1
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Feng R, Chen Y, Chen T, Hu Z, Peng T. DUF1127-containing protein and ProQ had opposite effects on biofilm formation in Vibrio alginolyticus. BMC Microbiol 2024; 24:330. [PMID: 39244528 PMCID: PMC11380419 DOI: 10.1186/s12866-024-03486-z] [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: 06/11/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024] Open
Abstract
The RNA binding protein is crucial for gene regulation at the post transcription level. In this study, functions of the DUF1127-containing protein and ProQ, which are RNA-binding proteins, were revealed in Vibrio alginolyticus. DUF1127 deletion increased the ability of biofilm formation, whereas ProQ deletion reduced the amount of biofilm. Moreover, extracellular proteinase secretion was significantly reduced in the DUF1127 deletion strain. ProQ, not DUF1127-containing protein, can help the cell to defense oxidative stress. Deletion of DUF1127 resulted in a higher ROS level in the cell, however, ProQ deletion showed no difference. RNA-seq unveiled the expression of genes involved in extracellular protease secretion were significantly downregulated and biofilm synthesis-related genes, such as rbsB and alsS, were differentially expressed in the DUF1127 deletion strain. ProQ affected the expression of genes involved in biofilm synthesis (flgC and flgE), virulence (betB and hutG), and oxidative stress. Moreover, the DUF1127-containing and ProQ affected the mRNA levels of various regulators, such as LysR and BetI. Overall, our study revealed that the DUF1127-containing protein and ProQ have crucial functions on biofilm formation in V. alginolyticus.
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Affiliation(s)
- Ruonan Feng
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China
| | - Ying Chen
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China
| | - Tongxian Chen
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China
- Dongguan Nancheng Business District North School, Dongguan, 523000, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China
| | - Tao Peng
- School of Resources and Environmental Engineering, Jiangsu University of Technology, 1801 Zhongwu Avenue, Changzhou, 213001, China.
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China.
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2
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Morón Á, Ortiz-Miravalles L, Peñalver M, García-Del Portillo F, Pucciarelli MG, Ortega AD. Rli51 Attenuates Transcription of the Listeria Pathogenicity Island 1 Gene mpl and Functions as a Trans-Acting sRNA in Intracellular Bacteria. Int J Mol Sci 2024; 25:9380. [PMID: 39273334 PMCID: PMC11394854 DOI: 10.3390/ijms25179380] [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: 07/25/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Listeria pathogenicity island 1 (LIPI-1) is a genetic region containing a cluster of genes essential for virulence of the bacterial pathogen Listeria monocytogenes. Main virulence factors in LIPI-1 include long 5' untranslated regions (5'UTRs), among which is Rli51, a small RNA (sRNA) in the 5'UTR of the Zn-metalloprotease-coding mpl. So far, Rli51 function and molecular mechanisms have remained obscure. Here, we show that Rli51 exhibits a dual mechanism of regulation, functioning as a cis- and as a trans-acting sRNA. Under nutrient-rich conditions, rli51-mpl transcription is prematurely terminated, releasing a short 121-nucleotide-long sRNA. Rli51 is predicted to function as a transcription attenuator that can fold into either a terminator or a thermodynamically more stable antiterminator. We show that the sRNA Rli21/RliI binds to a single-stranded RNA loop in Rli51, which is essential to mediate premature transcription termination, suggesting that sRNA binding could stabilize the terminator fold. During intracellular infection, rli51 transcription is increased, which generates a higher abundance of the short Rli51 sRNA and allows for transcriptional read-through into mpl. Comparative intracellular bacterial transcriptomics in rli51-null mutants and the wild-type reference strain EGD-e suggests that Rli51 upregulates iron-scavenging proteins and downregulates virulence factors from LIPI-1. MS2 affinity purification confirmed that Rli51 binds transcripts of the heme-binding protein Lmo2186 and Lmo0937 in vivo. These results prove that Rli51 functions as a trans-acting sRNA in intracellular bacteria. Our research shows a growth condition-dependent mechanism of regulation for Rli51, preventing unintended mpl transcription in extracellular bacteria and regulating genes important for virulence in intracellular bacteria.
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Affiliation(s)
- Álvaro Morón
- Department of Cell Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
| | - Laura Ortiz-Miravalles
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
| | - Marcos Peñalver
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
| | | | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
| | - Alvaro Darío Ortega
- Department of Cell Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
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3
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Goh KJ, Altuvia Y, Argaman L, Raz Y, Bar A, Lithgow T, Margalit H, Gan YH. RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae. Nucleic Acids Res 2024; 52:9119-9138. [PMID: 38804271 PMCID: PMC11347178 DOI: 10.1093/nar/gkae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) can infect healthy individuals, in contrast to classical strains that commonly cause nosocomial infections. The recent convergence of hypervirulence with carbapenem-resistance in K. pneumoniae can potentially create 'superbugs' that are challenging to treat. Understanding virulence regulation of hvKp is thus critical. Accumulating evidence suggest that posttranscriptional regulation by small RNAs (sRNAs) plays a role in bacterial virulence, but it has hardly been studied in K. pneumoniae. We applied RIL-seq to a prototypical clinical isolate of hvKp to unravel the Hfq-dependent RNA-RNA interaction (RRI) network. The RRI network is dominated by sRNAs, including predicted novel sRNAs, three of which we validated experimentally. We constructed a stringent subnetwork composed of RRIs that involve at least one hvKp virulence-associated gene and identified the capsule gene loci as a hub target where multiple sRNAs interact. We found that the sRNA OmrB suppressed both capsule production and hypermucoviscosity when overexpressed. Furthermore, OmrB base-pairs within kvrA coding region and partially suppresses translation of the capsule regulator KvrA. This agrees with current understanding of capsule as a major virulence and fitness factor. It emphasizes the intricate regulatory control of bacterial phenotypes by sRNAs, particularly of genes critical to bacterial physiology and virulence.
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Affiliation(s)
- Kwok Jian Goh
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Yael Altuvia
- 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
| | - Yair Raz
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - 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
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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4
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Hamrock FJ, Ryan D, Shaibah A, Ershova AS, Mogre A, Sulimani MM, Ben Taarit S, Reichardt S, Hokamp K, Westermann AJ, Kröger C. Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO. Nucleic Acids Res 2024:gkae668. [PMID: 39149883 DOI: 10.1093/nar/gkae668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies. Critical to adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. Forty sRNAs were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii. In-depth characterization uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including the transcript encoding outer membrane protein CarO. Aar initiates base-pairing with these mRNAs using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in multiple stress conditions suggesting a role in fine-tuning translation of the Aar-target molecules. Our study provides mechanistic insights into sRNA-mediated gene regulation in A. baumannii and represents a valuable resource for future RNA-centric research endeavours.
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Affiliation(s)
- Fergal J Hamrock
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Daniel Ryan
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
| | - Ali Shaibah
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Anna S Ershova
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aalap Mogre
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Maha M Sulimani
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Safa Ben Taarit
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Alexander J Westermann
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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Wei Y, Xin X, Zhang J, Liao Q, Rong Y, Zhong Y, Zhao M, Ma J, He S. Genome-wide sRNA and mRNA transcriptomic profiling insights into carbapenem-resistant Acinetobacter baumannii. Front Cell Infect Microbiol 2024; 14:1419989. [PMID: 39220286 PMCID: PMC11362675 DOI: 10.3389/fcimb.2024.1419989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Acinetobacter baumannii (AB) is rising as a human pathogen of critical priority worldwide as it is the leading cause of opportunistic infections in healthcare settings and carbapenem-resistant AB is listed as a "super bacterium" or "priority pathogen for drug resistance" by the World Health Organization. Methods Clinical isolates of A. baumannii were collected and tested for antimicrobial susceptibility. Among them, carbapenem-resistant and carbapenem-sensitive A. baumannii were subjected to prokaryotic transcriptome sequencing. The change of sRNA and mRNA expression was analyzed by bioinformatics and validated by quantitative reverse transcription-PCR. Results A total of 687 clinical isolates were collected, of which 336 strains of A. baumannii were resistant to carbapenem. Five hundred and six differentially expressed genes and nineteen differentially expressed sRNA candidates were discovered through transcriptomic profile analysis between carbapenem-resistant isolates and carbapenem-sensitive isolates. Possible binding sites were predicted through software for sRNA21 and adeK, sRNA27 and pgaC, sRNA29 and adeB, sRNA36 and katG, indicating a possible targeting relationship. A negative correlation was shown between sRNA21 and adeK (r = -0.581, P = 0.007), sRNA27 and pgaC (r = -0.612, P = 0.004), sRNA29 and adeB (r = -0.516, P = 0.020). Discussion This study preliminarily screened differentially expressed mRNA and sRNA in carbapenem-resistant A. baumannii, and explored possible targeting relationships, which will help further reveal the resistance mechanism and provide a theoretical basis for the development of drugs targeting sRNA for the prevention and treatment of carbapenem-resistant A. baumannii infection.
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Affiliation(s)
- Yong Wei
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Xuli Xin
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Jiachun Zhang
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Qifeng Liao
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Yan Rong
- Department of Pulmonary and Critical Care Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Ying Zhong
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Meiying Zhao
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Jianping Ma
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Song He
- Department of Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
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6
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Rios-Delgado G, McReynolds AKG, Pagella EA, Norambuena J, Briaud P, Zheng V, Munneke MJ, Kim J, Racine H, Carroll R, Zelzion E, Skaar E, Bose JL, Parker D, Lalaouna D, Boyd JM. The Staphylococcus aureus small non-coding RNA IsrR regulates TCA cycle activity and virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601953. [PMID: 39005296 PMCID: PMC11245030 DOI: 10.1101/2024.07.03.601953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Staphylococcus aureus has evolved mechanisms to cope with low iron (Fe) availability in host tissues. S. aureus uses the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that an S. aureus Δfur mutant has decreased expression of acnA, which codes for the Fe-dependent enzyme aconitase. Decreased acnA expression prevented the Δfur mutant from growing with amino acids as sole carbon and energy sources. Suppressor analysis determined that a mutation in isrR, which produces a regulatory RNA, permitted growth by decreasing isrR transcription. The decreased AcnA activity of the Δfur mutant was partially relieved by an ΔisrR mutation. Directed mutation of bases predicted to facilitate the interaction between the acnA transcript and IsrR, decreased the ability of IsrR to control acnA expression in vivo and IsrR bound to the acnA transcript in vitro. IsrR also bound to the transcripts coding the alternate TCA cycle proteins sdhC, mqo, citZ, and citM. Whole cell metal analyses suggest that IsrR promotes Fe uptake and increases intracellular Fe not ligated by macromolecules. Lastly, we determined that Fur and IsrR promote infection using murine skin and acute pneumonia models.
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Affiliation(s)
- Gustavo Rios-Delgado
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Aubrey K. G. McReynolds
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kanas City, KS, 66103, USA
| | - Emma A. Pagella
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kanas City, KS, 66103, USA
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Paul Briaud
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Vincent Zheng
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Matthew J. Munneke
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jisun Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, 07103, USA
| | - Hugo Racine
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, Strasbourg, 67000, France
| | - Ronan Carroll
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Ehud Zelzion
- Office of Advanced Research Computing, Rutgers University, 96 Frelinghuysen Road Piscataway, NJ 08854, USA
| | - Eric Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jeffrey L. Bose
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kanas City, KS, 66103, USA
| | - Dane Parker
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, 07103, USA
| | - David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, Strasbourg, 67000, France
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901, USA
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DeSouza NR, Jarboe T, Carnazza M, Quaranto D, Islam HK, Tiwari RK, Geliebter J. Long Non-Coding RNAs as Determinants of Thyroid Cancer Phenotypes: Investigating Differential Gene Expression Patterns and Novel Biomarker Discovery. BIOLOGY 2024; 13:304. [PMID: 38785786 PMCID: PMC11118935 DOI: 10.3390/biology13050304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Thyroid Cancer (TC) is the most common endocrine malignancy, with increasing incidence globally. Papillary thyroid cancer (PTC), a differentiated form of TC, accounts for approximately 90% of TC and occurs predominantly in women of childbearing age. Although responsive to current treatments, recurrence of PTC by middle age is common and is much more refractive to treatment. Undifferentiated TC, particularly anaplastic thyroid cancer (ATC), is the most aggressive TC subtype, characterized by it being resistant and unresponsive to all therapeutic and surgical interventions. Further, ATC is one of the most aggressive and lethal malignancies across all cancer types. Despite the differences in therapeutic needs in differentiated vs. undifferentiated TC subtypes, there is a critical unmet need for the identification of molecular biomarkers that can aid in early diagnosis, prognosis, and actionable therapeutic targets for intervention. Advances in the field of cancer genomics have enabled for the elucidation of differential gene expression patterns between tumors and healthy tissue. A novel category of molecules, known as non-coding RNAs, can themselves be differentially expressed, and extensively contribute to the up- and downregulation of protein coding genes, serving as master orchestrators of regulated and dysregulated gene expression patterns. These non-coding RNAs have been identified for their roles in driving carcinogenic patterns at various stages of tumor development and have become attractive targets for study. The identification of specific genes that are differentially expressed can give insight into mechanisms that drive carcinogenic patterns, filling the gaps of deciphering molecular and cellular processes that modulate TC subtypes, outside of well-known driver mutations.
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Affiliation(s)
- Nicole R. DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.); (T.J.); (H.K.I.); (R.K.T.)
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.); (T.J.); (H.K.I.); (R.K.T.)
| | - Michelle Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.); (T.J.); (H.K.I.); (R.K.T.)
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.); (T.J.); (H.K.I.); (R.K.T.)
| | - Humayun K. Islam
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.); (T.J.); (H.K.I.); (R.K.T.)
| | - Raj K. Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.); (T.J.); (H.K.I.); (R.K.T.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.); (T.J.); (H.K.I.); (R.K.T.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
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8
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Lozano-Velasco E, Inácio JM, Sousa I, Guimarães AR, Franco D, Moura G, Belo JA. miRNAs in Heart Development and Disease. Int J Mol Sci 2024; 25:1673. [PMID: 38338950 PMCID: PMC10855082 DOI: 10.3390/ijms25031673] [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: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Cardiovascular diseases (CVD) are a group of disorders that affect the heart and blood vessels. They include conditions such as myocardial infarction, coronary artery disease, heart failure, arrhythmia, and congenital heart defects. CVDs are the leading cause of death worldwide. Therefore, new medical interventions that aim to prevent, treat, or manage CVDs are of prime importance. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the posttranscriptional level and play important roles in various biological processes, including cardiac development, function, and disease. Moreover, miRNAs can also act as biomarkers and therapeutic targets. In order to identify and characterize miRNAs and their target genes, scientists take advantage of computational tools such as bioinformatic algorithms, which can also assist in analyzing miRNA expression profiles, functions, and interactions in different cardiac conditions. Indeed, the combination of miRNA research and bioinformatic algorithms has opened new avenues for understanding and treating CVDs. In this review, we summarize the current knowledge on the roles of miRNAs in cardiac development and CVDs, discuss the challenges and opportunities, and provide some examples of recent bioinformatics for miRNA research in cardiovascular biology and medicine.
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Affiliation(s)
- Estefania Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (D.F.)
| | - José Manuel Inácio
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
| | - Inês Sousa
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - Ana Rita Guimarães
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (D.F.)
| | - Gabriela Moura
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - José António Belo
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
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9
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Srivastava M, Dukeshire MR, Mir Q, Omoru OB, Manzourolajdad A, Janga SC. Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes. Brief Funct Genomics 2024; 23:46-54. [PMID: 36752040 PMCID: PMC10799312 DOI: 10.1093/bfgp/elac050] [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: 09/06/2022] [Revised: 10/24/2022] [Accepted: 11/11/2022] [Indexed: 02/09/2023] Open
Abstract
Long-range ribonucleic acid (RNA)-RNA interactions (RRI) are prevalent in positive-strand RNA viruses, including Beta-coronaviruses, and these take part in regulatory roles, including the regulation of sub-genomic RNA production rates. Crosslinking of interacting RNAs and short read-based deep sequencing of resulting RNA-RNA hybrids have shown that these long-range structures exist in severe acute respiratory syndrome coronavirus (SARS-CoV)-2 on both genomic and sub-genomic levels and in dynamic topologies. Furthermore, co-evolution of coronaviruses with their hosts is navigated by genetic variations made possible by its large genome, high recombination frequency and a high mutation rate. SARS-CoV-2's mutations are known to occur spontaneously during replication, and thousands of aggregate mutations have been reported since the emergence of the virus. Although many long-range RRIs have been experimentally identified using high-throughput methods for the wild-type SARS-CoV-2 strain, evolutionary trajectory of these RRIs across variants, impact of mutations on RRIs and interaction of SARS-CoV-2 RNAs with the host have been largely open questions in the field. In this review, we summarize recent computational tools and experimental methods that have been enabling the mapping of RRIs in viral genomes, with a specific focus on SARS-CoV-2. We also present available informatics resources to navigate the RRI maps and shed light on the impact of mutations on the RRI space in viral genomes. Investigating the evolution of long-range RNA interactions and that of virus-host interactions can contribute to the understanding of new and emerging variants as well as aid in developing improved RNA therapeutics critical for combating future outbreaks.
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Affiliation(s)
- Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Biology, Indiana University, 1001 East 3 St, Bloomington, Indiana 47405, USA
| | - Matthew R Dukeshire
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Okiemute Beatrice Omoru
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Amirhossein Manzourolajdad
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Computer Science, Colgate University, Hamilton, NY, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, Indiana 46202, USA
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana 46202, USA
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10
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Viering B, Balogh H, Cox CF, Kirpekar OK, Akers AL, Federico VA, Valenzano GZ, Stempel R, Pickett HL, Lundin PM, Blackledge MS, Miller HB. Loratadine Combats Methicillin-Resistant Staphylococcus aureus by Modulating Virulence, Antibiotic Resistance, and Biofilm Genes. ACS Infect Dis 2024; 10:232-250. [PMID: 38153409 PMCID: PMC10788911 DOI: 10.1021/acsinfecdis.3c00616] [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: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has evolved to become resistant to multiple classes of antibiotics. New antibiotics are costly to develop and deploy, and they have a limited effective lifespan. Antibiotic adjuvants are molecules that potentiate existing antibiotics through nontoxic mechanisms. We previously reported that loratadine, the active ingredient in Claritin, potentiates multiple cell-wall active antibiotics in vitro and disrupts biofilm formation through a hypothesized inhibition of the master regulatory kinase Stk1. Loratadine and oxacillin combined repressed the expression of key antibiotic resistance genes in the bla and mec operons. We hypothesized that additional genes involved in antibiotic resistance, biofilm formation, and other cellular pathways would be modulated when looking transcriptome-wide. To test this, we used RNA-seq to quantify transcript levels and found significant effects in gene expression, including genes controlling virulence, antibiotic resistance, metabolism, transcription (core RNA polymerase subunits and sigma factors), and translation (a plethora of genes encoding ribosomal proteins and elongation factor Tu). We further demonstrated the impacts of these transcriptional effects by investigating loratadine treatment on intracellular ATP levels, persister formation, and biofilm formation and morphology. Loratadine minimized biofilm formation in vitro and enhanced the survival of infected Caenorhabditis elegans. These pleiotropic effects and their demonstrated outcomes on MRSA virulence and survival phenotypes position loratadine as an attractive anti-infective against MRSA.
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Affiliation(s)
- Brianna
L. Viering
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Halie Balogh
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Chloe F. Cox
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Owee K. Kirpekar
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - A. Luke Akers
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Victoria A. Federico
- Department
of Biology, High Point University, High Point, North Carolina 27268, United States
| | - Gabriel Z. Valenzano
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Robin Stempel
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Hannah L. Pickett
- Department
of Biology, High Point University, High Point, North Carolina 27268, United States
| | - Pamela M. Lundin
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Meghan S. Blackledge
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Heather B. Miller
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
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11
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Li N, Yao S, Yu G, Lu L, Wang Z. tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments. Nucleic Acids Res 2024; 52:D345-D350. [PMID: 37811890 PMCID: PMC10767876 DOI: 10.1093/nar/gkad815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/22/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
tRFtarget 1.0 (http://trftarget.net/) is a platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments (tRFs) and target genes (or transcripts) across multiple organisms. Here, we introduce a newly released version of tRFtarget 2.0, in which we integrated 6 additional tRF sources, resulting in a comprehensive collection of 2614 high-quality tRF sequences spanning across 9 species, including 1944 Homo sapiens tRFs and one newly incorporated species Rattus norvegicus. We also expanded target genes by including ribosomal RNAs, long non-coding RNAs, and coding genes >50 kb in length. The predicted binding sites have surged up to approximately 6 billion, a 20.5-fold increase than that in tRFtarget 1.0. The manually curated publications relevant to tRF targets have increased to 400 and the gene-level experimental evidence has risen to 232. tRFtarget 2.0 introduces several new features, including a web-based tool that identifies potential binding sites of tRFs in user's own datasets, integration of standardized tRF IDs, and inclusion of external links to contents within the database. Additionally, we enhanced website framework and user interface. With these improvements, tRFtarget 2.0 is more user-friendly, providing researchers a streamlined and comprehensive platform to accelerate their research progress.
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Affiliation(s)
- Ningshan Li
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong 518172, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Siqiong Yao
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- SJTU-Yale Joint Center of Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangjun Yu
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong 518172, China
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
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12
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Raden M, Miladi M. How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA. Methods Mol Biol 2024; 2726:209-234. [PMID: 38780733 DOI: 10.1007/978-1-0716-3519-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Computational prediction of RNA-RNA interactions (RRI) is a central methodology for the specific investigation of inter-molecular RNA interactions and regulatory effects of non-coding RNAs like eukaryotic microRNAs or prokaryotic small RNAs. Available methods can be classified according to their underlying prediction strategies, each implicating specific capabilities and restrictions often not transparent to the non-expert user. Within this work, we review seven classes of RRI prediction strategies and discuss the advantages and limitations of respective tools, since such knowledge is essential for selecting the right tool in the first place.Among the RRI prediction strategies, accessibility-based approaches have been shown to provide the most reliable predictions. Here, we describe how IntaRNA, as one of the state-of-the-art accessibility-based tools, can be applied in various use cases for the task of computational RRI prediction. Detailed hands-on examples for individual RRI predictions as well as large-scale target prediction scenarios are provided. We illustrate the flexibility and capabilities of IntaRNA through the examples. Each example is designed using real-life data from the literature and is accompanied by instructions on interpreting the respective results from IntaRNA output. Our use-case driven instructions enable non-expert users to comprehensively understand and utilize IntaRNA's features for effective RRI predictions.
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Affiliation(s)
- Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany.
| | - Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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13
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Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods Mol Biol 2024; 2802:347-393. [PMID: 38819565 DOI: 10.1007/978-1-0716-3838-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Over the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large-scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible non-coding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of non-coding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Bioinformatics and Computational Biology research group, University of Vienna, Vienna, Austria
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
- Universidad National de Colombia, Bogotá, Colombia.
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.
- Santa Fe Institute, Santa Fe, NM, USA.
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14
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Ul Haq I, Müller P, Brantl S. Investigation of sRNA-mRNA Interactions in Bacillus subtilis In Vivo. Methods Mol Biol 2024; 2741:117-144. [PMID: 38217651 DOI: 10.1007/978-1-0716-3565-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
In this chapter, we describe in vivo methods for the analysis of interactions between an sRNA and its target mRNA in B. subtilis. All these methods have been either established or significantly improved in our group and successfully employed to characterize a number of sRNA/target mRNA systems in Bacillus subtilis. Whereas in Chap. 8, we describe a combination of in vitro methods, e.g., EMSA and RNA secondary structure probing, we focus here on the investigation of RNA-RNA interactions in vivo using compatible plasmids or chromosomal insertions and deletions, the elucidation of the mechanisms of action of regulatory sRNAs employing transcriptional and translational reporter gene fusions, as well as the determination of expression profiles, half-lives of sRNA and mRNA, and their intracellular concentrations, and, finally, the investigation of RNA chaperones that promote the sRNA/mRNA interaction. For an in-depth analysis of sRNA-mRNA interactions in B. subtilis, a combination of in vivo and in vitro methods should be applied.
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Affiliation(s)
- Inam Ul Haq
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Peter Müller
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Sabine Brantl
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Jena, Germany.
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15
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Lillebæk EMS, Kallipolitis BH. Experimental Validation of RNA-RNA Interactions by Electrophoretic Mobility Shift Assay. Methods Mol Biol 2024; 2741:195-206. [PMID: 38217655 DOI: 10.1007/978-1-0716-3565-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Regulatory RNAs in bacteria are known to act by base pairing with other RNAs. Interactions between two partner RNAs can be investigated by electrophoretic mobility shift assays. The regions predicted to be engaged in base pairing are analyzed by introducing mutations in one RNA that prevent RNA-RNA complex formation. Next, base pairing is restored by introducing complementary mutations in its partner RNA. Here, we describe the mutational strategy and experimental methods used to validate specific base pairing between two RNA species.
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16
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Neff SL, Hampton TH, Koeppen K, Sarkar S, Latario CJ, Ross BD, Stanton BA. Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development. mSystems 2023; 8:e0065323. [PMID: 37975659 PMCID: PMC10734502 DOI: 10.1128/msystems.00653-23] [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: 06/22/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Antimicrobial-resistant infections contribute to millions of deaths worldwide every year. In particular, the group of bacteria collectively known as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) pathogens are of considerable medical concern due to their virulence and exceptional ability to develop antibiotic resistance. New kinds of antimicrobial therapies are urgently needed to treat patients for whom existing antibiotics are ineffective. The Rocket-miR application predicts targets of human miRNAs in bacterial and fungal pathogens, rapidly identifying candidate miRNA-based antimicrobials. The application's target audience are microbiologists that have the laboratory resources to test the application's predictions. The Rocket-miR application currently supports 24 recognized human pathogens that are relevant to numerous diseases including cystic fibrosis, chronic obstructive pulmonary disease (COPD), urinary tract infections, and pneumonia. Furthermore, the application code was designed to be easily extendible to other human pathogens that commonly cause hospital-acquired infections.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Casey J. Latario
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Benjamin D. Ross
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
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17
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Tjaden B. TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning. Genome Biol 2023; 24:276. [PMID: 38041165 PMCID: PMC10691042 DOI: 10.1186/s13059-023-03117-2] [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: 06/26/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023] Open
Abstract
Small regulatory RNAs pervade prokaryotes, with the best-studied family of these non-coding genes corresponding to trans-acting regulators that bind via base pairing to their message targets. Given the increasing frequency with which these genes are being identified, it is important that methods for illuminating their regulatory targets keep pace. Using a machine learning approach, we investigate thousands of interactions between small RNAs and their targets, and we interrogate more than a hundred features indicative of these interactions. We present a new method, TargetRNA3, for predicting targets of small RNA regulators and show that it outperforms existing approaches. TargetRNA3 is available at https://cs.wellesley.edu/~btjaden/TargetRNA3 .
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Affiliation(s)
- Brian Tjaden
- Department of Computer Science, Wellesley College, Wellesley, MA, USA.
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18
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Tieng FYF, Abdullah-Zawawi MR, Md Shahri NAA, Mohamed-Hussein ZA, Lee LH, Mutalib NSA. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Brief Bioinform 2023; 25:bbad421. [PMID: 38040490 PMCID: PMC10753535 DOI: 10.1093/bib/bbad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023] Open
Abstract
RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA-RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA-RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | | | - Nur Alyaa Afifah Md Shahri
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), UKM, Selangor 43600, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, UKM, Selangor 43600, Malaysia
| | - Learn-Han Lee
- Sunway Microbiomics Centre, School of Medical and Life Sciences, Sunway University, Sunway City 47500, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, UKM, Kuala Lumpur 50300, Malaysia
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19
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Rojano-Nisimura AM, Simmons TR, Leistra AN, Mihailovic MK, Buchser R, Ekdahl AM, Joseph I, Curtis NC, Contreras LM. CsrA selectively modulates sRNA-mRNA regulator outcomes. Front Mol Biosci 2023; 10:1249528. [PMID: 38116378 PMCID: PMC10729762 DOI: 10.3389/fmolb.2023.1249528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/10/2023] [Indexed: 12/21/2023] Open
Abstract
Post-transcriptional regulation, by small RNAs (sRNAs) as well as the global Carbon Storage Regulator A (CsrA) protein, play critical roles in bacterial metabolic control and stress responses. The CsrA protein affects selective sRNA-mRNA networks, in addition to regulating transcription factors and sigma factors, providing additional avenues of cross talk between other stress-response regulators. Here, we expand the known set of sRNA-CsrA interactions and study their regulatory effects. In vitro binding assays confirm novel CsrA interactions with ten sRNAs, many of which are previously recognized as key regulatory nodes. Of those 10 sRNA, we identify that McaS, FnrS, SgrS, MicL, and Spot42 interact directly with CsrA in vivo. We find that the presence of CsrA impacts the downstream regulation of mRNA targets of the respective sRNA. In vivo evidence supports enhanced CsrA McaS-csgD mRNA repression and showcases CsrA-dependent repression of the fucP mRNA via the Spot42 sRNA. We additionally identify SgrS and FnrS as potential new sRNA sponges of CsrA. Overall, our results further support the expanding impact of the Csr system on cellular physiology via CsrA impact on the regulatory roles of these sRNAs.
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Affiliation(s)
| | - Trevor R. Simmons
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Abigail N. Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Mia K. Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Ryan Buchser
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Alyssa M. Ekdahl
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Isabella Joseph
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Nicholas C. Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Lydia M. Contreras
- Biochemistry Graduate Program, University of Texas at Austin, Austin, TX, United States
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
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20
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Wang Z, Chen M, Liu N, Zhao Y, Ru J, Qin C, Zhang T. Common and unique testosterone and 17 beta-estradiol degradation mechanisms in Comamonas testosteroni JLU460ET by transcriptome analysis. Front Microbiol 2023; 14:1238855. [PMID: 37954242 PMCID: PMC10637631 DOI: 10.3389/fmicb.2023.1238855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Strain C. testosteroni JLU460ET was isolated for testosterone and 17 beta-estradiol degradation by our group. In this study, strain C. testosteroni JLU460ET was induced by testosterone and 17 beta-estradiol and then subjected to transcriptome analysis. There were 2,047 upregulated genes after 3 h of testosterone induction, 2,040 upregulated genes after 13 h of testosterone induction, 2,078 upregulated genes after 3 h of 17 beta-estradiol induction, and 2,095 upregulated genes after 13 h of 17 beta-estradiol induction. Significantly upregulated genes were mainly involved in steroid and aromatic compound degradation. A 100 kb steroid-degrading gene cluster was found by transcriptome analysis, which included 92 annotated genes and 58 novel genes. Among them, MucB/RseB and Fiu are secretory proteins for sensing substrates in the environment. MFS-1 and TonB are transporters of testosterone and 17 beta-estradiol. Ring-cleavage enzymes and beta-oxidation enzymes are important for degradation. The genes upregulated by both substrates were almost the same, but the degree of induction by testosterone was higher than that by 17 beta-estradiol. Nine upregulated genes were selected for verification by quantitative real-time polymerase chain reaction (qRT-PCR). The qRT-PCR results were consistent with the transcriptome sequencing results. In this study, the common and unique metabolic mechanisms of testosterone and 17 beta-estradiol were compared by transcriptome analysis in C. testosteroni JLU460ET for the first time.
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Affiliation(s)
- Ze Wang
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, Jilin, China
| | - Mingming Chen
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, Jilin, China
| | - Na Liu
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Yongkang Zhao
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, Jilin, China
| | - Jintao Ru
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, Jilin, China
| | - Chuanyu Qin
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, Jilin, China
| | - Tingdi Zhang
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, Jilin, China
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21
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Zhu ZX, Liu Y, Wang J, Xie Y, Li RY, Ma Q, Tu Q, Melhem NA, Couldwell S, El-Araby RE, Tai A, Van Dyke TE, Karimbux N, Jeong YN, Chen JJ. A novel lncRNA-mediated epigenetic regulatory mechanism in periodontitis. Int J Biol Sci 2023; 19:5187-5203. [PMID: 37928259 PMCID: PMC10620817 DOI: 10.7150/ijbs.87977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/01/2023] [Indexed: 11/07/2023] Open
Abstract
Periodontitis is a highly prevalent chronic inflammatory disease with an exaggerated host immune response, resulting in periodontal tissue destruction and potential tooth loss. The long non-coding RNA, LncR-ANRIL, located on human chromosome 9p21, is recognized as a genetic risk factor for various conditions, including atherosclerosis, periodontitis, diabetes, and cancer. LncR-APDC is an ortholog of ANRIL located on mouse genome chr4. This study aims to comprehend the regulatory role of lncR-APDC in periodontitis progression. Our experimental findings, obtained from lncR-APDC gene knockout (KO) mice with induced experimental periodontitis (EP), revealed exacerbated bone loss and disrupted pro-inflammatory cytokine regulation. Downregulation of osteogenic differentiation occurred in bone marrow stem cells harvested from lncR-APDC-KO mice. Furthermore, single-cell RNA sequencing of periodontitis gingival tissue revealed alterations in the proportion and function of immune cells, including T and B cells, macrophages, and neutrophils, due to lncR-APDC silencing. Our findings also unveiled a previously unidentified epithelial cell subset that is distinctively presenting in the lncR-APDC-KO group. This epithelial subset, characterized by the positive expression of Krt8 and Krt18, engages in interactions with immune cells through a variety of ligand-receptor pairs. The expression of Tff2, now recognized for its role in chronic inflammatory conditions, exhibited a notable increase across various tissue and cell types in lncR-APDC deficient mice. Additionally, our investigation revealed the potential for a direct binding interaction between lncR-APDC and Tff2. Intra-gingival administration of AAV9-lncR-APDC was shown to have therapeutic effects in the EP model. In conclusion, our results suggest that lncR-APDC plays a critical role in the progression of periodontal disease and holds therapeutic potential for periodontitis. Furthermore, the presence of the distinctive epithelial subpopulation and significantly elevated Tff2 levels in the lncR-APDC-silenced EP model offer new perspectives on the epigenetic regulation of periodontitis pathogenesis.
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Affiliation(s)
- Zoe Xiaofang Zhu
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Yao Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jinghao Wang
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Ying Xie
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Rachel Yuantong Li
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Qian Ma
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Qisheng Tu
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Neiman A Melhem
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Sandrine Couldwell
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Rady E. El-Araby
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Albert Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
- Data Intensive Studies Center, Tufts University, Medford, MA, United States
| | - Thomas E. Van Dyke
- Clinical and Translational Research, Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Forsyth Institute, Boston, MA, United States
| | - Nadeem Karimbux
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Y. Natalie Jeong
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Jake Jinkun Chen
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
- Department of Genetics, Molecular and Cell Biology, Tufts University School of Medicine, Tufts School of Graduate Biomedical Sciences, 136 Harrison Ave, M&V Room 811, Boston, MA 02111, United States
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22
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Yu J, Qin M, Li J, Cui S. LncRNA SNHG4 sponges miR-200b to inhibit cell apoptosis in diabetic retinopathy. Arch Physiol Biochem 2023; 129:1117-1122. [PMID: 33822671 DOI: 10.1080/13813455.2021.1900873] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
This study aimed to investigate the role of long non-coding RNA (lncRNA) small nucleolar RNA host gene 4 (SNHG4) in diabetic retinopathy (DR). We found that SNHG4 was downregulated in DR. SNHG4 could directly interact with miR-200b, while overexpression of miR-200b did not affect the expression of SNHG4 in human retinal pigment epithelial cells ARPE-19. In contrast, overexpression of SNHG4 led to the upregulation of oxidation resistance 1 (Oxr1), a target of miR-200b. Cell apoptosis analysis showed that overexpression of miR-200b increased the apoptotic rate of ARPE-19 cells under high glucose treatment. Oxr1 and SNHG4 played opposite roles and reduced the effects of overexpression of miR-200b. In conclusion, SNHG4 may sponge miR-200b to inhibit cell apoptosis in DR by upregulating Oxr1.
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Affiliation(s)
- Jia Yu
- Department of Ophthalmology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, People's Republic of China
| | - Mei Qin
- Department of Ophthalmology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, People's Republic of China
| | - Juan Li
- Department of Ophthalmology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, People's Republic of China
| | - Shumin Cui
- Department of Ophthalmology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, People's Republic of China
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23
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Drummond IY, DePaolo A, Krieger M, Driscoll H, Eckstrom K, Spatafora GA. Small regulatory RNAs are mediators of the Streptococcus mutans SloR regulon. J Bacteriol 2023; 205:e0017223. [PMID: 37695854 PMCID: PMC10521355 DOI: 10.1128/jb.00172-23] [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: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
Dental caries is among the most prevalent chronic diseases worldwide. Streptococcus mutans, the chief causative agent of caries, uses a 25-kDa manganese-dependent SloR protein to coordinate the uptake of essential manganese with the transcription of its virulence attributes. Small non-coding RNAs (sRNAs) can either enhance or repress gene expression, and reports in the literature ascribe an emerging role for sRNAs in the environmental stress response. Herein, we focused our attention on 18-50 nt sRNAs as mediators of the S. mutans SloR and manganese regulons. Specifically, the results of RNA sequencing revealed 19 sRNAs in S. mutans, which were differentially transcribed in the SloR-proficient UA159 and SloR-deficient GMS584 strains, and 10 sRNAs that were differentially expressed in UA159 cells grown in the presence of low vs high manganese. We describe SmsR1532 and SmsR1785 as SloR- and manganese-responsive sRNAs that are processed from large transcripts and that bind SloR directly in their promoter regions. The predicted targets of these sRNAs include regulators of metal ion transport, growth management via a toxin-antitoxin operon, and oxidative stress tolerance. These findings support a role for sRNAs in coordinating intracellular metal ion homeostasis with virulence gene control in an important oral cariogen. IMPORTANCE Small regulatory RNAs (sRNAs) are critical mediators of environmental signaling, particularly in bacterial cells under stress, but their role in Streptococcus mutans is poorly understood. S. mutans, the principal causative agent of dental caries, uses a 25-kDa manganese-dependent protein, called SloR, to coordinate the regulated uptake of essential metal ions with the transcription of its virulence genes. In the present study, we identified and characterized sRNAs that are both SloR and manganese responsive. Taken together, this research can elucidate the details of regulatory networks that engage sRNAs in an important oral pathogen and that can enable the development of an effective anti-caries therapeutic.
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Affiliation(s)
| | | | - Madeline Krieger
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Heather Driscoll
- Department of Biology, Vermont Biomedical Research Network, Norwich University, Northfield, Vermont, USA
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, The Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, USA
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24
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Huang S, Zhang X, Song Z, Rahman MU, Fan B. Transcriptional Profiling and Transposon Mutagenesis Study of the Endophyte Pantoea eucalypti FBS135 Adapting to Nitrogen Starvation. Int J Mol Sci 2023; 24:14282. [PMID: 37762583 PMCID: PMC10532344 DOI: 10.3390/ijms241814282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The research on plant endophytes has been drawing a lot of attention in recent years. Pantoea belongs to a group of endophytes with plant growth-promoting activity and has been widely used in agricultural fields. In our earlier studies, Pantoea eucalypti FBS135 was isolated from healthy-growing Pinus massoniana and was able to promote pine growth. P. eucalypti FBS135 can grow under extremely low nitrogen conditions. To understand the mechanism of the low-nitrogen tolerance of this bacterium, the transcriptome of FBS135 in the absence of nitrogen was examined in this study. We found that FBS135 actively regulates its gene expression in response to nitrogen deficiency. Nearly half of the number (4475) of genes in FBS135 were differentially expressed under this condition, mostly downregulated, while it significantly upregulated many transportation-associated genes and some nitrogen metabolism-related genes. In the downregulated genes, the ribosome pathway-related ones were significantly enriched. Meanwhile, we constructed a Tn5 transposon library of FBS135, from which four genes involved in low-nitrogen tolerance were screened out, including the gene for the host-specific protein J, RNA polymerase σ factor RpoS, phosphoribosamine-glycine ligase, and serine acetyltransferase. Functional analysis of the genes revealed their potential roles in the adaptation to nitrogen limitation. The results obtained in this work shed light on the mechanism of endophytes represented by P. eucalypti FBS135, at the overall transcriptional level, to an environmentally limited nitrogen supply and provided a basis for further investigation on this topic.
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Affiliation(s)
- Shengquan Huang
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Xiuyu Zhang
- Department of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zongwen Song
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Mati Ur Rahman
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Ben Fan
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
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25
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Shenkutie AM, Gebrelibanos D, Yao M, Bedada Hundie G, Chow FWN, Leung PHM. Impairment of novel non-coding small RNA00203 inhibits biofilm formation and reduces biofilm-specific antibiotic resistance in Acinetobacter baumannii. Int J Antimicrob Agents 2023; 62:106889. [PMID: 37315907 DOI: 10.1016/j.ijantimicag.2023.106889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/12/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023]
Abstract
Small RNAs (sRNAs) are post-transcriptional regulators of many biological processes in bacteria, including biofilm formation and antibiotic resistance. The mechanisms by which sRNA regulates the biofilm-specific antibiotic resistance in Acinetobacter baumannii have not been reported to date. This study aimed to investigate the influence of sRNA00203 (53 nucleotides) on biofilm formation, antibiotic susceptibility, and expression of genes associated with biofilm formation and antibiotic resistance. The results showed that deletion of the sRNA00203-encoding gene decreased the biomass of biofilm by 85%. Deletion of the sRNA00203-encoding gene also reduced the minimum biofilm inhibitory concentrations for imipenem and ciprofloxacin 1024- and 128-fold, respectively. Knocking out of sRNA00203 significantly downregulated genes involved in biofilm matrix synthesis (pgaB), efflux pump production (novel00738), lipopolysaccharide biosynthesis (novel00626), preprotein translocase subunit (secA) and the CRP transcriptional regulator. Overall, the suppression of sRNA00203 in an A. baumannii ST1894 strain impaired biofilm formation and sensitized the biofilm cells to imipenem and ciprofloxacin. As sRNA00203 was found to be conserved in A. baumannii, a therapeutic strategy targeting sRNA00203 may be a potential solution for the treatment of biofilm-associated infections caused by A. baumannii. To the best of the authors' knowledge, this is the first study to show the impact of sRNA00203 on biofilm formation and biofilm-specific antibiotic resistance in A. baumannii.
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Affiliation(s)
- Abebe Mekuria Shenkutie
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China; Department of Microbiology, Immunology and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Daniel Gebrelibanos
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Mianzhi Yao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Gadissa Bedada Hundie
- Department of Microbiology, Immunology and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Franklin W N Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Polly H M Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
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26
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Glaser SF, Brezski A, Baumgarten N, Klangwart M, Heumüller AW, Maji RK, Leisegang MS, Guenther S, Zehendner CM, John D, Schulz MH, Zarnack K, Dimmeler S. Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4. Cell Rep 2023; 42:112824. [PMID: 37481725 DOI: 10.1016/j.celrep.2023.112824] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Circular RNAs are generated by backsplicing and control cellular signaling and phenotypes. Pericytes stabilize capillary structures and play important roles in the formation and maintenance of blood vessels. Here, we characterize hypoxia-regulated circular RNAs (circRNAs) in human pericytes and show that the circular RNA of procollagen-lysine,2-oxoglutarate 5-dioxygenase-2 (circPLOD2) is induced by hypoxia and regulates pericyte functions. Silencing of circPLOD2 affects pericytes and increases proliferation, migration, and secretion of soluble angiogenic proteins, thereby enhancing endothelial migration and network capability. Transcriptional and epigenomic profiling of circPLOD2-depleted cells reveals widespread changes in gene expression and identifies the transcription factor krüppel-like factor 4 (KLF4) as a key effector of the circPLOD2-mediated changes. KLF4 depletion mimics circPLOD2 silencing, whereas KLF4 overexpression reverses the effects of circPLOD2 depletion on proliferation and endothelial-pericyte interactions. Together, these data reveal an important function of circPLOD2 in controlling pericyte proliferation and capillary formation and show that the circPLOD2-mediated regulation of KLF4 significantly contributes to the transcriptional response to hypoxia.
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Affiliation(s)
- Simone Franziska Glaser
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany; German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Andre Brezski
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Nina Baumgarten
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany; German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Marius Klangwart
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany
| | - Andreas W Heumüller
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany
| | - Ranjan Kumar Maji
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany; German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Matthias S Leisegang
- German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Institute for Cardiovascular Physiology, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Stefan Guenther
- German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, 60590 Frankfurt, Germany; Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Christoph M Zehendner
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany
| | - David John
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany; German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Marcel H Schulz
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany; German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University, 60590 Frankfurt, Germany; German Center for Cardiovascular Research DZHK, Partner Site Frankfurt Rhine-Main, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, 60590 Frankfurt, Germany.
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27
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Ibéné M, Legendre A, Postic G, Angel E, Tahi F. C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data. Brief Bioinform 2023:bbad225. [PMID: 37337745 DOI: 10.1093/bib/bbad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 04/12/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023] Open
Abstract
RNAs can interact with other molecules in their environment, such as ions, proteins or other RNAs, to form complexes with important biological roles. The prediction of the structure of these complexes is therefore an important issue and a difficult task. We are interested in RNA complexes composed of several (more than two) interacting RNAs. We show how available knowledge on the considered RNAs can help predict their secondary structure. We propose an interactive tool for the prediction of RNA complexes, called C-RCPRed, that considers user knowledge and probing data (which can be generated experimentally or artificially). C-RCPred is based on a multi-objective optimization algorithm. Through an extensive benchmarking procedure, which includes state-of-the-art methods, we show the efficiency of the multi-objective approach and the positive impact of considering user knowledge and probing data on the prediction results. C-RCPred is freely available as an open-source program and web server on the EvryRNA website (https://evryrna.ibisc.univ-evry.fr).
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Affiliation(s)
- Mandy Ibéné
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Audrey Legendre
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Guillaume Postic
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Eric Angel
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Fariza Tahi
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
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28
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DeSouza NR, Quaranto D, Carnazza M, Jarboe T, Tiwari RK, Geliebter J. Interactome of Long Non-Coding RNAs: Transcriptomic Expression Patterns and Shaping Cancer Cell Phenotypes. Int J Mol Sci 2023; 24:9914. [PMID: 37373059 DOI: 10.3390/ijms24129914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
RNA biology has gained extensive recognition in the last two decades due to the identification of novel transcriptomic elements and molecular functions. Cancer arises, in part, due to the accumulation of mutations that greatly contribute to genomic instability. However, the identification of differential gene expression patterns of wild-type loci has exceeded the boundaries of mutational study and has significantly contributed to the identification of molecular mechanisms that drive carcinogenic transformation. Non-coding RNA molecules have provided a novel avenue of exploration, providing additional routes for evaluating genomic and epigenomic regulation. Of particular focus, long non-coding RNA molecule expression has been demonstrated to govern and direct cellular activity, thus evidencing a correlation between aberrant long non-coding RNA expression and the pathological transformation of cells. lncRNA classification, structure, function, and therapeutic utilization have expanded cancer studies and molecular targeting, and understanding the lncRNA interactome aids in defining the unique transcriptomic signatures of cancer cell phenotypes.
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Affiliation(s)
- Nicole R DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Michelle Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Raj K Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
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29
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Drummond IY, DePaolo A, Krieger M, Driscoll H, Eckstrom K, Spatafora GA. Small regulatory RNAs are mediators of the Streptococcus mutans SloR regulon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543485. [PMID: 37398324 PMCID: PMC10312646 DOI: 10.1101/2023.06.02.543485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Dental caries is among the most prevalent chronic infectious diseases worldwide. Streptococcus mutans , the chief causative agent of caries, uses a 25 kDa manganese dependent SloR protein to coordinate the uptake of essential manganese with the transcription of its virulence attributes. Small non-coding RNAs (sRNAs) can either enhance or repress gene expression and reports in the literature ascribe an emerging role for sRNAs in the environmental stress response. Herein, we identify 18-50 nt sRNAs as mediators of the S. mutans SloR and manganese regulons. Specifically, the results of sRNA-seq revealed 56 sRNAs in S. mutans that were differentially transcribed in the SloR-proficient UA159 and SloR-deficient GMS584 strains, and 109 sRNAs that were differentially expressed in UA159 cells grown in the presence of low versus high manganese. We describe SmsR1532 and SmsR1785 as SloR- and/or manganese-responsive sRNAs that are processed from large transcripts, and that bind SloR directly in their promoter regions. The predicted targets of these sRNAs include regulators of metal ion transport, growth management via a toxin-antitoxin operon, and oxidative stress tolerance. These findings support a role for sRNAs in coordinating intracellular metal ion homeostasis with virulence gene control in an important oral cariogen. IMPORTANCE Small regulatory RNAs (sRNAs) are critical mediators of environmental signaling, particularly in bacterial cells under stress, but their role in Streptococcus mutans is poorly understood. S. mutans, the principal causative agent of dental caries, uses a 25 kDa manganese-dependent protein, called SloR, to coordinate the regulated uptake of essential metal ions with the transcription of its virulence genes. In the present study, we identified and characterize sRNAs that are both SloR- and manganese-responsive. Taken together, this research can elucidate the details of regulatory networks that engage sRNAs in an important oral pathogen, and that can enable the development of an effective anti-caries therapeutic.
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30
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Shabbir S, Wang W, Nawaz M, Boruah P, Kulyar MFEA, Chen M, Wu B, Liu P, Dai Y, Sun L, Gou Q, Liu R, Hu G, Younis T, He M. Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress. Microb Cell Fact 2023; 22:88. [PMID: 37127628 PMCID: PMC10152622 DOI: 10.1186/s12934-023-02095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Acetic acid and furfural (AF) are two major inhibitors of microorganisms during lignocellulosic ethanol production. In our previous study, we successfully engineered Zymomonas mobilis 532 (ZM532) strain by genome shuffling, but the molecular mechanisms of tolerance to inhibitors were still unknown. Therefore, this study investigated the responses of ZM532 and its wild-type Z. mobilis (ZM4) to AF using multi-omics approaches (transcriptomics, genomics, and label free quantitative proteomics). Based on RNA-Seq data, two differentially expressed genes, ZMO_RS02740 (up-regulated) and ZMO_RS06525 (down-regulated) were knocked out and over-expressed through CRISPR-Cas technology to investigate their roles in AF tolerance. Overall, we identified 1865 and 14 novel DEGs in ZM532 and wild-type ZM4. In contrast, 1532 proteins were identified in ZM532 and wild-type ZM4. Among these, we found 96 important genes in ZM532 involving acid resistance mechanisms and survival rates against stressors. Furthermore, our knockout results demonstrated that growth activity and glucose consumption of mutant strains ZM532∆ZMO_RS02740 and ZM4∆ZMO_RS02740 decreased with increased fermentation time from 42 to 55 h and ethanol production up to 58% in ZM532 than that in ZM532∆ZMO_RS02740. Hence, these findings suggest ZMO_RS02740 as a protective strategy for ZM ethanol production under stressful conditions.
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Affiliation(s)
- Samina Shabbir
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Department of Chemistry, The Women University Multan, Multan, Pakistan
| | - Weiting Wang
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Mohsin Nawaz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Prerona Boruah
- School of Biotechnology and Bioinformatics, DY PATIL Deemed to Be University, Navi Mumbai, India
| | | | - Mao Chen
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Panting Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Yonghua Dai
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Lingling Sun
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Qiyu Gou
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Renbin Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Guoquan Hu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Tahira Younis
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Pakistan
| | - Mingxiong He
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
- Chengdu National Agricultural Science and Technology Center, Chengdu, People's Republic of China.
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31
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Rojano-Nisimura AM, Simmons TR, Leistra AN, Mihailovic MK, Buchser R, Ekdahl AM, Joseph I, Curtis NC, Contreras LM. CsrA Shows Selective Regulation of sRNA-mRNA Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534774. [PMID: 37034808 PMCID: PMC10081199 DOI: 10.1101/2023.03.29.534774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Post-transcriptional regulation, by small RNAs (sRNAs) as well as the global Carbon Storage Regulator A (CsrA) protein, play critical roles in bacterial metabolic control and stress responses. The CsrA protein affects selective sRNA-mRNA networks, in addition to regulating transcription factors and sigma factors, providing additional avenues of cross talk between other stress-response regulators. Here, we expand the known set of sRNA-CsrA interactions and study their regulatory effects. In vitro binding assays confirm novel CsrA interactions with ten sRNAs, many of which are previously recognized as key regulatory nodes. Of those 10 sRNA, we identify that McaS, FnrS, SgrS, MicL, and Spot42 interact with CsrA in vivo. We find that the presence of CsrA impacts the downstream regulation of mRNA targets of the respective sRNA. In vivo evidence supports enhanced CsrA McaS-csgD mRNA repression and showcase CsrA-dependent repression of the fucP mRNA via the Spot42 sRNA. We additionally identify SgrS and FnrS as potential new sRNA sponges of CsrA. Overall, our results further support the expanding impact of the Csr system on cellular physiology via CsrA impact on the regulatory roles of these sRNAs.
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Affiliation(s)
| | - Trevor R. Simmons
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Abigail N. Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Mia K. Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Ryan Buchser
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Alyssa M. Ekdahl
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Isabella Joseph
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Nicholas C. Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Lydia M. Contreras
- Biochemistry Graduate Program, University of Texas at Austin, 100 E. 24th Street Stop A6500, Austin, TX 78712, USA
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA
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32
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Homberg N, Galvão Ferrarini M, Gaspin C, Sagot MF. MicroRNA Target Identification: Revisiting Accessibility and Seed Anchoring. Genes (Basel) 2023; 14:genes14030664. [PMID: 36980936 PMCID: PMC10048102 DOI: 10.3390/genes14030664] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/23/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
By pairing to messenger RNAs (mRNAs for short), microRNAs (miRNAs) regulate gene expression in animals and plants. Accurately identifying which mRNAs interact with a given miRNA and the precise location of the interaction sites is crucial to reaching a more complete view of the regulatory network of an organism. Only a few experimental approaches, however, allow the identification of both within a single experiment. Computational predictions of miRNA–mRNA interactions thus remain generally the first step used, despite their drawback of a high rate of false-positive predictions. The major computational approaches available rely on a diversity of features, among which anchoring the miRNA seed and measuring mRNA accessibility are the key ones, with the first being universally used, while the use of the second remains controversial. Revisiting the importance of each is the aim of this paper, which uses Cross-Linking, Ligation, And Sequencing of Hybrids (CLASH) datasets to achieve this goal. Contrary to what might be expected, the results are more ambiguous regarding the use of the seed match as a feature, while accessibility appears to be a feature worth considering, indicating that, at least under some conditions, it may favour anchoring by miRNAs.
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Affiliation(s)
- Nicolas Homberg
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, 69622 Villeurbanne, France
- INRIA Lyon Centre, 69100 Villeurbanne, France
- UR0875 MIAT, INRAE, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, 69622 Villeurbanne, France
- INRIA Lyon Centre, 69100 Villeurbanne, France
| | - Christine Gaspin
- UR0875 MIAT, INRAE, Université de Toulouse, 31326 Castanet-Tolosan, France
- Correspondence: (C.G.); (M.-F.S.)
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, 69622 Villeurbanne, France
- INRIA Lyon Centre, 69100 Villeurbanne, France
- Correspondence: (C.G.); (M.-F.S.)
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33
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Tan Z, Fan J, He S, Zhang Z, Chu H. sRNA21, a novel small RNA, protects Mycobacterium abscessus against oxidative stress. J Gene Med 2023:e3492. [PMID: 36862004 DOI: 10.1002/jgm.3492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/04/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND During infection, Mycobacterium abscessus encounters numerous environmental changes and adapts to them using a variety of complex mechanisms. Non-coding small RNAs (sRNAs) have been shown in other bacteria to be involved in post-transcriptional regulatory pathways, including environmental stress adaptation. However, the potential role of sRNAs in the resistance to oxidative stress in M. abscessus was not clearly described. METHODS In the present study, we analyzed putative sRNAs identified by RNA-sequencing (RNA-seq) experiments in M. abscessus ATCC_19977 under oxidative stress, and the transcription profiles of sRNAs with differential expression were verified by quantitative reverse transcription-PCR (qRT-PCR). Six sRNA overexpression strains were constructed, and the differences in growth curves between these strains and the control strain were verified. An upregulated sRNA under oxidative stress was selected and named sRNA21. The survival ability of the sRNA21 overexpression strain was assessed, and computer-based approaches were used to predict the targets and pathways regulated by sRNA21. The total ATP production and NAD+ /NADH ratio of the sRNA21 overexpression strain were measured. The expression level of antioxidase-related genes and the activity of antioxidase were tested to confirm the interaction of sRNA21 with the predicted target genes in silico. RESULTS In total, 14 putative sRNAs were identified under oxidative stress, and the qRT-PCR analysis of six sRNAs showed comparable results to RNA-seq assays. Overexpression of sRNA21 in M. abscessus increased cell growth rate and intracellular ATP level before and after peroxide exposure. The expression of genes encoding alkyl hydroperoxidase and superoxide dismutase was significantly increased, and superoxide dismutase activity was enhanced in the sRNA21 overexpression strain. Meanwhile, after sRNA21 overexpression, the intracellular NAD+ /NADH ratio decreased, indicating changes in redox homeostasis. CONCLUSIONS Our findings show that sRNA21 is an oxidative stress-induced sRNA that increases M. abscessus survival and promotes the expression of antioxidant enzymes under oxidative stress. These findings may provide new insights into the adaptive transcriptional response of M. abscessus to oxidative stress.
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Affiliation(s)
- Zhili Tan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Junsheng Fan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Siyuan He
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Zhemin Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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34
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U A, Viswam P, Kattupalli D, Eppurathu Vasudevan S. Elucidation of transfer RNAs as stress regulating agents and the experimental strategies to conceive the functional role of tRNA-derived fragments in plants. Crit Rev Biotechnol 2023; 43:275-292. [PMID: 35382663 DOI: 10.1080/07388551.2022.2026288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In plants, the transfer RNAs (tRNAs) exhibit their profound influence in orchestrating diverse physiological activities like cell growth, development, and response to several surrounding stimuli. The tRNAs, which were known to restrict their function solely in deciphering the codons, are now emerging as frontline defenders in stress biology. The plants that are constantly confronted with a huge panoply of stresses rely on tRNA-mediated stress regulation by altering the tRNA abundance, curbing the transport of tRNAs, fragmenting the mature tRNAs during stress. Among them, the studies on the generation of transfer RNA-derived fragments (tRFs) and their biological implication in stress response have attained huge interest. In plants, the tRFs hold stable expression patterns and regulate biological functions under diverse environmental conditions. In this review, we discuss the fate of plant tRNAs upon stress and thereafter how the tRFs are metamorphosed into sharp ammunition to wrestle with stress. We also address the various methods developed to date for uncovering the role of tRFs and their function in plants.
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Affiliation(s)
- Aswathi U
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Pooja Viswam
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Divya Kattupalli
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
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35
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Ryan D, Bornet E, Prezza G, Alampalli SV, de Carvalho TF, Felchle H, Ebbecke T, Hayward R, Deutschbauer AM, Barquist L, Westermann AJ. An integrated transcriptomics-functional genomics approach reveals a small RNA that modulates Bacteroides thetaiotaomicron sensitivity to tetracyclines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528795. [PMID: 36824877 PMCID: PMC9949090 DOI: 10.1101/2023.02.16.528795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Gene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gut Bacteroides spp. Here, we map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo , such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. Thereby, we infer stress- and carbon source-specific transcriptional regulons, including conditional expression of capsular polysaccharides and polysaccharide utilization loci, and expand the annotation of small regulatory RNAs (sRNAs) in this organism. Integrating this comprehensive expression atlas with transposon mutant fitness data, we identify conditionally important sRNAs. One example is MasB, whose inactivation led to increased bacterial tolerance of tetracyclines. Using MS2 affinity purification coupled with RNA sequencing, we predict targets of this sRNA and discuss their potential role in the context of the MasB-associated phenotype. Together, this transcriptomic compendium in combination with functional sRNA genomics-publicly available through a new iteration of the 'Theta-Base' web browser (www.helmholtz-hiri.de/en/datasets/bacteroides-v2)-constitutes a valuable resource for the microbiome and sRNA research communities alike.
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36
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Chen G, Shi H, Ding H, Zhang X, Gu T, Zhu M, Tan W. Multi-scale analysis of nickel ion tolerance mechanism for thermophilic Sulfobacillus thermosulfidooxidans in bioleaching. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130245. [PMID: 36332278 DOI: 10.1016/j.jhazmat.2022.130245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Bioleaching is intensively investigated for recovering valuable metals such as Li, Co, Ni and Cu. Nickel ion stress threatens the health of microorganisms when Ni2+ starts to accumulate in the leachate during the bioleaching of materials that are rich in Ni, such as spent lithium-ion batteries. The possible mechanisms underlying the response of S. thermosulfidooxidans to nickel ion stress were analyzed using a multi-scale approach. Under the condition of nickel ion stress, high concentrations of nickel ions were immobilized by extracellular polymeric substances, while concentrations of nickel ions inside the cells remained low. The intracellular adenosine triphosphate (ATP) concentration and H+-ATPase activity increased to maintain normal cell growth and metabolic activities. Scavenging abilities of S. thermosulfidooxidans for hydrogen peroxide and superoxide anion were enhanced to reduce oxidative damage induced by nickel ion stress. There were 734 differentially expressed genes identified by RNA-seq under nickel ion stress. Most of them were involved in oxidative phosphorylation, glutathione metabolism and genetic information processing, responsible for intracellular energy utilization, intracellular antioxidant capacity and DNA damage repair, respectively. The results of this study are of major significance for in-depth understanding of the mechanisms of acidophilic microorganisms' resistance to metal ions.
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Affiliation(s)
- Guanglin Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hongjie Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Huili Ding
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Institute for Sustainable Energy and the Environment, Ohio University, Athens, OH, United States
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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37
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Web Services for RNA-RNA Interaction Prediction. Methods Mol Biol 2023; 2586:175-195. [PMID: 36705905 DOI: 10.1007/978-1-0716-2768-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Non-coding RNAs have various biological functions such as translational regulation, and RNA-RNA interactions play essential roles in the mechanisms of action of these RNAs. Therefore, RNA-RNA interaction prediction is an important problem in bioinformatics, and many tools have been developed for the computational prediction of RNA-RNA interactions. In addition to the development of novel algorithms with high accuracy, the development and maintenance of web services is essential for enhancing usability by experimental biologists. In this review, we survey web services for RNA-RNA interaction predictions and introduce how to use primary web services. We present various prediction tools, including general interaction prediction tools, prediction tools for specific RNA classes, and RNA-RNA interaction-based RNA design tools. Additionally, we discuss the future perspectives of the development of RNA-RNA interaction prediction tools and the sustainability of web services.
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38
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Small RNAs Activate Salmonella Pathogenicity Island 1 by Modulating mRNA Stability through the hilD mRNA 3' Untranslated Region. J Bacteriol 2023; 205:e0033322. [PMID: 36472436 PMCID: PMC9879128 DOI: 10.1128/jb.00333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is an enteric pathogen associated with foodborne disease. Salmonella invades the intestinal epithelium using a type three secretion system encoded on Salmonella pathogenicity island 1 (SPI-1). SPI-1 genes are tightly regulated by a complex feed-forward loop to ensure proper spatial and temporal expression. Most regulatory input is integrated at HilD, through control of hilD mRNA translation or HilD protein activity. The hilD mRNA possesses a 310-nucleotide 3' untranslated region (UTR) that influences HilD and SPI-1 expression, and this regulation is dependent on Hfq and RNase E, cofactors known to mediate small RNA (sRNA) activities. Thus, we hypothesized that the hilD mRNA 3' UTR is a target for sRNAs. Here, we show that two sRNAs, SdsR and Spot 42, regulate SPI-1 by targeting different regions of the hilD mRNA 3' UTR. Regulatory activities of these sRNAs depended on Hfq and RNase E, in agreement with previous roles found for both at the hilD 3' UTR. Salmonella mutants lacking SdsR and Spot 42 had decreased virulence in a mouse model of infection. Collectively, this work suggests that these sRNAs targeting the hilD mRNA 3' UTR increase hilD mRNA levels by interfering with RNase E-dependent mRNA degradation and that this regulatory effect is required for Salmonella invasiveness. Our work provides novel insights into mechanisms of sRNA regulation at bacterial mRNA 3' UTRs and adds to our knowledge of post-transcriptional regulation of the SPI-1 complex feed-forward loop. IMPORTANCE Salmonella enterica serovar Typhimurium is a prominent foodborne pathogen, infecting millions of people a year. To express virulence genes at the correct time and place in the host, Salmonella uses a complex regulatory network that senses environmental conditions. Known for their role in allowing quick responses to stress and virulence conditions, we investigated the role of small RNAs in facilitating precise expression of virulence genes. We found that the 3' untranslated region of the hilD mRNA, encoding a key virulence regulator, is a target for small RNAs and RNase E. The small RNAs stabilize hilD mRNA to allow proper expression of Salmonella virulence genes in the host.
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Krohmaly KI, Freishtat RJ, Hahn AL. Bioinformatic and experimental methods to identify and validate bacterial RNA-human RNA interactions. J Investig Med 2023; 71:23-31. [PMID: 36162901 DOI: 10.1136/jim-2022-002509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/21/2023]
Abstract
Ample evidence supports the importance of the microbiota on human health and disease. Recent studies suggest that extracellular vesicles are an important means of bacterial-host communication, in part via the transport of small RNAs (sRNAs). Bacterial sRNAs have been shown to co-precipitate with human and mouse RNA-induced silencing complex, hinting that some may regulate gene expression as eukaryotic microRNAs do. Bioinformatic tools, including those that can incorporate an sRNA's secondary structure, can be used to predict interactions between bacterial sRNAs and human messenger RNAs (mRNAs). Validation of these potential interactions using reproducible experimental methods is essential to move the field forward. This review will cover the evidence of interspecies communication via sRNAs, bioinformatic tools currently available to identify potential bacterial sRNA-host (specifically, human) mRNA interactions, and experimental methods to identify and validate those interactions.
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Affiliation(s)
- Kylie I Krohmaly
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Division of Emergency Medicine, Children's National Hospital, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Andrea L Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA.,Division of Infectious Diseases, Children's National Hospital, Washington, District of Columbia, USA
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40
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Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling. BIOLOGY 2022; 11:biology11121798. [PMID: 36552307 PMCID: PMC9775672 DOI: 10.3390/biology11121798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/27/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that regulate gene expression at the post-transcriptional level. They are suggested to be involved in most biological processes of the cell primarily by targeting messenger RNAs (mRNAs) for cleavage or translational repression. Their binding to their target sites is mediated by the Argonaute (AGO) family of proteins. Thus, miRNA target prediction is pivotal for research and clinical applications. Moreover, transfer-RNA-derived fragments (tRFs) and other types of small RNAs have been found to be potent regulators of Ago-mediated gene expression. Their role in mRNA regulation is still to be fully elucidated, and advancements in the computational prediction of their targets are in their infancy. To shed light on these complex RNA-RNA interactions, the availability of good quality high-throughput data and reliable computational methods is of utmost importance. Even though the arsenal of computational approaches in the field has been enriched in the last decade, there is still a degree of discrepancy between the results they yield. This review offers an overview of the relevant advancements in the field of bioinformatics and machine learning and summarizes the key strategies utilized for small RNA target prediction. Furthermore, we report the recent development of high-throughput sequencing technologies, and explore the role of non-miRNA AGO driver sequences.
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41
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Chen M, Liang H, Han C, Zhou P, Xing Z, Chen Q, Liu Y, Xie GA, Xie R. Engineering of global transcription factor FruR to redirect the carbon flow in Escherichia coli for enhancing L-phenylalanine biosynthesis. Microb Cell Fact 2022; 21:222. [PMID: 36289548 PMCID: PMC9609185 DOI: 10.1186/s12934-022-01954-7] [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] [Received: 09/09/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The catabolite repressor/activator protein (FruR) is a global regulatory protein known to control the expression of several genes concerned with carbon utilization and energy metabolism. This study aimed to illustrate effects of the FruR mutant on the L-phenylalanine (L-PHE) producing strain PHE01. RESULTS Random mutagenesis libraries of fruR generated in vitro were first integrated into the chromosome of PHE01 by CRISPR/Cas9 technique, and then the best mutant PHE07 (FruRE173K) was obtained. With this mutant, a final L-PHE concentration of 70.50 ± 1.02 g/L was achieved, which was 23.34% higher than that of PHE01. To better understand the mechanism, both transcriptomes and metabolomes of PHE07 were carried out and compared to that of PHE01. Specifically, the transcript levels of genes involved in gluconeogenesis pathway, pentose phosphate pathway, Krebs cycle, and glyoxylate shunt were up-regulated in the FruRE173K mutant, whereas genes aceEF, acnB, and icd were down-regulated. From the metabolite level, the FruRE173K mutation led to an accumulation of pentose phosphate pathway and Krebs cycle products, whereas the products of pyruvate metabolism pathway: acetyl-CoA and cis-aconic acid, were down-regulated. As a result of the altered metabolic flows, the utilization of carbon sources was improved and the supply of precursors (phosphoenolpyruvate and erythrose 4-phosphate) for L-PHE biosynthesis was increased, which together led to the enhanced production of L-PHE. CONCLUSION A novel strategy for L-PHE overproduction by modification of the global transcription factor FruR in E. coli was reported. Especially, these findings expand the scope of pathways affected by the fruR regulon and illustrate its importance as a global regulator in L-PHE production.
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Affiliation(s)
- Minliang Chen
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China ,Guangdong Provincial Key Laboratory of Research and Development and Application of Fermentation and Semi-Synthetic Drugs, Livzon New North River Pharmaceutical Co. Ltd, 1st Renmin Road, Qingyuan, 511500 People’s Republic of China
| | - Hengyu Liang
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China ,Jiaozuo Joincare Biotechnology Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China ,Guangdong Provincial Key Laboratory of Research and Development and Application of Fermentation and Semi-Synthetic Drugs, Livzon New North River Pharmaceutical Co. Ltd, 1st Renmin Road, Qingyuan, 511500 People’s Republic of China
| | - Chao Han
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China ,Guangdong Provincial Key Laboratory of Research and Development and Application of Fermentation and Semi-Synthetic Drugs, Livzon New North River Pharmaceutical Co. Ltd, 1st Renmin Road, Qingyuan, 511500 People’s Republic of China
| | - Peng Zhou
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China ,Guangdong Provincial Key Laboratory of Research and Development and Application of Fermentation and Semi-Synthetic Drugs, Livzon New North River Pharmaceutical Co. Ltd, 1st Renmin Road, Qingyuan, 511500 People’s Republic of China
| | - Zhiwei Xing
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China ,Jiaozuo Joincare Biotechnology Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China
| | - Qianqian Chen
- Guangdong Provincial Key Laboratory of Research and Development and Application of Fermentation and Semi-Synthetic Drugs, Livzon New North River Pharmaceutical Co. Ltd, 1st Renmin Road, Qingyuan, 511500 People’s Republic of China
| | - Yongyu Liu
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China
| | - Gou-an Xie
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China
| | - Rufei Xie
- Henan Joincare Biopharma Research Institute Co. Ltd, Jinyuan Street 8, Jiaozuo, 454000 People’s Republic of China
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Variant-Specific Analysis Reveals a Novel Long-Range RNA-RNA Interaction in SARS-CoV-2 Orf1a. Int J Mol Sci 2022; 23:ijms231911050. [PMID: 36232353 PMCID: PMC9570297 DOI: 10.3390/ijms231911050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 01/08/2023] Open
Abstract
Since the start of the COVID-19 pandemic, understanding the pathology of the SARS-CoV-2 RNA virus and its life cycle has been the priority of many researchers. Currently, new variants of the virus have emerged with various levels of pathogenicity and abundance within the human-host population. Although much of viral pathogenicity is attributed to the viral Spike protein’s binding affinity to human lung cells’ ACE2 receptor, comprehensive knowledge on the distinctive features of viral variants that might affect their life cycle and pathogenicity is yet to be attained. Recent in vivo studies into the RNA structure of the SARS-CoV-2 genome have revealed certain long-range RNA-RNA interactions. Using in silico predictions and a large population of SARS-CoV-2 sequences, we observed variant-specific evolutionary changes for certain long-range RRIs. We also found statistical evidence for the existence of one of the thermodynamic-based RRI predictions, namely Comp1, in the Beta variant sequences. A similar test that disregarded sequence variant information did not, however, lead to significant results. When performing population-based analyses, aggregate tests may fail to identify novel interactions due to variant-specific changes. Variant-specific analyses can result in de novo RRI identification.
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Lai KP, Tim Leung CC, Boncan DAT, Tam N, Lin X, Wang SY, Chan TF, Sun Wu RS, Chong Kong RY. Hypoxia-induced epigenetic transgenerational miRNAs dysregulation involved in reproductive impairment of ovary. Chem Biol Interact 2022; 367:110176. [PMID: 36096162 DOI: 10.1016/j.cbi.2022.110176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/03/2022]
Abstract
Hypoxia is a potent endocrine disruptor that is posing serious problems to the fish reproductive systems. Our previous studies reported that hypoxia could cause a transgenerational impairment of ovarian development and interfere hatching success in F2 offspring of marine medaka fish (Oryzias melastigma) through epigenetic regulation. As part of the epigenetic regulation, we investigated the involvement of microRNAs (miRNAs) in hypoxia-induced transgenerational reproductive impairments. In the present study, we used comparative small RNA sequencing to reveal that hypoxia caused miRNA dysregulation in ovaries of F0 hypoxia group and F2 transgenerational group. We found 4 common dysregulated miRNA in the F0 and F2 generations. Furthermore, integrated miRNA-mRNA analysis, followed by gene ontology enrichment analysis on the hypoxia-dysregulated miRNA-target genes further highlighted the importance of these dysregulated miRNAs in biological processes related to reproduction. More importantly, we identified 3 miRNA-mRNA pairs (novel miRNA-525-DIAPH2, novel miRNA-525-MYOCD, and novel miRNA-525-RAI14) that might play epigenetic roles in hypoxia-induced reproductive impairment. For the first time, our findings suggested the involvement of miRNA in hypoxia-induced reproductive impairments may be inherited via a transgenerational manner.
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Affiliation(s)
- Keng Po Lai
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, China; Department of Chemistry, The City University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, The City University of Hong Kong, Hong Kong SAR, China.
| | | | - Delbert Almerick T Boncan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nathan Tam
- Department of Chemistry, The City University of Hong Kong, Hong Kong SAR, China
| | - Xiao Lin
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, USA
| | - Simon Yuan Wang
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA, 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rudolf Shiu Sun Wu
- State Key Laboratory of Marine Pollution, The City University of Hong Kong, Hong Kong SAR, China; Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong SAR, China
| | - Richard Yuen Chong Kong
- Department of Chemistry, The City University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, The City University of Hong Kong, Hong Kong SAR, China.
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44
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Omoru OB, Pereira F, Janga SC, Manzourolajdad A. A Putative long-range RNA-RNA interaction between ORF8 and Spike of SARS-CoV-2. PLoS One 2022; 17:e0260331. [PMID: 36048827 PMCID: PMC9436084 DOI: 10.1371/journal.pone.0260331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/22/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing in-silico fragment-based predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. The patterns of sequence variation using data gathered worldwide further supported the predicted stability of the sub-interacting region (23679-23690 Spike) and (28031-28042 ORF8). Such RNA-RNA interactions can potentially impact viral life cycle including sub-genomic RNA production rates.
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Affiliation(s)
- Okiemute Beatrice Omoru
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States of America
| | - Filipe Pereira
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- IDENTIFICA Genetic Testing, Maia, Portugal
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, Indianapolis, Indiana, United States of America
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), Indianapolis, Indiana, United States of America
| | - Amirhossein Manzourolajdad
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States of America
- Department of Computer Science, Colgate University, Hamilton, NY, United States of America
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Bartl J, Zanini M, Bernardi F, Forget A, Blümel L, Talbot J, Picard D, Qin N, Cancila G, Gao Q, Nath S, Koumba IM, Wolter M, Kuonen F, Langini M, Beez T, Munoz C, Pauck D, Marquardt V, Yu H, Souphron J, Korsch M, Mölders C, Berger D, Göbbels S, Meyer FD, Scheffler B, Rotblat B, Diederichs S, Ramaswamy V, Suzuki H, Oro A, Stühler K, Stefanski A, Fischer U, Leprivier G, Willbold D, Steger G, Buell A, Kool M, Lichter P, Pfister SM, Northcott PA, Taylor MD, Borkhardt A, Reifenberger G, Ayrault O, Remke M. The HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors. Nat Commun 2022; 13:4061. [PMID: 35831316 PMCID: PMC9279496 DOI: 10.1038/s41467-022-31574-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 06/20/2022] [Indexed: 11/24/2022] Open
Abstract
Most lncRNAs display species-specific expression patterns suggesting that animal models of cancer may only incompletely recapitulate the regulatory crosstalk between lncRNAs and oncogenic pathways in humans. Among these pathways, Sonic Hedgehog (SHH) signaling is aberrantly activated in several human cancer entities. We unravel that aberrant expression of the primate-specific lncRNA HedgeHog Interacting Protein-AntiSense 1 (HHIP-AS1) is a hallmark of SHH-driven tumors including medulloblastoma and atypical teratoid/rhabdoid tumors. HHIP-AS1 is actively transcribed from a bidirectional promoter shared with SHH regulator HHIP. Knockdown of HHIP-AS1 induces mitotic spindle deregulation impairing tumorigenicity in vitro and in vivo. Mechanistically, HHIP-AS1 binds directly to the mRNA of cytoplasmic dynein 1 intermediate chain 2 (DYNC1I2) and attenuates its degradation by hsa-miR-425-5p. We uncover that neither HHIP-AS1 nor the corresponding regulatory element in DYNC1I2 are evolutionary conserved in mice. Taken together, we discover an lncRNA-mediated mechanism that enables the pro-mitotic effects of SHH pathway activation in human tumors. Long non-coding RNAs (lncRNAs) can contribute to cancers that are driven by Sonic hedgehog (SHH) signaling. Here the authors report that lncRNA HHIP-AS1 stabilises the mRNA of dynein complex 1, thereby, promoting the pro-mitotic effects of SHH-driven tumors.
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Affiliation(s)
- Jasmin Bartl
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany. .,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany. .,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany. .,Group for Interdisciplinary Neurobiology and Immunology-INI-research, Institute of Zoology University of Hamburg, Hamburg, Germany.
| | - Marco Zanini
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France
| | - Flavia Bernardi
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France
| | - Antoine Forget
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France
| | - Lena Blümel
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Julie Talbot
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France
| | - Daniel Picard
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Nan Qin
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Gabriele Cancila
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France
| | - Qingsong Gao
- St Jude Children's Research Hospital, Memphis, TN, USA
| | - Soumav Nath
- Institut für Physikalische Biologie and Biological-Medical Research Center (BMFZ), Heinrich Heine University, Düsseldorf, Germany.,IBI- (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, Jülich, Germany
| | - Idriss Mahoungou Koumba
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Marietta Wolter
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - François Kuonen
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology and Venereology, Hôpital de Beaumont, Lausanne University Hospital Center, CH- Lausanne, Lausanne, Switzerland
| | - Maike Langini
- Institute for Molecular Medicine, Proteome Research, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Thomas Beez
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Christopher Munoz
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - David Pauck
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Viktoria Marquardt
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Hua Yu
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France
| | - Judith Souphron
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France
| | - Mascha Korsch
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Christina Mölders
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Daniel Berger
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Sarah Göbbels
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Frauke-Dorothee Meyer
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Björn Scheffler
- DKFZ Division of Translational Neurooncology at the West German Cancer Center (WTZ), DKTK, partner site University Hospital Essen, Düsseldorf, Germany
| | - Barak Rotblat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva, Israel
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, DKTK, partner site Freiburg, Freiburg i.Br, Germany.,Division of RNA Biology & Cancer, DKFZ, Heidelberg, Germany
| | - Vijay Ramaswamy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hiromishi Suzuki
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anthony Oro
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University, Stanford, CA, USA
| | - Kai Stühler
- Molecular Proteomics Laboratory (MPL), BMFZ, Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory (MPL), BMFZ, Heinrich Heine University, Düsseldorf, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Gabriel Leprivier
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie and Biological-Medical Research Center (BMFZ), Heinrich Heine University, Düsseldorf, Germany.,IBI- (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, Jülich, Germany
| | - Gerhard Steger
- Institut für Physikalische Biologie and Biological-Medical Research Center (BMFZ), Heinrich Heine University, Düsseldorf, Germany
| | - Alexander Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marcel Kool
- Hopp Children´s Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children´s Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France. .,Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, Orsay, France.
| | - Marc Remke
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany. .,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, and DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany. .,Institute of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany, DKTK, partner site Essen/Düsseldorf, Düsseldorf, Germany.
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Bacteria reduce flagellin synthesis to evade microglia-astrocyte-driven immunity in the brain. Cell Rep 2022; 40:111033. [PMID: 35793624 DOI: 10.1016/j.celrep.2022.111033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 05/09/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
The immune response of brain cells to invading bacteria in vivo and the mechanism used by pathogenic bacteria to escape brain immune surveillance remain largely unknown. It is believed that microglia eliminate bacteria by phagocytosis based on in vitro data. Here we find that a small percentage of microglia in the brain engulf neonatal meningitis-causing Escherichia coli (NMEC), but more microglia are activated to produce tumor necrosis factor alpha (TNFα), which activates astrocytes to secrete complement component 3 (C3) involved in anti-bacterial activity. To evade anti-bacterial activity of the immune system, NMEC senses low concentration of threonine in cerebrospinal fluid (CSF) to down-modulate the expression of flagellin and reduce microglial TNFα and astrocyte C3 production. Our findings may help develop strategies for bacterial meningitis treatment.
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Menard G, Silard C, Suriray M, Rouillon A, Augagneur Y. Thirty Years of sRNA-Mediated Regulation in Staphylococcus aureus: From Initial Discoveries to In Vivo Biological Implications. Int J Mol Sci 2022; 23:ijms23137346. [PMID: 35806357 PMCID: PMC9266662 DOI: 10.3390/ijms23137346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/20/2022] [Accepted: 06/28/2022] [Indexed: 01/27/2023] Open
Abstract
Staphylococcus aureus is a widespread livestock and human pathogen that colonizes diverse microenvironments within its host. Its adaptation to the environmental conditions encountered within humans relies on coordinated gene expression. This requires a sophisticated regulatory network, among which regulatory RNAs (usually called sRNAs) have emerged as key players over the last 30 years. In S. aureus, sRNAs regulate target genes at the post-transcriptional level through base–pair interactions. The functional characterization of a subset revealed that they participate in all biological processes, including virulence, metabolic adaptation, and antibiotic resistance. In this review, we report 30 years of S. aureus sRNA studies, from their discovery to the in-depth characterizations of some of them. We also discuss their actual in vivo contribution, which is still lagging behind, and their place within the complex regulatory network. These shall be key aspects to consider in order to clearly uncover their in vivo biological functions.
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Affiliation(s)
- Guillaume Menard
- CHU Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), SB2H (Service de Bactériologie Hygiène-Hospitalière), University Rennes, UMR_S 1230, F-35000 Rennes, France; (G.M.); (M.S.)
| | - Chloé Silard
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
| | - Marie Suriray
- CHU Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), SB2H (Service de Bactériologie Hygiène-Hospitalière), University Rennes, UMR_S 1230, F-35000 Rennes, France; (G.M.); (M.S.)
| | - Astrid Rouillon
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
| | - Yoann Augagneur
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
- Correspondence: ; Tel.: +33-223234631
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A Reverse Genetic Approach for Studying sRNAs in Chlamydia trachomatis. mBio 2022; 13:e0086422. [PMID: 35726915 PMCID: PMC9426522 DOI: 10.1128/mbio.00864-22] [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: 11/20/2022] Open
Abstract
sRNAs are noncoding transcripts that play critical roles in posttranscriptional regulation in prokaryotes. In the intracellular bacterium Chlamydia, sRNAs have been identified, but functional studies have been limited to an E. coli heterologous system. We have developed an inducible sRNA overexpression system in Chlamydia trachomatis and used it to screen putative sRNAs for effects on the Chlamydia developmental cycle, which involves conversion between replicating (RB) and infectious (EB) chlamydial forms. Overexpression of 4 of 13 C. trachomatis sRNAs decreased production of infectious EBs. We performed detailed characterization of CtrR3 and CtrR7, the two sRNAs that caused the largest progeny defects in our screen. By quantifying chlamydial number and infectious progeny, and by visualizing chlamydial forms using electron microscopy, we showed that overexpression of CtrR3 prevented RB-to-EB conversion, whereas CtrR7 overexpression blocked bacterial replication. We also describe a workflow that allowed us to identify the mRNA targets of CtrR3 in Chlamydia. We first used MS2 aptamer affinity purification coupled with RNA sequencing as an unbiased approach to isolate interacting mRNAs. We then prioritized candidates based on sequence complementarity to the CtrR3 target recognition sequence, which we had identified with bioinformatic and mutational analyses. Finally, we tested putative targets with translational fusion assays in E. coli and C. trachomatis. Using this integrated approach, we provide experimental evidence that YtgB and CTL0389 are mRNA targets of CtrR3 in Chlamydia. These findings demonstrate how our C. trachomatis sRNA overexpression system can be used to investigate the functions and mRNA targets of chlamydial sRNAs.
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Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [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: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
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Fan D, Gong Y, Sun L, Zhang Y, Zhang J. Comparative transcriptome analysis to investigate the mechanism of anti-Helicobacter pylori activity of zinc. Microb Pathog 2022; 168:105611. [PMID: 35660509 DOI: 10.1016/j.micpath.2022.105611] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 03/22/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
As a potential anti-Helicobacter pylori agent, zinc causes impairment of Helicobacter pylori growth, and this property of zinc is of broad interest to biological investigators. However, little is known about the molecular mechanisms by which zinc inhibits the growth of Helicobacter pylori. Here, an in vitro experiment revealed that zinc at specific concentrations inhibits Helicobacter pylori growth. Furthermore, an RNA sequencing-based investigation of the global regulatory response to zinc revealed that exposure to zinc altered the Helicobacter pylori transcriptional profile in numerous ways. A high concentration of zinc induced the upregulation of genes related to ribosomal subunit, ribosome biosynthesis, chaperone and adhesins. However, flagellar assembly genes and some type IV secretion system genes were repressed. In addition, the expression levels of some genes that encode transporters of metal ions and that play key roles in Helicobacter pylori pathogenicity were altered under conditions of zinc-induced stress. In summary, high concentrations of zinc initiated antimicrobial activity to Helicobacter pylori under the combined effect of multiple repressed or altered pathogenetic genes and metabolic pathways associated with bacteria growth. This result has significant implications for understanding not only the antimicrobial activity mechanism of zinc but also the role of zinc-mediated homeostasis in Helicobacter pylori.
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Affiliation(s)
- Dongjie Fan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Yanan Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Lu Sun
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Yiyao Zhang
- Healthcare Security Bureau of Haidian District, Beijing, 100000, China.
| | - Jianzhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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