive extragenic palindrome (REP)—associated tyrosine transposase enzymes (RAYTs) bind REP DNA domains and catalyze their cleavage. Genomic sequence analyses identify potential noncoding REP sequences associated with RAYT-encoding genes. To probe the conformational space of potential RAYT DNA binding domains, we report here spectroscopic and calorimetric measurements that detect and partially characterize the solution conformational heterogeneity of REP oligonucleotides from six bacterial species. Our data reveal most of these REP oligonucleotides adopt multiple conformations, suggesting that RAYTs confront a landscape of potential DNA substrates in dynamic equilibrium that could be selected, enriched, and/or induced via differential binding. Thus, the transposase-bound DNA motif may not be the predominant conformation of the isolated REP domain. Intriguingly, for several REPs, the circular dichroism spectra suggest guanine tetraplexes as potential alternative or additional RAYT recognition elements, an observation consistent with these REP domains being highly nonrandom, with tetraplex-favoring 5′-G and 3′-C-rich segments. In fact, the conformational heterogeneity of REP domains detected and reported here, including the formation of noncanonical DNA secondary structures, may reflect a general feature required for recognition by RAYT transposases. Based on our biophysical data, we propose guanine tetraplexes as an additional DNA recognition element for binding by RAYT transposase enzymes. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 585–596, 2015.
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Affiliation(s)
- Tatsiana Charnavets
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Jaroslav Nunvar
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Iva Nečasová
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ, 08854
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ, 08854.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08903
| | - Bohdan Schneider
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
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Tourasse NJ, Shtaida N, Khozin-Goldberg I, Boussiba S, Vallon O. The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat. BMC Genomics 2015; 16:580. [PMID: 26238519 PMCID: PMC4524435 DOI: 10.1186/s12864-015-1792-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/22/2015] [Indexed: 11/10/2022] Open
Abstract
Background Lobosphaera incisa, formerly known as Myrmecia incisa and then Parietochloris incisa, is an oleaginous unicellular green alga belonging to the class Trebouxiophyceae (Chlorophyta). It is the richest known plant source of arachidonic acid, an ω-6 poly-unsaturated fatty acid valued by the pharmaceutical and baby-food industries. It is therefore an organism of high biotechnological interest, and we recently reported the sequence of its chloroplast genome. Results We now report the complete sequence of the mitochondrial genome of L. incisa from high-throughput Illumina short-read sequencing. The circular chromosome of 69,997 bp is predicted to encode a total of 64 genes, some harboring specific self-splicing group I and group II introns. Overall, the gene content is highly similar to that of the mitochondrial genomes of other Trebouxiophyceae, with 34 protein-coding, 3 rRNA, and 27 tRNA genes. Genes are distributed in two clusters located on different DNA strands, a bipartite arrangement that suggests expression from two divergent promoters yielding polycistronic primary transcripts. The L. incisa mitochondrial genome contains families of intergenic dispersed DNA repeat sequences that are not shared with other known mitochondrial genomes of Trebouxiophyceae. The most peculiar feature of the genome is a repetitive palindromic repeat, the LIMP (L. Incisa Mitochondrial Palindrome), found 19 times in the genome. It is formed by repetitions of an AACCA pentanucleotide, followed by an invariant 7-nt loop and a complementary repeat of the TGGTT motif. Analysis of the genome sequencing reads indicates that the LIMP can be a substrate for large-scale genomic rearrangements. We speculate that LIMPs can act as origins of replication. Deep sequencing of the L. incisa transcriptome also suggests that the LIMPs with long stems are sites of transcript processing. The genome also contains five copies of a related palindromic repeat, the HyLIMP, with a 10-nt motif related to that of the LIMP. Conclusions The mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression. Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.
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Affiliation(s)
- Nicolas J Tourasse
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 - Université Pierre et Marie Curie, Paris, France. .,Institut de Biologie Physico-Chimique, FRC CNRS 550, Université Pierre et Marie Curie, Paris, France. .,ARNA Laboratory, INSERM UMR 869, Université Bordeaux 2, Bordeaux, France.
| | - Nastassia Shtaida
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Olivier Vallon
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 - Université Pierre et Marie Curie, Paris, France
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