Conserved economics of transcription termination in eubacteria

Abstract

A secondary structure in the nascent RNA followed by a trail of U residues is believed to be necessary and sufficient to terminate transcription. Such structures represent an extremely economical mechanism of transcription termination since they function in the absence of any additional protein factors. We have developed a new algorithm, GeSTer, to identify putative terminators and analysed all available complete bacterial genomes. The algorithm classifies the structures into five classes. We find that potential secondary structure sequences are concentrated downstream of coding regions in most bacterial genomes. Interestingly, many of these structures are not followed by a discernible U-trail. However, irrespective of the nature of the trail sequence, the structures show a similar distribution, indicating that they serve the same purpose. In contrast, such a distribution is absent in archaeal genomes, indicating that they employ a distinct mechanism for transcription termination. The present algorithm represents the fastest and most accurate algorithm for identifying terminators in eubacterial genomes without being restricted by the classical Escherichia coli paradigm.

Figure 1

The anatomy of an imperfect palindrome. Features used to define a terminator structure by GeSTer. The numbers in parentheses denote the default number of bases (or base pairs) for each region. The trail consists of the 10 nt immediately following the structure.

Figure 2

Correlation of GC content with the basal ΔG of the region downstream of coding sequences. ΔG was calculated with a 60 base window using mfold as described (23). The line denoting the best linear regression fit is shown.

Figure 3

Relative orientation of adjacent genes on the genome. Adjacent genes in the genome could be both on the regular (A) or complementary strand (B). Alternatively, the genes could be oriented convergently (C) or divergently (D). The region between convergent genes constitutes the ‘pure downstream’ region while the region between divergent genes constitutes the ‘pure upstream’ region (see text).

Figure 4

Classification of terminators. The terminators are denoted schematically with the relevant regions highlighted. (A) L-shaped or E.coli type; (B) I-shaped or mycobacterial type; (C) V-shaped or Streptomyces type; (D) U-shaped or tandem type; (E) X-shaped or convergent type. The arrowhead denotes the direction of transcription. The individual structures in V-, U- and X-shaped structures could be either L- or I-shaped.

Figure 5

Representative distribution of putative terminators in bacteria. Distribution of all (red) and the best (magenta) structures identified by GeSTer in E.coli (A) and P.aeruginosa (C) with respect to the stop codon. The number of structures were aggregated over a window of 10 bases slid one base at a time. Distribution of the strongest structures (green) amongst the best candidate terminators in E.coli (B) and P.aeruginosa (D) aggregated over 10 bases. The strongest structures were selected with a ΔG filter of mean – SD of ΔG of all the best candidate structures, i.e. those structures with a ΔG lower than the mean by at least 1 SD.

Figure 6

Representative distribution of putative terminators in Archaea. Distribution of all (red) and the best (magenta) structures identified by GeSTer in Archaeoglobus fulgidus (A) and Halobacterium sp. (C) with respect to the stop codon. The number of structures were aggregated over a window of 10 bases slid one base at a time. Distribution of the strongest structures (green) amongst the best candidate terminators in A.fulgidus (B) and Halobacterium sp. (D). The strongest structures were selected with a ΔG filter of mean – SD of ΔG of all the best candidate structures, i.e. those structures with a ΔG lower than the mean by at least 1 SD.

Figure 7

Representative distribution of L- and I-shaped terminators in Bacteria. Distribution of the best candidate terminators (magenta) and their assignment as L- (light blue) or I-shaped (dark blue) structures in different bacteria is shown. The number of structures was aggregated over a window of 10 bases slid one base at a time.

Figure 7

Representative distribution of L- and I-shaped terminators in Bacteria. Distribution of the best candidate terminators (magenta) and their assignment as L- (light blue) or I-shaped (dark blue) structures in different bacteria is shown. The number of structures was aggregated over a window of 10 bases slid one base at a time.

Figure 8

Representative distribution of X-, U- and V-shaped terminators in Bacteria. Distribution of X- (red) and U-shaped (green) structures in E.coli (A and C) and P.aeruginosa (B and D), respectively. (E) The overall distribution of V-shaped structures in all bacteria. The number of structures were aggregated over a window of 10 bases slid one base at a time.

Figure 9

Correlation of GC content with a preference for I-shaped structures. The line denoting the best linear regression fit is shown.