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Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Nucleic Acids Res 2019; 47:10477-10488. [PMID: 31602466 PMCID: PMC6847099 DOI: 10.1093/nar/gkz855] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022] Open
Abstract
In all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine-Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position -3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.
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Affiliation(s)
- William D Baez
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Bappaditya Roy
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Zakkary A McNutt
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Ralf Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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Monteiro C, Neyret S, Leforestier J, Hervé du Penhoat C. Solution conformation of various uridine diphosphoglucose salts as probed by NMR spectroscopy. Carbohydr Res 2000; 329:141-55. [PMID: 11086694 DOI: 10.1016/s0008-6215(00)00166-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The solution conformations of uridine diphosphoglucose (UDP-Glc) under a variety of conditions (solvent, ionic strength, various mono- and divalent cations) have been studied by NMR spectroscopy (1H, 13C, 31P, and 25Mg). In the case of divalent cations (Ca2+, Mg2+, Mn2+) the phosphate oxygens are the preferred coordination sites and analysis of the 25Mg linewidths of solutions with various [Mg2+]/[UDP-Glc] ratios, indicates that the 1:1 Mg2+ UDP-Glc complex is the major species. From 13C relaxation data and hydrodynamic theory, it has been demonstrated that under all conditions UDP-Glc adopts a fairly extended overall shape and that magnesium ions lead to a significant increase in the average length of the UDP-Glc molecule as compared to monovalent cations. Thus, one of the roles of the metal ion in enzymic reactions involving nucleotide sugars may be to preorganize the nucleotide sugar.
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Affiliation(s)
- C Monteiro
- Centre de Recherches sur les Macromolécules Végétales, CNRS (associated with University Joseph Fourier), Grenoble, France
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Rundlöf T, Venable RM, Pastor RW, Kowalewski J, Widmalm G. Distinguishing Anisotropy and Flexibility of the Pentasaccharide LNF-1 in Solution by Carbon-13 NMR Relaxation and Hydrodynamic Modeling. J Am Chem Soc 1999. [DOI: 10.1021/ja992675b] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Torgny Rundlöf
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Richard M. Venable
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Richard W. Pastor
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Jozef Kowalewski
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Göran Widmalm
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
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Abdelkafi M, Leulliot N, Baumruk V, Bednárová L, Turpin PY, Namane A, Gouyette C, Huynh-Dinh T, Ghomi M. Structural features of the UCCG and UGCG tetraloops in very short hairpins as evidenced by optical spectroscopy. Biochemistry 1998; 37:7878-84. [PMID: 9601049 DOI: 10.1021/bi980011t] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Structures of the UCCG and UGCG tetraloops formed in octamer ribonucleotidic hairpin sequences, i.e., 5'-r[GC(UCCG)GC]-3' and 5'-r[GC(UGCG)GC]-3', have been studied in aqueous solution by methods of optical spectroscopy. UV absorption melting profiles of these short hairpins, containing only two closing GC base pairs in the stem, are consistent with a monophasic, completely reversible order-to-disorder transition and clearly confirm their unusual structural stability (with Tm congruent with 50 degrees C). To establish structural characteristics of these tetraloops, Raman and FTIR spectroscopies have been used and vibrational conformation markers arising from the phosphate backbone and various nucleosides have been analyzed. They have been assigned on the basis of known unambiguous vibrational markers established for DNA and RNA chains. Surprisingly, they are easily transferable to short oligonucleotidic sequences. Intensities and wavenumbers of these conformation markers have been monitored in the 0-70 degrees C temperature range, i.e., in going from an ordered to a disordered structure. The main structural features of the UCCG and UGCG tetraloops are similar to those previously found in the UUCG and UACG tetraloops by means of NMR and vibrational spectroscopies, except those of the second nucleosides of the tetraloops (rC and rG, respectively) which adopt a 3'-endo/anti rather than a 2'-endo/anti conformation.
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Affiliation(s)
- M Abdelkafi
- Laboratoire de Physicochimie Biomoléculaire et Cellulaire, URA CNRS 2056, Université Pierre et Marie Curie, Paris, France
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Kjellberg A, Torgny Rundlöf,, Kowalewski J, Widmalm G. Motional Properties of Two Vicinally Disubstituted Trisaccharides As Studied by Multiple-Field Carbon-13 NMR Relaxation. J Phys Chem B 1998. [DOI: 10.1021/jp971542e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandra Kjellberg
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Torgny Rundlöf,
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Jozef Kowalewski
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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