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Shanmuga Priya VG, Bhandare V, Muddapur UM, Swaminathan P, Fandilolu PM, Sonawane KD. Molecular modeling approach to identify inhibitors of Rv2004c (rough morphology and virulent strain gene), a DosR (dormancy survival regulator) regulon protein from Mycobacterium tuberculosis. J Biomol Struct Dyn 2022; 40:3242-3257. [DOI: 10.1080/07391102.2020.1846620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- V. G. Shanmuga Priya
- Department of Biotechnology, KLE Dr.M.S.Sheshgiri College of Engineering and Technology, Belagavi, India
| | - Vishwambhar Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, India
| | - Uday M. Muddapur
- Department of Biotechnology, B.V.B College of Engineering and Technology, KLE Technological University, Hubballi, India
| | - Priya Swaminathan
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, India
| | - Prayagraj M. Fandilolu
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, India
| | - Kailas D. Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, India
- Department of Microbiology, Shivaji University, Kolhapur, India
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Pollo-Oliveira L, Klassen R, Davis N, Ciftci A, Bacusmo JM, Martinelli M, DeMott MS, Begley TJ, Dedon PC, Schaffrath R, de Crécy-Lagard V. Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast. Biomolecules 2020; 10:E322. [PMID: 32085421 PMCID: PMC7072221 DOI: 10.3390/biom10020322] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/20/2022] Open
Abstract
Modifications found in the Anticodon Stem Loop (ASL) of tRNAs play important roles in regulating translational speed and accuracy. Threonylcarbamoyl adenosine (t6A37) and 5-methoxycarbonyl methyl-2-thiouridine (mcm5s2U34) are critical ASL modifications that have been linked to several human diseases. The model yeast Saccharomyces cerevisiae is viable despite the absence of both modifications, growth is however greatly impaired. The major observed consequence is a subsequent increase in protein aggregates and aberrant morphology. Proteomic analysis of the t6A-deficient strain (sua5 mutant) revealed a global mistranslation leading to protein aggregation without regard to physicochemical properties or t6A-dependent or biased codon usage in parent genes. However, loss of sua5 led to increased expression of soluble proteins for mitochondrial function, protein quality processing/trafficking, oxidative stress response, and energy homeostasis. These results point to a global function for t6A in protein homeostasis very similar to mcm5/s2U modifications.
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Affiliation(s)
- Leticia Pollo-Oliveira
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.P.-O.); (J.M.B.); (M.M.)
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (R.K.); (A.C.); (R.S.)
| | - Nick Davis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (N.D.); (M.S.D.); (P.C.D.)
| | - Akif Ciftci
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (R.K.); (A.C.); (R.S.)
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.P.-O.); (J.M.B.); (M.M.)
| | - Maria Martinelli
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.P.-O.); (J.M.B.); (M.M.)
| | - Michael S. DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (N.D.); (M.S.D.); (P.C.D.)
| | - Thomas J. Begley
- The RNA Institute, College of Arts and Science, University at Albany, SUNY, Albany, NY 12222, USA;
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (N.D.); (M.S.D.); (P.C.D.)
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (R.K.); (A.C.); (R.S.)
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.P.-O.); (J.M.B.); (M.M.)
- University of Florida Genetics Institute, Gainesville, FL 32608, USA
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Sierant M, Leszczynska G, Sadowska K, Komar P, Radzikowska-Cieciura E, Sochacka E, Nawrot B. Escherichia coli
tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA via
S-geranylated-intermediate. FEBS Lett 2018; 592:2248-2258. [DOI: 10.1002/1873-3468.13124] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Malgorzata Sierant
- Centre of Molecular and Macromolecular Studies; Polish Academy of Sciences; Lodz Poland
| | | | - Klaudia Sadowska
- Institute of Organic Chemistry; Lodz University of Technology; Poland
| | - Patrycja Komar
- Centre of Molecular and Macromolecular Studies; Polish Academy of Sciences; Lodz Poland
| | | | - Elzbieta Sochacka
- Institute of Organic Chemistry; Lodz University of Technology; Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies; Polish Academy of Sciences; Lodz Poland
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Zhang H, Li J, Wang R, Zhi J, Yin P, Xu J. Comparative analysis of expansin gene codon usage patterns among eight plant species. J Biomol Struct Dyn 2018; 37:910-917. [PMID: 29480091 DOI: 10.1080/07391102.2018.1442746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Expansins are essential components of plant cell wall and play an important role in plant growth, development, and stress resistance via loosening function. To understand the codon usage pattern of expansin genes, we gained the sequence data of expansin genes from eight plant species. Statistics analysis showed obvious codon characteristics between monocot and dicot plants. Comparably, expansin genes in monocot plants had really higher GC content, more high-frequency codons, and more optimal codons than that in dicot plants. Several monocot plants performed somehow as dicot plants in a few characters. Codon information of expansin genes might contribute to the understanding of the relationship and evolution clues between monocot and dicot plants. It further gained insight into the improvement of the gene expression and roles.
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Affiliation(s)
- Hao Zhang
- a National Engineering Laboratory for Tree Breeding , Beijing Forestry University , Beijing 100083 , China
| | - Jian Li
- a National Engineering Laboratory for Tree Breeding , Beijing Forestry University , Beijing 100083 , China
| | - Ruixue Wang
- a National Engineering Laboratory for Tree Breeding , Beijing Forestry University , Beijing 100083 , China
| | - Junkai Zhi
- a National Engineering Laboratory for Tree Breeding , Beijing Forestry University , Beijing 100083 , China
| | - Peng Yin
- a National Engineering Laboratory for Tree Breeding , Beijing Forestry University , Beijing 100083 , China
| | - Jichen Xu
- a National Engineering Laboratory for Tree Breeding , Beijing Forestry University , Beijing 100083 , China
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