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Category: Microbial Genetics and Molecular Biology
Biosynthesis and Function of Modified Nucleosides, Page 1 of 2
< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555818333/9781555810733_Chap11-1.gif /docserver/preview/fulltext/10.1128/9781555818333/9781555810733_Chap11-2.gifAbstract:
Modified nucleosides, which are derivatives of the four normal nucleosides, adenosine (A), guanosine (G), cytidine (C), and uridine (U), were found in nucleic acids as early as 1948. Modified nucleosides are contained in tRNA from all three phylogenetic domains—Archaea, Bacteria, and Eucarya—which were formerly called the kingdoms of archaebacteria, eubacteria, and eukaryotes, respectively. Although modified nucleosides are found in various positions in the tRNA, two positions, 34 and 37, contain the largest variety of modified nucleosides. This chapter presents an overview of the coding properties associated with modified nucleosides present in positions 34 and 37. Outside the anticodon, the modified nucleosides are usually “simple” modifications like methylated or thiolated derivatives, whereas all except one (archaeosine in tRNAs from Archaea) of the hypermodified nucleosides are present in the anticodon region and only in positions 34 and 37. Moreover, outside the anticodon region, only one or two kinds of modified nucleosides in each position are present, whereas a large variety of modified nucleosides are present in the anticodon region, especially in positions 34 and 37. During evolution, structural refinements of the individual tRNAs were presumably fulfilled by the evolution of the synthesis of the various modified nucleosides, including the hypermodified nucleoside. Modified nucleosides in the anticodon region exert their functions primarily in the decoding process, whereas modified nucleosides outside this region may primarily be involved in other tRNA interactions, such as interactions with translation factors or as sensors for environmental stress conditions.
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Genetic organization of E. coli trmA region (from reference 155 with permission). FIS = possible FIS binding site; tRNA T-arm homology = a sequence with extensive similarity to the T-loop of tRNAs; AdoMet binding = AdoMet binding site; and catalytic nucleophile = the catalytic nucleophile Cys-324. Also shown are the similarity between the PtrmA and the P1 promoter of rrn genes and the trmA transcriptional terminator (T) shared with the orfB gene. The btuB gene is the structural gene for the vitamin B12 receptor. The sequence is found in reference 157 .
Genetic organization of E. coli trmA region (from reference 155 with permission). FIS = possible FIS binding site; tRNA T-arm homology = a sequence with extensive similarity to the T-loop of tRNAs; AdoMet binding = AdoMet binding site; and catalytic nucleophile = the catalytic nucleophile Cys-324. Also shown are the similarity between the PtrmA and the P1 promoter of rrn genes and the trmA transcriptional terminator (T) shared with the orfB gene. The btuB gene is the structural gene for the vitamin B12 receptor. The sequence is found in reference 157 .
Genetic organization of E. coli trmD operon. Figures above the gene symbols indicate the number of protein molecules encoded from the respective genes per genome equivalents in cells grown at k = 1.0 hr−1. The Ω denotes a ρ-independent terminator. In vitro, 60% to 70% of the transcript terminates at the first such structure ( 55 ). Structures above the operon denote possible stem-loop structures that influence the translation of the 21K and trmD genes, respectively ( 406 ). The sequence is found in reference 54 .
Genetic organization of E. coli trmD operon. Figures above the gene symbols indicate the number of protein molecules encoded from the respective genes per genome equivalents in cells grown at k = 1.0 hr−1. The Ω denotes a ρ-independent terminator. In vitro, 60% to 70% of the transcript terminates at the first such structure ( 55 ). Structures above the operon denote possible stem-loop structures that influence the translation of the 21K and trmD genes, respectively ( 406 ). The sequence is found in reference 54 .
Genetic organization of E. coli hisT operon. Figures within the parentheses indicate the size of the protein encoded by the respective genes. Dyad symmetries and possible ρ-independent terminators are denoted as → ← and Ω, respectively. Transcriptions are shown by wavy lines and the transcription pattern is only tentative, since none of the transcripts has been shown to exist in vivo. The pattern is deduced from S1 mapping of a few areas of the operon, primer extension analysis, and analysis of polarity ( 39 , 271 , 337 ). It is presently unclear whether dedB and folC are part of the hisT operon ( 15 , 271 ). However, a chromosomally encoded transcript covering the intracistronic region between hisT and dedB is present ( 271 ). Furthermore, the ρ-independent terminator present between dedB and folC is not active ( 39 ), suggesting that transcripts extend to the ρ-independent terminator following the dedD gene. The promoters Ppdx, Pdiv, and Pint were located on the chromosome ( 14 , 15 ), whereas PfolC was located on a plasmid ( 39 ). The dedD gene seems to have its own promoter located within the folC gene ( 39 ). The overlap of the asd stop codon with the hisT start codon is also indicated, suggesting translational coupling of the expression of these two genes ( 14 ). The sequence is found in references 14 and 271 .
Genetic organization of E. coli hisT operon. Figures within the parentheses indicate the size of the protein encoded by the respective genes. Dyad symmetries and possible ρ-independent terminators are denoted as → ← and Ω, respectively. Transcriptions are shown by wavy lines and the transcription pattern is only tentative, since none of the transcripts has been shown to exist in vivo. The pattern is deduced from S1 mapping of a few areas of the operon, primer extension analysis, and analysis of polarity ( 39 , 271 , 337 ). It is presently unclear whether dedB and folC are part of the hisT operon ( 15 , 271 ). However, a chromosomally encoded transcript covering the intracistronic region between hisT and dedB is present ( 271 ). Furthermore, the ρ-independent terminator present between dedB and folC is not active ( 39 ), suggesting that transcripts extend to the ρ-independent terminator following the dedD gene. The promoters Ppdx, Pdiv, and Pint were located on the chromosome ( 14 , 15 ), whereas PfolC was located on a plasmid ( 39 ). The dedD gene seems to have its own promoter located within the folC gene ( 39 ). The overlap of the asd stop codon with the hisT start codon is also indicated, suggesting translational coupling of the expression of these two genes ( 14 ). The sequence is found in references 14 and 271 .
Genetic organization of E. coli miaA operon. The sequence is found in reference 73 . The location of the different promoters was established by H.-C. T. Tsui and M. Winkler ( 386a ). Also shown is the region of translational overlap between the mutL and miaA genes and that translation terminates with UGA for both genes.
Genetic organization of E. coli miaA operon. The sequence is found in reference 73 . The location of the different promoters was established by H.-C. T. Tsui and M. Winkler ( 386a ). Also shown is the region of translational overlap between the mutL and miaA genes and that translation terminates with UGA for both genes.
Structure of queuosine and its derivatives.
Structure of queuosine and its derivatives.
Presence of modified nucleosides in position 34 (wobble position). Data compiled from reference 367 . To the left of the different modified nucleosides are bars indicating which codons the tRNA is able to read well (filled circles). An open circle denotes less preferred pairing to that codon. Underlined nucleosides are for tRNAs from Mycoplasma. If not otherwise stated N is an uncharacterized modified nucleoside and U* indicates a modified U; V4 = cmnm5U; V5 = cmnm5s2U; V8 = mcnm5U; V9 =cmnm5Um.
Presence of modified nucleosides in position 34 (wobble position). Data compiled from reference 367 . To the left of the different modified nucleosides are bars indicating which codons the tRNA is able to read well (filled circles). An open circle denotes less preferred pairing to that codon. Underlined nucleosides are for tRNAs from Mycoplasma. If not otherwise stated N is an uncharacterized modified nucleoside and U* indicates a modified U; V4 = cmnm5U; V5 = cmnm5s2U; V8 = mcnm5U; V9 =cmnm5Um.
Synthesis of ms2io6A37 and mcmo5U and the links to the synthesis of chorismic acid.
Synthesis of ms2io6A37 and mcmo5U and the links to the synthesis of chorismic acid.
Presence of modified nucleosides in position 37 (next to the 3'-side of the anticodon) and the coding capacities of tRNAs. Note also that Salmonella typhimurium contains ms2io6A instead of ms2i6A in corresponding tRNAs (see Fig. 8 ) ( 51 ). For explanation of symbols, see Fig. 1. Y1 (yW) = wybutosine; Y2 (o2yW) = wybutoxosine; A4 = i6A; A5 = ms2i6A; Z1 = cis-zeatin or io6A; N for AAG codon is a modified A, probably a t6A derivative.
Presence of modified nucleosides in position 37 (next to the 3'-side of the anticodon) and the coding capacities of tRNAs. Note also that Salmonella typhimurium contains ms2io6A instead of ms2i6A in corresponding tRNAs (see Fig. 8 ) ( 51 ). For explanation of symbols, see Fig. 1. Y1 (yW) = wybutosine; Y2 (o2yW) = wybutoxosine; A4 = i6A; A5 = ms2i6A; Z1 = cis-zeatin or io6A; N for AAG codon is a modified A, probably a t6A derivative.
Enzymatic mechanism for the synthesis of m5U54. The figure is modified from reference 154 .
Enzymatic mechanism for the synthesis of m5U54. The figure is modified from reference 154 .