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Skeparnias I, Bou-Nader C, Anastasakis DG, Fan L, Wang YX, Hafner M, Zhang J. Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01340-4. [PMID: 38956168 DOI: 10.1038/s41594-024-01340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long noncoding RNA (lncRNA) has key roles in regulating transcription, splicing, tumorigenesis, etc. Its maturation and stabilization require precise processing by RNase P, which simultaneously initiates the biogenesis of a 3' cytoplasmic MALAT1-associated small cytoplasmic RNA (mascRNA). mascRNA was proposed to fold into a transfer RNA (tRNA)-like secondary structure but lacks eight conserved linking residues required by the canonical tRNA fold. Here we report crystal structures of human mascRNA before and after processing, which reveal an ultracompact, quasi-tRNA-like structure. Despite lacking all linker residues, mascRNA faithfully recreates the characteristic 'elbow' feature of tRNAs to recruit RNase P and ElaC homolog protein 2 (ELAC2) for processing, which exhibit distinct substrate specificities. Rotation and repositioning of the D-stem and anticodon regions preclude mascRNA from aminoacylation, avoiding interference with translation. Therefore, a class of metazoan lncRNA loci uses a previously unrecognized, unusually streamlined quasi-tRNA architecture to recruit select tRNA-processing enzymes while excluding others to drive bespoke RNA biogenesis, processing and maturation.
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Affiliation(s)
- Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
| | - Yun-Xing Wang
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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2
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Yin JZ, Keszei AFA, Houliston S, Filandr F, Beenstock J, Daou S, Kitaygorodsky J, Schriemer DC, Mazhab-Jafari MT, Gingras AC, Sicheri F. The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA. Structure 2024; 32:795-811.e6. [PMID: 38531363 DOI: 10.1016/j.str.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM. Structure and function analysis shows the HisRS-like domain of GCN2 has lost histidine and ATP binding but retains tRNA binding abilities. Hydrogen deuterium exchange mass spectrometry, site-directed mutagenesis and computational docking experiments support a tRNA binding model that is partially shifted from that employed by bona fide HisRS enzymes. These results demonstrate that the HisRS-like domain of GCN2 is a pseudoenzyme and advance our understanding of GCN2 regulation and function.
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Affiliation(s)
- Jay Z Yin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jonah Beenstock
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Salima Daou
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Julia Kitaygorodsky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad T Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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3
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Tatara Y, Kasai S, Kokubu D, Tsujita T, Mimura J, Itoh K. Emerging Role of GCN1 in Disease and Homeostasis. Int J Mol Sci 2024; 25:2998. [PMID: 38474243 PMCID: PMC10931611 DOI: 10.3390/ijms25052998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
GCN1 is recognized as a factor that is essential for the activation of GCN2, which is a sensor of amino acid starvation. This function is evolutionarily conserved from yeast to higher eukaryotes. However, recent studies have revealed non-canonical functions of GCN1 that are independent of GCN2, such as its participation in cell proliferation, apoptosis, and the immune response, beyond the borders of species. Although it is known that GCN1 and GCN2 interact with ribosomes to accomplish amino acid starvation sensing, recent studies have reported that GCN1 binds to disomes (i.e., ribosomes that collide each other), thereby regulating both the co-translational quality control and stress response. We propose that GCN1 regulates ribosome-mediated signaling by dynamically changing its partners among RWD domain-possessing proteins via unknown mechanisms. We recently demonstrated that GCN1 is essential for cell proliferation and whole-body energy regulation in mice. However, the manner in which ribosome-initiated signaling via GCN1 is related to various physiological functions warrants clarification. GCN1-mediated mechanisms and its interaction with other quality control and stress response signals should be important for proteostasis during aging and neurodegenerative diseases, and may be targeted for drug development.
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Affiliation(s)
- Yota Tatara
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Shuya Kasai
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Daichi Kokubu
- Diet and Well-Being Research Institute, KAGOME, Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
- Department of Vegetable Life Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Tadayuki Tsujita
- Laboratory of Biochemistry, Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga City 840-8502, Saga, Japan;
| | - Junsei Mimura
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Ken Itoh
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
- Department of Vegetable Life Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
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4
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Chrenková A, Bisiak F, Brodersen DE. Breaking bad nucleotides: understanding the regulatory mechanisms of bacterial small alarmone hydrolases. Trends Microbiol 2024:S0966-842X(23)00363-3. [PMID: 38262803 DOI: 10.1016/j.tim.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Guanosine tetra- and pentaphosphate nucleotides, (p)ppGpp, function as central secondary messengers and alarmones in bacterial cell biology, signalling a range of stress conditions, including nutrient starvation and exposure to cell-wall-targeting antibiotics, and are critical for survival. While activation of the stringent response and alarmone synthesis on starved ribosomes by members of the RSH (Rel) class of proteins is well understood, much less is known about how single-domain small alarmone synthetases (SASs) and their corresponding alarmone hydrolases, the small alarmone hydrolases (SAHs), are regulated and contribute to (p)ppGpp homeostasis. The substrate spectrum of these enzymes has recently been expanded to include hyperphosphorylated adenosine nucleotides, suggesting that they take part in a highly complex and interconnected signalling network. In this review, we provide an overview of our understanding of the SAHs and discuss their structure, function, regulation, and phylogeny.
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Affiliation(s)
- Adriana Chrenková
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Francesco Bisiak
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark.
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5
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Zhang J. Recognition of the tRNA structure: Everything everywhere but not all at once. Cell Chem Biol 2024; 31:36-52. [PMID: 38159570 PMCID: PMC10843564 DOI: 10.1016/j.chembiol.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
tRNAs are among the most abundant and essential biomolecules in cells. These spontaneously folding, extensively structured yet conformationally flexible anionic polymers literally bridge the worlds of RNAs and proteins, and serve as Rosetta stones that decipher and interpret the genetic code. Their ubiquitous presence, functional irreplaceability, and privileged access to cellular compartments and ribosomes render them prime targets for both endogenous regulation and exogenous manipulation. There is essentially no part of the tRNA that is not touched by another interaction partner, either as programmed or imposed by an external adversary. Recent progresses in genetic, biochemical, and structural analyses of the tRNA interactome produced a wealth of new knowledge into their interaction networks, regulatory functions, and molecular interfaces. In this review, I describe and illustrate the general principles of tRNA recognition by proteins and other RNAs, and discuss the underlying molecular mechanisms that deliver affinity, specificity, and functional competency.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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6
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Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas Č, Siksnys V, Tamulaitis G. Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Science 2023; 382:1036-1041. [PMID: 38033086 DOI: 10.1126/science.adj2107] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023]
Abstract
Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cAn) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we characterize a class of cAn-dependent effector proteins named CRISPR-Cas-associated messenger RNA (mRNA) interferase 1 (Cami1) consisting of a CRISPR-associated Rossmann fold sensor domain fused to winged helix-turn-helix and a RelE-family mRNA interferase domain. Upon activation by cyclic tetra-adenylate (cA4), Cami1 cleaves mRNA exposed at the ribosomal A-site thereby depleting mRNA and leading to cell growth arrest. The structures of apo-Cami1 and the ribosome-bound Cami1-cA4 complex delineate the conformational changes that lead to Cami1 activation and the mechanism of Cami1 binding to a bacterial ribosome, revealing unexpected parallels with eukaryotic ribosome-inactivating proteins.
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Affiliation(s)
- Irmantas Mogila
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Konstanty Keda
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Albertas Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Audrone Ruksenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
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7
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Guiraud P, Germain E, Byrne D, Maisonneuve E. The YmgB-SpoT interaction triggers the stringent response in Escherichia coli. J Biol Chem 2023; 299:105429. [PMID: 37926282 PMCID: PMC10704370 DOI: 10.1016/j.jbc.2023.105429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
Virtually all bacterial species synthesize (p)ppGpp (guanosine penta- or tetraphosphate), a pleiotropic regulator of the so-called stringent response, which controls many aspects of cellular physiology and metabolism. In Escherichia coli, (p)ppGpp levels are controlled by two homologous enzymes: the (p)ppGpp synthetase RelA and the bifunctional synthetase/hydrolase SpoT. We recently identified several protein candidates that can modulate (p)ppGpp levels in E. coli. In this work, we show that the putative two-component system connector protein YmgB can promote SpoT-dependent accumulation of ppGpp in E. coli. Importantly, we determined that the control of SpoT activities by YmgB is independent of its proposed role in the two-component Rcs system, and these two functions can be uncoupled. Using genetic and structure-function analysis, we show that the regulation of SpoT activities by YmgB occurs by functional and direct binding in vivo and in vitro to the TGS and Helical domains of SpoT. These results further support the role of these domains in controlling the reciprocal enzymatic states.
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Affiliation(s)
- Paul Guiraud
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix Marseille Univ (UMR7283), Marseille, France
| | - Elsa Germain
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix Marseille Univ (UMR7283), Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Institut de Microbiologie de la Méditerranée, CNRS-Aix Marseille Univ, Marseille, France
| | - Etienne Maisonneuve
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix Marseille Univ (UMR7283), Marseille, France.
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8
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Grucela PK, Zhang YE. Basal level of ppGpp coordinates Escherichia coli cell heterogeneity and ampicillin resistance and persistence. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:248-260. [PMID: 37933276 PMCID: PMC10625690 DOI: 10.15698/mic2023.11.808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/20/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
The universal stringent response alarmone ppGpp (guanosine penta and tetra phosphates) plays a crucial role in various aspects of fundamental cell physiology (e.g., cell growth rate, cell size) and thus bacterial tolerance to and survival of external stresses, including antibiotics. Besides transient antibiotic tolerance (persistence), ppGpp was recently found to contribute to E. coli resistance to ampicillin. How ppGpp regulates both the persistence and resistance to antibiotics remains incompletely understood. In this study, we first clarified that the absence of ppGpp in E. coli (ppGpp0 strain) resulted in a decreased minimal inhibition concentration (MIC) value of ampicillin but, surprisingly, a higher persistence level to ampicillin during exponential growth in MOPS rich medium. High basal ppGpp levels, thus lower growth rate, did not produce high ampicillin persistence. Importantly, we found that the high ampicillin persistence of the ppGpp0 strain is not due to dormant overnight carry-over cells. Instead, the absence of ppGpp produced higher cell heterogeneity, propagating during the regrowth and the killing phases, leading to higher ampicillin persistence. Consistently, we isolated a suppressor mutation of the ppGpp0 strain that restored the standard MIC value of ampicillin and reduced its cell heterogeneity and the ampicillin persistence level concomitantly. Altogether, we discussed the fundamental role of basal level of ppGpp in regulating cell homogeneity and ampicillin persistence.
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Affiliation(s)
| | - Yong Everett Zhang
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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9
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Bartoli J, Tempier AC, Guzzi NL, Piras CM, Cascales E, Viala JPM. Characterization of a (p)ppApp Synthetase Belonging to a New Family of Polymorphic Toxin Associated with Temperate Phages. J Mol Biol 2023; 435:168282. [PMID: 37730083 DOI: 10.1016/j.jmb.2023.168282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Polymorphic toxins (PTs) are a broad family of toxins involved in interbacterial competition and pathogenesis. PTs are modular proteins that are comprised of a conserved N-terminal domain responsible for its transport, and a variable C-terminal domain bearing toxic activity. Although the mode of transport has yet to be elucidated, a new family of putative PTs containing an N-terminal MuF domain, resembling the Mu coliphage F protein, was identified in prophage genetic elements. The C-terminal toxin domains of these MuF PTs are predicted to bear nuclease, metallopeptidase, ADP-ribosyl transferase and RelA_SpoT activities. In this study, we characterized the MuF-RelA_SpoT toxin associated with the temperate phage of Streptococcus pneumoniae SPNA45. We show that the RelA_SpoT domain has (p)ppApp synthetase activity, which is bactericidal under our experimental conditions. We further determine that the two genes located downstream encode two immunity proteins, one binding to and inactivating the toxin and the other detoxifying the cell via a pppApp hydrolase activity. Finally, based on protein sequence alignments, we propose a signature for (p)ppApp synthetases that distinguishes them from (p)ppGpp synthetases.
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Affiliation(s)
- Julia Bartoli
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Audrey C Tempier
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Noa L Guzzi
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France. https://twitter.com/NoaGzzi
| | - Chloé M Piras
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France. https://twitter.com/CascalesLab
| | - Julie P M Viala
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France.
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10
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Chen E, Shaffer MG, Bilodeau RE, West RE, Oberly PJ, Nolin TD, Culyba MJ. Clinical rel mutations in Staphylococcus aureus prime pathogen expansion under nutrient stress. mSphere 2023; 8:e0024923. [PMID: 37750686 PMCID: PMC10597345 DOI: 10.1128/msphere.00249-23] [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: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 09/27/2023] Open
Abstract
Persistent infection by Staphylococcus aureus has been linked to the bacterial stringent response (SR), a conserved stress response pathway regulated by the Rel protein. Rel synthesizes (p)ppGpp "alarmones" in response to amino acid starvation, which enables adaptation to stress by modulating bacterial growth and virulence. We previously identified five novel protein-altering mutations in rel that arose in patients with persistent methicillin-resistant S. aureus bacteremia. The mutations mapped to both the enzymatic and regulatory protein domains of Rel. Here, we set out to characterize the phenotype of these mutations to understand how they may have been selected in vivo. After introducing each mutation into S. aureus strain JE2, we analyzed growth, fitness, and antibiotic profiles. Despite being located in different protein domains, we found that all of the mutations converged on the same phenotype. Each shortened the time of lag phase growth and imparted a fitness advantage in nutritionally depleted conditions. Through quantification of intracellular (p)ppGpp, we link this phenotype to increased SR activation, specifically during the stationary phase of growth. In contrast to two previously identified clinical rel mutations, we find that our rel mutations do not cause antibiotic tolerance. Instead, our findings suggest that in vivo selection was due to an augmented SR that primes cells for growth in nutrient-poor conditions, which may be a strategy for evading host-imposed nutritional immunity. Importance Host and pathogen compete for available nutrition during infection. For bacteria, the stringent response (SR) regulator Rel responds to amino acid deprivation by signaling the cell to modulate its growth rate, metabolism, and virulence. In this report, we characterize five rel mutations that arose during cases of persistent methicillin-resistant Staphylococcus aureus bacteremia. We find that all of the mutations augmented SR signaling specifically under nutrient-poor conditions, enabling the cell to more readily grow and survive. Our findings reveal a strategy used by bacterial pathogens to evade the nutritional immunity imposed by host tissues during infection.
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Affiliation(s)
- Edwin Chen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marla G. Shaffer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert E. Bilodeau
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Raymond E. West
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Patrick J. Oberly
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Thomas D. Nolin
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Matthew J. Culyba
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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11
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Dominguez-Molina L, Talavera A, Cepauskas A, Kurata T, Echemendia-Blanco D, Hauryliuk V, Garcia-Pino A. Biochemical and X-ray analyses of the players involved in the faRel2/aTfaRel2 toxin-antitoxin operon. Acta Crystallogr F Struct Biol Commun 2023; 79:247-256. [PMID: 37728608 PMCID: PMC10565793 DOI: 10.1107/s2053230x23007288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/19/2023] [Indexed: 09/21/2023] Open
Abstract
The aTfaRel2/faRel2 operon from Coprobacillus sp. D7 encodes a bicistronic type II toxin-antitoxin (TA) module. The FaRel2 toxin is a toxic small alarmone synthetase (toxSAS) that inhibits translation through the pyrophosphorylation of uncharged tRNAs at the 3'-CCA end. The toxin is neutralized by the antitoxin ATfaRel2 through the formation of an inactive TA complex. Here, the production, biophysical analysis and crystallization of ATfaRel2 and FaRel2 as well as of the ATfaRel2-FaRel2 complex are reported. ATfaRel2 is monomeric in solution. The antitoxin crystallized in space group P21212 with unit-cell parameters a = 53.3, b = 34.2, c = 37.6 Å, and the best crystal diffracted to a resolution of 1.24 Å. Crystals of FaRel2 in complex with APCPP, a nonhydrolysable ATP analogue, belonged to space group P21, with unit-cell parameters a = 31.5, b = 60.6, c = 177.2 Å, β = 90.6°, and diffracted to 2.6 Å resolution. The ATfaRel2-FaRel2Y128F complex forms a heterotetramer in solution composed of two toxins and two antitoxins. This complex crystallized in two space groups: F4132, with unit-cell parameters a = b = c = 227.1 Å, and P212121, with unit-cell parameters a = 51.7, b = 106.2, c = 135.1 Å. The crystals diffracted to 1.98 and 2.1 Å resolution, respectively.
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Affiliation(s)
- Lucia Dominguez-Molina
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Albinas Cepauskas
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Dannele Echemendia-Blanco
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu Institute of Technology, Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
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12
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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13
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Li Y, Majumdar S, Treen R, Sharma MR, Corro J, Gamper HB, Manjari SR, Prusa J, Banavali NK, Stallings CL, Hou YM, Agrawal RK, Ojha AK. Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation. Proc Natl Acad Sci U S A 2023; 120:e2302006120. [PMID: 37216503 PMCID: PMC10235957 DOI: 10.1073/pnas.2302006120] [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: 02/04/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomes in vivo remains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in nonstarved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in a translation initiation complex reveals unknown interactions between the ACT domain of Rsh and components of the ribosomal L7/L12 stalk base, suggesting that the aminoacylation status of A-site tRNA is surveilled during the first cycle of elongation. Altogether, we propose a surveillance model of Rsh activation that originates from its constitutive interaction with the ribosomes entering the translation cycle.
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Affiliation(s)
- Yunlong Li
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
| | - Soneya Majumdar
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Ryan Treen
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
| | - Manjuli R. Sharma
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Jamie Corro
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
| | - Howard B. Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Swati R. Manjari
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Jerome Prusa
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO63110
| | - Nilesh K. Banavali
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO63110
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Rajendra K. Agrawal
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
| | - Anil K. Ojha
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
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14
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Gupta R, Hinnebusch AG. Differential requirements for P stalk components in activating yeast protein kinase Gcn2 by stalled ribosomes during stress. Proc Natl Acad Sci U S A 2023; 120:e2300521120. [PMID: 37043534 PMCID: PMC10120022 DOI: 10.1073/pnas.2300521120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023] Open
Abstract
The General Amino Acid Control is a conserved response to amino acid starvation involving activation of protein kinase Gcn2, which phosphorylates eukaryotic initiation factor 2 (eIF2α) with attendant inhibition of global protein synthesis and increased translation of yeast transcriptional activator GCN4. Gcn2 can be activated by either amino acid starvation or conditions that stall elongating ribosomes without reducing aminoacylation of tRNA, but it is unclear whether distinct molecular mechanisms operate in these two circumstances. We identified three regimes that activate Gcn2 in yeast cells by starvation-independent (SI) ribosome-stalling: treatment with tigecycline, eliminating the sole gene encoding tRNAArgUCC, and depletion of translation termination factor eRF1. We further demonstrated requirements for the tRNA- and ribosome-binding domains of Gcn2, the positive effector proteins Gcn1/Gcn20, and the tethering of at least one of two distinct P1/P2 heterodimers to the uL10 subunit of the ribosomal P stalk, for detectable activation by SI-ribosome stalling. Remarkably, no tethered P1/P2 proteins were required for strong Gcn2 activation elicited by starvation for histidine or branched-chain amino acids isoleucine/valine. These results indicate that Gcn2 activation has different requirements for the P stalk depending on how ribosomes are stalled. We propose that accumulation of deacylated tRNAs in amino acid-starved cells can functionally substitute for the P stalk in binding to the histidyl-tRNA synthetase-like domain of Gcn2 for eIF2α kinase activation by ribosomes stalled with A sites devoid of the eEF1A∙GTP∙aminoacyl-tRNA ternary complex.
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Affiliation(s)
- Ritu Gupta
- Section on Nutrient Control of Gene Expression, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD20892
| | - Alan G. Hinnebusch
- Section on Nutrient Control of Gene Expression, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD20892
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15
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Fung DK, Wang JD. The τ of alarmone hydrolysis. Nat Chem Biol 2023; 19:257-258. [PMID: 36470997 DOI: 10.1038/s41589-022-01200-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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16
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Tamman H, Ernits K, Roghanian M, Ainelo A, Julius C, Perrier A, Talavera A, Ainelo H, Dugauquier R, Zedek S, Thureau A, Pérez J, Lima-Mendez G, Hallez R, Atkinson GC, Hauryliuk V, Garcia-Pino A. Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint. Nat Chem Biol 2023; 19:334-345. [PMID: 36470996 PMCID: PMC9974481 DOI: 10.1038/s41589-022-01198-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022]
Abstract
Stringent factors orchestrate bacterial cell reprogramming through increasing the level of the alarmones (p)ppGpp. In Beta- and Gammaproteobacteria, SpoT hydrolyzes (p)ppGpp to counteract the synthetase activity of RelA. However, structural information about how SpoT controls the levels of (p)ppGpp is missing. Here we present the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and uncover the mechanism of intramolecular regulation of 'long'-stringent factors. In contrast to ribosome-associated Rel/RelA that adopt an elongated structure, SpoT assumes a compact τ-shaped structure in which the regulatory domains wrap around a Core subdomain that controls the conformational state of the enzyme. The Core is key to the specialization of long RelA-SpoT homologs toward either synthesis or hydrolysis: the short and structured Core of SpoT stabilizes the τ-state priming the hydrolase domain for (p)ppGpp hydrolysis, whereas the longer, more dynamic Core domain of RelA destabilizes the τ-state priming the monofunctional RelA for efficient (p)ppGpp synthesis.
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Affiliation(s)
- Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
| | - Karin Ernits
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Departement of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Andres Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Anthony Perrier
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Hanna Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Rémy Dugauquier
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Javier Pérez
- Synchrotron SOLEIL, Saint-Aubin - BP 48, Gif sur Yvette, France
| | - Gipsi Lima-Mendez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Régis Hallez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- WELBIO, Brussels, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medicine, University of Lund, Lund, Sweden.
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- University of Tartu, Institute of Technology, Tartu, Estonia.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
- WELBIO, Brussels, Belgium.
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17
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Abstract
As rapidly growing bacteria begin to exhaust essential nutrients, they enter a state of reduced growth, ultimately leading to stasis or quiescence. Investigation of the response to nutrient limitation has focused largely on the consequences of amino acid starvation, known as the "stringent response." Here, an uncharged tRNA in the A-site of the ribosome stimulates the ribosome-associated protein RelA to synthesize the hyperphosphorylated guanosine nucleotides (p)ppGpp that mediate a global slowdown of growth and biosynthesis. Investigations of the stringent response typically employ experimental methodologies that rapidly stimulate (p)ppGpp synthesis by abruptly increasing the fraction of uncharged tRNAs, either by explicit amino starvation or by inhibition of tRNA charging. Consequently, these methodologies inhibit protein translation, thereby interfering with the cellular pathways that respond to nutrient limitation. Thus, complete and/or rapid starvation is a problematic experimental paradigm for investigating bacterial responses to physiologically relevant nutrient-limited states.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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18
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Protein-Ligand Interactions in Scarcity: The Stringent Response from Bacteria to Metazoa, and the Unanswered Questions. Int J Mol Sci 2023; 24:ijms24043999. [PMID: 36835415 PMCID: PMC9965611 DOI: 10.3390/ijms24043999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
The stringent response, originally identified in Escherichia coli as a signal that leads to reprogramming of gene expression under starvation or nutrient deprivation, is now recognized as ubiquitous in all bacteria, and also as part of a broader survival strategy in diverse, other stress conditions. Much of our insight into this phenomenon derives from the role of hyperphosphorylated guanosine derivatives (pppGpp, ppGpp, pGpp; guanosine penta-, tetra- and tri-phosphate, respectively) that are synthesized on starvation cues and act as messengers or alarmones. These molecules, collectively referred to here as (p)ppGpp, orchestrate a complex network of biochemical steps that eventually lead to the repression of stable RNA synthesis, growth, and cell division, while promoting amino acid biosynthesis, survival, persistence, and virulence. In this analytical review, we summarize the mechanism of the major signaling pathways in the stringent response, consisting of the synthesis of the (p)ppGpp, their interaction with RNA polymerase, and diverse factors of macromolecular biosynthesis, leading to differential inhibition and activation of specific promoters. We also briefly touch upon the recently reported stringent-like response in a few eukaryotes, which is a very disparate mechanism involving MESH1 (Metazoan SpoT Homolog 1), a cytosolic NADPH phosphatase. Lastly, using ppGpp as an example, we speculate on possible pathways of simultaneous evolution of alarmones and their multiple targets.
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19
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Pseudomonas aeruginosa Citrate Synthase GltA Influences Antibiotic Tolerance and the Type III Secretion System through the Stringent Response. Microbiol Spectr 2023; 11:e0323922. [PMID: 36602339 PMCID: PMC9927146 DOI: 10.1128/spectrum.03239-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Carbohydrate metabolism plays essential roles in energy generation and providing carbon skeletons for amino acid syntheses. In addition, carbohydrate metabolism has been shown to influence bacterial susceptibility to antibiotics and virulence. In this study, we demonstrate that citrate synthase gltA mutation can increase the expression of the type III secretion system (T3SS) genes and antibiotic tolerance in Pseudomonas aeruginosa. The stringent response is activated in the gltA mutant, and deletion of the (p)ppGpp synthetase gene relA restores the antibiotic tolerance and expression of the T3SS genes to wild-type level. We further demonstrate that the intracellular level of cAMP is increased by the stringent response in the gltA mutant, which increases the expression of the T3SS master regulator gene exsA. Overall, our results reveal an essential role of GltA in metabolism, antibiotic tolerance, and virulence, as well as a novel regulatory mechanism of the stringent response-mediated regulation of the T3SS in P. aeruginosa. IMPORTANCE Rising antimicrobial resistance imposes a severe threat to human health. It is urgent to develop novel antimicrobial strategies by understanding bacterial regulation of virulence and antimicrobial resistance determinants. The stringent response plays an essential role in virulence and antibiotic tolerance. Pseudomonas aeruginosa is an opportunistic pathogen that causes acute and chronic infections in humans. The bacterium produces an arsenal of virulence factors and is highly resistant to a variety of antibiotics. In this study, we provide evidence that citrate synthase GltA plays a critical role in P. aeruginosa metabolism and influences the antibiotic tolerance and virulence. We further reveal a role of the stringent response in the regulation of the antibiotic tolerance and virulence. The significance of this work is in elucidation of novel regulatory pathways that control both antibiotic tolerance and virulence in P. aeruginosa.
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20
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Mehrez M, Romand S, Field B. New perspectives on the molecular mechanisms of stress signalling by the nucleotide guanosine tetraphosphate (ppGpp), an emerging regulator of photosynthesis in plants and algae. THE NEW PHYTOLOGIST 2023; 237:1086-1099. [PMID: 36349398 PMCID: PMC10107265 DOI: 10.1111/nph.18604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The nucleotides guanosine tetraphosphate and guanosine pentaphosphate (together (p)ppGpp) are found in a wide range of prokaryotic and eukaryotic organisms where they are associated with stress signalling. In this review, we will discuss recent research highlighting the role of (p)ppGpp signalling as a conserved regulator of photosynthetic activity in the chloroplasts of plants and algae, and the latest discoveries that open up new perspectives on the emerging roles of (p)ppGpp in acclimation to environmental stress. We explore how rapid advances in the study of (p)ppGpp signalling in prokaryotes are now revealing large gaps in our understanding of the molecular mechanisms of signalling by (p)ppGpp and related nucleotides in plants and algae. Filling in these gaps is likely to lead to the discovery of conserved as well as new plant- and algal-specific (p)ppGpp signalling mechanisms that will offer new insights into the taming of the chloroplast and the regulation of stress tolerance.
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Affiliation(s)
- Marwa Mehrez
- Aix‐Marseille University, CEA, CNRS, BIAM, UMR726513009MarseilleFrance
- Faculty of Sciences of Tunis, Laboratory of Molecular Genetics, Immunology and BiotechnologyUniversity of Tunis El Manar2092TunisTunisia
| | - Shanna Romand
- Aix‐Marseille University, CEA, CNRS, BIAM, UMR726513009MarseilleFrance
| | - Ben Field
- Aix‐Marseille University, CEA, CNRS, BIAM, UMR726513009MarseilleFrance
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21
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Alnahhas RN, Dunlop MJ. Advances in linking single-cell bacterial stress response to population-level survival. Curr Opin Biotechnol 2023; 79:102885. [PMID: 36641904 PMCID: PMC9899315 DOI: 10.1016/j.copbio.2022.102885] [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: 11/04/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 01/14/2023]
Abstract
Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.
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Affiliation(s)
- Razan N Alnahhas
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Biological Design Center, Boston University, Boston, MA 02215, United States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Biological Design Center, Boston University, Boston, MA 02215, United States.
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22
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Zhu M, Dai X. Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift. Nat Commun 2023; 14:467. [PMID: 36709335 PMCID: PMC9884231 DOI: 10.1038/s41467-023-36254-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Timely adaptation to nutrient downshift is crucial for bacteria to maintain fitness during feast and famine cycle in the natural niche. However, the molecular mechanism that ensures the timely adaption of bacterial growth to nutrient downshift remains poorly understood. Here, we quantitatively investigated the adaptation of Escherichia coli to various kinds of nutrient downshift. We found that relA deficient strain, which is devoid of stringent response, exhibits a significantly longer growth lag than wild type strain during adapting to both amino acid downshift and carbon downshift. Quantitative proteomics show that increased (p)ppGpp level promotes the growth adaption of bacteria to amino acid downshift via triggering the proteome resource re-allocation from ribosome synthesis to amino acid biosynthesis. Such type of proteome re-allocation is significantly delayed in the relA-deficient strain, which underlies its longer lag than wild type strain during amino acid downshift. During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. Our studies shed light on the fundamental strategy of bacteria to maintain fitness under nutrient-fluctuating environments.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
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23
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Ainelo A, Caballero-Montes J, Bulvas O, Ernits K, Coppieters ‘t Wallant K, Takada H, Craig SZ, Mazzucchelli G, Zedek S, Pichová I, Atkinson GC, Talavera A, Martens C, Hauryliuk V, Garcia-Pino A. The structure of DarB in complex with Rel NTD reveals nonribosomal activation of Rel stringent factors. SCIENCE ADVANCES 2023; 9:eade4077. [PMID: 36652515 PMCID: PMC9848473 DOI: 10.1126/sciadv.ade4077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Rel stringent factors are bifunctional ribosome-associated enzymes that catalyze both synthesis and hydrolysis of the alarmones (p)ppGpp. Besides the allosteric control by starved ribosomes and (p)ppGpp, Rel is regulated by various protein factors depending on specific stress conditions, including the c-di-AMP-binding protein DarB. However, how these effector proteins control Rel remains unknown. We have determined the crystal structure of the DarB2:RelNTD2 complex, uncovering that DarB directly engages the SYNTH domain of Rel to stimulate (p)ppGpp synthesis. This association with DarB promotes a SYNTH-primed conformation of the N-terminal domain region, markedly increasing the affinity of Rel for ATP while switching off the hydrolase activity of the enzyme. Binding to c-di-AMP rigidifies DarB, imposing an entropic penalty that precludes DarB-mediated control of Rel during normal growth. Our experiments provide the basis for understanding a previously unknown mechanism of allosteric regulation of Rel stringent factors independent of amino acid starvation.
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Affiliation(s)
- Andres Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Ondřej Bulvas
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Karin Ernits
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Kyo Coppieters ‘t Wallant
- Centre for Structural Biology and Bioinformatics, Universite Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Hiraku Takada
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Sophie Z. Craig
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Liège Université, B-4000 Liège, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Gemma C. Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Chloe Martens
- Centre for Structural Biology and Bioinformatics, Universite Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
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24
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Pang HW, Barrientos A. Rapid Cryopurification of the Yeast Mitochondrial Ribosome. Methods Mol Biol 2023; 2661:133-141. [PMID: 37166636 PMCID: PMC10654548 DOI: 10.1007/978-1-0716-3171-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cryogenic milling, or cryomilling, involves the use of liquid nitrogen to lower the temperature of the biological material and/or the milling process. When applied to the study of subcellular or suborganellar structures and processes, it allows for their rapid extraction from whole cells frozen in the physiological state of choice. This approach has proven to be useful for the study of yeast mitochondrial ribosomes. Following cryomilling of 100 mL of yeast culture, conveniently tagged mitochondrial ribosomes can be immunoprecipitated and purified in native conditions. These ribosomes are suitable for the application of downstream approaches. These include mitoribosome profiling to analyze the mitochondrial translatome or mass spectrometry analyses to assess the mitoribosome proteome in normal growth conditions or under stress, as described in this method.
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Affiliation(s)
- Hong Weng Pang
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
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25
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Antonov IV, O’Loughlin S, Gorohovski AN, O’Connor PB, Baranov PV, Atkins JF. Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing. RNA Biol 2023; 20:926-942. [PMID: 37968863 PMCID: PMC10732093 DOI: 10.1080/15476286.2023.2270812] [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: 11/17/2022] [Accepted: 10/02/2023] [Indexed: 11/17/2023] Open
Abstract
In Streptomyces species, the cell cycle involves a switch from an early and vegetative state to a later phase where secondary products including antibiotics are synthesized, aerial hyphae form and sporulation occurs. AdpA, which has two domains, activates the expression of numerous genes involved in the switch from the vegetative growth phase. The adpA mRNA of many Streptomyces species has a UUA codon in a linker region between 5' sequence encoding one domain and 3' sequence encoding its other and C-terminal domain. UUA codons are exceptionally rare in Streptomyces, and its functional cognate tRNA is not present in a fully modified and acylated form, in the early and vegetative phase of the cell cycle though it is aminoacylated later. Here, we report candidate recoding signals that may influence decoding of the linker region UUA. Additionally, a short ORF 5' of the main ORF has been identified with a GUG at, or near, its 5' end and an in-frame UUA near its 3' end. The latter is commonly 5 nucleotides 5' of the main ORF start. Ribosome profiling data show translation of that 5' region. Ten years ago, UUA-mediated translational bypassing was proposed as a sensor by a Streptomyces phage of its host's cell cycle stage and an effector of its lytic/lysogeny switch. We provide the first experimental evidence supportive of this proposal.
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Affiliation(s)
- Ivan V. Antonov
- Russian Academy of Science, Institute of Bioengineering, Research Center of Biotechnology, Moscow, Russia
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sinéad O’Loughlin
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Alessandro N. Gorohovski
- Russian Academy of Science, Institute of Bioengineering, Research Center of Biotechnology, Moscow, Russia
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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Molecular Characterization of Clinical Rel Mutations and Consequences for Resistance Expression and Fitness in Staphylococcus aureus. Antimicrob Agents Chemother 2022; 66:e0093822. [PMID: 36346240 PMCID: PMC9764984 DOI: 10.1128/aac.00938-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The stringent response (SR) is a universal stress response that acts as a global regulator of bacterial physiology and virulence, and is a contributor to antibiotic tolerance and resistance. In most bacteria, the SR is controlled by a bifunctional enzyme, Rel, which both synthesizes and hydrolyzes the alarmone (p)ppGpp via two distinct catalytic domains. The balance between these antagonistic activities is fine-tuned to the needs of the cell and, in a "relaxed" state, the hydrolase activity of Rel dominates. We have previously shown that two single amino acid substitutions in Rel (that were identified in clinical isolates from persistent infections) confer elevated basal concentrations of (p)ppGpp and consequent multidrug tolerance in Staphylococcus aureus. Here, we explore the molecular details of how these mutations bring about this increase in cellular (p)ppGpp and investigate the wider cellular consequences in terms of resistance expression, resistance development, and bacterial fitness. Using enzyme assays, we show that both these mutations drastically reduce the hydrolase activity of Rel, thereby shifting the balance of Rel activity in favor of (p)ppGpp synthesis. We also demonstrate that these mutations induce high-level, homogeneous expression of β-lactam resistance and confer a significant fitness advantage in the presence of bactericidal antibiotics (but a fitness cost in the absence of antibiotic). In contrast, these mutations do not appear to accelerate the emergence of endogenous resistance mutations in vitro. Overall, our findings reveal the complex nature of Rel regulation and the multifaceted implications of clinical Rel mutations in terms of antibiotic efficacy and bacteria survival.
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Mu H, Han F, Wang Q, Wang Y, Dai X, Zhu M. Recent functional insights into the magic role of (p)ppGpp in growth control. Comput Struct Biotechnol J 2022; 21:168-175. [PMID: 36544478 PMCID: PMC9747358 DOI: 10.1016/j.csbj.2022.11.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Rapid growth and survival are two key traits that enable bacterial cells to thrive in their natural habitat. The guanosine tetraphosphate and pentaphosphate [(p)ppGpp], also known as "magic spot", is a key second messenger inside bacterial cells as well as chloroplasts of plants and green algae. (p)ppGpp not only controls various stages of central dogma processes (replication, transcription, ribosome maturation and translation) and central metabolism but also regulates various physiological processes such as pathogenesis, persistence, motility and competence. Under extreme conditions such as nutrient starvation, (p)ppGpp-mediated stringent response is crucial for the survival of bacterial cells. This mini-review highlights some of the very recent progress on the key role of (p)ppGpp in bacterial growth control in light of cellular resource allocation and cell size regulation. We also briefly discuss some recent functional insights into the role of (p)ppGpp in plants and green algae from the angle of growth and development and further discuss several important open directions for future studies.
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28
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Lu Y, Yang L, An Y, Liu D, Yang G, He Q. Salt tolerance and ester production mechanisms of Candida etchellsii in Chinese horse bean-chili-paste. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Penugurti V, Mishra YG, Manavathi B. AMPK: An odyssey of a metabolic regulator, a tumor suppressor, and now a contextual oncogene. Biochim Biophys Acta Rev Cancer 2022; 1877:188785. [PMID: 36031088 DOI: 10.1016/j.bbcan.2022.188785] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022]
Abstract
Metabolic reprogramming is a unique but complex biochemical adaptation that allows solid tumors to tolerate various stresses that challenge cancer cells for survival. Under conditions of metabolic stress, mammalian cells employ adenosine monophosphate (AMP)-activated protein kinase (AMPK) to regulate energy homeostasis by controlling cellular metabolism. AMPK has been described as a cellular energy sensor that communicates with various metabolic pathways and networks to maintain energy balance. Earlier studies characterized AMPK as a tumor suppressor in the context of cancer. Later, a paradigm shift occurred in support of the oncogenic nature of AMPK, considering it a contextual oncogene. In support of this, various cellular and mouse models of tumorigenesis and clinicopathological studies demonstrated increased AMPK activity in various cancers. This review will describe AMPK's pro-tumorigenic activity in various malignancies and explain the rationale and context for using AMPK inhibitors in combination with anti-metabolite drugs to treat AMPK-driven cancers.
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Affiliation(s)
- Vasudevarao Penugurti
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Yasaswi Gayatri Mishra
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Bramanandam Manavathi
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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30
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Salinas Ibáñez ÁG, Origone AL, Liggieri CS, Barberis SE, Vega AE. Asclepain cI, a proteolytic enzyme from Asclepias curassavica L., a south American plant, against Helicobacter pylori. Front Microbiol 2022; 13:961958. [PMID: 36060760 PMCID: PMC9433900 DOI: 10.3389/fmicb.2022.961958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Helicobacter pylori is a Gram negative bacterium most frequently associated with human gastrointestinal infections worldwide. The increasing occurrence of antibiotic-resistant isolates of H. pylori constitutes a challenge. The eradication of the microorganism is currently being considered a “high priority” by the World Health Organization (WHO). In this context, bioactive compounds found in natural products seem to be an effective therapeutic option to develop new antibiotics against the pathogen. In this study, we investigated the effect of asclepain cI, the main purified proteolytic enzyme of the latex of petioles and stems from Asclepia curassavica L. (Asclepiadaceae), a South American native plant, against H. pylori; in order to obtain a natural therapeutic adjuvant and a safe nutraceutical product. Asclepain cI showed antibacterial activity against reference strains and drug-resistant clinical isolates of H. pylori in vitro. A range of minimal inhibitory concentration (MIC) from 1 to 2 μg/ml and minimal bactericidal concentration (MBC) from 2 to 4 μg/ml was obtained, respectively. The action of asclepain cI on the transcription of omp18, ureA, flaA genes showed a significantly decreased expression of the selected pathogenic factors. Furthermore, asclepain cI did not induce toxic effects at the concentrations assayed. Asclepain cI could be considered a highly feasible option to be used as a natural therapeutic adjuvant and a safe nutraceutical product against H. pylori.
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Affiliation(s)
- Ángel Gabriel Salinas Ibáñez
- Laboratorio de Microbiología e Inmunología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
- Instituto de Física Aplicada (INFAP) - Centro Científico Tecnológico (CCT) San Luis - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Luis, Argentina
| | - Anabella L. Origone
- Instituto de Física Aplicada (INFAP) - Centro Científico Tecnológico (CCT) San Luis - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Luis, Argentina
- Laboratorio de Control de Calidad y Desarrollo de Bromatología, Universidad Nacional de San Luis, San Luis, Argentina
| | - Constanza S. Liggieri
- Centro de Investigación de Proteínas Vegetales (CIProVe), Universidad Nacional de La Plata, La Plata, Argentina
| | - Sonia E. Barberis
- Instituto de Física Aplicada (INFAP) - Centro Científico Tecnológico (CCT) San Luis - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Luis, Argentina
- Laboratorio de Control de Calidad y Desarrollo de Bromatología, Universidad Nacional de San Luis, San Luis, Argentina
- *Correspondence: Sonia E. Barberis
| | - Alba E. Vega
- Laboratorio de Microbiología e Inmunología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
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Bisiak F, Chrenková A, Zhang SD, Pedersen JN, Otzen DE, Zhang YE, Brodersen DE. Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response. J Biol Chem 2022; 298:102142. [PMID: 35714769 PMCID: PMC9293644 DOI: 10.1016/j.jbc.2022.102142] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 11/04/2022] Open
Abstract
The bacterial stringent response involves wide-ranging metabolic reprogramming aimed at increasing long-term survivability during stress conditions. One of the hallmarks of the stringent response is the production of a set of modified nucleotides, known as alarmones, which affect a multitude of cellular pathways in diverse ways. Production and degradation of these molecules depend on the activity of enzymes from the RelA/SpoT homologous family, which come in both bifunctional (containing domains to both synthesize and hydrolyze alarmones) and monofunctional (consisting of only synthetase or hydrolase domain) variants, of which the structure, activity, and regulation of the bifunctional RelA/SpoT homologs have been studied most intensely. Despite playing an important role in guanosine nucleotide homeostasis in particular, mechanisms of regulation of the small alarmone hydrolases (SAHs) are still rather unclear. Here, we present crystal structures of SAH enzymes from Corynebacterium glutamicum (RelHCg) and Leptospira levettii (RelHLl) and show that while being highly similar, structural differences in substrate access and dimer conformations might be important for regulating their activity. We propose that a varied dimer form is a general property of the SAH family, based on current structural information as well as prediction models for this class of enzymes. Finally, subtle structural variations between monofunctional and bifunctional enzymes point to how these different classes of enzymes are regulated.
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Affiliation(s)
- Francesco Bisiak
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Adriana Chrenková
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Jannik N Pedersen
- Interdisciplinary Nanoscience Centre (iNano), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, DK-8000 Aarhus C, Denmark; Interdisciplinary Nanoscience Centre (iNano), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Yong E Zhang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 København N, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, DK-8000 Aarhus C, Denmark.
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Cellular perception of growth rate and the mechanistic origin of bacterial growth law. Proc Natl Acad Sci U S A 2022; 119:e2201585119. [PMID: 35544692 PMCID: PMC9171811 DOI: 10.1073/pnas.2201585119] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Many cellular activities in bacteria are organized according to their growth rate. The notion that ppGpp measures the cell’s growth rate is well accepted in the field of bacterial physiology. However, despite decades of interrogation and the identification of multiple molecular interactions that connects ppGpp to some aspects of cell growth, we lack a system-level, quantitative picture of how this alleged “measurement” is performed. Through quantitative experiments, we show that the ppGpp pool responds inversely to the rate of translational elongation in Escherichia coli. Together with its roles in inhibiting ribosome biogenesis and activity, ppGpp closes a key regulatory circuit that enables the cell to perceive and control the rate of its growth across conditions. The celebrated linear growth law relating the ribosome content and growth rate emerges as a consequence of keeping a supply of ribosome reserves while maintaining elongation rate in slow growth conditions. Further analysis suggests the elongation rate itself is detected by sensing the ratio of dwelling and translocating ribosomes, a strategy employed to collapse the complex, high-dimensional dynamics of the molecular processes underlying cell growth to perceive the physiological state of the whole.
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Abstract
The "magic spot" alarmones (pp)pGpp, previously implicated in Clostridioides difficile antibiotic survival, are synthesized by the RelA-SpoT homolog (RSH) of C. difficile (RSHCd) and RelQCd. These enzymes are transcriptionally activated by diverse environmental stresses. RSHCd has previously been reported to synthesize ppGpp, but in this study, we found that both clostridial enzymes exclusively synthesize pGpp. While direct synthesis of pGpp from a GMP substrate, and (p)ppGpp hydrolysis into pGpp by NUDIX hydrolases, have previously been reported, there is no precedent for a bacterium synthesizing pGpp exclusively. Hydrolysis of the 5' phosphate or pyrophosphate from GDP or GTP substrates is necessary for activity by the clostridial enzymes, neither of which can utilize GMP as a substrate. Both enzymes are remarkably insensitive to the size of their metal ion cofactor, tolerating a broad array of metals that do not allow activity in (pp)pGpp synthetases from other organisms. It is clear that while C. difficile utilizes alarmone signaling, its mechanisms of alarmone synthesis are not directly homologous to those in more completely characterized organisms. IMPORTANCE Despite the role of the stringent response in antibiotic survival and recurrent infections, it has been a challenging target for antibacterial therapies because it is so ubiquitous. This is an especially relevant consideration for the treatment of Clostridioides difficile infection (CDI), as exposure to broad-spectrum antibiotics that harm commensal microbes is a major risk factor for CDI. Here, we report that both of the alarmone synthetase enzymes that mediate the stringent response in this organism employ a unique mechanism that requires the hydrolysis of two phosphate bonds and synthesize the triphosphate alarmone pGpp exclusively. Inhibitors targeted against these noncanonical synthetases have the potential to be highly specific and minimize detrimental effects to stringent response pathways in commensal microbes.
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Tailor K, Sagar P, Dave K, Pohnerkar J. Fusion of the N-terminal 119 amino acids of RelA with the CTD domain render growth inhibitory effects of the latter, (p)ppGpp-dependent. Mol Genet Genomics 2022; 297:601-620. [PMID: 35238978 DOI: 10.1007/s00438-022-01873-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/10/2022] [Indexed: 10/18/2022]
Abstract
The guanosine nucleotide derivatives ppGpp and pppGpp are central to the remarkable capacity of bacteria to adapt to fluctuating environments and metabolic perturbations. They are synthesized by two proteins, RelA and SpoT in E. coli and the activities of each of the two enzymes are highly regulated for homeostatic control of intracellular (p)ppGpp levels. Characterization of the mutant studied here indicates that moderate level expression of RelA appreciably reduces growth of cells wherein the basal levels of (p)ppGpp are higher than in the wild type without elevating the levels further. Consistent with this result, a large part of the growth inhibition effect is reproduced by overexpression of RelA NTD-CTD fusion lacking the (p)ppGpp synthesis function. A null mutation in relA abolishes this growth inhibitory effect suggesting its requirement for basal level synthesis of (p)ppGpp. Accordingly, increase in the (p)ppGpp levels in the relA1 mutant by spoT202 mutation largely restored the growth inhibitory effects of overexpression of RelA NTD-CTD fusion. Expression of this construct consisting of 119 amino acids of the N-terminal hydrolytic domain (HD) fused in-frame with the CTD domain (±TGS domain) renders the growth inhibitory effects (p)ppGpp-responsive-inhibited growth only of spoT1 and spoT202 relA1 mutants. This finding uncovered an hitherto unrealized (p)ppGpp-dependent regulation of RelA-CTD function, unraveling the importance of RelA NTD-HD domain for its regulatory role. An incremental rise in the (p)ppGpp levels is proposed to progressively modulate the interaction of RelA-CTD with the ribosomes with possible implications in the feedback regulation of the (p)ppGpp synthesis function, a proposal that accounts for the nonlinear kinetics of (p)ppGpp synthesis and increased ratio of RelA:ribosomes, both in vitro as well as in vivo.
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Affiliation(s)
- Krishma Tailor
- Department of Biochemistry, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Prarthi Sagar
- Department of Biochemistry, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Keyur Dave
- Department of Biochemistry, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Jayashree Pohnerkar
- Department of Biochemistry, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India.
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Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Nat Commun 2022; 13:1069. [PMID: 35217658 PMCID: PMC8881573 DOI: 10.1038/s41467-022-28675-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/07/2022] [Indexed: 11/08/2022] Open
Abstract
The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli. Bacterial responses to nutrient limitation and other stress conditions are often modulated by the nucleotide-based second messenger (p)ppGpp. Here, the authors show that (p)ppGpp inhibits the SRP membrane-protein insertion and secretion pathway by binding to GTPases Ffh and FtsY.
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36
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Gastrointestinal Microbiota Dysbiosis Associated with SARS-CoV-2 Infection in Colorectal Cancer: The Implication of Probiotics. GASTROENTEROLOGY INSIGHTS 2022. [DOI: 10.3390/gastroent13010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The complexity of coronavirus disease 2019 (COVID-19)’s pathophysiology is such that microbial dysbiosis in the lung and gastrointestinal (GI) microbiota may be involved in its pathogenic process. GI microbiota dysbiosis has been associated with respiratory disorders, including COVID-19, as well as sporadic colorectal cancer (CRC) through imbalanced microbiota and compromised immune response. It is pertinent to understand the possible role of probiotics in stabilizing the microbial environment and maintaining the integrity of the respiratory and GI tracts in SARS-CoV-2 induced dysbiosis and colorectal carcinogenesis. The long-term implication of SARS-CoV-2 in GI dysbiosis via microbiota-gut-lung cross-talk could increase the risk of new CRC diagnosis or worsen the condition of previously diagnosed individuals. Recent knowledge shows that the immune-modulatory response to probiotics is shifting the beneficial use of probiotics towards the treatment of various diseases. In this review, we highlight the potential impact of probiotics on SARS-CoV-2 infection associated with CRC through microbiota imbalance in COVID-19 patients.
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Veetilvalappil VV, Aranjani JM, Mahammad FS, Joseph A. Awakening sleeper cells: a narrative review on bacterial magic spot synthetases as potential drug targets to overcome persistence. Curr Genet 2022; 68:49-60. [PMID: 34787710 PMCID: PMC8801413 DOI: 10.1007/s00294-021-01221-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 10/29/2022]
Abstract
Magic spot synthetases are emerging targets to overcome persistence caused by stringent response. The 'stringent response' is a bacterial stress survival mechanism, which results in the accumulation of alarmones (also called Magic spots) leading to the formation of dormant persister cells. These 'sleeper cells' evade antibiotic treatment and could result in relapse of infection. This review broadly investigates the phenomenon of stringent response and persistence, and specifically discusses the distribution, classification, and nomenclature of proteins such as Rel/SpoT homologs (RSH), responsible for alarmone synthesis. The authors further explain the relevance of RSH as potential drug targets to break the dormancy of persister cells commonly seen in biofilms. One of the significant factors that initiate alarmone synthesis is nutrient deficiency. In a starved condition, ribosome-associated RSH detects deacylated tRNA and initiates alarmone synthesis. Accumulation of alarmones has a considerable effect on bacterial physiology, virulence, biofilm formation, and persister cell formation. Preventing alarmone synthesis by inhibiting RSH responsible for alarmone synthesis will prevent or reduce persister cells' formation. Magic spot synthetases are thus potential targets that could be explored to overcome persistence seen in biofilms.
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Affiliation(s)
- Vimal Venu Veetilvalappil
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Jesil Mathew Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India.
| | - Fayaz Shaik Mahammad
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
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Wani AK, Akhtar N, Sher F, Navarrete AA, Américo-Pinheiro JHP. Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems. Arch Microbiol 2022; 204:144. [PMID: 35044532 DOI: 10.1007/s00203-022-02757-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 01/01/2023]
Abstract
Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.
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Affiliation(s)
- Atif Khurshid Wani
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Nahid Akhtar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Farooq Sher
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
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Salinas Ibáñez ÁG, Vallés D, Adaro M, Barberis S, Vega AE. Antimicrobial Effect of a Proteolytic Enzyme From the Fruits of Solanum granuloso-leprosum (Dunal) Against Helicobacter pylori. Front Nutr 2022; 8:699955. [PMID: 34977105 PMCID: PMC8717831 DOI: 10.3389/fnut.2021.699955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022] Open
Abstract
Helicobacter pylori is a gram-negative, helix-shaped, and microaerophilic bacteria that colonizes the human gastric mucosa, causing chronic infections, gastritis, peptic ulcer, lymphomas associated with lymphoid mucosa tissue, and gastric cancer. H. pylori is considered a Type 1 human carcinogen by WHO. The prevalence of the infection is estimated in more than half of the world population. Treatment of H. pylori infection includes antibiotics and proton pump inhibitors, but the increasing antibiotic resistance promotes the research of novel, more effective, and natural antibacterial compounds. The aim of this work was to study the effect of the partially purified proteolytic extract (RAP) of the fruits from Solanum granuloso-leprosum (Dunal), a South American native plant, and a purified fraction named granulosain I, against H. pylori, to obtain natural food additives for the production of anti-H. pylori functional foods. Furthermore, granulosain I and RAP could be used as natural adjuncts to conventional therapies. Granulosain I and RAP antibacterial activity was evaluated as minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) against H. pylori NCTC 11638 (reference strain) and twelve H. pylori wild strains, using a microdilution plating technique (Clinical and Laboratory Standards Institute). All the strains tested were susceptible to granulosain I with MIC from 156.25 to 312.5 μg/mL and MBC from 312.5 to 625 μg/mL, respectively. Besides, all the strains tested were susceptible to the RAP with MIC from 312.5 to 625 μg/mL and MBC from 625 to 1,250 μg/mL, respectively. The effect of granulosain I and RAP on the transcription of H. pylori genes encoding pathogenic factors, omp18, ureA, and flaA, with respect to a housekeeping gene (16S rRNA), was evaluated by RT-PCR technique. The band intensity between pathogenic factors and control gene was correlated under treated or untreated conditions, using the ImageJ program. Granulosain I and RAP significantly decreased the expression of pathogenic factors: omp18, ureA, and flaA. The combined inhibitory effect of granulosain I or RAP and an antibiotic such as, amoxicillin (AML, 10 μg), clarithromycin (CLA, 15 μg), levofloxacin (LEV, 5 μg), and metronidazole (MTZ, 5 μg) was evaluated, using the agar diffusion technique. Granulosain I and RAP showed significant synergistic effect on AML, CLA, and LEV, but no significant effect on MTZ was observed. Besides, granulosain I and RAP did not show toxicological effects at the concentrations studied. Finally, granulosain I and RAP could be used as safe natural food additives and as adjuvants for conventional therapies against H. pylori.
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Affiliation(s)
- Ángel Gabriel Salinas Ibáñez
- Laboratorio de Microbiología e Inmunología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.,Instituto de Física Aplicada (INFAP)-Centro Científico Tecnológico (CCT) San Luis-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Luis, Argentina
| | - Diego Vallés
- Laboratorio de Enzimas Hidrolíticas, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Mauricio Adaro
- Instituto de Física Aplicada (INFAP)-Centro Científico Tecnológico (CCT) San Luis-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Luis, Argentina.,Laboratorio de Control de Calidad y Desarrollo de Bromatología, Universidad Nacional de San Luis, San Luis, Argentina
| | - Sonia Barberis
- Instituto de Física Aplicada (INFAP)-Centro Científico Tecnológico (CCT) San Luis-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Luis, Argentina.,Laboratorio de Control de Calidad y Desarrollo de Bromatología, Universidad Nacional de San Luis, San Luis, Argentina
| | - Alba E Vega
- Laboratorio de Microbiología e Inmunología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
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Maki Y, Yoshida H. Ribosomal Hibernation-Associated Factors in Escherichia coli. Microorganisms 2021; 10:microorganisms10010033. [PMID: 35056482 PMCID: PMC8778775 DOI: 10.3390/microorganisms10010033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 01/30/2023] Open
Abstract
Bacteria convert active 70S ribosomes to inactive 100S ribosomes to survive under various stress conditions. This state, in which the ribosome loses its translational activity, is known as ribosomal hibernation. In gammaproteobacteria such as Escherichia coli, ribosome modulation factor and hibernation-promoting factor are involved in forming 100S ribosomes. The expression of ribosome modulation factor is regulated by (p)ppGpp (which is induced by amino acid starvation), cAMP-CRP (which is stimulated by reduced metabolic energy), and transcription factors involved in biofilm formation. This indicates that the formation of 100S ribosomes is an important strategy for bacterial survival under various stress conditions. In recent years, the structures of 100S ribosomes from various bacteria have been reported, enhancing our understanding of the 100S ribosome. Here, we present previous findings on the 100S ribosome and related proteins and describe the stress-response pathways involved in ribosomal hibernation.
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Kim N, Son JH, Kim K, Kim HJ, Shin M, Lee JC. DksA Modulates Antimicrobial Susceptibility of Acinetobacter baumannii. Antibiotics (Basel) 2021; 10:antibiotics10121472. [PMID: 34943684 PMCID: PMC8698368 DOI: 10.3390/antibiotics10121472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 11/05/2022] Open
Abstract
The stringent response regulators, (p)ppGpp and DksA, modulate various genes involved in physiological processes, virulence, and antimicrobial resistance in pathogenic bacteria. This study investigated the role of DksA in the antimicrobial susceptibility of Acinetobacter baumannii. The ∆dksA mutant (KM0248D) of A. baumannii ATCC 17978 and its complemented strain (KM0248C) were used, in addition to the ∆dksA mutant strain (NY0298D) of clinical 1656-2 strain. The microdilution assay was used to determine the minimum inhibitory concentrations (MICs) of antimicrobial agents. Quantitative real-time PCR was performed to analyze the expression of genes associated with efflux pumps. The KM0248D strain exhibited an increase of MICs to quinolones and tetracyclines, whereas KM0248D and NY0298D strains exhibited a decrease of MICs to aminoglycosides. The expression of genes associated with efflux pumps, including adeB, adeI/J, abeM, and/or tetA, was upregulated in both ∆dksA mutant strains. The deletion of dksA altered bacterial morphology in the clinical 1656-2 strain. In conclusion, DksA modulates the antimicrobial susceptibility of A. baumannii. The ∆dksA mutant strains of A. baumannii upregulate efflux pump gene expression, whereas (p)ppGpp-deficient mutants downregulate efflux pump gene expression. (p)ppGpp and DksA conduct opposite roles in the antimicrobial susceptibility of A. baumannii via efflux pump gene regulation.
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Shin J, Singal B, Grüber A, Wong DMK, Ragunathan P, Grüber G. Atomic structure of the regulatory TGS domain of Rel protein from Mycobacterium tuberculosis and its interaction with deacylated tRNA. FEBS Lett 2021; 595:3006-3018. [PMID: 34808002 DOI: 10.1002/1873-3468.14236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 11/09/2022]
Abstract
The stringent response is critical for the survival of Mycobacterium tuberculosis (Mtb) under nutrient starvation. The mechanism is mediated by a GTP pyrophosphokinase known as Rel, containing N-terminal synthetase and hydrolase domains and C-terminal regulatory domains, which include the TGS domain (ThrRS, GTPase, and SpoT proteins) that has been proposed to activate the synthetase domain via interaction with deacylated tRNA. Here, we present the NMR solution structure of the Mtb Rel TGS domain (MtRel TGS), consisting of five antiparallel β-strands and one helix-loop-helix motif. The interaction of MtRel TGS with deacylated tRNA is shown, indicating the critical amino acids of MtRel TGS in tRNA binding, and presenting the first structural evidence of MtRel TGS binding to deacylated tRNA in solution in the absence of the translational machinery.
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Affiliation(s)
- Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Bharti Singal
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Ardina Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - David Meng Kit Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
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Pulschen AA, Fernandes AZN, Cunha AF, Sastre DE, Matsuguma BE, Gueiros-Filho FJ. Many birds with one stone: targeting the (p)ppGpp signaling pathway of bacteria to improve antimicrobial therapy. Biophys Rev 2021; 13:1039-1051. [DOI: 10.1007/s12551-021-00895-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 10/25/2021] [Indexed: 12/19/2022] Open
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Preventing translational inhibition from ribosomal protein insufficiency by a herpes simplex virus-encoded ribosome-associated protein. Proc Natl Acad Sci U S A 2021; 118:2025546118. [PMID: 34725147 DOI: 10.1073/pnas.2025546118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
In addition to being required for protein synthesis, ribosomes and ribosomal proteins (RPs) also regulate messenger RNA translation in uninfected and virus-infected cells. By individually depleting 85 RPs using RNA interference, we found that overall protein synthesis in uninfected primary fibroblasts was more sensitive to RP depletion than those infected with herpes simplex virus-1 (HSV-1). Although representative RP depletion (uL3, uS4, uL5) inhibited protein synthesis in cells infected with two different DNA viruses (human cytomegalovirus, vaccinia virus), HSV-1-infected cell protein synthesis unexpectedly endured and required a single virus-encoded gene product, VP22. During individual RP insufficiency, VP22-expressing HSV-1 replicated better than a VP22-deficient variant. Furthermore, VP22 promotes polysome accumulation in virus-infected cells when uL3 or ribosome availability is limiting and cosediments with initiating and elongating ribosomes in infected and uninfected cells. This identifies VP22 as a virus-encoded, ribosome-associated protein that compensates for RP insufficiency to support viral protein synthesis and replication. Moreover, it reveals an unanticipated class of virus-encoded, ribosome-associated effectors that reduce the dependence of protein synthesis upon host RPs and broadly support translation during physiological stress such as infection.
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Ro C, Cashel M, Fernández-Coll L. The secondary messenger ppGpp interferes with cAMP-CRP regulon by promoting CRP acetylation in Escherichia coli. PLoS One 2021; 16:e0259067. [PMID: 34705884 PMCID: PMC8550359 DOI: 10.1371/journal.pone.0259067] [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: 06/10/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
The cAMP-CRP regulon coordinates transcription regulation of several energy-related genes, the lac operon among them. Lactose, or IPTG, induces the lac operon expression by binding to the LacI repressor, and releasing it from the promoter sequence. At the same time, the expression of the lac operon requires the presence of the CRP-cAMP complex, which promotes the binding of the RNA polymerase to the promoter region. The modified nucleotide cAMP accumulates in the absence of glucose and binds to the CRP protein, but its ability to bind to DNA can be impaired by lysine-acetylation of CRP. Here we add another layer of control, as acetylation of CRP seems to be modified by ppGpp. In cells grown in glycerol minimal media, ppGpp seems to repress the expression of lacZ, where ΔrelA mutants show higher expression of lacZ than in WT. These differences between the WT and ΔrelA strains seem to depend on the levels of acetylated CRP. During the growth in minimal media supplemented with glycerol, ppGpp promotes the acetylation of CRP by the Nε-lysine acetyltransferases YfiQ. Moreover, the expression of the different genes involved in the production and degradation of Acetyl-phosphate (ackA-pta) and the enzymatic acetylation of proteins (yfiQ) are stimulated by the presence of ppGpp, depending on the growth conditions.
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Affiliation(s)
- Chunghwan Ro
- Eunice Kennedy Shriver National Institute of Child Health and Development, NIH, Bethesda, Maryland, United States of America
| | - Michael Cashel
- Eunice Kennedy Shriver National Institute of Child Health and Development, NIH, Bethesda, Maryland, United States of America
| | - Llorenç Fernández-Coll
- Eunice Kennedy Shriver National Institute of Child Health and Development, NIH, Bethesda, Maryland, United States of America
- * E-mail:
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Kim N, Son JH, Kim K, Kim HJ, Kim YJ, Shin M, Lee JC. Global regulator DksA modulates virulence of Acinetobacter baumannii. Virulence 2021; 12:2750-2763. [PMID: 34696704 PMCID: PMC8583241 DOI: 10.1080/21505594.2021.1995253] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
DksA with (p)ppGpp regulates a wide range of gene transcriptions during the stringent response. The aim of this study was to identify a DksA ortholog in Acinetobacter baumannii and clarify the roles of DksA in bacterial physiology and virulence. The ∆dksA mutant and its complemented strains were constructed using A. baumannii ATCC 17978. The AlS_0248 in A. baumannii ATCC 17978 was identified to dksA using sequence homology, protein structure prediction, and gene expression patterns under different culture conditions. The ∆dksA mutant strain showed a filamentous morphology compared with the wild-type (WT) strain. Bacterial growth was decreased in the ∆dksA mutant strain under static conditions. Surface motility was decreased in the ∆dksA mutant strain compared with the WT strain. In contrast, biofilm formation was increased and biofilm-associated genes, such as bfmR/S and csuC/D/E, were upregulated in the ∆dksA mutant strain. The ∆dksA mutant strain produced less autoinducers than the WT strain. The expression of abaI and abaR was significantly decreased in the ∆dksA mutant strain. Furthermore, the ∆dksA mutant strain showed less bacterial burden and milder histopathological changes in the lungs of mice than the WT strain. Mice survival was also significantly different between the ∆dksA mutant and WT strains. Conclusively, DksA is directly or indirectly involved in regulating a wide range of genes associated with bacterial physiology and virulence, which contributes to the pathogenesis of A. baumannii. Thus, DksA is a potential anti-virulence target for A. baumannii infection.
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Affiliation(s)
- Nayeong Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Joo Hee Son
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Kyeongmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyo Jeong Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yoo Jeong Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Je Chul Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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In Silico Study of the RSH ( RelA/ SpoT Homologs) Gene Family and Expression Analysis in Response to PGPR Bacteria and Salinity in Brassica napus. Int J Mol Sci 2021; 22:ijms221910666. [PMID: 34639007 PMCID: PMC8509286 DOI: 10.3390/ijms221910666] [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: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 12/21/2022] Open
Abstract
Among several mechanisms involved in the plant stress response, synthesis of guanosine tetra and pentaphosphates (alarmones), homologous to the bacterial stringent response, is of crucial importance. Plant alarmones affect, among others, photosynthetic activity, metabolite accumulation, and nutrient remobilization, and thus regulate plant growth and development. The plant RSH (RelA/SpoT homolog) genes, that encode synthetases and/or hydrolases of alarmones, have been characterized in a limited number of plant species, e.g., Arabidopsis thaliana, Oryza sativa, and Ipomoea nil. Here, we used dry-to-wet laboratory research approaches to characterize RSH family genes in the polyploid plant Brassica napus. There are 12 RSH genes in the genome of rapeseed that belong to four types of RSH genes: 6 RSH1, 2 RSH2, 3 RSH3, and 1 CRSH. BnRSH genes contain 13-24 introns in RSH1, 2-6 introns in RSH2, 1-6 introns in RSH3, and 2-3 introns in the CRSH genes. In the promoter regions of the RSH genes, we showed the presence of regulatory elements of the response to light, plant hormones, plant development, and abiotic and biotic stresses. The wet-lab analysis showed that expression of BnRSH genes is generally not significantly affected by salt stress, but that the presence of PGPR bacteria, mostly of Serratia sp., increased the expression of BnRSH significantly. The obtained results show that BnRSH genes are differently affected by biotic and abiotic factors, which indicates their different functions in plants.
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(p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains. Mol Cell 2021; 81:3310-3322.e6. [PMID: 34416138 DOI: 10.1016/j.molcel.2021.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/26/2021] [Accepted: 07/21/2021] [Indexed: 01/03/2023]
Abstract
Amino acid starvation is sensed by Escherichia coli RelA and Bacillus subtilis Rel through monitoring the aminoacylation status of ribosomal A-site tRNA. These enzymes are positively regulated by their product-the alarmone nucleotide (p)ppGpp-through an unknown mechanism. The (p)ppGpp-synthetic activity of Rel/RelA is controlled via auto-inhibition by the hydrolase/pseudo-hydrolase (HD/pseudo-HD) domain within the enzymatic N-terminal domain region (NTD). We localize the allosteric pppGpp site to the interface between the SYNTH and pseudo-HD/HD domains, with the alarmone stimulating Rel/RelA by exploiting intra-NTD autoinhibition dynamics. We show that without stimulation by pppGpp, starved ribosomes cannot efficiently activate Rel/RelA. Compromised activation by pppGpp ablates Rel/RelA function in vivo, suggesting that regulation by the second messenger (p)ppGpp is necessary for mounting an acute starvation response via coordinated enzymatic activity of individual Rel/RelA molecules. Control by (p)ppGpp is lacking in the E. coli (p)ppGpp synthetase SpoT, thus explaining its weak synthetase activity.
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Emrizal R, Hamdani HY, Firdaus-Raih M. Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures. Int J Mol Sci 2021; 22:ijms22168553. [PMID: 34445259 PMCID: PMC8395288 DOI: 10.3390/ijms22168553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 12/12/2022] Open
Abstract
The increasing number and complexity of structures containing RNA chains in the Protein Data Bank (PDB) have led to the need for automated structure annotation methods to replace or complement expert visual curation. This is especially true when searching for tertiary base motifs and substructures. Such base arrangements and motifs have diverse roles that range from contributions to structural stability to more direct involvement in the molecule's functions, such as the sites for ligand binding and catalytic activity. We review the utility of computational approaches in annotating RNA tertiary base motifs in a dataset of PDB structures, particularly the use of graph theoretical algorithms that can search for such base motifs and annotate them or find and annotate clusters of hydrogen-bond-connected bases. We also demonstrate how such graph theoretical algorithms can be integrated into a workflow that allows for functional analysis and comparisons of base arrangements and sub-structures, such as those involved in ligand binding. The capacity to carry out such automatic curations has led to the discovery of novel motifs and can give new context to known motifs as well as enable the rapid compilation of RNA 3D motifs into a database.
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Affiliation(s)
- Reeki Emrizal
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia;
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia
| | - Hazrina Yusof Hamdani
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Pulau Pinang, Malaysia
- Correspondence: (H.Y.H.); (M.F.-R.)
| | - Mohd Firdaus-Raih
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia;
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia
- Correspondence: (H.Y.H.); (M.F.-R.)
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Abstract
Cellular life depends on transcription of DNA by RNA polymerase to express genetic information. RNA polymerase has evolved not just to read information from DNA and write it to RNA but also to sense and process information from the cellular and extracellular environments. Much of this information processing occurs during transcript elongation, when transcriptional pausing enables regulatory decisions. Transcriptional pauses halt RNA polymerase in response to DNA and RNA sequences and structures at locations and times that help coordinate interactions with small molecules and transcription factors important for regulation. Four classes of transcriptional pause signals are now evident after decades of study: elemental pauses, backtrack pauses, hairpin-stabilized pauses, and regulator-stabilized pauses. In this review, I describe current understanding of the molecular mechanisms of these four classes of pause signals, remaining questions about how RNA polymerase responds to pause signals, and the many exciting directions now open to understand pausing and the regulation of transcript elongation on a genome-wide scale. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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