1
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Young MK, Wang JD. From dusty shelves toward the spotlight: growing evidence for Ap4A as an alarmone in maintaining RNA stability and proteostasis. Curr Opin Microbiol 2024; 81:102536. [PMID: 39216180 PMCID: PMC11390322 DOI: 10.1016/j.mib.2024.102536] [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: 07/10/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Bacteria thrive in diverse environments and must withstand various stresses. A key stress response mechanism is the reprogramming of macromolecular biosynthesis and metabolic processes through alarmones - signaling nucleotides that accumulate intracellularly in response to metabolic stress. Diadenosine tetraphosphate (Ap4A), a putative alarmone, is produced in a noncanonical reaction by universally conserved aminoacyl-tRNA synthetases. Ap4A is ubiquitous across all domains of life and accumulates during heat and oxidative stress. Despite its early discovery in 1966, Ap4A's alarmone status remained inconclusive. Recent discoveries identified Ap4A as a precursor to RNA 5' caps in Escherichia coli. Additionally, Ap4A was found to directly bind to and allosterically inhibit the purine biosynthesis enzyme inosine 5'-monophosphate dehydrogenase, regulating guanosine triphosphate levels and enabling heat resistance in Bacillus subtilis. These findings, along with previous research, strongly suggest that Ap4A plays a crucial role as an alarmone, warranting further investigation to fully elucidate its functions.
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Affiliation(s)
- Megan Km Young
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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2
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Fung DK, Trinquier AE, Wang JD. Crosstalk between (p)ppGpp and other nucleotide second messengers. Curr Opin Microbiol 2023; 76:102398. [PMID: 37866203 PMCID: PMC10842992 DOI: 10.1016/j.mib.2023.102398] [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: 08/07/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023]
Abstract
In response to environmental cues, bacteria produce intracellular nucleotide messengers to regulate a wide variety of cellular processes and physiology. Studies on individual nucleotide messengers, such as (p)ppGpp or cyclic (di)nucleotides, have established their respective regulatory themes. As research on nucleotide signaling networks expands, recent studies have begun to uncover various crosstalk mechanisms between (p)ppGpp and other nucleotide messengers, including signal conversion, allosteric regulation, and target competition. The multiple layers of crosstalk implicate that (p)ppGpp is intricately linked to different nucleotide signaling pathways. From a physiological perspective, (p)ppGpp crosstalk enables fine-tuning and feedback regulation with other nucleotide messengers to achieve optimal adaptation.
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Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aude E Trinquier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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3
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Dobrogojski J, Nguyen VH, Kowalska J, Borek S, Pietrowska-Borek M. The Plasma Membrane Purinoreceptor P2K1/DORN1 Is Essential in Stomatal Closure Evoked by Extracellular Diadenosine Tetraphosphate (Ap 4A) in Arabidopsis thaliana. Int J Mol Sci 2023; 24:16688. [PMID: 38069010 PMCID: PMC10706190 DOI: 10.3390/ijms242316688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Dinucleoside polyphosphates (NpnNs) are considered novel signalling molecules involved in the induction of plant defence mechanisms. However, NpnN signal recognition and transduction are still enigmatic. Therefore, the aim of our research was the identification of the NpnN receptor and signal transduction pathways evoked by these nucleotides. Earlier, we proved that purine and pyrimidine NpnNs differentially affect the phenylpropanoid pathway in Vitis vinifera suspension-cultured cells. Here, we report, for the first time, that both diadenosine tetraphosphate (Ap4A) and dicytidine tetraphosphate (Cp4C)-induced stomatal closure in Arabidopsis thaliana. Moreover, we showed that plasma membrane purinoreceptor P2K1/DORN1 (does not respond to nucleotide 1) is essential for Ap4A-induced stomata movements but not for Cp4C. Wild-type Col-0 and the dorn1-3 A. thaliana knockout mutant were used. Examination of the leaf epidermis dorn1-3 mutant provided evidence that P2K1/DORN1 is a part of the signal transduction pathway in stomatal closure evoked by extracellular Ap4A but not by Cp4C. Reactive oxygen species (ROS) are involved in signal transduction caused by Ap4A and Cp4C, leading to stomatal closure. Ap4A induced and Cp4C suppressed the transcriptional response in wild-type plants. Moreover, in dorn1-3 leaves, the effect of Ap4A on gene expression was impaired. The interaction between P2K1/DORN1 and Ap4A leads to changes in the transcription of signalling hubs in signal transduction pathways.
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Affiliation(s)
- Jędrzej Dobrogojski
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Van Hai Nguyen
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (V.H.N.); (J.K.)
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (V.H.N.); (J.K.)
| | - Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
| | - Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
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4
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Gupta S, Jani J, Vijayasurya, Mochi J, Tabasum S, Sabarwal A, Pappachan A. Aminoacyl-tRNA synthetase - a molecular multitasker. FASEB J 2023; 37:e23219. [PMID: 37776328 DOI: 10.1096/fj.202202024rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
Aminoacyl-tRNA synthetases (AaRSs) are valuable "housekeeping" enzymes that ensure the accurate transmission of genetic information in living cells, where they aminoacylated tRNA molecules with their cognate amino acid and provide substrates for protein biosynthesis. In addition to their translational or canonical function, they contribute to nontranslational/moonlighting functions, which are mediated by the presence of other domains on the proteins. This was supported by several reports which claim that AaRS has a significant role in gene transcription, apoptosis, translation, and RNA splicing regulation. Noncanonical/ nontranslational functions of AaRSs also include their roles in regulating angiogenesis, inflammation, cancer, and other major physio-pathological processes. Multiple AaRSs are also associated with a broad range of physiological and pathological processes; a few even serve as cytokines. Therefore, the multifunctional nature of AaRSs suggests their potential as viable therapeutic targets as well. Here, our discussion will encompass a range of noncanonical functions attributed to Aminoacyl-tRNA Synthetases (AaRSs), highlighting their links with a diverse array of human diseases.
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Affiliation(s)
- Swadha Gupta
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Vijayasurya
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Jigneshkumar Mochi
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Saba Tabasum
- Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Akash Sabarwal
- Harvard Medical School, Boston, Massachusetts, USA
- Boston Children's Hospital, Boston, Massachusetts, USA
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
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5
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van der Does C, Braun F, Ren H, Albers SV. Putative nucleotide-based second messengers in archaea. MICROLIFE 2023; 4:uqad027. [PMID: 37305433 PMCID: PMC10249747 DOI: 10.1093/femsml/uqad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/07/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.
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Affiliation(s)
- Chris van der Does
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hongcheng Ren
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
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6
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Zegarra V, Mais CN, Freitag J, Bange G. The mysterious diadenosine tetraphosphate (AP4A). MICROLIFE 2023; 4:uqad016. [PMID: 37223742 PMCID: PMC10148737 DOI: 10.1093/femsml/uqad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
Dinucleoside polyphosphates, a class of nucleotides found amongst all the Trees of Life, have been gathering a lot of attention in the past decades due to their putative role as cellular alarmones. In particular, diadenosine tetraphosphate (AP4A) has been widely studied in bacteria facing various environmental challenges and has been proposed to be important for ensuring cellular survivability through harsh conditions. Here, we discuss the current understanding of AP4A synthesis and degradation, protein targets, their molecular structure where possible, and insights into the molecular mechanisms of AP4A action and its physiological consequences. Lastly, we will briefly touch on what is known with regards to AP4A beyond the bacterial kingdom, given its increasing appearance in the eukaryotic world. Altogether, the notion that AP4A is a conserved second messenger in organisms ranging from bacteria to humans and is able to signal and modulate cellular stress regulation seems promising.
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Affiliation(s)
- Victor Zegarra
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Johannes Freitag
- Department of Biology, Philipps University Marburg, Marburg 35043, Germany
| | - Gert Bange
- Corresponding author. Karl-von-Frisch Strasse 14, 35043 Marburg, Germany. E-mail:
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7
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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: 5.0] [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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8
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Mattay J. Noncanonical metabolite RNA caps: Classification, quantification, (de)capping, and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1730. [PMID: 35675554 DOI: 10.1002/wrna.1730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The 5' cap of eukaryotic mRNA is a hallmark for cellular functions from mRNA stability to translation. However, the discovery of novel 5'-terminal RNA caps derived from cellular metabolites has challenged this long-standing singularity in both eukaryotes and prokaryotes. Reminiscent of the 7-methylguanosine (m7G) cap structure, these noncanonical caps originate from abundant coenzymes such as NAD, FAD, or CoA and from metabolites like dinucleoside polyphosphates (NpnN). As of now, the significance of noncanonical RNA caps is elusive: they differ for individual transcripts, occur in distinct types of RNA, and change in response to environmental stimuli. A thorough comparison of their prevalence, quantity, and characteristics is indispensable to define the distinct classes of metabolite-capped RNAs. This is achieved by a structured analysis of all present studies covering functional, quantitative, and sequencing data which help to uncover their biological impact. The biosynthetic strategies of noncanonical RNA capping and the elaborate decapping machinery reveal the regulation and turnover of metabolite-capped RNAs. With noncanonical capping being a universal and ancient phenomenon, organisms have developed diverging strategies to adapt metabolite-derived caps to their metabolic needs, but ultimately to establish noncanonical RNA caps as another intriguing layer of RNA regulation. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Johanna Mattay
- Institute of Biochemistry, University of Münster, Münster, Germany
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9
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Giammarinaro PI, Young MKM, Steinchen W, Mais CN, Hochberg G, Yang J, Stevenson DM, Amador-Noguez D, Paulus A, Wang JD, Bange G. Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilis. Nat Microbiol 2022; 7:1442-1452. [PMID: 35953658 PMCID: PMC10439310 DOI: 10.1038/s41564-022-01193-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Diadenosine tetraphosphate (Ap4A) is a putative second messenger molecule that is conserved from bacteria to humans. Nevertheless, its physiological role and the underlying molecular mechanisms are poorly characterized. We investigated the molecular mechanism by which Ap4A regulates inosine-5'-monophosphate dehydrogenase (IMPDH, a key branching point enzyme for the biosynthesis of adenosine or guanosine nucleotides) in Bacillus subtilis. We solved the crystal structure of BsIMPDH bound to Ap4A at a resolution of 2.45 Å to show that Ap4A binds to the interface between two IMPDH subunits, acting as the glue that switches active IMPDH tetramers into less active octamers. Guided by these insights, we engineered mutant strains of B. subtilis that bypass Ap4A-dependent IMPDH regulation without perturbing intracellular Ap4A pools themselves. We used metabolomics, which suggests that these mutants have a dysregulated purine, and in particular GTP, metabolome and phenotypic analysis, which shows increased sensitivity of B. subtilis IMPDH mutant strains to heat compared with wild-type strains. Our study identifies a central role for IMPDH in remodelling metabolism and heat resistance, and provides evidence that Ap4A can function as an alarmone.
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Affiliation(s)
- Pietro I Giammarinaro
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Megan K M Young
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Wieland Steinchen
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Georg Hochberg
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Anja Paulus
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gert Bange
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany.
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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10
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Doamekpor SK, Sharma S, Kiledjian M, Tong L. Recent insights into noncanonical 5' capping and decapping of RNA. J Biol Chem 2022; 298:102171. [PMID: 35750211 PMCID: PMC9283932 DOI: 10.1016/j.jbc.2022.102171] [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: 04/26/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022] Open
Abstract
The 5' N7-methylguanosine cap is a critical modification for mRNAs and many other RNAs in eukaryotic cells. Recent studies have uncovered an RNA 5' capping quality surveillance mechanism, with DXO/Rai1 decapping enzymes removing incomplete caps and enabling the degradation of the RNAs, in a process we also refer to as "no-cap decay." It has also been discovered recently that RNAs in eukaryotes, bacteria, and archaea can have noncanonical caps (NCCs), which are mostly derived from metabolites and cofactors such as NAD, FAD, dephospho-CoA, UDP-glucose, UDP-N-acetylglucosamine, and dinucleotide polyphosphates. These NCCs can affect RNA stability, mitochondrial functions, and possibly mRNA translation. The DXO/Rai1 enzymes and selected Nudix (nucleotide diphosphate linked to X) hydrolases have been shown to remove NCCs from RNAs through their deNADding, deFADding, deCoAping, and related activities, permitting the degradation of the RNAs. In this review, we summarize the recent discoveries made in this exciting new area of RNA biology.
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Affiliation(s)
- Selom K. Doamekpor
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Sunny Sharma
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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11
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A distinct RNA recognition mechanism governs Np4 decapping by RppH. Proc Natl Acad Sci U S A 2022; 119:2117318119. [PMID: 35131855 PMCID: PMC8833179 DOI: 10.1073/pnas.2117318119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2021] [Indexed: 01/15/2023] Open
Abstract
Dinucleoside tetraphosphate alarmones function in bacteria as precursors to 5′-terminal nucleoside tetraphosphate (Np4) caps, becoming incorporated at high levels into RNA during stress and thereby influencing transcript lifetimes. However, little is known about how these noncanonical caps are removed as a prelude to RNA degradation. Here, we report that the RNA pyrophosphohydrolase RppH assumes a leading role in decapping those transcripts under conditions of disulfide stress and that it recognizes Np4-capped 5′ ends by an unexpected mechanism, generating a triphosphorylated RNA intermediate that must undergo further deprotection by RppH to trigger degradation. These findings help to explain the uneven distribution of Np4 caps on bacterial transcripts and have important implications for how gene expression is reprogrammed in response to stress. Dinucleoside tetraphosphates, often described as alarmones because their cellular concentration increases in response to stress, have recently been shown to function in bacteria as precursors to nucleoside tetraphosphate (Np4) RNA caps. Removal of this cap is critical for initiating 5′ end-dependent degradation of those RNAs, potentially affecting bacterial adaptability to stress; however, the predominant Np4 decapping enzyme in proteobacteria, ApaH, is inactivated by the very conditions of disulfide stress that enable Np4-capped RNAs to accumulate to high levels. Here, we show that, in Escherichia coli cells experiencing such stress, the RNA pyrophosphohydrolase RppH assumes a leading role in decapping those transcripts, preferring them as substrates over their triphosphorylated and diphosphorylated counterparts. Unexpectedly, this enzyme recognizes Np4-capped 5′ ends by a mechanism distinct from the one it uses to recognize other 5′ termini, resulting in a one-nucleotide shift in substrate specificity. The unique manner in which capped substrates of this kind bind to the active site of RppH positions the δ-phosphate, rather than the β-phosphate, for hydrolytic attack, generating triphosphorylated RNA as the primary product of decapping. Consequently, a second RppH-catalyzed deprotection step is required to produce the monophosphorylated 5′ terminus needed to stimulate rapid RNA decay. The unconventional manner in which RppH recognizes Np4-capped 5′ ends and its differential impact on the rates at which such termini are deprotected as a prelude to RNA degradation could have major consequences for reprogramming gene expression during disulfide stress.
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12
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Krüger L, Albrecht CJ, Schammann HK, Stumpf FM, Niedermeier ML, Yuan Y, Stuber K, Wimmer J, Stengel F, Scheffner M, Marx A. Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate. Nat Commun 2021; 12:5808. [PMID: 34608152 PMCID: PMC8490401 DOI: 10.1038/s41467-021-26075-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/10/2021] [Indexed: 01/14/2023] Open
Abstract
The nucleotides diadenosine triphosphate (Ap3A) and diadenosine tetraphosphate (Ap4A) are formed in prokaryotic and eukaryotic cells. Since their concentrations increase significantly upon cellular stress, they are considered to be alarmones triggering stress adaptive processes. However, their cellular roles remain elusive. To elucidate the proteome-wide interactome of Ap3A and Ap4A and thereby gain insights into their cellular roles, we herein report the development of photoaffinity-labeling probes and their employment in chemical proteomics. We demonstrate that the identified ApnA interactors are involved in many fundamental cellular processes including carboxylic acid and nucleotide metabolism, gene expression, various regulatory processes and cellular response mechanisms and only around half of them are known nucleotide interactors. Our results highlight common functions of these ApnAs across the domains of life, but also identify those that are different for Ap3A or Ap4A. This study provides a rich source for further functional studies of these nucleotides and depicts useful tools for characterization of their regulatory mechanisms in cells. Diadenosine polyphosphates (ApAs) are involved in cellular stress signaling but only a few molecular targets have been characterized so far. Here, the authors develop ApnA-based photoaffinity-labeling probes and use them to identify Ap3A and Ap4A binding proteins in human cell lysates.
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Affiliation(s)
- Lena Krüger
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Christoph J Albrecht
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Florian M Stumpf
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie L Niedermeier
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yizhi Yuan
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Katrin Stuber
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Josua Wimmer
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Florian Stengel
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.
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13
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Antoine L, Bahena-Ceron R, Devi Bunwaree H, Gobry M, Loegler V, Romby P, Marzi S. RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence. Genes (Basel) 2021; 12:1125. [PMID: 34440299 PMCID: PMC8394870 DOI: 10.3390/genes12081125] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.
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Affiliation(s)
| | | | | | | | | | | | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000 Strasbourg, France; (L.A.); (R.B.-C.); (H.D.B.); (M.G.); (V.L.); (P.R.)
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14
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Wiedermannová J, Julius C, Yuzenkova Y. The expanding field of non-canonical RNA capping: new enzymes and mechanisms. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201979. [PMID: 34017598 PMCID: PMC8131947 DOI: 10.1098/rsos.201979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Recent years witnessed the discovery of ubiquitous and diverse 5'-end RNA cap-like modifications in prokaryotes as well as in eukaryotes. These non-canonical caps include metabolic cofactors, such as NAD+/NADH, FAD, cell wall precursors UDP-GlcNAc, alarmones, e.g. dinucleotides polyphosphates, ADP-ribose and potentially other nucleoside derivatives. They are installed at the 5' position of RNA via template-dependent incorporation of nucleotide analogues as an initiation substrate by RNA polymerases. However, the discovery of NAD-capped processed RNAs in human cells suggests the existence of alternative post-transcriptional NC capping pathways. In this review, we compiled growing evidence for a number of these other mechanisms which produce various non-canonically capped RNAs and a growing repertoire of capping small molecules. Enzymes shown to be involved are ADP-ribose polymerases, glycohydrolases and tRNA synthetases, and may potentially include RNA 3'-phosphate cyclases, tRNA guanylyl transferases, RNA ligases and ribozymes. An emerging rich variety of capping molecules and enzymes suggests an unrecognized level of complexity of RNA metabolism.
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Affiliation(s)
| | | | - Yulia Yuzenkova
- Medical School, NUBI, Newcastle University, Newcastle upon Tyne, UK
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15
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Blaschke U, Skiebe E, Wilharm G. Novel Genes Required for Surface-Associated Motility in Acinetobacter baumannii. Curr Microbiol 2021; 78:1509-1528. [PMID: 33666749 PMCID: PMC7997844 DOI: 10.1007/s00284-021-02407-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/10/2021] [Indexed: 01/28/2023]
Abstract
Acinetobacter baumannii is an opportunistic and increasingly multi-drug resistant human pathogen rated as a critical priority one pathogen for the development of new antibiotics by the WHO in 2017. Despite the lack of flagella, A. baumannii can move along wet surfaces in two different ways: via twitching motility and surface-associated motility. While twitching motility is known to depend on type IV pili, the mechanism of surface-associated motility is poorly understood. In this study, we established a library of 30 A. baumannii ATCC® 17978™ mutants that displayed deficiency in surface-associated motility. By making use of natural competence, we also introduced these mutations into strain 29D2 to differentiate strain-specific versus species-specific effects of mutations. Mutated genes were associated with purine/pyrimidine/folate biosynthesis (e.g. purH, purF, purM, purE), alarmone/stress metabolism (e.g. Ap4A hydrolase), RNA modification/regulation (e.g. methionyl-tRNA synthetase), outer membrane proteins (e.g. ompA), and genes involved in natural competence (comEC). All tested mutants originally identified as motility-deficient in strain ATCC® 17978™ also displayed a motility-deficient phenotype in 29D2. By contrast, further comparative characterization of the mutant sets of both strains regarding pellicle biofilm formation, antibiotic resistance, and virulence in the Galleria mellonella infection model revealed numerous strain-specific mutant phenotypes. Our studies highlight the need for comparative analyses to characterize gene functions in A. baumannii and for further studies on the mechanisms underlying surface-associated motility.
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Affiliation(s)
- Ulrike Blaschke
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany.
| | - Evelyn Skiebe
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany
| | - Gottfried Wilharm
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany.
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16
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Meunier A, Cornet F, Campos M. Bacterial cell proliferation: from molecules to cells. FEMS Microbiol Rev 2021; 45:fuaa046. [PMID: 32990752 PMCID: PMC7794046 DOI: 10.1093/femsre/fuaa046] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
Bacterial cell proliferation is highly efficient, both because bacteria grow fast and multiply with a low failure rate. This efficiency is underpinned by the robustness of the cell cycle and its synchronization with cell growth and cytokinesis. Recent advances in bacterial cell biology brought about by single-cell physiology in microfluidic chambers suggest a series of simple phenomenological models at the cellular scale, coupling cell size and growth with the cell cycle. We contrast the apparent simplicity of these mechanisms based on the addition of a constant size between cell cycle events (e.g. two consecutive initiation of DNA replication or cell division) with the complexity of the underlying regulatory networks. Beyond the paradigm of cell cycle checkpoints, the coordination between the DNA and division cycles and cell growth is largely mediated by a wealth of other mechanisms. We propose our perspective on these mechanisms, through the prism of the known crosstalk between DNA replication and segregation, cell division and cell growth or size. We argue that the precise knowledge of these molecular mechanisms is critical to integrate the diverse layers of controls at different time and space scales into synthetic and verifiable models.
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Affiliation(s)
- Alix Meunier
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, IBCG, 165 rue Marianne Grunberg-Manago, 31062 Toulouse, France
| | - François Cornet
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, IBCG, 165 rue Marianne Grunberg-Manago, 31062 Toulouse, France
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, IBCG, 165 rue Marianne Grunberg-Manago, 31062 Toulouse, France
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17
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Ferguson F, McLennan AG, Urbaniak MD, Jones NJ, Copeland NA. Re-evaluation of Diadenosine Tetraphosphate (Ap 4A) From a Stress Metabolite to Bona Fide Secondary Messenger. Front Mol Biosci 2020; 7:606807. [PMID: 33282915 PMCID: PMC7705103 DOI: 10.3389/fmolb.2020.606807] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/19/2020] [Indexed: 01/14/2023] Open
Abstract
Cellular homeostasis requires adaption to environmental stress. In response to various environmental and genotoxic stresses, all cells produce dinucleoside polyphosphates (NpnNs), the best studied of which is diadenosine tetraphosphate (Ap4A). Despite intensive investigation, the precise biological roles of these molecules have remained elusive. However, recent studies have elucidated distinct and specific signaling mechanisms for these nucleotides in prokaryotes and eukaryotes. This review summarizes these key discoveries and describes the mechanisms of Ap4A and Ap4N synthesis, the mediators of the cellular responses to increased intracellular levels of these molecules and the hydrolytic mechanisms required to maintain low levels in the absence of stress. The intracellular responses to dinucleotide accumulation are evaluated in the context of the "friend" and "foe" scenarios. The "friend (or alarmone) hypothesis" suggests that ApnN act as bona fide secondary messengers mediating responses to stress. In contrast, the "foe" hypothesis proposes that ApnN and other NpnN are produced by non-canonical enzymatic synthesis as a result of physiological and environmental stress in critically damaged cells but do not actively regulate mitigating signaling pathways. In addition, we will discuss potential target proteins, and critically assess new evidence supporting roles for ApnN in the regulation of gene expression, immune responses, DNA replication and DNA repair. The recent advances in the field have generated great interest as they have for the first time revealed some of the molecular mechanisms that mediate cellular responses to ApnN. Finally, areas for future research are discussed with possible but unproven roles for intracellular ApnN to encourage further research into the signaling networks that are regulated by these nucleotides.
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Affiliation(s)
- Freya Ferguson
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom.,Materials Science Institute, Lancaster University, Lancaster, United Kingdom
| | - Alexander G McLennan
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael D Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Nigel J Jones
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nikki A Copeland
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom.,Materials Science Institute, Lancaster University, Lancaster, United Kingdom
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18
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Vargas-Blanco DA, Shell SS. Regulation of mRNA Stability During Bacterial Stress Responses. Front Microbiol 2020; 11:2111. [PMID: 33013770 PMCID: PMC7509114 DOI: 10.3389/fmicb.2020.02111] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5' ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.
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Affiliation(s)
- Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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19
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Fung DK, Yang J, Stevenson DM, Amador-Noguez D, Wang JD. Small Alarmone Synthetase SasA Expression Leads to Concomitant Accumulation of pGpp, ppApp, and AppppA in Bacillus subtilis. Front Microbiol 2020; 11:2083. [PMID: 32983059 PMCID: PMC7492591 DOI: 10.3389/fmicb.2020.02083] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
(p)ppGpp is a highly conserved bacterial alarmone which regulates many aspects of cellular physiology and metabolism. In Gram-positive bacteria such as B. subtilis, cellular (p)ppGpp level is determined by the bifunctional (p)ppGpp synthetase/hydrolase RelA and two small alarmone synthetases (SASs) YjbM (SasB) and YwaC (SasA). However, it is less clear whether these enzymes are also involved in regulation of alarmones outside of (p)ppGpp. Here we developed an improved LC-MS-based method to detect a broad spectrum of metabolites and alarmones from bacterial cultures with high efficiency. By characterizing the metabolomic signatures of SasA expressing B. subtilis, we identified strong accumulation of the (p)ppGpp analog pGpp, as well as accumulation of ppApp and AppppA. The induced accumulation of these alarmones is abolished in the catalytically dead sasA mutant, suggesting that it is a consequence of SasA synthetase activity. In addition, we also identified depletion of specific purine nucleotides and their precursors including IMP precursors FGAR, SAICAR and AICAR (ZMP), as well as GTP and GDP. Furthermore, we also revealed depletion of multiple pyrimidine precursors such as orotate and orotidine 5′-phosphate. Taken together, our work shows that induction of a single (p)ppGpp synthetase can cause concomitant accumulation and potential regulatory interplay of multiple alarmones.
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Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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20
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Trinquier A, Durand S, Braun F, Condon C. Regulation of RNA processing and degradation in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194505. [PMID: 32061882 DOI: 10.1016/j.bbagrm.2020.194505] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/13/2020] [Accepted: 02/11/2020] [Indexed: 12/22/2022]
Abstract
Messenger RNA processing and decay is a key mechanism to control gene expression at the post-transcriptional level in response to ever-changing environmental conditions. In this review chapter, we discuss the main ribonucleases involved in these processes in bacteria, with a particular but non-exclusive emphasis on the two best-studied paradigms of Gram-negative and Gram-positive bacteria, E. coli and B. subtilis, respectively. We provide examples of how the activity and specificity of these enzymes can be modulated at the protein level, by co-factor binding and by post-translational modifications, and how they can be influenced by specific properties of their mRNA substrates, such as 5' protective 'caps', nucleotide modifications, secondary structures and translation. 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)
- Aude Trinquier
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sylvain Durand
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Frédérique Braun
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Ciarán Condon
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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21
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Np 4A alarmones function in bacteria as precursors to RNA caps. Proc Natl Acad Sci U S A 2020; 117:3560-3567. [PMID: 32019889 DOI: 10.1073/pnas.1914229117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stresses that increase the cellular concentration of dinucleoside tetraphosphates (Np4Ns) have recently been shown to impact RNA degradation by inducing nucleoside tetraphosphate (Np4) capping of bacterial transcripts. However, neither the mechanism by which such caps are acquired nor the function of Np4Ns in bacteria is known. Here we report that promoter sequence changes upstream of the site of transcription initiation similarly affect both the efficiency with which Escherichia coli RNA polymerase incorporates dinucleoside polyphosphates at the 5' end of nascent transcripts in vitro and the percentage of transcripts that are Np4-capped in E. coli, clear evidence for Np4 cap acquisition by Np4N incorporation during transcription initiation in bacterial cells. E. coli RNA polymerase initiates transcription more efficiently with Np4As than with ATP, particularly when the coding strand nucleotide that immediately precedes the initiation site is a purine. Together, these findings indicate that Np4Ns function in bacteria as precursors to Np4 caps and that RNA polymerase has evolved a predilection for synthesizing capped RNA whenever such precursors are abundant.
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22
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Pietrowska-Borek M, Dobrogojski J, Sobieszczuk-Nowicka E, Borek S. New Insight into Plant Signaling: Extracellular ATP and Uncommon Nucleotides. Cells 2020; 9:E345. [PMID: 32024306 PMCID: PMC7072326 DOI: 10.3390/cells9020345] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
New players in plant signaling are described in detail in this review: extracellular ATP (eATP) and uncommon nucleotides such as dinucleoside polyphosphates (NpnN's), adenosine 5'-phosphoramidate (NH2-pA), and extracellular NAD+ and NADP+ (eNAD(P)+). Recent molecular, physiological, and biochemical evidence implicating concurrently the signaling role of eATP, NpnN's, and NH2-pA in plant biology and the mechanistic events in which they are involved are discussed. Numerous studies have shown that they are often universal signaling messengers, which trigger a signaling cascade in similar reactions and processes among different kingdoms. We also present here, not described elsewhere, a working model of the NpnN' and NH2-pA signaling network in a plant cell where these nucleotides trigger induction of the phenylpropanoid and the isochorismic acid pathways yielding metabolites protecting the plant against various types of stresses. Through these signals, the plant responds to environmental stimuli by intensifying the production of various compounds, such as anthocyanins, lignin, stilbenes, and salicylic acid. Still, more research needs to be performed to identify signaling networks that involve uncommon nucleotides, followed by omic experiments to define network elements and processes that are controlled by these signals.
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Affiliation(s)
- Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Jędrzej Dobrogojski
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (E.S.-N.); (S.B.)
| | - Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (E.S.-N.); (S.B.)
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23
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Clark DL, Velleman SG, Bernier M, McCormick J, Blakeslee JJ. Research Note: The effect of selection for 16-week body weight on turkey serum metabolome. Poult Sci 2020; 99:517-525. [PMID: 32416838 PMCID: PMC7587827 DOI: 10.3382/ps/pez493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/06/2019] [Indexed: 11/24/2022] Open
Abstract
The phenotype of modern commercial turkeys is substantially different than that of unselected, heritage turkey lines. These phenotypic changes have arisen from alterations in the genome/transcriptome, as well as the influence of many external factors on growth performance including nutrition, environment, and management. To investigate the phenotypic changes resulting from genetic selection for increased body weight, The Ohio State University maintains 2 unique genetic turkey lines: the randombred control (RBC2) line, which is comprised of genetics from 1960 era commercial turkeys and has been maintained without conscious selection for any trait; and the F line, which was originally selected from the RBC2 line and has been selected for increased 16 wk body weight for over 50 generations. This study used broad-spectrum mass-spectrometry profiling techniques to identify and quantify differences in the metabolome of the serum of F and RBC2 turkey lines. Serum samples from both F and RBC2 turkeys were subject to quantitative time of flight liquid chromatography tandem mass spectrometry analyses. Principle component analyses showed distinct populations of metabolites in the F vs. RBC2 serum, suggesting that increased body weight is associated with the accumulation of several metabolites. Comparing the spectral features to online databases resulted in the selection of 104 features with potentially identifiable chemical structures. Of these 104 features, 25 were found at higher levels in the serum of the RBC2 line turkeys, while 79 were found at a greater abundance in the F line turkeys. A more detailed analysis of these 104 features allowed for the putative identification of 49 compounds, which were clustered into 6 functional groups: 1) energy metabolism; 2) vitamins; 3) hormones and signaling molecules; 4) lipid derivatives, fatty acid metabolites, and membrane components; 5) amino acid/protein metabolism; and 6) microbial metabolites. Further validation and experimentation is needed to confirm the identity of these metabolites and understand their biological relevance and association with selection for increased body weight.
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Affiliation(s)
- Daniel L Clark
- Ohio Agricultural Research and Development Center, Department of Animal Sciences, The Ohio State University, Wooster, OH 44691.
| | - Sandra G Velleman
- Ohio Agricultural Research and Development Center, Department of Animal Sciences, The Ohio State University, Wooster, OH 44691
| | - Matthew Bernier
- Campus Chemical Instrumentation Center (CCIC), The Ohio State University, Columbus, OH 43210
| | - Janet McCormick
- Ohio Agricultural Research and Development Center, Department of Animal Sciences, The Ohio State University, Wooster, OH 44691
| | - Joshua J Blakeslee
- Ohio Agricultural Research and Development Center, Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 44691; Ohio Agricultural Research and Development Center, OARDC Metabolite Analysis Cluster, The Ohio State University, Wooster, OH 44691
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24
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Yu J, Liu Z, Liang Y, Luo F, Zhang J, Tian C, Motzik A, Zheng M, Kang J, Zhong G, Liu C, Fang P, Guo M, Razin E, Wang J. Second messenger Ap 4A polymerizes target protein HINT1 to transduce signals in FcεRI-activated mast cells. Nat Commun 2019; 10:4664. [PMID: 31604935 PMCID: PMC6789022 DOI: 10.1038/s41467-019-12710-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/25/2019] [Indexed: 02/01/2023] Open
Abstract
Signal transduction systems enable organisms to monitor their external environments and accordingly adjust the cellular processes. In mast cells, the second messenger Ap4A binds to the histidine triad nucleotide-binding protein 1 (HINT1), disrupts its interaction with the microphthalmia-associated transcription factor (MITF), and eventually activates the transcription of genes downstream of MITF in response to immunostimulation. How the HINT1 protein recognizes and is regulated by Ap4A remain unclear. Here, using eight crystal structures, biochemical experiments, negative stain electron microscopy, and cellular experiments, we report that Ap4A specifically polymerizes HINT1 in solution and in activated rat basophilic leukemia cells. The polymerization interface overlaps with the area on HINT1 for MITF interaction, suggesting a possible competitive mechanism to release MITF for transcriptional activation. The mechanism depends precisely on the length of the phosphodiester linkage of Ap4A. These results highlight a direct polymerization signaling mechanism by the second messenger.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zaizhou Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yuanyuan Liang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Feng Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Jie Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Cuiping Tian
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Alex Motzik
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, 91120, Israel
| | - Mengmeng Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Guisheng Zhong
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Min Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Kangma BioTech, Co., Ltd, 1131 Cailun Road, Shanghai, 201203, China
| | - Ehud Razin
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, 91120, Israel.
- NUS-HUJ-CREATE Cellular and Molecular Mechanisms of Inflammation Program, Department of Microbiology and Immunology, National University of Singapore, Singapore, 117597, Singapore.
| | - Jing Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
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25
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Shan L, Fan W, Wang W, Tang W, Yang Z, Wang Z, Liu Y, Shen Z, Dai Y, Cheng S, Jacobson O, Zhai K, Hu J, Ma Y, Kiesewetter DO, Gao G, Chen X. Organosilica-Based Hollow Mesoporous Bilirubin Nanoparticles for Antioxidation-Activated Self-Protection and Tumor-Specific Deoxygenation-Driven Synergistic Therapy. ACS NANO 2019; 13:8903-8916. [PMID: 31374171 DOI: 10.1021/acsnano.9b02477] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A major concern about glucose oxidase (GOx)-mediated cancer starvation therapy is its ability to induce serious oxidative damage to normal tissues through the massive production of H2O2 byproducts in the oxygen-involved glucose decomposition reaction, which may be addressed by using a H2O2 scavenger, known as an antioxidation agent. Surprisingly, H2O2 removal accelerates the aerobic glycometabolism of tumors by activating the H2O2-dependent "redox signaling" pathway of cancer cells. Simultaneous oxygen depletion further aggravates tumor hypoxia to increase the toxicity of a bioreductive prodrug, such as tirapazamine (TPZ), thereby improving the effectiveness of cancer starvation therapy and bioreductive chemotherapy. Herein, a "nitrogen-protected silica template" method is proposed to design a nanoantioxidant called an organosilica-based hollow mesoporous bilirubin nanoparticle (HMBRN), which can act as an excellent nanocarrier to codeliver GOx and TPZ. In addition to efficient removal of H2O2 for self-protection of normal tissues via antioxidation, GOx/TPZ-coloaded HMBRN can also rapidly deplete intratumoral glucose/oxygen to promote a synergistic starvation-enhanced bioreductive chemotherapeutic effect for the substantial suppression of solid tumor growth. Distinct from the simple combination of two treatments, this study introduces antioxidation-activated self-protection nanotechnology for the significant improvement of tumor-specific deoxygenation-driven synergistic treatment efficacy without additional external energy input, thus realizing the renaissance of precise endogenous cancer therapy with negligible side effects.
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Affiliation(s)
- Lingling Shan
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering , Suzhou University , Suzhou 234000 , China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Wenpei Fan
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Weiwei Wang
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering , Suzhou University , Suzhou 234000 , China
| | - Wei Tang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Zhen Yang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Zhantong Wang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Yijing Liu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Zheyu Shen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Yunlu Dai
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Siyuan Cheng
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Orit Jacobson
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Kefeng Zhai
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering , Suzhou University , Suzhou 234000 , China
| | - Junkai Hu
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Ying Ma
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Dale O Kiesewetter
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
| | - Guizhen Gao
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering , Suzhou University , Suzhou 234000 , China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States
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26
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Luciano DJ, Levenson-Palmer R, Belasco JG. Stresses that Raise Np 4A Levels Induce Protective Nucleoside Tetraphosphate Capping of Bacterial RNA. Mol Cell 2019; 75:957-966.e8. [PMID: 31178354 DOI: 10.1016/j.molcel.2019.05.031] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022]
Abstract
Present in all realms of life, dinucleoside tetraphosphates (Np4Ns) are generally considered signaling molecules. However, only a single pathway for Np4N signaling has been delineated in eukaryotes, and no receptor that mediates the influence of Np4Ns has ever been identified in bacteria. Here we show that, under disulfide stress conditions that elevate cellular Np4N concentrations, diverse Escherichia coli mRNAs and sRNAs acquire a cognate Np4 cap. Purified E. coli RNA polymerase and lysyl-tRNA synthetase are both capable of adding such 5' caps. Cap removal by either of two pyrophosphatases, ApaH or RppH, triggers rapid RNA degradation in E. coli. ApaH, the predominant decapping enzyme, functions as both a sensor and an effector of disulfide stress, which inactivates it. These findings suggest that the physiological changes attributed to elevated Np4N concentrations in bacteria may result from widespread Np4 capping, leading to altered RNA stability and consequent changes in gene expression.
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Affiliation(s)
- Daniel J Luciano
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Rose Levenson-Palmer
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA.
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Alarmone Ap4A is elevated by aminoglycoside antibiotics and enhances their bactericidal activity. Proc Natl Acad Sci U S A 2019; 116:9578-9585. [PMID: 31004054 PMCID: PMC6511005 DOI: 10.1073/pnas.1822026116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This paper demonstrates that aminoglycoside antibiotics induce the production of the Ap4A in bacteria. Increased intracellular Ap4A, in turn, promotes bacterial cell killing by this class of antibiotics, which correlated well with elevated damage to the bacterial membrane upon aminoglycoside treatment. These findings reveal a striking connection between aminoglycoside killing and the Ap4A production particularly under conditions of oxidative stress. Importantly, the results of this study suggest that targeting Ap4A degradation or inducing its hypersynthesis during therapy with aminoglycosides might help solve the well-known toxicity issue associated with this class of antibiotics by reducing the level of drug needed for effective treatment. Second messenger molecules play important roles in the responses to various stimuli that can determine a cell's fate under stress conditions. Here, we report that lethal concentrations of aminoglycoside antibiotics result in the production of a dinucleotide alarmone metabolite–diadenosine tetraphosphate (Ap4A), which promotes bacterial cell killing by this class of antibiotics. We show that the treatment of Escherichia coli with lethal concentrations of kanamycin (Kan) dramatically increases the production of Ap4A. This elevation of Ap4A is dependent on the production of a hydroxyl radical and involves the induction of the Ap4A synthetase lysyl-tRNA synthetase (LysU). Ectopic alteration of intracellular Ap4A concentration via the elimination of the Ap4A phosphatase diadenosine tetraphosphatase (ApaH) and the overexpression of LysU causes over a 5,000-fold increase in bacterial killing by aminoglycosides. This increased susceptibility to aminoglycosides correlates with bacterial membrane disruption. Our findings provide a role for the alarmone Ap4A and suggest that blocking Ap4A degradation or increasing its synthesis might constitute an approach to enhance aminoglycoside killing potency by broadening their therapeutic index and thereby allowing lower nontoxic dosages of these antibiotics to be used in the treatment of multidrug-resistant infections.
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Hernández-Morales R, Becerra A, Lazcano A. Alarmones as Vestiges of a Bygone RNA World. J Mol Evol 2019; 87:37-51. [PMID: 30604017 DOI: 10.1007/s00239-018-9883-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/15/2018] [Indexed: 12/11/2022]
Abstract
All known alarmones are ribonucleotides or ribonucleotide derivatives that are synthesized when cells are under stress conditions, triggering a stringent response that affects major processes such as replication, gene expression, and metabolism. The ample phylogenetic distribution of alarmones (e.g., cAMP, Ap(n)A, cGMP, AICAR, and ZTP) suggests that they are very ancient molecules that may have already been present in cellular systems prior to the evolutionary divergence of the Archaea, Bacteria, and Eukarya domains. Their chemical structure, wide biological distribution, and functional role in highly conserved cellular processes support the possibility that these modified nucleotides are molecular fossils of an epoch in the evolution of chemical signaling and metabolite sensing during which RNA molecules played a much more conspicuous role in biological catalysis and genetic information.
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Affiliation(s)
- Ricardo Hernández-Morales
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Mexico City, Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Mexico City, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Mexico City, Mexico. .,Miembro de El Colegio Nacional, Donceles 104, Centro Histórico, 06000, Mexico City, Mexico.
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29
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Catalase Expression in Azospirillum brasilense Sp7 Is Regulated by a Network Consisting of OxyR and Two RpoH Paralogs and Including an RpoE1→RpoH5 Regulatory Cascade. Appl Environ Microbiol 2018; 84:AEM.01787-18. [PMID: 30217849 DOI: 10.1128/aem.01787-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/01/2018] [Indexed: 12/19/2022] Open
Abstract
The genome of Azospirillum brasilense encodes five RpoH sigma factors: two OxyR transcription regulators and three catalases. The aim of this study was to understand the role they play during oxidative stress and their regulatory interconnection. Out of the 5 paralogs of RpoH present in A. brasilense, inactivation of only rpoH1 renders A. brasilense heat sensitive. While transcript levels of rpoH1 were elevated by heat stress, those of rpoH3 and rpoH5 were upregulated by H2O2 Catalase activity was upregulated in A. brasilense and its rpoH::km mutants in response to H2O2 except in the case of the rpoH5::km mutant, suggesting a role for RpoH5 in regulating inducible catalase. Transcriptional analysis of the katN, katAI, and katAII genes revealed that the expression of katN and katAII was severely compromised in the rpoH3::km and rpoH5::km mutants, respectively. Regulation of katN and katAII by RpoH3 and RpoH5, respectively, was further confirmed in an Escherichia coli two-plasmid system. Regulation of katAII by OxyR2 was evident by a drastic reduction in growth, KatAII activity, and katAII::lacZ expression in an oxyR2::km mutant. This study reports the involvement of RpoH3 and RpoH5 sigma factors in regulating oxidative stress response in alphaproteobacteria. We also report the regulation of an inducible catalase by a cascade of alternative sigma factors and an OxyR. Out of the three catalases in A. brasilense, those corresponding to katN and katAII are regulated by RpoH3 and RpoH5, respectively. The expression of katAII is regulated by a cascade of RpoE1→RpoH5 and OxyR2.IMPORTANCE In silico analysis of the A. brasilense genome showed the presence of multiple paralogs of genes involved in oxidative stress response, which included 2 OxyR transcription regulators and 3 catalases. So far, Deinococcus radiodurans and Vibrio cholerae are known to harbor two paralogs of OxyR, and Sinorhizobium meliloti harbors three catalases. We do not yet know how the expression of multiple catalases is regulated in any bacterium. Here we show the role of multiple RpoH sigma factors and OxyR in regulating the expression of multiple catalases in A. brasilense Sp7. Our work gives a glimpse of systems biology of A. brasilense used for responding to oxidative stress.
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30
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Mukkayyan N, Sharan D, Ajitkumar P. A Symmetric Molecule Produced by Mycobacteria Generates Cell-Length Asymmetry during Cell-Division and Thereby Cell-Length Heterogeneity. ACS Chem Biol 2018; 13:1447-1454. [PMID: 29757604 DOI: 10.1021/acschembio.8b00080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Diadenosine polyphosphates, Ap(2-7)A, which contain two adenosines in a 5',5' linkage through phosphodiester bonds involving 2-7 phosphates, regulate diverse cellular functions in all organisms, from bacteria to humans, under normal and stress conditions. We had earlier reported consistent occurrence of asymmetric constriction during division (ACD) in 20-30% of dividing mycobacterial cells in culture, irrespective of different growth media, implying exogenous action of some factor of mycobacterial origin. Consistent with this premise, concentrated culture supernatant (CCS), but not the equivalent volume-wise concentrated unused medium, dramatically enhanced the ACD proportion to 70-90%. Mass spectrometry and biochemical analyses of the bioactive fraction from CCS revealed the ACD-effecting factor to be Ap6A. Synthetic Ap6A showed a mass spectrometry profile, biochemical characteristics, and bioactivity identical to native Ap6A in the CCS. Thus, the present work reveals a novel role for Ap6A in generating cell-length asymmetry during mycobacterial cell-division and thereby cell-length heterogeneity in the population.
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Affiliation(s)
- Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
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31
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Götz KH, Hacker SM, Mayer D, Dürig JN, Stenger S, Marx A. Inhibitors of the Diadenosine Tetraphosphate Phosphorylase Rv2613c of Mycobacterium tuberculosis. ACS Chem Biol 2017; 12:2682-2689. [PMID: 28892605 DOI: 10.1021/acschembio.7b00653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intracellular concentration of diadenosine tetraphospate (Ap4A) increases upon exposure to stress conditions. Despite being discovered over 50 years ago, the cellular functions of Ap4A are still enigmatic. If and how the varied Ap4A is a signal and involved in the signaling pathways leading to an appropriate cellular response remain to be discovered. Because the turnover of Ap4A by Ap4A cleaving enzymes is rapid, small molecule inhibitors for these enzymes would provide tools for the more detailed study of the role of Ap4A. Here, we describe the development of a high-throughput screening assay based on a fluorogenic Ap4A substrate for the identification and optimization of small molecule inhibitors for Ap4A cleaving enzymes. As proof-of-concept we screened a library of over 42 000 compounds toward their inhibitory activity against the Ap4A phosphorylase (Rv2613c) of Mycobacterium tuberculosis (Mtb). A sulfanylacrylonitril derivative with an IC50 of 260 ± 50 nM in vitro was identified. Multiple derivatives were synthesized to further optimize their properties with respect to their in vitro IC50 values and their cytotoxicity against human cells (HeLa). In addition, we selected two hits to study their antimycobacterial activity against virulent Mtb to show that they might be candidates for further development of antimycobacterial agents against multidrug-resistant Mtb.
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Affiliation(s)
- Kathrin H. Götz
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Stephan M. Hacker
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Daniel Mayer
- Institute
for Medical Microbiology and Hygiene, University Hospital of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
| | - Jan-Niklas Dürig
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Steffen Stenger
- Institute
for Medical Microbiology and Hygiene, University Hospital of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
| | - Andreas Marx
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
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32
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Arif SM, Varshney U, Vijayan M. Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1. J Struct Biol 2017; 199:165-176. [PMID: 28705712 DOI: 10.1016/j.jsb.2017.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 10/19/2022]
Abstract
Diadenosine polyphosphates (ApnA, n=2-6), particularly Ap4A, are involved in several important physiological processes. The substantial sequence identity of the Nudix hydrolase domain (domain 1) of Mycobacterium smegmatis MutT1 (MsMutT1) with a known Ap4A hydrolase suggested that MsMutT1 could also hydrolyse diadenosine polyphosphates. Biochemical experiments yielded results in conformity with this suggestion, with Ap4A as the best among the substrates. ATP is a product in all experiments; small amounts of ADP were also observed in the experiments involving Ap4A and Ap6A. Hydrolysis was inhibited by fluoride ions in all cases. The mechanism of action and its inhibition in relation to ApnA were explored through the X-ray analysis of the crystals of the MsMutT1 complexes with Ap5A; Ap5A and MnCl2; Ap4A; ATP; and ATP.NaF.MgCl2. The aggregation pattern of molecules in the first four crystals is similar to that found in a majority of MsMutT1-NTP crystals. Substrate molecules occupy the primary binding site and ATP occupies a site at an intermolecular interface, in the first two. ATP occupies both the sites in the third and fourth crystal. The protein-ligand interactions observed in these crystal structures lead to an explanation of the molecular mechanism of hydrolysis of ApnA by MsMutT1. The fifth crystal exhibits a new packing arrangement. The structure of the complex provides an explanation for the fluoride inhibition of the activity of the enzyme. It would thus appear that MutT1 has a major role involving the hydrolysis of diadenosine polyphosphates, which could be elucidated at the molecular level.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - U Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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33
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Despotović D, Brandis A, Savidor A, Levin Y, Fumagalli L, Tawfik DS. Diadenosine tetraphosphate (Ap4A) - an E. coli alarmone or a damage metabolite? FEBS J 2017; 284:2194-2215. [PMID: 28516732 DOI: 10.1111/febs.14113] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 05/15/2017] [Indexed: 12/21/2022]
Abstract
Under stress, metabolism is changing: specific up- or down-regulation of proteins and metabolites occurs as well as side effects. Distinguishing specific stress-signaling metabolites (alarmones) from side products (damage metabolites) is not trivial. One example is diadenosine tetraphosphate (Ap4A) - a side product of aminoacyl-tRNA synthetases found in all domains of life. The earliest observations suggested that Ap4A serves as an alarmone for heat stress in Escherichia coli. However, despite 50 years of research, the signaling mechanisms associated with Ap4A remain unknown. We defined a set of criteria for distinguishing alarmones from damage metabolites to systematically classify Ap4A. In a nutshell, no indications for a signaling cascade that is triggered by Ap4A were found; rather, we found that Ap4A is efficiently removed in a constitutive, nonregulated manner. Several fold perturbations in Ap4A concentrations have no effect, yet accumulation at very high levels is toxic due to disturbance of zinc homeostasis, and also because Ap4A's structural overlap with ATP can result in spurious binding and inactivation of ATP-binding proteins. Overall, Ap4A met all criteria for a damage metabolite. While we do not exclude any role in signaling, our results indicate that the damage metabolite option should be considered as the null hypothesis when examining Ap4A and other metabolites whose levels change upon stress.
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Affiliation(s)
- Dragana Despotović
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Laura Fumagalli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Italy
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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Kimura Y, Tanaka C, Sasaki K, Sasaki M. High concentrations of intracellular Ap4A and/or Ap5A in developing Myxococcus xanthus cells inhibit sporulation. MICROBIOLOGY-SGM 2017; 163:86-93. [PMID: 27902428 DOI: 10.1099/mic.0.000403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Diadenosine polyphosphates (ApnA) are thought to act as signalling molecules regulating stress responses and biofilm formation in prokaryotes. However, ApnA function in Myxococcus xanthus remains unknown. Here, we investigated the role of ApnA in M. xanthus, using the wild-type and ApnA hydrolase (apaH) mutant strains exposed to various stress conditions. In both wild-type and apaH mutant cells cultured on starvation medium (CF agar), the levels of intracellular diadenosine tetraphosphate (Ap4A) and pentaphosphate (Ap5A) increased several fold during the first 16 h of development and decreased gradually thereafter. The levels of Ap4A and Ap5A in the apaH mutant were about 5- and 11-fold higher than those in the wild-type strain at 16 h, respectively. ApnA hydrolase activity of the wild-type strain increased 1.5-fold during the first 8 h of development, and it then gradually decreased. The apaH mutant formed spores 1-2 days after the wild-type strain did, and the yield of viable spores was 5.5 % of that in the wild-type strain 5 days after inoculation onto CF agar. These results suggest the possibility that high intracellular levels of Ap4A and/or Ap5A may inhibit M. xanthus sporulation at the early stage of development and that the bacteria reduce intracellular Ap4A and Ap5A accumulation through ApnA hydrolase activity.
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Affiliation(s)
- Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Chihiro Tanaka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Katsuho Sasaki
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Masashi Sasaki
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
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35
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Oka M, Takegawa K, Kimura Y. Lysyl-tRNA synthetase from Myxococcus xanthus catalyzes the formation of diadenosine penta- and hexaphosphates from adenosine tetraphosphate. Arch Biochem Biophys 2016; 604:152-8. [PMID: 27392456 DOI: 10.1016/j.abb.2016.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/23/2016] [Accepted: 07/02/2016] [Indexed: 11/18/2022]
Abstract
Myxococcus xanthus lysyl-tRNA synthetase (LysS) produces diadenosine tetraphosphate (Ap4A) from ATP in the presence of Mn(2+); in the present study, it also generated Ap4 from ATP and triphosphate. When ATP and Ap4 were incubated with LysS and pyrophosphatase, first Ap4A, Ap5A, and ADP, and then Ap5, Ap6A, and Ap3A were generated. The results suggest that in the first step, LysS can form lysyl-AMP and lysyl-ADP intermediates from Ap4 and release triphosphate and diphosphate, respectively, whereas in the second step, it can produce Ap5 from lysyl-ADP with triphosphate, and Ap6A from lysyl-ADP with Ap4. In addition, in the presence of Ap4 and pyrophosphatase, but absence of ATP, LysS also generates diadenosine oligophosphates (ApnAs: n = 3-6). These results indicate that LysS has the ability to catalyze the formation of various ApnAs from Ap4 in the presence of pyrophosphatase. Furthermore, the formation of Ap4A by LysS was inhibited by tRNA(Lys) in the presence of 1 mM ATP. To the best of our knowledge, this is the first report of Ap5A and Ap6A synthesis by lysyl-tRNA synthetase.
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Affiliation(s)
- Manami Oka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Kyusyu University, Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan.
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36
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Boylston JA, Brenner C. A knockdown with smoke model reveals FHIT as a repressor of Heme oxygenase 1. Cell Cycle 2015; 13:2913-30. [PMID: 25486479 DOI: 10.4161/15384101.2014.946858] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fragile histidine triad (FHIT) gene deletions are among the earliest and most frequent events in carcinogenesis, particularly in carcinogen-exposed tissues. Though FHIT has been established as an authentic tumor suppressor, the mechanism underlying tumor suppression remains opaque. Most experiments designed to clarify FHIT function have analyzed the consequence of re-expressing FHIT in FHIT-negative cells. However, carcinogenesis occurs in cells that transition from FHIT-positive to FHIT-negative. To better understand cancer development, we induced FHIT loss in human bronchial epithelial cells with RNA interference. Because FHIT is a demonstrated target of carcinogens in cigarette smoke, we combined FHIT silencing with cigarette smoke extract (CSE) exposure and measured gene expression consequences by RNA microarray. The data indicate that FHIT loss enhances the expression of a set of oxidative stress response genes after exposure to CSE, including the cytoprotective enzyme heme oxygenase 1 (HMOX1) at the RNA and protein levels. Data are consistent with a mechanism in which Fhit protein is required for accumulation of the transcriptional repressor of HMOX1, Bach1 protein. We posit that by allowing superinduction of oxidative stress response genes, loss of FHIT creates a survival advantage that promotes carcinogenesis.
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Key Words
- ARE, antioxidant response element
- ApppA, diadenosine triphosphate
- BACH1
- BACH1, BTB and CNC homology 1 gene
- BMC, bone marrow cell
- CPT, camptothecin
- CSE, cigarette smoke extract
- Cigarette smoke
- FHIT
- FHIT, fragile histidine triad gene
- HMOX1
- HMOX1, heme oxygenase 1 gene
- MMC, mitomycin C
- NRF2
- Nrf2, nuclear factor erythroid derived 2-like 2 protein
- Oxidative Stress
- RNAi, RNA interference
- ROS, reactive oxygen species
- qRT-PCR, quantitative real time PCR
- siRNA, short interfering RNA
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Affiliation(s)
- Jennifer A Boylston
- a Department of Biochemistry and Program in Molecular and Cellular Biology; Carver College of Medicine ; University of Iowa ; Iowa City , IA USA
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Marriott AS, Copeland NA, Cunningham R, Wilkinson MC, McLennan AG, Jones NJ. Diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) is synthesized in response to DNA damage and inhibits the initiation of DNA replication. DNA Repair (Amst) 2015. [PMID: 26204256 DOI: 10.1016/j.dnarep.2015.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The level of intracellular diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) increases several fold in mammalian cells treated with non-cytotoxic doses of interstrand DNA-crosslinking agents such as mitomycin C. It is also increased in cells lacking DNA repair proteins including XRCC1, PARP1, APTX and FANCG, while >50-fold increases (up to around 25 μM) are achieved in repair mutants exposed to mitomycin C. Part of this induced Ap4A is converted into novel derivatives, identified as mono- and di-ADP-ribosylated Ap4A. Gene knockout experiments suggest that DNA ligase III is primarily responsible for the synthesis of damage-induced Ap4A and that PARP1 and PARP2 can both catalyze its ADP-ribosylation. Degradative proteins such as aprataxin may also contribute to the increase. Using a cell-free replication system, Ap4A was found to cause a marked inhibition of the initiation of DNA replicons, while elongation was unaffected. Maximum inhibition of 70-80% was achieved with 20 μM Ap4A. Ap3A, Ap5A, Gp4G and ADP-ribosylated Ap4A were without effect. It is proposed that Ap4A acts as an important inducible ligand in the DNA damage response to prevent the replication of damaged DNA.
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Affiliation(s)
- Andrew S Marriott
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Nikki A Copeland
- Division of Biomedical and Life Sciences, University of Lancaster, Lancaster LA1 4YG, UK
| | - Ryan Cunningham
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark C Wilkinson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Alexander G McLennan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Nigel J Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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Enzymatic characterization of a class II lysyl-tRNA synthetase, LysS, from Myxococcus xanthus. Arch Biochem Biophys 2015; 579:33-9. [PMID: 26048731 DOI: 10.1016/j.abb.2015.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/21/2022]
Abstract
Lysyl-tRNA synthetases efficiently produce diadenosine tetraphosphate (Ap4A) from lysyl-AMP with ATP in the absence of tRNA. We characterized recombinant class II lysyl-tRNA synthetase (LysS) from Myxococcus xanthus and found that it is monomeric and requires Mn(2+) for the synthesis of Ap4A. Surprisingly, Zn(2+) inhibited enzyme activity in the presence of Mn(2+). When incubated with ATP, Mn(2+), lysine, and inorganic pyrophosphatase, LysS first produced Ap4A and ADP, then converted Ap4A to diadenosine triphosphate (Ap3A), and finally converted Ap3A to ADP, the end product of the reaction. Recombinant LysS retained Ap4A synthase activity without lysine addition. Additionally, when incubated with Ap4A (minus pyrophosphatase), LysS converted Ap4A mainly ATP and AMP, or ADP in the presence or absence of lysine, respectively. These results demonstrate that M. xanthus LysS has different enzymatic properties from class II lysyl-tRNA synthetases previously reported.
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Patzak A, Carlström M, Sendeski MM, Lai EY, Liu ZZ, Sällström J, Flöge J, Heintz B, Jankowski J, Jankowski V. Diadenosine pentaphosphate modulates glomerular arteriolar tone and glomerular filtration rate. Acta Physiol (Oxf) 2015; 213:285-93. [PMID: 25394939 DOI: 10.1111/apha.12425] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/28/2014] [Accepted: 11/09/2014] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Mechanisms and participating substances involved in the reduction of glomerular filtration (GFR) in contrast-induced acute kidney injury (CI-AKI) are still matter of debate. We hypothesized that diadenosine polyphosphates are released by the action of contrast media on tubular cells and may act on glomerular arterioles and reduce GFR. METHODS Freshly isolated rat tubules were treated with the contrast medium iodixanol (47 mg iodine per mL) at 37 °C for 20 min. The content of Apn A (n = 3-6) in the supernatant of treated tubules and in the plasma of healthy persons and patients with AKI was analysed using reversed-phase chromatography, affinity chromatography and mass spectrometry. GFR was obtained in conscious mice by inulin clearance. Concentration response curves for Apn A (n = 3-6, 10(-12) -10(-5) mol L(-1) ) were measured in isolated perfused glomerular arterioles. RESULTS Iodixanol treatment of tubules significantly increased the concentration of Apn A (n = 3-5) in the supernatant. Ap6 A was below the detection limit. AKI patient shows higher concentrations of Apn A compared to healthy. Application of Ap5 A significantly reduced the GFR in conscious mice. Ap5 A reduced afferent arteriolar diameters, but did not influence efferent arterioles. The constrictor effect on afferent arterioles was strong immediately after application, but weakened with time. Then, non-selective P2 inhibitor suramin blocked the Ap5 A-induced constriction. CONCLUSION The data suggest that Ap5 A plays a role in the pathophysiology of CI-AKI. We show a contrast media-induced release of Ap5 A from tubules, which might increase afferent arteriolar resistance and reduce the GFR.
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Affiliation(s)
- A. Patzak
- Institute of Vegetative Physiology; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - M. Carlström
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
| | - M. M. Sendeski
- Institute of Vegetative Physiology; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - E. Y. Lai
- Department of Physiology; Zhejiang University School of Medicine; Hangzhou China
| | - Z. Z. Liu
- Institute of Vegetative Physiology; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - J. Sällström
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
| | - J. Flöge
- Division of Nephrology and Clinical Immunology; RWTH University of Aachen; Aachen Germany
| | - B. Heintz
- Division of Nephrology and Clinical Immunology; RWTH University of Aachen; Aachen Germany
| | - J. Jankowski
- Institute of Molecular Cardiovascular Research; RWTH University of Aachen; Aachen Germany
| | - V. Jankowski
- Institute of Molecular Cardiovascular Research; RWTH University of Aachen; Aachen Germany
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Monrás JP, Collao B, Molina-Quiroz RC, Pradenas GA, Saona LA, Durán-Toro V, Ordenes-Aenishanslins N, Venegas FA, Loyola DE, Bravo D, Calderón PF, Calderón IL, Vásquez CC, Chasteen TG, Lopez DA, Pérez-Donoso JM. Microarray analysis of the Escherichia coli response to CdTe-GSH Quantum Dots: understanding the bacterial toxicity of semiconductor nanoparticles. BMC Genomics 2014; 15:1099. [PMID: 25496196 PMCID: PMC4300170 DOI: 10.1186/1471-2164-15-1099] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/26/2014] [Indexed: 02/06/2023] Open
Abstract
Background Most semiconductor nanoparticles used in biomedical applications are made of heavy metals and involve synthetic methods that require organic solvents and high temperatures. This issue makes the development of water-soluble nanoparticles with lower toxicity a major topic of interest. In a previous work our group described a biomimetic method for the aqueous synthesis of CdTe-GSH Quantum Dots (QDs) using biomolecules present in cells as reducing and stabilizing agents. This protocol produces nanoparticles with good fluorescent properties and less toxicity than those synthesized by regular chemical methods. Nevertheless, biomimetic CdTe-GSH nanoparticles still display some toxicity, so it is important to know in detail the effects of these semiconductor nanoparticles on cells, their levels of toxicity and the strategies that cells develop to overcome it. Results In this work, the response of E. coli exposed to different sized-CdTe-GSH QDs synthesized by a biomimetic protocol was evaluated through transcriptomic, biochemical, microbiological and genetic approaches. It was determined that: i) red QDs (5 nm) display higher toxicity than green (3 nm), ii) QDs mainly induce expression of genes involved with Cd+2 stress (zntA and znuA) and tellurium does not contribute significantly to QDs-mediated toxicity since cells incorporate low levels of Te, iii) red QDs also induce genes related to oxidative stress response and membrane proteins, iv) Cd2+ release is higher in red QDs, and v) QDs render the cells more sensitive to polymyxin B. Conclusion Based on the results obtained in this work, a general model of CdTe-GSH QDs toxicity in E. coli is proposed. Results indicate that bacterial toxicity of QDs is mainly associated with cadmium release, oxidative stress and loss of membrane integrity. The higher toxicity of red QDs is most probably due to higher cadmium content and release from the nanoparticle as compared to green QDs. Moreover, QDs-treated cells become more sensitive to polymyxin B making these biomimetic QDs candidates for adjuvant therapies against bacterial infections. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1099) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - José M Pérez-Donoso
- Bionanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Universidad Andres Bello, Santiago, Chile.
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Lee CR, Kim M, Park YH, Kim YR, Seok YJ. RppH-dependent pyrophosphohydrolysis of mRNAs is regulated by direct interaction with DapF in Escherichia coli. Nucleic Acids Res 2014; 42:12746-57. [PMID: 25313159 PMCID: PMC4227774 DOI: 10.1093/nar/gku926] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Similar to decapping of eukaryotic mRNAs, the RppH-catalyzed conversion of 5′-terminal triphosphate to monophosphate has recently been identified as the rate-limiting step for the degradation of a subset of mRNAs in Escherichia coli. However, the regulation of RppH pyrophosphohydrolase activity is not well understood. Because the overexpression of RppH alone does not affect the decay rate of most target mRNAs, the existence of a mechanism regulating its activity has been suggested. In this study, we identified DapF, a diaminopimelate (DAP) epimerase catalyzing the stereoinversion of L,L-DAP to meso-DAP, as a regulator of RppH. DapF showed a high affinity interaction with RppH and increased its RNA pyrophosphohydrolase activity. The simultaneous overexpression of both DapF and RppH increased the decay rates of RppH target RNAs by about a factor of two. Together, our data suggest that the cellular level of DapF is a critical factor regulating the RppH-catalyzed pyrophosphate removal and the subsequent degradation of target mRNAs.
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Affiliation(s)
- Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
| | - Miri Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Young-Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Yeon-Ran Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Yeong-Jae Seok
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-742, Korea
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42
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Alva-Pérez J, Arellano-Reynoso B, Hernández-Castro R, Suárez-Güemes F. The invA gene of Brucella melitensis is involved in intracellular invasion and is required to establish infection in a mouse model. Virulence 2014; 5:563-74. [PMID: 24667775 DOI: 10.4161/viru.28589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Some of the mechanisms underlying the invasion and intracellular survival of B. melitensis are still unknown, including the role of a subfamily of NUDIX enzymes, which have been described in other bacterial species as invasins and are present in Brucella spp. We have generated a mutation in the coding gene of one of these proteins, the invA gene (BMEI0215) of B. melitensis strain 133, to understand its role in virulence. HeLa cell invasion results showed that mutant strain survival was decreased 5-fold compared with that of the parental strain at 2 h pi (P<0.001). In a goat macrophage infection assay, mutant strain replication was 8-fold less than in the parental strain at 24 h pi (P<0.001); yet, at 48 h pi, no significant differences in intracellular replication were observed. Additionally, colocalization of the invA mutant with calregulin was significantly lower at 24 h pi compared with that of the parental strain. Furthermore, the mutant strain exhibited a low level of colocalization with cathepsin D, which was similar to the parental strain colocalization at 24 h pi. In vivo infection results demonstrated that spleen colonization was significantly lower with the mutant than with the parental strain. The immune response, measured in terms of antibody switching and IFN-γ transcription, was similar for Rev1 and infection with the mutant, although it was lower than the immune response elicited by the parental strain. Consequently, these results indicate that the invA gene is important during invasion but not for intracellular replication. Additionally, mutation of the invA gene results in in vivo attenuation.
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Affiliation(s)
- Jorge Alva-Pérez
- Department of Microbiology and Immunology; College of Veterinary Medicine; National Autonomous University of Mexico; Mexico DF, Mexico
| | - Beatriz Arellano-Reynoso
- Department of Microbiology and Immunology; College of Veterinary Medicine; National Autonomous University of Mexico; Mexico DF, Mexico
| | - Rigoberto Hernández-Castro
- Department of Ecology of Pathogen Agents; General Hospital "Dr. Manuel Gea González"; National Health Department; Mexico DF, Mexico
| | - Francisco Suárez-Güemes
- Department of Microbiology and Immunology; College of Veterinary Medicine; National Autonomous University of Mexico; Mexico DF, Mexico
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Álvarez-Ordóñez A, Begley M, Clifford T, Deasy T, Collins B, Hill C. Transposon mutagenesis reveals genes involved in osmotic stress and drying in Cronobacter sakazakii. Food Res Int 2014. [DOI: 10.1016/j.foodres.2013.10.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kokotas H, Kroupis C, Chiras D, Grigoriadou M, Lamnissou K, Petersen MB, Kitsos G. Biomarkers in primary open angle glaucoma. Clin Chem Lab Med 2013; 50:2107-19. [PMID: 22745021 DOI: 10.1515/cclm-2012-0048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/20/2012] [Indexed: 11/15/2022]
Abstract
Glaucoma, a leading cause of blindness worldwide, is currently defined as a disturbance of the structural or functional integrity of the optic nerve that causes characteristic atrophic changes in the optic nerve, which may lead to specific visual field defects over time. This disturbance usually can be arrested or diminished by adequate lowering of intraocular pressure (IOP). Glaucoma can be divided roughly into two main categories, ‘ open angle ’ and ‘ closed angle ’ glaucoma.Open angle, chronic glaucoma tends to progress at a slower rate and patients may not notice loss of vision until the disease has progressed significantly. Primary open angle glaucoma(POAG) is described distinctly as a multifactorial optic neuropathy that is chronic and progressive with a characteristic acquired loss of optic nerve fibers. Such loss develops in the presence of open anterior chamber angles, characteristic visual field abnormalities, and IOP that is too high for the healthy eye. It manifests by cupping and atrophy of the optic disc, in the absence of other known causes of glaucomatous disease. Several biological markers have been implicated with the disease. The purpose of this study was to summarize the current knowledge regarding the non-genetic molecular markers which have been predicted to have an association with POAG but have not yet been validated.
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Affiliation(s)
- Haris Kokotas
- Department of Genetics, Institute of Child Health , Aghia Sophia Children's Hospital, Athens, Greece.
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45
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Guo M, Schimmel P. Essential nontranslational functions of tRNA synthetases. Nat Chem Biol 2013; 9:145-53. [PMID: 23416400 DOI: 10.1038/nchembio.1158] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/28/2012] [Indexed: 12/25/2022]
Abstract
Nontranslational functions of vertebrate aminoacyl tRNA synthetases (aaRSs), which catalyze the production of aminoacyl-tRNAs for protein synthesis, have recently been discovered. Although these new functions were thought to be 'moonlighting activities', many are as critical for cellular homeostasis as their activity in translation. New roles have been associated with their cytoplasmic forms as well as with nuclear and secreted extracellular forms that affect pathways for cardiovascular development and the immune response and mTOR, IFN-γ and p53 signaling. The associations of aaRSs with autoimmune disorders, cancers and neurological disorders further highlight nontranslational functions of these proteins. New architecture elaborations of the aaRSs accompany their functional expansion in higher organisms and have been associated with the nontranslational functions for several aaRSs. Although a general understanding of how these functions developed is limited, the expropriation of aaRSs for essential nontranslational functions may have been initiated by co-opting the amino acid-binding site for another purpose.
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Affiliation(s)
- Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA
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Structures of yeast Apa2 reveal catalytic insights into a canonical AP₄A phosphorylase of the histidine triad superfamily. J Mol Biol 2013; 425:2687-98. [PMID: 23628156 DOI: 10.1016/j.jmb.2013.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 11/23/2022]
Abstract
The homeostasis of intracellular diadenosine 5',5″'-P(1),P(4)-tetraphosphate (Ap4A) in the yeast Saccharomyces cerevisiae is maintained by two 60% sequence-identical paralogs of Ap4A phosphorylases (Apa1 and Apa2). Enzymatic assays show that, compared to Apa1, Apa2 has a relatively higher phosphorylase activity towards Ap3A (5',5″'-P(1),P(3)-tetraphosphate), Ap4A, and Ap5A (5',5″'-P(1),P(5)-tetraphosphate), and Ap4A is the favorable substrate for both enzymes. To decipher the catalytic insights, we determined the crystal structures of Apa2 in the apo-, AMP-, and Ap4A-complexed forms at 2.30, 2.80, and 2.70Å resolution, respectively. Apa2 is an α/β protein with a core domain of a twisted eight-stranded antiparallel β-sheet flanked by several α-helices, similar to the galactose-1-phosphate uridylyltransferase (GalT) members of the histidine triad (HIT) superfamily. However, a unique auxiliary domain enables an individual Apa2 monomer to possess an intact substrate-binding cleft, which is distinct from previously reported dimeric GalT proteins. This cleft is perfectly complementary to the favorable substrate Ap4A, the AMP and ATP moieties of which are perpendicular to each other, leaving the α-phosphate group exposed at the sharp turn against the catalytic residue His161. Structural comparisons combined with site-directed mutagenesis and activity assays enable us to define the key residues for catalysis. Furthermore, multiple-sequence alignment reveals that Apa2 and homologs represent canonical Ap4A phosphorylases, which could be grouped as a unique branch in the GalT family.
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Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C. The proteomic response to mutants of the Escherichia coli RNA degradosome. MOLECULAR BIOSYSTEMS 2013; 9:750-7. [PMID: 23403814 PMCID: PMC3709862 DOI: 10.1039/c3mb25513a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The Escherichia coli RNA degradosome recognizes and degrades RNA through the coordination of four main protein components, the endonuclease RNase E, the exonuclease PNPase, the RhlB helicase and the metabolic enzyme enolase. To help our understanding of the functions of the RNA degradosome, we quantified expression changes of >2300 proteins using mass spectrometry based shotgun proteomics in E. coli strains deficient in rhlB, eno, pnp (which displays temperature sensitive growth), or rne(1-602) which encodes a C-terminal truncation mutant of RNase E and is deficient in degradosome assembly. Global protein expression changes are most similar between the pnp and rhlB mutants, confirming the functional relationship between the genes. We observe down-regulation of protein chaperones including GroEL and DnaK (which associate with the degradosome), a decrease in translation related proteins in Δpnp, ΔrhlB and rne(1-602) cells, and a significant increase in the abundance of aminoacyl-tRNA synthetases. Analysis of the observed proteomic changes points to a shared motif, CGCTGG, that may be associated with RNA degradosome targets. Further, our data provide information on the expression modulation of known degradosome-associated proteins, such as DeaD and RNase G, as well as other RNA helicases and RNases - suggesting or confirming functional complementarity in some cases. Taken together, our results emphasize the role of the RNA degradosome in the modulation of the bacterial proteome and provide the first large-scale proteomic description of the response to perturbation of this major pathway of RNA degradation.
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Affiliation(s)
- Li Zhou
- University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX
- Department of Molecular Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ang B Zhang
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York, NY
| | - Rong Wang
- University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX
- National Heart Lung and Blood Institute, NIH, NIH, Bethesda, Maryland, USA
| | - Edward M Marcotte
- University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX
| | - Christine Vogel
- University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York, NY
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Fraga H, Fontes R. Enzymatic synthesis of mono and dinucleoside polyphosphates. Biochim Biophys Acta Gen Subj 2011; 1810:1195-204. [PMID: 21978831 DOI: 10.1016/j.bbagen.2011.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 09/09/2011] [Accepted: 09/19/2011] [Indexed: 01/08/2023]
Abstract
BACKGROUND Mono and dinucleoside polyphosphates (p(n)Ns and Np(n)Ns) exist in living organisms and induce diverse biological effects through interaction with intracellular and cytoplasmic membrane proteins. The source of these compounds is associated with secondary activities of a diverse group of enzymes. SCOPE OF REVIEW Here we discuss the mechanisms that can promote their synthesis at a molecular level. Although all the enzymes described in this review are able to catalyse the in vitro synthesis of Np(n)Ns (and/or p(n)N), it is not clear which ones are responsible for their in vivo accumulation. MAJOR CONCLUSIONS Despite the large amount of knowledge already available, important questions remain to be answered and a more complete understanding of p(n)Ns and Np(n)Ns synthesis mechanisms is required. With the possible exception of (GTP:GTP guanylyltransferase of Artemia), all enzymes able to catalyse the synthesis of p(n)Ns and Np(n)Ns are unspecific and the factors that can promote their synthesis relative to the canonical enzyme activities are unclear. GENERAL SIGNIFICANCE The fact that p(n)Ns and Np(n)Ns syntheses are promiscuous activities of housekeeping enzymes does not reduce its physiological or pathological importance. Here we resume the current knowledge regarding their enzymatic synthesis and point the open questions on the field.
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Affiliation(s)
- Hugo Fraga
- Department of Biochemistry, Universitat Autonoma de Barcelona, Spain
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Borbély G, Surányi G, Kós P. Stress responses of cyanobacteria and the pleiotropic effects of light deprivation. FEMS Microbiol Ecol 2011. [DOI: 10.1111/j.1574-6941.1990.tb01680.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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50
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Di-adenosine tetraphosphate (Ap4A) metabolism impacts biofilm formation by Pseudomonas fluorescens via modulation of c-di-GMP-dependent pathways. J Bacteriol 2010; 192:3011-23. [PMID: 20154123 DOI: 10.1128/jb.01571-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dinucleoside tetraphosphates are common constituents of the cell and are thought to play diverse biological roles in organisms ranging from bacteria to humans. In this study we characterized two independent mechanisms by which di-adenosine tetraphosphate (Ap4A) metabolism impacts biofilm formation by Pseudomonas fluorescens. Null mutations in apaH, the gene encoding nucleoside tetraphosphate hydrolase, resulted in a marked increase in the cellular level of Ap4A. Concomitant with this increase, Pho regulon activation in low-inorganic-phosphate (P(i)) conditions was severely compromised. As a consequence, an apaH mutant was not sensitive to Pho regulon-dependent inhibition of biofilm formation. In addition, we characterized a Pho-independent role for Ap4A metabolism in regulation of biofilm formation. In P(i)-replete conditions Ap4A metabolism was found to impact expression and localization of LapA, the major adhesin regulating surface commitment by P. fluorescens. Increases in the level of c-di-GMP in the apaH mutant provided a likely explanation for increased localization of LapA to the outer membrane in response to elevated Ap4A concentrations. Increased levels of c-di-GMP in the apaH mutant were associated with increases in the level of GTP, suggesting that elevated levels of Ap4A may promote de novo purine biosynthesis. In support of this suggestion, supplementation with adenine could partially suppress the biofilm and c-di-GMP phenotypes of the apaH mutant. We hypothesize that changes in the substrate (GTP) concentration mediated by altered flux through nucleotide biosynthetic pathways may be a significant point of regulation for c-di-GMP biosynthesis and regulation of biofilm formation.
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