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Humphrey ED, Sukhodolets MV. Isolation and Partial Characterization of Novel, Structurally Uniform (Hfq 6) n≥8 Assemblies Carrying Accessory Transcription and Translation Factors. Biochemistry 2024; 63:1647-1662. [PMID: 38869079 DOI: 10.1021/acs.biochem.3c00728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In growing E. coli cells, the transcription-translation complexes (TTCs) form characteristic foci; however, the exact molecular composition of these superstructures is not known with certainty. Herein, we report that, during our recently developed "fast" procedures for purification of E. coli RNA polymerase (RP), a fraction of the RP's α/RpoA subunits is displaced from the core RP complexes and copurifies with multiprotein superstructures carrying the nucleic acid-binding protein Hfq and the ribosomal protein S6. We show that the main components of these large multiprotein assemblies are fixed protein copy-number (Hfq6)n≥8 complexes; these complexes have a high level of structural uniformity and are distinctly unlike the previously described (Hfq6)n "head-to-tail" polymers. We describe purification of these novel, structurally uniform (Hfq6)n≥8 complexes to near homogeneity and show that they also contain small nonprotein molecules and accessory S6. We demonstrate that Hfq, S6, and RP have similar solubility profiles and present evidence pointing to a role of the Hfq C-termini in superstructure formation. Taken together, our data offer new insights into the composition of the macromolecular assemblies likely acting as scaffolds for transcription complexes and ribosomes during bacterial cells' active growth.
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Affiliation(s)
- Elijah D Humphrey
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
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2
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Bruce-Tagoe TA, Bhaskar S, Kavle RR, Jeevanandam J, Acquah C, Ohemeng-Boahen G, Agyei D, Danquah MK. Advances in aptamer-based biosensors for monitoring foodborne pathogens. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2024; 61:1252-1271. [PMID: 38910921 PMCID: PMC11190136 DOI: 10.1007/s13197-023-05889-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/27/2023] [Accepted: 10/21/2023] [Indexed: 06/25/2024]
Abstract
Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05889-8.
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Affiliation(s)
| | - Shyju Bhaskar
- Department of Food Science, University of Otago, Dunedin, 9056 New Zealand
| | - Ruchita Rao Kavle
- Department of Food Science, University of Otago, Dunedin, 9056 New Zealand
| | - Jaison Jeevanandam
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Caleb Acquah
- Faculty of Health Sciences, University of Ottawa, Ottawa, ON K1H 8M5 Canada
| | - Godfred Ohemeng-Boahen
- Department of Chemical Engineering, Kwame Nkrumah University of Science and Technology, UPO, Kumasi, Ghana
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, 9056 New Zealand
| | - Michael K. Danquah
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN 37403 USA
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3
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Wang WS, Lin-Chao S. Hfq-Antisense RNA I Binding Regulates RNase E-Dependent RNA Stability and ColE1 Plasmid Copy Number. Int J Mol Sci 2024; 25:3955. [PMID: 38612765 PMCID: PMC11012335 DOI: 10.3390/ijms25073955] [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: 02/26/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
The mechanisms and consequences of gene regulation by Hfq on trans-encoded small RNAs (sRNAs) have been well studied and documented. Recent employment of Genomic SELEX to search for Hfq-binding motifs has indicated that Hfq might frequently regulate gene expression controlled by cis-antisense RNAs. Here, we use the classic ColE1 plasmid antisense RNA-based regulation model (i.e., RNA I) to study the role of Hfq in controlling antisense regulatory functions. We show that Hfq exhibits a high binding affinity for RNA I and that binding limits RNase E cleavage, thereby stabilizing RNA I and reducing the plasmid copy number. Full-length RNA I displays a binding affinity for Hfq in the sub-micromolar range. In vivo overexpression of Hfq prolongs RNA I stability and reduces the ColE1 plasmid copy number, whereas deletion of hfq reduces RNA I stability and increases the plasmid copy number. RNA I predominantly binds to the proximal face of Hfq and exhibits competitive ability against a chromosome-borne proximal face-bound sRNA (DsrA) for Hfq binding. Through its strong promoter and high gene dosage features, plasmid-encoded antisense RNA I results in high RNA I expression, so it may antagonize the effects of trans-encoded RNAs in controlling target gene expression.
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Affiliation(s)
- Wei-Syuan Wang
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11490, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Sue Lin-Chao
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11490, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
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4
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Anand D, Jakkala K, Nair RR, Sharan D, Pradhan A, Mukkayyan N, Ajitkumar P. Complete identity and expression of StfZ, the cis-antisense RNA to the mRNA of the cell division gene ftsZ, in Escherichia coli. Front Microbiol 2022; 13:920117. [PMID: 36338044 PMCID: PMC9628754 DOI: 10.3389/fmicb.2022.920117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria regulate FtsZ protein levels through transcriptional and translational mechanisms for proper cell division. A cis-antisense RNA, StfZ, produced from the ftsA-ftsZ intergenic region, was proposed to regulate FtsZ level in Escherichia coli. However, its structural identity remained unknown. In this study, we determined the complete sequence of StfZ and identified the isoforms and its promoters. We find that under native physiological conditions, StfZ is expressed at a 1:6 ratio of StfZ:ftsZ mRNA at all growth phases from three promoters as three isoforms of 366, 474, and 552 nt RNAs. Overexpression of StfZ reduces FtsZ protein level, increases cell length, and blocks cell division without affecting the ftsZ mRNA stability. We did not find differential expression of StfZ under the stress conditions of heat shock, cold shock, or oxidative stress, or at any growth phase. These data indicated that the cis-encoded StfZ antisense RNA to ftsZ mRNA may be involved in the fine tuning of ftsZ mRNA levels available for translation as per the growth-phase-specific requirement at all phases of growth and cell division.
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Affiliation(s)
- Deepak Anand
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Biology, Lund University, Lund, Sweden
- *Correspondence: Deepak Anand,
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology, The University of Chicago, Chicago, IL, United States
| | - Atul Pradhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, United States
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5
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Bano N, Ehlinger C, Yang TY, Swanson M, Allen S. Considerations in the Immunogenicity Assessment Strategy for Oligonucleotide Therapeutics (ONTs). AAPS J 2022; 24:93. [DOI: 10.1208/s12248-022-00741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
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Satish S, Dey A, Tharmavaram M, Khatri N, Rawtani D. Risk assessment of selected pharmaceuticals on wildlife with nanomaterials based aptasensors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155622. [PMID: 35508236 DOI: 10.1016/j.scitotenv.2022.155622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
Pharmaceuticals have improved human and veterinary health tremendously over the years. But the implications of the presence of pharmaceuticals in the environment on terrestrial, avian, and aquatic organisms are still not fully comprehended. The bioaccumulation and biomagnifications of these chemicals through the food chain have long-term effects on the wildlife. The detection and quantification of such pharmaceutical residues in the environment is a tedious process and quicker methods are needed. Aptasensors are one such quick and reliable method for the identification of pharmaceutical residues in the wildlife. Aptasensors are a class of biosensors that work on the principles of biological recognition of elements. The aptamers are unique biological recognition elements with high specificity and affinity to various targets. Their efficiency makes them a very promising candidate for such sensitive research. In this review, the pharmaceutical threats to wildlife and their detection techniques using aptasensors have been discussed.
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Affiliation(s)
- Swathi Satish
- School of Pharmacy, National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India
| | - Aayush Dey
- School of Doctoral Studies & Research (SDSR), National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India
| | - Maithri Tharmavaram
- School of Pharmacy, National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India
| | - Nitasha Khatri
- Gujarat Environment Management Institute, Department of Forest and Environment, Sector 10B, Jivraj Mehta Bhavan, Gandhinagar, Gujarat, India
| | - Deepak Rawtani
- School of Pharmacy, National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India.
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7
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Nnachi RC, Sui N, Ke B, Luo Z, Bhalla N, He D, Yang Z. Biosensors for rapid detection of bacterial pathogens in water, food and environment. ENVIRONMENT INTERNATIONAL 2022; 166:107357. [PMID: 35777116 DOI: 10.1016/j.envint.2022.107357] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Conventional techniques (e.g., culture-based method) for bacterial detection typically require a central laboratory and well-trained technicians, which may take several hours or days. However, recent developments within various disciplines of science and engineering have led to a major paradigm shift in how microorganisms can be detected. The analytical sensors which are widely used for medical applications in the literature are being extended for rapid and on-site monitoring of the bacterial pathogens in food, water and the environment. Especially, within the low-resource settings such as low and middle-income countries, due to the advantages of low cost, rapidness and potential for field-testing, their use is indispensable for sustainable development of the regions. Within this context, this paper discusses analytical methods and biosensors which can be used to ensure food safety, water quality and environmental monitoring. In brief, most of our discussion is focused on various rapid sensors including biosensors and microfluidic chips. The analytical performances such as the sensitivity, specificity and usability of these sensors, as well as a brief comparison with the conventional techniques for bacteria detection, form the core part of the discussion. Furthermore, we provide a holistic viewpoint on how future research should focus on exploring the synergy of different sensing technologies by developing an integrated multiplexed, sensitive and accurate sensors that will enable rapid detection for food safety, water and environmental monitoring.
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Affiliation(s)
- Raphael Chukwuka Nnachi
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Ning Sui
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Bowen Ke
- Laboratory of Anesthesiology & Critical Care Medicine, Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 61004, PR China
| | - Zhenhua Luo
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern Ireland, United Kingdom; Healthcare Technology Hub, Ulster University, Jordanstown Shore Road, BT37 0QB, Northern Ireland, United Kingdom
| | - Daping He
- School of Science, Wuhan University of Technology, Wuhan 430070, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom.
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8
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Liu R, Zhang F, Sang Y, Katouzian I, Jafari SM, Wang X, Li W, Wang J, Mohammadi Z. Screening, identification, and application of nucleic acid aptamers applied in food safety biosensing. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Li D, Liu L, Huang Q, Tong T, Zhou Y, Li Z, Bai Q, Liang H, Chen L. Recent advances on aptamer-based biosensors for detection of pathogenic bacteria. World J Microbiol Biotechnol 2021; 37:45. [PMID: 33554321 DOI: 10.1007/s11274-021-03002-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/08/2021] [Indexed: 01/10/2023]
Abstract
As a significant constituent in biosphere, bacteria have a great influence on human activity. The detection of pathogen bacteria is closely related to the human health. However, the traditional methods for detection of pathogenic bacteria are time-consuming and difficult for quantification, although they are practical and reliable. Therefore, novel strategies for rapid, sensitive, and cost-effective detection are in great demand. Aptamer is a kind of oligonucleotide that selected by repeated screening in vitro or systematic evolution of ligands by exponential enrichment (SELEX) technology. Over the past years, owing to high affinity and specificity of aptamers, a variety of aptamer-based biosensors have been designed and applied for pathogen detection. In this review, we have discussed the recent advances on the applications of aptamer-based biosensors in detection of pathogenic bacteria. In addition, we also point out some problems in current methods and look forward to the further development of aptamer-based biosensors for pathogen detection.
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Affiliation(s)
- Danliang Li
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China.,Key Laboratory of Hengyang for Health Hazard Factors Inspection and Quarantine, Hengyang, China
| | - Luyao Liu
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China.,Key Laboratory of Hengyang for Health Hazard Factors Inspection and Quarantine, Hengyang, China
| | - Qiaoling Huang
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China.,Key Laboratory of Hengyang for Health Hazard Factors Inspection and Quarantine, Hengyang, China
| | - Ting Tong
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China.,Key Laboratory of Hengyang for Health Hazard Factors Inspection and Quarantine, Hengyang, China
| | - You Zhou
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China.,Key Laboratory of Hengyang for Health Hazard Factors Inspection and Quarantine, Hengyang, China
| | - Zhongyu Li
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, China
| | - Qinqin Bai
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China
| | - Hao Liang
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China. .,Key Laboratory of Hengyang for Health Hazard Factors Inspection and Quarantine, Hengyang, China.
| | - Lili Chen
- Department of health inspection and quarantine, College of Public Health, University of South China, Hengyang, China. .,Key Laboratory of Hengyang for Health Hazard Factors Inspection and Quarantine, Hengyang, China. .,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, Hunan, China.
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10
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Choi O, Kang B, Lee Y, Lee Y, Kim J. Pantoea ananatis carotenoid production confers toxoflavin tolerance and is regulated by Hfq-controlled quorum sensing. Microbiologyopen 2020; 10:e1143. [PMID: 33269542 PMCID: PMC7883899 DOI: 10.1002/mbo3.1143] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/09/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
Carotenoids are widely used in functional foods, cosmetics, and health supplements, and their importance and scope of use are continuously expanding. Here, we characterized carotenoid biosynthetic genes of the plant‐pathogenic bacterium Pantoea ananatis, which carries a carotenoid biosynthetic gene cluster (including crtE, X, Y, I, B, and Z) on a plasmid. Reverse transcription–polymerase chain reaction (RT‐PCR) analysis revealed that the crtEXYIB gene cluster is transcribed as a single transcript and crtZ is independently transcribed in the opposite direction. Using splicing by overlap extension with polymerase chain reaction (SOE by PCR) based on asymmetric amplification, we reassembled crtE–B, crtE–B–I, and crtE–B–I–Y. High‐performance liquid chromatography confirmed that Escherichia coli expressing the reassembled crtE–B, crtE–B–I, and crtE–B–I–Y operons produced phytoene, lycopene, and β‐carotene, respectively. We found that the carotenoids conferred tolerance to UV radiation and toxoflavin. Pantoea ananatis shares rice environments with the toxoflavin producer Burkholderia glumae and is considered to be the first reported example of producing and using carotenoids to withstand toxoflavin. We confirmed that carotenoid production by P. ananatis depends on RpoS, which is positively regulated by Hfq/ArcZ and negatively regulated by ClpP, similar to an important regulatory network of E. coli (HfqArcZ →RpoS Ͱ ClpXP). We also demonstrated that Hfq‐controlled quorum signaling de‐represses EanR to activate RpoS, thereby initiating carotenoid production. Survival genes such as those responsible for the production of carotenoids of the plant‐pathogenic P. ananatis must be expressed promptly to overcome stressful environments and compete with other microorganisms. This mechanism is likely maintained by a brake with excellent performance, such as EanR.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju, Korea
| | - Yongsang Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju, Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju, Korea
| | - Jinwoo Kim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea.,Division of Applied Life Science, Gyeongsang National University, Jinju, Korea.,Department of Plant Medicine, Gyeongsang National University, Jinju, Korea
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11
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Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020; 21:E8774. [PMID: 33233573 PMCID: PMC7699794 DOI: 10.3390/ijms21228774] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia; (D.B.); (A.K.)
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12
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Emamjomeh A, Zahiri J, Asadian M, Behmanesh M, Fakheri BA, Mahdevar G. Identification, Prediction and Data Analysis of Noncoding RNAs: A Review. Med Chem 2019; 15:216-230. [PMID: 30484409 DOI: 10.2174/1573406414666181015151610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 06/03/2018] [Accepted: 09/30/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs. OBJECTIVE The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA's roles in cellular processes and drugs design, briefly. METHOD In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases. RESULTS The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs. CONCLUSION ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.
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Affiliation(s)
- Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Asadian
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Barat A Fakheri
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Ghasem Mahdevar
- Department of Mathematics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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13
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Kim W, Choi JS, Kim D, Shin D, Suk S, Lee Y. Mechanisms for Hfq-Independent Activation of rpoS by DsrA, a Small RNA, in Escherichia coli. Mol Cells 2019; 42:426-439. [PMID: 31085808 PMCID: PMC6537650 DOI: 10.14348/molcells.2019.0040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Many small RNAs (sRNAs) regulate gene expression by base pairing to their target messenger RNAs (mRNAs) with the help of Hfq in Escherichia coli. The sRNA DsrA activates translation of the rpoS mRNA in an Hfq-dependent manner, but this activation ability was found to partially bypass Hfq when DsrA is overproduced. The precise mechanism by which DsrA bypasses Hfq is unknown. In this study, we constructed strains lacking all three rpoS-activating sRNAs (i.e., ArcZ, DsrA, and RprA) in hfq+ and Hfq- backgrounds, and then artificially regulated the cellular DsrA concentration in these strains by controlling its ectopic expression. We then examined how the expression level of rpoS was altered by a change in the concentration of DsrA. We found that the translation and stability of the rpoS mRNA are both enhanced by physiological concentrations of DsrA regardless of Hfq, but that depletion of Hfq causes a rapid degradation of DsrA and thereby decreases rpoS mRNA stability. These results suggest that the observed Hfq dependency of DsrA-mediated rpoS activation mainly results from the destabilization of DsrA in the absence of Hfq, and that DsrA itself contributes to the translational activation and stability of the rpoS mRNA in an Hfq-independent manner.
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Affiliation(s)
- Wonkyong Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Jee Soo Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Daun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Doohang Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Shinae Suk
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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14
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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15
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Berry KE, Hochschild A. A bacterial three-hybrid assay detects Escherichia coli Hfq-sRNA interactions in vivo. Nucleic Acids Res 2018; 46:e12. [PMID: 29140461 PMCID: PMC5778611 DOI: 10.1093/nar/gkx1086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/21/2017] [Accepted: 10/20/2017] [Indexed: 01/08/2023] Open
Abstract
The interaction of RNA molecules with proteins is a critical aspect of gene regulation across all domains of life. Here, we report the development of a bacterial three-hybrid (B3H) assay to genetically detect RNA-protein interactions. The basis for this three-hybrid assay is a transcription-based bacterial two-hybrid assay that has been used widely to detect and dissect protein-protein interactions. In the three-hybrid assay, a DNA-bound protein with a fused RNA-binding moiety (the coat protein of bacteriophage MS2 (MS2CP)) is used to recruit a hybrid RNA upstream of a test promoter. The hybrid RNA consists of a constant region that binds the tethered MS2CP and a variable region. Interaction between the variable region of the hybrid RNA and a target RNA-binding protein that is fused to a subunit of Escherichia coli RNA polymerase (RNAP) stabilizes the binding of RNAP to the test promoter, thereby activating transcription of a reporter gene. We demonstrate that this three-hybrid assay detects interaction between non-coding small RNAs (sRNAs) and the hexameric RNA chaperone Hfq from E. coli and enables the identification of Hfq mutants with sRNA-binding defects. Our findings suggest that this B3H assay will be broadly applicable for the study of RNA-protein interactions.
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Affiliation(s)
- Katherine E Berry
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Hochschild
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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16
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Kinghorn AB, Fraser LA, Liang S, Shiu SCC, Tanner JA. Aptamer Bioinformatics. Int J Mol Sci 2017; 18:E2516. [PMID: 29186809 PMCID: PMC5751119 DOI: 10.3390/ijms18122516] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/17/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several enclaves of aptamer bioinformatics, including simulation of aptamer selection, fragment-based aptamer design, patterning of libraries, identification of lead aptamers from high-throughput sequencing (HTS) data and in silico aptamer optimization.
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Affiliation(s)
| | | | | | | | - Julian A. Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR China; (A.B.K.); (L.A.F.); (S.L.); (S.C.-C.S.)
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17
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Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mücke N, Wilmanns M, Gibson TJ, Barabas O. Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. Sci Rep 2017; 7:9903. [PMID: 28852099 PMCID: PMC5575007 DOI: 10.1038/s41598-017-10085-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/02/2017] [Indexed: 11/18/2022] Open
Abstract
The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confirm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN)X motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, fhlA. A systematic computational survey also shows that phylogenetically conserved (ARN)X motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN)X motif containing sRNAs with target mRNAs on a “speed-dating” fashion, thereby supporting their regulatory function.
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Affiliation(s)
- Eike C Schulz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Markus Seiler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, 60438, Frankfurt a.M., Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Franka Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Vladimir Rybin
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Vivian Pogenberg
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany
| | - Norbert Mücke
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Matthias Wilmanns
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
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18
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Chen J, Gottesman S. Hfq links translation repression to stress-induced mutagenesis in E. coli. Genes Dev 2017; 31:1382-1395. [PMID: 28794186 PMCID: PMC5580658 DOI: 10.1101/gad.302547.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Here, Chen et al. show an example of Hfq repressing translation in the absence of sRNAs via major remodeling of the mRNA. They demonstrate that, by interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis. Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA–RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis. Here we report that Hfq deploys dual mechanisms to control mutS expression. First, Hfq binds directly to an (AAN)3 motif within the mutS 5′ untranslated region (UTR), repressing translation in the absence of sRNA partners both in vivo and in vitro. Second, Hfq acts in a canonical pathway, promoting base-pairing of ArcZ sRNA with the mutS leader to inhibit translation. Most importantly, using pathway-specific mutS chromosomal alleles that specifically abrogate either regulatory pathway or both, we demonstrate that tight control of MutS levels in stationary phase contributes to stress-induced mutagenesis. By interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis.
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Affiliation(s)
- Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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19
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Aptamer-assisted novel technologies for detecting bacterial pathogens. Biomed Pharmacother 2017; 93:737-745. [PMID: 28700978 DOI: 10.1016/j.biopha.2017.07.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/18/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Nowadays, all people are at risk of infectious diseases that are mainly caused by bacteria causing infection. There is a permanent demand for an appropriate detection method that is affordable, practical, careful, rapid, sensitive, efficient and economical. Aptamers are single stranded DNA or RNA oligonucleotides, which can be recognized specifically and bind to their target molecules and also, be exploited in diagnostic applications. Recently, aptamer-based systems have offered great potentials in applications for the recognition of several important bacterial pathogens from clinical and food specimens. There are several reports appraising the diagnostic applicability of aptamer-based systems for the detection of pathogens. As for its excellent sensitivity, as well as its rapid and efficient detectability, this technique may be practical to indicate bacterial targets with less sample size and may consume less time than traditional methods These systems offer a promising approach for the sensitive and quick detection of food-borne and clinical agents. This review provides an overview of aptamer-based methods as a novel approach for detecting bacterial pathogens.
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20
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Nguyen Quang N, Perret G, Ducongé F. Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers. Pharmaceuticals (Basel) 2016; 9:ph9040076. [PMID: 27973417 PMCID: PMC5198051 DOI: 10.3390/ph9040076] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022] Open
Abstract
Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. Simultaneously to the amplification of high-affinity candidates, the diversity in the pool is exponentially reduced after several rounds of in vitro selection. Until now, cloning and Sanger sequencing of about 100 sequences was usually used to identify the enriched candidates. However, High-Throughput Sequencing (HTS) is now extensively used to replace such low throughput sequencing approaches. Providing a deeper analysis of the library, HTS is expected to accelerate the identification of aptamers as well as to identify aptamers with higher affinity. It is also expected that it can provide important information on the binding site of the aptamers. Nevertheless, HTS requires handling a large amount of data that is only possible through the development of new in silico methods. Here, this review presents these different strategies that have been recently developed to improve the identification and characterization of aptamers using HTS.
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Affiliation(s)
- Nam Nguyen Quang
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), 18 route du panorama, 92260 Fontenay-aux-Roses, France.
- Neurodegenerative Diseases Laboratory, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Université Paris-Sud, UMR 9199, 92260 Fontenay-aux-Roses, France.
| | - Gérald Perret
- LFB Biotechnologies, 3 avenue des Tropiques, 91958 Courtaboeuf CEDEX, France.
| | - Frédéric Ducongé
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), 18 route du panorama, 92260 Fontenay-aux-Roses, France.
- Neurodegenerative Diseases Laboratory, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Université Paris-Sud, UMR 9199, 92260 Fontenay-aux-Roses, France.
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21
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Teng J, Yuan F, Ye Y, Zheng L, Yao L, Xue F, Chen W, Li B. Aptamer-Based Technologies in Foodborne Pathogen Detection. Front Microbiol 2016; 7:1426. [PMID: 27672383 PMCID: PMC5018482 DOI: 10.3389/fmicb.2016.01426] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/29/2016] [Indexed: 11/13/2022] Open
Abstract
Aptamers are single stranded DNA or RNA ligands, which can be selected by a method called systematic evolution of ligands by exponential enrichment (SELEX); and they can specifically recognize and bind to their targets. These unique characteristics of aptamers offer great potentials in applications such as pathogen detection and biomolecular screening. Pathogen detection is the critical means in detecting and identifying the problems related to public health and food safety; and only the rapid, sensitive and efficient detection technologies can enable the users to make the accurate assessments on the risks of infections (humans and animals) or contaminations (foods and other commodities) caused by various pathogens. This article reviews the development in the field of the aptamer-based approaches for pathogen detection, including whole-cell SELEX and Genomic SELEX. Nowadays, a variety of aptamer-based biosensors have been developed for pathogen detection. Thus, in this review, we also cover the development in aptamer-based biosensors including optical biosensors for multiple pathogen detection by multiple-labeling or label-free models such as fluorescence detection and surface plasmon resonance, electrochemical biosensors and lateral chromatography test strips, and their applications in pathogen detection and biomolecular screening. While notable progress has been made in the field in the last decade, challenges or drawbacks in their applications such as pathogen detection and biomolecular screening remain to be overcome.
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Affiliation(s)
- Jun Teng
- College of Food Science and Engineering, Hefei University of Technology, HefeiChina
| | - Fang Yuan
- Animal Quarantine Laboratory, Jiangsu Entry-Exit Inspection and Quarantine Bureau, NanjingChina
| | - Yingwang Ye
- College of Food Science and Engineering, Hefei University of Technology, HefeiChina
| | - Lei Zheng
- College of Food Science and Engineering, Hefei University of Technology, HefeiChina
| | - Li Yao
- College of Food Science and Engineering, Hefei University of Technology, HefeiChina
| | - Feng Xue
- Animal Quarantine Laboratory, Jiangsu Entry-Exit Inspection and Quarantine Bureau, NanjingChina
| | - Wei Chen
- College of Food Science and Engineering, Hefei University of Technology, HefeiChina
| | - Baoguang Li
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MDUSA
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22
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Jijakli K, Khraiwesh B, Fu W, Luo L, Alzahmi A, Koussa J, Chaiboonchoe A, Kirmizialtin S, Yen L, Salehi-Ashtiani K. The in vitro selection world. Methods 2016; 106:3-13. [PMID: 27312879 DOI: 10.1016/j.ymeth.2016.06.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/23/2016] [Accepted: 06/07/2016] [Indexed: 12/20/2022] Open
Abstract
Through iterative cycles of selection, amplification, and mutagenesis, in vitro selection provides the ability to isolate molecules of desired properties and function from large pools (libraries) of random molecules with as many as 10(16) distinct species. This review, in recognition of a quarter of century of scientific discoveries made through in vitro selection, starts with a brief overview of the method and its history. It further covers recent developments in in vitro selection with a focus on tools that enhance the capabilities of in vitro selection and its expansion from being purely a nucleic acids selection to that of polypeptides and proteins. In addition, we cover how next generation sequencing and modern biological computational tools are being used to complement in vitro selection experiments. On the very least, sequencing and computational tools can translate the large volume of information associated with in vitro selection experiments to manageable, analyzable, and exploitable information. Finally, in vivo selection is briefly compared and contrasted to in vitro selection to highlight the unique capabilities of each method.
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Affiliation(s)
- Kenan Jijakli
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Basel Khraiwesh
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Weiqi Fu
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Liming Luo
- Department of Pathology & Immunology, Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amnah Alzahmi
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Joseph Koussa
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry Program, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Laising Yen
- Department of Pathology & Immunology, Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates.
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23
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Zheng A, Panja S, Woodson SA. Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria. J Mol Biol 2016; 428:2259-2264. [PMID: 27049793 DOI: 10.1016/j.jmb.2016.03.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 12/20/2022]
Abstract
The Sm-protein Hfq facilitates interactions between small non-coding RNA (sRNA) and target mRNAs. In enteric Gram-negative bacteria, Hfq is required for sRNA regulation, and hfq deletion results in stress intolerance and reduced virulence. By contrast, the role of Hfq in Gram-positive is less established and varies among species. The RNA binding and RNA annealing activity of Hfq from Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus subtilis, and Staphylococcus aureus were compared using minimal RNAs and fluorescence spectroscopy. The results show that RNA annealing activity increases with the number of arginines in a semi-conserved patch on the rim of the Hfq hexamer and correlates with the previously reported requirement for Hfq in sRNA regulation. Thus, the amino acid sequence of the arginine patch can predict the chaperone function of Hfq in sRNA regulation in different organisms.
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Affiliation(s)
- Amy Zheng
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Subrata Panja
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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24
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Zurla C, Jung J, Santangelo PJ. Can we observe changes in mRNA "state"? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related processes. Analyst 2016; 141:548-62. [PMID: 26605378 PMCID: PMC4701657 DOI: 10.1039/c5an01959a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA binding proteins (RBP) regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNA) through their interactions with specific cis-acting elements within target RNAs. Post-transcriptional regulatory mechanisms are directly involved in the control of the immune response and stress response and their alterations play a crucial role in cancer related processes. In this review, we discuss mRNAs and RNA binding proteins relevant to tumorigenesis, current methodologies for detecting RNA interactions, and last, we describe a novel method to detect such interactions, which combines peptide modified, RNA imaging probes (FMTRIPs) with proximity ligation (PLA) and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity in situ.
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Affiliation(s)
- C Zurla
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - J Jung
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - P J Santangelo
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
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25
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van Nues RW, Castro-Roa D, Yuzenkova Y, Zenkin N. Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate. Nucleic Acids Res 2015; 44:2577-92. [PMID: 26609136 PMCID: PMC4824073 DOI: 10.1093/nar/gkv1302] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/08/2015] [Indexed: 11/23/2022] Open
Abstract
Coupled transcription and translation in bacteria are tightly regulated. Some small RNAs (sRNAs) control aspects of this coupling by modifying ribosome access or inducing degradation of the message. Here, we show that sRNA IsrA (IS61 or McaS) specifically associates with core enzyme of RNAP in vivo and in vitro, independently of σ factor and away from the main nucleic-acids-binding channel of RNAP. We also show that, in the cells, IsrA exists as ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase. Our findings suggest that IsrA might be directly involved in transcription or can participate in regulation of gene expression by delivering proteins associated with it to target mRNAs through its interactions with transcribing RNAP and through regions of sequence-complementarity with the target. In this eukaryotic-like model only in the context of a complex with its target, IsrA and its associated proteins become active. In this manner, in the form of sRNPs, bacterial sRNAs could regulate a number of targets with various outcomes, depending on the set of associated proteins.
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Affiliation(s)
- Rob W van Nues
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Daniel Castro-Roa
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
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26
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Abstract
To fully understand the regulation of gene expression, it is critical to quantitatively define whether and how RNA-binding proteins (RBPs) discriminate between alternative binding sites in RNAs. Here, we describe new methods that measure protein binding to large numbers of RNA variants, and ways to analyse and interpret data obtained by these approaches, including affinity distributions and free energy landscapes. We discuss how the new methodologies and the associated concepts enable the development of inclusive, quantitative models for RNA-protein interactions that transcend the traditional binary classification of RBPs as either specific or nonspecific.
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27
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Abstract
Long non-coding RNAs (lncRNAs) are associated to a plethora of cellular functions, most of which require the interaction with one or more RNA-binding proteins (RBPs); similarly, RBPs are often able to bind a large number of different RNAs. The currently available knowledge is already drawing an intricate network of interactions, whose deregulation is frequently associated to pathological states. Several different techniques were developed in the past years to obtain protein–RNA binding data in a high-throughput fashion. In parallel, in silico inference methods were developed for the accurate computational prediction of the interaction of RBP–lncRNA pairs. The field is growing rapidly, and it is foreseeable that in the near future, the protein–lncRNA interaction network will rise, offering essential clues for a better understanding of lncRNA cellular mechanisms and their disease-associated perturbations.
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28
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Patenge N, Pappesch R, Khani A, Kreikemeyer B. Genome-wide analyses of small non-coding RNAs in streptococci. Front Genet 2015; 6:189. [PMID: 26042151 PMCID: PMC4438229 DOI: 10.3389/fgene.2015.00189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023] Open
Abstract
Streptococci represent a diverse group of Gram-positive bacteria, which colonize a wide range of hosts among animals and humans. Streptococcal species occur as commensal as well as pathogenic organisms. Many of the pathogenic species can cause severe, invasive infections in their hosts leading to a high morbidity and mortality. The consequence is a tremendous suffering on the part of men and livestock besides the significant financial burden in the agricultural and healthcare sectors. An environmentally stimulated and tightly controlled expression of virulence factor genes is of fundamental importance for streptococcal pathogenicity. Bacterial small non-coding RNAs (sRNAs) modulate the expression of genes involved in stress response, sugar metabolism, surface composition, and other properties that are related to bacterial virulence. Even though the regulatory character is shared by this class of RNAs, variation on the molecular level results in a high diversity of functional mechanisms. The knowledge about the role of sRNAs in streptococci is still limited, but in recent years, genome-wide screens for sRNAs have been conducted in an increasing number of species. Bioinformatics prediction approaches have been employed as well as expression analyses by classical array techniques or next generation sequencing. This review will give an overview of whole genome screens for sRNAs in streptococci with a focus on describing the different methods and comparing their outcome considering sRNA conservation among species, functional similarities, and relevance for streptococcal infection.
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Affiliation(s)
- Nadja Patenge
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
| | - Roberto Pappesch
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
| | - Afsaneh Khani
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
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Cho KH, Kim JH. Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens. Front Genet 2015; 6:110. [PMID: 25859258 PMCID: PMC4374534 DOI: 10.3389/fgene.2015.00110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/03/2015] [Indexed: 01/19/2023] Open
Abstract
Due to recent advances of bioinformatics and high throughput sequencing technology, discovery of regulatory non-coding RNAs in bacteria has been increased to a great extent. Based on this bandwagon, many studies searching for trans-acting small non-coding RNAs in streptococci have been performed intensively, especially in the important human pathogen, group A and B streptococci. However, studies for cis-encoded non-coding antisense RNAs in streptococci have been scarce. A recent study shows antisense RNAs are involved in virulence gene regulation in group B streptococcus, S. agalactiae. This suggests antisense RNAs could have important roles in the pathogenesis of streptococcal pathogens. In this review, we describe recent discoveries of chromosomal cis-encoded antisense RNAs in streptococcal pathogens and other low GC Gram (+) bacteria to provide a guide for future studies.
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Affiliation(s)
- Kyu Hong Cho
- Department of Biology, Indiana State University Terre Haute, IN, USA
| | - Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Science Washington, DC, USA
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Van Assche E, Van Puyvelde S, Vanderleyden J, Steenackers HP. RNA-binding proteins involved in post-transcriptional regulation in bacteria. Front Microbiol 2015; 6:141. [PMID: 25784899 PMCID: PMC4347634 DOI: 10.3389/fmicb.2015.00141] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/06/2015] [Indexed: 11/19/2022] Open
Abstract
Post-transcriptional regulation is a very important mechanism to control gene expression in changing environments. In the past decade, a lot of interest has been directed toward the role of small RNAs (sRNAs) in bacterial post-transcriptional regulation. However, sRNAs are not the only molecules controlling gene expression at this level, RNA-binding proteins (RBPs) play an important role as well. CsrA and Hfq are the two best studied bacterial proteins of this type, but recently, additional proteins involved in post-transcriptional control have been identified. This review focuses on the general working mechanisms of post-transcriptionally active RBPs, which include (i) adaptation of the susceptibility of mRNAs and sRNAs to RNases, (ii) modulating the accessibility of the ribosome binding site of mRNAs, (iii) recruiting and assisting in the interaction of mRNAs with other molecules and (iv) regulating transcription terminator/antiterminator formation, and gives an overview of both the well-studied and the newly identified proteins that are involved in post-transcriptional regulatory processes. Additionally, the post-transcriptional mechanisms by which the expression or the activity of these proteins is regulated, are described. For many of the newly identified proteins, however, mechanistic questions remain. Most likely, more post-transcriptionally active proteins will be identified in the future.
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Affiliation(s)
- Elke Van Assche
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
| | - Sandra Van Puyvelde
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
| | - Jos Vanderleyden
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
| | - Hans P Steenackers
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
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Darmostuk M, Rimpelova S, Gbelcova H, Ruml T. Current approaches in SELEX: An update to aptamer selection technology. Biotechnol Adv 2015; 33:1141-61. [PMID: 25708387 DOI: 10.1016/j.biotechadv.2015.02.008] [Citation(s) in RCA: 416] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/26/2015] [Accepted: 02/13/2015] [Indexed: 12/21/2022]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a well-established and efficient technology for the generation of oligonucleotides with a high target affinity. These SELEX-derived single stranded DNA and RNA molecules, called aptamers, were selected against various targets, such as proteins, cells, microorganisms, chemical compounds etc. They have a great potential in the use as novel antibodies, in cancer theragnostics and in biomedical research. Vast interest in aptamers stimulated continuous development of SELEX, which underwent numerous modifications since its first application in 1990. Novel modifications made the selection process more efficient, cost-effective and significantly less time-consuming. This article brings a comprehensive and up-to-date review of recent advances in SELEX methods and pinpoints advantages, main obstacles and limitations. The post-SELEX strategies and examples of application are also briefly outlined in this review.
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Affiliation(s)
- Mariia Darmostuk
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Silvie Rimpelova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Helena Gbelcova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic; Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, Bratislava 811 08, Slovak Republic.
| | - Tomas Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
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Abstract
The Sm-like protein Hfq (host factor Q-beta phage) facilitates regulation by bacterial small noncoding RNAs (sRNAs) in response to stress and other environmental signals. Here, we present a low-resolution model of Escherichia coli Hfq bound to the rpoS mRNA, a bacterial stress response gene that is targeted by three different sRNAs. Selective 2'-hydroxyl acylation and primer extension, small-angle X-ray scattering, and Monte Carlo molecular dynamics simulations show that the distal face and lateral rim of Hfq interact with three sites in the rpoS leader, folding the RNA into a compact tertiary structure. These interactions are needed for sRNA regulation of rpoS translation and position the sRNA target adjacent to an sRNA binding region on the proximal face of Hfq. Our results show how Hfq specifically distorts the structure of the rpoS mRNA to enable sRNA base pairing and translational control.
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Möller P, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F. Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PLoS One 2014; 9:e110427. [PMID: 25330313 PMCID: PMC4201532 DOI: 10.1371/journal.pone.0110427] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/14/2014] [Indexed: 01/18/2023] Open
Abstract
As matchmaker between mRNA and sRNA interactions, the RNA chaperone Hfq plays a key role in riboregulation of many bacteria. Often, the global influence of Hfq on the transcriptome is reflected by substantially altered proteomes and pleiotropic phenotypes in hfq mutants. Using quantitative proteomics and co-immunoprecipitation combined with RNA-sequencing (RIP-seq) of Hfq-bound RNAs, we demonstrate the pervasive role of Hfq in nutrient acquisition, metabolism and motility of the plant pathogen Agrobacterium tumefaciens. 136 of 2544 proteins identified by iTRAQ (isobaric tags for relative and absolute quantitation) were affected in the absence of Hfq. Most of them were associated with ABC transporters, general metabolism and motility. RIP-seq of chromosomally encoded Hfq3xFlag revealed 1697 mRNAs and 209 non-coding RNAs (ncRNAs) associated with Hfq. 56 ncRNAs were previously undescribed. Interestingly, 55% of the Hfq-bound ncRNAs were encoded antisense (as) to a protein-coding sequence suggesting that A. tumefaciens Hfq plays an important role in asRNA-target interactions. The exclusive enrichment of 296 mRNAs and 31 ncRNAs under virulence conditions further indicates a role for post-transcriptional regulation in A. tumefaciens-mediated plant infection. On the basis of the iTRAQ and RIP-seq data, we assembled a comprehensive model of the Hfq core regulon in A. tumefaciens.
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Affiliation(s)
- Philip Möller
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | | | - Konrad U. Förstner
- Research Center for Infectious Diseases (ZINF), Julius-Maximilian's University of Würzburg, Würzburg, Germany
| | - Tuan-Nan Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Cynthia M. Sharma
- Research Center for Infectious Diseases (ZINF), Julius-Maximilian's University of Würzburg, Würzburg, Germany
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
- * E-mail:
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Becker A, Overlöper A, Schlüter JP, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E. Riboregulation in plant-associated α-proteobacteria. RNA Biol 2014; 11:550-62. [PMID: 25003187 DOI: 10.4161/rna.29625] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The symbiotic α-rhizobia Sinorhizobium meliloti, Bradyrhizobium japonicum, Rhizobium etli and the related plant pathogen Agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. These metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. Here we summarize the recent knowledge on their small non-coding RNAs (sRNAs) including conservation, function, and interaction of the sRNAs with the RNA chaperone Hfq. In each of these organisms, an inventory of hundreds of cis- and trans-encoded sRNAs with regulatory potential was uncovered by high-throughput approaches and used for the construction of 39 sRNA family models. Genome-wide analyses of hfq mutants and co-immunoprecipitation with tagged Hfq revealed a major impact of the RNA chaperone on the physiology of plant-associated α-proteobacteria including symbiosis and virulence. Highly conserved members of the SmelC411 family are the AbcR sRNAs, which predominantly regulate ABC transport systems. AbcR1 of A. tumefaciens controls the uptake of the plant-generated signaling molecule GABA and is a central regulator of nutrient uptake systems. It has similar functions in S. meliloti and the human pathogen Brucella abortus. As RNA degradation is an important process in RNA-based gene regulation, a short overview on ribonucleases in plant-associated α-proteobacteria concludes this review.
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Affiliation(s)
- Anke Becker
- LOEWE Centre for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; Marburg, Germany
| | | | - Jan-Philip Schlüter
- LOEWE Centre for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; Marburg, Germany
| | - Jan Reinkensmeier
- Center for Biotechnology (CeBiTec); Bielefeld University; Bielefeld, Germany
| | - Marta Robledo
- LOEWE Centre for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; Marburg, Germany
| | - Robert Giegerich
- Center for Biotechnology (CeBiTec); Bielefeld University; Bielefeld, Germany
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Bilusic I, Popitsch N, Rescheneder P, Schroeder R, Lybecker M. Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation. RNA Biol 2014; 11:641-54. [PMID: 24922322 PMCID: PMC4152368 DOI: 10.4161/rna.29299] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hfq is a global regulator of gene expression in bacteria undergoing adaptation to changing environmental conditions. Its major function is to promote RNA-RNA interactions between regulatory small RNAs (sRNAs) and their target mRNAs. Previously, we demonstrated that Hfq binds many antisense RNAs (asRNAs) in vitro and hypothesized that Hfq may play a role in regulating gene expression via asRNAs. To investigate the E. coli Hfq-binding transcriptome in more detail, we co-immunoprecipitated and deep-sequenced RNAs bound to Hfq in vivo. We detected many new Hfq-binding sRNAs and observed that almost 300 mRNAs bind to Hfq. Among these, several are known to be sRNA targets. We identified 25 novel RNAs, which are transcribed from within protein coding regions and named them intragenic RNAs (intraRNAs). Furthermore, 67 asRNAs were co-immunoprecipitated with Hfq, demonstrating that Hfq binds antisense transcripts in vivo. Northern blot analyses confirmed the deep sequencing results and demonstrated that many of the novel Hfq-binding RNAs identified are regulated by Hfq.
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Affiliation(s)
- Ivana Bilusic
- Department of Biochemistry and Cell Biology; Max F Perutz Laboratories; University of Vienna; Vienna, Austria
| | - Niko Popitsch
- Center for Integrative Bioinformatics Vienna; Max F Perutz Laboratories; Medical University of Vienna; University of Vienna; Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna; Max F Perutz Laboratories; Medical University of Vienna; University of Vienna; Vienna, Austria
| | - Renée Schroeder
- Department of Biochemistry and Cell Biology; Max F Perutz Laboratories; University of Vienna; Vienna, Austria
| | - Meghan Lybecker
- Department of Biochemistry and Cell Biology; Max F Perutz Laboratories; University of Vienna; Vienna, Austria
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37
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Moreno R, Hernández-Arranz S, La Rosa R, Yuste L, Madhushani A, Shingler V, Rojo F. The Crc and Hfq proteins of Pseudomonas putida cooperate in catabolite repression and formation of ribonucleic acid complexes with specific target motifs. Environ Microbiol 2014; 17:105-18. [PMID: 24803210 DOI: 10.1111/1462-2920.12499] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/28/2014] [Indexed: 12/22/2022]
Abstract
The Crc protein is a global regulator that has a key role in catabolite repression and optimization of metabolism in Pseudomonads. Crc inhibits gene expression post-transcriptionally, preventing translation of mRNAs bearing an AAnAAnAA motif [the catabolite activity (CA) motif] close to the translation start site. Although Crc was initially believed to bind RNA by itself, this idea was recently challenged by results suggesting that a protein co-purifying with Crc, presumably the Hfq protein, could account for the detected RNA-binding activity. Hfq is an abundant protein that has a central role in post-transcriptional gene regulation. Herein, we show that the Pseudomonas putida Hfq protein can recognize the CA motifs of RNAs through its distal face and that Crc facilitates formation of a more stable complex at these targets. Crc was unable to bind RNA in the absence of Hfq. However, pull-down assays showed that Crc and Hfq can form a co-complex with RNA containing a CA motif in vitro. Inactivation of the hfq or the crc gene impaired catabolite repression to a similar extent. We propose that Crc and Hfq cooperate in catabolite repression, probably through forming a stable co-complex with RNAs containing CA motifs to result in inhibition of translation initiation.
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Affiliation(s)
- Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049, Madrid, Spain
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38
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Weichenrieder O. RNA binding by Hfq and ring-forming (L)Sm proteins: a trade-off between optimal sequence readout and RNA backbone conformation. RNA Biol 2014; 11:537-49. [PMID: 24828406 PMCID: PMC4152361 DOI: 10.4161/rna.29144] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The eukaryotic Sm and the Sm-like (LSm) proteins form a large family that includes LSm proteins in archaea and the Hfq proteins in bacteria. Commonly referred to as the (L)Sm protein family, the various members play important roles in RNA processing, decay, and riboregulation. Particularly interesting from a structural point of view is their ability to assemble into doughnut-shaped rings, which allows them to bind preferentially the uridine-rich 3′-end of RNA oligonucleotides. With an emphasis on Hfq, this review compares the RNA-binding properties of the various (L)Sm rings that were recently co-crystallized with RNA substrates, and it discusses how these properties relate to physiological function.
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Affiliation(s)
- Oliver Weichenrieder
- Department of Biochemistry; Max Planck Institute for Developmental Biology; Tübingen, Germany
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Sakai Y, Abe K, Nakashima S, Yoshida W, Ferri S, Sode K, Ikebukuro K. Improving the gene-regulation ability of small RNAs by scaffold engineering in Escherichia coli. ACS Synth Biol 2014; 3:152-62. [PMID: 24328142 DOI: 10.1021/sb4000959] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Noncoding small RNAs are involved in transcriptional and post-transcriptional gene regulation of target mRNAs by modulating mRNA elongation, stability, or translational efficiency. Many natural trans-encoded small RNAs contain a scaffold that allows binding of the RNA chaperone protein Hfq for conditional gene regulation. Here, we improved the gene regulation abilities of small RNAs by directly fusing the natural Escherichia coli trans-encoded small RNA-derived scaffolds, including Hfq-binding and rho-independent transcription terminator sequences, to the 3' end of the small RNAs that mediate RNA-based gene regulation. As target small RNAs to improve their gene regulation abilities, we selected small RNAs of artificial post-transcriptional riboregulators and transcriptional attenuators. Four different small RNA scaffolds were fused to the riboregulator and attenuator-derived small RNAs. Mutations were introduced into the best small RNA scaffold to improve its gene-regulation ability further. As a result, mutations predicted to stabilize the secondary structures of the small RNA scaffolds dramatically increased its ability to regulate gene expression of both the post-transcriptional riboregulator and transcriptional attenuator systems. We believe our engineered small RNA scaffolds are applicable to other RNA regulators for improving regulatory activity, and engineered small RNA scaffolds may present a valuable strategy to regulate target gene expression strongly.
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Affiliation(s)
- Yuta Sakai
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koichi Abe
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Saki Nakashima
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wataru Yoshida
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Stefano Ferri
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Torres-Quesada O, Reinkensmeier J, Schlüter JP, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jiménez-Zurdo JI. Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti. RNA Biol 2014; 11:563-79. [PMID: 24786641 DOI: 10.4161/rna.28239] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The RNA chaperone Hfq is a global post-transcriptional regulator in bacteria. Here, we used RNAseq to analyze RNA populations from the legume symbiont Sinorhizobium meliloti that were co-immunoprecipitated (CoIP-RNA) with a FLAG-tagged Hfq in five growth/stress conditions. Hfq-bound transcripts (1315) were largely identified in stressed bacteria and derived from small RNAs (sRNAs), both trans-encoded (6.4%) and antisense (asRNAs; 6.3%), and mRNAs (86%). Pull-down with Hfq recovered a small proportion of annotated S. meliloti sRNAs (14% of trans-sRNAs and 2% of asRNAs) suggesting a discrete impact of this protein in sRNA pathways. Nonetheless, Hfq selectively stabilized CoIP-enriched sRNAs, anticipating that these interactions are functionally significant. Transcription of 26 Hfq-bound sRNAs was predicted to occur from promoters recognized by the major stress σ factors σ(E2) or σ(H1/2). Recovery rates of sRNAs in each of the CoIP-RNA libraries suggest a large impact of Hfq-assisted riboregulation in S. meliloti osmoadaptation. Hfq directly targeted 18% of the predicted S. meliloti mRNAs, which encode functionally diverse proteins involved in transport and metabolism, σ(E2)-dependent stress responses, quorum sensing, flagella biosynthesis, ribosome, and membrane assembly or symbiotic nitrogen fixation. Canonical targeting of the 5' regions of two of the ABC transporter mRNAs by the homologous Hfq-binding AbcR1 and AbcR2 sRNAs leading to inhibition of protein synthesis was confirmed in vivo. We therefore provide a comprehensive resource for the systems-level deciphering of hitherto unexplored S. meliloti stress and symbiotic post-transcriptional regulons and the identification of Hfq-dependent sRNA-mRNA regulatory pairs.
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Affiliation(s)
- Omar Torres-Quesada
- Grupo de Ecología Genética de la Rizosfera; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas; CSIC, Granada, Spain
| | - Jan Reinkensmeier
- Center for Biotechnology (CeBiTec); Bielefeld University; Bielefeld, Germany
| | - Jan-Philip Schlüter
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology; Philipps-Universität Marburg; Marburg, Germany
| | - Marta Robledo
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology; Philipps-Universität Marburg; Marburg, Germany
| | - Alexandra Peregrina
- Grupo de Ecología Genética de la Rizosfera; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas; CSIC, Granada, Spain
| | - Robert Giegerich
- Center for Biotechnology (CeBiTec); Bielefeld University; Bielefeld, Germany
| | - Nicolás Toro
- Grupo de Ecología Genética de la Rizosfera; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas; CSIC, Granada, Spain
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology; Philipps-Universität Marburg; Marburg, Germany
| | - Jose I Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas; CSIC, Granada, Spain
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41
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Hess WR, Berghoff BA, Wilde A, Steglich C, Klug G. Riboregulators and the role of Hfq in photosynthetic bacteria. RNA Biol 2014; 11:413-26. [PMID: 24651049 PMCID: PMC4152350 DOI: 10.4161/rna.28035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/29/2014] [Indexed: 12/25/2022] Open
Abstract
Anoxygenic and oxygenic bacteria directly convert solar energy into biomass using photosynthesis. The formation and composition of photosynthetic complexes has to be tightly controlled in response to environmental conditions, as exposure to sunlight can be harmful due to the generation of reactive oxygen species and the damaging effects of UV irradiation. Therefore, photosynthetic bacteria are exposed to a particular set of regulatory challenges in addition to those that also affect other bacteria, requiring sophisticated regulatory systems. Indeed, hundreds of potential regulatory RNAs have been identified in photosynthetic model bacteria as well as antisense RNAs (asRNAs) of up to several kb in length that protect certain mRNAs from degradation. The trans-acting small non-coding RNAs (sRNAs), PcrZ and PsrR1, control pigment and photosystem biogenesis in Rhodobacter sphaeroides and cyanobacteria, respectively. The asRNAs IsrR and As1_flv4 act as negative regulators and the asRNAs PsbA2R and PsbA3R as positive effectors of photosynthesis gene expression in Synechocystis 6803.
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Affiliation(s)
- Wolfgang R Hess
- Faculty of Biology; Institute for Biology III; University of Freiburg; Freiburg, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology; University of Giessen; Giessen, Germany
| | - Annegret Wilde
- Faculty of Biology; Institute for Biology III; University of Freiburg; Freiburg, Germany
| | - Claudia Steglich
- Faculty of Biology; Institute for Biology III; University of Freiburg; Freiburg, Germany
| | - Gabriele Klug
- Institute for Microbiology and Molecular Biology; University of Giessen; Giessen, Germany
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Kakoschke T, Kakoschke S, Magistro G, Schubert S, Borath M, Heesemann J, Rossier O. The RNA chaperone Hfq impacts growth, metabolism and production of virulence factors in Yersinia enterocolitica. PLoS One 2014; 9:e86113. [PMID: 24454955 PMCID: PMC3893282 DOI: 10.1371/journal.pone.0086113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/05/2013] [Indexed: 11/18/2022] Open
Abstract
To adapt to changes in environmental conditions, bacteria regulate their gene expression at the transcriptional but also at the post-transcriptional level, e.g. by small RNAs (sRNAs) which modulate mRNA stability and translation. The conserved RNA chaperone Hfq mediates the interaction of many sRNAs with their target mRNAs, thereby playing a global role in fine-tuning protein production. In this study, we investigated the significance of Hfq for the enteropathogen Yersina enterocolitica serotype O:8. Hfq facilitated optimal growth in complex and minimal media. Our comparative protein analysis of parental and hfq-negative strains suggested that Hfq promotes lipid metabolism and transport, cell redox homeostasis, mRNA translation and ATP synthesis, and negatively affects carbon and nitrogen metabolism, transport of siderophore and peptides and tRNA synthesis. Accordingly, biochemical tests indicated that Hfq represses ornithine decarboxylase activity, indole production and utilization of glucose, mannitol, inositol and 1,2-propanediol. Moreover, Hfq repressed production of the siderophore yersiniabactin and its outer membrane receptor FyuA. In contrast, hfq mutants exhibited reduced urease production. Finally, strains lacking hfq were more susceptible to acidic pH and oxidative stress. Unlike previous reports in other Gram-negative bacteria, Hfq was dispensable for type III secretion encoded by the virulence plasmid. Using a chromosomally encoded FLAG-tagged Hfq, we observed increased production of Hfq-FLAG in late exponential and stationary phases. Overall, Hfq has a profound effect on metabolism, resistance to stress and modulates the production of two virulence factors in Y. enterocolitica, namely urease and yersiniabactin.
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Affiliation(s)
- Tamara Kakoschke
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Munich, Germany
| | - Sara Kakoschke
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Munich, Germany
| | - Giuseppe Magistro
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Munich, Germany
| | - Marc Borath
- Protein Analysis Unit, Adolf-Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Munich, Germany
| | - Ombeline Rossier
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Munich, Germany
- * E-mail:
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Antagonistic functions between the RNA chaperone Hfq and an sRNA regulate sensitivity to the antibiotic colicin. EMBO J 2013; 32:2764-78. [PMID: 24065131 DOI: 10.1038/emboj.2013.205] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 08/14/2013] [Indexed: 11/09/2022] Open
Abstract
The RNA chaperone Hfq is a key regulator of the function of small RNAs (sRNAs). Hfq has been shown to facilitate sRNAs binding to target mRNAs and to directly regulate translation through the action of sRNAs. Here, we present evidence that Hfq acts as the repressor of cirA mRNA translation in the absence of sRNA. Hfq binding to cirA prevents translation initiation, which correlates with cirA mRNA instability. In contrast, RyhB pairing to cirA mRNA promotes changes in RNA structure that displace Hfq, thereby allowing efficient translation as well as mRNA stabilization. Because CirA is a receptor for the antibiotic colicin Ia, in addition to acting as an Fur (Ferric Uptake Regulator)-regulated siderophore transporter, translational activation of cirA mRNA by RyhB promotes colicin sensitivity under conditions of iron starvation. Altogether, these results indicate that Fur and RyhB modulate an unexpected feed-forward loop mechanism related to iron physiology and colicin sensitivity.
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Guenther UP, Yandek LE, Niland CN, Campbell FE, Anderson D, Anderson VE, Harris ME, Jankowsky E. Hidden specificity in an apparently nonspecific RNA-binding protein. Nature 2013; 502:385-8. [PMID: 24056935 PMCID: PMC3800043 DOI: 10.1038/nature12543] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/14/2013] [Indexed: 12/27/2022]
Abstract
Nucleic-acid-binding proteins are generally viewed as either specific or nonspecific, depending on characteristics of their binding sites in DNA or RNA. Most studies have focused on specific proteins, which identify cognate sites by binding with highest affinities to regions with defined signatures in sequence, structure or both. Proteins that bind to sites devoid of defined sequence or structure signatures are considered nonspecific. Substrate binding by these proteins is poorly understood, and it is not known to what extent seemingly nonspecific proteins discriminate between different binding sites, aside from those sequestered by nucleic acid structures. Here we systematically examine substrate binding by the apparently nonspecific RNA-binding protein C5, and find clear discrimination between different binding site variants. C5 is the protein subunit of the transfer RNA processing ribonucleoprotein enzyme RNase P from Escherichia coli. The protein binds 5' leaders of precursor tRNAs at a site without sequence or structure signatures. We measure functional binding of C5 to all possible sequence variants in its substrate binding site, using a high-throughput sequencing kinetics approach (HITS-KIN) that simultaneously follows processing of thousands of RNA species. C5 binds different substrate variants with affinities varying by orders of magnitude. The distribution of functional affinities of C5 for all substrate variants resembles affinity distributions of highly specific nucleic acid binding proteins. Unlike these specific proteins, C5 does not bind its physiological RNA targets with the highest affinity, but with affinities near the median of the distribution, a region that is not associated with a sequence signature. We delineate defined rules governing substrate recognition by C5, which reveal specificity that is hidden in cellular substrates for RNase P. Our findings suggest that apparently nonspecific and specific RNA-binding modes may not differ fundamentally, but represent distinct parts of common affinity distributions.
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Affiliation(s)
- Ulf-Peter Guenther
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Faner MA, Feig AL. Identifying and characterizing Hfq-RNA interactions. Methods 2013; 63:144-59. [PMID: 23707622 DOI: 10.1016/j.ymeth.2013.04.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 11/15/2022] Open
Abstract
To regulate stress responses and virulence, bacteria use small regulatory RNAs (sRNAs). These RNAs can up or down regulate target mRNAs through base pairing by influencing ribosomal access and RNA decay. A large class of these sRNAs, called trans-encoded sRNAs, requires the RNA binding protein Hfq to facilitate base pairing between the regulatory RNA and its target mRNA. The resulting network of regulation is best characterized in Escherichia coli and Salmonella typhimurium, but the importance of Hfq dependent sRNA regulation is recognized in a diverse population of bacteria. In this review we present the approaches and methods used to discover Hfq binding RNAs, characterize their interactions and elucidate their functions.
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Affiliation(s)
- M A Faner
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, United States
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Abstract
Over the past years, small non-coding RNAs (sRNAs) emerged as important modulators of gene expression in bacteria. Guided by partial sequence complementarity, these sRNAs interact with target mRNAs and eventually affect transcript stability and translation. The physiological function of sRNAs depends on the protein Hfq, which binds sRNAs in the cell and promotes the interaction with their mRNA targets. This important physiological function of Hfq as a central hub of sRNA-mediated regulation made it one of the most intensely studied proteins in bacteria. Recently, a new model for sRNA binding by Hfq has been proposed that involves the direct recognition of the sRNA 3' end and interactions of the sRNA body with the lateral RNA-binding surface of Hfq. This review summarizes the current understanding of the RNA binding properties of Hfq and its (s)RNA complexes. Moreover, the implications of the new binding model for sRNA-mediated regulation are discussed.
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Affiliation(s)
- Evelyn Sauer
- Biozentrum, University of Basel, Basel, Switzerland.
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Lalaouna D, Simoneau-Roy M, Lafontaine D, Massé E. Regulatory RNAs and target mRNA decay in prokaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:742-7. [PMID: 23500183 DOI: 10.1016/j.bbagrm.2013.02.013] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
Recent advances in prokaryote genetics have highlighted the important and complex roles of small regulatory RNAs (sRNAs). Although blocking mRNA translation is often the main function of sRNAs, these molecules can also induce the degradation of target mRNAs using a mechanism that drastically differs from eukaryotic RNA interference (RNAi). Whereas RNAi relies on RNase III-like machinery that is specific to double-strand RNAs, sRNA-mediated mRNA degradation in Escherichia coli and Samonella typhimurium depends on RNase E, a single-strand specific endoribonuclease. Surprisingly, the latest descriptions of sRNA-mediated mRNA degradation in various bacteria suggest a variety of previously unsuspected mechanisms. In this review, we focus on recently characterized mechanisms in which sRNAs can bind to target mRNAs to induce decay. These new mechanisms illustrate how sRNAs and mRNA structures, including riboswitches, act cooperatively with protein partners to initiate the decay of mRNAs. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- David Lalaouna
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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Abstract
The RNA chaperone Hfq is a key player in small RNA (sRNA)-mediated regulation of target mRNAs in many bacteria. The absence of this protein causes pleiotropic phenotypes such as impaired stress regulation and, occasionally, loss of virulence. Hfq promotes rapid sRNA-target mRNA base pairing to allow for fast, adaptive responses. For this to happen, sRNAs and/or mRNAs must be bound by Hfq. However, when the intra- or extracellular environment changes, so does the intracellular RNA pool, and this, in turn, requires a correspondingly rapid change in the pool of Hfq-bound RNAs. Biochemical studies have suggested tight binding of Hfq to many RNAs, indicating very slow dissociation rates. In contrast, the changing pool of binding-competent RNAs must compete for access to this helper protein in a minute time frame (known response time for regulation). How rapid exchange of RNAs on Hfq in vivo can be reconciled with biochemically stable and very slowly dissociating Hfq-RNA complexes is the topic of this review. Several recent reports suggest that the time scale discrepancy can be resolved by an “active cycling” model: rapid exchange of RNAs on Hfq is not limited by slow intrinsic dissociation rates, but is driven by the concentration of free RNA. Thus, transient binding of competitor RNA to Hfq-RNA complexes increases cycling rates and solves the strong binding/high turnover paradox.
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Affiliation(s)
- E Gerhart H Wagner
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden.
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49
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Dambach M, Irnov I, Winkler WC. Association of RNAs with Bacillus subtilis Hfq. PLoS One 2013; 8:e55156. [PMID: 23457461 PMCID: PMC3574147 DOI: 10.1371/journal.pone.0055156] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/23/2012] [Indexed: 11/18/2022] Open
Abstract
The prevalence and characteristics of small regulatory RNAs (sRNAs) have not been well characterized for Bacillus subtilis, an important model system for Gram-positive bacteria. However, B. subtilis was recently found to synthesize many candidate sRNAs during stationary phase. In the current study, we performed deep sequencing on Hfq-associated RNAs and found that a small subset of sRNAs associates with Hfq, an enigmatic RNA-binding protein that stabilizes sRNAs in Gram-negatives, but whose role is largely unknown in Gram-positive bacteria. We also found that Hfq associated with antisense RNAs, antitoxin transcripts, and many mRNA leaders. Several new candidate sRNAs and mRNA leader regions were also discovered by this analysis. Additionally, mRNA fragments overlapping with start or stop codons associated with Hfq, while, in contrast, relatively few full-length mRNAs were recovered. Deletion of hfq reduced the intracellular abundance of several representative sRNAs, suggesting that B. subtilis Hfq-sRNA interactions may be functionally significant in vivo. In general, we anticipate this catalog of Hfq-associated RNAs to serve as a resource in the functional characterization of Hfq in B. subtilis.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Gene Deletion
- Gene Expression Regulation, Bacterial
- Host Factor 1 Protein/analysis
- Host Factor 1 Protein/genetics
- Host Factor 1 Protein/metabolism
- Open Reading Frames
- RNA, Antisense/analysis
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Michael Dambach
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Irnov Irnov
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Wade C. Winkler
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, United States of America
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Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M. Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs. BMC Genomics 2012; 13 Suppl 7:S13. [PMID: 23282220 PMCID: PMC3521395 DOI: 10.1186/1471-2164-13-s7-s13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may also have similar functions for Burkholderia pseudomallei, a soil bacterium that can adapt to diverse environmental conditions, which causes the disease melioidosis and is also able to infect a wide variety of hosts. RESULTS By integrating several proven sRNA prediction programs into a computational pipeline, available Burkholderia spp. genomes were screened to identify sRNA gene candidates. Orthologous sRNA candidates were then identified via comparative analysis. From the total prediction, 21 candidates were found to have Rfam homologs. RT-PCR and sequencing of candidate sRNA genes of unknown functions revealed six putative sRNAs which were highly conserved in Burkholderia spp. and two that were unique to B. pseudomallei present in a normal culture conditions transcriptome. The validated sRNAs include potential cis-acting elements associated with the modulation of methionine metabolism and one B. pseudomallei-specific sRNA that is expected to bind to the Hfq protein. CONCLUSIONS The use of the pipeline developed in this study and subsequent comparative analysis have successfully aided in the discovery and shortlisting of sRNA gene candidates for validation. This integrated approach identified 29 B. pseudomallei sRNA genes - of which 21 have Rfam homologs and 8 are novel.
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Affiliation(s)
- Jia-Shiun Khoo
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
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