Chapter 25 : Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes

Structures of the modified bases in tRNA and rRNA discussed in this chapter. Abbreviations for the modified bases and the enzymes that catalyze the modifications, which are enclosed in dotted lines, are indicated. Structures were redrawn or modified from Limbach et al. (1995) . Positions refer to eubacterial or eukaryotic tRNA unless rRNA is indicated. (A) i6A37, N 6-Isopentenyladenosine; (B) ms2i6A37, 2-methylthio-N 6-isopentenyladenosine; (C) Ψ (various positions), pseudouridine; (D)m6 2A2058 (in 23S rRNA) or 1518 and 1519 in 16S rRNA, N 6,N 6-dimethyladenosine; (E) s4U8, 4-thiouridine; (F) mcm5s2U34, 5-methoxycarbonylmethyl-2-thiouridine; (G) m2 2G26 , N 2,N 2-dimethylguanosine; (H) m5sU54, ribosylthymine; (I) ms2io6A37, 2-methylthio-N 6-(cis-hydroxyisopentenyl)adenosine; ( J) m6t6A37, N 6-methyl-N 6-threonylcarbamoyladenosine; (K) m2A37, 2-methyladenosine; (L) s2C32, 2-thiocytidine; (M) m1G37, 1-methylguanosine; (N) D, 5,6-dihydrouridine (various positions); (O) m7G46, 7-methylguanosine; (P) Q34, queuosine; (Q) preQ,34, 7-aminomethyl-7-deazaguanosine; (R) t6A37, N 6-threonylcarbamoyladenosine; (S) Ar(p)64, 2′-O-ribosyladenosine (phosphate); (T) m5C34, 48, 49, 5-methylcytidine; (U) m1А14, 58, 1-methyladenosine; (V) mnm5s2U34, 5-methylaminomethyl-2-thiouridine.

Structure of the monocistronic trmA operon (m5U54 methyltransferase; Fig. 1H ) in E. coli (89.65 min) and S. typhimurium. The locations of the FIS protein binding site and stringent discriminator in the P trmA promoter and the bifunctional transcription terminator structure at the ends of trmA and orfB ( yijD) are indicated. The divergently transcribed btuB gene encodes an outer membrane protein involved in vitamin B12 uptake. See text for additional details. Adapted from Björk (1995a) .

Structure of the E. coli (9.17 min) and S. typhimurium queA-tgt locus, which catalyzes Q34 biosynthesis ( Fig. IP ). tgt encodes the preQ,34 transglycosylase that inserts preQ, into tRNA ( Fig. 1Q ), and queA encodes epoxy-queuosine synthase, which catalyzes a step in the conversion of the inserted preQ,34 to Q34 (see Slany and Kersten, 1992 ). The locations of promoters and terminators are indicated along with transcripts detected on Northern blots ( Pogliano and Beckwith, 1994 ; Slany and Kersten, 1992 ). The relationship between the queA-tgt operon and the downstream yajC, secD, and secF genes is discussed in the text. Adapted from Björk (1995a) , based on data from Poghano and Beckwith (1994)V and Slany and Kersten (1992) .

Structure of the multifunctional trmD operon (m1G37 methyltransferase; Fig. 1M ) of E. coli (59.10 min) and S. typhimurium. The four genes of the operon rpsP (ribosomal protein S16), 21K (function unknown), trmD, and rplS (ribosomal protein L19) are transcribed into the single long mRNA indicated. The locations of the promoter (P), Rho-factor independent attenuator before the first (rpsP) gene, and terminator (T) at the end of the operon are indicated along with folded secondary structures in the mRNA that are thought to inhibit translation of the 21K and TrmD proteins. Control of the adjacent ffb (protein component of signal recognition protein) and yfiB (16K) (nonessential protein) genes is separate from that of the trmD operon. See text for additional details. Adapted from Björk (1995a) .

Structure of the multifunctional miaA operon (i6A37 prenyltransferase; Fig. 1A ) in E. coli K-12 (94.75 min). The figure is drawn to scale. Besides miaA, the multifunctional operon, which has no intercistronic spaces between urfl, urf2, amiB, and miaA, includes amiB (cell wall amidase), mutL (DNA mismatch repair), hfq (RNA chaperon global regulator), and the hflA region (protease). The locations of multiple standard Eσ70-specific promoters (P), heat shock Eσ32-specific promoters (P-HS), transcript processing sites (PT), transcriptional attenuators (Atn), and the transcription terminator at the end of the operon (TERM) are indicated. The Hfq chaperone is thought to act as a negative regulator of MiaA expression by destabilizing the miaA transcript. See text for additional details. Adapted from Tsui et al. (1996) .

Structure of the multifunctional ksgA operon (m6 2A1518 and 1519 dimethyltransferase; Fig. ID ) of E. coli (1.11 min). Besides ksgA, the operon consists of surA (peptidyl-prolyl cis-trans isomerase), pdxA (pyridoxine 5′-phosphate ring closure), apaG (unknown function), and apaH (diadenosine [AppppA] tetraphosphatase). The positions of the mapped P ksgA and P apaGH promoters are indicated. The locations of the P surA and P pdxA promoters are approximate. About 50% of ksgA transcription originates from promoters upstream from Р ksgA . See text for other details. Adapted from Roa et al. (1989) , based on Tormo et al. (1990) and van Gemen et al. (1987) .

Structure and transcriptional control of the rrnB rRNA operon of E. coli (89.74 min). The upper figure shows the structure of the entire operon, which extends from the PI and P2 promoters to the T1 and T2 transcription terminators and includes genes for 16S rRNA, tRNA2 Glu, 23S rRNA, and 5S rRNA. The lower figure shows the FIS binding sites and Up elements that contribute to expression from the P1 and P2 promoters and the box A element that functions in transcription antitermination of the nontranslated operon. See text and Gourse et al. (1996) for additional details. Adapted from Gourse et al. (1996) .

Antiattenuation model for induction of ermC operon (m62A2058 dimethyltransferase; Fig. 1D ) expression by the antibiotic erythromycin in B. subtilis and other gram-positive bacteria. The top two alternative mRNA secondary structures, which sequester the ermC ribosome binding site (RBS), form when the ermC leader transcript is translated in the absence of erythromycin. The bottom structure, which allows ermC translation, forms when ribosomes stall during translation of the leader peptide in the presence of erythromycin. See text for additional details. Adapted from Vellanoweth (1993) . Start leader, translation start codon of leader peptide; stop leader, translation stop codon of leader peptide; ermC SD, Shine-Dalgarno sequence preceding ermC; ermC start, ermC translation start codon.

Model for regulation of Tgt (Q34) transglycosylase activity by phosphorylation by protein kinase С (PKC) in mammalian cells. The unphosphorylated form of the Tgt enzyme (top) exists as a heterodimer containing a catalytic and a regulatory subunit. Phosphorylation of the regulatory subunit by PKC (bottom) causes the subunits to dissociate releasing the active catalytic subunit. Based on Morris et al. (1995) .

Differential expression of yeast TRM1 (m2 2G26 dimethyltransferase; Fig. 1G ) and MOD5 (i6A37 prenyltransferase; Fig. 1A ) that leads to isozyme sorting in yeast. (A) Transcription and translation start points in TRM1 and MOD5. TRM1 is transcribed from two different promoters. The larger isozyme (Trm1p-I) is translated from ATG1 in the longer transcript, and the smaller isozyme (Trm1p-II) is translated from ATG17, which is the first start codon in the shorter transcript. MOD5 is also transcribed from two promoters, but both transcripts contain the ATG1 and ATG12 translation start codons. The larger (Mod5p-I) and smaller (Mod5p-II) isozymes are translated from ATG1 and ATG12, respectively, in the larger bifunc-tional transcript. See text and Martin and Hopper (1994) for additional details. (B) Signals for targeting and isozyme distribution of the TRM1 and MOD5 gene products in yeast. The amino acid sequences of the isozymes are indicated by the lines. Open boxes, regions sufficient for efficient targeting to mitochondria; shaped box in Trm1p-I, region that improves import into mitochondria; hatched boxes, nuclear targeting or localization signals. + and –, present and absent, respectively, in the indicated subcellular compartments. See text and Martin and Hopper (1994) for additional details. Adapted from Martin and Hopper (1994) .