1
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Khan D, Ramachandiran I, Vasu K, China A, Khan K, Cumbo F, Halawani D, Terenzi F, Zin I, Long B, Costain G, Blaser S, Carnevale A, Gogonea V, Dutta R, Blankenberg D, Yoon G, Fox PL. Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6A site accessibility. Nat Commun 2024; 15:4284. [PMID: 38769304 DOI: 10.1038/s41467-024-48549-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is an autosomal recessive disorder characterized by defective central nervous system myelination. Exome sequencing of two siblings with severe cognitive and motor impairment and progressive hypomyelination characteristic of HLD revealed homozygosity for a missense single-nucleotide variant (SNV) in EPRS1 (c.4444 C > A; p.Pro1482Thr), encoding glutamyl-prolyl-tRNA synthetase, consistent with HLD15. Patient lymphoblastoid cell lines express markedly reduced EPRS1 protein due to dual defects in nuclear export and cytoplasmic translation of variant EPRS1 mRNA. Variant mRNA exhibits reduced METTL3 methyltransferase-mediated writing of N6-methyladenosine (m6A) and reduced reading by YTHDC1 and YTHDF1/3 required for efficient mRNA nuclear export and translation, respectively. In contrast to current models, the variant does not alter the sequence of m6A target sites, but instead reduces their accessibility for modification. The defect was rescued by antisense morpholinos predicted to expose m6A sites on target EPRS1 mRNA, or by m6A modification of the mRNA by METTL3-dCas13b, a targeted RNA methylation editor. Our bioinformatic analysis predicts widespread occurrence of SNVs associated with human health and disease that similarly alter accessibility of distal mRNA m6A sites. These results reveal a new RNA-dependent etiologic mechanism by which SNVs can influence gene expression and disease, consequently generating opportunities for personalized, RNA-based therapeutics targeting these disorders.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fabio Cumbo
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Dalia Halawani
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Isaac Zin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Briana Long
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Amanda Carnevale
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Grace Yoon
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Department of Paediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA.
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2
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Tare P, Bhowmick T, Katagi G, China A, Nagaraja V. Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS Omega 2023; 8:47510-47519. [PMID: 38144119 PMCID: PMC10733919 DOI: 10.1021/acsomega.3c04754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 12/26/2023]
Abstract
RNA polymerases (RNAPs) across the bacterial kingdom have retained a conserved structure and function. In spite of the remarkable similarity of the enzyme in different bacteria, a wide variation is found in the promoter-polymerase interaction, transcription initiation, and termination. However, the transcription elongation was considered to be a monotonic process, although the rate of elongation could vary in different bacteria. Such variations in RNAP elongation rates could be important to fine-tune the transcription, which in turn would influence cellular metabolism and growth rates. Here, we describe a quantitative study to measure the transcription rates for the RNAPs from three bacteria, namely, Mycobacterium tuberculosis, Mycobacterium smegmatis, and Escherichia coli, which exhibit different growth kinetics. The RNA synthesis rates of the RNAPs were calculated from the real-time elongation kinetic profile using surface plasmon resonance through a computational flux flow model. The computational model revealed the modular process of elongation, with different rate profiles for the three RNAPs. Notably, the transcription elongation rates of these RNAPs followed the trend in the growth rates of these bacteria.
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Affiliation(s)
- Priyanka Tare
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Tuhin Bhowmick
- Department
of Physics, Indian Institute of Science, Bangalore 560012, India
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Gurunath Katagi
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Arnab China
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
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3
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Khan D, Terenzi F, Liu G, Ghosh PK, Ye F, Nguyen K, China A, Ramachandiran I, Chakraborty S, Stefan J, Khan K, Vasu K, Dong F, Willard B, Karn J, Gack MU, Fox PL. A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon. Nat Commun 2023; 14:3385. [PMID: 37296097 PMCID: PMC10250186 DOI: 10.1038/s41467-023-39091-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, generates multiple protein-coding, subgenomic RNAs (sgRNAs) from a longer genomic RNA, all bearing identical termini with poorly understood roles in regulating viral gene expression. Insulin and interferon-gamma, two host-derived, stress-related agents, and virus spike protein, induce binding of glutamyl-prolyl-tRNA synthetase (EPRS1), within an unconventional, tetra-aminoacyl-tRNA synthetase complex, to the sgRNA 3'-end thereby enhancing sgRNA expression. We identify an EPRS1-binding sarbecoviral pan-end activating RNA (SPEAR) element in the 3'-end of viral RNAs driving agonist-induction. Translation of another co-terminal 3'-end feature, ORF10, is necessary for SPEAR-mediated induction, independent of Orf10 protein expression. The SPEAR element enhances viral programmed ribosomal frameshifting, thereby expanding its functionality. By co-opting noncanonical activities of a family of essential host proteins, the virus establishes a post-transcriptional regulon stimulating global viral RNA translation. A SPEAR-targeting strategy markedly reduces SARS-CoV-2 titer, suggesting a pan-sarbecoviral therapeutic modality.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Prabar K Ghosh
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fengchun Ye
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kien Nguyen
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Shruti Chakraborty
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jennifer Stefan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Franklin Dong
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
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4
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Vasu K, Ramachandiran I, Terenzi F, Khan D, China A, Khan K, Chechi A, Baleanu-Gogonea C, Gogonea V, Fox PL. The zinc-binding domain of mammalian prolyl-tRNA synthetase is indispensable for catalytic activity and organism viability. iScience 2021; 24:102215. [PMID: 33748704 PMCID: PMC7960942 DOI: 10.1016/j.isci.2021.102215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/26/2021] [Accepted: 02/17/2021] [Indexed: 01/10/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) participate in decoding the genome by catalyzing conjugation of amino acids to their cognate tRNAs. During evolution, biochemical and environmental conditions markedly influenced the sequence and structure of the 20 AARSs, revealing adaptations dictating canonical and orthogonal activities. Here, we investigate the function of the appended Zn2+-binding domain (ZBD) in the bifunctional AARS, glutamyl-prolyl-tRNA synthetase (GluProRS). We developed GluProRS mutant mice by CRISPR-Cas9 with a deletion of 29 C-terminal amino acids, including two of four Zn2+-coordinating cysteines. Homozygous ZBD mutant mice die before embryonic day 12.5, but heterozygous mice are healthy. ZBD disruption profoundly reduces GluProRS canonical function by dual mechanisms: it induces rapid proteasomal degradation of the protein and inhibits ProRS aminoacylation activity, likely by sub-optimal positioning of ATP in the spatially adjacent catalytic domain. Collectively, our studies reveal the ZBD as a critical determinant of ProRS activity and GluProRS stability in vitro and in vivo. Conserved zinc-binding domain (ZBD) of GluProRS is required for Pro-tRNA charging ZBD stabilizes GluProRS and positions C-terminal carboxylate in the catalytic site Embryonic lethality in mice with defective GluProRS ZBD reveals in vivo essentiality Locked nucleic acid qPCR assay for CRISPR-mediated screening of chimeric mutant mice
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Affiliation(s)
- Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Aayushi Chechi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | - Valentin Gogonea
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.,Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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5
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Halawani D, Gogonea V, DiDonato JA, Pipich V, Yao P, China A, Topbas C, Vasu K, Arif A, Hazen SL, Fox PL. Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains. J Biol Chem 2018; 293:8843-8860. [PMID: 29643180 DOI: 10.1074/jbc.m117.807503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/26/2018] [Indexed: 02/02/2023] Open
Abstract
Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH-S-transferase-C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST-C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems.
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Affiliation(s)
- Dalia Halawani
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Valentin Gogonea
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and .,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Joseph A DiDonato
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Vitaliy Pipich
- the Jülich Center for Neutron Science, Outstation at Maier-Leibnitz Zentrum, Forschungszentrum Jülich, GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany, and
| | - Peng Yao
- the Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, New York 14642
| | - Arnab China
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Celalettin Topbas
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Kommireddy Vasu
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Abul Arif
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Stanley L Hazen
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,Center for Cardiovascular Diagnostics and Prevention, and Department of Cardiovascular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Paul L Fox
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
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6
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Thiagarajan PS, Sinyuk M, Turaga SM, Mulkearns-Hubert EE, Hale JS, Rao V, Demelash A, Saygin C, China A, Alban TJ, Hitomi M, Torre-Healy LA, Alvarado AG, Jarrar A, Wiechert A, Adorno-Cruz V, Fox PL, Calhoun BC, Guan JL, Liu H, Reizes O, Lathia JD. Cx26 drives self-renewal in triple-negative breast cancer via interaction with NANOG and focal adhesion kinase. Nat Commun 2018; 9:578. [PMID: 29422613 PMCID: PMC5805730 DOI: 10.1038/s41467-018-02938-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/09/2018] [Indexed: 12/18/2022] Open
Abstract
Tumors adapt their phenotypes during growth and in response to therapies through dynamic changes in cellular processes. Connexin proteins enable such dynamic changes during development, and their dysregulation leads to disease states. The gap junction communication channels formed by connexins have been reported to exhibit tumor-suppressive functions, including in triple-negative breast cancer (TNBC). However, we find that connexin 26 (Cx26) is elevated in self-renewing cancer stem cells (CSCs) and is necessary and sufficient for their maintenance. Cx26 promotes CSC self-renewal by forming a signaling complex with the pluripotency transcription factor NANOG and focal adhesion kinase (FAK), resulting in NANOG stabilization and FAK activation. This FAK/NANOG-containing complex is not formed in mammary epithelial or luminal breast cancer cells. These findings challenge the paradigm that connexins are tumor suppressors in TNBC and reveal a unique function for Cx26 in regulating the core self-renewal signaling that controls CSC maintenance. Connexin proteins are usually considered as tumor suppressors. Here, the authors show that connexin 26 (Cx26) regulates the self-renewal of breast cancer stem cells via a ternary complex with FAK and NANOG.
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Affiliation(s)
- Praveena S Thiagarajan
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA.,Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Maksim Sinyuk
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Soumya M Turaga
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Erin E Mulkearns-Hubert
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - James S Hale
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Vinay Rao
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Abeba Demelash
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Caner Saygin
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Arnab China
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Tyler J Alban
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA.,Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Masahiro Hitomi
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA.,Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Luke A Torre-Healy
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Alvaro G Alvarado
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Awad Jarrar
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Andrew Wiechert
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA
| | - Valery Adorno-Cruz
- Case Comprehensive Cancer Center, Cleveland, OH, 44195, USA.,Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Departments of Pharmacology and Medicine, Northwestern University School of Medicine, Chicago, IL, 60611, USA
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA.,Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA.,Case Comprehensive Cancer Center, Cleveland, OH, 44195, USA
| | | | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Huiping Liu
- Case Comprehensive Cancer Center, Cleveland, OH, 44195, USA.,Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Departments of Pharmacology and Medicine, Northwestern University School of Medicine, Chicago, IL, 60611, USA
| | - Ofer Reizes
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA. .,Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA. .,Case Comprehensive Cancer Center, Cleveland, OH, 44195, USA.
| | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44915, USA. .,Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA. .,Case Comprehensive Cancer Center, Cleveland, OH, 44195, USA.
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7
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Arif A, Terenzi F, Potdar AA, Jia J, Sacks J, China A, Halawani D, Vasu K, Li X, Brown JM, Chen J, Kozma SC, Thomas G, Fox PL. EPRS is a critical mTORC1-S6K1 effector that influences adiposity in mice. Nature 2017; 542:357-361. [PMID: 28178239 PMCID: PMC5480610 DOI: 10.1038/nature21380] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/11/2017] [Indexed: 12/26/2022]
Abstract
Metabolic pathways that contribute to adiposity and ageing are activated by the mammalian target of rapamycin complex 1 (mTORC1) and p70 ribosomal protein S6 kinase 1 (S6K1) axis. However, known mTORC1-S6K1 targets do not account for observed loss-of-function phenotypes, suggesting that there are additional downstream effectors of this pathway. Here we identify glutamyl-prolyl-tRNA synthetase (EPRS) as an mTORC1-S6K1 target that contributes to adiposity and ageing. Phosphorylation of EPRS at Ser999 by mTORC1-S6K1 induces its release from the aminoacyl tRNA multisynthetase complex, which is required for execution of noncanonical functions of EPRS beyond protein synthesis. To investigate the physiological function of EPRS phosphorylation, we generated Eprs knock-in mice bearing phospho-deficient Ser999-to-Ala (S999A) and phospho-mimetic (S999D) mutations. Homozygous S999A mice exhibited low body weight, reduced adipose tissue mass, and increased lifespan, similar to S6K1-deficient mice and mice with adipocyte-specific deficiency of raptor, an mTORC1 constituent. Substitution of the EprsS999D allele in S6K1-deficient mice normalized body mass and adiposity, indicating that EPRS phosphorylation mediates S6K1-dependent metabolic responses. In adipocytes, insulin stimulated S6K1-dependent EPRS phosphorylation and release from the multisynthetase complex. Interaction screening revealed that phospho-EPRS binds SLC27A1 (that is, fatty acid transport protein 1, FATP1), inducing its translocation to the plasma membrane and long-chain fatty acid uptake. Thus, EPRS and FATP1 are terminal mTORC1-S6K1 axis effectors that are critical for metabolic phenotypes.
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Affiliation(s)
- Abul Arif
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Fulvia Terenzi
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Jie Jia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Jessica Sacks
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Arnab China
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Dalia Halawani
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Kommireddy Vasu
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Xiaoxia Li
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - J Mark Brown
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Jie Chen
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Sara C Kozma
- Catalan Institute of Oncology, ICO, Bellvitge Biomedical Research Institute, IDIBELL, Barcelona, Spain.,Department of Physiological Sciences II, Faculty of Medicine, University of Barcelona, 08908 Barcelona, Spain
| | - George Thomas
- Catalan Institute of Oncology, ICO, Bellvitge Biomedical Research Institute, IDIBELL, Barcelona, Spain.,Department of Physiological Sciences II, Faculty of Medicine, University of Barcelona, 08908 Barcelona, Spain.,Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
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8
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Ghosh S, Padmanabhan B, Godbole AA, Tare P, Ahmed W, Vasu K, China A, Kumar R, Mitra A, Nagaraja V. Transcriptional regulation of topology modulators and transcription regulators of Mycobacterium tuberculosis. Biochem Biophys Res Commun 2016; 475:257-63. [PMID: 27207833 DOI: 10.1016/j.bbrc.2016.05.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a formidable pathogen which has the ability to survive the hostile environment of the host by evading the host defense system. The re-configuration of its transcriptional and metabolic process allows the pathogen to confront the adverse environment within the host macrophages. The factors that assist the transcription and modulate the DNA topology would have to play a key role in the regulation of global gene expression of the organism. How transcription of these essential housekeeping genes alters in response to growth conditions and environmental stress has not been addressed together in a set of experimental conditions in Mtb. Now, we have mapped the transcription start sites (TSS) and promoters of several genes that play a central role in the regulation of DNA topology and transcription in Mtb. Using in vivo reporter assays, we validated the activity of the identified promoter elements in different growth conditions. The variation in transcript abundance of these essential genes was also analyzed in growth phase-dependent manner. These data provide the first glimpse into the specific adaptive changes in the expression of genes involved in transcription and DNA topology modulation in Mtb.
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Affiliation(s)
- Soumitra Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Bhavna Padmanabhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Kommireddy Vasu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Arnab China
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Rupesh Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Anirban Mitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
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Tare P, China A, Nagaraja V. Distinct and contrasting transcription initiation patterns at Mycobacterium tuberculosis promoters. PLoS One 2012; 7:e43900. [PMID: 22970148 PMCID: PMC3436766 DOI: 10.1371/journal.pone.0043900] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 07/30/2012] [Indexed: 11/18/2022] Open
Abstract
Although sequencing of Mycobacterium tuberculosis genome lead to better understanding of transcription units and gene functions, interactions occurring during transcription initiation between RNA polymerase and promoters is yet to be elucidated. Different stages of transcription initiation include promoter specific binding of RNAP, isomerization, abortive initiation and promoter clearance. We have now analyzed these events with four promoters of M. tuberculosis viz. PgyrB1, PgyrR, PrrnPCL1 and PmetU. The promoters differed from each other in their rates of open complex formation, decay, promoter clearance and abortive transcription. The equilibrium binding and kinetic studies of various steps revealed distinct rate limiting events for each of the promoter, which also differed markedly in their characteristics from the respective promoters of Mycobacterium smegmatis. Surprisingly, the transcription at gyr promoter was enhanced in the presence of initiating nucleotides and decreased in the presence of alarmone, pppGpp, a pattern typically seen with rRNA promoters studied so far. The gyr promoter of M. smegmatis, on the other hand, was not subjected to pppGpp mediated regulation. The marked differences in the transcription initiation pathway seen with rrn and gyr promoters of M. smegmatis and M. tuberculosis suggest that such species specific differences in the regulation of expression of the crucial housekeeping genes could be one of the key determinants contributing to the differences in growth rate and lifestyle of the two organisms. Moreover, the distinct rate limiting steps during transcription initiation of each one of the promoters studied point at variations in their intracellular regulation.
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Affiliation(s)
- Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Arnab China
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- * E-mail:
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Prabha S, China A, Rao DN, Nagaraja V. WITHDRAWN: Stimulation of the Mycobacterium tuberculosis transcription elongation by MtbMfd. Tuberculosis (Edinb) 2011:S1472-9792(11)00213-7. [PMID: 22129656 DOI: 10.1016/j.tube.2011.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Revised: 11/03/2011] [Accepted: 11/08/2011] [Indexed: 11/20/2022]
Abstract
This article has been withdrawn at the request of the author(s). The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Swayam Prabha
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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China A, Tare P, Nagaraja V. Comparison of promoter-specific events during transcription initiation in mycobacteria. Microbiology (Reading) 2010; 156:1942-1952. [PMID: 20299402 DOI: 10.1099/mic.0.038620-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA-protein interactions that occur during transcription initiation play an important role in regulating gene expression. To initiate transcription, RNA polymerase (RNAP) binds to promoters in a sequence-specific fashion. This is followed by a series of steps governed by the equilibrium binding and kinetic rate constants, which in turn determine the overall efficiency of the transcription process. We present here the first detailed kinetic analysis of promoter-RNAP interactions during transcription initiation in the sigma(A)-dependent promoters P(rrnAPCL1), P(rrnB) and P(gyr) of Mycobacterium smegmatis. The promoters show comparable equilibrium binding affinity but differ significantly in open complex formation, kinetics of isomerization and promoter clearance. Furthermore, the two rrn promoters exhibit varied kinetic properties during transcription initiation and appear to be subjected to different modes of regulation. In addition to distinct kinetic patterns, each one of the housekeeping promoters studied has its own rate-limiting step in the initiation pathway, indicating the differences in their regulation.
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Affiliation(s)
- Arnab China
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, India
| | - Valakunja Nagaraja
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore - 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, India
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Malshetty V, Kurthkoti K, China A, Mallick B, Yamunadevi S, Sang PB, Srinivasan N, Nagaraja V, Varshney U. Novel insertion and deletion mutants of RpoB that render Mycobacterium smegmatis RNA polymerase resistant to rifampicin-mediated inhibition of transcription. Microbiology (Reading) 2010; 156:1565-1573. [PMID: 20150242 DOI: 10.1099/mic.0.036970-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The startling increase in the occurrence of rifampicin (Rif) resistance in the clinical isolates of Mycobacterium tuberculosis worldwide is posing a serious concern to tuberculosis management. The majority of Rif resistance in bacteria arises from mutations in the RpoB subunit of the RNA polymerase. We isolated M. smegmatis strains harbouring either an insertion (6 aa) or a deletion (10 aa) in their RpoB proteins. Although these strains showed a compromised fitness for growth in 7H9 Middlebrook medium, their resistance to Rif was remarkably high. The attenuated growth of the strains correlated with decreased specific activities of the RNA polymerases from the mutants. While the RNA polymerases from the parent or a mutant strain (harbouring a frequently occurring mutation, H442Y, in RpoB) were susceptible to Rif-mediated inhibition of transcription from calf thymus DNA, those from the insertion and deletion mutants were essentially refractory to such inhibition. Three-dimensional structure modelling revealed that the RpoB amino acids that interact with Rif are either deleted or unable to interact with Rif due to their unsuitable spatial positioning in these mutants. We discuss possible uses of the RpoB mutants in studying transcriptional regulation in mycobacteria and as potential targets for drug design.
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Affiliation(s)
- Vidyasagar Malshetty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Krishna Kurthkoti
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Arnab China
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Bratati Mallick
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Subburaj Yamunadevi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pau Biak Sang
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Valakunja Nagaraja
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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Dinakaran M, Senthilkumar P, Yogeeswari P, China A, Nagaraja V, Sriram D. Synthesis, Antimycobacterial Activities and Phototoxic Evaluation of 5H-thiazolo[3,2-a]quinoline-4-carboxylic Acid Derivatives. Med Chem 2008; 4:482-91. [DOI: 10.2174/157340608785700225] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dinakaran M, Senthilkumar P, Yogeeswari P, China A, Nagaraja V, Sriram D. Antimycobacterial activities of novel 2-(sub)-3-fluoro/nitro-5,12-dihydro-5-oxobenzothiazolo[3,2-a]quinoline-6-carboxylic acid. Bioorg Med Chem 2008; 16:3408-18. [DOI: 10.1016/j.bmc.2007.11.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Revised: 11/02/2007] [Accepted: 11/03/2007] [Indexed: 10/22/2022]
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Senthilkumar P, Dinakaran M, Yogeeswari P, Sriram D, China A, Nagaraja V. Synthesis and antimycobacterial activities of novel 6-nitroquinolone-3-carboxylic acids. Eur J Med Chem 2008; 44:345-58. [PMID: 18502542 DOI: 10.1016/j.ejmech.2008.02.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 02/15/2008] [Accepted: 02/29/2008] [Indexed: 11/25/2022]
Abstract
Various 1-(substituted)-1,4-dihydro-6-nitro-4-oxo-7-(sub-secondary amino)-quinoline-3-carboxylic acids were synthesized from 2,4-dichlorobenzoic acid by six step synthesis. The compounds were evaluated for antimycobacterial in vitro and in vivo against Mycobacterium tuberculosis H37Rv (MTB), multi-drug resistant Mycobacterium tuberculosis (MDR-TB) and Mycobacterium smegmatis (MC(2)) and also tested for the ability to inhibit the supercoiling activity of DNA gyrase from M. smegmatis. Among the 48 synthesized compounds, 7-(4-((benzo[d][1,3]dioxol-5-yl)methyl)piperazin-1-yl)-1-cyclopropyl-1,4-dihydro-6-nitro-4-oxoquinoline-3-carboxylic acid (8c) was found to be the most active compound in vitro with MIC of 0.08 and 0.16 microM against MTB and MDR-TB, respectively. In the in vivo animal model 8c decreased the bacterial load in lung and spleen tissues with 2.78 and 4.15-log10 protections, respectively, at the dose of 50 mg/kg body weight.
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Affiliation(s)
- Palaniappan Senthilkumar
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India
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Dinakaran M, Senthilkumar P, Yogeeswari P, China A, Nagaraja V, Sriram D. Novel ofloxacin derivatives: synthesis, antimycobacterial and toxicological evaluation. Bioorg Med Chem Lett 2007; 18:1229-36. [PMID: 18068979 DOI: 10.1016/j.bmcl.2007.11.110] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 11/23/2007] [Accepted: 11/28/2007] [Indexed: 10/22/2022]
Abstract
Thirty novel 9-fluoro-2,3-dihydro-8,10-(mono/di-sub)-3-methyl-8-nitro-7-oxo-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acids were synthesized from 2,3,4,5-tetrafluoro benzoic acid and evaluated for in vitro and in vivo antimycobacterial activities against Mycobacterium tuberculosis H37Rv (MTB), multi-drug resistant Mycobacterium tuberculosis (MDR-TB), and Mycobacterium smegmatis (MC(2)) and also tested for the ability to inhibit the supercoiling activity of DNA gyrase from mycobacteria. Among the synthesized compounds, 10-[2-carboxy-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl]-9-fluoro-2,3-dihydro-3-methyl-8-nitro-7-oxo-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid was found to be the most active compound in vitro with MIC99 of 0.19 microM and 0.09 microM against MTB and MTR-TB, respectively. In the in vivo animal model also the same compound decreased the bacterial load in lung and spleen tissues with 1.91 and 2.91--log10 protections, respectively, at the dose of 50mg/kg body weight. Compound 10-[(4-((4-chlorophenyl)(phenyl)methyl)piperazin-1-yl)]-9-fluoro-2,3-dihydro-3-methyl-8-nitro-7-oxo-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid was found to be the most active in the inhibition of the supercoiling activity of DNA gyrase with an IC(50) of 10.0 microg/mL. The results demonstrate the potential and importance of developing new oxazino quinolone derivatives against mycobacterial infections.
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Affiliation(s)
- Murugesan Dinakaran
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India
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Kamal A, Ahmed S, Reddy K, A. Khan M, Shetty R, Siddhardha B, Murty U, China A, Nagaraja V. Synthesis and Biological Evaluation of a New Series of Benzothiazole-Benzothiadiazine Conjugates as Antibacterial Agents. LETT DRUG DES DISCOV 2007. [DOI: 10.2174/157018007782794563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Senthilkumar P, Dinakaran M, Banerjee D, Devakaram RV, Yogeeswari P, China A, Nagaraja V, Sriram D. Synthesis and antimycobacterial evaluation of newer 1-cyclopropyl-1,4-dihydro-6-fluoro-7-(substituted secondary amino)-8-methoxy-5-(sub)-4-oxoquinoline-3-carboxylic acids. Bioorg Med Chem 2007; 16:2558-69. [PMID: 18078756 DOI: 10.1016/j.bmc.2007.11.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 11/16/2007] [Accepted: 11/17/2007] [Indexed: 11/28/2022]
Abstract
Thirty-four newer 1-cyclopropyl-1,4-dihydro-6-fluoro-7-(substituted secondary amino)-8-methoxy-5-(sub)-4-oxoquinoline-3-carboxylic acids were synthesized from 1,2,3,4-tetrafluoro benzene and evaluated for in vitro and in vivo antimycobacterial activities against Mycobacterium tuberculosis H37Rv (MTB), multi-drug resistant M. tuberculosis (MDR-TB) and Mycobacterium smegmatis (MC(2)) and also tested for the ability to inhibit the supercoiling activity of DNA gyrase. Among the synthesized compounds, 7-(1-(4-methoxybenzyl)-3,4,5,6,7,8-hexahydroisoquinolin-2(1H)-yl)-1-cyclopropyl-6-fluoro-1,4-dihydro-8-methoxy-5-nitro-4-oxoquinoline-3-carboxylic acid (13n) was found to be the most active compound in vitro with MIC of 0.16 and 0.33 microM against MTB and MDR-TB, respectively. In the in vivo animal model 13n decreased the bacterial load in lung and spleen tissues with 2.54 and 2.92-log10 protections, respectively, at the dose of 50mg/kg body weight. Compound 13n also inhibited the supercoiling activity of mycobacterial DNA gyrase with IC(50) of 30.0 microg/ml.
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Affiliation(s)
- Palaniappan Senthilkumar
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India
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Senthilkumar P, Dinakaran M, Yogeeswari P, China A, Nagaraja V, Sriram D. Antimycobacterial activities of novel fluoroquinolones. Biomed Pharmacother 2007; 63:27-35. [PMID: 18031974 DOI: 10.1016/j.biopha.2007.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 10/03/2007] [Indexed: 11/28/2022] Open
Abstract
Fifty-one novel 1-(cyclopropyl/2,4-difluorophenyl/t-butyl)-1,4-dihydro-6-fluoro-7-(sub secondary amino)-4-oxoquinoline-3-carboxylic acids were synthesized and evaluated for their antimycobacterial in vitro and in vivo against Mycobacterium tuberculosis H37Rv (MTB), multi-drug resistant Mycobacterium tuberculosis (MDR-TB) and Mycobacterium smegmatis (MC(2)) and also tested for the ability to inhibit the supercoiling activity of DNA gyrase from M. smegmatis. Among the synthesized compounds, 7-(3-(diethylcarbamoyl)piperidin-1-yl)-1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxoquinoline-3-carboxylic acid (7l) was found to be the most active compound in vitro with MIC of 0.09 microM against MTB and MDR-TB respectively. In the in vivo animal model 7l decreased the mycobacterial load in lung and spleen tissues with 2.53- and 4.88-log10 protections respectively at a dose of 50mg/kg body weight.
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Affiliation(s)
- Palaniappan Senthilkumar
- Medicinal Chemistry Research Laboratory, Pharmacy Group, Birla Institute of Technology and Science, Pilani, Rajasthan, India
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Sriram D, Senthilkumar P, Dinakaran M, Yogeeswari P, China A, Nagaraja V. Antimycobacterial Activities of Novel 1-(Cyclopropyl/tert-butyl/4-fluorophenyl)-1,4-dihydro- 6-nitro-4-oxo-7-(substituted secondary amino)-1,8-naphthyridine-3-carboxylic Acid. J Med Chem 2007; 50:6232-9. [DOI: 10.1021/jm700999n] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dharmarajan Sriram
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India, and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Palaniappan Senthilkumar
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India, and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Murugesan Dinakaran
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India, and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Perumal Yogeeswari
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India, and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Arnab China
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India, and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Valakunja Nagaraja
- Medicinal Chemistry Research Laboratory, Pharmacy group, Birla Institute of Technology and Science, Pilani 333031, India, and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Jain V, Saleem-Batcha R, China A, Chatterji D. Molecular dissection of the mycobacterial stringent response protein Rel. Protein Sci 2006; 15:1449-64. [PMID: 16731979 PMCID: PMC2242531 DOI: 10.1110/ps.062117006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 03/08/2006] [Accepted: 03/09/2006] [Indexed: 10/24/2022]
Abstract
Latency in Mycobacterium tuberculosis poses a barrier in its complete eradication. Overexpression of certain genes is one of the factors that help these bacilli survive inside the host during latency. Among these genes, rel, which leads to the expression of Rel protein, plays an important role by synthesizing the signaling molecule ppGpp using GDP and ATP as substrates, thereby changing bacterial physiology. In Gram-negative bacteria, the protein is thought to be activated in vivo in the presence of ribosome by sensing uncharged tRNA. In the present report, we show that Rel protein from Mycobacterium smegmatis, which is highly homologous to M. tuberculosis Rel, is functional even in the absence of ribosome and uncharged tRNA. From the experiments presented here, it appears that the activity of Rel(Msm) is regulated by the domains present at the C terminus, as the deletion of these domains results in higher synthesis activity, with little change in hydrolysis of ppGpp. However, in the presence of tRNA, though the synthesis activity of the full-length protein increases to a certain extent, the hydrolysis activity undergoes drastic reduction. Full-length Rel undergoes multimerization involving interchain disulfide bonds. The synthesis of pppGpp by the full-length protein is enhanced in the reduced environment in vitro, whereas the hydrolysis activity does not change significantly. Mutations of cysteines to serines result in monomerization with a simultaneous increase in the synthesis activity. Finally, it has been possible to identify the unique cysteine, of six present in Rel, required for tRNA-mediated synthesis of ppGpp.
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Affiliation(s)
- Vikas Jain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Gupta R, China A, Manjunatha UH, Ponnanna NM, Nagaraja V. A complex of DNA gyrase and RNA polymerase fosters transcription in Mycobacterium smegmatis. Biochem Biophys Res Commun 2006; 343:1141-5. [PMID: 16579974 DOI: 10.1016/j.bbrc.2006.02.195] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 02/23/2006] [Indexed: 11/24/2022]
Abstract
We report here the existence of a complex between RNA polymerase (RNAP) and DNA gyrase in Mycobacterium smegmatis. The interaction between the two enzymes was detected during our attempts to purify DNA gyrase from M. smegmatis. RNAP subunits co-eluted along with DNA gyrase in two different affinity chromatography column procedures employed to purify the latter enzyme. A complex containing both the enzymes was isolated through gel filtration chromatography and sucrose density gradient centrifugation of the cell free extracts. The complex exhibited both DNA supercoiling and transcription activities. Reduction in the transcription activity of the complex in the presence of DNA gyrase inhibitor indicates a role for DNA gyrase in stimulating transcription.
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Affiliation(s)
- Richa Gupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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