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Wang X, Wang L, Wang Y, Fu X, Wang X, Wu H, Wang H, Lu Z. sRNA molecules participate in hyperosmotic stress response regulation in Sphingomonas melonis TY. Appl Environ Microbiol 2024; 90:e0215823. [PMID: 38289134 PMCID: PMC10880617 DOI: 10.1128/aem.02158-23] [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: 12/01/2023] [Accepted: 12/21/2023] [Indexed: 02/22/2024] Open
Abstract
Drought and salinity are ubiquitous environmental factors that pose hyperosmotic threats to microorganisms and impair their efficiency in performing environmental functions. However, bacteria have developed various responses and regulatory systems to cope with these abiotic challenges. Posttranscriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions can lead to the induction of specific small RNA molecules (sRNAs) that participate in stress response regulation. Here, we report a candidate functional sRNA landscape of Sphingomonas melonis TY under hyperosmotic stress, and 18 sRNAs were found with a clear response to hyperosmotic stress. These findings will help in the comprehensive analysis of sRNA regulation in Sphingomonas species. Weighted correlation network analysis revealed a 263 nucleotide sRNA, SNC251, which was transcribed from its own promoter and showed the most significant correlation with hyperosmotic response factors. Deletion of snc251 affected biofilm formation and multiple cellular processes, including ribosome-related pathways, aromatic compound degradation, and the nicotine degradation capacity of S. melonis TY, while overexpression of SNC251 facilitated biofilm formation by TY under hyperosmotic stress. Two genes involved in the TonB system were further verified to be activated by SNC251, which also indicated that SNC251 is a trans-acting sRNA. Briefly, this research reports a landscape of sRNAs participating in the hyperosmotic stress response in S. melonis and reveals a novel sRNA, SNC251, which contributes to the S. melonis TY biofilm formation and thus enhances its hyperosmotic stress response ability.IMPORTANCESphingomonas species play a vital role in plant defense and pollutant degradation and survive extensively under drought or salinity. Previous studies have focused on the transcriptional and translational responses of Sphingomonas under hyperosmotic stress, but the posttranscriptional regulation of small RNA molecules (sRNAs) is also crucial for quickly modulating cellular processes to adapt dynamically to osmotic environments. In addition, the current knowledge of sRNAs in Sphingomonas is extremely scarce. This research revealed a novel sRNA landscape of Sphingomonas melonis and will greatly enhance our understanding of sRNAs' acting mechanisms in the hyperosmotic stress response.
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Affiliation(s)
- Xiaoyu Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Lvjing Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Yihan Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xueni Fu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
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Liu W, Pang Y, Yu X, Lu D, Yang Y, Meng F, Xu C, Yuan L, Nan Y. Pan-cancer analysis of NUDT21 and its effect on the proliferation of human head and neck squamous cell carcinoma. Aging (Albany NY) 2024; 16:3363-3385. [PMID: 38349866 DOI: 10.18632/aging.205539] [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: 11/01/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Based on bioinformatics research of NUDT21 in pan-cancer, we aimed to clarify the mechanism of NUDT21 in HHNC by experiment. METHODS The correlation between differential expression of NUDT21 in pan-cancer and survival prognosis, genomic instability, tumor stemness, DNA repair, RNA methylation and with immune microenvironment were analyzed by the application of different pan-cancer analysis web databases. In addition, immunohistochemistry staining and genetic detection of NUDT21 in HHNCC tumor tissues by immunohistochemistry and qRT-PCR. Then, through in vitro cell experiments, NUDT21 was knocked down by lentivirus to detect the proliferation, cycle, apoptosis of FaDu and CNE-2Z cells, and finally by PathScan intracellular signaling array reagent to detect the apoptotic protein content. RESULTS Based on the pan-cancer analysis, we found that elevated expression of NUDT21 in most cancers was significantly correlated with TMB, MSI, neoantigens and chromosomal ploidy, and in epigenetics, elevated NUDT21 expression was strongly associated with genomic stability, mismatch repair genes, tumor stemness, and RNA methylation. Based on immunosuppressive score, we found that NUDT21 plays an essential role in the immunosuppressive environment by suppressing immune checkpointing effect in most cancers. In addition, using HHNSCC as a study target, PCR and pathological detection of NUDT21 in tumor tissues was significantly increased than that in paracancerous normal tissues. In vitro cellular assays, silencing NUDT21 inhibited proliferation and promoted apoptosis in FaDu and CNE-2Z cells, and blocked the cell cycle in the G2/M phase. Therefore, the experiments confirmed that NUDT21 promotes the proliferation of FaDu by suppressing the expression of apoptotic.
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Affiliation(s)
- Wenjing Liu
- Key Laboratory of Ningxia Minority Medicine Modernization Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yingna Pang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Xiaolu Yu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Doudou Lu
- Clinical Medical College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yating Yang
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Fandi Meng
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Chengbi Xu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Ling Yuan
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yi Nan
- Key Laboratory of Ningxia Minority Medicine Modernization Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
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Ciganda M, Sotelo-Silveira J, Dubey AP, Pandey P, Smith JT, Shen S, Qu J, Smircich P, Read LK. Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state. RNA (NEW YORK, N.Y.) 2023; 29:1881-1895. [PMID: 37730435 PMCID: PMC10653379 DOI: 10.1261/rna.079625.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Trypanosoma brucei occupies distinct niches throughout its life cycle, within both the mammalian and tsetse fly hosts. The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. In kinetoplastid protozoa, including T. brucei, posttranscriptional control mechanisms are the primary means of gene regulation, and these are often mediated by RNA-binding proteins. DRBD18 is a T. brucei RNA-binding protein that reportedly interacts with ribosomal proteins and translation factors. Here, we tested a role for DRBD18 in translational control. We validate the DRBD18 interaction with translating ribosomes and the translation initiation factor, eIF3a. We further show that DRBD18 depletion by RNA interference leads to altered polysomal profiles with a specific depletion of heavy polysomes. Ribosome profiling analysis reveals that 101 transcripts change in translational efficiency (TE) upon DRBD18 depletion: 41 exhibit decreased TE and 60 exhibit increased TE. A further 66 transcripts are buffered, that is, changes in transcript abundance are compensated by changes in TE such that the total translational output is expected not to change. In DRBD18-depleted cells, a set of transcripts that codes for procyclic form-specific proteins is translationally repressed while, conversely, transcripts that code for bloodstream form- and metacyclic form-specific proteins are translationally enhanced. RNA immunoprecipitation/qRT-PCR indicates that DRBD18 associates with members of both repressed and enhanced cohorts. These data suggest that DRBD18 contributes to the maintenance of the procyclic state through both positive and negative translational control of specific mRNAs.
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Affiliation(s)
- Martin Ciganda
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - José Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay
| | - Ashutosh P Dubey
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Parul Pandey
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Joseph T Smith
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo and NYS Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo and NYS Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, USA
| | - Pablo Smircich
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay
- Sección Genómica Funcional, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Laurie K Read
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
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Zhang J, Liu Y, Li C, Xiao Q, Zhang D, Chen Y, Rosenecker J, Ding X, Guan S. Recent Advances and Innovations in the Preparation and Purification of In Vitro-Transcribed-mRNA-Based Molecules. Pharmaceutics 2023; 15:2182. [PMID: 37765153 PMCID: PMC10536309 DOI: 10.3390/pharmaceutics15092182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic poses a disruptive impact on public health and the global economy. Fortunately, the development of COVID-19 vaccines based on in vitro-transcribed messenger RNA (IVT mRNA) has been a breakthrough in medical history, benefiting billions of people with its high effectiveness, safety profile, and ease of large-scale production. This success is the result of decades of continuous RNA research, which has led to significant improvements in the stability and expression level of IVT mRNA through various approaches such as sequence optimization and improved preparation processes. IVT mRNA sequence optimization has been shown to have a positive effect on enhancing the mRNA expression level. The innovation of IVT mRNA purification technology is also indispensable, as the purity of IVT mRNA directly affects the success of downstream vaccine preparation processes and the potential for inducing unwanted side effects in therapeutic applications. Despite the progress made, challenges related to IVT mRNA sequence design and purification still require further attention to enhance the quality of IVT mRNA in the future. In this review, we discuss the latest innovative progress in IVT mRNA design and purification to further improve its clinical efficacy.
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Affiliation(s)
- Jingjing Zhang
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Yuheng Liu
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Chao Li
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Qin Xiao
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Dandan Zhang
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Yang Chen
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Joseph Rosenecker
- Department of Pediatrics, Ludwig-Maximilians University of Munich, 80337 Munich, Germany;
| | - Xiaoyan Ding
- Department of Pediatrics, Ludwig-Maximilians University of Munich, 80337 Munich, Germany;
| | - Shan Guan
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
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Ciganda M, Sotelo-Silveira J, Smith JT, Shen S, Qu J, Smircich P, Read LK. Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527724. [PMID: 36798237 PMCID: PMC9934708 DOI: 10.1101/2023.02.08.527724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Trypanosoma brucei occupies distinct niches throughout its life cycle, within both the mammalian and tsetse fly hosts. The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. Whereas most well-studied organisms rely on transcriptional control as the main regulator of gene expression, post-transcriptional control mechanisms are particularly important in T. brucei , and these are often mediated by RNA-binding proteins. DRBD18 is a T. brucei RNA-binding protein that interacts with ribosomal proteins and translation factors. Here, we tested a role for DRBD18 in translational control. We show that DRBD18 depletion by RNA interference leads to altered polysomal profiles with a specific depletion of heavy polysomes. Ribosome profiling analysis reveals that 101 transcripts change in translational efficiency (TE) upon DRBD18 depletion: 41 exhibit decreased TE and 60 exhibit increased TE. A further 66 transcripts are buffered, i.e . changes in transcript abundance are compensated by changes in TE such that the total translational output is expected not to change. Proteomic analysis validates these data. In DRBD18-depleted cells, a cohort of transcripts that codes for procyclic form-specific proteins is translationally repressed while, conversely, transcripts that code for bloodstream form- and metacyclic form-specific proteins are translationally enhanced. These data suggest that DRBD18 contributes to the maintenance of the procyclic state through both positive and negative translational control of specific mRNAs.
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Alternative RNA Conformations: Companion or Combatant. Genes (Basel) 2022; 13:genes13111930. [DOI: 10.3390/genes13111930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/04/2022] Open
Abstract
RNA molecules, in one form or another, are involved in almost all aspects of cell physiology, as well as in disease development. The diversity of the functional roles of RNA comes from its intrinsic ability to adopt complex secondary and tertiary structures, rivaling the diversity of proteins. The RNA molecules form dynamic ensembles of many interconverting conformations at a timescale of seconds, which is a key for understanding how they execute their cellular functions. Given the crucial role of RNAs in various cellular processes, we need to understand the RNA molecules from a structural perspective. Central to this review are studies aimed at revealing the regulatory role of conformational equilibria in RNA in humans to understand genetic diseases such as cancer and neurodegenerative diseases, as well as in pathogens such as bacteria and viruses so as to understand the progression of infectious diseases. Furthermore, we also summarize the prior studies on the use of RNA structures as platforms for the rational design of small molecules for therapeutic applications.
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Ma XX, Qiu YY, Chang ZG, Gao JF, Jiang RR, Li CL, Wang CR, Chang QC. Identification of Myoferlin, a Potential Serodiagnostic Antigen of Clonorchiasis, via Immunoproteomic Analysis of Sera From Different Infection Periods and Excretory-Secretory Products of Clonorchis sinensis. Front Cell Infect Microbiol 2021; 11:779259. [PMID: 34733798 PMCID: PMC8558468 DOI: 10.3389/fcimb.2021.779259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
Clonorchiasis, which is caused by Clonorchis sinensis, is an important foodborne disease worldwide. The excretory-secretory products (ESPs) of C. sinensis play important roles in host-parasite interactions by acting as causative agents. In the present study, the ESPs and sera positive for C. sinensis were collected to identify proteins specific to the sera of C. sinensis (i.e., proteins that do not cross-react with Fasciola hepatica and Schistosoma japonicum) at different infection periods. Briefly, white Japanese rabbits were artificially infected with C. sinensis, and their sera were collected at 7 days post-infection (dpi), 14 dpi, 35 dpi, and 77 dpi. To identify the specific proteins in C. sinensis, a co-immunoprecipitation (Co-IP) assay was conducted using shotgun liquid chromatography tandem-mass spectrometry (LC-MS/MS) to pull down the sera roots of C. sinensis, F. hepatica, and S. japonicum. For the annotated proteins, 32, 18, 39, and 35 proteins specific to C. sinensis were pulled down by the infected sera at 7, 14, 35, and 77 dpi, respectively. Three proteins, Dynein light chain-1, Dynein light chain-2 and Myoferlin were detected in all infection periods. Of these proteins, myoferlin is known to be overexpressed in several human cancers and could be a promising biomarker and therapeutic target for cancer cases. Accordingly, this protein was selected for further studies. To achieve a better expression, myoferlin was truncated into two parts, Myof1 and Myof2 (1,500 bp and 810 bp), based on the antigenic epitopes provided by bioinformatics. The estimated molecular weight of the recombinant proteins was 57.3 ku (Myof1) and 31.3 ku (Myof2). Further, both Myof1 and Myof2 could be probed by the sera from rabbits infected with C. sinensis. No cross-reaction occurred with the positive sera of S. japonica, F. hepatica, and negative controls. Such findings indicate that myoferlin may be an important diagnostic antigen present in the ESPs. Overall, the present study provides new insights into proteomic changes between ESPs and hosts in different infection periods by LC-MS/MS. Moreover, myoferlin, as a biomarker, may be used to develop an objective method for future diagnosis of clonorchiasis.
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Affiliation(s)
- Xiao-Xiao Ma
- School of Public Health, Shantou University, Shantou, China.,College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yang-Yuan Qiu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhi-Guang Chang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jun-Feng Gao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | | | - Chun-Lin Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qiao-Cheng Chang
- School of Public Health, Shantou University, Shantou, China.,College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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Identification of a non-coding RNA and its putative involvement in the regulation of tetanus toxin synthesis in Clostridium tetani. Sci Rep 2021; 11:4157. [PMID: 33603121 PMCID: PMC7892561 DOI: 10.1038/s41598-021-83623-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/29/2021] [Indexed: 11/17/2022] Open
Abstract
Clostridium tetani produces the tetanus toxin (TeNT), one of the most powerful bacterial toxins known to humankind and responsible for tetanus. The regulation of toxin expression is complex and involves the alternative sigma factor TetR as well as other regulators. Here, a transcriptional analysis of the TeNT-encoding large plasmid of C. tetani identified a putative non-coding small RNA (sRNA), located in close vicinity of the 3′ untranslated region of the tent gene. A northern blot experiment could identify a respective sRNA with a size of approx. 140 nucleotides. Sequence analysis showed that the sRNA contains a 14-nucleotide region that is complementary to a 5′ located region of tent. In order to investigate the function of the sRNA, we applied a RNA interference approach targeting the sRNA in two C. tetani wild-type strains; the constructed antisense C. tetani strains showed an approx. threefold increase in both extracellular and total TeNT production compared to the respective wild-type strains. In addition, recombinant C. tetani strains were constructed that contained tent-locus harboring plasmids with and without the sRNA. However, the introduction of the tent-locus without the sRNA in a C. tetani strain lacking the wild-type TeNT-encoding large plasmid resulted in a lower TeNT production compared to the same strain with recombinant tent-locus with the sRNA. This suggests that the expression or the effect of the sRNA is modulated by the C. tetani genetic background, notably that of the wild-type TeNT-encoding large plasmid. In addition, some recombinant strains exhibited modulated growth patterns, characterized by premature bacterial cell lysis. Taken together, our data indicate that the sRNA acts as a negative regulator of TeNT synthesis, with a possible impact on the growth of C. tetani. We hypothesize that the role of this sRNA is to limit toxin levels in the exponential growth phase in order to prevent premature bacterial lysis.
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Menendez-Gil P, Toledo-Arana A. Bacterial 3'UTRs: A Useful Resource in Post-transcriptional Regulation. Front Mol Biosci 2021; 7:617633. [PMID: 33490108 PMCID: PMC7821165 DOI: 10.3389/fmolb.2020.617633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Bacterial messenger RNAs (mRNAs) are composed of 5′ and 3′ untranslated regions (UTRs) that flank the coding sequences (CDSs). In eukaryotes, 3′UTRs play key roles in post-transcriptional regulatory mechanisms. Shortening or deregulation of these regions is associated with diseases such as cancer and metabolic disorders. Comparatively, little is known about the functions of 3′UTRs in bacteria. Over the past few years, 3′UTRs have emerged as important players in the regulation of relevant bacterial processes such as virulence, iron metabolism, and biofilm formation. This MiniReview is an update for the different 3′UTR-mediated mechanisms that regulate gene expression in bacteria. Some of these include 3′UTRs that interact with the 5′UTR of the same transcript to modulate translation, 3′UTRs that are targeted by specific ribonucleases, RNA-binding proteins and small RNAs (sRNAs), and 3′UTRs that act as reservoirs of trans-acting sRNAs, among others. In addition, recent findings regarding a differential evolution of bacterial 3′UTRs and its impact in the species-specific expression of orthologous genes are also discussed.
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Affiliation(s)
- Pilar Menendez-Gil
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC) - Gobierno de Navarra, Navarra, Spain
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC) - Gobierno de Navarra, Navarra, Spain
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Menendez-Gil P, Caballero CJ, Catalan-Moreno A, Irurzun N, Barrio-Hernandez I, Caldelari I, Toledo-Arana A. Differential evolution in 3'UTRs leads to specific gene expression in Staphylococcus. Nucleic Acids Res 2020; 48:2544-2563. [PMID: 32016395 PMCID: PMC7049690 DOI: 10.1093/nar/gkaa047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 12/05/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
The evolution of gene expression regulation has contributed to species differentiation. The 3′ untranslated regions (3′UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3′UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3′UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3′UTR of orthologous genes and demonstrated that 3′UTR sequence variations affect protein production. This suggested that species-specific functional 3′UTRs might be specifically selected during evolution. 3′UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3′UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3′UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3′UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.
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Affiliation(s)
- Pilar Menendez-Gil
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Carlos J Caballero
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Arancha Catalan-Moreno
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Naiara Irurzun
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000-Strasbourg, France
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
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11
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New sequencing methodologies reveal interplay between multiple RNA-binding proteins and their RNAs. Curr Genet 2020; 66:713-717. [PMID: 32193580 DOI: 10.1007/s00294-020-01066-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 01/18/2023]
Abstract
It is now established that base-pairing regulatory RNAs are key players in post-transcriptional regulatory networks where they affect the translation and/or stability of their target RNAs. In many cases, the base-pairing between two RNAs is facilitated by an RNA-binding protein (RBP) that serves as an RNA chaperone. Recent advances in sequencing methods have revealed the RNA populations bound by the RBPs, yielding insights valuable into regulatory networks. Further analyses of these networks can improve our understanding of the roles played by RBPs in the regulation of gene expression by regulatory RNAs, especially when multiple RBPs are involved. For example, using an RNA sequencing-based methodology that captures RNA-RNA pairs on RBP, an interplay between two RBPs in bacteria that compete on the same RNA-RNA pair was revealed. In this case, one protein promotes negative regulation of the target RNA, while the second protein can block this regulation. In this mini-review, I outline the exciting future directions that can be taken to deepen our understanding of the roles played by RBPs in post-transcriptional regulation, and discuss how the different sequencing methods can assist in deciphering the relationships among RBPs, and between the RBPs and the RNAs they bind. Having a more detailed picture of the RBPs-RNAs network will elucidate how bacteria can have nuanced control of gene expression, critical for survival in the varied environments in which bacteria live.
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Dos Santos RF, Arraiano CM, Andrade JM. New molecular interactions broaden the functions of the RNA chaperone Hfq. Curr Genet 2019; 65:1313-1319. [PMID: 31104083 DOI: 10.1007/s00294-019-00990-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/09/2023]
Abstract
The RNA chaperone Hfq is an important bacterial post-transcriptional regulator. Most studies on Hfq are focused on the role of this protein on small non-coding RNAs (sRNAs) and messenger RNAs (mRNAs). The most well-characterized function of Hfq is its role as RNA matchmaker, promoting the base-pairing between sRNAs and their mRNA targets. However, novel substrates and previous unrecognized functions of Hfq have now been identified, which expanded the regulatory spectrum of this protein. Hfq was recently found to bind rRNA and act as a new ribosome biogenesis factor, affecting rRNA processing, ribosome assembly, translational efficiency and translational fidelity. Hfq was also found to bind tRNAs, which could provide an additional mechanism for its role on the accuracy of protein synthesis. The list of substrates does not include RNA exclusively since Hfq was shown to bind DNA, playing an important role in DNA compaction. Additionally, Hfq is also capable to establish many protein-protein interactions. Overall, the functions of the RNA-binding protein Hfq have been expanded beyond its function in small RNA-mediated regulation. The identification of additional substrates and new functions provides alternative explanations for the importance of the chaperone Hfq as a global regulator.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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