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Pradhan UK, Naha S, Das R, Gupta A, Parsad R, Meher PK. RBProkCNN: Deep learning on appropriate contextual evolutionary information for RNA binding protein discovery in prokaryotes. Comput Struct Biotechnol J 2024; 23:1631-1640. [PMID: 38660008 PMCID: PMC11039349 DOI: 10.1016/j.csbj.2024.04.034] [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: 02/16/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
RNA-binding proteins (RBPs) are central to key functions such as post-transcriptional regulation, mRNA stability, and adaptation to varied environmental conditions in prokaryotes. While the majority of research has concentrated on eukaryotic RBPs, recent developments underscore the crucial involvement of prokaryotic RBPs. Although computational methods have emerged in recent years to identify RBPs, they have fallen short in accurately identifying prokaryotic RBPs due to their generic nature. To bridge this gap, we introduce RBProkCNN, a novel machine learning-driven computational model meticulously designed for the accurate prediction of prokaryotic RBPs. The prediction process involves the utilization of eight shallow learning algorithms and four deep learning models, incorporating PSSM-based evolutionary features. By leveraging a convolutional neural network (CNN) and evolutionarily significant features selected through extreme gradient boosting variable importance measure, RBProkCNN achieved the highest accuracy in five-fold cross-validation, yielding 98.04% auROC and 98.19% auPRC. Furthermore, RBProkCNN demonstrated robust performance with an independent dataset, showcasing a commendable 95.77% auROC and 95.78% auPRC. Noteworthy is its superior predictive accuracy when compared to several state-of-the-art existing models. RBProkCNN is available as an online prediction tool (https://iasri-sg.icar.gov.in/rbprokcnn/), offering free access to interested users. This tool represents a substantial contribution, enriching the array of resources available for the accurate and efficient prediction of prokaryotic RBPs.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Ritwika Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Rajender Parsad
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
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2
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Yan S, Zhang G, Luo W, Xu M, Peng R, Du Z, Liu Y, Bai Z, Xiao X, Qin S. PROTAC technology: From drug development to probe technology for target deconvolution. Eur J Med Chem 2024; 276:116725. [PMID: 39083982 DOI: 10.1016/j.ejmech.2024.116725] [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] [Received: 06/13/2024] [Revised: 07/19/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
Drug development remains a critical focus within the global pharmaceutical industry. To date, more than 80 % of disease targets are considered difficult to target. The emergence of PROTAC technology has, to some extent, alleviated this challenge. Since introduction, PROTAC technology has evolved through the peptide E3 ligase ligand phase and the small molecule E3 ligase ligand phase. Currently, multiple PROTAC molecules are in the clinical research phase, showing promising potential for addressing drug resistance, disease recurrence, and intractable targets. Target deconvolution is a crucial step in the drug discovery and development process. Due to the exceptional targeting ability and specificity of PROTAC, it is widely used and promoted as an innovative technology for discovering new drug targets, leading to significant breakthroughs. The use of PROTAC probe requires only a catalytic dose and weak interaction with the target protein to achieve target degradation. Thus, it offers substantial advantages over traditional probes, particularly in identifying new targets that are low-abundance or difficult to target. This review provides a comprehensive overview of the advancements made by PROTAC technology in drug development and drug target discovery, while also systematically reviewing the workflow of PROTAC probe. With the ongoing development of PROTAC technology, PROTAC probe is poised to become a key research area in future drug target deconvolution.
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Affiliation(s)
- Si Yan
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China
| | - Guangshuai Zhang
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China
| | - Wei Luo
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Mengwei Xu
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Rui Peng
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Ziwei Du
- Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Yan Liu
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Zhaofang Bai
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China.
| | - Xiaohe Xiao
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China.
| | - Shuanglin Qin
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China.
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Chu LC, Christopoulou N, McCaughan H, Winterbourne S, Cazzola D, Wang S, Litvin U, Brunon S, Harker PJ, McNae I, Granneman S. pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data. Life Sci Alliance 2024; 7:e202402787. [PMID: 39079742 PMCID: PMC11289467 DOI: 10.26508/lsa.202402787] [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: 04/22/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologies, is difficult to quantify as experimental approaches for validating the results are generally low throughput. To address this, we introduce pyRBDome, a pipeline for enhancing RNA-binding proteome data in silico. It aligns the experimental results with RNA-binding site (RBS) predictions from distinct machine-learning tools and integrates high-resolution structural data when available. Its statistical evaluation of RBDome data enables quick identification of likely genuine RNA-binders in experimental datasets. Furthermore, by leveraging the pyRBDome results, we have enhanced the sensitivity and specificity of RBS detection through training new ensemble machine-learning models. pyRBDome analysis of a human RBDome dataset, compared with known structural data, revealed that although UV-cross-linked amino acids were more likely to contain predicted RBSs, they infrequently bind RNA in high-resolution structures. This discrepancy underscores the limitations of structural data as benchmarks, positioning pyRBDome as a valuable alternative for increasing confidence in RBDome datasets.
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Affiliation(s)
- Liang-Cui Chu
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Niki Christopoulou
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Hugh McCaughan
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Sophie Winterbourne
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Davide Cazzola
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
| | - Shichao Wang
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Ulad Litvin
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Salomé Brunon
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris, France
| | - Patrick Jb Harker
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Cancer Biomarker Centre, University of Manchester, Manchester, UK
| | - Iain McNae
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Sander Granneman
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
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Börner J, Grützner J, Gerken F, Klug G. The Impact of the Major Endoribonucleases RNase E and RNase III and of the sRNA StsR on Photosynthesis Gene Expression in Rhodobacter sphaeroides Is Growth-Phase-Dependent. Int J Mol Sci 2024; 25:9123. [PMID: 39201809 PMCID: PMC11354728 DOI: 10.3390/ijms25169123] [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: 07/26/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Rhodobacter sphaeroides is a facultative phototrophic bacterium that performs aerobic respiration when oxygen is available. Only when oxygen is present at low concentrations or absent are pigment-protein complexes formed, and anoxygenic photosynthesis generates ATP. The regulation of photosynthesis genes in response to oxygen and light has been investigated for decades, with a focus on the regulation of transcription. However, many studies have also revealed the importance of regulated mRNA processing. This study analyzes the phenotypes of wild type and mutant strains and compares global RNA-seq datasets to elucidate the impact of ribonucleases and the small non-coding RNA StsR on photosynthesis gene expression in Rhodobacter. Most importantly, the results demonstrate that, in particular, the role of ribonuclease E in photosynthesis gene expression is strongly dependent on growth phase.
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Affiliation(s)
- Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany (F.G.)
| | | | | | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany (F.G.)
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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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6
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Moonitz SA, Do NT, Noriega R. Electrostatic modulation of multiple binding events between loquacious-PD and double-stranded RNA. Phys Chem Chem Phys 2024; 26:20739-20744. [PMID: 39049620 DOI: 10.1039/d4cp02151g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Electrostatics can alter the RNA-binding properties of proteins that display structure selectivity without sequence specificity. Loquacious-PD relies on this broad scope response to mediate the interaction of endonucleases with double stranded RNAs. Multimodal spectroscopic probes with in situ perturbations reveal an efficient and stable binding mechanism that disfavors high protein density complexes and is sensitive to local electrostatics.
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Affiliation(s)
- Sasha A Moonitz
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
| | - Nhat T Do
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
| | - Rodrigo Noriega
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
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7
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Pan X, Ouyang H, Xiao X, Zhou X, Lai L. Analysis of different expression RNA binding protein genes in mouse microglia cell from the brains of mice 72 h after subarachnoid hemorrhage or sham operation. BMC Med Genomics 2024; 17:194. [PMID: 39095742 PMCID: PMC11295691 DOI: 10.1186/s12920-024-01972-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 07/28/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND The prognosis of brain injury caused by subarachnoid hemorrhage (SAH) is poor. Previous studies showed that abnormal function of RBPs might be involved in brain injury, neuroinflammation and further affect microglia homeostasis. However, no studies have systematically analyzed the genome-wide abnormal expression of RBPs genes in microglia during SAH. METHODS RNA-seq data of microglia from the SAH mouse group (SAH) and control sham-operated mouse group (sham) were downloaded from the GEO database in GSE167957, including four samples from the sham group and four samples from the SAH group for subsequent analysis.Utilizing GO and KEGG functional enrichment analyses, we conducted a comprehensive study of differentially expressed genes (DEGs), alternative splicing patterns, and co-expression networks to gain deeper insights into the differential expression of RNA-binding proteins (RBPs) and differential alternative splicing events (ASEs) between the SAH (subarachnoid hemorrhage) and sham groups. This analysis aimed to elucidate the potential mechanisms underlying the aberrant expression of RBPs in microglia during brain injury caused by SAH. RESULTS ASEs and co-expression analyses of differentially expressed RBPs and differential ASEs were carried out in microglia in terms of gene expression. GO and KEGG functional enrichment analysis showed that aberrantly expressed RBPs such as Mcm7, Mtdh, SRSF3, and Hnrnpa2b1 may affect and regulate downstream Csnk1d, Uckl1 and other protein phosphorylation-related genes by alterative splicing. CONCLUSION RBPs were aberrantly expressed in microglia during the development of brain injury secondary to SAH, regulating alterative splicing of downstream genes and influencing the progression of SAH brain injury in this study. This implies that RBPs are important for the identification of new therapeutic targets for brain injury after SAH.
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Affiliation(s)
- Xinyi Pan
- Jiangxi Medical College, Huan kui Academy, Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Hengyang Ouyang
- Jiangxi Medical College, Huan kui Academy, Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Xue Xiao
- Jiangxi Medical College, Huan kui Academy, Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Xiaobing Zhou
- Department of Neurosurgery, The first affiliated hospital,Jiangxi Medical college,Nanchang University, Nanchang, Jiangxi, China
| | - Lingfeng Lai
- Department of Neurosurgery, The first affiliated hospital,Jiangxi Medical college,Nanchang University, Nanchang, Jiangxi, China.
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Nguyen LD, LeBlanc H, Berry KE. Improved constructs for bait RNA display in a bacterial three-hybrid assay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604302. [PMID: 39091812 PMCID: PMC11291032 DOI: 10.1101/2024.07.23.604302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We have previously developed a transcription-based bacterial three-hybrid (B3H) assay as a genetic approach to probe RNA-protein interactions inside of E. coli cells. This system offers a straightforward path to identify and assess the consequences of mutations in RBPs with molecular phenotypes of interest. One limiting factor in detecting RNA-protein interactions in the B3H assay is RNA misfolding arising from incorrect base-pair interactions with neighboring RNA sequences in a hybrid RNA. To support correct folding of hybrid bait RNAs, we have explored the use of a highly stable stem ("GC clamp") to isolate regions of a hybrid RNA as discrete folding units. In this work, we introduce new bait RNA constructs to 1) insulate the folding of individual components of the hybrid RNA with GC clamps and 2) express bait RNAs that do not encode their own intrinsic terminator. We find that short GC clamps (5 or 7 bp long) are more effective than a longer 13bp GC clamp in the B3H assay. These new constructs increase the number of Hfq-sRNA and -5'UTR interactions that are detectable in the B3H system and improve the signal-to-noise ratio of many of these interactions. We therefore recommend the use of constructs containing short GC clamps for the expression of future B3H bait RNAs. With these new constructs, a broader range of RNA-protein interactions are detectable in the B3H assay, expanding the utility and impact of this genetic tool as a platform to search for and interrogate mechanisms of additional RNA-protein interactions.
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Affiliation(s)
- Linh D. Nguyen
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Hannah LeBlanc
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Katherine E. Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
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9
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Ratwatte A, Somathilaka S, Balasubramaniam S, Gilad AA. Nonlinear classifiers for wet-neuromorphic computing using gene regulatory neural network. BIOPHYSICAL REPORTS 2024; 4:100158. [PMID: 38848994 PMCID: PMC11231448 DOI: 10.1016/j.bpr.2024.100158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/20/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
The gene regulatory network (GRN) of biological cells governs a number of key functionalities that enable them to adapt and survive through different environmental conditions. Close observation of the GRN shows that the structure and operational principles resemble an artificial neural network (ANN), which can pave the way for the development of wet-neuromorphic computing systems. Genes are integrated into gene-perceptrons with transcription factors (TFs) as input, where the TF concentration relative to half-maximal RNA concentration and gene product copy number influences transcription and translation via weighted multiplication before undergoing a nonlinear activation function. This process yields protein concentration as the output, effectively turning the entire GRN into a gene regulatory neural network (GRNN). In this paper, we establish nonlinear classifiers for molecular machine learning using the inherent sigmoidal nonlinear behavior of gene expression. The eigenvalue-based stability analysis, tailored to system parameters, confirms maximum-stable concentration levels, minimizing concentration fluctuations and computational errors. Given the significance of the stabilization phase in GRNN computing and the dynamic nature of the GRN, alongside potential changes in system parameters, we utilize the Lyapunov stability theorem for temporal stability analysis. Based on this GRN-to-GRNN mapping and stability analysis, three classifiers are developed utilizing two generic multilayer sub-GRNNs and a sub-GRNN extracted from the Escherichia coli GRN. Our findings also reveal the adaptability of different sub-GRNNs to suit different application requirements.
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Affiliation(s)
- Adrian Ratwatte
- School of Computing, University of Nebraska-Lincoln, 104 Schorr Center, Lincoln, Nebraska, USA.
| | - Samitha Somathilaka
- School of Computing, University of Nebraska-Lincoln, 104 Schorr Center, Lincoln, Nebraska, USA; VistaMilk Research Centre, Walton Institute for Information and Communication Systems Science, South East Technological University, Waterford, Ireland
| | | | - Assaf A Gilad
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA; Department of Radiology, Michigan State University, East Lansing, Michigan, USA
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10
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Siemers M, Lippegaus A, Papenfort K. ChimericFragments: computation, analysis and visualization of global RNA networks. NAR Genom Bioinform 2024; 6:lqae035. [PMID: 38633425 PMCID: PMC11023125 DOI: 10.1093/nargab/lqae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
RNA-RNA interactions are a key feature of post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA duplex formation on a genome-wide scale, computational methods for the analysis and interpretation of the underlying data are lagging behind. Here, we present ChimericFragments, an analysis framework for RNA-seq experiments that produce chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and provides an interactive graph-based visualization for data exploration and interpretation. ChimericFragments detects true RNA-RNA interactions with high precision and is compatible with several widely used experimental procedures such as RIL-seq, LIGR-seq or CLASH. We further demonstrate that ChimericFragments enables the systematic detection of novel RNA regulators and RNA-target pairs with crucial roles in microbial physiology and virulence. ChimericFragments is written in Julia and available at: https://github.com/maltesie/ChimericFragments.
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Affiliation(s)
- Malte Siemers
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
- Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Anne Lippegaus
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
| | - Kai Papenfort
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
- Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
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11
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Monti M, Herman R, Mancini L, Capitanchik C, Davey K, Dawson CS, Ule J, Thomas GH, Willis AE, Lilley KS, Villanueva E. Interrogation of RNA-protein interaction dynamics in bacterial growth. Mol Syst Biol 2024; 20:573-589. [PMID: 38531971 PMCID: PMC11066096 DOI: 10.1038/s44320-024-00031-y] [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: 09/26/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, showcasing how this approach can reveal the function of uncharacterised proteins and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
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Affiliation(s)
- Mie Monti
- MRC Toxicology Unit, University of Cambridge, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Reyme Herman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Leonardo Mancini
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Charlotte Capitanchik
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Karen Davey
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, University of Cambridge, CB2 1QR, Cambridge, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK.
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK.
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12
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Zhu Y, Ponath F, Cosi V, Vogel J. A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum. Nucleic Acids Res 2024; 52:3950-3970. [PMID: 38281181 DOI: 10.1093/nar/gkae010] [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: 10/30/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
The common oral microbe Fusobacterium nucleatum has recently drawn attention after it was found to colonize tumors throughout the human body. Fusobacteria are also interesting study systems for bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. To search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that co-purified with 19 different sRNAs. This approach revealed strong enrichment of the KH domain proteins KhpA and KhpB with nearly all tested sRNAs, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the stability of several of their target transcripts. Transcriptome studies combined with biochemical and genetic analyses suggest that KhpA/B have several physiological functions, including being required for ethanolamine utilization. Our RBP search and the discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.
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Affiliation(s)
- Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Valentina Cosi
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
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13
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Vogt LN, Panis G, Schäpers A, Peschek N, Huber M, Papenfort K, Viollier PH, Fröhlich KS. Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus. mBio 2024; 15:e0315323. [PMID: 38511926 PMCID: PMC11005374 DOI: 10.1128/mbio.03153-23] [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: 11/21/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The alphaproteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate the translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the Hfq-bound sRNA RusT is transcriptionally controlled by the NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis, we determine 16 candidate target transcripts that are deregulated, many of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limited.IMPORTANCEThe conserved RNA-binding protein Hfq contributes significantly to the adaptation of bacteria to different environmental conditions. Hfq not only stabilizes associated sRNAs but also promotes inter-molecular base-pairing interactions with target transcripts. Hfq plays a pivotal role for growth and survival, controlling central metabolism and cell wall synthesis in the oligotroph Caulobacter crescentus. However, direct evidence for Hfq-dependent post-transcriptional regulation and potential oligotrophy in C. crescentus has been lacking. Here, we identified sRNAs and mRNAs associated with Hfq in vivo, and demonstrated the requirement of Hfq for sRNA-mediated regulation, particularly of outer membrane transporters in C. crescentus.
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Affiliation(s)
- Laura N. Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Anna Schäpers
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Nikolai Peschek
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michaela Huber
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Kathrin S. Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
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14
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Jenniches L, Michaux C, Popella L, Reichardt S, Vogel J, Westermann AJ, Barquist L. Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives. Proc Natl Acad Sci U S A 2024; 121:e2308814121. [PMID: 38527194 PMCID: PMC10998600 DOI: 10.1073/pnas.2308814121] [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: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in posttranscriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 min, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with cross-linking and immunoprecipitation followed by RNA sequencing (CLIP-seq) revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for ProQ in the oxidative stress response. Our findings provide insights into posttranscriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.
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Affiliation(s)
- Laura Jenniches
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
| | - Charlotte Michaux
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Linda Popella
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
- Faculty of Medicine, University of Würzburg, Würzburg97080, Germany
| | - Alexander J. Westermann
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
- Faculty of Medicine, University of Würzburg, Würzburg97080, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, ONL5L 1C6Canada
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15
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Yang N, Zhang N, Lu G, Zeng S, Xing Y, Du L. RNA-binding proteins potentially regulate the alternative splicing of cell cycle-associated genes in proliferative diabetic retinopathy. Sci Rep 2024; 14:6731. [PMID: 38509306 PMCID: PMC10954754 DOI: 10.1038/s41598-024-57516-x] [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: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 03/22/2024] Open
Abstract
RNA-binding proteins (RBPs) contribute to the pathogenesis of proliferative diabetic retinopathy (PDR) by regulating gene expression through alternative splicing events (ASEs). However, the RBPs differentially expressed in PDR and the underlying mechanisms remain unclear. Thus, this study aimed to identify the differentially expressed genes in the neovascular membranes (NVM) and retinas of patients with PDR. The public transcriptome dataset GSE102485 was downloaded from the Gene Expression Omnibus database, and samples of PDR and normal retinas were analyzed. A mouse model of oxygen-induced retinopathy was used to confirm the results. The top 20 RBPs were screened for co-expression with alternative splicing genes (ASGs). A total of 403 RBPs were abnormally expressed in the NVM and retina samples. Functional analysis demonstrated that the ASGs were enriched in cell cycle pathways. Cell cycle-associated ASEs and an RBP-AS regulatory network, including 15 RBPs and their regulated ASGs, were extracted. Splicing factor proline/glutamine rich (SFPQ), microtubule-associated protein 1 B (MAP1B), heat-shock protein 90-alpha (HSP90AA1), microtubule-actin crosslinking factor 1 (MACF1), and CyclinH (CCNH) expression remarkably differed in the mouse model. This study provides novel insights into the RBP-AS interaction network in PDR and for developing screening and treatment options to prevent diabetic retinopathy-related blindness.
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Affiliation(s)
- Ning Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ningzhi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Guojing Lu
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Siyu Zeng
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lei Du
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China.
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16
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Dolcemascolo R, Heras-Hernández M, Goiriz L, Montagud-Martínez R, Requena-Menéndez A, Ruiz R, Pérez-Ràfols A, Higuera-Rodríguez RA, Pérez-Ropero G, Vranken WF, Martelli T, Kaiser W, Buijs J, Rodrigo G. Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria. eLife 2024; 12:RP91777. [PMID: 38363283 PMCID: PMC10942595 DOI: 10.7554/elife.91777] [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] [Indexed: 02/17/2024] Open
Abstract
The RNA recognition motif (RRM) is the most common RNA-binding protein domain identified in nature. However, RRM-containing proteins are only prevalent in eukaryotic phyla, in which they play central regulatory roles. Here, we engineered an orthogonal post-transcriptional control system of gene expression in the bacterium Escherichia coli with the mammalian RNA-binding protein Musashi-1, which is a stem cell marker with neurodevelopmental role that contains two canonical RRMs. In the circuit, Musashi-1 is regulated transcriptionally and works as an allosteric translation repressor thanks to a specific interaction with the N-terminal coding region of a messenger RNA and its structural plasticity to respond to fatty acids. We fully characterized the genetic system at the population and single-cell levels showing a significant fold change in reporter expression, and the underlying molecular mechanism by assessing the in vitro binding kinetics and in vivo functionality of a series of RNA mutants. The dynamic response of the system was well recapitulated by a bottom-up mathematical model. Moreover, we applied the post-transcriptional mechanism engineered with Musashi-1 to specifically regulate a gene within an operon, implement combinatorial regulation, and reduce protein expression noise. This work illustrates how RRM-based regulation can be adapted to simple organisms, thereby adding a new regulatory layer in prokaryotes for translation control.
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Affiliation(s)
- Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Biotechnology, Polytechnic University of ValenciaValenciaSpain
| | - María Heras-Hernández
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
| | - Lucas Goiriz
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Applied Mathematics, Polytechnic University of ValenciaValenciaSpain
| | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Biotechnology, Polytechnic University of ValenciaValenciaSpain
| | | | - Raúl Ruiz
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
| | - Anna Pérez-Ràfols
- Giotto Biotech SRLSesto FiorentinoItaly
- Magnetic Resonance Center (CERM), Department of Chemistry Ugo Schiff, Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of FlorenceSesto FiorentinoItaly
| | - R Anahí Higuera-Rodríguez
- Dynamic Biosensors GmbHPlaneggGermany
- Department of Physics, Technical University of MunichGarchingGermany
| | - Guillermo Pérez-Ropero
- Ridgeview Instruments ABUppsalaSweden
- Department of Chemistry – BMC, Uppsala UniversityUppsalaSweden
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit BrusselBrusselsBelgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles – Vrije Universiteit BrusselBrusselsBelgium
| | | | | | - Jos Buijs
- Ridgeview Instruments ABUppsalaSweden
- Department of Immunology, Genetics, and Pathology, Uppsala UniversityUppsalaSweden
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
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17
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Putzeys L, Wicke L, Brandão A, Boon M, Pires DP, Azeredo J, Vogel J, Lavigne R, Gerovac M. Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches. Curr Opin Microbiol 2024; 77:102419. [PMID: 38271748 PMCID: PMC10884466 DOI: 10.1016/j.mib.2023.102419] [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: 08/14/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
In the last decade, powerful high-throughput sequencing approaches have emerged to analyse microbial transcriptomes at a global scale. However, to date, applications of these approaches to microbial viruses such as phages remain scarce. Tailoring these techniques to virus-infected bacteria promises to obtain a detailed picture of the underexplored RNA biology and molecular processes during infection. In addition, transcriptome study of stress and perturbations induced by phages in their infected bacterial hosts is likely to reveal new fundamental mechanisms of bacterial metabolism and gene regulation. Here, we provide references and blueprints to implement emerging transcriptomic approaches towards addressing transcriptome architecture, RNA-RNA and RNA-protein interactions, RNA modifications, structures and heterogeneity of transcription profiles in infected cells that will provide guides for future directions in phage-centric therapeutic applications and microbial synthetic biology.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Ana Brandão
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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18
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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19
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Cardoza E, Singh H. From Stress Tolerance to Virulence: Recognizing the Roles of Csps in Pathogenicity and Food Contamination. Pathogens 2024; 13:69. [PMID: 38251376 PMCID: PMC10819108 DOI: 10.3390/pathogens13010069] [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: 10/30/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Be it for lab studies or real-life situations, bacteria are constantly exposed to a myriad of physical or chemical stresses that selectively allow the tolerant to survive and thrive. In response to environmental fluctuations, the expression of cold shock domain family proteins (Csps) significantly increases to counteract and help cells deal with the harmful effects of stresses. Csps are, therefore, considered stress adaptation proteins. The primary functions of Csps include chaperoning nucleic acids and regulating global gene expression. In this review, we focus on the phenotypic effects of Csps in pathogenic bacteria and explore their involvement in bacterial pathogenesis. Current studies of csp deletions among pathogenic strains indicate their involvement in motility, host invasion and stress tolerance, proliferation, cell adhesion, and biofilm formation. Through their RNA chaperone activity, Csps regulate virulence-associated genes and thereby contribute to bacterial pathogenicity. Additionally, we outline their involvement in food contamination and discuss how foodborne pathogens utilize the stress tolerance roles of Csps against preservation and sanitation strategies. Furthermore, we highlight how Csps positively and negatively impact pathogens and the host. Overall, Csps are involved in regulatory networks that influence the expression of genes central to stress tolerance and virulence.
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Affiliation(s)
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS University, Vile Parle West, Mumbai 400056, India
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20
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Zamba-Campero M, Soliman D, Yu H, Lasseter AG, Chang YY, Liu J, Aravind L, Jewett MW, Storz G, Adams PP. Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574855. [PMID: 38260563 PMCID: PMC10802407 DOI: 10.1101/2024.01.09.574855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Flagella propel pathogens through their environments yet are expensive to synthesize and are immunogenic. Thus, complex hierarchical regulatory networks control flagellar gene expression. Spirochetes are highly motile bacteria, but peculiarly in the Lyme spirochete Borrelia burgdorferi, the archetypal flagellar regulator σ28 is absent. We rediscovered gene bb0268 in B. burgdorferi as flgV, a broadly-conserved gene in the flagellar superoperon alongside σ28 in many Spirochaetes, Firmicutes and other phyla, with distant homologs in Epsilonproteobacteria. We found that B. burgdorferi FlgV is localized within flagellar motors. B. burgdorferi lacking flgV construct fewer and shorter flagellar filaments and are defective in cell division and motility. During the enzootic cycle, B. burgdorferi lacking flgV survive and replicate in Ixodes ticks but are attenuated for dissemination and infection in mice. Our work defines infection timepoints when spirochete motility is most crucial and implicates FlgV as a broadly distributed structural flagellar component that modulates flagellar assembly.
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Affiliation(s)
- Maxime Zamba-Campero
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Soliman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaxin Yu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Amanda G. Lasseter
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
| | - Yuen-Yan Chang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mollie W. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Philip P. Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
- Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA
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21
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García-Tomsig NI, Lagares A, Becker A, Valverde C, Jiménez-Zurdo JI. An Integrated Affinity Chromatography-Based Approach to Unravel the sRNA Interactome in Nitrogen-Fixing Rhizobia. Methods Mol Biol 2024; 2741:363-380. [PMID: 38217663 DOI: 10.1007/978-1-0716-3565-0_19] [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
The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs. We describe here an MS2 affinity chromatography-based procedure adapted to unravel the sRNA interactome in nitrogen-fixing legume endosymbiotic bacteria. The method consists of tagging of the bait sRNA at its 5'-end with the MS2 aptamer followed by pulse overexpression and immobilization of the chimeric transcript from cell lysates by an MS2-MBP fusion protein conjugated to an amylose resin. The sRNA-binding proteins and target mRNAs are further profiled by mass spectrometry and RNAseq, respectively.
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Affiliation(s)
- Natalia Isabel García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio Lagares
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Argentina
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo (CBMS), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires, Argentina
| | - José Ignacio Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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22
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Stenum TS, Holmqvist E. Global Identification of RNA-Binding Proteins in Bacteria. Methods Mol Biol 2024; 2741:347-361. [PMID: 38217662 DOI: 10.1007/978-1-0716-3565-0_18] [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
RNA-binding proteins (RBPs) are at the heart of many biological processes and are therefore essential for cellular life. Following identification of single RBPs by classical genetics and molecular biology methods, approaches for RBP discovery on a systems level have recently emerged. For instance, RNA interactome capture (RIC) enables the global purification of RBPs cross-linked to polyadenylated RNA using oligo(dT) probes. RIC was originally developed for eukaryotic organisms but was recently established for capturing RBPs in bacteria. In this chapter, we provide a detailed step-by-step protocol for performing RIC in bacteria. The protocol is based on its application to Escherichia coli but should be amenable for charting other genetically tractable bacterial species.
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Affiliation(s)
| | - Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
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23
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Liu F, Chen Z, Zhang S, Wu K, Bei C, Wang C, Chao Y. In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub. Nat Commun 2023; 14:8106. [PMID: 38062076 PMCID: PMC10703908 DOI: 10.1038/s41467-023-43632-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
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Affiliation(s)
- Fang Liu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziying Chen
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center & Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuo Zhang
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kejing Wu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China.
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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24
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Sumitha MK, Kalimuthu M, Aarthy M, Paramasivan R, Kumar A, Gupta B. In silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA-binding proteins in Aedes aegypti. Parasitol Res 2023; 122:2847-2857. [PMID: 37735272 DOI: 10.1007/s00436-023-07969-2] [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] [Received: 01/14/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023]
Abstract
RNA-binding proteins (RBPs) are the proteins that bind RNAs and regulate their functioning. RBPs in mosquitoes are gaining attention due to their ability to bind flaviviruses and regulate their replication and transmission. Despite their relevance, RBPs in mosquitoes are not explored much. In this study, we screened the whole genome of Aedes aegypti, the primary vector of several pathogenic viruses, and identified the proteins containing RNA recognition motif (RRM), the most abundant protein domain in eukaryotes. Using several in silico strategies, a total of 135 RRM-containing RBPs were identified in Ae. aegypti. The proteins were characterized based on their available annotations and the sequence similarity with Drosophila melanogaster. Ae. aegypti RRM-containing RBPs included serine/arginine-rich (SR) proteins, polyadenylate-binding proteins (PABP), heteronuclear ribonucleoproteins (hnRNP), small nuclear ribonucleoproteins (snRNP), splicing factors, eukaryotic initiation factors, transformers, and nucleolysins. Phylogenetic analysis revealed that the proteins and the domain organization are conserved among Ae. aegypti, Bombyx mori, and Drosophila melanogaster. However, the gene length and the intron-exon organization varied across the insect species. Expression analysis of the genes encoding RBPs using publicly available RNA sequencing data for different developmental time points of the mosquito life cycle starting from the ovary and eggs up to the adults revealed stage-specific expression with several genes preferentially expressed in early embryonic stages and blood-fed female ovaries. This is the first database for the Ae. aegypti RBPs that can serve as the reference base for future investigations. Stage-specific genes can be further explored to determine their role in mosquito growth and development with a focus on developing novel mosquito control strategies.
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Affiliation(s)
- Melveettil Kishor Sumitha
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Mariapillai Kalimuthu
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Murali Aarthy
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Rajaiah Paramasivan
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Bhavna Gupta
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India.
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25
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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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26
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Melamed S, Zhang A, Jarnik M, Mills J, Silverman A, Zhang H, Storz G. σ 28-dependent small RNA regulation of flagella biosynthesis. eLife 2023; 12:RP87151. [PMID: 37843988 PMCID: PMC10578931 DOI: 10.7554/elife.87151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here, we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor σ28 (fliA) in Escherichia coli. Interestingly, the four sRNAs have varied effects on flagellin protein levels, flagella number and cell motility. UhpU, corresponding to the 3´ UTR of a metabolic gene, likely has hundreds of targets including a transcriptional regulator at the top flagella regulatory cascade connecting metabolism and flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs and act on ribosomal protein mRNAs connecting ribosome production and flagella synthesis. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.
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Affiliation(s)
- Sahar Melamed
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Aixia Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Michal Jarnik
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Joshua Mills
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Aviezer Silverman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Hongen Zhang
- Bioinformatics and Scientific Computing Core, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
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27
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Ghandour R, Papenfort K. Small regulatory RNAs in Vibrio cholerae. MICROLIFE 2023; 4:uqad030. [PMID: 37441523 PMCID: PMC10335731 DOI: 10.1093/femsml/uqad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Vibrio cholerae is a major human pathogen causing the diarrheal disease, cholera. Regulation of virulence in V. cholerae is a multifaceted process involving gene expression changes at the transcriptional and post-transcriptional level. Whereas various transcription factors have been reported to modulate virulence in V. cholerae, small regulatory RNAs (sRNAs) have now been established to also participate in virulence control and the regulation of virulence-associated processes, such as biofilm formation, quorum sensing, stress response, and metabolism. In most cases, these sRNAs act by base-pairing with multiple target transcripts and this process typically requires the aid of an RNA-binding protein, such as the widely conserved Hfq protein. This review article summarizes the functional roles of sRNAs in V. cholerae, their underlying mechanisms of gene expression control, and how sRNAs partner with transcription factors to modulate complex regulatory programs. In addition, we will discuss regulatory principles discovered in V. cholerae that not only apply to other Vibrio species, but further extend into the large field of RNA-mediated gene expression control in bacteria.
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Affiliation(s)
- Rabea Ghandour
- Friedrich Schiller University Jena, Institute of Microbiology, 07745 Jena, Germany
| | - Kai Papenfort
- Corresponding author. Institute of Microbiology, General Microbiology, Friedrich Schiller University Jena, Winzerlaer Straße 2, 07745 Jena, Germany. Tel: +49-3641-949-311; E-mail:
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28
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Grützner J, Börner J, Jäger A, Klug G. The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides. Int J Mol Sci 2023; 24:ijms24119515. [PMID: 37298460 DOI: 10.3390/ijms24119515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In natural habitats, bacteria frequently need to adapt to changing environmental conditions. Regulation of transcription plays an important role in this process. However, riboregulation also contributes substantially to adaptation. Riboregulation often acts at the level of mRNA stability, which is determined by sRNAs, RNases, and RNA-binding proteins. We previously identified the small RNA-binding protein CcaF1, which is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides. Rhodobacter is a facultative phototroph that can perform aerobic and anaerobic respiration, fermentation, and anoxygenic photosynthesis. Oxygen concentration and light conditions decide the pathway for ATP production. Here, we show that CcaF1 promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins. Levels of mRNAs for transcriptional regulators of photosynthesis genes are not affected by CcaF1. RIP-Seq analysis compares the binding of CcaF1 to RNAs during microaerobic and photosynthetic growth. The stability of the pufBA mRNA for proteins of the light-harvesting I complex is increased by CcaF1 during phototrophic growth but decreased during microaerobic growth. This research underlines the importance of RNA-binding proteins in adaptation to different environments and demonstrates that an RNA-binding protein can differentially affect its binding partners in dependence upon growth conditions.
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Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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29
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Fuchs M, Lamm-Schmidt V, Lenče T, Sulzer J, Bublitz A, Wackenreuter J, Gerovac M, Strowig T, Faber F. A network of small RNAs regulates sporulation initiation in Clostridioides difficile. EMBO J 2023:e112858. [PMID: 37140366 DOI: 10.15252/embj.2022112858] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
The obligate anaerobic, enteric pathogen Clostridioides difficile persists in the intestinal tract by forming antibiotic-resistant endospores that contribute to relapsing and recurrent infections. Despite the importance of sporulation for C. difficile pathogenesis, environmental cues and molecular mechanisms that regulate sporulation initiation remain ill-defined. Here, by using RIL-seq to globally capture the Hfq-dependent RNA-RNA interactome, we discovered a network of small RNAs that bind to mRNAs encoding sporulation-related genes. We show that two of these small RNAs, SpoX and SpoY, regulate translation of the master regulator of sporulation, Spo0A, in an opposing manner, which ultimately leads to altered sporulation rates. Infection of antibiotic-treated mice with SpoX and SpoY deletion mutants revealed a global effect on gut colonization and intestinal sporulation. Our work uncovers an elaborate RNA-RNA interactome controlling the physiology and virulence of C. difficile and identifies a complex post-transcriptional layer in the regulation of spore formation in this important human pathogen.
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Affiliation(s)
- Manuela Fuchs
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Vanessa Lamm-Schmidt
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Tina Lenče
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Johannes Sulzer
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Arne Bublitz
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Janet Wackenreuter
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Milan Gerovac
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig, Germany
| | - Franziska Faber
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
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30
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FinO/ProQ-family proteins: an evolutionary perspective. Biosci Rep 2023; 43:232566. [PMID: 36787218 PMCID: PMC9977716 DOI: 10.1042/bsr20220313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/15/2023] Open
Abstract
RNA-binding proteins are key actors of post-transcriptional networks. Almost exclusively studied in the light of their interactions with RNA ligands and the associated functional events, they are still poorly understood as evolutionary units. In this review, we discuss the FinO/ProQ family of bacterial RNA chaperones, how they evolve and spread across bacterial populations and what properties and opportunities they provide to their host cells. We reflect on major conserved and divergent themes within the family, trying to understand how the same ancestral RNA-binding fold, augmented with additional structural elements, could yield either highly specialised proteins or, on the contrary, globally acting regulatory hubs with a pervasive impact on gene expression. We also consider dominant convergent evolutionary trends that shaped their RNA chaperone activity and recurrently implicated the FinO/ProQ-like proteins in bacterial DNA metabolism, translation and virulence. Finally, we offer a new perspective in which FinO/ProQ-family regulators emerge as active evolutionary players with both negative and positive roles, significantly impacting the evolutionary modes and trajectories of their bacterial hosts.
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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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Man-Bovenkerk S, Schipper K, van Sorge NM, Speijer D, van der Ende A, Pannekoek Y. Neisseria meningitidis Sibling Small Regulatory RNAs Connect Metabolism with Colonization by Controlling Propionate Use. J Bacteriol 2023; 205:e0046222. [PMID: 36856428 PMCID: PMC10029713 DOI: 10.1128/jb.00462-22] [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] [Received: 12/02/2022] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Neisseria meningitidis (meningococcus) colonizes the human nasopharynx, primarily as a commensal, but sporadically causing septicemia and meningitis. During colonization and invasion, it encounters different niches with specific nutrient compositions. Small noncoding RNAs (sRNAs) are used to fine-tune expression of genes, allowing adaptation to their physiological differences. We have previously characterized sRNAs (Neisseria metabolic switch regulators [NmsRs]) controlling switches between cataplerotic and anaplerotic metabolism. Here, we extend the NmsR regulon by studying methylcitrate lyase (PrpF) and propionate kinase (AckA-1) involved in the methylcitrate cycle and serine hydroxymethyltransferase (GlyA) and 3-hydroxyacid dehydrogenase (MmsB) involved in protein degradation. These proteins were previously shown to be dysregulated in a ΔnmsRs strain. Levels of transcription of target genes and NmsRs were assessed by reverse transcriptase quantitative PCR (RT-qPCR). We also used a novel gene reporter system in which the 5' untranslated region (5' UTR) of the target gene is fused to mcherry to study NmsRs-target gene interaction in the meningococcus. Under nutrient-rich conditions, NmsRs downregulate expression of PrpF and AckA-1 by direct interaction with the 5' UTR of their mRNA. Overexpression of NmsRs impaired growth under nutrient-limiting growth conditions with pyruvate and propionic acid as the only carbon sources. Our data strongly suggest that NmsRs downregulate propionate metabolism by lowering methylcitrate enzyme activity under nutrient-rich conditions. Under nutrient-poor conditions, NmsRs are downregulated, increasing propionate metabolism, resulting in higher tricarboxylic acid (TCA) activities. IMPORTANCE Neisseria meningitidis colonizes the human nasopharynx, forming a reservoir for the sporadic occurrence of epidemic invasive meningococcal disease like septicemia and meningitis. Propionic acid generated by other bacteria that coinhabit the human nasopharynx can be utilized by meningococci for replication in this environment. Here, we showed that sibling small RNAs, designated NmsRs, riboregulate propionic acid utilization by meningococci and, thus, colonization. Under conditions mimicking the nasopharyngeal environment, NmsRs are downregulated. This leads to the conversion of propionic acid to pyruvate and succinate, resulting in higher tricarboxylic acid cycle activity, allowing colonization of the nasopharynx. NmsRs link metabolic state with colonization, which is a crucial step on the trajectory to invasive meningococcal disease.
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Affiliation(s)
- Sandra Man-Bovenkerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Kim Schipper
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Nina M. van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
- Amsterdam UMC, Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam, The Netherlands
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
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Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends Biochem Sci 2023; 48:119-141. [PMID: 36150954 PMCID: PMC10043782 DOI: 10.1016/j.tibs.2022.08.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/25/2023]
Abstract
Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.
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Affiliation(s)
- Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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34
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Islam MS, Hardwick SW, Quell L, Durica‐Mitic S, Chirgadze DY, Görke B, Luisi BF. Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis. EMBO J 2023; 42:e112574. [PMID: 36504162 PMCID: PMC9841335 DOI: 10.15252/embj.2022112574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 12/14/2022] Open
Abstract
Biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled by intricate post-transcriptional networks mediated by GlmZ, a small regulatory RNA (sRNA). GlmZ stimulates translation of the mRNA encoding GlcN6P synthtase in Escherichia coli, but when bound by RapZ protein, the sRNA becomes inactivated through cleavage by the endoribonuclease RNase E. Here, we report the cryoEM structure of the RapZ:GlmZ complex, revealing a complementary match of the RapZ tetrameric quaternary structure to structural repeats in the sRNA. The nucleic acid is contacted by RapZ mostly through a highly conserved domain that shares an evolutionary relationship with phosphofructokinase and suggests links between metabolism and riboregulation. We also present the structure of a precleavage intermediate formed between the binary RapZ:GlmZ complex and RNase E that reveals how GlmZ is presented and recognised by the enzyme. The structures provide a framework for understanding how other encounter complexes might guide recognition and action of endoribonucleases on target transcripts, and how structured substrates in polycistronic precursors may be recognised for processing by RNase E.
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Affiliation(s)
- Md Saiful Islam
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Laura Quell
- Department of Microbiology, Immunobiology and Genetics, Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Svetlana Durica‐Mitic
- Department of Microbiology, Immunobiology and Genetics, Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | | | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Ben F Luisi
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523326. [PMID: 36711508 PMCID: PMC9882015 DOI: 10.1101/2023.01.09.523326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Yusuf Adeshina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Igor Bychkov
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Yan Xia
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Ragul Gowthaman
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Sven A. Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | | | - David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Erica A. Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140
| | - Petr B. Makhov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City KS 66160
| | - Manoj M. Pillai
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - Yanis Boumber
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140
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Chen F, Cocaign-Bousquet M, Girbal L, Nouaille S. 5'UTR sequences influence protein levels in Escherichia coli by regulating translation initiation and mRNA stability. Front Microbiol 2022; 13:1088941. [PMID: 36620028 PMCID: PMC9810816 DOI: 10.3389/fmicb.2022.1088941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
A set of 41 synthetic 5'UTRs with different theoretical translation initiation rates were generated to explore the role of 5'UTRs in the regulation of protein levels in Escherichia coli. The roles of the synthetic 5'UTRs in regulating the expression of different reporter genes were analyzed in vivo. Protein levels varied substantially between the different constructs but for most of the 5'UTRs, protein levels were not correlated with theoretical translation initiation rates. Large variations in mRNA concentrations were measured with the different 5'UTRs even though the same concentration of transcription inducer was used in each case. 5'UTRs were also found to strongly affect mRNA stability, and these changes in mRNA stability often contributed to observed differences in mRNA concentration. Unexpectedly, the effect of the 5'UTRs on mRNA half-lives was found to vary depending on the downstream reporter gene. These results clearly demonstrate that 5'UTRs contribute to gene expression regulation at the level of translation initiation and of mRNA stability, to an extent that depends on the nature of the downstream gene.
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Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli. mBio 2022; 13:e0237122. [PMID: 36226957 PMCID: PMC9765468 DOI: 10.1128/mbio.02371-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The regulatory function of many bacterial small RNAs (sRNAs) requires the binding of the RNA chaperone Hfq to the 3' portion of the sRNA intrinsic terminator, and therefore sRNA signaling might be regulated by modulating its terminator. Here, using a multicopy screen developed with the terminator of sRNA SgrS, we identified an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof) that attenuate SgrS termination in Escherichia coli. Analyses of CyaR and YgjH, a putative tRNA binding protein, suggested that the CyaR activity was indirect and the effect of YgjH was moderate. Overproduction of the protein attenuators CspD and Rof resulted in more frequent readthrough at terminators of SgrS and two other sRNAs, and regulation by SgrS of target mRNAs was reduced. The effect of Rof, a known inhibitor of Rho, was mimicked by bicyclomycin or by a rho mutant, suggesting an unexpected role for Rho in sRNA termination. CspD, a member of the cold shock protein family, bound both terminated and readthrough transcripts, stabilizing them and attenuating termination. By RNA sequencing analysis of the CspD overexpression strain, we found global effects of CspD on gene expression across some termination sites. We further demonstrated effects of endogenous CspD under slow growth conditions where cspD is highly expressed. These findings provided evidence of changes in the efficiency of intrinsic termination, confirming this as an additional layer of the regulation of sRNA signaling. IMPORTANCE Growing evidence suggests that the modulation of intrinsic termination and readthrough of transcription is more widespread than previously appreciated. For small RNAs, proper termination plays a critical role in their regulatory function. Here, we present a multicopy screen approach to identify factors that attenuate small RNA termination and therefore abrogate signaling dependent on the small RNA. This study highlights a new aspect of regulation of small RNA signaling as well as the modulation of intrinsic termination.
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38
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Rasmussen RA, Wang S, Camarillo JM, Sosnowski V, Cho BK, Goo Y, Lucks J, O’Halloran T. Zur and zinc increase expression of E. coli ribosomal protein L31 through RNA-mediated repression of the repressor L31p. Nucleic Acids Res 2022; 50:12739-12753. [PMID: 36533433 PMCID: PMC9825181 DOI: 10.1093/nar/gkac1086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can adapt in response to numerous stress conditions. One such stress condition is zinc depletion. The zinc-sensing transcription factor Zur regulates the way numerous bacterial species respond to severe changes in zinc availability. Under zinc sufficient conditions, Zn-loaded Zur (Zn2-Zur) is well-known to repress transcription of genes encoding zinc uptake transporters and paralogues of a few ribosomal proteins. Here, we report the discovery and mechanistic basis for the ability of Zur to up-regulate expression of the ribosomal protein L31 in response to zinc in E. coli. Through genetic mutations and reporter gene assays, we find that Zur achieves the up-regulation of L31 through a double repression cascade by which Zur first represses the transcription of L31p, a zinc-lacking paralogue of L31, which in turn represses the translation of L31. Mutational analyses show that translational repression by L31p requires an RNA hairpin structure within the l31 mRNA and involves the N-terminus of the L31p protein. This work uncovers a new genetic network that allows bacteria to respond to host-induced nutrient limiting conditions through a sophisticated ribosomal protein switching mechanism.
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Affiliation(s)
- Rebecca A Rasmussen
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
| | - Suning Wang
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Jeannie M Camarillo
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
| | - Victoria Sosnowski
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
| | - Byoung-Kyu Cho
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
- Mass Spectrometry Technology Access Center, Washington University in St Louis, School of Medicine, USA
| | - Young Ah Goo
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
- Mass Spectrometry Technology Access Center, Washington University in St Louis, School of Medicine, USA
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Thomas V O’Halloran
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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Zhong X, Ma J, Bai Q, Zhu Y, Zhang Y, Gu Q, Pan Z, Liu G, Wu Z, Yao H. Identification of the RNA-binding domain-containing protein RbpA that acts as a global regulator of the pathogenicity of Streptococcus suis serotype 2. Virulence 2022; 13:1304-1314. [PMID: 35903019 PMCID: PMC9341378 DOI: 10.1080/21505594.2022.2103233] [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: 11/12/2022] Open
Abstract
Streptococcus suis serotype 2 (SS2), an emerging zoonotic pathogen, causes swine diseases and human cases of streptococcal toxic shock syndrome. RNA-binding proteins (RBPs) can modulate gene expression through post-transcriptional regulation. In this study, we identified an RBP harbouring an S1 domain, named RbpA, which facilitated SS2 adhesion to host epithelial cells and contributed to bacterial pathogenicity. Comparative proteomic analysis identified 145 proteins that were expressed differentially between ΔrbpA strain and wild-type strain, including several virulence-associated factors, such as the extracellular protein factor (EF), SrtF pilus, IgA1 protease, SBP2 pilus, and peptidoglycan-binding LysM’ proteins. The mechanisms underlying the regulatory effects of RbpA on their encoding genes were explored, and it was found that RbpA regulates gene expression through diverse mechanisms, including post-transcriptional regulation, and thus acts as a global regulator. These results partly reveal the pathogenic mechanism mediated by RbpA, improving our understanding of the regulatory systems of S. suis and providing new insights into bacterial pathogenicity.
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Affiliation(s)
- Xiaojun Zhong
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Jiale Ma
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qiankun Bai
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yinchu Zhu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yue Zhang
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qibing Gu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zihao Pan
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Guangjin Liu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zongfu Wu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Huochun Yao
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Chihara K, Gerovac M, Hör J, Vogel J. Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq). RNA (NEW YORK, N.Y.) 2022; 29:rna.079439.122. [PMID: 36328526 PMCID: PMC9808575 DOI: 10.1261/rna.079439.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
New methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar concept as the established Grad-seq approach. In Grad-seq, cellular RNA and protein complexes of a bacterium of interest are separated in a glycerol gradient, followed by high-throughput RNA-sequencing and mass spectrometry analyses of individual gradient fractions. New RNA-protein complexes are predicted based on the similarity of their elution profiles. In SEC-seq, we have replaced the glycerol gradient with separation by size exclusion chromatography, which shortens operation times and offers greater potential for automation. Applying SEC-seq to Escherichia coli, we find that the method provides a higher resolution than Grad-seq in the lower molecular weight range up to ~500 kDa. This is illustrated by the ability of SEC-seq to resolve two distinct, but similarly sized complexes of the global translational repressor CsrA with either of its antagonistic small RNAs, CsrB and CsrC. We also characterized changes in the SEC-seq profiles of the small RNA MicA upon deletion of its RNA chaperones Hfq and ProQ and investigated the redistribution of these two proteins upon RNase treatment. Overall, we demonstrate that SEC-seq is a tractable and reproducible method for the global profiling of bacterial RNA-protein complexes that offers the potential to discover yet-unrecognized associations between bacterial RNAs and proteins.
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Affiliation(s)
- Kotaro Chihara
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany
| | | | - Jens Hör
- Weizmann Institute, Rehovot, Israel
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Smirnov A. How global RNA-binding proteins coordinate the behaviour of RNA regulons: an information approach. Comput Struct Biotechnol J 2022; 20:6317-6338. [DOI: 10.1016/j.csbj.2022.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
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Pleiotropic Effects of Hfq on the Cytochrome c Content and Pyomelanin Production in Shewanella oneidensis. Appl Environ Microbiol 2022; 88:e0128922. [PMID: 36073941 PMCID: PMC9499022 DOI: 10.1128/aem.01289-22] [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: 11/20/2022] Open
Abstract
Shewanella oneidensis is the best understood model microorganism for the study of diverse cytochromes (cytos) c that support its unparallel respiratory versatility. Although RNA chaperone Hfq has been implicated in regulation of cyto c production, little is known about the biological pathways that it affects in this bacterium. In this study, from a spontaneous mutant that secretes pyomelanin and has a lowered cyto c content, we identified Hfq to be the regulator that critically associates with both phenotypes in S. oneidensis. We found that expression of the key genes in biosynthesis and degradation of heme is differentially affected by Hfq at under- and overproduced levels, and through modulating heme levels, Hfq influences the cyto c content. Although Hfq in excess results in overproduction of the enzymes responsible for both generation and removal of homogentisic acid (HGA), the precursor of pyomelanin, it is compromised activity of HmgA that leads to excretion and polymerization of HGA to form pyomelanin. We further show that Hfq mediates HmgA activity by lowering intracellular iron content because HmgA is an iron-dependent enzyme. Overall, our work highlights the significance of Hfq-mediated posttranscriptional regulation in the physiology of S. oneidensis, unraveling unexpected mechanisms by which Hfq affects cyto c biosynthesis and pyomelanin production. IMPORTANCE In bacteria, Hfq has been implicated in regulation of diverse biological processes posttranslationally. In S. oneidensis, Hfq affects the content of cytos c that serve as the basis of its respiratory versatility and potential application in bioenergy and bioremediation. In this study, we found that Hfq differentially regulates heme biosynthesis and degradation, leading to altered cyto c contents. Hfq in excess causes a synthetic effect on HmgA, an enzyme responsible for pyomelanin formation. Overall, the data presented manifest that the biological processes in a given bacterium regulated by Hfq are highly complex, amounting to required coordination among multiple physiological aspects to allow cells to respond to environmental changes promptly.
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Köbel T, Melo Palhares R, Fromm C, Szymanski W, Angelidou G, Glatter T, Georg J, Berghoff BA, Schindler D. An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria. ACS Synth Biol 2022; 11:2989-3003. [PMID: 36044590 PMCID: PMC9486967 DOI: 10.1021/acssynbio.2c00164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic biology approaches life from the perspective of an engineer. Standardized and de novo design of genetic parts to subsequently build reproducible and controllable modules, for example, for circuit design, is a key element. To achieve this, natural systems and elements often serve as a blueprint for researchers. Regulation of protein abundance is controlled at DNA, mRNA, and protein levels. Many tools for the activation or repression of transcription or the destabilization of proteins are available, but easy-to-handle minimal regulatory elements on the mRNA level are preferable when translation needs to be modulated. Regulatory RNAs contribute considerably to regulatory networks in all domains of life. In particular, bacteria use small regulatory RNAs (sRNAs) to regulate mRNA translation. Slowly, sRNAs are attracting the interest of using them for broad applications in synthetic biology. Here, we promote a "plug and play" plasmid toolset to quickly and efficiently create synthetic sRNAs to study sRNA biology or their application in bacteria. We propose a simple benchmarking assay by targeting the acrA gene of Escherichia coli and rendering cells sensitive toward the β-lactam antibiotic oxacillin. We further highlight that it may be necessary to test multiple seed regions and sRNA scaffolds to achieve the desired regulatory effect. The described plasmid toolset allows quick construction and testing of various synthetic sRNAs based on the user's needs.
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Affiliation(s)
- Tania
S. Köbel
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany
| | - Rafael Melo Palhares
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christin Fromm
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Witold Szymanski
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Georgia Angelidou
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Timo Glatter
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Jens Georg
- Institut
für Biologie III, Albert-Ludwigs-Universität
Freiburg, Schänzlestraße
1, 79104 Freiburg, Germany
| | - Bork A. Berghoff
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany,
| | - Daniel Schindler
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,
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Martinez-Monge A, Pastor I, Bustamante C, Manosas M, Ritort F. Measurement of the specific and non-specific binding energies of Mg 2+ to RNA. Biophys J 2022; 121:3010-3022. [PMID: 35864738 PMCID: PMC9463699 DOI: 10.1016/j.bpj.2022.07.020] [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] [Indexed: 11/02/2022] Open
Abstract
Determining the non-specific and specific electrostatic contributions of magnesium binding to RNA is a challenging problem. We introduce a single-molecule method based on measuring the folding energy of a native RNA in magnesium and at its equivalent sodium concentration. The latter is defined so that the folding energy in sodium equals the non-specific electrostatic contribution in magnesium. The sodium equivalent can be estimated according to the empirical 100/1 rule (1 M NaCl is equivalent to 10 mM MgCl2), which is a good approximation for most RNAs. The method is applied to an RNA three-way junction (3WJ) that contains specific Mg2+ binding sites and misfolds into a double hairpin structure without binding sites. We mechanically pull the RNA with optical tweezers and use fluctuation theorems to determine the folding energies of the native and misfolded structures in magnesium (10 mM MgCl2) and at the equivalent sodium condition (1 M NaCl). While the free energies of the misfolded structure are equal in magnesium and sodium, they are not for the native structure, the difference being due to the specific binding energy of magnesium to the 3WJ, which equals ΔG≃ 10 kcal/mol. Besides stabilizing the 3WJ, Mg2+ also kinetically rescues it from the misfolded structure over timescales of tens of seconds in a force-dependent manner. The method should generally be applicable to determine the specific binding energies of divalent cations to other tertiary RNAs.
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Affiliation(s)
- A Martinez-Monge
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain
| | - Isabel Pastor
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carlos Bustamante
- Departments of Chemistry, Physics and Molecular and Cell Biology, University of California Berkeley, Berkeley, California; Howard Hughes Medical Institute University of California Berkeley, Berkeley, California; Kavli Energy Nanosciences Institute, University of California Berkeley, Berkeley, California
| | - Maria Manosas
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain.
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain.
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45
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Identification and Characterization of an RRM-Containing, RNA Binding Protein in Acinetobacter baumannii. Biomolecules 2022; 12:biom12070922. [PMID: 35883478 PMCID: PMC9313427 DOI: 10.3390/biom12070922] [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: 05/23/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative pathogen, known to acquire resistance to antibiotics used in the clinic. The RNA-binding proteome of this bacterium is poorly characterized, in particular for what concerns the proteins containing RNA Recognition Motif (RRM). Here, we browsed the A. baumannii proteome for homologous proteins to the human HuR(ELAVL1), an RNA binding protein containing three RRMs. We identified a unique locus that we called AB-Elavl, coding for a protein with a single RRM with an average of 34% identity to the first HuR RRM. We also widen the research to the genomes of all the bacteria, finding 227 entries in 12 bacterial phyla. Notably we observed a partial evolutionary divergence between the RNP1 and RNP2 conserved regions present in the prokaryotes in comparison to the metazoan consensus sequence. We checked the expression at the transcript and protein level, cloned the gene and expressed the recombinant protein. The X-ray and NMR structural characterization of the recombinant AB-Elavl revealed that the protein maintained the typical β1α1β2β3α2β4 and three-dimensional organization of eukaryotic RRMs. The biochemical analyses showed that, although the RNP1 and RNP2 show differences, it can bind to AU-rich regions like the human HuR, but with less specificity and lower affinity. Therefore, we identified an RRM-containing RNA-binding protein actually expressed in A. baumannii.
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46
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Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli. mSystems 2022; 7:e0008622. [PMID: 35695420 PMCID: PMC9426608 DOI: 10.1128/msystems.00086-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The RNA chaperones, cold shock proteins CspC and CspE, are important in stress response and adaptation. We studied their role in the pathogenesis of a virulent Escherichia coli, representative of extraintestinal pathogenic E. coli (ExPEC) which are serum resistant and septicemic. We performed a global analysis to identify transcripts that interact with these cold shock proteins (CSPs), focusing on virulence-related genes. We used CLIP-seq, which combines UV cross-linking, immunoprecipitation and RNA sequencing. A large number of transcripts bound to the CSPs were identified, and many bind both CspC and CspE. Many transcripts were of genes involved in protein synthesis, transcription and energy metabolism. In addition, there were virulence-related genes, (i.e., fur and ryhB), essential for iron homeostasis. The CLIP-seq results were validated on two transcripts, clpX and tdcA, reported as virulence-associated. Deletion of either CspC or CspE significantly decreased their transcript levels and in a double deletion mutant cspC/cspE, the transcript stability of tdcA and clpX was reduced by 32-fold and 10-fold, respectively. We showed that these two genes are important for virulence, as deleting either of them resulted in loss of serum resistance, a requirement for sepsis. As several virulence-related transcripts interact with CspC or CspE, we determined the importance of these proteins for growth in serum and showed that deletion of either gene significantly reduced serum survival. This phenotype could be partially complemented by cspE and fully complemented by cspC. These results indicate that the two RNA chaperones are essential for virulence, and that CspC particularly critical. IMPORTANCE Virulent Escherichia coli strains that cause infections outside the intestinal tract—extraintestinal pathogenic E. coli (ExPEC)—constitute a major clinical problem worldwide. They are involved in several distinct conditions, including urinary tract infections, newborn meningitis, and sepsis. Due to increasing antibiotic resistance, these strains are a main factor in hospital and community-acquired infections. Because many strains, which do not cross-react immunologically are involved, developing a simple vaccine is not possible. Therefore, it is essential to understand the pathogenesis of these bacteria to identify potential targets for developing drugs or vaccines. One of the least investigated systems involves RNA binding proteins, important for stability of transcripts and global gene regulation. Two such proteins are CspC and CspE (“cold shock proteins”), RNA chaperones involved in stress adaptation. Here we performed a global analysis to identify the transcripts which are affected by these two chaperones, with focus on virulence-associated transcripts.
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47
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The RNA-Binding Protein ProQ Impacts Exopolysaccharide Biosynthesis and Second Messenger Cyclic di-GMP Signaling in the Fire Blight Pathogen Erwinia amylovora. Appl Environ Microbiol 2022; 88:e0023922. [PMID: 35416685 DOI: 10.1128/aem.00239-22] [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: 11/20/2022] Open
Abstract
Erwinia amylovora is a plant-pathogenic bacterium that causes fire blight disease in many economically important plants, including apples and pears. This bacterium produces three exopolysaccharides (EPSs), amylovoran, levan, and cellulose, and forms biofilms in host plant vascular tissues, which are crucial for pathogenesis. Here, we demonstrate that ProQ, a conserved bacterial RNA chaperone, was required for the virulence of E. amylovora in apple shoots and for biofilm formation in planta. In vitro experiments revealed that the deletion of proQ increased the production of amylovoran and cellulose. Prc is a putative periplasmic protease, and the prc gene is located adjacent to proQ. We found that Prc and the associated lipoprotein NlpI negatively affected amylovoran production, whereas Spr, a peptidoglycan hydrolase degraded by Prc, positively regulated amylovoran. Since the prc promoter is likely located within proQ, our data showed that proQ deletion significantly reduced the prc mRNA levels. We used a genome-wide transposon mutagenesis experiment to uncover the involvement of the bacterial second messenger c-di-GMP in ProQ-mediated cellulose production. The deletion of proQ resulted in elevated intracellular c-di-GMP levels and cellulose production, which were restored to wild-type levels by deleting genes encoding c-di-GMP biosynthesis enzymes. Moreover, ProQ positively affected the mRNA levels of genes encoding c-di-GMP-degrading phosphodiesterase enzymes via a mechanism independent of mRNA decay. In summary, our study revealed a detailed function of E. amylovora ProQ in coordinating cellulose biosynthesis and, for the first time, linked ProQ with c-di-GMP metabolism and also uncovered a role of Prc in the regulation of amylovoran production. IMPORTANCE Fire blight, caused by the bacterium Erwinia amylovora, is an important disease affecting many rosaceous plants, including apple and pear, that can lead to devastating economic losses worldwide. Similar to many xylem-invading pathogens, E. amylovora forms biofilms that rely on the production of exopolysaccharides (EPSs). In this paper, we identified the RNA-binding protein ProQ as an important virulence regulator. ProQ played a central role in controlling the production of EPSs and participated in the regulation of several conserved bacterial signal transduction pathways, including the second messenger c-di-GMP and the periplasmic protease Prc-mediated systems. Since ProQ has recently been recognized as a global posttranscriptional regulator in many bacteria, these findings provide new insights into multitiered regulatory mechanisms for the precise control of virulence factor production in bacterial pathogens.
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48
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Zhang J, Yan K, Chen Q, Liu B. PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning. Bioinformatics 2022; 38:2135-2143. [PMID: 35176130 DOI: 10.1093/bioinformatics/btac106] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/18/2021] [Accepted: 02/15/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION RNA-binding proteins (RBPs) play crucial roles in post-transcriptional regulation. Accurate identification of RBPs helps to understand gene expression, regulation, etc. In recent years, some computational methods were proposed to identify RBPs. However, these methods fail to accurately identify RBPs from some specific species with limited data, such as bacteria. RESULTS In this study, we introduce a computational method called PreRBP-TL for identifying species-specific RBPs based on transfer learning. The weights of the prediction model were initialized by pretraining with the large general RBP dataset and then fine-tuned with the small species-specific RPB dataset by using transfer learning. The experimental results show that the PreRBP-TL achieves better performance for identifying the species-specific RBPs from Human, Arabidopsis, Escherichia coli and Salmonella, outperforming eight state-of-the-art computational methods. It is anticipated PreRBP-TL will become a useful method for identifying RBPs. AVAILABILITY AND IMPLEMENTATION For the convenience of researchers to identify RBPs, the web server of PreRBP-TL was established, freely available at http://bliulab.net/PreRBP-TL. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jun Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China
| | - Ke Yan
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Qingcai Chen
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China
| | - Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China.,School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China.,Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
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49
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Ponath F, Hör J, Vogel J. An overview of gene regulation in bacteria by small RNAs derived from mRNA 3' ends. FEMS Microbiol Rev 2022; 46:6564598. [PMID: 35388892 PMCID: PMC9438474 DOI: 10.1093/femsre/fuac017] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past two decades, small noncoding RNAs (sRNAs) that regulate mRNAs by short base pairing have gone from a curiosity to a major class of post-transcriptional regulators in bacteria. They are integral to many stress responses and regulatory circuits, affecting almost all aspects of bacterial life. Following pioneering sRNA searches in the early 2000s, the field quickly focused on conserved sRNA genes in the intergenic regions of bacterial chromosomes. Yet, it soon emerged that there might be another rich source of bacterial sRNAs—processed 3′ end fragments of mRNAs. Several such 3′ end-derived sRNAs have now been characterized, often revealing unexpected, conserved functions in diverse cellular processes. Here, we review our current knowledge of these 3′ end-derived sRNAs—their biogenesis through ribonucleases, their molecular mechanisms, their interactions with RNA-binding proteins such as Hfq or ProQ and their functional scope, which ranges from acting as specialized regulators of single metabolic genes to constituting entire noncoding arms in global stress responses. Recent global RNA interactome studies suggest that the importance of functional 3′ end-derived sRNAs has been vastly underestimated and that this type of cross-regulation between genes at the mRNA level is more pervasive in bacteria than currently appreciated.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Jens Hör
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
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50
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RNase III Participates in the Adaptation to Temperature Shock and Oxidative Stress in Escherichia coli. Microorganisms 2022; 10:microorganisms10040699. [PMID: 35456749 PMCID: PMC9032294 DOI: 10.3390/microorganisms10040699] [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: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/05/2023] Open
Abstract
Bacteria thrive in ever-changing environments by quickly remodeling their transcriptome and proteome via complex regulatory circuits. Regulation occurs at multiple steps, from the transcription of genes to the post-translational modification of proteins, via both protein and RNA regulators. At the post-transcriptional level, the RNA fate is balanced through the binding of ribosomes, chaperones and ribonucleases. We aim to decipher the role of the double-stranded-RNA-specific endoribonuclease RNase III and to evaluate its biological importance in the adaptation to modifications of the environment. The inactivation of RNase III affects a large number of genes and leads to several phenotypical defects, such as reduced thermotolerance in Escherichia coli. In this study, we reveal that RNase III inactivation leads to an increased sensitivity to temperature shock and oxidative stress. We further show that RNase III is important for the induction of the heat shock sigma factor RpoH and for the expression of the superoxide dismutase SodA.
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