1
|
König F, Svensson SL, Sharma CM. Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni. Nat Commun 2024; 15:5240. [PMID: 38897989 PMCID: PMC11187230 DOI: 10.1038/s41467-024-48986-8] [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: 07/06/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
Like for many bacteria, flagella are crucial for Campylobacter jejuni motility and virulence. Biogenesis of the flagellar machinery requires hierarchical transcription of early, middle (RpoN-dependent), and late (FliA-dependent) genes. However, little is known about post-transcriptional regulation of flagellar biogenesis by small RNAs (sRNAs). Here, we characterized two sRNAs with opposing effects on C. jejuni filament assembly and motility. We demonstrate that CJnc230 sRNA (FlmE), encoded downstream of the flagellar hook protein, is processed from the RpoN-dependent flgE mRNA by RNase III, RNase Y, and PNPase. We identify mRNAs encoding a flagella-interaction regulator and the anti-sigma factor FlgM as direct targets of CJnc230 repression. CJnc230 overexpression upregulates late genes, including the flagellin flaA, culminating in longer flagella and increased motility. In contrast, overexpression of the FliA-dependent sRNA CJnc170 (FlmR) reduces flagellar length and motility. Overall, our study demonstrates how the interplay of two sRNAs post-transcriptionally fine-tunes flagellar biogenesis through balancing of the hierarchically-expressed components.
Collapse
Affiliation(s)
- Fabian König
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, 97080, Würzburg, Germany
| | - Sarah L Svensson
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, 97080, Würzburg, Germany
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cynthia M Sharma
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, 97080, Würzburg, Germany.
| |
Collapse
|
2
|
Barrault M, Chabelskaya S, Coronel-Tellez RH, Toffano-Nioche C, Jacquet E, Bouloc P. Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity. Nucleic Acids Res 2024:gkae506. [PMID: 38869061 DOI: 10.1093/nar/gkae506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Pathogenic bacteria employ complex systems to cope with metal ion shortage conditions and propagate in the host. IsrR is a regulatory RNA (sRNA) whose activity is decisive for optimum Staphylococcus aureus fitness upon iron starvation and for full virulence. IsrR down-regulates several genes encoding iron-containing enzymes to spare iron for essential processes. Here, we report that IsrR regulates the tricarboxylic acid (TCA) cycle by controlling aconitase (CitB), an iron-sulfur cluster-containing enzyme, and its transcriptional regulator, CcpE. This IsrR-dependent dual-regulatory mechanism provides an RNA-driven feedforward loop, underscoring the tight control required to prevent aconitase expression. Beyond its canonical enzymatic role, aconitase becomes an RNA-binding protein with regulatory activity in iron-deprived conditions, a feature that is conserved in S. aureus. Aconitase not only negatively regulates its own expression, but also impacts the enzymes involved in both its substrate supply and product utilization. This moonlighting activity concurrently upregulates pyruvate carboxylase expression, allowing it to compensate for the TCA cycle deficiency associated with iron scarcity. These results highlight the cascade of complex posttranscriptional regulations controlling S. aureus central metabolism in response to iron deficiency.
Collapse
Affiliation(s)
- Maxime Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Svetlana Chabelskaya
- Université de Rennes 1, BRM (Bacterial regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Rodrigo H Coronel-Tellez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR2301, 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
3
|
Peng A, Yin G, Zuo W, Zhang L, Du G, Chen J, Wang Y, Kang Z. Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology. Synth Syst Biotechnol 2024; 9:223-233. [PMID: 38385150 PMCID: PMC10877136 DOI: 10.1016/j.synbio.2024.01.013] [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: 12/10/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.
Collapse
Affiliation(s)
- Anqi Peng
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wenjie Zuo
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Luyao Zhang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| |
Collapse
|
4
|
Kirsebom LA, Liu F, McClain WH. The discovery of a catalytic RNA within RNase P and its legacy. J Biol Chem 2024; 300:107318. [PMID: 38677513 PMCID: PMC11143913 DOI: 10.1016/j.jbc.2024.107318] [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: 09/18/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Sidney Altman's discovery of the processing of one RNA by another RNA that acts like an enzyme was revolutionary in biology and the basis for his sharing the 1989 Nobel Prize in Chemistry with Thomas Cech. These breakthrough findings support the key role of RNA in molecular evolution, where replicating RNAs (and similar chemical derivatives) either with or without peptides functioned in protocells during the early stages of life on Earth, an era referred to as the RNA world. Here, we cover the historical background highlighting the work of Altman and his colleagues and the subsequent efforts of other researchers to understand the biological function of RNase P and its catalytic RNA subunit and to employ it as a tool to downregulate gene expression. We primarily discuss bacterial RNase P-related studies but acknowledge that many groups have significantly contributed to our understanding of archaeal and eukaryotic RNase P, as reviewed in this special issue and elsewhere.
Collapse
Affiliation(s)
- Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, California, USA.
| | - William H McClain
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| |
Collapse
|
5
|
Ju X, Li S, Froom R, Wang L, Lilic M, Delbeau M, Campbell EA, Rock JM, Liu S. Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome. Nature 2024; 627:424-430. [PMID: 38418874 PMCID: PMC10937400 DOI: 10.1038/s41586-024-07105-9] [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: 11/14/2022] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that is responsible for major health and economic costs worldwide1. Mtb encounters diverse environments during its life cycle and responds to these changes largely by reprogramming its transcriptional output2. However, the mechanisms of Mtb transcription and how they are regulated remain poorly understood. Here we use a sequencing method that simultaneously determines both termini of individual RNA molecules in bacterial cells3 to profile the Mtb transcriptome at high resolution. Unexpectedly, we find that most Mtb transcripts are incomplete, with their 5' ends aligned at transcription start sites and 3' ends located 200-500 nucleotides downstream. We show that these short RNAs are mainly associated with paused RNA polymerases (RNAPs) rather than being products of premature termination. We further show that the high propensity of Mtb RNAP to pause early in transcription relies on the binding of the σ-factor. Finally, we show that a translating ribosome promotes transcription elongation, revealing a potential role for transcription-translation coupling in controlling Mtb gene expression. In sum, our findings depict a mycobacterial transcriptome that prominently features incomplete transcripts resulting from RNAP pausing. We propose that the pausing phase constitutes an important transcriptional checkpoint in Mtb that allows the bacterium to adapt to environmental changes and could be exploited for TB therapeutics.
Collapse
Affiliation(s)
- Xiangwu Ju
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Ruby Froom
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Ling Wang
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Madeleine Delbeau
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
6
|
Poirier KM, Luallen RJ, Rivera DE. RNA fluorescence in situ hybridization (FISH) as a method to visualize bacterial colonization in the C. elegans gut. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001044. [PMID: 38481555 PMCID: PMC10935869 DOI: 10.17912/micropub.biology.001044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/05/2024] [Accepted: 02/25/2024] [Indexed: 03/17/2024]
Abstract
Caenorhabditis elegans is an excellent model to study host-microbe interactions as it is easy to visualize bacterial presence in their intestine. However, previous studies have shown that utilizing transgenic, fluorescent protein-expressing bacteria is not a reliable method to distinguish living bacteria from dead bacteria in the lumen of C. elegans . In this study, we compared methods for visualizing bacterial presence within the C. elegans intestine and found that RNA f luorescent i n s itu h ybridization (RNA FISH) could distinguish the difference between intact and dead bacteria. Thus, we propose RNA FISH as the preferred method to visualize live bacterial presence in the intestines of C. elegans prior to fixation.
Collapse
Affiliation(s)
- Kayla M Poirier
- Department of Biology, San Diego State University, San Diego, California, United States
| | - Robert J Luallen
- Department of Biology, San Diego State University, San Diego, California, United States
| | - Dalaena E Rivera
- Department of Biology, San Diego State University, San Diego, California, United States
| |
Collapse
|
7
|
Chamberlain AR, Huynh L, Huang W, Taylor DJ, Harris ME. The specificity landscape of bacterial ribonuclease P. J Biol Chem 2024; 300:105498. [PMID: 38013087 PMCID: PMC10731613 DOI: 10.1016/j.jbc.2023.105498] [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: 07/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Developing quantitative models of substrate specificity for RNA processing enzymes is a key step toward understanding their biology and guiding applications in biotechnology and biomedicine. Optimally, models to predict relative rate constants for alternative substrates should integrate an understanding of structures of the enzyme bound to "fast" and "slow" substrates, large datasets of rate constants for alternative substrates, and transcriptomic data identifying in vivo processing sites. Such data are either available or emerging for bacterial ribonucleoprotein RNase P a widespread and essential tRNA 5' processing endonuclease, thus making it a valuable model system for investigating principles of biological specificity. Indeed, the well-established structure and kinetics of bacterial RNase P enabled the development of high throughput measurements of rate constants for tRNA variants and provided the necessary framework for quantitative specificity modeling. Several studies document the importance of conformational changes in the precursor tRNA substrate as well as the RNA and protein subunits of bacterial RNase P during binding, although the functional roles and dynamics are still being resolved. Recently, results from cryo-EM studies of E. coli RNase P with alternative precursor tRNAs are revealing prospective mechanistic relationships between conformational changes and substrate specificity. Yet, extensive uncharted territory remains, including leveraging these advances for drug discovery, achieving a complete accounting of RNase P substrates, and understanding how the cellular context contributes to RNA processing specificity in vivo.
Collapse
Affiliation(s)
| | - Loc Huynh
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
| |
Collapse
|
8
|
Han S, Byun JW, Lee M. Comparative Transcriptomic Analysis of Flagellar-Associated Genes in Salmonella Typhimurium and Its rnc Mutant. J Microbiol 2024; 62:33-48. [PMID: 38182942 DOI: 10.1007/s12275-023-00099-5] [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: 09/27/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/07/2024]
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a globally recognized foodborne pathogen that affects both animals and humans. Endoribonucleases mediate RNA processing and degradation in the adaptation of bacteria to environmental changes and have been linked to the pathogenicity of S. Typhimurium. Not much is known about the specific regulatory mechanisms of these enzymes in S. Typhimurium, particularly in the context of environmental adaptation. Thus, this study carried out a comparative transcriptomic analysis of wild-type S. Typhimurium SL1344 and its mutant (∆rnc), which lacks the rnc gene encoding RNase III, thereby elucidating the detailed regulatory characteristics that can be attributed to the rnc gene. Global gene expression analysis revealed that the ∆rnc strain exhibited 410 upregulated and 301 downregulated genes (fold-change > 1.5 and p < 0.05), as compared to the wild-type strain. Subsequent bioinformatics analysis indicated that these differentially expressed genes are involved in various physiological functions, in both the wild-type and ∆rnc strains. This study provides evidence for the critical role of RNase III as a general positive regulator of flagellar-associated genes and its involvement in the pathogenicity of S. Typhimurium.
Collapse
Affiliation(s)
- Seungmok Han
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Ji-Won Byun
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Minho Lee
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.
| |
Collapse
|
9
|
Wu R, Barnes S, Dahlin H, Khamrui S, Ingle S, Xiang Y, Shi Y, Bechhofer D, Lazarus M. Structural insights into RNA cleavage by a novel family of bacterial RNases. RESEARCH SQUARE 2023:rs.3.rs-3788707. [PMID: 38234822 PMCID: PMC10793500 DOI: 10.21203/rs.3.rs-3788707/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Processing of RNA is a key regulatory mechanism for all living systems. We recently discovered a novel family of endoribonucleases that is conserved across all bacteria. Here, using crystallography, cryo-EM microscopy, biochemical, biophysical, and mass spectrometry techniques, we are able to shed light on a novel RNA cleavage mechanism in bacteria. We show that YicC, the prototypical member of this family, forms a hexameric channel that closes down on a 26-mer RNA substrate, and find that it cleaves across an RNA hairpin to generate several short fragments.
Collapse
Affiliation(s)
- Ruoxi Wu
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | - Yi Shi
- Icahn School of Medicine at Mount Sinai
| | | | | |
Collapse
|
10
|
Mugunthan S, Wong LL, Winnerdy FR, Summers S, Bin Ismail MH, Foo YH, Jaggi TK, Meldrum OW, Tiew PY, Chotirmall SH, Rice SA, Phan AT, Kjelleberg S, Seviour T. RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms. Nat Commun 2023; 14:7772. [PMID: 38012164 PMCID: PMC10682433 DOI: 10.1038/s41467-023-43533-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
The extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.
Collapse
Affiliation(s)
- Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- St John's Island National Marine Laboratory c/o Tropical Marine Science Institute, National University of Singapore, 119227, Singapore
| | | | - Yong Hwee Foo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), Nanyang Technological University, Singapore, 636921, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Oliver W Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- The iThree Institute, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Canberra, Australia
| | - Anh Tuân Phan
- School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, 8000, Denmark.
| |
Collapse
|
11
|
Błaszczyk E, Płociński P, Lechowicz E, Brzostek A, Dziadek B, Korycka-Machała M, Słomka M, Dziadek J. Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs. Sci Rep 2023; 13:20717. [PMID: 38001315 PMCID: PMC10673834 DOI: 10.1038/s41598-023-47944-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
In reference to gene annotation, more than half of the tRNA species synthesized by Mycobacterium tuberculosis require the enzymatic addition of the cytosine-cytosine-adenine (CCA) tail, which is indispensable for amino acid charging and tRNA functionality. It makes the mycobacterial CCA-adding enzyme essential for survival of the bacterium and a potential target for novel pipelines in drug discovery avenues. Here, we described the rv3907c gene product, originally annotated as poly(A)polymerase (rv3907c, PcnA) as a functional CCA-adding enzyme (CCAMtb) essential for viability of M. tuberculosis. The depletion of the enzyme affected tRNAs maturation, inhibited bacilli growth, and resulted in abundant accumulation of polyadenylated RNAs. We determined the enzymatic activities displayed by the mycobacterial CCAMtb in vitro and studied the effects of inhibiting of its transcription in bacterial cells. We are the first to properly confirm the existence of RNA polyadenylation in mycobacteria, a previously controversial phenomenon, which we found promoted upon CCA-adding enzyme downexpression.
Collapse
Affiliation(s)
- Ewelina Błaszczyk
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Przemysław Płociński
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Ewelina Lechowicz
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | | | - Marcin Słomka
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 139, 90-235, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland.
| |
Collapse
|
12
|
Cornman RS. Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus. PeerJ 2023; 11:e16455. [PMID: 38025724 PMCID: PMC10655722 DOI: 10.7717/peerj.16455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues. Methods Short-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly. Results At least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with 'Africanized' honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1-100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species. Discussion Collectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage.
Collapse
|
13
|
Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Bacterial cGAS senses a viral RNA to initiate immunity. Nature 2023; 623:1001-1008. [PMID: 37968393 PMCID: PMC10686824 DOI: 10.1038/s41586-023-06743-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023]
Abstract
Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. As the mammalian cyclase OAS1 also binds viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.
Collapse
Affiliation(s)
- Dalton V Banh
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Adrian Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | | | - Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
14
|
Chatterjee A, Zhang K, Parker KM. Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16086-16096. [PMID: 37811805 DOI: 10.1021/acs.est.3c05019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.
Collapse
Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
15
|
Iyer KV, Müller M, Tittel LS, Winz ML. Molecular Highway Patrol for Ribosome Collisions. Chembiochem 2023; 24:e202300264. [PMID: 37382189 DOI: 10.1002/cbic.202300264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
During translation, messenger RNAs (mRNAs) are decoded by ribosomes which can stall for various reasons. These include chemical damage, codon composition, starvation, or translation inhibition. Trailing ribosomes can collide with stalled ribosomes, potentially leading to dysfunctional or toxic proteins. Such aberrant proteins can form aggregates and favor diseases, especially neurodegeneration. To prevent this, both eukaryotes and bacteria have evolved different pathways to remove faulty nascent peptides, mRNAs and defective ribosomes from the collided complex. In eukaryotes, ubiquitin ligases play central roles in triggering downstream responses and several complexes have been characterized that split affected ribosomes and facilitate degradation of the various components. As collided ribosomes signal translation stress to affected cells, in eukaryotes additional stress response pathways are triggered when collisions are sensed. These pathways inhibit translation and modulate cell survival and immune responses. Here, we summarize the current state of knowledge about rescue and stress response pathways triggered by ribosome collisions.
Collapse
Affiliation(s)
- Kaushik Viswanathan Iyer
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Max Müller
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lena Sophie Tittel
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marie-Luise Winz
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| |
Collapse
|
16
|
Myers TM, Ingle S, Weiss CA, Sondermann H, Lee V, Bechhofer D, Winkler W. Bacillus subtilis NrnB is expressed during sporulation and acts as a unique 3'-5' exonuclease. Nucleic Acids Res 2023; 51:9804-9820. [PMID: 37650646 PMCID: PMC10570053 DOI: 10.1093/nar/gkad662] [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: 04/22/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023] Open
Abstract
All cells employ a combination of endo- and exoribonucleases to degrade long RNA polymers to fragments 2-5 nucleotides in length. These short RNA fragments are processed to monoribonucleotides by nanoRNases. Genetic depletion of nanoRNases has been shown to increase abundance of short RNAs. This deleteriously affects viability, virulence, and fitness, indicating that short RNAs are a metabolic burden. Previously, we provided evidence that NrnA is the housekeeping nanoRNase for Bacillus subtilis. Herein, we investigate the biological and biochemical functions of the evolutionarily related protein, B. subtilis NrnB (NrnBBs). These experiments show that NrnB is surprisingly different from NrnA. While NrnA acts at the 5' terminus of RNA substrates, NrnB acts at the 3' terminus. Additionally, NrnA is expressed constitutively under standard growth conditions, yet NrnB is selectively expressed during endospore formation. Furthermore, NrnA processes only short RNAs, while NrnB unexpectedly processes both short RNAs and longer RNAs. Indeed, inducible expression of NrnB can even complement the loss of the known global 3'-5' exoribonucleases, indicating that it acts as a general exonuclease. Together, these data demonstrate that NrnB proteins, which are widely found in Firmicutes, Epsilonproteobacteria and Archaea, are fundamentally different than NrnA proteins and may be used for specialized purposes.
Collapse
Affiliation(s)
- Tanner M Myers
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD 20742, USA
| | - Shakti Ingle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cordelia A Weiss
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Vincent T Lee
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - David H Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wade C Winkler
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD 20742, USA
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
17
|
Gruffaz C, Smirnov A. GTPase Era at the heart of ribosome assembly. Front Mol Biosci 2023; 10:1263433. [PMID: 37860580 PMCID: PMC10582724 DOI: 10.3389/fmolb.2023.1263433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.
Collapse
Affiliation(s)
- Christelle Gruffaz
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
| | - Alexandre Smirnov
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| |
Collapse
|
18
|
Chen XY, Hu SS, Xu XC, Tang JL, Tang DJ. RNase D Is Involved in 5S rRNA Degradation and Exopolysaccharide Production in Xanthomonas campestris pv. campestris. PHYTOPATHOLOGY 2023; 113:1822-1832. [PMID: 37160665 DOI: 10.1094/phyto-09-22-0327-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ribonucleases (RNases) play critical roles in RNA metabolism and are collectively essential for cell viability. However, most knowledge about bacterial RNases comes from the studies on Escherichia coli; very little is known about the RNases in plant pathogens. The crucifer black rot pathogen Xanthomonas campestris pv. campestris (Xcc) encodes 15 RNases, but none of them has been functionally characterized. Here, we report the physiological function of the exoribonuclease RNase D in Xcc and provide evidence demonstrating that the Xcc RNase D is involved in 5S rRNA degradation and exopolysaccharide (EPS) production. Our work shows that the growth and virulence of Xcc were not affected by deletion of RNase D but were severely attenuated by RNase D overexpression. However, deletion of RNase D in Xcc resulted in a significant reduction in EPS production. In addition, either deletion or overexpression of RNase D in Xcc did not influence the tRNAs tested, inconsistent with the finding in E. coli that the primary function of RNase D is to participate in tRNA maturation and its overexpression degrades tRNAs. More importantly, deletion, overexpression, and in vitro enzymatic analyses revealed that the Xcc RNase D degrades 5S rRNA but not 16S and 23S rRNAs that share an operon with 5S rRNA. Our results suggest that Xcc employs RNase D to realize specific modulation of the cellular 5S rRNA content after transcription and maturation whenever necessary. The finding expands our knowledge about the function of RNase D in bacteria.
Collapse
Affiliation(s)
- Xin-Yi Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Shan-Shan Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Xiao-Can Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Dong-Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| |
Collapse
|
19
|
Broglia L, Le Rhun A, Charpentier E. Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiol Rev 2023; 47:fuad049. [PMID: 37656885 PMCID: PMC10503654 DOI: 10.1093/femsre/fuad049] [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: 03/23/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target recognition. Recent advances in high-throughput RNA sequencing (RNA-seq) approaches have provided a better understanding of the roles and modes of action of bacterial RNases. Global studies aiming to identify direct targets of RNases have highlighted the diversity of RNase activity and RNA-based mechanisms of gene expression regulation. Here, we review recent RNA-seq approaches used to study bacterial RNases, with a focus on the methods for identifying direct RNase targets.
Collapse
Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Center for Human Technologies, Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Institute for Biology, Humboldt University, D-10115 Berlin, Germany
| |
Collapse
|
20
|
Iqbal A, Yang Y. Utilizing Dichloromethane as an Extremely Proficient Substitute for Phenol/Chloroform in Extracting RNA with Exceptional Purity from Woody Tissues of Coconut. Methods Protoc 2023; 6:75. [PMID: 37736958 PMCID: PMC10514881 DOI: 10.3390/mps6050075] [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: 08/04/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Procuring high-grade RNA from mature coconut tissues is a tricky and labor-intensive process due to the intricate scaffold of polysaccharides, polyphenols, lipids, and proteins that form firm complexes with nucleic acids. However, we have effectively developed a novel method for the first time, letting the retrieval of high-grade RNA from the roots, endosperm, and mesocarp of mature coconut trees take place. In this method, we exploited dichloromethane as a replacement to phenol/chloroform for RNA recovery from mature coconut tissues. The amount of high-grade RNA acquired from the roots of mature coconut trees was 120.7 µg/g, with an A260/280 ratio of 1.95. Similarly, the mature coconut mesocarp yielded 134.6 µg/g FW of quality RNA with A260/280 ratio of 1.98, whereas the mature coconut endosperm produced 120.4 µg/g FW of quality RNA with A260/280 ratio of 2.01. Furthermore, the RNA isolation using the dichloromethane method exhibited excellent performance in downstream experiments, particularly in RT-PCR for cDNA production and amplification. On the contrary, the RNA plant kit, TRIZOL, and Cetyl Trimethyl Ammonium Bromide (CTAB) methods were unsuccessful in isolating substantial quantities of RNA with exceptional purities from the mentioned coconut tissues. In view of these findings, we conclude that the newly developed method will be pivotal in effectively extracting RNA with high purity from mature coconut tissues.
Collapse
Affiliation(s)
- Amjad Iqbal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Science, Wenchang 571339, China
- Department of Food Science & Technology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Science, Wenchang 571339, China
| |
Collapse
|
21
|
Huang L, Tam KS, Xie W. Structural and Biochemical Studies of the Novel Hexameric Endoribonuclease YicC. ACS Chem Biol 2023; 18:1738-1747. [PMID: 37535940 DOI: 10.1021/acschembio.3c00091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The decay of mRNA is an essential process to bacteria. The newly identified E. coli protein YicC is a founding member of the UPF0701 family, and biochemical studies indicated that it is an RNase involved in mRNA degradation. However, its biochemical properties and catalytic mechanism are poorly understood. Here, we report the crystal structure of YicC, which shows an extended shape consisting of modular domains. While the backbone trace of the monomer forms a unique, nearly closed loop, the three monomers present in the asymmetric unit make a "shoulder-by-shoulder" trimer. In vitro RNA cleavage assays indicated that this endoribonuclease mainly recognizes the consensus GUG motif, with a preference for an extended CGUG sequence. Additionally, the active enzyme exists as a hexamer in solution and assumes a funnel shape. Structural analysis indicated that the hexamer interface is mainly formed by the hexamerization domain consisting of D71-D124 and that the disruption of the oligomeric form greatly diminished the enzymatic activity. By studying the surface charge potential and the sequence conservation, we identified a series of residues that play critical functional roles, which helps to reveal the catalytic mechanism of this divalent metal-ion-dependent RNase. Last but not least, we discovered that the catalytic domain of YicC did not share similarity with any known nuclease fold, suggesting that the enzyme adopts a novel fold to perform its catalysis and in vivo functions. In summary, our investigations into YicC provide an in-depth understanding of the functions of the UPF0701 protein family and the DUF1732 domain in general.
Collapse
Affiliation(s)
- Lin Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - King Sing Tam
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| |
Collapse
|
22
|
Neto NAS, Aguiar TKB, Costa RJP, Mesquita FP, Oliveira LLBD, Moraes MEAD, Montenegro RC, Carneiro RF, Nagano CS, Freitas CDT, Souza PFN. United we stand, divided we fall: in-depth proteomic evaluation of the synergistic effect of Mo-CBP 3-PepI and Ciprofloxacin against Staphylococcus aureus biofilms. BIOFOULING 2023; 39:838-852. [PMID: 37955278 DOI: 10.1080/08927014.2023.2279992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
Staphylococcus aureus forms biofilms, a structure that protects bacterial cells, conferring more resistance to difficult treatment. Synthetic peptides surge as an alternative to overcome the biofilm of multidrug-resistant pathogens. Mo-CBP3-PepI, when combined with Ciprofloxacin, reduced preformed S. aureus biofilm by 50% at low concentrations (0.2 and 6.2 μg. mL-1, respectively). The goal of this study was to evaluate the proteomic profile of biofilms after treatment with the Mo-CBP3-PepI combined with ciprofloxacin. Here, proteomic analysis confirmed with more depth previously described mechanisms and revealed changes in the accumulation of proteins related to DNA and protein metabolism, cell wall biosynthesis, redox metabolism, quorum sensing, and biofilm formation. Some proteins related to DNA and protein metabolism were reduced, while other proteins, like redox system proteins, disappeared in Ciprofloxacin+Mo-CBP3-PepI treatment. Our results indicated a synergistic effect of these two molecules with several mechanisms against S. aureus biofilm and opened new doors for combined treatments with other drugs.
Collapse
Affiliation(s)
- Nilton A S Neto
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Tawanny K B Aguiar
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Rayara J P Costa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Felipe P Mesquita
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Lais L B de Oliveira
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Maria E A de Moraes
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Raquel C Montenegro
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Rômulo F Carneiro
- Department of Fisheries Engineering, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
| | - Celso S Nagano
- Department of Fisheries Engineering, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
| | - Cleverson D T Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Pedro F N Souza
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| |
Collapse
|
23
|
Wang N, Li P, Cheng Y, Song H, Xu C. Stem-loop structures control mRNA processing of the cellulosomal cip-cel operon in Ruminiclostridium cellulolyticum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:106. [PMID: 37386549 DOI: 10.1186/s13068-023-02357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 06/11/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND Anaerobic, mesophilic, and cellulolytic Ruminiclostridium cellulolyticum produces an efficient cellulolytic extracellular complex named cellulosome, which consist of a non-catalytic multi-functional integrating subunit, organizing the various catalytic subunits into the complex. Main components of cellulosome were encoded by the cip-cel operon in R. cellulolyticum, and their stoichiometry is controlled by the mechanism of selective RNA processing and stabilization, which allows to confer each processed RNA portion from the cip-cel mRNA on different fates due to their stability and resolve the potential contradiction between the equimolar stoichiometry of transcripts with a within a transcription unit and the non-equimolar stoichiometry of subunits. RESULTS In this work, RNA processing events were found to occur at six intergenic regions (IRs) harboring stem-loop structures in cip-cel operon. These stem-loops not only stabilize processed transcripts at their both ends, but also act as cleavage signals specifically recognized by endoribonucleases. We further demonstrated that cleavage sites were often located downstream or 3' end of their associated stem-loops that could be classified into two types, with distinct GC-rich stems being required for RNA cleavage. However, the cleavage site in IR4 was found to be located upstream of the stem-loop, as determined by the bottom AT-pair region of this stem-loop, together with its upstream structure. Thus, our findings reveal the structural requirements for processing of cip-cel transcripts, which can be potentially used to control the stoichiometry of gene expression in an operon. CONCLUSIONS Our findings reveal that stem-loop structures acting as RNA cleavage signals not only can be recognized by endoribonucleases and determine the location of cleavage sites but also determine the stoichiometry of their flanking processed transcripts by controlling stability in cip-cel operon. These features represent a complexed regulation of cellulosome in the post-transcriptional level, which can be exploited for designing synthetic elements to control gene expression.
Collapse
Affiliation(s)
- Na Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Ping Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Ying Cheng
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Chenggang Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China.
| |
Collapse
|
24
|
Kolberg T, von Löhneysen S, Ozerova I, Wellner K, Hartmann R, Stadler P, Mörl M. Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA. Nucleic Acids Res 2023; 51:e63. [PMID: 37114986 PMCID: PMC10287922 DOI: 10.1093/nar/gkad312] [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: 01/24/2023] [Revised: 03/21/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Structural analysis of RNA is an important and versatile tool to investigate the function of this type of molecules in the cell as well as in vitro. Several robust and reliable procedures are available, relying on chemical modification inducing RT stops or nucleotide misincorporations during reverse transcription. Others are based on cleavage reactions and RT stop signals. However, these methods address only one side of the RT stop or misincorporation position. Here, we describe Led-Seq, a new approach based on lead-induced cleavage of unpaired RNA positions, where both resulting cleavage products are investigated. The RNA fragments carrying 2', 3'-cyclic phosphate or 5'-OH ends are selectively ligated to oligonucleotide adapters by specific RNA ligases. In a deep sequencing analysis, the cleavage sites are identified as ligation positions, avoiding possible false positive signals based on premature RT stops. With a benchmark set of transcripts in Escherichia coli, we show that Led-Seq is an improved and reliable approach based on metal ion-induced phosphodiester hydrolysis to investigate RNA structures in vivo.
Collapse
Affiliation(s)
- Tim Kolberg
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Sarah von Löhneysen
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Iuliia Ozerova
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Karolin Wellner
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Roland K Hartmann
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| |
Collapse
|
25
|
Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
Collapse
Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
| |
Collapse
|
26
|
Huang J, Liu X, Sun Y, Li Z, Lin MH, Hamilton K, Mandel CR, Sandmeir F, Conti E, Oyala PH, Tong L. An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11. J Biol Chem 2023; 299:103047. [PMID: 36822327 PMCID: PMC10064220 DOI: 10.1016/j.jbc.2023.103047] [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: 01/19/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023] Open
Abstract
Human cleavage and polyadenylation specificity factor (CPSF)73 (also known as CPSF3) is the endoribonuclease that catalyzes the cleavage reaction for the 3'-end processing of pre-mRNAs. The active site of CPSF73 is located at the interface between a metallo-β-lactamase domain and a β-CASP domain. Two metal ions are coordinated by conserved residues, five His and two Asp, in the active site, and they are critical for the nuclease reaction. The metal ions have long been thought to be zinc ions, but their exact identity has not been examined. Here we present evidence from inductively coupled plasma mass spectrometry and X-ray diffraction analyses that a mixture of metal ions, including Fe, Zn, and Mn, is present in the active site of CPSF73. The abundance of the various metal ions is different in samples prepared from different expression hosts. Zinc is present at less than 20% abundance in a sample expressed in insect cells, but the sample is active in cleaving a pre-mRNA substrate in a reconstituted canonical 3'-end processing machinery. Zinc is present at 75% abundance in a sample expressed in human cells, which has comparable endonuclease activity. We also observe a mixture of metal ions in the active site of the CPSF73 homolog INTS11, the endonuclease for Integrator. Taken together, our results provide further insights into the role of metal ions in the activity of CPSF73 and INTS11 for RNA 3'-end processing.
Collapse
Affiliation(s)
- Ji Huang
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Xiangyang Liu
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Yadong Sun
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Zhuang Li
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Keith Hamilton
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Corey R Mandel
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Felix Sandmeir
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York, USA.
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Jain C. Suppression of multiple phenotypic and RNA processing defects by over-expression of Oligoribonuclease in Escherichia coli. J Biol Chem 2023; 299:104567. [PMID: 36870683 PMCID: PMC10124918 DOI: 10.1016/j.jbc.2023.104567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 03/06/2023] Open
Abstract
Oligoribonuclease (Orn) is an essential Ribonuclease (RNase) from Escherichia coli (E. coli), which plays a critical role in the conversion of short RNA molecules (NanoRNAs) to mononucleotides. Although no additional functions have been ascribed to Orn since its discovery nearly 50 years ago, it was observed in this study that the growth defects caused by a lack of two other RNases that do not digest NanoRNAs, PNPase and RNase PH, could be suppressed by Orn over-expression. Further analyses showed that Orn over-expression can alleviate the growth defects caused by an absence of other RNases even when its expression was increased by a small degree, and it can carry out molecular reactions that are normally performed by RNase T and RNase PH. In addition, biochemical assays revealed that Orn can fully digest single stranded RNAs within a variety of structural contexts. These studies provide new insights into Orn function and its ability to participate in multiple aspects of E. coli RNA metabolism.
Collapse
Affiliation(s)
- Chaitanya Jain
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, USA.
| |
Collapse
|
29
|
Zou Z, Younas T, Dumsday G, Haritos VS, He L. Rapid production of multimeric RNA aptamers stabilized by a designed pseudo-circular structure in E. coli. Biotechnol J 2023; 18:e2200390. [PMID: 36427490 DOI: 10.1002/biot.202200390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
RNA aptamers bind specifically and selectively to various macromolecules, cell surfaces, and viruses and find broad applications as biosensors, diagnostics, and in therapeutic treatments and drug delivery. Currently, RNA aptamer production is via in vitro methods. Herein, a new E. coli-based approach has been demonstrated for the rapid production of multimeric RNA aptamer transcripts that are protected from degradation by burying the 5' and 3' ends of the transcript in a designed double-stranded spacer. Multimeric and fluorescent RNA aptamers were produced stably in vivo and readily isolated from RNase III-deficient cells, and their full functionalities were shown by binding assays and fluorescence measurements. This approach shows promise as a rapid and scalable bioprocess for the production of RNA aptamers at low cost.
Collapse
Affiliation(s)
- Zongsheng Zou
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
| | - Tayyaba Younas
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
| | - Geoff Dumsday
- CSIRO Manufacturing, Ian Wark Laboratory, Clayton, VIC, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
| | - Lizhong He
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
| |
Collapse
|
30
|
Jones GH. Streptomyces RNases - Function and impact on antibiotic synthesis. Front Microbiol 2023; 14:1096228. [PMID: 37113221 PMCID: PMC10126417 DOI: 10.3389/fmicb.2023.1096228] [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: 11/11/2022] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Streptomyces are soil dwelling bacteria that are notable for their ability to sporulate and to produce antibiotics and other secondary metabolites. Antibiotic biosynthesis is controlled by a variety of complex regulatory networks, involving activators, repressors, signaling molecules and other regulatory elements. One group of enzymes that affects antibiotic synthesis in Streptomyces is the ribonucleases. In this review, the function of five ribonucleases, RNase E, RNase J, polynucleotide phosphorylase, RNase III and oligoribonuclease, and their impact on antibiotic production will be discussed. Mechanisms for the effects of RNase action on antibiotic synthesis are proposed.
Collapse
|
31
|
Badhwar P, Ahmad I, Sharma R, Taneja B. Structural investigation and gene deletion studies of mycobacterial oligoribonuclease reveal modulation of c-di-GMP-mediated phenotypes. Int J Biol Macromol 2022; 223:161-172. [PMID: 36356862 DOI: 10.1016/j.ijbiomac.2022.11.029] [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: 08/04/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger required for normal physiology as well as survival under hypoxic and reductive stress conditions of mycobacterial cells. Complete degradation of c-di-GMP is necessary for signal termination and maintaining its homeostasis inside the cells. Homeostasis of c-di-GMP in mycobacteria is brought about by the bifunctional diguanylate cyclase (DGC) that synthesizes c-di-GMP from two molecules of GTP and also catalyses the asymmetric cleavage of c-di-GMP to linear pGpG through its phosphodiesterase activity. However, the mycobacterial enzyme for the last step of degradation from pGpG to GMP has not been characterized thus far. Here, we present the identification of oligoribonuclease (Orn) as the most likely phosphodiesterase to degrade pGpG to GMP through AlphaFold-empowered structural homology that exhibited in vitro phosphodiesterase activity on pGpG substrates. In order to understand the physiological role of Orn in mycobacteria, we created a deletion mutant of orn in M. smegmatis and analysed the phenotypes that are associated with c-di-GMP signaling. We find that orn plays important roles in vivo and is required not only for proper growth of M. smegmatis in normal and stress conditions but also for biofilm formation.
Collapse
Affiliation(s)
- Pooja Badhwar
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Iftekhar Ahmad
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhupesh Taneja
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
32
|
Kaur R, Nikkel DJ, Aboelnga MM, Wetmore SD. The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1. J Phys Chem B 2022; 126:10672-10683. [PMID: 36485014 DOI: 10.1021/acs.jpcb.2c06756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.
Collapse
Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.,Chemistry Department, Faculty of Science, Damietta University, New Damietta 34517, Egypt
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| |
Collapse
|
33
|
Wei G, Li S, Ye S, Wang Z, Zarringhalam K, He J, Wang W, Shao Z. High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5. Int J Mol Sci 2022; 23:ijms232415995. [PMID: 36555635 PMCID: PMC9788540 DOI: 10.3390/ijms232415995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Alkanes are widespread in the ocean, and Alcanivorax is one of the most ubiquitous alkane-degrading bacteria in the marine ecosystem. Small RNAs (sRNAs) are usually at the heart of regulatory pathways, but sRNA-mediated alkane metabolic adaptability still remains largely unknown due to the difficulties of identification. Here, differential RNA sequencing (dRNA-seq) modified with a size selection (~50-nt to 500-nt) strategy was used to generate high-resolution sRNAs profiling in the model species Alcanivorax dieselolei B-5 under alkane (n-hexadecane) and non-alkane (acetate) conditions. As a result, we identified 549 sRNA candidates at single-nucleotide resolution of 5'-ends, 63.4% of which are with transcription start sites (TSSs), and 36.6% of which are with processing sites (PSSs) at the 5'-ends. These sRNAs originate from almost any location in the genome, regardless of intragenic (65.8%), antisense (20.6%) and intergenic (6.2%) regions, and RNase E may function in the maturation of sRNAs. Most sRNAs locally distribute across the 15 reference genomes of Alcanivorax, and only 7.5% of sRNAs are broadly conserved in this genus. Expression responses to the alkane of several core conserved sRNAs, including 6S RNA, M1 RNA and tmRNA, indicate that they may participate in alkane metabolisms and result in more actively global transcription, RNA processing and stresses mitigation. Two novel CsrA-related sRNAs are identified, which may be involved in the translational activation of alkane metabolism-related genes by sequestering the global repressor CsrA. The relationships of sRNAs with the characterized genes of alkane sensing (ompS), chemotaxis (mcp, cheR, cheW2), transporting (ompT1, ompT2, ompT3) and hydroxylation (alkB1, alkB2, almA) were created based on the genome-wide predicted sRNA-mRNA interactions. Overall, the sRNA landscape lays the ground for uncovering cryptic regulations in critical marine bacterium, among which both the core and species-specific sRNAs are implicated in the alkane adaptive metabolisms.
Collapse
Affiliation(s)
- Guangshan Wei
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Sujie Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Sida Ye
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Zining Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jianguo He
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Correspondence: (W.W.); (Z.S.)
| | - Zongze Shao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: (W.W.); (Z.S.)
| |
Collapse
|
34
|
Martinez J, Ross PA, Gu X, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Hoffmann AA, Sinkins SP. Genomic and Phenotypic Comparisons Reveal Distinct Variants of Wolbachia Strain wAlbB. Appl Environ Microbiol 2022; 88:e0141222. [PMID: 36318064 PMCID: PMC9680635 DOI: 10.1128/aem.01412-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
The intracellular bacterium Wolbachia inhibits virus replication and is being harnessed around the world to fight mosquito-borne diseases through releases of mosquitoes carrying the symbiont. Wolbachia strains vary in their ability to invade mosquito populations and suppress viruses in part due to differences in their density within the insect and associated fitness costs. Using whole-genome sequencing, we demonstrate the existence of two variants in wAlbB, a Wolbachia strain being released in natural populations of Aedes aegypti mosquitoes. The two variants display striking differences in genome architecture and gene content. Differences in the presence/absence of 52 genes between variants include genes located in prophage regions and others potentially involved in controlling the symbiont's density. Importantly, we show that these genetic differences correlate with variation in wAlbB density and its tolerance to heat stress, suggesting that different wAlbB variants may be better suited for field deployment depending on local environmental conditions. Finally, we found that the wAlbB genome remained stable following its introduction in a Malaysian mosquito population. Our results highlight the need for further genomic and phenotypic characterization of Wolbachia strains in order to inform ongoing Wolbachia-based programs and improve the selection of optimal strains in future field interventions. IMPORTANCE Dengue is a viral disease transmitted by Aedes mosquitoes that threatens around half of the world population. Recent advances in dengue control involve the introduction of Wolbachia bacterial symbionts with antiviral properties into mosquito populations, which can lead to dramatic decreases in the incidence of the disease. In light of these promising results, there is a crucial need to better understand the factors affecting the success of such strategies, in particular the choice of Wolbachia strain for field releases and the potential for evolutionary changes. Here, we characterized two variants of a Wolbachia strain used for dengue control that differ at the genomic level and in their ability to replicate within the mosquito. We also found no evidence for the evolution of the symbiont within the 2 years following its deployment in Malaysia. Our results have implications for current and future Wolbachia-based health interventions.
Collapse
Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Perran A. Ross
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Xinyue Gu
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| |
Collapse
|
35
|
Zhang W, Yao Y, Zhou H, He J, Wang J, Li L, Gao M, Liu X, Shi Y, Lin J, Liu J, Chen H, Feng Y, Zhou Z, Yu Y, Hua X. Interactions between host epithelial cells and Acinetobacter baumannii promote the emergence of highly antibiotic resistant and highly mucoid strains. Emerg Microbes Infect 2022; 11:2556-2569. [PMID: 36227610 PMCID: PMC9621264 DOI: 10.1080/22221751.2022.2136534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Acinetobacter baumannii is an important nosocomial pathogen. Upon colonizing a host, A. baumannii are subjected to selective pressure by immune defenses as they adapt to the host environment. However, the mechanism of this pathoadaptation is unknown. Here, we established an in vitro system to evolve A. baumannii driven by the continuous selective pressure exerted by epithelial cells, and we used a combination of experimental evolution, phenotypic characterization and multi-omics analysis to address the underlying mechanism. When continuously exposed to selective pressure by pulmonary epithelial cells, A. baumannii showed ptk mutation-mediated mucoid conversion (reduced adhesion and increased anti-phagocytic ability) by enhancement of capsular exopolysaccharide chain length; rsmG mutation-mediated deficiency of 7-methylguanosine modification in the 524th nucleotide of 16S rRNA, which increased ribosome translation efficiency; and rnaseI mutation-mediated changes in outer membrane permeability and efflux pump expression. Together, these mutations altered susceptibility to a variety of antimicrobial agents, including the novel antibiotic cefiderocol, by regulating siderophore and siderophore-receptor biosynthesis. In conclusion, pulmonary epithelial cells modulate A. baumannii pathoadaptation, implicating the host–microbe interaction in the survival and persistence of A. baumannii.
Collapse
Affiliation(s)
- Wang Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yue Yao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Jingfen Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Li Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaochen Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Ya Shi
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, Zhejiang, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China.,Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huan Chen
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, Zhejiang, China
| | - Yu Feng
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| |
Collapse
|
36
|
Kimura N, Takayama KI, Yamada Y, Kume H, Fujimura T, Inoue S. Ribonuclease H2 Subunit A Preserves Genomic Integrity and Promotes Prostate Cancer Progression. CANCER RESEARCH COMMUNICATIONS 2022; 2:870-883. [PMID: 36923313 PMCID: PMC10010380 DOI: 10.1158/2767-9764.crc-22-0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/15/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Homeostasis of genomic integrity should be regulated to promote proliferation and inhibit DNA damage-induced cell death in cancer. Ribonuclease H2 (RNase H2) maintains genome stability by controlling DNA:RNA hybrid and R-loop levels. Here, we identified that RNase H2 subunit A (RNASEH2A), a component of RNase H2, is highly expressed in castration-resistant prostate cancer (CRPC) tissues compared with localized prostate cancer. Interestingly, we showed that RNASEH2A suppressed R-loop levels to prevent cell apoptosis induced by DNA damage in prostate cancer cells. Both in vivo and in vitro studies revealed that RNASEH2A promotes cell growth and migration via the negative regulation of p53 and positive regulation of AR and AR-V7. Mechanistically, epigenetic regulation followed by R-loop accumulation in these promoters was observed for these gene regulations. Importantly, IHC analysis demonstrated that R-loop formation increased in CRPC tissues and correlated with RNASEH2A expression levels. Notably, two small molecules targeting RNase H2 activity were found to suppress CRPC tumor growth with no significant toxic effects. Collectively, we propose that RNASEH2A overexpression is a hallmark of prostate cancer progression by maintaining genomic stability to prevent R-loop-mediated apoptosis induction. Targeting RNase H2 activity could be a potential strategy for treating CRPC tumors. Significance RNASEH2A was demonstrated to be highly upregulated in aggressive prostate cancer to degrade R-loop accumulation and preserve genomic stability for tumor growth, suggesting that RNase H2 activity could be a promising therapeutic target.
Collapse
Affiliation(s)
- Naoki Kimura
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Yuta Yamada
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | | | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan.,Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| |
Collapse
|
37
|
Bakke M. A Comprehensive Analysis of ATP Tests: Practical Use and Recent Progress in the Total Adenylate Test for the Effective Monitoring of Hygiene. J Food Prot 2022; 85:1079-1095. [PMID: 35503956 DOI: 10.4315/jfp-21-384] [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: 10/15/2021] [Accepted: 04/26/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Rapid hygiene monitoring tests based on the presence of ATP have been widely used in the food industry to ensure that adequate cleanliness is maintained. In this study, the practical applications and limitations of these tests and recent technological progress for facilitating more accurate control were evaluated. The presence of ATP on a surface indicates improper cleaning and the presence of contaminants, including organic debris and bacteria. Food residues are indicators of insufficient cleaning and are direct hazards because they may provide safe harbors for bacteria, provide sources of nutrients for bacterial growth, interfere with the antimicrobial activity of disinfectants, and support the formation of biofilms. Residues of allergenic foods on a surface may increase the risk of allergen cross-contact. However, ATP tests cannot detect bacteria or allergenic proteins directly. To ensure efficient use of commercially available ATP tests, in-depth knowledge is needed regarding their practical applications, methods for determining pass-fail limits, and differences in performance. Conventional ATP tests have limitations due to possible hydrolysis of ATP to ADP and AMP, which further hinders the identification of food residues. To overcome this problem, a total adenylate test was developed that could detect ATP+ADP+AMP (A3 test). The A3 test is suitable for the detection of adenylates from food residues and useful for verification of hygiene levels. The A3 test in conjunction with other methods, such as microorganism culture and food allergen tests, may be a useful strategy for identifying contamination sources and facilitating effective hygiene management. HIGHLIGHTS
Collapse
Affiliation(s)
- Mikio Bakke
- Kikkoman Biochemifa Company, Marketing & Planning Division, 2-1-1 Nishi-shinbashi, Minato-ku, Tokyo 105-0003, Japan
| |
Collapse
|
38
|
Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
Collapse
|
39
|
Babu VMP, Sankari S, Ghosal A, Walker GC. A Mutant Era GTPase Suppresses Phenotypes Caused by Loss of Highly Conserved YbeY Protein in Escherichia coli. Front Microbiol 2022; 13:896075. [PMID: 35663862 PMCID: PMC9159920 DOI: 10.3389/fmicb.2022.896075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 12/03/2022] Open
Abstract
Ribosome assembly is a complex fundamental cellular process that involves assembling multiple ribosomal proteins and several ribosomal RNA species in a highly coordinated yet flexible and resilient manner. The highly conserved YbeY protein is a single-strand specific endoribonuclease, important for ribosome assembly, 16S rRNA processing, and ribosome quality control. In Escherichia coli, ybeY deletion results in pleiotropic phenotypes including slow growth, temperature sensitivity, accumulation of precursors of 16S rRNA, and impaired formation of fully assembled 70S subunits. Era, an essential highly conserved GTPase protein, interacts with many ribosomal proteins, and its depletion results in ribosome assembly defects. YbeY has been shown to interact with Era together with ribosomal protein S11. In this study, we have analyzed a suppressor mutation, era(T99I), that can partially suppress a subset of the multiple phenotypes of ybeY deletion. The era(T99I) allele was able to improve 16S rRNA processing and ribosome assembly at 37°C. However, it failed to suppress the temperature sensitivity and did not improve 16S rRNA stability. The era(T99I) allele was also unable to improve the 16S rRNA processing defects caused by the loss of ribosome maturation factors. We also show that era(T99I) increases the GroEL levels in the 30S ribosome fractions independent of YbeY. We propose that the mechanism of suppression is that the changes in Era's structure caused by the era(T99I) mutation affect its GTP/GDP cycle in a way that increases the half-life of RNA binding to Era, thereby facilitating alternative processing of the 16S RNA precursor. Taken together, this study offers insights into the role of Era and YbeY in ribosome assembly and 16S rRNA processing events.
Collapse
Affiliation(s)
| | | | | | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
40
|
Herzel L, Stanley JA, Yao CC, Li GW. Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome. Nucleic Acids Res 2022; 50:5029-5046. [PMID: 35524564 PMCID: PMC9122600 DOI: 10.1093/nar/gkac295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
Collapse
Affiliation(s)
- Lydia Herzel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Julian A Stanley
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Chun-Chen Yao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| |
Collapse
|
41
|
Putzeys L, Boon M, Lammens EM, Kuznedelov K, Severinov K, Lavigne R. Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages. Comput Struct Biotechnol J 2022; 20:2624-2638. [PMID: 35685363 PMCID: PMC9163698 DOI: 10.1016/j.csbj.2022.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
- Corresponding author.
| |
Collapse
|
42
|
Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community. THE ISME JOURNAL 2022; 16:1442-1452. [PMID: 35066567 PMCID: PMC9039033 DOI: 10.1038/s41396-022-01191-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/31/2021] [Accepted: 01/06/2022] [Indexed: 01/16/2023]
Abstract
Species loss within a microbial community can increase resource availability and spur adaptive evolution. Environmental shifts that cause species loss or fluctuations in community composition are expected to become more common, so it is important to understand the evolutionary forces that shape the stability and function of the emergent community. Here we study experimental cultures of a simple, ecologically stable community of Saccharomyces cerevisiae and Lactobacillus plantarum, in order to understand how the presence or absence of a species impacts coexistence over evolutionary timescales. We found that evolution in coculture led to drastically altered evolutionary outcomes for L. plantarum, but not S. cerevisiae. Both monoculture- and co-culture-evolved L. plantarum evolved dozens of mutations over 925 generations of evolution, but only L. plantarum that had evolved in isolation from S. cerevisiae lost the capacity to coexist with S. cerevisiae. We find that the evolutionary loss of ecological stability corresponds with fitness differences between monoculture-evolved L. plantarum and S. cerevisiae and genetic changes that repeatedly evolve across the replicate populations of L. plantarum. This work shows how coevolution within a community can prevent destabilising evolution in individual species, thereby preserving ecological diversity and stability, despite rapid adaptation.
Collapse
|
43
|
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: 25] [Impact Index Per Article: 12.5] [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.
Collapse
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
| |
Collapse
|
44
|
Daniels PW, Hama Soor T, Levicky Q, Hettema EH, Mitchell P. Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1. RNA (NEW YORK, N.Y.) 2022; 28:493-507. [PMID: 35082142 PMCID: PMC8925975 DOI: 10.1261/rna.078939.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The 3' exonucleolytic processing of stable RNAs is conserved throughout biology. Yeast strains lacking the exoribonuclease Rex1 are defective in the 3' processing of stable RNAs, including 5S rRNA and tRNA. The equivalent RNA processing steps in Escherichia coli are carried out by RNase T. Rex1 is larger than RNase T, the catalytic DEDD domain being embedded within uncharacterized amino- and carboxy-terminal regions. Here we report that both amino- and carboxy-terminal regions of Rex1 are essential for its function, as shown by genetic analyses and 5S rRNA profiling. Full-length Rex1, but not mutants lacking amino- or carboxy-terminal regions, accurately processed a 3' extended 5S rRNA substrate. Crosslinking analyses showed that both amino- and carboxy-terminal regions of Rex1 directly contact RNA in vivo. Sequence homology searches identified YFE9 in Schizosaccharomyces pombe and SDN5 in Arabidopsis thaliana as closely related proteins to Rex1. In addition to the DEDD domain, these proteins share a domain, referred to as the RYS (Rex1, YFE9 and SDN5) domain, that includes elements of both the amino- and caroxy-terminal flanking regions. We also characterize a nuclear localization signal in the amino-terminal region of Rex1. These studies reveal a novel dual domain structure at the core of Rex1-related ribonucleases, wherein the catalytic DEDD domain and the RYS domain are aligned such that they both contact the bound substrate. The domain organization of Rex1 is distinct from that of other previously characterized DEDD family nucleases and expands the known repertoire of structures for this fundamental family of RNA processing enzymes.
Collapse
Affiliation(s)
- Peter W Daniels
- Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN Sheffield, United Kingdom
| | - Taib Hama Soor
- Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN Sheffield, United Kingdom
| | - Quentin Levicky
- Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN Sheffield, United Kingdom
| | - Ewald H Hettema
- Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN Sheffield, United Kingdom
| | - Phil Mitchell
- Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN Sheffield, United Kingdom
| |
Collapse
|
45
|
Analysis of mRNA Decay Intermediates in Bacillus subtilis 3′ Exoribonuclease and RNA Helicase Mutant Strains. mBio 2022; 13:e0040022. [PMID: 35311531 PMCID: PMC9040804 DOI: 10.1128/mbio.00400-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Bacillus subtilis genome encodes four 3′ exoribonucleases: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Previous work showed that PNPase, encoded by the pnpA gene, is the major 3′ exonuclease involved in mRNA turnover; in a pnpA deletion strain, numerous mRNA decay intermediates accumulate. Whether B. subtilis mRNA decay occurs in the context of a degradosome complex is controversial. In this study, global mapping of mRNA decay intermediate 3′ ends within coding sequences was performed in strains that were either deleted for or had an inactivating point mutation in the pnpA gene. The patterns of 3′-end accumulation in these strains were highly similar, which may have implications for the role of a degradosome in mRNA decay. A comparison with mapped 3′ ends in a strain lacking CshA, the major RNA helicase, indicated that many mRNAs require both PNPase and CshA for efficient decay. Transcriptome sequencing (RNA-seq) analysis of strains lacking RNase R suggested that this enzyme did not play a major role in mRNA turnover in the wild-type strain. Strains were constructed that contained only one of the four known 3′ exoribonucleases. When RNase R was the only 3′ exonuclease present, it was able to degrade a model mRNA efficiently, showing processive decay even through a strong stem-loop structure that inhibits PNPase processivity. Strains containing only RNase PH or only YhaM were also insensitive to this RNA secondary structure, suggesting the existence of another, as-yet-unidentified, 3′ exoribonuclease.
Collapse
|
46
|
Jones SP, Goossen C, Lewis SD, Delaney AM, Gleghorn ML. Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes. J Struct Biol X 2022; 6:100066. [PMID: 35340590 PMCID: PMC8943300 DOI: 10.1016/j.yjsbx.2022.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
RNases are varied in the RNA structures and sequences they target for cleavage and are an important type of enzyme in cells. Despite the numerous examples of RNases known, and of those with determined three-dimensional structures, relatively few examples exist with the RNase bound to intact cognate RNA substrate prior to cleavage. To better understand RNase structure and sequence specificity for RNA targets, in vitro methods used to assemble these enzyme complexes trapped in a pre-cleaved state have been developed for a number of different RNases. We have surveyed the Protein Data Bank for such structures and in this review detail methodologies that have successfully been used and relate them to the corresponding structures. We also offer ideas and suggestions for future method development. Many strategies within this review can be used in combination with X-ray crystallography, as well as cryo-EM, and other structure-solving techniques. Our hope is that this review will be used as a guide to resolve future yet-to-be-determined RNase-substrate complex structures.
Collapse
Affiliation(s)
- Seth P. Jones
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Christian Goossen
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Lothrop St, Pittsburgh, PA 15261, United States
| | - Sean D. Lewis
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Mayo Clinic, 200 1st St SW, Rochester, MN 5590, United States
| | - Annie M. Delaney
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Michael L. Gleghorn
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| |
Collapse
|
47
|
Garcia Gonzalez J, Hernandez FJ. Nuclease activity: an exploitable biomarker in bacterial infections. Expert Rev Mol Diagn 2022; 22:265-294. [PMID: 35240900 DOI: 10.1080/14737159.2022.2049249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications. AREAS COVERED This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected. EXPERT OPINION Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.
Collapse
Affiliation(s)
- Javier Garcia Gonzalez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| |
Collapse
|
48
|
Zhang J, Hess WR, Zhang C. "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria. MLIFE 2022; 1:21-39. [PMID: 38818322 PMCID: PMC10989914 DOI: 10.1002/mlf2.12015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 06/01/2024]
Abstract
RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes. In bacteria, the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis, but not much is known in other bacteria. Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO2 and solar energy. A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria. Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E. coli and B. subtilis, and only a limited number of them have been experimentally investigated. In this review, we summarize the current knowledge about these RNA-turnover-related proteins in cyanobacteria. Although many of them are biochemically similar to their counterparts in E. coli and B. subtilis, they appear to have distinct cellular functions, suggesting a different mechanism of RNA turnover regulation in cyanobacteria. The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field.
Collapse
Affiliation(s)
- Ju‐Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Cheng‐Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
- Institut WUT‐AMUAix‐Marseille University and Wuhan University of TechnologyWuhanChina
| |
Collapse
|
49
|
Ulyanova V, Nadyrova A, Dudkina E, Kuznetsova A, Ahmetgalieva A, Faizullin D, Surchenko Y, Novopashina D, Zuev Y, Kuznetsov N, Ilinskaya O. Structural and Functional Differences between Homologous Bacterial Ribonucleases. Int J Mol Sci 2022; 23:ijms23031867. [PMID: 35163789 PMCID: PMC8837141 DOI: 10.3390/ijms23031867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 02/04/2023] Open
Abstract
Small cationic guanyl-preferring ribonucleases (RNases) produced by the Bacillus species share a similar protein tertiary structure with a high degree of amino acid sequence conservation. However, they form dimers that differ in conformation and stability. Here, we have addressed the issues (1) whether the homologous RNases also have distinctions in catalytic activity towards different RNA substrates and interactions with the inhibitor protein barstar, and (2) whether these differences correlate with structural features of the proteins. Circular dichroism and dynamic light scattering assays revealed distinctions in the structures of homologous RNases. The activity levels of the RNases towards natural RNA substrates, as measured spectrometrically by acid-soluble hydrolysis products, were similar and decreased in the row high-polymeric RNA >>> transport RNA > double-stranded RNA. However, stopped flow kinetic studies on model RNA substrates containing the guanosine residue in a hairpin stem or a loop showed that the cleavage rates of these enzymes were different. Moreover, homologous RNases were inhibited by the barstar with diverse efficiency. Therefore, minor changes in structure elements of homologous proteins have a potential to significantly effect molecule stability and functional activities, such as catalysis or ligand binding.
Collapse
Affiliation(s)
- Vera Ulyanova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
- Correspondence:
| | - Alsu Nadyrova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Elena Dudkina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Aleksandra Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Albina Ahmetgalieva
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Dzhigangir Faizullin
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (D.F.); (Y.Z.)
| | - Yulia Surchenko
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Darya Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (D.F.); (Y.Z.)
| | - Nikita Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Olga Ilinskaya
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| |
Collapse
|
50
|
Abstract
Detailed studies of the Gram-negative model bacterium, Escherichia coli, have demonstrated that post-transcriptional events exert important and possibly greater control over gene regulation than transcription initiation or effective translation. Thus, over the past 30 years, considerable effort has been invested in understanding the pathways of mRNA turnover in E. coli. Although it is assumed that most of the ribonucleases and accessory proteins involved in mRNA decay have been identified, our understanding of the regulation of mRNA decay is still incomplete. Furthermore, the vast majority of the studies on mRNA decay have been conducted on exponentially growing cells. Thus, the mechanism of mRNA decay as currently outlined may not accurately reflect what happens when cells find themselves under a variety of stress conditions, such as, nutrient starvation, changes in pH and temperature, as well as a host of others. While the cellular machinery for degradation is relatively constant over a wide range of conditions, intracellular levels of specific ribonucleases can vary depending on the growth conditions. Substrate competition will also modulate ribonucleolytic activity. Post-transcriptional modifications of transcripts by polyadenylating enzymes may favor a specific ribonuclease activity. Interactions with small regulatory RNAs and RNA binding proteins add additional complexities to mRNA functionality and stability. Since many of the ribonucleases are found at the inner membrane, the physical location of a transcript may help determine its half-life. Here we discuss the properties and role of the enzymes involved in mRNA decay as well as the multiple factors that may affect mRNA decay under various in vivo conditions.
Collapse
Affiliation(s)
| | - Sidney R. Kushner
- Department of Genetics, University of Georgia, Athens GA 30602,Department of Microbiology, University of Georgia, Athens GA 30602,To whom correspondence should be addressed:
| |
Collapse
|