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Chapter 15 : Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression

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Abstract:

Aminoacyl-tRNA synthetases (AARS) form a class of essential enzymes whose main role is to ligate amino acids to tRNAs. This chapter reviews what is known about the AARS genes, their chromosomal localization, their organization, and the regulation of their expression. It focuses exclusively on bacterial systems, mainly and , for which a great deal of information is available.

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15

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Gene Expression and Regulation
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Amino Acid Addition
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Figures

Image of Figure 1
Figure 1

The AARS genes. The AARS genes are shown in bold with other contiguous genes. Positions are given in min and come from DNA sequence alignment of a revised, integrated genomic restriction map ( ). The genes for which no DNA sequence data are available are indicated in italics and come from the E. linkage map ( ). Asterisks indicate that the gene has not been mapped accurately. Arrows indicate the direction of transcription. Co-transcribed genes are covered by a single arrow. The genes within brackets are placed on DNA fragments whose complete sequence is known ( ). The replication origin is shown as oriC at 84 min.

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15
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Image of Figure 2a
Figure 2a

Regulatory regions of the AARS genes. Panel A shows the sequences from −197 to −98 and panel B from −97 to +2. Nucleotides are numbered from the base 5' to the first nucleotide (-1) of the initiation codons. When regulatory regions are longer than 197 nucleotides or when the genetic organization is complex, as explained later in the legend, more than 197 nucleotides are shown. The orientation of the genes or open reading frames is shown by arrows. When transcription is from left to right, the -10 and -35 regions of the promoters are underlined, with “−10” and “−35” indicated over the sequence, and transcription initiation sites are indicated with right arrows. If transcription is from right to left, the −10 and −35 regions are overlined, with “−10” and “−35” indicated under the sequence, and transcription initiation sites are indicated with left arrows. Dotted underlining of the −10 and −35 regions means that they were identified with a search protocol ( ) in the regulatory regions when no experimental data were available. The regions with dyad symmetry are shown with arrows over the sequence. Open reading frames are underlined with their names over the sequence. Putative rho-independent transcription terminators are identified by the dyad symmetry and the letter t over the downstream T residues. The Shine-Dalgarno sequences are underlined, with “SD” written over the sequence. The initiation codons are also underlined. GATC sequences recognized by the methylase are boxed. Putative Fis protein binding sites are underlined, with FIS under the sequence. Putative integration host factor protein binding sites are underlined, with IHF under the sequence. In general, a line in panel A joins to the corresponding line in panel B. The two exceptions are and for which the sequences downstream of the ATGs in panel A are not shown and the corresponding sequences in panel B show only the ends of and The 5' end of the in vivo synthesized mRNA is known ( ). The dyad symmetry around the -10 region corresponds to a region protected by AlaRS ( ); the significance of the upstream dyad symmetry is not known. The 5' and 3' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping ( ). The synthetase gene is preceded by (ending with an UAA codon), whose putative rho-independent transcription termination site is shown. The 5' and 3' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping, respectively ( ). The gene is expressed divergently from whose putative transcription initiation signals are shown ( ). The 5' and 3' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping ( ). The 5' and 3' ends of the in vivo and in vitro synthesized mRNA are known by S1 mapping and the molecular weight (MW) is known by Northern blot analysis ( ). The synthetase gene is preceded by whose transcription termination site is shown. The 5' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping and the MW, by Northern blot ( ). The overlined nucleotides and the dyad symmetry after the third transcription initiation site correspond to a tRNA-like structure (see text). Panel A shows the upstream sequences. Panel B shows the putative promoter and the translation initiation site (with the ATG) on the first line; the second line shows the end of the short intergenic region, and the translation initiation site with the ATG. Only sequence information is available ( ). The open reading frame terminating 27 nucleotides upstream of is indicated as “orf.” The gene is located immediately downstream of which encodes a protein of unknown function ( ). The 5' end of the in vivo synthesized mRNA of is known by S1 mapping and its MW, by Northern blot ( ). Panel A shows the leftward promoter (on the first line), the intergenic region (straddling the first and second lines), and the rightward promoter with its ATG initiation codon (on the second line). Panel B shows the end of and the internal promoter. The sequence of is interrupted (at the “||”) from eight nucleotides downstream of the internal transcription initiation site to two nucleotides upstream of its translation termination codon. The 5' ends of in vivo synthesized mRNAs are known by S1 mapping and primer extension and their MW by Northern blot ( ). sequence information only ( ). The gene coding for a 19-kDa lipoprotein ( ) starts 17 nucleotides downstream of the U of the UAA translation termination codon of panel A shows the upstream sequences with the end of (on the first line and the beginning of the second line), the intergenic region, and the promoter and its initiation codon. Panel B shows the end of the short intergenic region, and the translation initiation site of The 5' and 3' ends of the mRNA are approximately known by S1 mapping of in vivo synthesized transcripts; the MW of the transcript has been determined by Northern blot ( ). The 5' ends of in vivo synthesized mRNAs are known by primer extension ( ). The regions protected by the Lrp protein are overlined ( ). The nucleotides duplicated by the IS2 insertions in the promoter are underlined. The orientations of the two insertions are different and are indicated as (I) and (II) ( ). Panel A shows the upstream sequences with the upstream promoter, with its transcription initiation site and a 235-nucleotide-long interruption of the mRNA (first line), the tRNA-like structures (line two), the internal terminator, and the leftward translation initiation site. Panel B shows the −10 and −35 regions, the downstream promoter, and the translation initiation site of The 5' and 3' ends of in vitro and in vivo transcripts were determined with either S1 or primer extension mapping ( ). Panel A shows the promoter with the 3' end of the putative integration host factor binding site, the leader peptide the attenuator, and the sequences upstream of Panel B shows the rest of the upstream sequences and the translation initiation site on the first line; the second line shows the end of the intergenic region, and the translation initiation site of The 5' end of the in vitro synthesized mRNA and the 3' end of the attenuated leader are known by SI mapping ( ). The 5' end of in vivo synthesized mRNA is known by primer extension ( ). Sequence information only ( ). The 5' end of in vivo synthesized mRNA is known by primer extension ( ). The different domains of the translational operator are indicated. The anticodon-like sequence CGT of domain 2 is underlined. The 5' end of in vivo synthesized mRNA is approximately known by S1 mapping ( ). The 5' end of in vivo synthesized mRNA is approximately known by RNAse T2 mapping ( ). The 5' end is known by S1 mapping of in vitro and in vivo transcripts and primer extension of in vivo transcripts, and the 3' end is known by in vitro transcripts of the mRNA ( ).

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15
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Image of Figure 2b
Figure 2b

Regulatory regions of the AARS genes. Panel A shows the sequences from −197 to −98 and panel B from −97 to +2. Nucleotides are numbered from the base 5' to the first nucleotide (-1) of the initiation codons. When regulatory regions are longer than 197 nucleotides or when the genetic organization is complex, as explained later in the legend, more than 197 nucleotides are shown. The orientation of the genes or open reading frames is shown by arrows. When transcription is from left to right, the -10 and -35 regions of the promoters are underlined, with “−10” and “−35” indicated over the sequence, and transcription initiation sites are indicated with right arrows. If transcription is from right to left, the −10 and −35 regions are overlined, with “−10” and “−35” indicated under the sequence, and transcription initiation sites are indicated with left arrows. Dotted underlining of the −10 and −35 regions means that they were identified with a search protocol ( ) in the regulatory regions when no experimental data were available. The regions with dyad symmetry are shown with arrows over the sequence. Open reading frames are underlined with their names over the sequence. Putative rho-independent transcription terminators are identified by the dyad symmetry and the letter t over the downstream T residues. The Shine-Dalgarno sequences are underlined, with “SD” written over the sequence. The initiation codons are also underlined. GATC sequences recognized by the methylase are boxed. Putative Fis protein binding sites are underlined, with FIS under the sequence. Putative integration host factor protein binding sites are underlined, with IHF under the sequence. In general, a line in panel A joins to the corresponding line in panel B. The two exceptions are and for which the sequences downstream of the ATGs in panel A are not shown and the corresponding sequences in panel B show only the ends of and The 5' end of the in vivo synthesized mRNA is known ( ). The dyad symmetry around the -10 region corresponds to a region protected by AlaRS ( ); the significance of the upstream dyad symmetry is not known. The 5' and 3' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping ( ). The synthetase gene is preceded by (ending with an UAA codon), whose putative rho-independent transcription termination site is shown. The 5' and 3' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping, respectively ( ). The gene is expressed divergently from whose putative transcription initiation signals are shown ( ). The 5' and 3' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping ( ). The 5' and 3' ends of the in vivo and in vitro synthesized mRNA are known by S1 mapping and the molecular weight (MW) is known by Northern blot analysis ( ). The synthetase gene is preceded by whose transcription termination site is shown. The 5' ends of the in vivo synthesized mRNA are known by primer extension and S1 mapping and the MW, by Northern blot ( ). The overlined nucleotides and the dyad symmetry after the third transcription initiation site correspond to a tRNA-like structure (see text). Panel A shows the upstream sequences. Panel B shows the putative promoter and the translation initiation site (with the ATG) on the first line; the second line shows the end of the short intergenic region, and the translation initiation site with the ATG. Only sequence information is available ( ). The open reading frame terminating 27 nucleotides upstream of is indicated as “orf.” The gene is located immediately downstream of which encodes a protein of unknown function ( ). The 5' end of the in vivo synthesized mRNA of is known by S1 mapping and its MW, by Northern blot ( ). Panel A shows the leftward promoter (on the first line), the intergenic region (straddling the first and second lines), and the rightward promoter with its ATG initiation codon (on the second line). Panel B shows the end of and the internal promoter. The sequence of is interrupted (at the “||”) from eight nucleotides downstream of the internal transcription initiation site to two nucleotides upstream of its translation termination codon. The 5' ends of in vivo synthesized mRNAs are known by S1 mapping and primer extension and their MW by Northern blot ( ). sequence information only ( ). The gene coding for a 19-kDa lipoprotein ( ) starts 17 nucleotides downstream of the U of the UAA translation termination codon of panel A shows the upstream sequences with the end of (on the first line and the beginning of the second line), the intergenic region, and the promoter and its initiation codon. Panel B shows the end of the short intergenic region, and the translation initiation site of The 5' and 3' ends of the mRNA are approximately known by S1 mapping of in vivo synthesized transcripts; the MW of the transcript has been determined by Northern blot ( ). The 5' ends of in vivo synthesized mRNAs are known by primer extension ( ). The regions protected by the Lrp protein are overlined ( ). The nucleotides duplicated by the IS2 insertions in the promoter are underlined. The orientations of the two insertions are different and are indicated as (I) and (II) ( ). Panel A shows the upstream sequences with the upstream promoter, with its transcription initiation site and a 235-nucleotide-long interruption of the mRNA (first line), the tRNA-like structures (line two), the internal terminator, and the leftward translation initiation site. Panel B shows the −10 and −35 regions, the downstream promoter, and the translation initiation site of The 5' and 3' ends of in vitro and in vivo transcripts were determined with either S1 or primer extension mapping ( ). Panel A shows the promoter with the 3' end of the putative integration host factor binding site, the leader peptide the attenuator, and the sequences upstream of Panel B shows the rest of the upstream sequences and the translation initiation site on the first line; the second line shows the end of the intergenic region, and the translation initiation site of The 5' end of the in vitro synthesized mRNA and the 3' end of the attenuated leader are known by SI mapping ( ). The 5' end of in vivo synthesized mRNA is known by primer extension ( ). Sequence information only ( ). The 5' end of in vivo synthesized mRNA is known by primer extension ( ). The different domains of the translational operator are indicated. The anticodon-like sequence CGT of domain 2 is underlined. The 5' end of in vivo synthesized mRNA is approximately known by S1 mapping ( ). The 5' end of in vivo synthesized mRNA is approximately known by RNAse T2 mapping ( ). The 5' end is known by S1 mapping of in vitro and in vivo transcripts and primer extension of in vivo transcripts, and the 3' end is known by in vitro transcripts of the mRNA ( ).

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15
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Image of Figure 3
Figure 3

Chromosomal location of AARS. The AARS (in bold) are shown with other contiguous or nearby genes. Positions are given in degrees (on the 360° map) and come from the revised genetic map of ( ) except those for the and genes ( ) and for the and genes ( ). Genes for which no DNA sequence data are available are in italics. Asterisks indicate genes that have been mapped by hybridization with an ordered collection of DNA fragments cloned in yeast artificial chromosomes ( ) and, accordingly, for which the limits of their possible position on the chromosome is given. Arrows show the direction of transcription. Co-transcribed genes are covered by a single arrow, but arrows covering only a single gene do not exclude co-transcription of adjacent genes. Genes within brackets areplaced on a DNA segment whose complete sequence is known. The position of the biosynthetic operon (247°) is indicated, since it contains the same regulatory elements as the majority of AARS genes (see text).

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15
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Image of Figure 4
Figure 4

Conserved regulatory sequences in 5' noncoding regions of us, and AARS and biosynthetic genes. The sequences shown are located at various distances upstream of the initiation codon. For an operon, the initiation codon is that of the first gene indicated on the left. Secondary structures resembling a factor-independent transcription terminator are indicated by inverted arrows. Regions of conserved sequence are boxed and, for clarity, have been separated for the spp. (A) and and (B). They comprise the T-box element and a second shorter consensus in the promoter proximal half of the terminator stem showing some complementarity to the central part of the T-box (see text). Bct = Bsu = Bst = LL = Lc =

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15
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Image of Figure 5
Figure 5

Schematic diagram of conserved regulatory structures of T-box/terminator containing AARS genes in spp. The schematic diagram is based on the 3-domain (I, II, and III) structural model of the leader ( ) and shows common features shared by genes containing T-box/terminator. The boxed segment containing the T-box and the terminator is shown in detail in Fig. 4 , where the known sequences are aligned. +1 indicates the transcription start point. The small subdivided box in domain I represents the “specifier codon” ( ) (see text) specific for the appropriate amino acid; the specifier codon is found at the identical position in the leaders of most tRNA synthetase genes. Between stem-loops II and III, which can vary in their extension, is a perfectly conserved CGUUA sequence. Additional somewhat less well conserved sequences are marked by an asterisk and a number: *1 = CAGAGA, *2 = GxUG ( ).

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15
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Image of Figure 6
Figure 6

Effect of a T-box deletion in presence or absence of intact terminator structure. The regulatory region (wild-type and modified versions) has been fused to the gene. The resulting transcriptional fusions have been integrated in the chromosome in single copy and their expression quantified by measuring the β-galactose activity. The values given are relative (reproduced and modified from [ ]) and are based on those of a wild-type fusion representing 100%. The T-box element is indicated by a box. The 6-bp deletion within the T-box element (-GGGTGG-, compare Fig. 4 ) is the same in the fusions B and D (i.e., in the presence or absence of an intact terminator structure). The terminator stem-loop structure is indicated diagrammatically. In fusion C and D, the half of the stem loop proximal to the gene is deleted.

Citation: Putzer H, Grunberg-Manago M, Springer M. 1995. Bacterial Aminoacyl-tRNA Synthetases: Genes and Regulation of Expression , p 293-333. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch15
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References

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