1
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Bao Y, Cao X, Landick R. RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations. Nucleic Acids Res 2024; 52:4556-4574. [PMID: 38554114 PMCID: PMC11077087 DOI: 10.1093/nar/gkae209] [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: 09/14/2023] [Revised: 03/03/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024] Open
Abstract
Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). A surface-exposed domain inserted into the catalytic trigger loop (TL) of Escherichia coli RNAP, called SI3, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ΔSI3*). ΔSI3* increased transcription rate in vitro relative to ΔSI3, possibly explaining its viability, but retained both positive and negative effects of ΔSI3 on pausing. ΔSI3* inhibited pauses stabilized by nascent RNA structures (pause hairpins; PHs) but enhanced other pauses. Using NET-seq, we found that ΔSI3*-enhanced pauses resemble the consensus elemental pause sequence whereas sequences at ΔSI3*-suppressed pauses, which exhibited greater association with PHs, were more divergent. ΔSI3*-suppressed pauses also were associated with apparent pausing one nucleotide upstream from the consensus sequence, often generating tandem pause sites. These '-2 pauses' were stimulated by pyrophosphate in vitro and by addition of apyrase to degrade residual NTPs during NET-seq sample processing. We propose that some pauses are readily reversible by pyrophosphorolysis or single-nucleotide cleavage. Our results document multiple ways that SI3 modulates pausing in vivo and may explain discrepancies in consensus pause sequences in some NET-seq studies.
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Affiliation(s)
- Yu Bao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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2
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Palo MZ, Zhu J, Mishanina TV, Landick R. Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects. Biochemistry 2021; 60:3323-3336. [PMID: 34705427 DOI: 10.1021/acs.biochem.1c00528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In all domains of life, multisubunit RNA polymerases (RNAPs) catalyze both the extension of mRNA transcripts by nucleotide addition and the hydrolysis of RNA, which enables proofreading by removal of misincorporated nucleotides. A highly conserved catalytic module within RNAPs called the trigger loop (TL) functions as the key controller of these activities. The TL is proposed to act as a positional catalyst of phosphoryl transfer and transcript cleavage via electrostatic and steric contacts with substrates in its folded helical form. The function of a near-universally conserved TL histidine that contacts NTP phosphates is of particular interest. Despite its exceptional conservation, substitutions of the TL His with Gln support efficient catalysis in bacterial and yeast RNAPs. Unlike bacterial TLs, which contain a nearby Arg, the TL His is the only acid-base catalyst candidate in the eukaryotic RNAPII TL. Nonetheless, replacement of the TL His with Leu is reported to support cell growth in yeast, suggesting that even hydrogen bonding and polarity at this position may be dispensable for efficient catalysis by RNAPII. To test how a TL His-to-Leu substitution affects the enzymatic functions of RNAPII, we compared its rates of nucleotide addition, pyrophosphorolysis, and RNA hydrolysis to those of the wild-type RNAPII enzyme. The His-to-Leu substitution slightly reduced rates of phosphoryl transfer with little if any effect on intrinsic transcript cleavage. These findings indicate that the highly conserved TL His is neither an obligate acid-base catalyst nor a polar contact for NTP phosphates but instead functions as a positional catalyst mainly through steric effects.
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Affiliation(s)
- Michael Z Palo
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junqiao Zhu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tatiana V Mishanina
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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3
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Abstract
Phosphate is an essential nutrient for life and is a critical component of bone formation, a major signaling molecule, and structural component of cell walls. Phosphate is also a component of high-energy compounds (i.e., AMP, ADP, and ATP) and essential for nucleic acid helical structure (i.e., RNA and DNA). Phosphate plays a central role in the process of mineralization, normal serum levels being associated with appropriate bone mineralization, while high and low serum levels are associated with soft tissue calcification. The serum concentration of phosphate and the total body content of phosphate are highly regulated, a process that is accomplished by the coordinated effort of two families of sodium-dependent transporter proteins. The three isoforms of the SLC34 family (SLC34A1-A3) show very restricted tissue expression and regulate intestinal absorption and renal excretion of phosphate. SLC34A2 also regulates the phosphate concentration in multiple lumen fluids including milk, saliva, pancreatic fluid, and surfactant. Both isoforms of the SLC20 family exhibit ubiquitous expression (with some variation as to which one or both are expressed), are regulated by ambient phosphate, and likely serve the phosphate needs of the individual cell. These proteins exhibit similarities to phosphate transporters in nonmammalian organisms. The proteins are nonredundant as mutations in each yield unique clinical presentations. Further research is essential to understand the function, regulation, and coordination of the various phosphate transporters, both the ones described in this review and the phosphate transporters involved in intracellular transport.
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Affiliation(s)
- Nati Hernando
- University of Zurich-Irchel, Institute of Physiology, Zurich, Switzerland; Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; and Robley Rex VA Medical Center, Louisville, Kentucky
| | - Kenneth Gagnon
- University of Zurich-Irchel, Institute of Physiology, Zurich, Switzerland; Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; and Robley Rex VA Medical Center, Louisville, Kentucky
| | - Eleanor Lederer
- University of Zurich-Irchel, Institute of Physiology, Zurich, Switzerland; Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; and Robley Rex VA Medical Center, Louisville, Kentucky
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4
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Gottesman ME, Mustaev A. Change in inorganic phosphate physical state can regulate transcription. Transcription 2019; 10:187-194. [PMID: 31668122 DOI: 10.1080/21541264.2019.1682454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Inorganic phosphate (Pi), a ubiquitous metabolite, is involved in all major biochemical pathways. We demonstrate that, in vitro, MgHPO4 (the intracellular Pi form) at physiological concentrations can exist in a metastable supersaturated dissolved state or as a precipitate. We have shown that in solution, MgHPO4 strongly stimulates exonuclease nascent transcript cleavage by RNA polymerase. We report here that MgHPO4 precipitate selectively and efficiently inhibits transcription initiation in vitro. In view of the MgHPO4 solubility and in vitro sensitivity of RNA synthesis to MgHPO4 precipitate, at physiological concentrations, MgHPO4 should cause a 50-98% inhibition of cellular RNA synthesis, thus exerting a strong regulatory action. The effects of Pi on transcription in vivo will, therefore, reflect the physical state of intracellular Pi.
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Affiliation(s)
- Max E Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY, USA
| | - Arkady Mustaev
- Public Health Research Institute & Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ, USA
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5
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Gottesman ME, Mustaev A. Ribonucleoside-5'-diphosphates (NDPs) support RNA polymerase transcription, suggesting NDPs may have been substrates for primordial nucleic acid biosynthesis. J Biol Chem 2019; 294:11785-11792. [PMID: 31189650 DOI: 10.1074/jbc.ra119.009074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/21/2019] [Indexed: 01/28/2023] Open
Abstract
A better understanding of the structural basis for the preferences of RNA and DNA polymerases for nucleoside-5'-triphosphates (NTPs) could help define the catalytic mechanisms for nucleotidyl transfer during RNA and DNA synthesis and the origin of primordial nucleic acid biosynthesis. We show here that ribonucleoside-5'-diphosphates (NDPs) can be utilized as substrates by RNA polymerase (RNAP). We found that NDP incorporation is template-specific and that noncognate NDPs are not incorporated. Compared with the natural RNAP substrates, NTPs, the Km of RNAP for NDPs was increased ∼4-fold, whereas the V max was decreased ∼200-fold. These properties could be accounted for by molecular modeling of NTP/RNAP co-crystal structures. This finding suggested that the terminal phosphate residue in NTP (not present in NDP) is important for positioning the nucleotide for nucleolytic attack in the nucleotidyl transfer reaction. Strikingly, a mutational substitution of the active-center βR1106 side chain involved in NTP positioning also strongly inhibited NDP-directed synthesis, even though this residue does not contact NDP. Substitutions in the structurally analogous side chain in RB69 DNA polymerase (Arg-482) and HIV reverse transcriptase (Lys-65) were previously observed to inhibit dNDP incorporation. The unexpected involvement of these residues suggests that they affect a step in catalysis common for nucleic acid polymerases. The substrate activity of NDPs with RNAP along with those reported for DNA polymerases reinforces the hypothesis that NDPs may have been used for nucleic acid biosynthesis by primordial enzymes, whose evolution then led to the use of the more complex triphosphate derivatives.
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Affiliation(s)
- Max E Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032
| | - Arkady Mustaev
- Public Health Research Institute and Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, New Jersey 07103
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6
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Belogurov GA, Artsimovitch I. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase. J Mol Biol 2019; 431:3975-4006. [PMID: 31153902 DOI: 10.1016/j.jmb.2019.05.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
Abstract
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation.
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Affiliation(s)
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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7
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Firrincieli A, Presentato A, Favoino G, Marabottini R, Allevato E, Stazi SR, Scarascia Mugnozza G, Harfouche A, Petruccioli M, Turner RJ, Zannoni D, Cappelletti M. Identification of Resistance Genes and Response to Arsenic in Rhodococcus aetherivorans BCP1. Front Microbiol 2019; 10:888. [PMID: 31133997 PMCID: PMC6514093 DOI: 10.3389/fmicb.2019.00888] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/08/2019] [Indexed: 11/28/2022] Open
Abstract
Arsenic (As) ranks among the priority metal(loid)s that are of public health concern. In the environment, arsenic is present in different forms, organic or inorganic, featured by various toxicity levels. Bacteria have developed different strategies to deal with this toxicity involving different resistance genetic determinants. Bacterial strains of Rhodococcus genus, and more in general Actinobacteria phylum, have the ability to cope with high concentrations of toxic metalloids, although little is known on the molecular and genetic bases of these metabolic features. Here we show that Rhodococcus aetherivorans BCP1, an extremophilic actinobacterial strain able to tolerate high concentrations of organic solvents and toxic metalloids, can grow in the presence of high concentrations of As(V) (up to 240 mM) under aerobic growth conditions using glucose as sole carbon and energy source. Notably, BCP1 cells improved their growth performance as well as their capacity of reducing As(V) into As(III) when the concentration of As(V) is within 30–100 mM As(V). Genomic analysis of BCP1 compared to other actinobacterial strains revealed the presence of three gene clusters responsible for organic and inorganic arsenic resistance. In particular, two adjacent and divergently oriented ars gene clusters include three arsenate reductase genes (arsC1/2/3) involved in resistance mechanisms against As(V). A sequence similarity network (SSN) and phylogenetic analysis of these arsenate reductase genes indicated that two of them (ArsC2/3) are functionally related to thioredoxin (Trx)/thioredoxin reductase (TrxR)-dependent class and one of them (ArsC1) to the mycothiol (MSH)/mycoredoxin (Mrx)-dependent class. A targeted transcriptomic analysis performed by RT-qPCR indicated that the arsenate reductase genes as well as other genes included in the ars gene cluster (possible regulator gene, arsR, and arsenite extrusion genes, arsA, acr3, and arsD) are transcriptionally induced when BCP1 cells were exposed to As(V) supplied at two different sub-lethal concentrations. This work provides for the first time insights into the arsenic resistance mechanisms of a Rhodococcus strain, revealing some of the unique metabolic requirements for the environmental persistence of this bacterial genus and its possible use in bioremediation procedures of toxic metal contaminated sites.
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Affiliation(s)
- Andrea Firrincieli
- Department for the Innovation in Biological Systems, Agro-Food and Forestry, University of Tuscia, Viterbo, Italy
| | - Alessandro Presentato
- Department of Biotechnology, University of Verona, Verona, Italy.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Giusi Favoino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Rosita Marabottini
- Department for the Innovation in Biological Systems, Agro-Food and Forestry, University of Tuscia, Viterbo, Italy
| | - Enrica Allevato
- Department for the Innovation in Biological Systems, Agro-Food and Forestry, University of Tuscia, Viterbo, Italy
| | - Silvia Rita Stazi
- Department for the Innovation in Biological Systems, Agro-Food and Forestry, University of Tuscia, Viterbo, Italy
| | - Giuseppe Scarascia Mugnozza
- Department for the Innovation in Biological Systems, Agro-Food and Forestry, University of Tuscia, Viterbo, Italy
| | - Antoine Harfouche
- Department for the Innovation in Biological Systems, Agro-Food and Forestry, University of Tuscia, Viterbo, Italy
| | - Maurizio Petruccioli
- Department for the Innovation in Biological Systems, Agro-Food and Forestry, University of Tuscia, Viterbo, Italy
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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8
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Ka Man Tse C, Xu J, Xu L, Sheong FK, Wang S, Chow HY, Gao X, Li X, Cheung PPH, Wang D, Zhang Y, Huang X. Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate. Nat Catal 2019; 2:228-235. [PMID: 31179024 PMCID: PMC6548511 DOI: 10.1038/s41929-019-0227-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
RNA polymerase II (Pol II) utilises the same active site for polymerization and intrinsic cleavage. Pol II proofreads the nascent transcript by its intrinsic nuclease activity to maintain high transcriptional fidelity critical for cell growth and viability. The detailed catalytic mechanism of intrinsic cleavage remains unknown. Here, we combined ab initio quantum mechanics/molecular mechanics studies and biochemical cleavage assays to show that Pol II utilises downstream phosphate oxygen to activate the attacking nucleophile in hydrolysis, while the newly formed 3'-end is protonated through active-site water without a defined general acid. Experimentally, alteration of downstream phosphate oxygen either by 2'-5' sugar linkage or stereo-specific thio-substitution of phosphate oxygen drastically reduced cleavage rate. We showed by N7-modification that guanine nucleobase does not directly involve as acid-base catalyst. Our proposed mechanism provides important insights into the understanding of intrinsic transcriptional cleavage reaction, an essential step of transcriptional fidelity control.
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Affiliation(s)
- Carmen Ka Man Tse
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Jun Xu
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Liang Xu
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Chemistry, Sun Yat-Sen University, Guangzhou, China
| | - Fu Kit Sheong
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Shenglong Wang
- Department of Chemistry, New York University, New York, New York 10003 United States
| | - Hoi Yee Chow
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Xin Gao
- Computational Bioscience Research Centre (CBRC), CEMSE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Peter Pak-Hang Cheung
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Dong Wang
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003 United States
- NYU-ECNU Centre for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xuhui Huang
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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9
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Treviño S, Díaz A, Sánchez-Lara E, Sanchez-Gaytan BL, Perez-Aguilar JM, González-Vergara E. Vanadium in Biological Action: Chemical, Pharmacological Aspects, and Metabolic Implications in Diabetes Mellitus. Biol Trace Elem Res 2019; 188:68-98. [PMID: 30350272 PMCID: PMC6373340 DOI: 10.1007/s12011-018-1540-6] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Vanadium compounds have been primarily investigated as potential therapeutic agents for the treatment of various major health issues, including cancer, atherosclerosis, and diabetes. The translation of vanadium-based compounds into clinical trials and ultimately into disease treatments remains hampered by the absence of a basic pharmacological and metabolic comprehension of such compounds. In this review, we examine the development of vanadium-containing compounds in biological systems regarding the role of the physiological environment, dosage, intracellular interactions, metabolic transformations, modulation of signaling pathways, toxicology, and transport and tissue distribution as well as therapeutic implications. From our point of view, the toxicological and pharmacological aspects in animal models and humans are not understood completely, and thus, we introduced them in a physiological environment and dosage context. Different transport proteins in blood plasma and mechanistic transport determinants are discussed. Furthermore, an overview of different vanadium species and the role of physiological factors (i.e., pH, redox conditions, concentration, and so on) are considered. Mechanistic specifications about different signaling pathways are discussed, particularly the phosphatases and kinases that are modulated dynamically by vanadium compounds because until now, the focus only has been on protein tyrosine phosphatase 1B as a vanadium target. Particular emphasis is laid on the therapeutic ability of vanadium-based compounds and their role for the treatment of diabetes mellitus, specifically on that of vanadate- and polioxovanadate-containing compounds. We aim at shedding light on the prevailing gaps between primary scientific data and information from animal models and human studies.
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Affiliation(s)
- Samuel Treviño
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 14 Sur y Av. San Claudio, Col. San Manuel, C.P. 72570 Puebla, PUE Mexico
| | - Alfonso Díaz
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 14 Sur y Av. San Claudio, Col. San Manuel, C.P. 72570 Puebla, PUE Mexico
| | - Eduardo Sánchez-Lara
- Centro de Química, ICUAP, Benemérita Universidad Autónoma de Puebla, 14 Sur y Av. San Claudio, Col. San Manuel, C.P. 72570 Puebla, PUE Mexico
| | - Brenda L. Sanchez-Gaytan
- Centro de Química, ICUAP, Benemérita Universidad Autónoma de Puebla, 14 Sur y Av. San Claudio, Col. San Manuel, C.P. 72570 Puebla, PUE Mexico
| | - Jose Manuel Perez-Aguilar
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 14 Sur y Av. San Claudio, Col. San Manuel, C.P. 72570 Puebla, PUE Mexico
| | - Enrique González-Vergara
- Centro de Química, ICUAP, Benemérita Universidad Autónoma de Puebla, 14 Sur y Av. San Claudio, Col. San Manuel, C.P. 72570 Puebla, PUE Mexico
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10
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Esyunina D, Kulbachinskiy A. Interactions in the active site of Deinococcus radiodurans RNA polymerase during RNA proofreading. Biochem Biophys Res Commun 2018; 509:161-166. [PMID: 30579600 DOI: 10.1016/j.bbrc.2018.12.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022]
Abstract
Co-transcriptional RNA proofreading by RNA polymerase (RNAP) is essential for accurate mRNA synthesis and reactivation of stalled transcription complexes, which can otherwise compromise genome integrity. RNAP from the stress-resistant bacterium Deinococcus radiodurans exhibits high levels of RNA cleavage in comparison with RNAP from Escherichia coli, which allows it to remove misincorporated nucleotides with high efficiency. Here, we show that the rate of RNA cleavage by D. radiodurans RNAP depends on the structure of the (mis)matched RNA 3'-nucleotide and its contacts with the active site. These interactions likely position the reactive phosphodiester bond in the cleavage-competent conformation, thus facilitating its hydrolysis catalyzed by metal ions in the active center. The universal RNA cleavage factor GreA largely alleviates defects in RNA cleavage caused by modifications in the RNA 3'-nucleotide or in its binding pocket in RNAP, suggesting that GreA functionally substitutes for these contacts. The results demonstrate that various RNAPs rely on a conserved mechanism for RNA proofreading, which can be modulated by changes in accessory parts of the active center.
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Affiliation(s)
- Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
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