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Sharma R, Mishanina TV. A riboswitch-controlled TerC family transporter Alx tunes intracellular manganese concentration in Escherichia coli at alkaline pH. J Bacteriol 2024; 206:e0016824. [PMID: 38869303 PMCID: PMC11270866 DOI: 10.1128/jb.00168-24] [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: 04/19/2024] [Accepted: 05/11/2024] [Indexed: 06/14/2024] Open
Abstract
Cells use transition metal ions as structural components of biomolecules and cofactors in enzymatic reactions, making transition metal ions integral cellular components. Organisms optimize metal ion concentration to meet cellular needs by regulating the expression of proteins that import and export that metal ion, often in a metal ion concentration-dependent manner. One such regulation mechanism is via riboswitches, which are 5'-untranslated regions of an mRNA that undergo conformational changes to promote or inhibit the expression of the downstream gene, commonly in response to a ligand. The yybP-ykoY family of bacterial riboswitches shares a conserved aptamer domain that binds manganese ions (Mn2+). In Escherichia coli, the yybP-ykoY riboswitch precedes and regulates the expression of two different genes: mntP, which based on genetic evidence encodes an Mn2+ exporter, and alx, which encodes a putative metal ion transporter whose cognate ligand is currently in question. The expression of alx is upregulated by both elevated concentrations of Mn2+ and alkaline pH. With metal ion measurements and gene expression studies, we demonstrate that the alkalinization of media increases the cytoplasmic manganese pool, which, in turn, enhances alx expression. The Alx-mediated Mn2+ export prevents the toxic buildup of the cellular manganese, with the export activity maximal at alkaline pH. We pinpoint a set of acidic residues in the predicted transmembrane segments of Alx that play a critical role in Mn2+ export. We propose that Alx-mediated Mn2+ export serves as a primary protective mechanism that fine tunes the cytoplasmic manganese content, especially during alkaline stress.IMPORTANCEBacteria use clever ways to tune gene expression upon encountering certain environmental stresses, such as alkaline pH in parts of the human gut and high concentration of a transition metal ion manganese. One way by which bacteria regulate the expression of their genes is through the 5'-untranslated regions of messenger RNA called riboswitches that bind ligands to turn expression of genes on/off. In this work, we have investigated the roles and regulation of alx and mntP, the two genes in Escherichia coli regulated by the yybP-ykoY riboswitches, in alkaline pH and high concentration of Mn2+. This work highlights the intricate ways through which bacteria adapt to their surroundings, utilizing riboregulatory mechanisms to maintain Mn2+ levels amidst varying environmental factors.
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Affiliation(s)
- Ravish Sharma
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Tatiana V. Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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2
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Hsieh YYP, Sun W, Young JM, Cheung R, Hogan DA, Dandekar AA, Malik HS. Widespread fungal-bacterial competition for magnesium lowers bacterial susceptibility to polymyxin antibiotics. PLoS Biol 2024; 22:e3002694. [PMID: 38900845 PMCID: PMC11218974 DOI: 10.1371/journal.pbio.3002694] [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: 04/02/2024] [Revised: 07/02/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024] Open
Abstract
Fungi and bacteria coexist in many polymicrobial communities, yet the molecular basis of their interactions remains poorly understood. Here, we show that the fungus Candida albicans sequesters essential magnesium ions from the bacterium Pseudomonas aeruginosa. To counteract fungal Mg2+ sequestration, P. aeruginosa expresses the Mg2+ transporter MgtA when Mg2+ levels are low. Thus, loss of MgtA specifically impairs P. aeruginosa in co-culture with C. albicans, but fitness can be restored by supplementing Mg2+. Using a panel of fungi and bacteria, we show that Mg2+ sequestration is a general mechanism of fungal antagonism against gram-negative bacteria. Mg2+ limitation enhances bacterial resistance to polymyxin antibiotics like colistin, which target gram-negative bacterial membranes. Indeed, experimental evolution reveals that P. aeruginosa evolves C. albicans-dependent colistin resistance via non-canonical means; antifungal treatment renders resistant bacteria colistin-sensitive. Our work suggests that fungal-bacterial competition could profoundly impact polymicrobial infection treatment with antibiotics of last resort.
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Affiliation(s)
- Yu-Ying Phoebe Hsieh
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Wanting Sun
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Janet M. Young
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Robin Cheung
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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3
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H, Elliot MA. Multifactorial genetic control and magnesium levels govern the production of a Streptomyces antibiotic with unusual cell density dependence. mSystems 2024; 9:e0136823. [PMID: 38493407 PMCID: PMC11019849 DOI: 10.1128/msystems.01368-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/18/2024] Open
Abstract
Streptomyces bacteria are renowned both for their antibiotic production capabilities and for their cryptic metabolic potential. Their metabolic repertoire is subject to stringent genetic control, with many of the associated biosynthetic gene clusters being repressed by the conserved nucleoid-associated protein Lsr2. In an effort to stimulate new antibiotic production in wild Streptomyces isolates, we leveraged the activity of an Lsr2 knockdown construct and successfully enhanced antibiotic production in the wild Streptomyces isolate WAC07094. We determined that this new activity stemmed from increased levels of the angucycline-like family member saquayamycin. Saquayamycin has both antibiotic and anti-cancer activities, and intriguingly, beyond Lsr2-mediated repression, we found saquayamycin production was also suppressed at high density on solid or in liquid growth media; its levels were greatest in low-density cultures. This density-dependent control was exerted at the level of the cluster-situated regulatory gene sqnR and was mediated in part through the activity of the PhoRP two-component regulatory system, where deleting phoRP led to both constitutive antibiotic production and sqnR expression. This suggests that PhoP functions to repress the expression of sqnR at high cell density. We further discovered that magnesium supplementation could alleviate this density dependence, although its action was independent of PhoP. Finally, we revealed that the nitrogen-responsive regulators GlnR and AfsQ1 could relieve the repression exerted by Lsr2 and PhoP. Intriguingly, we found that this low density-dependent production of saquayamycin was not unique to WAC07094; saquayamycin production by another wild isolate also exhibited low-density activation, suggesting that this spatial control may serve an important ecological function in their native environments.IMPORTANCEStreptomyces specialized metabolic gene clusters are subject to complex regulation, and their products are frequently not observed under standard laboratory growth conditions. For the wild Streptomyces isolate WAC07094, production of the angucycline-family compound saquayamycin is subject to a unique constellation of control factors. Notably, it is produced primarily at low cell density, in contrast to the high cell density production typical of most antibiotics. This unusual density dependence is conserved in other saquayamycin producers and is driven by the pathway-specific regulator SqnR, whose expression is influenced by both nutritional and genetic elements. Collectively, this work provides new insights into an intricate regulatory system governing antibiotic production and indicates there may be benefits to including low-density cultures in antibiotic screening platforms.
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Affiliation(s)
- Hindra
- Institute of Infectious Disease Research and Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Marie A. Elliot
- Institute of Infectious Disease Research and Department of Biology, McMaster University, Hamilton, Ontario, Canada
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4
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Vishnu N, Venkatesan M, Madaris TR, Venkateswaran MK, Stanley K, Ramachandran K, Chidambaram A, Madesh AK, Yang W, Nair J, Narkunan M, Muthukumar T, Karanam V, Joseph LC, Le A, Osidele A, Aslam MI, Morrow JP, Malicdan MC, Stathopulos PB, Madesh M. ERMA (TMEM94) is a P-type ATPase transporter for Mg 2+ uptake in the endoplasmic reticulum. Mol Cell 2024; 84:1321-1337.e11. [PMID: 38513662 PMCID: PMC10997467 DOI: 10.1016/j.molcel.2024.02.033] [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: 04/22/2023] [Revised: 10/16/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Intracellular Mg2+ (iMg2+) is bound with phosphometabolites, nucleic acids, and proteins in eukaryotes. Little is known about the intracellular compartmentalization and molecular details of Mg2+ transport into/from cellular organelles such as the endoplasmic reticulum (ER). We found that the ER is a major iMg2+ compartment refilled by a largely uncharacterized ER-localized protein, TMEM94. Conventional and AlphaFold2 predictions suggest that ERMA (TMEM94) is a multi-pass transmembrane protein with large cytosolic headpiece actuator, nucleotide, and phosphorylation domains, analogous to P-type ATPases. However, ERMA uniquely combines a P-type ATPase domain and a GMN motif for ERMg2+ uptake. Experiments reveal that a tyrosine residue is crucial for Mg2+ binding and activity in a mechanism conserved in both prokaryotic (mgtB and mgtA) and eukaryotic Mg2+ ATPases. Cardiac dysfunction by haploinsufficiency, abnormal Ca2+ cycling in mouse Erma+/- cardiomyocytes, and ERMA mRNA silencing in human iPSC-cardiomyocytes collectively define ERMA as an essential component of ERMg2+ uptake in eukaryotes.
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Affiliation(s)
- Neelanjan Vishnu
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Manigandan Venkatesan
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Travis R Madaris
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Mridula K Venkateswaran
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Kristen Stanley
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Karthik Ramachandran
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Adhishree Chidambaram
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Abitha K Madesh
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Wenli Yang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jyotsna Nair
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Melanie Narkunan
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Tharani Muthukumar
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Varsha Karanam
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Leroy C Joseph
- Department of Medicine, College of Physicians and Surgeons of Columbia University, 650 W 168 Street, New York, NY 10032, USA
| | - Amy Le
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Ayodeji Osidele
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - M Imran Aslam
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - John P Morrow
- Department of Medicine, College of Physicians and Surgeons of Columbia University, 650 W 168 Street, New York, NY 10032, USA
| | - May C Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, and the Common Fund, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Western University, London, ON N6A 5C1, Canada
| | - Muniswamy Madesh
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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5
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Wu Y, Zhu L, Zhang Y, Xu W. Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304852. [PMID: 37658499 DOI: 10.1002/smll.202304852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Indexed: 09/03/2023]
Abstract
Riboswitches have received significant attention over the last two decades for their multiple functionalities and great potential for applications in various fields. This article highlights and reviews the recent advances in biosensing and biotherapy. These fields involve a wide range of applications, such as food safety detection, environmental monitoring, metabolic engineering, live cell imaging, wearable biosensors, antibacterial drug targets, and gene therapy. The discovery, origin, and optimization of riboswitches are summarized to help readers better understand their multidimensional applications. Finally, this review discusses the multidimensional challenges and development of riboswitches in order to further expand their potential for novel applications.
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Affiliation(s)
- Yifan Wu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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6
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Bar A, Argaman L, Eldar M, Margalit H. TRS: a method for determining transcript termini from RNAtag-seq sequencing data. Nat Commun 2023; 14:7843. [PMID: 38030608 PMCID: PMC10687069 DOI: 10.1038/s41467-023-43534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/12/2023] [Indexed: 12/01/2023] Open
Abstract
In bacteria, determination of the 3' termini of transcripts plays an essential role in regulation of gene expression, affecting the functionality and stability of the transcript. Several experimental approaches were developed to identify the 3' termini of transcripts, however, these were applied only to a limited number of bacteria and growth conditions. Here we present a straightforward approach to identify 3' termini from widely available RNA-seq data without the need for additional experiments. Our approach relies on the observation that the RNAtag-seq sequencing protocol results in overabundance of reads mapped to transcript 3' termini. We present TRS (Termini by Read Starts), a computational pipeline exploiting this property to identify 3' termini in RNAtag-seq data, and show that the identified 3' termini are highly reliable. Since RNAtag-seq data are widely available for many bacteria and growth conditions, our approach paves the way for studying bacterial transcription termination in an unprecedented scope.
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Affiliation(s)
- Amir Bar
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel
| | - Michal Eldar
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel.
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7
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Palmgren M. P-type ATPases: Many more enigmas left to solve. J Biol Chem 2023; 299:105352. [PMID: 37838176 PMCID: PMC10654040 DOI: 10.1016/j.jbc.2023.105352] [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: 07/03/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023] Open
Abstract
P-type ATPases constitute a large ancient super-family of primary active pumps that have diverse substrate specificities ranging from H+ to phospholipids. The significance of these enzymes in biology cannot be overstated. They are structurally related, and their catalytic cycles alternate between high- and low-affinity conformations that are induced by phosphorylation and dephosphorylation of a conserved aspartate residue. In the year 1988, all P-type sequences available by then were analyzed and five major families, P1 to P5, were identified. Since then, a large body of knowledge has accumulated concerning the structure, function, and physiological roles of members of these families, but only one additional family, P6 ATPases, has been identified. However, much is still left to be learned. For each family a few remaining enigmas are presented, with the intention that they will stimulate interest in continued research in the field. The review is by no way comprehensive and merely presents personal views with a focus on evolution.
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Affiliation(s)
- Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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8
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Pokorzynski ND, Groisman EA. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiol Mol Biol Rev 2023; 87:e0019822. [PMID: 37358444 PMCID: PMC10521370 DOI: 10.1128/mmbr.00198-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.
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Affiliation(s)
- Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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Metaane S, Monteil V, Douché T, Giai Gianetto Q, Matondo M, Maufrais C, Norel F. Loss of CorA, the primary magnesium transporter of Salmonella, is alleviated by MgtA and PhoP-dependent compensatory mechanisms. PLoS One 2023; 18:e0291736. [PMID: 37713445 PMCID: PMC10503707 DOI: 10.1371/journal.pone.0291736] [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: 06/09/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of stationary phase cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have recently shown that a ΔrpoS mutation decreases the magnesium content and expression level of the housekeeping Mg2+-transporter CorA in stationary phase Salmonella. The other two Mg2+-transporters of Salmonella are encoded by the PhoP-activated mgtA and mgtB genes and are expressed under magnesium starvation. The σS control of corA prompted us to evaluate the impact of CorA in stationary phase Salmonella cells, by using global and analytical proteomic analyses and physiological assays. The ΔcorA mutation conferred a competitive disadvantage to exit from stationary phase, and slightly impaired motility, but had no effect on total and free cellular magnesium contents. In contrast to the wild-type strain, the ΔcorA mutant produced MgtA, but not MgtB, in the presence of high extracellular magnesium concentration. Under these conditions, MgtA production in the ΔcorA mutant did not require PhoP. Consistently, a ΔmgtA, but not a ΔphoP, mutation slightly reduced the magnesium content of the ΔcorA mutant. Synthetic phenotypes were observed when the ΔphoP and ΔcorA mutations were combined, including a strong reduction in growth and motility, independently of the extracellular magnesium concentration. The abundance of several proteins involved in flagella formation, chemotaxis and secretion was lowered by the ΔcorA and ΔphoP mutations in combination, but not alone. These findings unravel the importance of PhoP-dependent functions in the absence of CorA when magnesium is sufficient. Altogether, our data pinpoint a regulatory network, where the absence of CorA is sensed by the cell and compensated by MgtA and PhoP- dependent mechanisms.
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Affiliation(s)
- Selma Metaane
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Véronique Monteil
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Thibaut Douché
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Quentin Giai Gianetto
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Mariette Matondo
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Corinne Maufrais
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Françoise Norel
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
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10
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Liang Y, Zhang J, Xu C, Wang J, Han W, Yang J, Wu S, An J, Liu J, Zhang Z, Shi J, Zhang K. Biomimetic Mineralized CRISPR/Cas RNA Nanoparticles for Efficient Tumor-Specific Multiplex Gene Editing. ACS NANO 2023; 17:15025-15043. [PMID: 37481734 DOI: 10.1021/acsnano.3c04116] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
CRISPR/Cas9 systems have great potential to achieve sophisticated gene therapy and cell engineering by editing multiple genomic loci. However, to achieve efficient multiplex gene editing, the delivery system needs adequate capacity to transfect all CRISPR/Cas9 RNA species at the required stoichiometry into the cytosol of each individual cell. Herein, inspired by biomineralization in nature, we develop an all-in-one biomimetic mineralized CRISPR/Cas9 RNA delivery system. This system allows for precise control over the coencapsulation ratio between Cas9 mRNA and multiple sgRNAs, while also exhibiting a high RNA loading capacity. In addition, it enhances the storage stability of RNA at 4 °C for up to one month, and the surface of the nanoparticles can be easily functionalized for precise targeting of RNA nanoparticles in vivo at nonliver sites. Based on the above characteristics, as a proof-of-concept, our system was able to achieve significant gene-editing at each target gene (Survivin: 31.9%, PLK1: 24.41%, HPV: 23.2%) and promote apoptosis of HeLa cells in the mouse model, inhibiting tumor growth without obvious off-target effects in liver tissue. This system addresses various challenges associated with multicomponent RNA delivery in vivo, providing an innovative strategy for the RNA-based CRISPR/Cas9 gene editing.
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Affiliation(s)
- Yan Liang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jingge Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Chenlu Xu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jinjin Wang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Wenshuai Han
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jiali Yang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Sixuan Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jingyi An
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Junjie Liu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
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11
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Yao Y, Sun H, Wurihan, Gegeheng, Gezi, Skarstad K, Fan L, Morigen. A DnaA-dependent riboswitch for transcription attenuation of the his operon. MLIFE 2023; 2:126-140. [PMID: 38817620 PMCID: PMC10989985 DOI: 10.1002/mlf2.12075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/01/2024]
Abstract
Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the release of the arrested ribosome from the leader mRNA molecule. In this study, we first report a possible example of the DnaA-dependent riboswitch for transcription attenuation in Escherichia coli. We show that (i) DnaA regulates the transcription of the structural genes but not that of the leader hisL gene; (ii) DnaA might bind to rDnaA boxes present in the HisL-SL RNA, and subsequently attenuate the transcription of the operon; (iii) the HisL-SL RNA and rDnaA boxes are phylogenetically conserved and evolutionarily important; and (iv) the translating ribosome is required for deattenuation of the his operon, whereas tRNAHis strengthens attenuation. This mechanism seems to be phylogenetically conserved in Gram-negative bacteria and evolutionarily important.
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Affiliation(s)
- Yuan Yao
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Hongwei Sun
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Wurihan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gegeheng
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gezi
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Kirsten Skarstad
- Department of Molecular Cell Biology and Department of MicrobiologyOslo University HospitalOsloNorway
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Morigen
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
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12
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Sharma R, Mishanina TV. A riboswitch-controlled manganese exporter (Alx) tunes intracellular Mn 2+ concentration in E. coli at alkaline pH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539761. [PMID: 37214827 PMCID: PMC10197570 DOI: 10.1101/2023.05.07.539761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells use transition metal ions as structural components of biomolecules and cofactors in enzymatic reactions, making transition metals vital cellular components. The buildup of a particular metal ion in certain stress conditions becomes harmful to the organism due to the misincorporation of the excess ion into biomolecules, resulting in perturbed enzymatic activity or metal-catalyzed formation of reactive oxygen species. Organisms optimize metal concentration by regulating the expression of proteins that import and export that metal, often in a metal concentration-dependent manner. One such regulation mechanism is via riboswitches, which are 5'-untranslated regions (UTR) of an mRNA that undergo conformational changes to promote or inhibit the expression of the downstream gene, commonly in response to a ligand. The yybP-ykoY family of bacterial riboswitches shares a conserved aptamer domain that binds manganese (Mn2+). In E. coli, the yybP-ykoY riboswitch precedes and regulates the expression of two genes: mntP, which based on extensive genetic evidence encodes an Mn2+ exporter, and alx, which encodes a putative metal ion transporter whose cognate ligand is currently in question. Expression of alx is upregulated by both elevated intracellular concentrations of Mn2+ and alkaline pH. With metal ion measurements and gene expression studies, we demonstrate that the alkalinization of media increases cytoplasmic Mn2+ content, which in turn enhances alx expression. Alx then exports excess Mn2+ to prevent toxic buildup of the metal inside the cell, with the export activity maximal at alkaline pH. Using mutational and complementation experiments, we pinpoint a set of acidic residues in the predicted transmembrane segments of Alx that play a crucial role in its Mn2+ export. We propose that Alx-mediated Mn2+ export provides a primary protective layer that fine-tunes the cytoplasmic Mn2+ levels, especially during alkaline stress.
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Affiliation(s)
- Ravish Sharma
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Tatiana V. Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
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13
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Bai S, Han X, Feng D. Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1139744. [PMID: 36890896 PMCID: PMC9987563 DOI: 10.3389/fpls.2023.1139744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.
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Affiliation(s)
- Shiyan Bai
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends Biochem Sci 2023; 48:119-141. [PMID: 36150954 PMCID: PMC10043782 DOI: 10.1016/j.tibs.2022.08.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/25/2023]
Abstract
Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.
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Affiliation(s)
- Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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15
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Cui M, Zhang D, Wang Q, Chao J. An intelligent, autocatalytic, DNAzyme biocircuit for amplified imaging of intracellular microRNAs. NANOSCALE 2023; 15:578-587. [PMID: 36533380 DOI: 10.1039/d2nr05165f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
DNAzymes hold great promise as transducing agents for the analysis of intracellular biomarkers. However, their low intracellular delivery efficiency and limited signal amplification capability (including an additional supply of cofactors) hinder their application in low-abundance biomarker analysis. Herein, a general strategy to design an intelligent, autocatalytic, DNAzyme biocircuit is developed for amplified microRNA imaging in living cells. The DNAzyme biocircuit is constructed based on a nanodevice composed of catalytic hairpin assembly (CHA) and DNAzyme biocatalytic functional units, sustained by Au nanoparticles (AuNPs) and MnO2 nanosheets (CD/AM nanodevices). Once the CD/AM nanodevices are endocytosed by cells, the MnO2 nanosheets are reduced by intracellular glutathione (GSH), which not only releases the different units of the DNAzyme circuit, but also generates the cofactor Mn2+ for DNAzyme autocatalysis. The intracellular analytes could trigger the coordinated cross-activation of CHA and autocatalytic DNAzymes on AuNPs, enabling reliable and accurate detection of miRNAs in living cells. This intelligent autocatalytic multilayer DNAzyme biocircuit can effectively avoid signal leakage and obtain high amplification gain, expanding the application of programmable complex DNA nanocircuits in biosensing, nanomaterial assembly, and biomedicine.
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Affiliation(s)
- Meirong Cui
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Dan Zhang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Qingfu Wang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Jie Chao
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
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16
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Zou Z, Pan M, Mo F, Jiang Q, Feng A, Zhou Y, Wang F, Liu X. High-fidelity ATP imaging via an isothermal cascade catalytic amplifier. Chem Sci 2022; 13:12198-12207. [PMID: 36349106 PMCID: PMC9601329 DOI: 10.1039/d2sc04560e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/29/2022] [Indexed: 09/19/2023] Open
Abstract
Artificial catalytic DNA circuits that can identify, transduce and amplify the biomolecule of interest have supplemented a powerful toolkit for visualizing various biomolecules in cancer cells. However, the non-specific response in normal tissues and the low abundance of analytes hamper their extensive biosensing and biomedicine applications. Herein, by combining tumor-responsive MnO2 nanoparticles with a specific stimuli-activated cascade DNA amplifier, we propose a multiply guaranteed and amplified ATP-sensing platform via the successive cancer-selective probe exposure and stimulation procedures. Initially, the GSH-degradable MnO2 nanocarrier, acting as a tumor-activating module, ensures the accurate delivery of the cascade DNA amplifier into GSH-rich cancer cells and simultaneously provides adequate Mn2+ cofactors for facilitating the DNAzyme biocatalysis. Then, the released cascade amplifier, acting as an ATP-monitoring module, fulfills the precise and sensitive analysis of low-abundance ATP in cancer cells where the catalyzed hairpin assembly (CHA) is integrated with the DNAzyme biocatalyst for higher signal gain. Additionally, the cascade catalytic amplifier achieved tumor-specific activated photodynamic therapy (PDT) after integrating an activatable photosensitizer into the system. This homogeneous cascade catalytic aptasensing circuit can detect low-abundance endogenous ATP of cancer cells, due to its intrinsically rich recognition repertoire and avalanche-mimicking hierarchical acceleration, thus demonstrating broad prospects for analyzing clinically important biomolecules and the associated physiological processes.
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Affiliation(s)
- Zhiqiao Zou
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P.R. China
| | - Min Pan
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University Wuhan 430072 P.R. China
| | - Fengye Mo
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P.R. China
| | - Qunying Jiang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P.R. China
| | - Ailing Feng
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P.R. China
| | - Yizhuo Zhou
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P.R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P.R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P.R. China
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17
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Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch. Commun Biol 2022; 5:1120. [PMID: 36273041 PMCID: PMC9588036 DOI: 10.1038/s42003-022-04096-z] [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] [Received: 06/15/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
Riboswitches normally regulate gene expression through structural changes in response to the specific binding of cellular metabolites or metal ions. Taking add adenine riboswitch as an example, we explore the influences of metal ions (especially for K+ and Mg2+ ions) on the structure and dynamics of riboswitch aptamer (with and without ligand) by using molecular dynamic (MD) simulations. Our results show that a two-state transition marked by the structural deformation at the connection of J12 and P1 (CJ12-P1) is not only related to the binding of cognate ligands, but also strongly coupled with the change of metal ion environments. Moreover, the deformation of the structure at CJ12-P1 can be transmitted to P1 directly connected to the expression platform in multiple ways, which will affect the structure and stability of P1 to varying degrees, and finally change the regulation state of this riboswitch. Molecular dynamic simulations are employed to assess the influence of metal ions on riboswitch structure and dynamics, suggesting a conformational control of riboswitch aptamers by metal ions before ligand binding.
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18
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Giarimoglou N, Kouvela A, Maniatis A, Papakyriakou A, Zhang J, Stamatopoulou V, Stathopoulos C. A Riboswitch-Driven Era of New Antibacterials. Antibiotics (Basel) 2022; 11:antibiotics11091243. [PMID: 36140022 PMCID: PMC9495366 DOI: 10.3390/antibiotics11091243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022] Open
Abstract
Riboswitches are structured non-coding RNAs found in the 5′ UTR of important genes for bacterial metabolism, virulence and survival. Upon the binding of specific ligands that can vary from simple ions to complex molecules such as nucleotides and tRNAs, riboswitches change their local and global mRNA conformations to affect downstream transcription or translation. Due to their dynamic nature and central regulatory role in bacterial metabolism, riboswitches have been exploited as novel RNA-based targets for the development of new generation antibacterials that can overcome drug-resistance problems. During recent years, several important riboswitch structures from many bacterial representatives, including several prominent human pathogens, have shown that riboswitches are ideal RNA targets for new compounds that can interfere with their structure and function, exhibiting much reduced resistance over time. Most interestingly, mainstream antibiotics that target the ribosome have been shown to effectively modulate the regulatory behavior and capacity of several riboswitches, both in vivo and in vitro, emphasizing the need for more in-depth studies and biological evaluation of new antibiotics. Herein, we summarize the currently known compounds that target several main riboswitches and discuss the role of mainstream antibiotics as modulators of T-box riboswitches, in the dawn of an era of novel inhibitors that target important bacterial regulatory RNAs.
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Affiliation(s)
- Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Alexandros Maniatis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi, 15341 Athens, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-997932
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19
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Pavlova N, Penchovsky R. Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics (Basel) 2022; 11:antibiotics11091177. [PMID: 36139956 PMCID: PMC9495176 DOI: 10.3390/antibiotics11091177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.
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20
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White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Na + riboswitches regulate genes for diverse physiological processes in bacteria. Nat Chem Biol 2022; 18:878-885. [PMID: 35879547 PMCID: PMC9337991 DOI: 10.1038/s41589-022-01086-4] [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: 09/20/2021] [Accepted: 06/10/2022] [Indexed: 01/31/2023]
Abstract
Organisms presumably have mechanisms to monitor and physiologically adapt to changes in cellular Na+ concentrations. Only a single bacterial protein has previously been demonstrated to selectively sense Na+ and regulate gene expression. Here we report a riboswitch class, previously called the ‘DUF1646 motif’, whose members selectively sense Na+ and regulate the expression of genes relevant to sodium biology. Many proteins encoded by Na+-riboswitch-regulated genes are annotated as metal ion transporters, whereas others are involved in mitigating osmotic stress or harnessing Na+ gradients for ATP production. Na+ riboswitches exhibit dissociation constants in the low mM range, and strongly reject all other alkali and alkaline earth ions. Likewise, only Na+ triggers riboswitch-mediated transcription and gene expression changes. These findings reveal that some bacteria use Na+ riboswitches to monitor, adjust and exploit Na+ concentrations and gradients, and in some instances collaborate with c-di-AMP riboswitches to coordinate gene expression during osmotic stress. ![]()
Only one protein factor is known that senses Na+ and controls gene expression. The Breaker Laboratory describes a bacterial riboswitch class selective for Na+ that regulates genes important for Na+ homeostasis, pH maintenance, osmotic stress response and ATP synthesis.
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Affiliation(s)
- Neil White
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Anna Sun
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA. .,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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21
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Franken GAC, Huynen MA, Martínez-Cruz LA, Bindels RJM, de Baaij JHF. Structural and functional comparison of magnesium transporters throughout evolution. Cell Mol Life Sci 2022; 79:418. [PMID: 35819535 PMCID: PMC9276622 DOI: 10.1007/s00018-022-04442-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/22/2022] [Accepted: 06/21/2022] [Indexed: 12/16/2022]
Abstract
Magnesium (Mg2+) is the most prevalent divalent intracellular cation. As co-factor in many enzymatic reactions, Mg2+ is essential for protein synthesis, energy production, and DNA stability. Disturbances in intracellular Mg2+ concentrations, therefore, unequivocally result in delayed cell growth and metabolic defects. To maintain physiological Mg2+ levels, all organisms rely on balanced Mg2+ influx and efflux via Mg2+ channels and transporters. This review compares the structure and the function of prokaryotic Mg2+ transporters and their eukaryotic counterparts. In prokaryotes, cellular Mg2+ homeostasis is orchestrated via the CorA, MgtA/B, MgtE, and CorB/C Mg2+ transporters. For CorA, MgtE, and CorB/C, the motifs that form the selectivity pore are conserved during evolution. These findings suggest that CNNM proteins, the vertebrate orthologues of CorB/C, also have Mg2+ transport capacity. Whereas CorA and CorB/C proteins share the gross quaternary structure and functional properties with their respective orthologues, the MgtE channel only shares the selectivity pore with SLC41 Na+/Mg2+ transporters. In eukaryotes, TRPM6 and TRPM7 Mg2+ channels provide an additional Mg2+ transport mechanism, consisting of a fusion of channel with a kinase. The unique features these TRP channels allow the integration of hormonal, cellular, and transcriptional regulatory pathways that determine their Mg2+ transport capacity. Our review demonstrates that understanding the structure and function of prokaryotic magnesiotropic proteins aids in our basic understanding of Mg2+ transport.
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Affiliation(s)
- G A C Franken
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - M A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L A Martínez-Cruz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park, Derio, 48160, Bizkaia, Spain
| | - R J M Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - J H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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22
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Mahendran G, Jayasinghe OT, Thavakumaran D, Arachchilage GM, Silva GN. Key players in regulatory RNA realm of bacteria. Biochem Biophys Rep 2022; 30:101276. [PMID: 35592614 PMCID: PMC9111926 DOI: 10.1016/j.bbrep.2022.101276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network. The three major classes of prokaryotic ncRNAs and their characterized mechanisms of operation in gene regulation. sRNAs emerging as major players in global gene regulatory networks. Riboswitch mediated gene control mechanisms through on/off switches in response to ligand binding. RNA thermo sensors for temperature-dependent gene expression. Therapeutic importance of ncRNAs and computational approaches involved in the discovery of ncRNAs.
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Affiliation(s)
- Gowthami Mahendran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Oshadhi T. Jayasinghe
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dhanushika Thavakumaran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Gayan Mirihana Arachchilage
- Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA
- PTC Therapeutics Inc, South Plainfield, NJ, 07080, USA
| | - Gayathri N. Silva
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Corresponding author.
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23
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Sadhanala HK, Pagidi S, Yadav S, Beiderman M, Grinberg I, Fixler D, Gedanken A. Boron‐doped Carbon Dots with Surface Oxygen Functional Groups as a Highly Sensitive and Label‐free Photoluminescence Probe for the Enhanced Detection of Mg
2+
Ions. ChemistrySelect 2022. [DOI: 10.1002/slct.202201261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Sudhakar Pagidi
- Department of Chemistry Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Suhas Yadav
- Department of Chemistry Bar-Ilan University Ramat-Gan 5290002 Israel
| | | | - Ilya Grinberg
- Department of Chemistry Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Dror Fixler
- Faculty of Engineering Bar-Ilan University Ramat Gan 5290002 Israel
| | - Aharon Gedanken
- Department of Chemistry Bar-Ilan University Ramat-Gan 5290002 Israel
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24
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Salmonella Central Carbon Metabolism Enhances Bactericidal Killing by Fluoroquinolone Antibiotics. Antimicrob Agents Chemother 2022; 66:e0234421. [PMID: 35658490 DOI: 10.1128/aac.02344-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The efficacy of killing by bactericidal antibiotics has been reported to depend in large part on the ATP levels, with low levels of ATP leading to increased persistence after antibiotic challenge. Here, we show that an atp operon deletion strain of Salmonella enterica serovar Typhimurium lacking the ATP synthase was at least 10-fold more sensitive to killing by the fluoroquinolone antibiotic ciprofloxacin and yet showed either increased survival or no significant difference compared with the wild-type strain when challenged with aminoglycoside or β-lactam antibiotics, respectively. The increased cell killing and reduced bacterial survival (persistence) after fluoroquinolone challenge were found to involve metabolic compensation for the loss of the ATP synthase through central carbon metabolism reactions and increased NAD(P)H levels. We conclude that the intracellular ATP levels per se do not correlate with bactericidal antibiotic persistence to fluoroquinolone killing; rather, the central carbon metabolic pathways active at the time of challenge and the intracellular target of the antibiotic determine the efficacy of treatment.
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Iron-responsive riboswitches. Curr Opin Chem Biol 2022; 68:102135. [DOI: 10.1016/j.cbpa.2022.102135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022]
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Coordination of Phosphate and Magnesium Metabolism in Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1362:135-150. [PMID: 35288878 DOI: 10.1007/978-3-030-91623-7_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The majority of cellular phosphate (PO4-3; Pi) exists as nucleoside triphosphates, mainly adenosine triphosphate (ATP), and ribosomal RNA (rRNA). ATP and rRNA are also the largest cytoplasmic reservoirs of magnesium (Mg2+), the most abundant divalent cation in living cells. The co-occurrence of these ionic species in the cytoplasm is not coincidental. Decades of work in the Pi and Mg2+ starvation responses of two model enteric bacteria, Escherichia coli and Salmonella enterica, have led to the realization that the metabolisms of Pi and Mg2+ are interconnected. Bacteria must acquire these nutrients in a coordinated manner to achieve balanced growth and avoid loss of viability. In this chapter, we will review how bacteria sense and respond to fluctuations in environmental and intracellular Pi and Mg2+ levels. We will also discuss how these two compounds are functionally linked, and how cells elicit physiological responses to maintain their homeostasis.
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Abstract
More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.
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Affiliation(s)
- Ronald R. Breaker
- Corresponding Author: Ronald R. Breaker - Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, United States; Phone: 203-432-9389; , Twitter: @RonBreaker
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Cai X, Wang Q, Fang Y, Yao D, Zhan Y, An B, Yan B, Cai J. Attenuator LRR - a regulatory tool for modulating gene expression in Gram-positive bacteria. Microb Biotechnol 2021; 14:2538-2551. [PMID: 33720523 PMCID: PMC8601186 DOI: 10.1111/1751-7915.13797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
With the rapid development of synthetic biology in recent years, particular attention has been paid to RNA devices, especially riboswitches, because of their significant and diverse regulatory roles in prokaryotic and eukaryotic cells. Due to the limited performance and context-dependence of riboswitches, only a few of them (such as theophylline, tetracycline and ciprofloxacin riboswitches) have been utilized as regulatory tools in biotechnology. In the present study, we demonstrated that a ribosome-dependent ribo-regulator, LRR, discovered in our previous work, exhibits an attractive regulatory performance. Specifically, it offers a 60-fold change in expression in the presence of retapamulin and a low level of leaky expression of about 1-2% without antibiotics. Moreover, LRR can be combined with different promoters and performs well in Bacillus thuringiensis, B. cereus, B. amyloliquefaciens, and B. subtilis. Additionally, LRR also functions in the Gram-negative bacterium Escherichia coli. Furthermore, we demonstrate its ability to control melanin metabolism in B. thuringiensis BMB171. Our results show that LRR can be applied to regulate gene expression, construct genetic circuits and tune metabolic pathways, and has great potential for many applications in synthetic biology.
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Affiliation(s)
- Xia Cai
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Qian Wang
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Yu Fang
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Die Yao
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Yunda Zhan
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Baoju An
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Bing Yan
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Jun Cai
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin300071China
- Tianjin Key Laboratory of Microbial Functional GenomicsTianjin300071China
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Abstract
Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5' leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.
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Affiliation(s)
- Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA; .,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA;
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Abstract
Phosphorus (P) is essential for life. As the fifth-most-abundant element in living cells, P is required for the synthesis of an array of biological molecules including (d)NTPs, nucleic acids, and membranes. Organisms typically acquire environmental P as inorganic phosphate (Pi). While essential for growth and viability, excess intracellular Pi is toxic for both bacteria and eukaryotes. Using the bacterium Salmonella enterica serovar Typhimurium as a model, we establish that Pi cytotoxicity is manifested following its assimilation into adenosine triphosphate (ATP), which acts as a chelating agent for Mg2+ and other cations. Our findings identify physiological processes disrupted by excessive Pi and how bacteria tune P assimilation to cytoplasmic Mg2+ levels. Phosphorus (P) is an essential component of core biological molecules. In bacteria, P is acquired mainly as inorganic orthophosphate (Pi) and assimilated into adenosine triphosphate (ATP) in the cytoplasm. Although P is essential, excess cytosolic Pi hinders growth. We now report that bacteria limit Pi uptake to avoid disruption of Mg2+-dependent processes that result, in part, from Mg2+ chelation by ATP. We establish that the MgtC protein inhibits uptake of the ATP precursor Pi when Salmonella enterica serovar Typhimurium experiences cytoplasmic Mg2+ starvation. This response prevents ATP accumulation and overproduction of ribosomal RNA that together ultimately hinder bacterial growth and result in loss of viability. Even when cytoplasmic Mg2+ is not limiting, excessive Pi uptake increases ATP synthesis, depletes free cytoplasmic Mg2+, inhibits protein synthesis, and hinders growth. Our results provide a framework to understand the molecular basis for Pi toxicity. Furthermore, they suggest a regulatory logic that governs P assimilation based on its intimate connection to cytoplasmic Mg2+ homeostasis.
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Groisman EA, Duprey A, Choi J. How the PhoP/PhoQ System Controls Virulence and Mg 2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution. Microbiol Mol Biol Rev 2021; 85:e0017620. [PMID: 34191587 PMCID: PMC8483708 DOI: 10.1128/mmbr.00176-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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Petrovskaya LE, Ziganshin RH, Kryukova EA, Zlobinov AV, Gapizov SS, Shingarova LN, Mironov VA, Lomakina GY, Dolgikh DA, Kirpichnikov MP. Increased Synthesis of a Magnesium Transporter MgtA During Recombinant Autotransporter Expression in Escherichia coli. Appl Biochem Biotechnol 2021; 193:3672-3703. [PMID: 34351586 DOI: 10.1007/s12010-021-03634-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/01/2022]
Abstract
Overproduction of the membrane proteins in Escherichia coli cells is a common approach to obtain sufficient material for their functional and structural studies. However, the efficiency of this process can be limited by toxic effects which decrease the viability of the host and lead to low yield of the product. During the expression of the esterase autotransporter AT877 from Psychrobacter cryohalolentis K5T, we observed significant growth inhibition of the C41(DE3) cells in comparison with the same cells producing other recombinant proteins. Induction of AT877 synthesis also resulted in the elevated expression of a magnesium transporter MgtA and decreased ATP content of the cells. To characterize the response to overexpression of the autotransporter in bacterial cells, we performed a comparative analysis of their proteomic profile by mass spectrometry. According to the obtained data, E. coli cells which synthesize AT877 experience complex stress condition presumably associated with secretion apparatus overloading and improper localization of the recombinant protein. Several response pathways were shown to be activated by AT877 overproduction including Cpx, PhoP/PhoQ, Psp, and σE The obtained results open new opportunities for optimization of the recombinant membrane protein expression in E. coli for structural studies and biotechnological applications.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia.
| | - Rustam H Ziganshin
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
| | - Alexander V Zlobinov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Sultan Sh Gapizov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Lyudmila N Shingarova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Vasiliy A Mironov
- Roche Diagnostics Rus LLC, Letnikovskaya str. 2/2, Moscow, 115114, Russia
| | - Galina Yu Lomakina
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991, Russia
- Bauman Moscow State Technical University, Baumanskaya 2-ya, 5/1, Moscow, 105005, Russia
| | - Dmitriy A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
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Low Cytoplasmic Magnesium Increases the Specificity of the Lon and ClpAP Proteases. J Bacteriol 2021; 203:e0014321. [PMID: 33941609 DOI: 10.1128/jb.00143-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteolysis is a fundamental property of all living cells. In the bacterium Salmonella enterica serovar Typhimurium, the HspQ protein controls the specificities of the Lon and ClpAP proteases. Upon acetylation, HspQ stops being a Lon substrate and no longer enhances proteolysis of the Lon substrate Hha. The accumulated HspQ protein binds to the protease adaptor ClpS, hindering proteolysis of ClpS-dependent substrates of ClpAP, such as Oat, a promoter of antibiotic persistence. HspQ is acetylated by the protein acetyltransferase Pat from acetyl coenzyme A (acetyl-CoA) bound to the acetyl-CoA binding protein Qad. We now report that low cytoplasmic Mg2+ promotes qad expression, which protects substrates of Lon and ClpSAP by increasing HspQ amounts. The qad promoter is activated by PhoP, a regulatory protein highly activated in low cytoplasmic Mg2+ that also represses clpS transcription. Both the qad gene and PhoP repression of the clpS promoter are necessary for antibiotic persistence. PhoP also promotes qad transcription in Escherichia coli, which shares a similar PhoP box in the qad promoter region with S. Typhimurium, Salmonella bongori, and Enterobacter cloacae. Our findings identify cytoplasmic Mg2+ and the PhoP protein as critical regulators of protease specificity in multiple enteric bacteria. IMPORTANCE The bacterium Salmonella enterica serovar Typhimurium narrows down the spectrum of substrates degraded by the proteases Lon and ClpAP in response to low cytoplasmic Mg2+, a condition that decreases protein synthesis. This control is exerted by PhoP, a transcriptional regulator activated in low cytoplasmic Mg2+ that governs proteostasis and is conserved in enteric bacteria. The uncovered mechanism enables bacteria to control the abundance of preexisting proteins.
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34
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Wang X, Wei W, Zhao J. Using a Riboswitch Sensor to Detect Co 2+/Ni 2+ Transport in E. coli. Front Chem 2021; 9:631909. [PMID: 33659237 PMCID: PMC7917058 DOI: 10.3389/fchem.2021.631909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Intracellular concentrations of essential mental ions must be tightly maintained to avoid metal deprivation and toxicity. However, their levels in cells are still difficult to monitor. In this report, the combination of a Co2+Ni2+-specific riboswitch and an engineered downstream mCherry fluorescent protein allowed a highly sensitive and selective whole-cell Co2+/Ni2+ detection process. The sensors were applied to examine the resistance system of Co2+/Ni2+ in E. coli, and the sensors were able to monitor the effects of genetic deletions. These results indicate that riboswitch-based sensors can be employed in the study of related cellular processes.
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Affiliation(s)
- Xiaoying Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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35
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Yuwen Z, Mei H, Li H, Pu S. A novel diarylethene probe with high selective recognition of CN- and Mg2+and its application. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Blanc-Potard AB, Groisman EA. How Pathogens Feel and Overcome Magnesium Limitation When in Host Tissues. Trends Microbiol 2020; 29:98-106. [PMID: 32807623 DOI: 10.1016/j.tim.2020.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 12/29/2022]
Abstract
Host organisms utilize nutritional immunity to limit the availability of nutrients essential to an invading pathogen. Nutrients may include amino acids, nucleotide bases, and transition metals, the essentiality of which varies among pathogens. The mammalian macrophage protein Slc11a1 (previously Nramp1) mediates resistance to several intracellular pathogens. Slc11a1 is proposed to restrict growth of Salmonella enterica serovar Typhimurium in host tissues by causing magnesium deprivation. This is intriguing because magnesium is the most abundant divalent cation in all living cells. A pathogen's response to factors such as Slc11a1 that promote nutritional immunity may therefore reflect what the pathogen 'feels' in its cytoplasm, rather than the nutrient concentration in host cell compartments.
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Affiliation(s)
- Anne-Béatrice Blanc-Potard
- Laboratory of Pathogen Host Interactions, Université Montpellier, case 107, Place Eugène Bataillon, 34095, Montpellier cedex 5, France; CNRS, UMR5235, 34095, Montpellier Cedex 05, France.
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA; Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA.
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Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter. Proc Natl Acad Sci U S A 2020; 117:20235-20243. [PMID: 32753384 DOI: 10.1073/pnas.2006116117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
All cells require Mg2+ to replicate and proliferate. The macrophage protein Slc11a1 is proposed to protect mice from invading microbes by causing Mg2+ starvation in host tissues. However, the Mg2+ transporter MgtB enables the facultative intracellular pathogen Salmonella enterica serovar Typhimurium to cause disease in mice harboring a functional Slc11a1 protein. Here, we report that, unexpectedly, the Salmonella small protein MgtR promotes MgtB degradation by the protease FtsH, which raises the question: How does Salmonella preserve MgtB to promote survival inside macrophages? We establish that the Salmonella small protein MgtU prevents MgtB proteolysis, even when MgtR is absent. Like MgtB, MgtU is necessary for survival in Slc11a1 +/+ macrophages, resistance to oxidative stress, and growth under Mg2+ limitation conditions. The Salmonella Mg2+ transporter MgtA is not protected by MgtU despite sharing 50% amino acid identity with MgtB and being degraded in an MgtR- and FtsH-dependent manner. Surprisingly, the mgtB, mgtR, and mgtU genes are part of the same transcript, providing a singular example of transcript-specifying proteins that promote and hinder degradation of the same target. Our findings demonstrate that small proteins can confer pathogen survival inside macrophages by altering the abundance of related transporters, thereby furthering homeostasis.
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38
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Dey S, Purkait R, Mallick D, Sinha C. A Vanillinyl‐Hydrazone Schiff Base: Recognition of Mg
2+
, Zn
2+
, Cd
2+
and I
−
by Turn‐On Fluorescence Method. ChemistrySelect 2020. [DOI: 10.1002/slct.202002271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sunanda Dey
- Department of Chemistry Jadavpur University Kolkata 700 032 India
| | - Rakesh Purkait
- Department of Chemistry Jadavpur University Kolkata 700 032 India
| | - Debashis Mallick
- Department of Chemistry Mrinalini Datta Mahavidyapith Kolkata 700 051 India
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Abstract
Antibiotics constitute one of the cornerstones of modern medicine. However, individuals may succumb to a bacterial infection if a pathogen survives exposure to antibiotics. The ability of bacteria to survive bactericidal antibiotics results from genetic changes in the preexisting bacterial genome, from the acquisition of genes from other organisms, and from nonheritable phenomena that give rise to antibiotic tolerance. Nonheritable antibiotic tolerance can be exhibited by a large fraction of the bacterial population or by a small subpopulation referred to as persisters. Nonheritable resistance to antibiotics has been ascribed to the activity of toxins that are part of toxin-antitoxin modules, to the universal energy currency ATP, and to the signaling molecule guanosine (penta) tetraphosphate. However, these molecules are dispensable for nonheritable resistance to antibiotics in many organisms. By contrast, nutrient limitation, treatment with bacteriostatic antibiotics, or expression of genes that slow bacterial growth invariably promote nonheritable resistance. We posit that antibiotic persistence results from conditions promoting feedback inhibition among core cellular processes, resulting phenotypically in a slowdown or halt in bacterial growth.
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40
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Sherlock ME, Breaker RR. Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes. RNA (NEW YORK, N.Y.) 2020; 26:675-693. [PMID: 32165489 PMCID: PMC7266159 DOI: 10.1261/rna.074997.120] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Comparative sequence analyses have been used to discover numerous classes of structured noncoding RNAs, some of which are riboswitches that specifically recognize small-molecule or elemental ion ligands and influence expression of adjacent downstream genes. Determining the correct identity of the ligand for a riboswitch candidate typically is aided by an understanding of the genes under its regulatory control. Riboswitches whose ligands were straightforward to identify have largely been associated with well-characterized metabolic pathways, such as coenzyme or amino acid biosynthesis. Riboswitch candidates whose ligands resist identification, collectively known as orphan riboswitches, are often associated with genes coding for proteins of unknown function, or genes for various proteins with no established link to one another. The cognate ligands for 16 former orphan riboswitch motifs have been identified to date. The successful pursuit of the ligands for these classes has provided insight into areas of biology that are not yet fully explored, such as ion homeostasis, signaling networks, and other previously underappreciated biochemical or physiological processes. Herein we discuss the strategies and methods used to match ligands with orphan riboswitch classes, and overview the lessons learned to inform and motivate ongoing efforts to identify ligands for the many remaining candidates.
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Affiliation(s)
- Madeline E Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
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41
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Wei J, Wang H, Wu Q, Gong X, Ma K, Liu X, Wang F. A Smart, Autocatalytic, DNAzyme Biocircuit for in Vivo, Amplified, MicroRNA Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911712] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
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42
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Wei J, Wang H, Wu Q, Gong X, Ma K, Liu X, Wang F. A Smart, Autocatalytic, DNAzyme Biocircuit for in Vivo, Amplified, MicroRNA Imaging. Angew Chem Int Ed Engl 2020; 59:5965-5971. [PMID: 31961985 DOI: 10.1002/anie.201911712] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/30/2019] [Indexed: 01/07/2023]
Abstract
DNAzymes have been recognized as promising transducing agents for visualizing endogenous biomarkers, but their inefficient intracellular delivery and limited amplification capacity (including insufficient cofactor supply) preclude their extensive biological application. Herein, an autocatalytic DNAzyme (ACD) biocircuit is constructed for amplified microRNA imaging in vivo based on a hybridization chain reaction (HCR) and DNAzyme biocatalysis, sustained by a honeycomb MnO2 nanosponge (hMNS). The hMNS not only delivers DNA probes, but also supplies Mn2+ as a DNAzyme cofactor and magnetic resonance imaging (MRI) agent. Through the subsequent cross-activation of HCR and DNAzyme amplicons, the ACD amplifies the limited signal resulting from miRNA recognition. The hMNS/ACD system was used to image microRNA in vivo, thus demonstrating its great promise in cancer diagnosis.
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Affiliation(s)
- Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
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Pohland AC, Schneider D. Mg2+ homeostasis and transport in cyanobacteria - at the crossroads of bacterial and chloroplast Mg2+ import. Biol Chem 2020; 400:1289-1301. [PMID: 30913030 DOI: 10.1515/hsz-2018-0476] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/19/2019] [Indexed: 12/29/2022]
Abstract
Magnesium cation (Mg2+) is the most abundant divalent cation in living cells, where it is required for various intracellular functions. In chloroplasts and cyanobacteria, established photosynthetic model systems, Mg2+ is the central ion in chlorophylls, and Mg2+ flux across the thylakoid membrane is required for counterbalancing the light-induced generation of a ΔpH across the thylakoid membrane. Yet, not much is known about Mg2+ homoeostasis, transport and distribution within cyanobacteria. However, Mg2+ transport across membranes has been studied in non-photosynthetic bacteria, and first observations and findings are reported for chloroplasts. Cyanobacterial cytoplasmic membranes appear to contain the well-characterized Mg2+ channels CorA and/or MgtE, which both facilitate transmembrane Mg2+ flux down the electrochemical gradient. Both Mg2+ channels are typical for non-photosynthetic bacteria. Furthermore, Mg2+ transporters of the MgtA/B family are also present in the cytoplasmic membrane to mediate active Mg2+ import into the bacterial cell. While the cytoplasmic membrane of cyanobacteria resembles a 'classical' bacterial membrane, essentially nothing is known about Mg2+ channels and/or transporters in thylakoid membranes of cyanobacteria or chloroplasts. As discussed here, at least one Mg2+ channelling protein must be localized within thylakoid membranes. Thus, either one of the 'typical' bacterial Mg2+ channels has a dual localization in the cytoplasmic plus the thylakoid membrane, or another, yet unidentified channel is present in cyanobacterial thylakoid membranes.
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Affiliation(s)
- Anne-Christin Pohland
- Institut für Pharmazie und Biochemie, Johannes-Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes-Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany
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Abstract
RNA molecules fold into complex three-dimensional structures that sample alternate conformations ranging from minor differences in tertiary structure dynamics to major differences in secondary structure. This allows them to form entirely different substructures with each population potentially giving rise to a distinct biological outcome. The substructures can be partitioned along an existing energy landscape given a particular static cellular cue or can be shifted in response to dynamic cues such as ligand binding. We review a few key examples of RNA molecules that sample alternate conformations and how these are capitalized on for control of critical regulatory functions.
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Affiliation(s)
- Marie Teng-Pei Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Victoria D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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45
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Venkata Subbaiah KC, Hedaya O, Wu J, Jiang F, Yao P. Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine. Comput Struct Biotechnol J 2019; 17:1326-1338. [PMID: 31741723 PMCID: PMC6849081 DOI: 10.1016/j.csbj.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 01/12/2023] Open
Abstract
Alteration of RNA structure by environmental signals is a fundamental mechanism of gene regulation. For example, the riboswitch is a noncoding RNA regulatory element that binds a small molecule and causes a structural change in the RNA, thereby regulating transcription, splicing, or translation of an mRNA. The role of riboswitches in metabolite sensing and gene regulation in bacteria and other lower species was reported almost two decades ago, but riboswitches have not yet been discovered in mammals. An analog of the riboswitch, the protein-directed RNA switch (PDRS), has been identified as an important regulatory mechanism of gene expression in mammalian cells. RNA-binding proteins and microRNAs are two major executors of PDRS via their interaction with target transcripts in mammals. These protein-RNA interactions influence cellular functions by integrating environmental signals and intracellular pathways from disparate stimuli to modulate stability or translation of specific mRNAs. The discovery of a riboswitch in eukaryotes that is composed of a single class of thiamine pyrophosphate (TPP) suggests that additional ligand-sensing RNAs may be present to control eukaryotic or mammalian gene expression. In this review, we focus on protein-directed RNA switch mechanisms in mammals. We offer perspectives on the potential discovery of mammalian protein-directed and compound-dependent RNA switches that are related to human disease and medicine.
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Affiliation(s)
- Kadiam C Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Omar Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
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Antimicrobial Properties of Magnesium Open Opportunities to Develop Healthier Food. Nutrients 2019; 11:nu11102363. [PMID: 31623397 PMCID: PMC6835631 DOI: 10.3390/nu11102363] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/15/2019] [Accepted: 09/21/2019] [Indexed: 02/07/2023] Open
Abstract
Magnesium is a vital mineral that takes part in hundreds of enzymatic reactions in the human body. In the past several years, new information emerged in regard to the antibacterial effect of magnesium. Here we elaborate on the recent knowledge of its antibacterial effect with emphasis on its ability to impair bacterial adherence and formation complex community of bacterial cells called biofilm. We further talk about its ability to impair biofilm formation in milk that provides opportunity for developing safer and qualitative dairy products. Finally, we describe the pronounced advantages of enrichment of food with magnesium ions, which result in healthier and more efficient food products.
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Regulation of Bacterial Gene Expression by Transcription Attenuation. Microbiol Mol Biol Rev 2019; 83:83/3/e00019-19. [PMID: 31270135 DOI: 10.1128/mmbr.00019-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A wide variety of mechanisms that control gene expression in bacteria are based on conditional transcription termination. Generally, in these mechanisms, a transcription terminator is located between a promoter and a downstream gene(s), and the efficiency of the terminator is controlled by a regulatory effector that can be a metabolite, protein, or RNA. The most common type of regulation involving conditional termination is transcription attenuation, in which the primary regulatory target is an essential element of a single terminator. The terminator can be either intrinsic or Rho dependent, with each presenting unique regulatory targets. Transcription attenuation mechanisms can be divided into five classes based primarily on the manner in which transcription termination is rendered conditional. This review summarizes each class of control mechanisms from a historical perspective, describes important examples in a physiological context and the current state of knowledge, highlights major advances, and discusses expectations of future discoveries.
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Gupta A, Swati D. Riboswitches in Archaea. Comb Chem High Throughput Screen 2019; 22:135-149. [DOI: 10.2174/1386207322666190425143301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 03/15/2019] [Accepted: 04/13/2019] [Indexed: 12/15/2022]
Abstract
Background:
Riboswitches are cis-acting, non-coding RNA elements found in the
5’UTR of bacterial mRNA and 3’ UTR of eukaryotic mRNA, that fold in a complex manner to act
as receptors for specific metabolites hence altering their conformation in response to the change in
concentrations of a ligand or metabolite. Riboswitches function as gene regulators in numerous
bacteria, archaea, fungi, algae and plants.
Aim and Objective:
This study identifies different classes of riboswitches in the Archaeal domain
of life. Previous studies have suggested that riboswitches carry a conserved aptameric domain in
different domains of life. Since Archaea are considered to be the most idiosyncratic organisms it
was interesting to look for the conservation pattern of riboswitches in these obviously strange
microorganisms.
Materials and Methods:
Completely sequenced Archaeal Genomes present in the NCBI repository
were used for studying riboswitches and other ncRNAs. The sequence files in FASTA format were
downloaded from NCBI Genome database and information related to these genomes was retrieved
from GenBank. Three bioinformatics approaches were used namely, ab initio, consensus structure
prediction and statistical model-based prediction for identifying riboswitches.
Results:
Archaeal genomes have a sporadic distribution of putative riboswitches like the TPP,
FMN, Guanidine, Lysine and c-di-AMP riboswitches, which are known to occur in bacteria. Also,
a class of riboswitch sensing c-di-GMP, a second messenger, has been identified in a few Archaeal
organisms.
Conclusion:
This study clearly reveals that bioinformatics methods are likely to play a major role
in identifying conserved riboswitches and in establishing how widespread these classes are in all
domains of life, even though the final confirmation may come from wet lab methods.
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Affiliation(s)
- Angela Gupta
- Department of Bioinformatics, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
| | - D. Swati
- Department of Bioinformatics, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
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A review on native and denaturing purification methods for non-coding RNA (ncRNA). J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1120:71-79. [PMID: 31071581 DOI: 10.1016/j.jchromb.2019.04.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/20/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022]
Abstract
Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.
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Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors. NANOMATERIALS 2019; 9:nano9020233. [PMID: 30744040 PMCID: PMC6410142 DOI: 10.3390/nano9020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/10/2023]
Abstract
Genetically encodable sensors have been widely used in the detection of intracellular molecules ranging from metal ions and metabolites to nucleic acids and proteins. These biosensors are capable of monitoring in real-time the cellular levels, locations, and cell-to-cell variations of the target compounds in living systems. Traditionally, the majority of these sensors have been developed based on fluorescent proteins. As an exciting alternative, genetically encoded RNA-based molecular sensors (GERMS) have emerged over the past few years for the intracellular imaging and detection of various biological targets. In view of their ability for the general detection of a wide range of target analytes, and the modular and simple design principle, GERMS are becoming a popular choice for intracellular analysis. In this review, we summarize different design principles of GERMS based on various RNA recognition modules, transducer modules, and reporting systems. Some recent advances in the application of GERMS for intracellular imaging are also discussed. With further improvement in biostability, sensitivity, and robustness, GERMS can potentially be widely used in cell biology and biotechnology.
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