1
|
Morón Á, Ortiz-Miravalles L, Peñalver M, García-Del Portillo F, Pucciarelli MG, Ortega AD. Rli51 Attenuates Transcription of the Listeria Pathogenicity Island 1 Gene mpl and Functions as a Trans-Acting sRNA in Intracellular Bacteria. Int J Mol Sci 2024; 25:9380. [PMID: 39273334 PMCID: PMC11394854 DOI: 10.3390/ijms25179380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Listeria pathogenicity island 1 (LIPI-1) is a genetic region containing a cluster of genes essential for virulence of the bacterial pathogen Listeria monocytogenes. Main virulence factors in LIPI-1 include long 5' untranslated regions (5'UTRs), among which is Rli51, a small RNA (sRNA) in the 5'UTR of the Zn-metalloprotease-coding mpl. So far, Rli51 function and molecular mechanisms have remained obscure. Here, we show that Rli51 exhibits a dual mechanism of regulation, functioning as a cis- and as a trans-acting sRNA. Under nutrient-rich conditions, rli51-mpl transcription is prematurely terminated, releasing a short 121-nucleotide-long sRNA. Rli51 is predicted to function as a transcription attenuator that can fold into either a terminator or a thermodynamically more stable antiterminator. We show that the sRNA Rli21/RliI binds to a single-stranded RNA loop in Rli51, which is essential to mediate premature transcription termination, suggesting that sRNA binding could stabilize the terminator fold. During intracellular infection, rli51 transcription is increased, which generates a higher abundance of the short Rli51 sRNA and allows for transcriptional read-through into mpl. Comparative intracellular bacterial transcriptomics in rli51-null mutants and the wild-type reference strain EGD-e suggests that Rli51 upregulates iron-scavenging proteins and downregulates virulence factors from LIPI-1. MS2 affinity purification confirmed that Rli51 binds transcripts of the heme-binding protein Lmo2186 and Lmo0937 in vivo. These results prove that Rli51 functions as a trans-acting sRNA in intracellular bacteria. Our research shows a growth condition-dependent mechanism of regulation for Rli51, preventing unintended mpl transcription in extracellular bacteria and regulating genes important for virulence in intracellular bacteria.
Collapse
Affiliation(s)
- Álvaro Morón
- Department of Cell Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
| | - Laura Ortiz-Miravalles
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
| | - Marcos Peñalver
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
| | | | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
| | - Alvaro Darío Ortega
- Department of Cell Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biologia Molecular Severo Ochoa (CBM) CSIC-UAM, 28049 Madrid, Spain
| |
Collapse
|
2
|
Erdem M, Cicek M, Erson-Bensan AE. Versatile RNA: overlooked gems of the transcriptome. FEBS J 2023; 290:4843-4851. [PMID: 36719259 DOI: 10.1111/febs.16742] [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: 10/31/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/01/2023]
Abstract
The critical role of RNA, its use and targetability concerning different aspects of human health are gaining more attention because our understanding of the versatility of RNA has dramatically evolved over the last decades. We now appreciate that RNA is far more critical than a messenger molecule and possesses many complicated functions. As a multifunctional molecule with its sequence, flexible structures and enzymatic abilities, RNA is genuinely powerful. Mammalian transcriptomes consist of a dynamically regulated plethora of coding and noncoding RNA types. However, some aspects of RNA metabolism remain to be explored. In this Viewpoint, we focus on the transcriptome's unconventional and possibly overlooked aspects to emphasize the importance of RNA in mammalian systems.
Collapse
Affiliation(s)
- Murat Erdem
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mustafa Cicek
- Department of Biology, Kamil Ozdag Faculty of Science, Karamanoglu Mehmetbey University, Karaman, Turkey
| | | |
Collapse
|
3
|
Diallo I, Ho J, Lalaouna D, Massé E, Provost P. RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria. Front Mol Biosci 2022; 9:914991. [PMID: 35720117 PMCID: PMC9203972 DOI: 10.3389/fmolb.2022.914991] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 12/21/2022] Open
Abstract
RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of an eukaryotic 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma and, by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16 nt). Here we report the detailed profiling of vsRNAs in Escherichia coli, E. coli-derived outer membrane vesicles (OMVs) and five other bacterial strains (Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella enterica serovar Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001). vsRNAs of 8–15 nt in length [RNAs (8-15 nt)] were found to be more abundant than RNAs of 16–30 nt in length [RNAs (16–30 nt)]. vsRNA biotypes were distinct and varied within and across bacterial species and accounted for one third of reads identified in the 8–30 nt window. The tRNA-derived fragments (tRFs) have appeared as a major biotype among the vsRNAs, notably Ile-tRF and Ala-tRF, and were selectively loaded in OMVs. tRF-derived vsRNAs appear to be thermodynamically stable with at least 2 G-C basepairs and stem-loop structure. The analyzed tRF-derived vsRNAs are predicted to target several human host mRNAs with diverse functions. Bacterial vsRNAs and OMV-derived vsRNAs could be novel players likely modulating the intricate relationship between pathogens and their hosts.
Collapse
Affiliation(s)
- Idrissa Diallo
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Jeffrey Ho
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - David Lalaouna
- CRCHUS, RNA Group, Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Eric Massé
- CRCHUS, RNA Group, Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Patrick Provost
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- *Correspondence: Patrick Provost,
| |
Collapse
|
4
|
The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa. Genes (Basel) 2021; 12:genes12122030. [PMID: 34946978 PMCID: PMC8700879 DOI: 10.3390/genes12122030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.
Collapse
|
5
|
Tiwari B, Habermann K, Arif MA, Top O, Frank W. Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:656657. [PMID: 34211484 PMCID: PMC8239388 DOI: 10.3389/fpls.2021.656657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/21/2021] [Indexed: 05/19/2023]
Abstract
The biological significance of non-coding RNAs (ncRNAs) has been firmly established to be important for the regulation of genes involved in stress acclimation. Light plays an important role for the growth of plants providing the energy for photosynthesis; however, excessive light conditions can also cause substantial defects. Small RNAs (sRNAs) are a class of non-coding RNAs that regulate transcript levels of protein-coding genes and mediate epigenetic silencing. Next generation sequencing facilitates the identification of small non-coding RNA classes such as miRNAs (microRNAs) and small-interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), but changes in the ncRNA transcriptome in response to high light are poorly understood. We subjected Arabidopsis plants to high light conditions and performed a temporal in-depth study of the transcriptome data after 3 h, 6 h, and 2 days of high light treatment. We identified a large number of high light responsive miRNAs and sRNAs derived from NAT gene pairs, lncRNAs and TAS transcripts. We performed target predictions for differentially expressed miRNAs and correlated their expression levels through mRNA sequencing data. GO analysis of the targets revealed an overrepresentation of genes involved in transcriptional regulation. In A. thaliana, sRNA-mediated regulation of gene expression in response to high light treatment is mainly carried out by miRNAs and sRNAs derived from NAT gene pairs, and from lncRNAs. This study provides a deeper understanding of sRNA-dependent regulatory networks in high light acclimation.
Collapse
|
6
|
Li S, Edelmann D, Berghoff BA, Georg J, Evguenieva-Hackenberg E. Bioinformatic prediction reveals posttranscriptional regulation of the chromosomal replication initiator gene dnaA by the attenuator sRNA rnTrpL in Escherichia coli. RNA Biol 2020; 18:1324-1338. [PMID: 33164661 DOI: 10.1080/15476286.2020.1846388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DnaA is the initiator protein of chromosome replication, but the regulation of its homoeostasis in enterobacteria is not well understood. The DnaA level remains stable at different growth rates, suggesting a link between metabolism and dnaA expression. In a bioinformatic prediction, which we made to unravel targets of the sRNA rnTrpL in Enterobacteriaceae, the dnaA mRNA was the most conserved target candidate. The sRNA rnTrpL is derived from the transcription attenuator of the tryptophan biosynthesis operon. In Escherichia coli, its level is higher in minimal than in rich medium due to derepressed transcription without external tryptophan supply. Overexpression and deletion of the rnTrpL gene decreased and increased, respectively, the levels of dnaA mRNA. The decrease of the dnaA mRNA level upon rnTrpL overproduction was dependent on hfq and rne. Base pairing between rnTrpL and dnaA mRNA in vivo was validated. In minimal medium, the oriC level was increased in the ΔtrpL mutant, in line with the expected DnaA overproduction and increased initiation of chromosome replication. In line with this, chromosomal rnTrpL mutation abolishing the interaction with dnaA increased both the dnaA mRNA and the oriC level. Moreover, upon addition of tryptophan to minimal medium cultures, the oriC level in the wild type was increased. Thus, rnTrpL is a base-pairing sRNA that posttranscriptionally regulates dnaA in E. coli. Furthermore, our data suggest that rnTrpL contributes to the DnaA homoeostasis in dependence on the nutrient availability, which is represented by the tryptophan level in the cell.
Collapse
Affiliation(s)
- Siqi Li
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Daniel Edelmann
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | |
Collapse
|
7
|
Melior H, Li S, Madhugiri R, Stötzel M, Azarderakhsh S, Barth-Weber S, Baumgardt K, Ziebuhr J, Evguenieva-Hackenberg E. Transcription attenuation-derived small RNA rnTrpL regulates tryptophan biosynthesis gene expression in trans. Nucleic Acids Res 2020; 47:6396-6410. [PMID: 30993322 PMCID: PMC6614838 DOI: 10.1093/nar/gkz274] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/01/2019] [Accepted: 04/12/2019] [Indexed: 01/06/2023] Open
Abstract
Ribosome-mediated transcription attenuation is a basic posttranscriptional regulation mechanism in bacteria. Liberated attenuator RNAs arising in this process are generally considered nonfunctional. In Sinorhizobium meliloti, the tryptophan (Trp) biosynthesis genes are organized into three operons, trpE(G), ppiD-trpDC-moaC-moeA, and trpFBA-accD-folC, of which only the first one, trpE(G), contains a short ORF (trpL) in the 5′-UTR and is regulated by transcription attenuation. Under conditions of Trp sufficiency, transcription is terminated between trpL and trpE(G), and a small attenuator RNA, rnTrpL, is produced. Here, we show that rnTrpL base-pairs with trpD and destabilizes the polycistronic trpDC mRNA, indicating rnTrpL-mediated downregulation of the trpDC operon in trans. Although all three trp operons are regulated in response to Trp availability, only in the two operons trpE(G) and trpDC the Trp-mediated regulation is controlled by rnTrpL. Together, our data show that the trp attenuator coordinates trpE(G) and trpDC expression posttranscriptionally by two fundamentally different mechanisms: ribosome-mediated transcription attenuation in cis and base-pairing in trans. Also, we present evidence that rnTrpL-mediated regulation of trpDC genes expression in trans is conserved in Agrobacterium and Bradyrhizobium, suggesting that the small attenuator RNAs may have additional conserved functions in the control of bacterial gene expression.
Collapse
Affiliation(s)
- Hendrik Melior
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, 35392, Germany
| | - Siqi Li
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, 35392, Germany
| | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University, Giessen, 35392, Germany
| | - Maximilian Stötzel
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, 35392, Germany
| | - Saina Azarderakhsh
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, 35392, Germany
| | - Susanne Barth-Weber
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, 35392, Germany
| | - Kathrin Baumgardt
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, 35392, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, 35392, Germany
| | | |
Collapse
|
8
|
Bédard ASV, Hien EDM, Lafontaine DA. Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194501. [PMID: 32036061 DOI: 10.1016/j.bbagrm.2020.194501] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/17/2022]
Abstract
Riboswitches are RNA sensors that have been shown to modulate the expression of downstream genes by altering their structure upon metabolite binding. Riboswitches are unique among cellular regulators in that metabolite detection is strictly performed using RNA interactions with the sensed metabolite and in which no regulatory protein is needed to mediate the interaction. However, recent studies have shed light on riboswitch control mechanisms relying on protein regulators to harness metabolite binding for the mediation of gene expression, thereby increasing the range of cellular factors involved in riboswitch regulation. The interaction between riboswitches and proteins adds another level of evolutionary pressure as riboswitches must maintain key residues for metabolite detection, structural switching and protein binding sites. Here, we review regulatory mechanisms involving Escherichia coli riboswitches that have recently been shown to rely on regulatory proteins. We also discuss the implication of such protein-based riboswitch regulatory mechanisms for genetic regulation.
Collapse
Affiliation(s)
- Anne-Sophie Vézina Bédard
- Department of biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Elsa D M Hien
- Department of biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Daniel A Lafontaine
- Department of biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada.
| |
Collapse
|
9
|
Carvalho Barbosa C, Calhoun SH, Wieden HJ. Non-coding RNAs: what are we missing? Biochem Cell Biol 2020; 98:23-30. [DOI: 10.1139/bcb-2019-0037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Over the past two decades, the importance of small non-coding RNAs (sncRNAs) as regulatory molecules has become apparent in all three domains of life (archaea, bacteria, eukaryotes). In fact, sncRNAs play an important role in the control of gene expression at both the transcriptional and the post-transcriptional level, with crucial roles in fine-tuning cell responses during internal and external stress. Multiple pathways for sncRNA biogenesis and diverse mechanisms of regulation have been reported, and although biogenesis and mechanisms of sncRNAs in prokaryotes and eukaryotes are different, remarkable similarities exist. Here, we briefly review and compare the major sncRNA classes that act post-transcriptionally, and focus on recent discoveries regarding the ribosome as a target of regulation and the conservation of these mechanisms between prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- Cristina Carvalho Barbosa
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Sydnee H. Calhoun
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
10
|
Ren J, Lee J, Na D. Recent advances in genetic engineering tools based on synthetic biology. J Microbiol 2020; 58:1-10. [PMID: 31898252 DOI: 10.1007/s12275-020-9334-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/19/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022]
Abstract
Genome-scale engineering is a crucial methodology to rationally regulate microbiological system operations, leading to expected biological behaviors or enhanced bioproduct yields. Over the past decade, innovative genome modification technologies have been developed for effectively regulating and manipulating genes at the genome level. Here, we discuss the current genome-scale engineering technologies used for microbial engineering. Recently developed strategies, such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, multiplex automated genome engineering (MAGE), promoter engineering, CRISPR-based regulations, and synthetic small regulatory RNA (sRNA)-based knockdown, are considered as powerful tools for genome-scale engineering in microbiological systems. MAGE, which modifies specific nucleotides of the genome sequence, is utilized as a genome-editing tool. Contrastingly, synthetic sRNA, CRISPRi, and CRISPRa are mainly used to regulate gene expression without modifying the genome sequence. This review introduces the recent genome-scale editing and regulating technologies and their applications in metabolic engineering.
Collapse
Affiliation(s)
- Jun Ren
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jingyu Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
| |
Collapse
|
11
|
Romanova EV, Bukin YS, Mikhailov KV, Logacheva MD, Aleoshin VV, Sherbakov DY. Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. Mol Phylogenet Evol 2019; 144:106710. [PMID: 31846708 DOI: 10.1016/j.ympev.2019.106710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
The evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding. The additional tRNA gene findings were verified using phylogenetic analysis and genetic distance analysis. The majority of remolded tRNA genes (seven out of ten cases) were found in the mt genomes of endemic amphipod species from Lake Baikal. All additional mt tRNA genes arose independently in the Baikalian amphipods, indicating the unusual plasticity of tRNA gene evolution in these species assemblages. The possible reasons for the unusual abundance of additional tRNA genes in the mt genomes of Baikalian amphipods are discussed. The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional cases of duplicated tRNA genes overlooked by using less specific Metazoa-wide models. The application of these models for mt tRNA gene prediction will be useful for the correct annotation of mt genomes of amphipods and probably other crustaceans.
Collapse
Affiliation(s)
- Elena V Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation.
| | - Yurij S Bukin
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
| | - Kirill V Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria D Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry Yu Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
| |
Collapse
|
12
|
Ethanolamine Utilization and Bacterial Microcompartment Formation Are Subject to Carbon Catabolite Repression. J Bacteriol 2019; 201:JB.00703-18. [PMID: 30833356 DOI: 10.1128/jb.00703-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/24/2019] [Indexed: 12/13/2022] Open
Abstract
Ethanolamine (EA) is a compound prevalent in the gastrointestinal (GI) tract that can be used as a carbon, nitrogen, and/or energy source. Enterococcus faecalis, a GI commensal and opportunistic pathogen, contains approximately 20 ethanolamine utilization (eut) genes encoding the necessary regulatory, enzymatic, and structural proteins for this process. Here, using a chemically defined medium, two regulatory factors that affect EA utilization were examined. First, the functional consequences of loss of the small RNA (sRNA) EutX on the efficacy of EA utilization were investigated. One effect observed, as loss of this negative regulator causes an increase in eut gene expression, was a concomitant increase in the number of catabolic bacterial microcompartments (BMCs) formed. However, despite this increase, the growth of the strain was repressed, suggesting that the overall efficacy of EA utilization was negatively affected. Second, utilizing a deletion mutant and a complement, carbon catabolite control protein A (CcpA) was shown to be responsible for the repression of EA utilization in the presence of glucose. A predicted cre site in one of the three EA-inducible promoters, PeutS, was identified as the target of CcpA. However, CcpA was shown to affect the activation of all the promoters indirectly through the two-component system EutV and EutW, whose genes are under the control of the PeutS promoter. Moreover, a bioinformatics analysis of bacteria predicted to contain CcpA and cre sites revealed that a preponderance of BMC-containing operons are likely regulated by carbon catabolite repression (CCR).IMPORTANCE Ethanolamine (EA) is a compound commonly found in the gastrointestinal (GI) tract that can affect the behavior of human pathogens that can sense and utilize it, such as Enterococcus faecalis and Salmonella Therefore, it is important to understand how the genes that govern EA utilization are regulated. In this work, we investigated two regulatory factors that control this process. One factor, a small RNA (sRNA), is shown to be important for generating the right levels of gene expression for maximum efficiency. The second factor, a transcriptional repressor, is important for preventing expression when other preferred sources of energy are available. Furthermore, a global bioinformatics analysis revealed that this second mechanism of transcriptional regulation likely operates on similar genes in related bacteria.
Collapse
|
13
|
Singh P, Kumar N, Jethva M, Yadav S, Kumari P, Thakur A, Kushwaha HR. Riboswitch regulation in cyanobacteria is independent of their habitat adaptations. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:315-324. [PMID: 29515325 PMCID: PMC5834989 DOI: 10.1007/s12298-018-0504-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 12/13/2017] [Accepted: 01/02/2018] [Indexed: 01/17/2024]
Abstract
Cyanobacteria are one of the ancient bacterial species occupying a variety of habitats with diverse metabolic preferences. RNA regulators like riboswitches play significant role in controlling the gene expression in prokaryotes. The taxonomic distribution of riboswitches suggests that they might be one of the oldest mechanisms of gene control system. In this paper, we analyzed the distribution of different riboswitch families in various cyanobacterial genomes. It was observed that only four riboswitch classes were abundant in cyanobacteria, B12-element (Cob)/AdoCbl/AdoCbl-variant riboswitch being the most abundant. The analysis suggests that riboswitch mode of regulation is present in cyanobacterial species irrespective of their habitat types. A large number of unidentified genes regulated by riboswitches listed in this analysis indicate the wide range of targets for these riboswitch families. The analysis revealed a large number of genes regulated by riboswitches which may assist in elaborating the diversity among the cyanobacterial species.
Collapse
Affiliation(s)
- Payal Singh
- Synthetic Biology and Biofuel, ternational Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Nilesh Kumar
- Synthetic Biology and Biofuel, ternational Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Minesh Jethva
- Synthetic Biology and Biofuel, ternational Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Saurabh Yadav
- Department of Biotechnology, Hemwati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand India
| | | | | | | |
Collapse
|
14
|
Abstract
Ethanolamine (EA) is a valuable source of carbon and/or nitrogen for bacteria capable of its catabolism. Because it is derived from the membrane phospholipid phosphatidylethanolamine, it is particularly prevalent in the gastrointestinal tract, which is membrane rich due to turnover of the intestinal epithelium and the resident microbiota. Intriguingly, many gut pathogens carry the eut (ethanolamine utilization) genes. EA utilization has been studied for about 50 years, with most of the early work occurring in just a couple of species of Enterobacteriaceae. Once the metabolic pathways and enzymes were characterized by biochemical approaches, genetic screens were used to map the various activities to the eut genes. With the rise of genomics, the diversity of bacteria containing the eut genes and surprising differences in eut gene content were recognized. Some species contain nearly 20 genes and encode many accessory proteins, while others contain only the core catabolic enzyme. Moreover, the eut genes are regulated by very different mechanisms, depending on the organism and the eut regulator encoded. In the last several years, exciting progress has been made in elucidating the complex regulatory mechanisms that govern eut gene expression. Furthermore, a new appreciation for how EA contributes to infection and colonization in the host is emerging. In addition to providing an overview of EA-related biology, this minireview will give special attention to these recent advances.
Collapse
|
15
|
Discovery of new RNA classes and global RNA-binding proteins. Curr Opin Microbiol 2017; 39:152-160. [PMID: 29179042 DOI: 10.1016/j.mib.2017.11.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022]
Abstract
The identification of new RNA functions and the functional annotation of transcripts in genomes represent exciting yet challenging endeavours of modern biology. Crucial insights into the biological roles of RNA molecules can be gained from the identification of the proteins with which they form specific complexes. Modern interactome techniques permit to profile RNA-protein interactions in a genome-wide manner and identify new RNA classes associated with globally acting RNA-binding proteins. Applied to a variety of organisms, these methods are already revolutionising our understanding of RNA-mediated biological processes. Here, we focus on one such approach-Gradient sequencing or Grad-seq-which has recently guided the discovery of protein ProQ and its associated small RNAs as a new domain of post-transcriptional control in bacteria.
Collapse
|
16
|
Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR. Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments. J Biotechnol 2017; 261:85-96. [DOI: 10.1016/j.jbiotec.2017.06.1203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 12/14/2022]
|
17
|
Álvarez-Fraga L, Rumbo-Feal S, Pérez A, Gómez MJ, Gayoso C, Vallejo JA, Ohneck EJ, Valle J, Actis LA, Beceiro A, Bou G, Poza M. Global assessment of small RNAs reveals a non-coding transcript involved in biofilm formation and attachment in Acinetobacter baumannii ATCC 17978. PLoS One 2017; 12:e0182084. [PMID: 28763494 PMCID: PMC5538643 DOI: 10.1371/journal.pone.0182084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/12/2017] [Indexed: 12/30/2022] Open
Abstract
Many strains of Acinetobacter baumannii have been described as being able to form biofilm. Small non-coding RNAs (sRNAs) control gene expression in many regulatory circuits in bacteria. The aim of the present work was to provide a global description of the sRNAs produced both by planktonic and biofilm-associated (sessile) cells of A. baumannii ATCC 17978, and to compare the corresponding gene expression profiles to identify sRNAs molecules associated to biofilm formation and virulence. sRNA was extracted from both planktonic and sessile cells and reverse transcribed. cDNA was subjected to 454-pyrosequencing using the GS-FLX Titanium chemistry. The global analysis of the small RNA transcriptome revealed different sRNA expression patterns in planktonic and biofilm associated cells, with some of the transcripts only expressed or repressed in sessile bacteria. A total of 255 sRNAs were detected, with 185 of them differentially expressed in the different types of cells. A total of 9 sRNAs were expressed only in biofilm cells, while the expression of other 21 coding regions were repressed only in biofilm cells. Strikingly, the expression level of the sRNA 13573 was 120 times higher in biofilms than in planktonic cells, an observation that prompted us to further investigate the biological role of this non-coding transcript. Analyses of an isogenic mutant and over-expressing strains revealed that the sRNA 13573 gene is involved in biofilm formation and attachment to A549 human alveolar epithelial cells. The present work serves as a basis for future studies examining the complex regulatory network that regulate biofilm biogenesis and attachment to eukaryotic cells in A. baumannii ATCC 17978.
Collapse
Affiliation(s)
- Laura Álvarez-Fraga
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Soraya Rumbo-Feal
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Astrid Pérez
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Manuel J. Gómez
- Department of Molecular Evolution, Center for Astrobiology, INTA-CSIC, Torrejón de Ardoz, Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Carmen Gayoso
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Juan A. Vallejo
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Emily J. Ohneck
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Jaione Valle
- Departamento de Biofilms Microbianos, Instituto de Agrobiotecnología, Navarra, Spain
| | - Luis A. Actis
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Alejandro Beceiro
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Germán Bou
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
- * E-mail: (GB); (MP)
| | - Margarita Poza
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
- * E-mail: (GB); (MP)
| |
Collapse
|
18
|
Mateescu B, Kowal EJK, van Balkom BWM, Bartel S, Bhattacharyya SN, Buzás EI, Buck AH, de Candia P, Chow FWN, Das S, Driedonks TAP, Fernández-Messina L, Haderk F, Hill AF, Jones JC, Van Keuren-Jensen KR, Lai CP, Lässer C, Liegro ID, Lunavat TR, Lorenowicz MJ, Maas SLN, Mäger I, Mittelbrunn M, Momma S, Mukherjee K, Nawaz M, Pegtel DM, Pfaffl MW, Schiffelers RM, Tahara H, Théry C, Tosar JP, Wauben MHM, Witwer KW, Nolte-'t Hoen ENM. Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper. J Extracell Vesicles 2017; 6:1286095. [PMID: 28326170 PMCID: PMC5345583 DOI: 10.1080/20013078.2017.1286095] [Citation(s) in RCA: 519] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/25/2016] [Indexed: 02/07/2023] Open
Abstract
The release of RNA-containing extracellular vesicles (EV) into the extracellular milieu has been demonstrated in a multitude of different in vitro cell systems and in a variety of body fluids. RNA-containing EV are in the limelight for their capacity to communicate genetically encoded messages to other cells, their suitability as candidate biomarkers for diseases, and their use as therapeutic agents. Although EV-RNA has attracted enormous interest from basic researchers, clinicians, and industry, we currently have limited knowledge on which mechanisms drive and regulate RNA incorporation into EV and on how RNA-encoded messages affect signalling processes in EV-targeted cells. Moreover, EV-RNA research faces various technical challenges, such as standardisation of EV isolation methods, optimisation of methodologies to isolate and characterise minute quantities of RNA found in EV, and development of approaches to demonstrate functional transfer of EV-RNA in vivo. These topics were discussed at the 2015 EV-RNA workshop of the International Society for Extracellular Vesicles. This position paper was written by the participants of the workshop not only to give an overview of the current state of knowledge in the field, but also to clarify that our incomplete knowledge – of the nature of EV(-RNA)s and of how to effectively and reliably study them – currently prohibits the implementation of gold standards in EV-RNA research. In addition, this paper creates awareness of possibilities and limitations of currently used strategies to investigate EV-RNA and calls for caution in interpretation of the obtained data.
Collapse
Affiliation(s)
- Bogdan Mateescu
- Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zürich) , Zurich , Switzerland
| | - Emma J K Kowal
- Department of Biology, Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Bas W M van Balkom
- Department of Nephrology and Hypertension, UMC Utrecht , Utrecht , the Netherlands
| | - Sabine Bartel
- Experimental Asthma Research, Priority Area Asthma & Allergy, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL) , Borstel , Germany
| | - Suvendra N Bhattacharyya
- Department of Science and Technology, CSIR-Indian Institute of Chemical Biology , Kolkata , India
| | - Edit I Buzás
- Department of Genetics, Cell- and Immunobiology, Semmelweis University , Budapest , Hungary
| | - Amy H Buck
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh , Edinburgh , UK
| | | | - Franklin W N Chow
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh , Edinburgh , UK
| | - Saumya Das
- Cardiovascular Research Institute, Massachusetts General Hospital , Boston , MA , USA
| | - Tom A P Driedonks
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University , Utrecht , the Netherlands
| | | | - Franziska Haderk
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University , Bundoora , Australia
| | - Jennifer C Jones
- Molecular Immunogenetics & Vaccine Research Section, Vaccine Branch, CCR, NCI , Bethesda , MD , USA
| | | | - Charles P Lai
- Institute of Biomedical Engineering, National Tsing Hua University , Hsinchu , Taiwan
| | - Cecilia Lässer
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School, Boston, MA, USA; Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Italia di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo , Palermo , Italy
| | - Taral R Lunavat
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School, Boston, MA, USA; Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magdalena J Lorenowicz
- Center for Molecular Medicine, University Medical Center Utrecht & Regenerative Medicine Center , Utrecht , the Netherlands
| | - Sybren L N Maas
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School , Boston , MA , USA
| | - Imre Mäger
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Institute of Technology, University of Tartu, Tartu, Estonia
| | - Maria Mittelbrunn
- Instituto de Investigación del Hospital 12 de Octubre , Madrid , Spain
| | - Stefan Momma
- Institute of Neurology (Edinger Institute), Frankfurt University Medical School , Frankfurt am Main , Germany
| | - Kamalika Mukherjee
- Department of Science and Technology, CSIR-Indian Institute of Chemical Biology , Kolkata , India
| | - Muhammed Nawaz
- Department of Pathology and Forensic Medicine, Ribeirão Preto School of Medicine, University of Sao Paulo , Sao Paulo , Brazil
| | - D Michiel Pegtel
- Department of Pathology, Exosomes Research Group, VU University Medical Center , Amsterdam , the Netherlands
| | - Michael W Pfaffl
- Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich (TUM) Weihenstephan , Freising , Germany
| | - Raymond M Schiffelers
- Laboratory Clinical Chemistry & Haematology, University Medical Center Utrecht , Utrecht , the Netherlands
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Institute of Biomedical & Health Sciences, Hiroshima University , Hiroshima , Japan
| | - Clotilde Théry
- Institut Curie, PSL Research University, INSERM U932 , Paris , France
| | - Juan Pablo Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Nuclear Research Center, Faculty of Science, Universidad de la República , Montevideo , Uruguay
| | - Marca H M Wauben
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University , Utrecht , the Netherlands
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology and Department of Neurology, The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University , Utrecht , the Netherlands
| |
Collapse
|