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Santoscoy MC, Jarboe LR. Production of cholesterol-like molecules impacts Escherichia coli robustness, production capacity, and vesicle trafficking. Metab Eng 2022; 73:134-143. [PMID: 35842218 DOI: 10.1016/j.ymben.2022.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/26/2022] [Accepted: 07/03/2022] [Indexed: 10/17/2022]
Abstract
The economic viability of bioprocesses is constrained by the limited range of operating conditions that can be tolerated by the cell factory. Engineering of the microbial cell membrane is one strategy that can increase robustness and thus alter this range. In this work, we targeted cellular components that contribute to maintenance of appropriate membrane function, such as: flotillin-like proteins, membrane structural proteins, and membrane lipids. Specifically, we exploited the promiscuity of squalene hopene cyclase (SHC) to produce polycyclic terpenoids with properties analogous to cholesterol. Strains producing these cholesterol-like molecules were visualized by AFM and height features were observed. Production of these cholesterol-like molecules was associated with increased tolerance towards a diversity of chemicals, particularly alcohols, and membrane trafficking processes such as lipid droplet accumulation and production of extracellular vesicles. This engineering approach improved the production titers for wax-esters and ethanol by 80- and 10-fold, respectively. Expression of SHC resulted in the production of steroids. Strains engineered to also express truncated squalene synthase (tERG9) produced diplopterol and generally did not perform as well. Increased expression of several membrane-associated proteins, such as YqiK, was observed to impact vesicle trafficking and further improve tolerance relative to SHC alone, but did not improve bio-production. Deletion of YbbJ increased lipid droplet accumulation as well as production of intracellular wax esters. This work serves as a proof of concept for engineering strategies targeting membrane physiology and trafficking to expand the production capacity of microbial cell factories.
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Affiliation(s)
- Miguel C Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
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2
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Shin J, Naskar A, Ko D, Kim S, Kim KS. Bioconjugated Thymol-Zinc Oxide Nanocomposite as a Selective and Biocompatible Antibacterial Agent against Staphylococcus Species. Int J Mol Sci 2022; 23:6770. [PMID: 35743214 PMCID: PMC9224476 DOI: 10.3390/ijms23126770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
Owing to the rapid spread of antibiotic resistance among Staphylococcus species, effective and low-risk alternatives to antibiotics are being actively searched. Thymol (THO), the most abundant component of the oil extracted from thyme, can be considered as a natural antibacterial alternative. However, the low antibacterial activity and non-selectivity of THO limit its usage as a universal anti-Staphylococcus agent. Herein, we report the bioconjugation of THO with ZnO nanoparticle (ZO), which resulted in the TZ nanocomposite (NC), as a potent and selective antibacterial agent against Staphylococcus species, particularly S. epidermidis. The cell-free supernatant (CFS) of ATCC 25923 cultures was employed for the production of TZ NC. Successful production of TZ NC was confirmed via X-ray diffraction (XRD), Fourier-transform infrared (FT-IR) spectroscopy, and ultraviolet-visible (UV-Vis) studies. TZ NC had selective efficacy against Staphylococcus species, with MIC values 2-32-fold lower than THO. The antibacterial mechanisms of TZ NC are proposed to involve membrane rupture, suppression of biofilm formation, and modulation of new cell wall and protein-synthesis-associated cellular pathways. Its biocompatibility against HCT116 cells was also checked. Our findings suggest that the TZ nanocomposite could improve the selectivity and bactericidal activity of THO against target species.
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Affiliation(s)
- Joonho Shin
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (J.S.); (A.N.)
| | - Atanu Naskar
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (J.S.); (A.N.)
| | - Dongjoon Ko
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (D.K.); (S.K.)
| | - Semi Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (D.K.); (S.K.)
| | - Kwang-sun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (J.S.); (A.N.)
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Mikolčević P, Hloušek-Kasun A, Ahel I, Mikoč A. ADP-ribosylation systems in bacteria and viruses. Comput Struct Biotechnol J 2021; 19:2366-2383. [PMID: 34025930 PMCID: PMC8120803 DOI: 10.1016/j.csbj.2021.04.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/30/2022] Open
Abstract
ADP-ribosylation is an ancient posttranslational modification present in all kingdoms of life. The system likely originated in bacteria where it functions in inter- and intra-species conflict, stress response and pathogenicity. It was repeatedly adopted via lateral transfer by eukaryotes, including humans, where it has a pivotal role in epigenetics, DNA-damage repair, apoptosis, and other crucial pathways including the immune response to pathogenic bacteria and viruses. In other words, the same ammunition used by pathogens is adapted by eukaryotes to fight back. While we know quite a lot about the eukaryotic system, expanding rather patchy knowledge on bacterial and viral ADP-ribosylation would give us not only a better understanding of the system as a whole but a fighting advantage in this constant arms race. By writing this review we hope to put into focus the available information and give a perspective on how this system works and can be exploited in the search for therapeutic targets in the future. The relevance of the subject is especially highlighted by the current situation of being amid the world pandemic caused by a virus harbouring and dependent on a representative of such a system.
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Affiliation(s)
- Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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4
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021; 59:341-359. [PMID: 33779951 DOI: 10.1007/s12275-021-0650-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/16/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021:10.1007/s12275-021-0650-3. [PMID: 33565052 DOI: 10.1007/s12275-021-0650-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Ranjith K, Sharma S, Shivaji S. Microbes of the human eye: Microbiome, antimicrobial resistance and biofilm formation. Exp Eye Res 2021; 205:108476. [PMID: 33549582 DOI: 10.1016/j.exer.2021.108476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND The review focuses on the bacteria associated with the human eye using the dual approach of detecting cultivable bacteria and the total microbiome using next generation sequencing. The purpose of this review was to highlight the connection between antimicrobial resistance and biofilm formation in ocular bacteria. METHODS Pubmed was used as the source to catalogue culturable bacteria and ocular microbiomes associated with the normal eyes and those with ocular diseases, to ascertain the emergence of anti-microbial resistance with special reference to biofilm formation. RESULTS This review highlights the genetic strategies used by microorganisms to evade the lethal effects of anti-microbial agents by tracing the connections between candidate genes and biofilm formation. CONCLUSION The eye has its own microbiome which needs to be extensively studied under different physiological conditions; data on eye microbiomes of people from different ethnicities, geographical regions etc. are also needed to understand how these microbiomes affect ocular health.
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Affiliation(s)
- Konduri Ranjith
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India.
| | - Savitri Sharma
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India.
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India.
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The YmdB protein regulates biofilm formation dependent on the repressor SinR in Bacillus cereus 0-9. World J Microbiol Biotechnol 2020; 36:165. [PMID: 33000364 DOI: 10.1007/s11274-020-02933-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
YmdB, which can regulate biofilm formation independently, has been reported to exist in Bacillus subtilis. The B. cereus 0-9 genome also encodes a YmdB-like protein, which has measureable phosphodiesterase activity, and 72.35% sequence identity to YmdB protein of B. subtilis 168. In this work, we studied the function of YmdB protein and its encoding gene, ymdB, in B. cereus 0-9. Our results indicated that YmdB protein is critical for the biofilm formation of B. cereus 0-9. In ΔymdB mutant, the transcriptional levels of sinR and hag were up-regulated, and those of genes closely related to biofilm formation, such as sipW, tasA and calY, were down-regulated. Deletion of ymdB gene stimulates the swarming motility of B. cereus 0-9, and enhances it to travel outward, but reduces its ability to form complex spatial structures on the solid surface of MSgg plates. Hence, it is considered that YmdB plays a key role in biofilm formation, and this effect is likely achieved through the function of repressor SinR in B. cereus 0-9. Furthermore, by comparing the amino acid sequences of YmdB by Basic Local Alignment Search Tool (BLAST) in Genebank, we found that YmdB homologues are present in a variety of bacteria (Including Gram-negative bacteria) except B. subtilis and B. cereus. All these bacteria come at different evolutionary distances and belong to different genera. Therefore, we believe that YmdB exists in many types of bacteria and plays an important role in the stress-resistance of bacteria to adapt to the environment. These results can help us to further understand the biocontrol characteristics of B. cereus 0-9.
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Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
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Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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Cafiso V, Stracquadanio S, Lo Verde F, Dovere V, Zega A, Pigola G, Aranda J, Stefani S. COL R Acinetobacter baumannii sRNA Signatures: Computational Comparative Identification and Biological Targets. Front Microbiol 2020; 10:3075. [PMID: 32010115 PMCID: PMC6978653 DOI: 10.3389/fmicb.2019.03075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/19/2019] [Indexed: 11/25/2022] Open
Abstract
Multidrug-Resistant (MDR) and Extensively Drug Resistant (XDR) Acinetobacter baumannii (Ab) represent a serious cause of healthcare-associated infections worldwide. Currently, the available treatment options are very restricted and colistin-based therapies are last-line treatments of these infections, even though colistin resistant (COLR) Ab have rarely been isolated yet. In bacteria, small non-coding RNAs (sRNAs) have been implicated in regulatory pathways of different biological functions, however, no knowledge exists about the sRNA role on the biological adaptation in COLRAb. Our study investigated two Italian XDR isogenic colistin-susceptible/resistant (COLS/R) Ab strain-pairs to discover new sRNA signatures. Comparative sRNA transcriptome (sRNAome) analyses were carried out by Illumina RNA-seq using both a Tru-Seq and a Short Insert library, whilst Ab ATCC 17978 and ACICU Reference Genome assembly, mapping, annotation and statistically significant differential expression (q-value ≤ 0.01) of the raw reads were performed by the Rockhopper tool. A computational filtering, sorting only similarly statistically significant differentially expressed (DE) sRNAs mapping on the same gene in both COLRAb isolates was conducted. COLR vs. COLS sRNAome, analyzed integrating the DE sRNAs obtained from the two different libraries, revealed some statistically significant DE sRNAs in COLRAb. In detail, we found: (i) two different under-expressed cis-acting sRNAs (AbsRNA1 and AbsRNA2) mapping in antisense orientation the 16S rRNA gene A1S_r01, (ii) one under-expressed cis-acting sRNA (AbsRNA3) targeting the A1S_2505 gene (hypothetical protein), (iii) one under-expressed microRNA-size small RNA fragment (AbsRNA4) and its pre-microAbsRNA4 targeting the A1S_0501 gene (hypothetical protein), (iv) as well as an over-expressed microRNA-size small RNA fragment (AbsRNA5) and its pre-microAbsRNA5 targeting the A1S_3097 gene (signal peptide). Custom TaqMan® probe-based real-time qPCRs validated the expression pattern of the selected sRNA candidates shown by RNA-seq. Furthermore, analysis on sRNA ΔA1S_r01, ΔA1S_2505 as well as the over-expressed A1S_3097 mutants revealed no effects on colistin resistance. Our study, for the first time, found the sRNAome signatures of clinical COLRAb with a computational prediction of their targets related to protein synthesis, host-microbe interaction and other different biological functions, including biofilm production, cell-cycle control, virulence, and antibiotic-resistance.
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Affiliation(s)
- Viviana Cafiso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Flavia Lo Verde
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Veronica Dovere
- Department of Translational Research and New Technology in Medicine and Surgery, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Alessandra Zega
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giuseppe Pigola
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Jesús Aranda
- Departament de Genètica i Microbiologia, Facultat de Biociènces, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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Chen H, Tang Y, Weir MD, Gao J, Imazato S, Oates TW, Lei L, Wang S, Hu T, Xu HHK. Effects of S. mutans gene-modification and antibacterial monomer dimethylaminohexadecyl methacrylate on biofilm growth and acid production. Dent Mater 2019; 36:296-309. [PMID: 31839202 DOI: 10.1016/j.dental.2019.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/17/2019] [Accepted: 12/02/2019] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Antibacterial quaternary ammonium monomers (QAMs) are used in resins. The rnc gene in Streptococcus mutans (S. mutans) plays a key role in resisting antibiotics. The objectives of this study were to investigate for the first time: (1) the effects of rnc deletion on S. mutans biofilms and acid production; (2) the combined effects of rnc deletion with dimethylaminohexadecyl methacrylate (DMAHDM) on biofilm-inhibition efficacy. METHODS Parent S. mutans strain UA159 (ATCC 700610) and the rnc-deleted S. mutans were used. Bacterial growth, minimum inhibitory concentration (MIC), and minimal bactericidal concentration (MBC) were measured to analyze the bacterial susceptibility of the parent and rnc-deleted S. mutans against DMAHDM, with the gold-standard chlorhexidine (CHX) as control. Biofilm biomass, polysaccharide and lactic acid production were measured. RESULTS The drug-susceptibility of the rnc-deleted S. mutans to DMAHDM or CHX was 2-fold higher than parent S. mutans. The drug-susceptibility did not increase after 10 passages (p < 0.05). Deleting the rnc gene increased the biofilm susceptibility to DMAHDM or CHX by 2-fold. The rnc-deletion in S. mutans reduced biofilm biomass, polysaccharide and lactic acid production, even at no drugs. DMAHDM was nearly 40 % more potent than the gold-standard CHX. The combination of rnc deletion+DMAHDM treatment achieved the greatest reduction in biofilm biomass, polysaccharide synthesis, and lactic acid production. SIGNIFICANCE Gene modification by deleting the rnc in S. mutans reduced the biofilm growth and acid production, and the rnc deletion+DMAHDM method showed the greatest biofilm-inhibition efficacy, for the first time. The dual strategy of antibacterial monomer+bacterial gene modification shows great potential to control biofilms and inhibit caries.
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Affiliation(s)
- Hong Chen
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China; Department of Advanced Oral Sciences and Therapeutics, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Yunhao Tang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Michael D Weir
- Department of Advanced Oral Sciences and Therapeutics, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Jianghong Gao
- Department of Advanced Oral Sciences and Therapeutics, University of Maryland Dental School, Baltimore, MD 21201, USA; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, Department of Preventive Dentistry, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Satoshi Imazato
- Department of Biomaterials Science, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Thomas W Oates
- Department of Advanced Oral Sciences and Therapeutics, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Lei Lei
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Suping Wang
- Department of Advanced Oral Sciences and Therapeutics, University of Maryland Dental School, Baltimore, MD 21201, USA; Department of Operative Dentistry and Endodontics & Periodontics and Stomatology Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China.
| | - Tao Hu
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Hockin H K Xu
- Department of Advanced Oral Sciences and Therapeutics, University of Maryland Dental School, Baltimore, MD 21201, USA; Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Ranjith K, Ramchiary J, Prakash JSS, Arunasri K, Sharma S, Shivaji S. Gene Targets in Ocular Pathogenic Escherichia coli for Mitigation of Biofilm Formation to Overcome Antibiotic Resistance. Front Microbiol 2019; 10:1308. [PMID: 31293528 PMCID: PMC6598151 DOI: 10.3389/fmicb.2019.01308] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
The present work is an attempt to establish the functionality of genes involved in biofilm formation and antibiotic resistance in an ocular strain of Escherichia coli (L-1216/2010) which was isolated and characterized from the Vitreous fluid of a patient with Endophthalmitis. For this purpose, seven separate gene-specific knockout mutants were generated by homologous recombination in ocular E. coli. The genes that were mutated included three transmembrane genes ytfR (ABC transporter ATP-binding protein), mdtO (multidrug efflux system) and tolA (inner membrane protein), ryfA coding for non-coding RNA and three metabolic genes mhpA (3-3-hydroxyphenylpropionate 1,2-dioxygenase), mhpB (2,3-di hydroxyphenylpropionate 1,2-dioxygenase), and bdcR (regulatory gene of bdcA). Mutants were validated by sequencing and Reverse transcription-PCR and monitored for biofilm formation by XTT method and confocal microscopy. The antibiotic susceptibility of the mutants was also ascertained. The results indicated that biofilm formation was inhibited in five mutants (ΔbdcR, ΔmhpA, ΔmhpB, ΔryfA, and ΔtolA) and the thickness of biofilm reduced from 17.2 μm in the wildtype to 1.5 to 4.8 μm in the mutants. Mutants ΔytfR and ΔmdtO retained the potential to form biofilm. Complementation of the mutants with the wild type gene restored biofilm formation potential in all mutants except in ΔmhpB. The 5 mutants which lost their ability to form biofilm (ΔbdcR, ΔmhpA, ΔmhpB, ΔtolA, and ΔryfA) did not exhibit any change in their susceptibility to Ceftazidime, Cefuroxime, Ciprofloxacin, Gentamicin, Cefotaxime, Sulfamethoxazole, Imipenem, Erythromycin, and Streptomycin in the planktonic phase compared to wild type ocular E. coli. But ΔmdtO was the only mutant with altered MIC to Sulfamethoxazole, Imipenem, Erythromycin, and Streptomycin both in the planktonic and biofilm phase. This is the first report demonstrating the involvement of the metabolic genes mhpA and mhpB and bdcR (regulatory gene of bdcA) in biofilm formation in ocular E. coli. In addition we provide evidence that tolA and ryfA are required for biofilm formation while ytfR and mdtO are not required. Mitigation of biofilm formation to overcome antibiotic resistance could be achieved by targeting the genes bdcR, mhpA, mhpB, ryfA, and tolA.
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Affiliation(s)
- Konduri Ranjith
- Jhaveri Microbiology Centre - Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India.,Research Scholar, Manipal Academy of Higher Education, Manipal, India
| | - Jahnabi Ramchiary
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Jogadhenu S S Prakash
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Kotakonda Arunasri
- Jhaveri Microbiology Centre - Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India
| | - Savitri Sharma
- Jhaveri Microbiology Centre - Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre - Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India
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12
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Palazzo L, Mikoč A, Ahel I. ADP-ribosylation: new facets of an ancient modification. FEBS J 2017; 284:2932-2946. [PMID: 28383827 PMCID: PMC7163968 DOI: 10.1111/febs.14078] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/20/2017] [Accepted: 04/04/2017] [Indexed: 12/11/2022]
Abstract
Rapid response to environmental changes is achieved by uni- and multicellular organisms through a series of molecular events, often involving modification of macromolecules, including proteins, nucleic acids and lipids. Amongst these, ADP-ribosylation is of emerging interest because of its ability to modify different macromolecules in the cells, and its association with many key biological processes, such as DNA-damage repair, DNA replication, transcription, cell division, signal transduction, stress and infection responses, microbial pathogenicity and aging. In this review, we provide an update on novel pathways and mechanisms regulated by ADP-ribosylation in organisms coming from all kingdoms of life.
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Affiliation(s)
- Luca Palazzo
- Sir William Dunn School of PathologyUniversity of OxfordUK
| | - Andreja Mikoč
- Division of Molecular BiologyRuđer Bošković InstituteZagrebCroatia
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordUK
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Kim M, Kim M, Kim KS. YmdB-mediated down-regulation of sucA inhibits biofilm formation and induces apramycin susceptibility in Escherichia coli. Biochem Biophys Res Commun 2016; 483:252-257. [PMID: 28034758 DOI: 10.1016/j.bbrc.2016.12.157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/23/2016] [Indexed: 11/16/2022]
Abstract
Antibiotic resistance associated with biofilm formation is a major concern when treating bacterial infections with drugs. The genes and pathways involved in biofilm formation have been extensively studied and are also involved in antibiotic resistance. Recent studies show that overexpression of Escherichia coli (E. coli) YmdB protein alters gene expression profiles and inhibits biofilm formation. Therefore, it is expected that YmdB and its regulated genes play a key role in development of biofilm and antibiotic resistance phenotypes. The present study screened antibiotics to identify those whose susceptibility profiles were regulated by YmdB levels. This protocol identified apramycin. Additional screening for genes negatively regulated by inactivation of RNase III activity via YmdB overexpression revealed that a gene associated with the tricarboxylic acid cycle gene, sucA, was necessary for the YmdB-like phenotype. Taken together, these data suggest that regulation of RNase III activity by trans-acting factors may be the key to identifying genes or pathways connecting biofilm and antibiotic resistance phenotypes. This information could be used to reduce the emergence of biofilm-associated multidrug-resistant bacteria.
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Affiliation(s)
- Moonjeong Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 46241, South Korea
| | - Minji Kim
- Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, South Korea
| | - Kwang-Sun Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 46241, South Korea.
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14
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Lalić J, Posavec Marjanović M, Palazzo L, Perina D, Sabljić I, Žaja R, Colby T, Pleše B, Halasz M, Jankevicius G, Bucca G, Ahel M, Matić I, Ćetković H, Luić M, Mikoč A, Ahel I. Disruption of Macrodomain Protein SCO6735 Increases Antibiotic Production in Streptomyces coelicolor. J Biol Chem 2016; 291:23175-23187. [PMID: 27634042 PMCID: PMC5087735 DOI: 10.1074/jbc.m116.721894] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/31/2016] [Indexed: 12/30/2022] Open
Abstract
ADP-ribosylation is a post-translational modification that can alter the physical and chemical properties of target proteins and that controls many important cellular processes. Macrodomains are evolutionarily conserved structural domains that bind ADP-ribose derivatives and are found in proteins with diverse cellular functions. Some proteins from the macrodomain family can hydrolyze ADP-ribosylated substrates and therefore reverse this post-translational modification. Bacteria and Streptomyces, in particular, are known to utilize protein ADP-ribosylation, yet very little is known about their enzymes that synthesize and remove this modification. We have determined the crystal structure and characterized, both biochemically and functionally, the macrodomain protein SCO6735 from Streptomyces coelicolor This protein is a member of an uncharacterized subfamily of macrodomain proteins. Its crystal structure revealed a highly conserved macrodomain fold. We showed that SCO6735 possesses the ability to hydrolyze PARP-dependent protein ADP-ribosylation. Furthermore, we showed that expression of this protein is induced upon DNA damage and that deletion of this protein in S. coelicolor increases antibiotic production. Our results provide the first insights into the molecular basis of its action and impact on Streptomyces metabolism.
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Affiliation(s)
| | | | - Luca Palazzo
- the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | | | | - Roko Žaja
- the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
- the Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Thomas Colby
- the Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany, and
| | | | | | - Gytis Jankevicius
- the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Giselda Bucca
- the School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Moulsecoomb, Brighton BN2 4GJ, United Kingdom
| | - Marijan Ahel
- the Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Ivan Matić
- the Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany, and
| | | | | | | | - Ivan Ahel
- the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom,
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15
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Paudyal S, Alfonso-Prieto M, Carnevale V, Redhu SK, Klein ML, Nicholson AW. Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB. Proteins 2015; 83:459-72. [PMID: 25546632 PMCID: PMC4329070 DOI: 10.1002/prot.24751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 01/06/2023]
Abstract
Ribonuclease III is a conserved bacterial endonuclease that cleaves double-stranded(ds) structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control that in turn confer global post-transcriptional regulation. The Escherichia coli macrodomain protein YmdB directly interacts with RNase III, and an increase in YmdB amount in vivo correlates with a reduction in RNase III activity. Here, a computational-based structural analysis was performed to identify atomic-level features of the YmdB-RNase III interaction. The docking of monomeric E. coli YmdB with a homology model of the E. coli RNase III homodimer yields a complex that exhibits an interaction of the conserved YmdB residue R40 with specific RNase III residues at the subunit interface. Surface Plasmon Resonance (SPR) analysis provided a KD of 61 nM for the complex, corresponding to a binding free energy (ΔG) of −9.9 kcal/mol. YmdB R40 and RNase III D128 were identified by in silico alanine mutagenesis as thermodynamically important interacting partners. Consistent with the prediction, the YmdB R40A mutation causes a 16-fold increase in KD (ΔΔG = +1.8 kcal/mol), as measured by SPR, and the D128A mutation in both RNase III subunits (D128A/D128′A) causes an 83-fold increase in KD (ΔΔG = +2.7 kcal/mol). The greater effect of the D128A/D128′A mutation may reflect an altered RNase III secondary structure, as revealed by CD spectroscopy, which also may explain the significant reduction in catalytic activity in vitro. The features of the modeled complex relevant to potential RNase III regulatory mechanisms are discussed. Proteins 2015; 83:459–472. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Samridhdi Paudyal
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122
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