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Moon JH, Woo J, Park JY, Noh MH, Kim D, Jung GY. Biosensor-guided evolution boosts itaconic acid production, unveiling unique insights into the stringent response. BIORESOURCE TECHNOLOGY 2025; 426:132326. [PMID: 40024573 DOI: 10.1016/j.biortech.2025.132326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 01/20/2025] [Accepted: 02/27/2025] [Indexed: 03/04/2025]
Abstract
Acetate is a cost-effective and sustainable carbon source that, despite its potential, remains underutilized. This study employed biosensor-assisted adaptive laboratory evolution (ALE) to enhance itaconic acid production and acetate metabolism in Escherichia coli. The evolved E. coli W strains exhibited 65% increase in itaconic acid production and 71% increase in growth rate, and 45% increase in itaconic acid yield. A common 31-kb genomic deletion was identified in the evolved strains, with two genes, ecw_m2276 and ecw_m2277, driving the observed phenotypic changes. The evolved strains exhibited an intensified stringent response, which enhanced the acetate-utilizing pathway and resulted in over a 5,000% increase in the expression of the glyoxylate shunt, thereby boosting microbial growth. Overexpression of relA further replicated these enhanced phenotypes. Our findings highlight not only significant physiological improvements but also present a novel strategy for enhancing microbial growth and bioproduction from acetate, offering valuable insights for industrial biotechnology applications.
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Affiliation(s)
- Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jihoon Woo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Myung Hyun Noh
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan 44429, Republic of Korea.
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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2
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Zegarra V, Weiland P, Plitzko PA, Thiery J, Czech L, Willmund F, Bedrunka P, Bange G. Structural and mechanistic basis for the regulation of the chloroplast signal recognition particle by (p)ppGpp. FEBS Lett 2025; 599:1373-1385. [PMID: 39935135 DOI: 10.1002/1873-3468.70008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 01/20/2025] [Accepted: 01/24/2025] [Indexed: 02/13/2025]
Abstract
The alarmones (p)ppGpp play a critical role in chloroplasts by acting as signalling molecules that regulate gene expression, protein synthesis and chloroplast (cp) development, particularly in response to stress and nutrient availability. However, the underlying molecular mechanisms are still poorly understood. Here, we show that (p)ppGpp binds to the GTPase-containing NG domains of the chloroplast signal recognition particle (SRP) and its receptor, preventing their GTP-dependent association through a competitive mechanism. The structure of (cp)FtsY bound to ppGpp reveals that the alarmone employs the same binding mode as its GDP counterpart and hinders chloroplast SRP:FtsY complex formation via its pyrophosphate moiety. Consequently, (p)ppGpp also inhibits the mutual stimulation of the two GTPases present in the (cp)SRP54:FtsY complex. Taken together, our findings provide the first description of how the alarmones (p)ppGpp may regulate the SRP-dependent protein trafficking pathway in plants.
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Affiliation(s)
- Victor Zegarra
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Germany
| | - Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
- Center for Tumor Biology and Immunology, Department of Medicine, Philipps-University Marburg, Germany
| | - Pauline Anka Plitzko
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Germany
| | - Julia Thiery
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
| | - Felix Willmund
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
- Department of Biology, Philipps-University Marburg, Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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3
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Maciąg-Dorszyńska M, Olszewski P, Karczewska M, Boss L. Toxin-antitoxin genes are differentially expressed in Escherichia coli relA and spoT mutans cultured under nitrogen, fatty acid, or carbon starvation conditions. Front Microbiol 2025; 15:1528825. [PMID: 39895937 PMCID: PMC11783221 DOI: 10.3389/fmicb.2024.1528825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 12/23/2024] [Indexed: 02/04/2025] Open
Abstract
Introduction The stringent response is one of the fundamental mechanisms that control and modulate bacterial adaptation to stress conditions, such as nutrient limitation. The accumulation of stringent response effectors, (p)ppGpp, causes differential expression of approximately 500 genes, including genes of bacterial endogenous toxin-antitoxin (TA) systems. However, the exact link between (p)ppGpp and toxin-antitoxin systems' activation, as well as toxin-antitoxin role in stress adaptation remains disputed. Methods In this study, we performed a complex analysis of changes (RNA-Seq) in the toxin-antitoxin operons' transcription in response to nitrogen, fatty acid, or carbon starvation, in bacteria with different abilities of (p)ppGpp accumulation. Results and discussion Although we observed that in some cases (p)ppGpp accumulation appears to be crucial for transcriptional activation of TA genes (e.g., ghoST, ryeA), our data indicates that the general pattern of chromosomally encoded TA gene expression in E. coli differs depending on the nutrient distribution in the environment, regardless of the alarmone accumulation.
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Affiliation(s)
- Monika Maciąg-Dorszyńska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Paweł Olszewski
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Monika Karczewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Lidia Boss
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
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4
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Kago G, Turnbough CL, Salazar JC, Payne SM. (p)ppGpp is required for virulence of Shigella flexneri. Infect Immun 2024; 92:e0033423. [PMID: 38099658 PMCID: PMC10790822 DOI: 10.1128/iai.00334-23] [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: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024] Open
Abstract
Infection by the enteric pathogen Shigella flexneri requires transit through the gastrointestinal tract and invasion of and replication within the cells of the host colonic epithelium. This process exposes the pathogen to a range of diverse microenvironments. Furthermore, the unique composition and physical environment of the eukaryotic cell cytosol represents a stressful environment for S. flexneri, and extensive physiological adaptations are needed for the bacterium to thrive. In this work, we show that disrupting synthesis of the stringent response alarmone (p)ppGpp in S. flexneri diminished expression of key virulence genes, including ipaA, ipaB, ipaC, and icsA, and it reduced bacterial invasion and intercellular spread. Deletion of the (p)ppGpp synthase gene relA alone had no effect on S. flexneri virulence, but disruption of both relA and the (p)ppGpp synthase/hydrolase gene spoT resulted in loss of (p)ppGpp synthesis and virulence. While the relA spoT deletion mutant was able to invade a cultured human epithelial cell monolayer, albeit at reduced levels, it was unable to maintain the infection and spread to adjacent cells, as indicated by loss of plaque formation. Complementation with spoT on a plasmid vector restored plaque formation. Thus, SpoT alone is sufficient to provide the necessary level of (p)ppGpp for virulence. These results indicate that (p)ppGpp is required for S. flexneri virulence and adaptation to the intracellular environment, adding to the repertoire of signaling pathways that affect Shigella pathogenesis.
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Affiliation(s)
- Grace Kago
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Charles L. Turnbough
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan Carlos Salazar
- Programa de Microbiología y Micología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Shelley M. Payne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, USA
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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: 11] [Impact Index Per Article: 5.5] [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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6
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Leiva LE, Zegarra V, Bange G, Ibba M. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria. Microbiol Mol Biol Rev 2023; 87:e0004422. [PMID: 36853029 PMCID: PMC10029340 DOI: 10.1128/mmbr.00044-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
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7
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Ender A, Grafl N, Kolberg T, Findeiß S, Stadler PF, Mörl M. Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes. RNA (NEW YORK, N.Y.) 2022; 28:551-567. [PMID: 35022261 PMCID: PMC8925977 DOI: 10.1261/rna.078814.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Removal of the 5'-leader region is an essential step in the maturation of tRNA molecules in all domains of life. This reaction is catalyzed by various RNase P activities, ranging from ribonucleoproteins with ribozyme activity to protein-only forms. In Escherichia coli, the efficiency of RNase P-mediated cleavage can be controlled by computationally designed riboswitch elements in a ligand-dependent way, where the 5'-leader sequence of a tRNA precursor is either sequestered in a hairpin structure or presented as a single-stranded region accessible for maturation. In the presented work, the regulatory potential of such artificial constructs is tested on different forms of eukaryotic RNase P enzymes-two protein-only RNase P enzymes (PRORP1 and PRORP2) from Arabidopsis thaliana and the ribonucleoprotein of Homo sapiens The PRORP enzymes were analyzed in vitro as well as in vivo in a bacterial RNase P complementation system. We also tested in HEK293T cells whether the riboswitches remain functional with human nuclear RNase P. While the regulatory principle of the synthetic riboswitches applies for all tested RNase P enzymes, the results also show differences in the substrate requirements of the individual enzyme versions. Hence, such designed RNase P riboswitches represent a novel tool to investigate the impact of the structural composition of the 5'-leader on substrate recognition by different types of RNase P enzymes.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Nadine Grafl
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Tim Kolberg
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, 04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
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8
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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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9
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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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Adaptive Laboratory Evolution as a Means To Generate Lactococcus lactis Strains with Improved Thermotolerance and Ability To Autolyze. Appl Environ Microbiol 2021; 87:e0103521. [PMID: 34406823 DOI: 10.1128/aem.01035-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis subsp. lactis (referred to here as L. lactis) is a model lactic acid bacterium and one of the main constituents of the mesophilic cheese starter used for producing soft or semihard cheeses. Most dairy L. lactis strains grow optimally at around 30°C and are not particularly well adapted to the elevated temperatures (37 to 39°C) to which they are often exposed during cheese production. To overcome this challenge, we used adaptive laboratory evolution (ALE) in milk, using a setup where the temperature was gradually increased over time, and isolated two evolved strains (RD01 and RD07) better able to tolerate high growth temperatures. One of these, strain RD07, was isolated after 1.5 years of evolution (400 generations) and efficiently acidified milk at 41°C, which has not been reported for industrial L. lactis strains until now. Moreover, RD07 appeared to autolyze 2 to 3 times faster than its parent strain, which is another highly desired property of dairy lactococci and rarely observed in the L. lactis subspecies used in this study. Model cheese trials indicated that RD07 could potentially accelerate cheese ripening. Transcriptomics analysis revealed the potential underlying causes responsible for the enhanced growth at high temperatures for the mutants. These included downregulation of the pleiotropic transcription factor CodY and overexpression of genes, which most likely lowered the guanidine nucleotide pool. Cheese trials at ARLA Foods using RD01 blended with the commercial Flora Danica starter culture, including a 39.5°C cooking step, revealed better acidification and flavor formation than the pure starter culture. IMPORTANCE In commercial mesophilic starter cultures, L. lactis is generally more thermotolerant than Lactococcus cremoris, whereas L. cremoris is more prone to autolysis, which is the key to flavor and aroma formation. In this study, we found that adaptation to higher thermotolerance can improve autolysis. Using whole-genome sequencing and RNA sequencing, we attempt to determine the underlying reason for the observed behavior. In terms of dairy applications, there are obvious advantages associated with using L. lactis strains with high thermotolerance, as these are less affected by curd cooking, which generally hampers the performance of the mesophilic starter. Cheese ripening, the costliest part of cheese manufacturing, can be reduced using autolytic strains. Thus, the solution presented here could simplify starter cultures, make the cheese manufacturing process more efficient, and enable novel types of harder cheese variants.
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11
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Bange G, Brodersen DE, Liuzzi A, Steinchen W. Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp. Annu Rev Microbiol 2021; 75:383-406. [PMID: 34343020 DOI: 10.1146/annurev-micro-042621-122343] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Under stressful growth conditions and nutrient starvation, bacteria adapt by synthesizing signaling molecules that profoundly reprogram cellular physiology. At the onset of this process, called the stringent response, members of the RelA/SpoT homolog (RSH) protein superfamily are activated by specific stress stimuli to produce several hyperphosphorylated forms of guanine nucleotides, commonly referred to as (p)ppGpp. Some bifunctional RSH enzymes also harbor domains that allow for degradation of (p)ppGpp by hydrolysis. (p)ppGpp synthesis or hydrolysis may further be executed by single-domain alarmone synthetases or hydrolases, respectively. The downstream effects of (p)ppGpp rely mainly on direct interaction with specific intracellular effectors, which are widely used throughout most cellular processes. The growing number of identified (p)ppGpp targets allows us to deduce both common features of and differences between gram-negative and gram-positive bacteria. In this review, we give an overview of (p)ppGpp metabolism with a focus on the functional and structural aspects of the enzymes involved and discuss recent findings on alarmone-regulated cellular effectors. 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)
- Gert Bange
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Anastasia Liuzzi
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Wieland Steinchen
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
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12
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Pausch P, Abdelshahid M, Steinchen W, Schäfer H, Gratani FL, Freibert SA, Wolz C, Turgay K, Wilson DN, Bange G. Structural Basis for Regulation of the Opposing (p)ppGpp Synthetase and Hydrolase within the Stringent Response Orchestrator Rel. Cell Rep 2021; 32:108157. [PMID: 32937119 DOI: 10.1016/j.celrep.2020.108157] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase and synthetase activity and a stress-perceiving and regulatory C-terminal domain (CTD). CTD-mediated binding of Rel to stalled ribosomes boosts (p)ppGpp synthesis. However, how the opposing activities of the NTD are controlled in the absence of stress was poorly understood. Here, we demonstrate on the RSH-type protein Rel that the critical regulative elements reside within the TGS (ThrRS, GTPase, and SpoT) subdomain of the CTD, which associates to and represses the synthetase to concomitantly allow for activation of the hydrolase. Furthermore, we show that Rel forms homodimers, which appear to control the interaction with deacylated-tRNA, but not the enzymatic activity of Rel. Collectively, our study provides a detailed molecular view into the mechanism of stringent response repression in the absence of stress.
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Affiliation(s)
- Patrick Pausch
- Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Strasse, C07, Philipps-University Marburg, 35043 Marburg, Germany
| | - Maha Abdelshahid
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Strasse, C07, Philipps-University Marburg, 35043 Marburg, Germany
| | - Heinrich Schäfer
- Leibniz University of Hannover, Institute for Microbiology & Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117 Berlin, Germany
| | - Fabio Lino Gratani
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Sven-Andreas Freibert
- Center for Synthetic Microbiology & Institute for Cytobiology and Cytopathology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Kürşad Turgay
- Leibniz University of Hannover, Institute for Microbiology & Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117 Berlin, Germany.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Gert Bange
- Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Strasse, C07, Philipps-University Marburg, 35043 Marburg, Germany.
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13
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Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Res 2021; 49:1784-1800. [PMID: 33469651 PMCID: PMC7897497 DOI: 10.1093/nar/gkaa1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022] Open
Abstract
We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Maja Etzel
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Stefan Hammer
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, Inselstr. 22, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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14
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Takada H, Roghanian M, Caballero-Montes J, Van Nerom K, Jimmy S, Kudrin P, Trebini F, Murayama R, Akanuma G, Garcia-Pino A, Hauryliuk V. Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis. Nucleic Acids Res 2021; 49:444-457. [PMID: 33330919 PMCID: PMC7797070 DOI: 10.1093/nar/gkaa1187] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
In the Gram-positive Firmicute bacterium Bacillus subtilis, amino acid starvation induces synthesis of the alarmone (p)ppGpp by the RelA/SpoT Homolog factor Rel. This bifunctional enzyme is capable of both synthesizing and hydrolysing (p)ppGpp. To detect amino acid deficiency, Rel monitors the aminoacylation status of the ribosomal A-site tRNA by directly inspecting the tRNA’s CCA end. Here we dissect the molecular mechanism of B. subtilis Rel. Off the ribosome, Rel predominantly assumes a ‘closed’ conformation with dominant (p)ppGpp hydrolysis activity. This state does not specifically select deacylated tRNA since the interaction is only moderately affected by tRNA aminoacylation. Once bound to the vacant ribosomal A-site, Rel assumes an ‘open’ conformation, which primes its TGS and Helical domains for specific recognition and stabilization of cognate deacylated tRNA on the ribosome. The tRNA locks Rel on the ribosome in a hyperactivated state that processively synthesises (p)ppGpp while the hydrolysis is suppressed. In stark contrast to non-specific tRNA interactions off the ribosome, tRNA-dependent Rel locking on the ribosome and activation of (p)ppGpp synthesis are highly specific and completely abrogated by tRNA aminoacylation. Binding pppGpp to a dedicated allosteric site located in the N-terminal catalytic domain region of the enzyme further enhances its synthetase activity.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Steffi Jimmy
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Pavel Kudrin
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Fabio Trebini
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu-Kubotamachi, Akita, 010-0874, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium.,WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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15
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Kushwaha GS, Patra A, Bhavesh NS. Structural Analysis of (p)ppGpp Reveals Its Versatile Binding Pattern for Diverse Types of Target Proteins. Front Microbiol 2020; 11:575041. [PMID: 33224117 PMCID: PMC7674647 DOI: 10.3389/fmicb.2020.575041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/06/2020] [Indexed: 11/25/2022] Open
Abstract
(p)ppGpp, highly phosphorylated guanosine, are global regulatory nucleotides that modulate several biochemical events in bacterial physiology ranging from core central dogma to various metabolic pathways. Conventionally, (p)ppGpp collectively refers to two nucleotides, ppGpp, and pppGpp in the literature. Initially, (p)ppGpp has been discovered as a transcription regulatory molecule as it binds to RNA polymerase and regulates transcriptional gene regulation. During the past decade, several other target proteins of (p)ppGpp have been discovered and as of now, more than 30 proteins have been reported to be regulated by the binding of these two signaling nucleotides. The regulation of diverse biochemical activities by (p)ppGpp requires fine-tuned molecular interactions with various classes of proteins so that it can moderate varied functions. Here we report a structural dynamics of (p)ppGpp in the unbound state using well-defined computational tools and its interactions with target proteins to understand the differential regulation by (p)ppGpp at the molecular level. We carried out replica exchange molecular dynamics simulation studies to enhance sampling of conformations during (p)ppGpp simulation. The detailed comparative analysis of torsion angle conformation of ribose sugar of unbound (p)ppGpp and bound states of (p)ppGpp was carried out. The structural dynamics shows that two linear phosphate chains provide plasticity to (p)ppGpp nucleotides for the binding to diverse proteins. Moreover, the intermolecular interactions between (p)ppGpp and target proteins were characterized through various physicochemical parameters including, hydrogen bonds, van der Waal’s interactions, aromatic stacking, and side chains of interacting residues of proteins. Surprisingly, we observed that interactions of (p)ppGpp to target protein have a consensus binding pattern for a particular functional class of enzymes. For example, the binding of (p)ppGpp to RNA polymerase is significantly different from the binding of (p)ppGpp to the proteins involved in the ribosome biogenesis pathway. Whereas, (p)ppGpp binding to enzymes involved in nucleotide metabolism facilitates the functional regulation through oligomerization. Analysis of these datasets revealed that guanine base-specific contacts are key determinants to discriminate functional class of protein. Altogether, our studies provide significant information to understand the differential interaction pattern of (p)ppGpp to its target and this information may be useful to design antibacterial compounds based on (p)ppGpp analogs.
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Affiliation(s)
- Gajraj Singh Kushwaha
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.,KIIT Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT) (Deemed to be University), Bhubaneswar, India
| | - Anupam Patra
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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16
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Ovchinnikov SV, Bikmetov D, Livenskyi A, Serebryakova M, Wilcox B, Mangano K, Shiriaev DI, Osterman IA, Sergiev PV, Borukhov S, Vazquez-Laslop N, Mankin AS, Severinov K, Dubiley S. Mechanism of translation inhibition by type II GNAT toxin AtaT2. Nucleic Acids Res 2020; 48:8617-8625. [PMID: 32597957 PMCID: PMC7470980 DOI: 10.1093/nar/gkaa551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Type II toxin–antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin–antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin–antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the AtaT2 activity induces ribosome stalling at all four glycyl codons but does not evoke a stringent response. In vitro, AtaT2 acetylates the aminoacyl moiety of isoaccepting glycyl tRNAs, thus precluding their participation in translation. Our study broadens the known target specificity of GNAT toxins beyond the earlier described isoleucine and formyl methionine tRNAs, and suggest that various GNAT toxins may have evolved to specificaly target other if not all individual aminoacyl tRNAs.
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Affiliation(s)
- Stepan V Ovchinnikov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Dmitry Bikmetov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia
| | - Alexei Livenskyi
- Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Marina Serebryakova
- Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Brendan Wilcox
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Dmitrii I Shiriaev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ilya A Osterman
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Petr V Sergiev
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Nora Vazquez-Laslop
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Waksman Institute for Microbiology, Piscataway, NJ 08854-8020, USA
| | - Svetlana Dubiley
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia
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17
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Planson AG, Sauveplane V, Dervyn E, Jules M. Bacterial growth physiology and RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194502. [PMID: 32044462 DOI: 10.1016/j.bbagrm.2020.194502] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/31/2022]
Abstract
Bacteria are sophisticated systems with high capacity and flexibility to adapt to various environmental conditions. Each prokaryote however possesses a defined metabolic network, which sets its overall metabolic capacity, and therefore the maximal growth rate that can be reached. To achieve optimal growth, bacteria adopt various molecular strategies to optimally adjust gene expression and optimize resource allocation according to the nutrient availability. The resulting physiological changes are often accompanied by changes in the growth rate, and by global regulation of gene expression. The growth-rate-dependent variation of the abundances in the cellular machineries, together with condition-specific regulatory mechanisms, affect RNA metabolism and fate and pose a challenge for rational gene expression reengineering of synthetic circuits. This article is part of a Special Issue entitled: RNA and gene control in bacteria, edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Anne-Gaëlle Planson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Etienne Dervyn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Matthieu Jules
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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18
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Sinha AK, Winther KS, Roghanian M, Gerdes K. Fatty acid starvation activates RelA by depleting lysine precursor pyruvate. Mol Microbiol 2019; 112:1339-1349. [PMID: 31400173 DOI: 10.1111/mmi.14366] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 12/22/2022]
Abstract
Bacteria undergoing nutrient starvation induce the ubiquitous stringent response, resulting in gross physiological changes that reprograms cell metabolism from fast to slow growth. The stringent response is mediated by the secondary messengers pppGpp and ppGpp collectively referred to as (p)ppGpp or 'alarmone'. In Escherichia coli, two paralogs, RelA and SpoT, synthesize (p)ppGpp. RelA is activated by amino acid starvation, whereas SpoT, which can also degrade (p)ppGpp, responds to fatty acid (FA), carbon and phosphate starvation. Here, we discover that FA starvation leads to rapid activation of RelA and reveal the underlying mechanism. We show that FA starvation leads to depletion of lysine that, in turn, leads to the accumulation of uncharged tRNALys and activation of RelA. SpoT was also activated by FA starvation but to a lower level and with a delayed kinetics. Next, we discovered that pyruvate, a precursor of lysine, is depleted by FA starvation. We also propose a mechanism that explains how FA starvation leads to pyruvate depletion. Together our results raise the possibility that RelA may be a major player under many starvation conditions previously thought to depend principally on SpoT. Interestingly, FA starvation provoked a ~100-fold increase in relA dependent ampicillin tolerance.
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Affiliation(s)
- Anurag Kumar Sinha
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Skovbo Winther
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Kenn Gerdes
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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19
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Kushwaha GS, Oyeyemi BF, Bhavesh NS. Stringent response protein as a potential target to intervene persistent bacterial infection. Biochimie 2019; 165:67-75. [PMID: 31302165 DOI: 10.1016/j.biochi.2019.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/07/2019] [Indexed: 01/25/2023]
Abstract
More than half of the world's population is infected with persistent bacterial infections, consequently, persisters are gradually becoming a major public health concern. During the persistent phase, bacterial pathogens deploy many regulatory strategies to compensate unfavorable host environmental conditions. The stringent response is one of such gene regulatory mechanisms which is stimulated by nutrient starvation. It is regulated by the synthesis of highly phosphorylated signaling nucleotides, (p)ppGpp or alarmone. (p)ppGpp is synthesized by ppGpp synthetases, and these proteins are classified as RelA/SpoT homolog (RSH) proteins. Subsequently, (p)ppGpp modulate several molecular and biochemical processes ranging from transcription to metabolism. Imperativeness of (p)ppGpp synthetases has been investigated by numerous approaches including microbiology and animal studies, thereby establishing that Rel enzyme deleted strains of pathogenic bacteria were unable to transform in persister form. In this review, we summarize recent findings to corroborate the rationality to consider (p)ppGpp synthetase as a potential target in discovering a novel class of antimicrobial agents to combat persistent infections. Moreover, inhibition studies on Mycobacterium tuberculosis (p)ppGpp synthetase shows that these inhibitors prevent dormant state transition and biofilm formation. Also, we have highlighted the structural biology of (p)ppGpp synthetases, which may provide significant information that could be used in structure-based inhibitor design.
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Affiliation(s)
- Gajraj Singh Kushwaha
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Bolaji Fatai Oyeyemi
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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