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Chapter 23 : Regulation by Termination-Antitermination: a Genomic Approach

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Abstract:

A variety of transcription termination-antitermination regulatory processes, often called transcription attenuation mechanisms, have been discovered in phage and microbial species. This chapter discusses known and predicted examples of regulation by antitermination-termination at sites specifying an intrinsic terminator, deduced by examining the entire genome. In many mechanisms of transcription attenuation, the termination decision is based on whether an RNA antiterminator (AT) structure has been previously formed. To identify the operons of that may be regulated by transcription termination-antitermination, a computer program that searches the genome for overlapping AT/terminator (T) elements was developed based on nucleotide sequence and free energy criteria. The program designed was used to search the entire genome sequence of for sequences that could specify transcript AAT, AT, and T structures. The number of gene sequences identified that were preceded by potential AT and T structures was dependent on the parameters employed in the program. Conservation of the specific transcription attenuation regulatory mechanisms used for many genes encoding aminoacyl-tRNA synthetases or amino acid biosynthetic enzymes of and other gram-positive organisms has been well documented by Grundy and Henkin.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23

Key Concept Ranking

Transcription Termination
0.51430106
RNA Polymerase
0.5138889
Transcription Initiation
0.5113954
Bacillus subtilis
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Figures

Image of FIGURE 1a
FIGURE 1a

Characteristics of the presumed AT/T or AAT/AT/T regulatory regions preceding genes (A), (B), (C), and (D). Sequences corresponding to the -35 and -10 elements of the putative sigma A promoter preceding each gene are indicated in outlined letters. Sequences corresponding to the T, AT, and AAT structures are underlined with a single solid line, a single wavy line, and double solid lines, respectively. Common bases in the AT and T structures are in boldface, and common bases in the AAT and AT structures are in boldface italics. A more complete description of these sequences and structures can be obtained from our website (http://cmgm.stanford.edu/∼merino/Bacillus_subtilis/index.html .

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
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Image of FIGURE 1b
FIGURE 1b

Characteristics of the presumed AT/T or AAT/AT/T regulatory regions preceding genes (A), (B), (C), and (D). Sequences corresponding to the -35 and -10 elements of the putative sigma A promoter preceding each gene are indicated in outlined letters. Sequences corresponding to the T, AT, and AAT structures are underlined with a single solid line, a single wavy line, and double solid lines, respectively. Common bases in the AT and T structures are in boldface, and common bases in the AAT and AT structures are in boldface italics. A more complete description of these sequences and structures can be obtained from our website (http://cmgm.stanford.edu/∼merino/Bacillus_subtilis/index.html .

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
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Image of FIGURE 1c
FIGURE 1c

Characteristics of the presumed AT/T or AAT/AT/T regulatory regions preceding genes (A), (B), (C), and (D). Sequences corresponding to the -35 and -10 elements of the putative sigma A promoter preceding each gene are indicated in outlined letters. Sequences corresponding to the T, AT, and AAT structures are underlined with a single solid line, a single wavy line, and double solid lines, respectively. Common bases in the AT and T structures are in boldface, and common bases in the AAT and AT structures are in boldface italics. A more complete description of these sequences and structures can be obtained from our website (http://cmgm.stanford.edu/∼merino/Bacillus_subtilis/index.html .

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
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Image of FIGURE 1d
FIGURE 1d

Characteristics of the presumed AT/T or AAT/AT/T regulatory regions preceding genes (A), (B), (C), and (D). Sequences corresponding to the -35 and -10 elements of the putative sigma A promoter preceding each gene are indicated in outlined letters. Sequences corresponding to the T, AT, and AAT structures are underlined with a single solid line, a single wavy line, and double solid lines, respectively. Common bases in the AT and T structures are in boldface, and common bases in the AAT and AT structures are in boldface italics. A more complete description of these sequences and structures can be obtained from our website (http://cmgm.stanford.edu/∼merino/Bacillus_subtilis/index.html .

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
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References

/content/book/10.1128/9781555817992.chap23
1. Aymerich, S., , and M. Steinmetz . 1987 . Cloning and preliminary characterization of the sacS locus from Bacillus subtilis which controls the regulation of the exoenzyme levansucrase . Mol. Gen. Genet . 208:114120.
2. Cassan, M., , J. Ronceray, , and J. C. Patte . 1983 . Nucleotide sequence of the promoter region of the E. coli lysC gene . Nucleic Acids Res . 11:61576166.
3. Ebbole, D. J., , and H. Zalkin . 1987 . Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis . J. Biol. Chem. 262:82748287.
4. Grandoni, J. A., , S. B. Fulmer, , V. Brizzio, , S. A. Zahler, , and J. M. Calvo . 1993 . Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine . J. Bacteriol . 175: 75817593.
5. Grundy, F. J., , and T. M. Henkin . 1993 . tRNA as a positive regulator of transcription antitermination in B. subtilis . Cell 74:475482.
6. Grundy, F. J., , and T. M. Henkin . 1994 . Conservation of transcription antitermination mechanisms in aminoacyltRNA synthetase and amino acid biosynthesis genes in gram-positive bacteria . J. Mol. Biol . 235:798804.
7. Grundy, F. J., , and T. M. Henkin . 1998 . The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria . Mol. Microbiol . 30:737749.
8. Henkin, T. M. 1996 . Control of transcription termination in prokaryotes . Annu. Rev. Genet. 30:3557.
9. Kochhar, S., , and H. Paulus . 1996 . Lysine-induced premature transcription termination in the lysC operon of Bacillus subtilis . Microbiology 142:16351639.
10. Landick, R., , C. L. Turnbough, , Jr., and C. Yanofsky. 1996 . Transcription attenuation, p. 1263-1286. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, , E. C. C,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaecter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, vol. 1. American Society for Microbiology, Washington D.C.
11. Lee, F., , and C. Yanofsky . 1977 . Transcription termination at the trp operon attenuators of Escherichia coli and Salmonella typhimurium: RNA secondary structure and regulation of termination . Proc. Natl. Acad. Sci. USA 74: 43654369.
12. Lu, Y., , R. J. Turner, , and R. L. Switzer . 1995 . Roles of the three transcriptional attenuators of the Bacillus subtilis pyrimidine biosynthetic operon in the regulation of its expression . J. Bacteriol . 177:13151325.
13. Lu, Y., , R. J. Turner, , and R. L. Switzer . 1996 . Function of RNA secondary structures in transcriptional attenuation of the Bacillus subtilis pyr operon . Proc. Natl. Acad. Sci. USA 93:1446214467.
14. Mulligan, M. E., , D. K. Hawley, , R. Entriken, , and W. R. McClure . 1984 . Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity . Nucleic Acids Res . 12: 789800.
15. Pearson, W. R. 2000 . Flexible sequence similarity searching with the FAST A3 program package . Methods Mol. Biol . 132:185219.
16. Piatt, P., , and J. P. Richardson, . 1992 . Escherichia coli rho factor: protein and enzyme of transcription termination, p. 365388. In S. L. McKnight, and K. R. Yamamoto (ed.) Transcription Regulation, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
17. Roberts, J. W., 1996 . Transcription termination and its control, p. 2745. In E. C. C. Lin, and A. S. Lynch (ed.), Regulation of Gene Expression in Escherichia coli. R. G. Landes Company and Chapman Hall, Austin, Tex.
18. Sarsero, J. P., , E. Merino, , and C. Yanofsky . 2000 . A Bacillus subtilis operon containing genes of unknown function senses tRNATrp charging and regulates expression of the genes of tryptophan biosynthesis . Proc. Natl. Acad Sci. USA 97:26562661.
19. Shimotsu, H., , M. I. Kuroda, , C. Yanofsky, , and D. J. Henner . 1986 . Novel form of transcription attenuation regulates expression the Bacillus subtilis tryptophan operon . J. Bacteriol . 166:461471.
20. Turner, R. J., , Y. Lu, , and R. L. Switzer . 1994 . Regulation of the Bacillus subtilis pyrimidine biosynthetic (pyr) gene cluster by an autogenous transcriptional attenuation mechanism . J. Bacteriol . 176:37083722.
21. Yanofsky, C. 2000 . Transcription attenuation: once viewed as a novel regulatory strategy . J. Bacteriol . 182:18.
22. Zuker, M., , and P. Stiegler . 1981 . Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information . Nucleic Acids Res . 9:133148.

Tables

Generic image for table
TABLE 1

genes known or proposed to be regulated by antiterminator and terminator sequences and structures

The homologous gene is also known to be regulated by attentuation.

The homologous gene of was found by our program to have an attenuator.

Gene regulated by the T-box mechanism ( ).

Gene regulated by the S-box mechanism ( ).

Gene regulated by TRAP (trp RNA-binding attenuation protein) ( ).

Direction of transcription of the upstream gene. S, same direction, D, opposite direction.

Sequences that form antiterminator structures are in italics, and those that form terminator structures are in boldface.

Coding sequences are in upper case, and intergenic sequences are in lower case.

Based on GenBank sequence annotations, our program reads the upstream sequence of every gene. This sequence is considered as the analysis window and its default value is 300 nt. In this window, the program searches for a run of t's (rts) that would correspond to a run of u's in RNA. The size of the rts selected is 6 nt, at least five of which must be “ts”. tttatt or tttttc are examples of acceptable rts. The arbitrarily selected maximum acceptable space between the its and the first base of the downstream gene, is 110 nt. For every rts, the program looks for the most stable secondary structure that could be formed within the first upstream 60 nt. Initially, the secondary structure that could be formed from this 60 nt is predicted using the FoldRNA program ( ). Trie only secondary structure that is considered part of a T is the stem-and'loop structure (SLS). If the sequence analyzed contains more than one SLS, only the one closest to the rts is considered in the analysis. In the event that the folding predictions yield structures different than an SLS (e.g., cloverleaf like), the first nt of the 60 nt long sequence is removed and the search for the SLS is repeated recursively until the program finds the sequence, which when folded, corresponds to the most stable SLS. This SLS is considered part of a T only if the base at the bottom of the stem is no more than 4 nt from the rts, the maximum number of loops in the structure is 3, and if the free energy of the structure is at least —0.2 kcal/mol per nucleotide.

For every T found, the program then searches for the presence of an associated AT. The program begins by scanning a 60-nt sequence upstream of the middle of the main T loop. The program then finds the most stable SLS using the procedure described in the T analysis. An SLS is considered an AT on the basis of the following somewhat arbitrary preferences: If at least 3 bases of its stem overlap with the T sequence, the maximum number of loops of the structure is 4, and if it has a free energy that is at least one fourth that of its corresponding T. The previous analysis is also repeated on each AT, searching for its corresponding AAT structure. To consider the AAT and AT as mutually exclusive structures, they must share at least 3 bases. The free energy of the AAT must be at least one fourth that of its associated AT. Finally, the program looks for promoter sequences in the 300-bp upstream region of the AT/T elements using the algorithm proposed by Mulligan et al. ( ). It also searches for some other regulatory sequence in the RNA leader region, such as the T-box sequence ( ), or the TRAP binding site ( ).

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
Generic image for table
TABLE 2a

genes known or proposed to be regulated by anti-antiterminator, antiterminator, and terminator sequences and structures

The homologous gene is also known to be regulated by attenuation.

The homologous gene of was found by our program to have an attenuator.

Gene regulated by the T-box mechanism ( ).

Gene regulated by the S-box mechanism ( ).

Gene regulated by TRAP (trp RNA–binding attenuation protein ( ).

Direction of transcription of the upstream gene. S, same direction, D, opposite direction.

Sequences that form anti-antiterminator structures are underlined, those that form antiterminator structures are in italics, and those that form terminator structures are in boldface.

Coding sequences are in upper case, and intergenic sequences are in lower case.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
Generic image for table
TABLE 2b

genes known or proposed to be regulated by anti-antiterminator, antiterminator, and terminator sequences and structures

The homologous gene is also known to be regulated by attenuation.

The homologous gene of was found by our program to have an attenuator.

Gene regulated by the T-box mechanism ( ).

Gene regulated by the S-box mechanism ( ).

Gene regulated by TRAP (trp RNA–binding attenuation protein ( ).

Direction of transcription of the upstream gene. S, same direction, D, opposite direction.

Sequences that form anti-antiterminator structures are underlined, those that form antiterminator structures are in italics, and those that form terminator structures are in boldface.

Coding sequences are in upper case, and intergenic sequences are in lower case.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
Generic image for table
TABLE 2c

genes known or proposed to be regulated by anti-antiterminator, antiterminator, and terminator sequences and structures

The homologous gene is also known to be regulated by attenuation.

The homologous gene of was found by our program to have an attenuator.

Gene regulated by the T-box mechanism ( ).

Gene regulated by the S-box mechanism ( ).

Gene regulated by TRAP (trp RNA–binding attenuation protein ( ).

Direction of transcription of the upstream gene. S, same direction, D, opposite direction.

Sequences that form anti-antiterminator structures are underlined, those that form antiterminator structures are in italics, and those that form terminator structures are in boldface.

Coding sequences are in upper case, and intergenic sequences are in lower case.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
Generic image for table
TABLE 2d

genes known or proposed to be regulated by anti-antiterminator, antiterminator, and terminator sequences and structures

The homologous gene is also known to be regulated by attenuation.

The homologous gene of was found by our program to have an attenuator.

Gene regulated by the T-box mechanism ( ).

Gene regulated by the S-box mechanism ( ).

Gene regulated by TRAP (trp RNA–binding attenuation protein ( ).

Direction of transcription of the upstream gene. S, same direction, D, opposite direction.

Sequences that form anti-antiterminator structures are underlined, those that form antiterminator structures are in italics, and those that form terminator structures are in boldface.

Coding sequences are in upper case, and intergenic sequences are in lower case.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
Generic image for table
TABLE 2e

genes known or proposed to be regulated by anti-antiterminator, antiterminator, and terminator sequences and structures

The homologous gene is also known to be regulated by attenuation.

The homologous gene of was found by our program to have an attenuator.

Gene regulated by the T-box mechanism ( ).

Gene regulated by the S-box mechanism ( ).

Gene regulated by TRAP (trp RNA–binding attenuation protein ( ).

Direction of transcription of the upstream gene. S, same direction, D, opposite direction.

Sequences that form anti-antiterminator structures are underlined, those that form antiterminator structures are in italics, and those that form terminator structures are in boldface.

Coding sequences are in upper case, and intergenic sequences are in lower case.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
Generic image for table
TABLE 2f

genes known or proposed to be regulated by anti-antiterminator, antiterminator, and terminator sequences and structures

The homologous gene is also known to be regulated by attenuation.

The homologous gene of was found by our program to have an attenuator.

Gene regulated by the T-box mechanism ( ).

Gene regulated by the S-box mechanism ( ).

Gene regulated by TRAP (trp RNA–binding attenuation protein ( ).

Direction of transcription of the upstream gene. S, same direction, D, opposite direction.

Sequences that form anti-antiterminator structures are underlined, those that form antiterminator structures are in italics, and those that form terminator structures are in boldface.

Coding sequences are in upper case, and intergenic sequences are in lower case.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23
Generic image for table
TABLE 3

Homologous genes of and both of which appear to be regulated by transcription attenuation

is not regulated by attenuation ( ), but its paralog, , is regulated by antiterminator-terminator structures.

Length of the fragments with maximum similarity in the alignment of their corresponding protein sequences.

Percentage of identical residues common to the aligned protein sequences.

Percentage of biochemically equivalent residues common to the aligned protein sequences.

Citation: Merino E, Yanofsky C. 2002. Regulation by Termination-Antitermination: a Genomic Approach, p 323-336. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch23

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