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Małecka EM, Woodson SA. RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone. Nat Commun 2024; 15:2069. [PMID: 38453956 PMCID: PMC10920880 DOI: 10.1038/s41467-024-46316-6] [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: 10/24/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024] Open
Abstract
RNA-guided enzymes must quickly search a vast sequence space for their targets. This search is aided by chaperones such as Hfq, a protein that mediates regulation by bacterial small RNAs (sRNAs). How RNA binding proteins enhance this search is little known. Using single-molecule Förster resonance energy transfer, we show that E. coli Hfq performs a one-dimensional scan in which compaction of the target RNA delivers sRNAs to sites distant from the location of Hfq recruitment. We also show that Hfq can transfer an sRNA between different target sites in a single mRNA, favoring the most stable duplex. We propose that compaction and segmental transfer, combined with repeated cycles of base pairing, enable the kinetic selection of optimal sRNA targets. Finally, we show that RNA compaction and sRNA transfer require conserved arginine patches. We suggest that arginine patches are a widespread strategy for enabling the movement of RNA across protein surfaces.
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Affiliation(s)
- Ewelina M Małecka
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.,5, Baltimore, MD, 21218, USA.
- Laboratory of Single-Molecule Biophysics, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, Warsaw, 02-109, Poland.
| | - Sarah A Woodson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.,5, Baltimore, MD, 21218, USA.
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2
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Cai H, Roca J, Zhao YF, Woodson SA. Dynamic Refolding of OxyS sRNA by the Hfq RNA Chaperone. J Mol Biol 2022; 434:167776. [PMID: 35934049 PMCID: PMC10044511 DOI: 10.1016/j.jmb.2022.167776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 10/16/2022]
Abstract
The Sm protein Hfq chaperones small non-coding RNAs (sRNAs) in bacteria, facilitating sRNA regulation of target mRNAs. Hfq acts in part by remodeling the sRNA and mRNA structures, yet the basis for this remodeling activity is not understood. To understand how Hfq remodels RNA, we used single-molecule Förster resonance energy transfer (smFRET) to monitor conformational changes in OxyS sRNA upon Hfq binding. The results show that E. coli Hfq first compacts OxyS, bringing its 5' and 3 ends together. Next, Hfq destabilizes an internal stem-loop in OxyS, allowing the RNA to adopt a more open conformation that is stabilized by a conserved arginine on the rim of Hfq. The frequency of transitions between compact and open conformations depend on interactions with Hfqs flexible C-terminal domain (CTD), being more rapid when the CTD is deleted, and slower when OxyS is bound to Caulobacter crescentus Hfq, which has a shorter and more stable CTD than E. coli Hfq. We propose that the CTDs gate transitions between OxyS conformations that are stabilized by interaction with one or more arginines. These results suggest a general model for how basic residues and intrinsically disordered regions of RNA chaperones act together to refold RNA.
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Affiliation(s)
- Huahuan Cai
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA; Department of Chemistry, College of Chemistry and Chemical Engineering, and Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China
| | - Jorjethe Roca
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA
| | - Yu-Fen Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, and Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China; Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Sarah A Woodson
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA.
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3
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Meng X, He M, Xia P, Wang J, Wang H, Zhu G. Functions of Small Non-Coding RNAs in Salmonella–Host Interactions. BIOLOGY 2022; 11:biology11091283. [PMID: 36138763 PMCID: PMC9495376 DOI: 10.3390/biology11091283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary In the process of infecting the host, Salmonella senses and adapts to the environment within the host, breaks through the host’s defense system, and survives and multiplies in the host cell. As a class of universal regulators encoded in intergenic space, an increasing number of small non-coding RNAs (sRNAs) have been found to be involved in a series of processes during Salmonella infection, and they play an important role in interactions with the host cell. In this review, we discuss how sRNAs help Salmonella resist acidic environmental stress by regulating acid resistance genes and modulate adhesion and invasion to non-phagocytic cells by regulating virulent genes such as fimbrial subunits and outer membrane proteins. In addition, sRNAs help Salmonella adapt to oxidative stress within host cells and promote survival within macrophages. Although the function of a variety of sRNAs has been studied during host–Salmonella interactions, many of sRNAs’ functions remain to be discovered. Abstract Salmonella species infect hosts by entering phagocytic and non-phagocytic cells, causing diverse disease symptoms, such as fever, gastroenteritis, and even death. Therefore, Salmonella has attracted much attention. Many factors are involved in pathogenesis, for example, the capsule, enterotoxins, Salmonella pathogenicity islands (SPIs), and corresponding regulators. These factors are all traditional proteins associated with virulence and regulation. Recently, small non-coding RNAs (sRNAs) have also been reported to function as critical regulators. Salmonella has become a model organism for studying sRNAs. sRNAs regulate gene expression by imperfect base-pairing with targets at the post-transcriptional level. sRNAs are involved in diverse biological processes, such as virulence, substance metabolism, and adaptation to stress environments. Although some studies have reported the crucial roles of sRNAs in regulating host–pathogen interactions, the function of sRNAs in host–Salmonella interactions has rarely been reviewed. Here, we review the functions of sRNAs during the infection of host cells by Salmonella, aiming to deepen our understanding of sRNA functions and the pathogenic mechanism of Salmonella.
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Affiliation(s)
- Xia Meng
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
- Correspondence:
| | - Mengping He
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
| | - Pengpeng Xia
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
| | - Jinqiu Wang
- Department of Animal Husbandry and Veterinary Medicine, Beijing Agricultural Vocational College, Beijing 102442, China
| | - Heng Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
| | - Guoqiang Zhu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
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4
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Naskulwar K, Peña-Castillo L. sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction. RNA Biol 2021; 19:44-54. [PMID: 34965197 PMCID: PMC8794260 DOI: 10.1080/15476286.2021.2012058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A multitude of sRNAs have been identified in many bacterial species; however, their function has yet to be elucidated. A key step to understand sRNAs function is to identify the mRNAs these sRNAs bind to. There are several computational methods for sRNA target prediction, and the most accurate one is CopraRNA which is based on comparative-genomics. However, species-specific sRNAs are quite common and CopraRNA cannot be used for these sRNAs. The most commonly used transcriptome-wide sRNA target prediction method and second-most-accurate method is IntaRNA. However, IntaRNA can take hours to run on a bacterial transcriptome. Here we present sRNARFTarget, a machine-learning-based method for transcriptome-wide sRNA target prediction applicable to any sRNA. We comparatively assessed the performance of sRNARFTarget, CopraRNA and IntaRNA in three bacterial species. Our results show that sRNARFTarget outperforms IntaRNA in terms of accuracy, ranking of true interacting pairs, and running time. However, CopraRNA substantially outperforms the other two programsin terms of accuracy. Thus, we suggest using CopraRNA when homolog sequences of the sRNA are available, and sRNARFTarget for transcriptome-wide prediction or for species-specific sRNAs. sRNARFTarget is available at https://github.com/BioinformaticsLabAtMUN/sRNARFTarget.
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Affiliation(s)
- Kratika Naskulwar
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Canada
| | - Lourdes Peña-Castillo
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Canada
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5
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Małecka EM, Sobańska D, Olejniczak M. Bacterial Chaperone Protein Hfq Facilitates the Annealing of Sponge RNAs to Small Regulatory RNAs. J Mol Biol 2021; 433:167291. [PMID: 34624296 DOI: 10.1016/j.jmb.2021.167291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/15/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023]
Abstract
Bacterial small RNAs (sRNAs) in association with the chaperone protein Hfq regulate the expression of many target mRNAs. Since sRNAs' action is crucial to engendering a response to changing environmental conditions, their activity needs to be regulated. One such mechanism occurs at the post-transcriptional level and involves sponge RNAs, which sequester sRNAs affecting their regulatory output. Both types of RNAs were identified on Hfq, but it is not known how Hfq interacts with RNA sponges and stimulates their base-pairing with sRNAs. Here, we used biochemical methods to demonstrate that sponge RNAs resemble sRNAs by their structure and their modes of Hfq binding. Hfq facilitates the annealing of AgvB and 3'ETSleuZ sponge RNAs to targeted sRNAs: GcvB and RybB, respectively, and each surface of the protein plays a particular role in the process. Moreover, we found that the efficiency of sponge RNA interactions with sRNAs can be improved; therefore, we propose that natural RNA sponges might not sequester sRNAs optimally.
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Affiliation(s)
- Ewelina M Małecka
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Daria Sobańska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland. https://twitter.com/SobanskaD
| | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
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6
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Liu H, Shi F, Tan S, Yu X, Lai W, Li Y. Engineering a Bifunctional ComQXPA-P srfA Quorum-Sensing Circuit for Dynamic Control of Gene Expression in Corynebacterium glutamicum. ACS Synth Biol 2021; 10:1761-1774. [PMID: 34165971 DOI: 10.1021/acssynbio.1c00149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Corynebacterium glutamicum is an important industrial workhorse for the production of amino acids and other chemicals. However, the engineering of C. glutamicum is inflexible due to the lack of dynamic regulation tools. In this study, a quorum sensing (QS) circuit and its modulated hfq-sRNA cassette were constructed, and the dynamic control of gene expression by these bifunctional circuits was researched. First, the ComQXPA-PsrfA QS system of Bacillus subtilis was harnessed and modified to create an upregulating QS circuit, in which the transcription of genes controlled by the PsrfA promoter may be promoted at high cell density. This QS circuit successfully activated the expression of green fluorescent protein (GFP) to 6.35-fold in a cell density-dependent manner in C. glutamicum. Next, the hfq-sRNA-mediated downregulating circuit under the control of the ComQXPA-PsrfA QS system was established, and the expression of GFP was autonomously repressed by 96.1%. Next, to fine-tune these two QS circuits, a library of synthetic PsrfA based promoters was constructed, and a series of mutant PsrfAM promoters with 0.4-1.5-fold strength of native PsrfA were selected. Subsequently, the ComQXPA-PsrfAM QS circuit was utilized to upregulate the expression of red fluorescent protein, and the same QS-based hfq-sRNA system was utilized to downregulate the expression of GFP simultaneously. Last, this bifunctional ComQXPA-PsrfAM QS circuit was verified again by fine-tuning the expression of α-amylase. Therefore, the engineered ComQXPA-PsrfAM QS cassette can be applied as a novel bifunctional QS circuit to flexibly control gene expression in C. glutamicum.
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Affiliation(s)
- Haiyan Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Feng Shi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Shuyu Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xinping Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenmei Lai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yongfu Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
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7
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Faigenbaum-Romm R, Reich A, Gatt YE, Barsheshet M, Argaman L, Margalit H. Hierarchy in Hfq Chaperon Occupancy of Small RNA Targets Plays a Major Role in Their Regulation. Cell Rep 2021; 30:3127-3138.e6. [PMID: 32130912 PMCID: PMC7059120 DOI: 10.1016/j.celrep.2020.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/15/2020] [Accepted: 02/04/2020] [Indexed: 11/28/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are posttranscriptional regulators of gene expression that base pair with complementary sequences on target mRNAs, often in association with the chaperone Hfq. Here, using experimentally identified sRNA-target pairs, along with gene expression measurements, we assess basic principles of regulation by sRNAs. We show that the sRNA sequence dictates the target repertoire, as point mutations in the sRNA shift the target set correspondingly. We distinguish two subsets of targets: targets showing changes in expression levels under overexpression of their sRNA regulator and unaffected targets that interact more sporadically with the sRNA. These differences among targets are associated with their Hfq occupancy, rather than with the sRNA-target base-pairing potential. Our results suggest that competition among targets over Hfq binding plays a major role in the regulatory outcome, possibly awarding targets with higher Hfq binding efficiency an advantage in the competition over binding to the sRNA. Basic concepts of regulation by small RNAs are revealed from large-scale data Small changes in the small RNA sequence shift the target repertoire accordingly A regulatory sRNA affects the expression levels of only a subset of its targets Competition among targets over Hfq binding plays a major role in their regulation
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Affiliation(s)
- Raya Faigenbaum-Romm
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Avichai Reich
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Meshi Barsheshet
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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8
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Stepwise sRNA targeting of structured bacterial mRNAs leads to abortive annealing. Mol Cell 2021; 81:1988-1999.e4. [PMID: 33705712 DOI: 10.1016/j.molcel.2021.02.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/08/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
Abstract
Bacterial small RNAs (sRNAs) regulate the expression of hundreds of transcripts via base pairing mediated by the Hfq chaperone protein. sRNAs and the mRNA sites they target are heterogeneous in sequence, length, and secondary structure. To understand how Hfq can flexibly match diverse sRNA and mRNA pairs, we developed a single-molecule Förster resonance energy transfer (smFRET) platform that visualizes the target search on timescales relevant in cells. Here we show that unfolding of target secondary structure on Hfq creates a kinetic energy barrier that determines whether target recognition succeeds or aborts before a stable anti-sense complex is achieved. Premature dissociation of the sRNA can be alleviated by strong RNA-Hfq interactions, explaining why sRNAs have different target recognition profiles. We propose that the diverse sequences and structures of Hfq substrates create an additional layer of information that tunes the efficiency and selectivity of non-coding RNA regulation in bacteria.
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9
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Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA. Nat Commun 2021; 12:874. [PMID: 33558533 PMCID: PMC7870926 DOI: 10.1038/s41467-021-21144-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Base-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA-mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24-31% and increase koff by 14-25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.
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10
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Dos Santos RF, Arraiano CM, Andrade JM. New molecular interactions broaden the functions of the RNA chaperone Hfq. Curr Genet 2019; 65:1313-1319. [PMID: 31104083 DOI: 10.1007/s00294-019-00990-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/09/2023]
Abstract
The RNA chaperone Hfq is an important bacterial post-transcriptional regulator. Most studies on Hfq are focused on the role of this protein on small non-coding RNAs (sRNAs) and messenger RNAs (mRNAs). The most well-characterized function of Hfq is its role as RNA matchmaker, promoting the base-pairing between sRNAs and their mRNA targets. However, novel substrates and previous unrecognized functions of Hfq have now been identified, which expanded the regulatory spectrum of this protein. Hfq was recently found to bind rRNA and act as a new ribosome biogenesis factor, affecting rRNA processing, ribosome assembly, translational efficiency and translational fidelity. Hfq was also found to bind tRNAs, which could provide an additional mechanism for its role on the accuracy of protein synthesis. The list of substrates does not include RNA exclusively since Hfq was shown to bind DNA, playing an important role in DNA compaction. Additionally, Hfq is also capable to establish many protein-protein interactions. Overall, the functions of the RNA-binding protein Hfq have been expanded beyond its function in small RNA-mediated regulation. The identification of additional substrates and new functions provides alternative explanations for the importance of the chaperone Hfq as a global regulator.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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11
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Hoekzema M, Romilly C, Holmqvist E, Wagner EGH. Hfq-dependent mRNA unfolding promotes sRNA-based inhibition of translation. EMBO J 2019; 38:embj.2018101199. [PMID: 30833291 PMCID: PMC6443205 DOI: 10.15252/embj.2018101199] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 01/11/2023] Open
Abstract
Small RNAs post‐transcriptionally regulate many processes in bacteria. Base‐pairing of sRNAs near ribosome‐binding sites in mRNAs inhibits translation, often requiring the RNA chaperone Hfq. In the canonical model, Hfq simultaneously binds sRNAs and mRNA targets to accelerate pairing. Here, we show that the Escherichia coli sRNAs OmrA and OmrB inhibit translation of the diguanylate cyclase DgcM (previously: YdaM), a player in biofilm regulation. In OmrA/B repression of dgcM, Hfq is not required as an RNA interaction platform, but rather unfolds an inhibitory RNA structure that impedes OmrA/B binding. This restructuring involves distal face binding of Hfq and is supported by RNA structure mapping. A corresponding mutant protein cannot support inhibition in vitro and in vivo; proximal and rim mutations have negligible effects. Strikingly, OmrA/B‐dependent translational inhibition in vitro is restored, in complete absence of Hfq, by a deoxyoligoribonucleotide that base‐pairs to the biochemically mapped Hfq site in dgcM mRNA. We suggest that Hfq‐dependent RNA structure remodeling can promote sRNA access, which represents a mechanism distinct from an interaction platform model.
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Affiliation(s)
- Mirthe Hoekzema
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Cédric Romilly
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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12
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Lee YJ, Kim SJ, Amrofell MB, Moon TS. Establishing a Multivariate Model for Predictable Antisense RNA-Mediated Repression. ACS Synth Biol 2019; 8:45-56. [PMID: 30517781 DOI: 10.1021/acssynbio.8b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent advances in our understanding of RNA folding and functions have facilitated the use of regulatory RNAs such as synthetic antisense RNAs (asRNAs) to modulate gene expression. However, despite the simple and universal complementarity rule, predictable asRNA-mediated repression is still challenging due to the intrinsic complexity of native asRNA-mediated gene regulation. To address this issue, we present a multivariate model, based on the change in free energy of complex formation (Δ GCF) and percent mismatch of the target binding region, which can predict synthetic asRNA-mediated repression efficiency in diverse contexts. First, 69 asRNAs that bind to multiple target mRNAs were designed and tested to create the predictive model. Second, we showed that the same model is effective predicting repression of target genes in both plasmids and chromosomes. Third, using our model, we designed asRNAs that simultaneously modulated expression of a toxin and its antitoxin to demonstrate tunable control of cell growth. Fourth, we tested and validated the same model in two different biotechnologically important organisms: Escherichia coli Nissle 1917 and Bacillus subtilis 168. Last, multiple parameters, including target locations, the presence of an Hfq binding site, GC contents, and gene expression levels, were revisited to define the conditions under which the multivariate model should be used for accurate prediction. Together, 434 different strain-asRNA combinations were tested, validating the predictive model in a variety of contexts, including multiple target genes and organisms. The result presented in this study is an important step toward achieving predictable tunability of asRNA-mediated repression.
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Affiliation(s)
- Young Je Lee
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Soo-Jung Kim
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew B. Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Kwiatkowska J, Wroblewska Z, Johnson KA, Olejniczak M. The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs. RNA (NEW YORK, N.Y.) 2018; 24:1761-1784. [PMID: 30217864 PMCID: PMC6239178 DOI: 10.1261/rna.067777.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/07/2018] [Indexed: 05/08/2023]
Abstract
MgrR is an Hfq-dependent sRNA, whose transcription is controlled by the level of Mg2+ ions in Escherichia coli MgrR belongs to Class II sRNAs because its stability in the cell is affected by mutations in Hfq differently than canonical, Class I sRNAs. Here, we examined the effect of mutations in RNA binding sites of Hfq on the kinetics of the annealing of MgrR to two different target mRNAs, eptB and ygdQ, by global data fitting of the reaction kinetics monitored by gel electrophoresis of intermediates and products. The data showed that the mutation on the rim of the Hfq ring trapped MgrR on Hfq preventing the annealing of MgrR to either mRNA. The mutation in the distal face slowed the ternary complex formation and affected the release of MgrR-mRNA complexes from Hfq, while the mutation in the proximal face weakened the MgrR binding to Hfq and in this way affected the annealing. Moreover, competition assays established that MgrR bound to both faces of Hfq and competed against other sRNAs. Further studies showed that uridine-rich sequences located in less structurally stable regions served as Hfq binding sites in each mRNA. Overall, the data show that the binding of MgrR sRNA to both faces of the Hfq ring enables it to efficiently anneal to target mRNAs. It also confers on MgrR a competitive advantage over other sRNAs, which could contribute to efficient cellular response to changes in magnesium homeostasis.
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Affiliation(s)
- Joanna Kwiatkowska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Zuzanna Wroblewska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Kenneth A Johnson
- Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
| | - Mikolaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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14
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Wang C, Pu T, Lou W, Wang Y, Gao Z, Hu B, Fan J. Hfq, a RNA Chaperone, Contributes to Virulence by Regulating Plant Cell Wall-Degrading Enzyme Production, Type VI Secretion System Expression, Bacterial Competition, and Suppressing Host Defense Response in Pectobacterium carotovorum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1166-1178. [PMID: 30198820 DOI: 10.1094/mpmi-12-17-0303-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hfq is a RNA chaperone and participates in a wide range of cellular processes and pathways. In this study, mutation of hfq gene from Pectobacterium carotovorum subsp. carotovorum PccS1 led to significantly reduced virulence and plant cell wall-degrading enzyme (PCWDE) activities. In addition, the mutant exhibited decreased biofilm formation and motility and greatly attenuated carbapenem production as well as secretion of hemolysin coregulated protein (Hcp) as compared with wild-type strain PccS1. Moreover, a higher level of callose deposition was induced in Nicotiana benthamiana leaves when infiltrated with the mutant. A total of 26 small (s)RNA deletion mutants were obtained among a predicted 27 sRNAs, and three mutants exhibited reduced virulence in the host plant. These results suggest that hfq plays a key role in Pectobacterium virulence by positively impacting PCWDE production, secretion of the type VI secretion system, bacterial competition, and suppression of host plant responses.
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Affiliation(s)
- Chunting Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianxin Pu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangying Lou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujie Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zishu Gao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Baishi Hu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaqin Fan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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15
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Kim J, Mannaa M, Kim N, Lee C, Kim J, Park J, Lee HH, Seo YS. The Roles of Two hfq Genes in the Virulence and Stress Resistance of Burkholderia glumae. THE PLANT PATHOLOGY JOURNAL 2018; 34:412-425. [PMID: 30369851 PMCID: PMC6200039 DOI: 10.5423/ppj.oa.06.2018.0097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/09/2018] [Accepted: 07/22/2018] [Indexed: 05/08/2023]
Abstract
The Hfq protein is a global small RNA chaperone that interacts with regulatory bacterial small RNAs (sRNA) and plays a role in the post-transcriptional regulation of gene expression. The roles of Hfq in the virulence and pathogenicity of several infectious bacteria have been reported. This study was conducted to elucidate the functions of two hfq genes in Burkholderia glumae, a causal agent of rice grain rot. Therefore, mutant strains of the rice-pathogenic B. glumae BGR1, targeting each of the two hfq genes, as well as the double defective mutant were constructed and tested for several phenotypic characteristics. Bacterial swarming motility, toxoflavin production, virulence in rice, siderophore production, sensitivity to H2O2, and lipase production assays were conducted to compare the mutant strains with the wild-type B. glumae BGR1 and complementation strains. The hfq1 gene showed more influence on bacterial motility and toxoflavin production than the hfq2 gene. Both genes were involved in the full virulence of B. glumae in rice plants. Other biochemical characteristics such as siderophore production and sensitivity to H2O2 induced oxidative stress were also found to be regulated by the hfq1 gene. However, lipase activity was shown to be unassociated with both tested genes. To the best of our knowledge, this is the first study to elucidate the functions of two hfq genes in B. glumae. Identification of virulence-related factors in B. glumae will facilitate the development of efficient control measures.
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Affiliation(s)
| | | | - Namgyu Kim
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Chaeyeong Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Juyun Kim
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
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16
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Tello M, Avalos F, Orellana O. Codon usage and modular interactions between messenger RNA coding regions and small RNAs in Escherichia coli. BMC Genomics 2018; 19:657. [PMID: 30189833 PMCID: PMC6127932 DOI: 10.1186/s12864-018-5038-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/27/2018] [Indexed: 01/04/2023] Open
Abstract
Background Small RNAs (sRNAs) are key regulators of gene expression in bacteria. In addition to modulating translation initiation, sRNAs can interact with mRNA coding regions to regulate mRNA stability and translation efficiency, enhancing or impeding progression of the ribosome along the mRNA. Since most amino acids are decoded by more than one codon (synonymous) we asked as to whether there is a codon bias in the interaction of sRNAs with coding regions of mRNAs. Therefore, we explored whether there are differences in codon usage or tRNA availability according to whether an mRNA is regulated by sRNAs or not. We also explored these parameters in the coding interaction regions in mRNAs. We focused our analysis on sRNAs that regulate multiple mRNAs. Results We found differences in codon adaptation index and tRNA adaptation index between sRNA-regulated and non-sRNA-regulated mRNAs. Interestingly, the sRNA-mRNA interacting regions tended to be enriched in unpreferred codons decoded by scarce tRNAs. We also found that sRNAs with multiple targets often contained modular segments capable of recognizing conserved motifs among these mRNAs. Conclusions Our results show that sRNAs in E. coli tend to recognize mRNA coding regions in which the ribosome is predicted to advance at low speeds. Identified motifs in interacting regions are conserved among mRNAs that are recognized by the same sRNA. Electronic supplementary material The online version of this article (10.1186/s12864-018-5038-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mario Tello
- Centro de Biotecnología Acuícola, Departamento de Biología, Universidad de Santiago de Chile, Alameda 3363, 9170022, Estación Central, Chile
| | - Felipe Avalos
- Centro de Biotecnología Acuícola, Departamento de Biología, Universidad de Santiago de Chile, Alameda 3363, 9170022, Estación Central, Chile
| | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina Universidad de Chile. Independencia 1027, 8380453, Santiago, Chile.
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17
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Andrade JM, Dos Santos RF, Chelysheva I, Ignatova Z, Arraiano CM. The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity. EMBO J 2018; 37:embj.201797631. [PMID: 29669858 DOI: 10.15252/embj.201797631] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 02/28/2018] [Accepted: 03/13/2018] [Indexed: 11/09/2022] Open
Abstract
Ribosome biogenesis is a complex process involving multiple factors. Here, we show that the widely conserved RNA chaperone Hfq, which can regulate sRNA-mRNA basepairing, plays a critical role in rRNA processing and ribosome assembly in Escherichia coli Hfq binds the 17S rRNA precursor and facilitates its correct processing and folding to mature 16S rRNA Hfq assists ribosome assembly and associates with pre-30S particles but not with mature 30S subunits. Inactivation of Hfq strikingly decreases the pool of mature 70S ribosomes. The reduction in ribosome levels depends on residues located in the distal face of Hfq but not on residues found in the proximal and rim surfaces which govern interactions with the sRNAs. Our results indicate that Hfq-mediated regulation of ribosomes is independent of its function as sRNA-regulator. Furthermore, we observed that inactivation of Hfq compromises translation efficiency and fidelity, both features of aberrantly assembled ribosomes. Our work expands the functions of the Sm-like protein Hfq beyond its function in small RNA-mediated regulation and unveils a novel role of Hfq as crucial in ribosome biogenesis and translation.
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Affiliation(s)
- José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Irina Chelysheva
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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18
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Identification of New Bacterial Small RNA Targets Using MS2 Affinity Purification Coupled to RNA Sequencing. Methods Mol Biol 2018; 1737:77-88. [PMID: 29484588 DOI: 10.1007/978-1-4939-7634-8_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small regulatory RNAs (sRNAs) are ubiquitous regulatory molecules expressed in living cells. In prokaryotes, sRNAs usually bind to target mRNAs to either promote their degradation or interfere with translation initiation. Because a single sRNA can regulate a considerable number of target mRNAs, we seek to identify those targets rapidly and reliably. Here, we present a robust method based on the co-purification of target mRNAs bound to MS2-tagged sRNAs expressed in vivo. After purification of the tagged-sRNA, we use RNAseq to determine the identity of all RNA interacting partners and their enrichment level. We describe how to analyze the RNAseq data through the Galaxy Project Platform bioinformatics tools to identify new mRNA targets. This technique is applicable to most sRNAs of E. coli and Salmonella.
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19
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van der Feltz C, DeHaven AC, Hoskins AA. Stress-induced Pseudouridylation Alters the Structural Equilibrium of Yeast U2 snRNA Stem II. J Mol Biol 2017; 430:524-536. [PMID: 29079482 DOI: 10.1016/j.jmb.2017.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/09/2017] [Accepted: 10/14/2017] [Indexed: 12/21/2022]
Abstract
In yeast, the U2 small nuclear ribonucleic acid (snRNA) component of the spliceosome is targeted for additional post-transcriptional modifications in response to cellular stress. Uridines 56 and 93 are both modified to pseudouridines (Ψ) during nutrient deprivation, while U56 is also pseudouridylated during heat shock. Both positions are located within stem II, which must toggle between two mutually exclusive structures during splicing. Stem IIa forms during spliceosome assembly, and stem IIc forms during the catalytic steps. We have studied how uridine 56 and 93 pseudouridylation impacts conformational switching of stem II. Using single-molecule Förster resonance energy transfer, we show that Ψ56 dampens conformational dynamics of stem II and stabilizes stem IIc. In contrast, Ψ93 increases dynamics of non-stem IIc conformations. Pseudouridylation impacts conformational switching of stem II by Mg2+ or the U2 protein Cus2; however, when Mg2+ and Cus2 are used in combination, the impacts of pseudouridylation can be suppressed. These results show that stress-induced post-transcriptional modification of U56 and U93 alters snRNA conformational dynamics by distinct mechanisms and that protein and metal cofactors of the spliceosome alter how snRNAs respond to these modifications.
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Affiliation(s)
- Clarisse van der Feltz
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA
| | - Alexander C DeHaven
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA.
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20
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Olejniczak M, Storz G. ProQ/FinO-domain proteins: another ubiquitous family of RNA matchmakers? Mol Microbiol 2017; 104:905-915. [PMID: 28370625 DOI: 10.1111/mmi.13679] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2017] [Indexed: 02/02/2023]
Abstract
Small RNAs (sRNAs), particularly those that act by limited base pairing with mRNAs, are part of most regulatory networks in bacteria. In many cases, the base-pairing interaction is facilitated by the RNA chaperone Hfq. However, not all bacteria encode Hfq and some base-pairing sRNAs do not require Hfq raising the possibility of other RNA chaperones. Candidates are proteins with homology to FinO, a factor that promotes base pairing between the FinP antisense sRNA and the traJ mRNA to control F plasmid transfer. Recent papers have shown that the Salmonella enterica FinO-domain protein ProQ binds a large suite of sRNAs, including the RaiZ sRNA, which represses translation of the hupA mRNA, and the Legionella pneumophila protein RocC binds the RocR sRNA, which blocks expression of competence genes. Here we discuss what is known about FinO-domain structures, including the recently solved Escherichia coli ProQ structure, as well as the RNA binding properties of this family of proteins and evidence they act as chaperones. We compare these properties with those of Hfq. We further summarize what is known about the physiological roles of FinO-domain proteins and enumerate outstanding questions whose answers will establish whether they constitute a second major class of RNA chaperones.
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Affiliation(s)
- Mikolaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan, 61-614, Poland
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institutes of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
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