Promoter propagation in prokaryotes

Abstract

Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. In many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large impact on rapid adaptation of novel or cryptic functions. Querying all publicly available prokaryotic genomes (1362) uncovered >4000 families of highly conserved PMPs (50 to 100 long with ≥80% nt identity) in 1043 genomes from 424 different genera. The genomes with the largest number of PMP families are Anabaena variabilis (28 families), Geobacter uraniireducens (27 families) and Cyanothece PCC7424 (25 families). Family size varied from 2 to 93 homologous promoters (in Desulfurivibrio alkaliphilus). Some PMPs are present in particular species, but some are conserved across distant genera. The identified PMPs represent a conservative dataset of very recent or conserved events of mobilization of non-coding DNA and thus they constitute evidence of an extensive reservoir of recyclable regulatory sequences for rapid transcriptional rewiring.

Figure 1.

Identification of PMPs. Dashed boxes represent 100 nt defined promoters (green arrows), downstream CDSs (dark blue and pink arrows) and upstream CDSs (orange and blue arrows) used for BLAST alignments. Those regions were taken ±50 nt of the TLS of the downstream CDSs. Two promoters are considered mobile if they align over >50 nt with at least 80% identity (green shadow), while their upstream CDSs (A and C) and downstream CDSs (B and D) do not align.

Figure 2.

PMP regulating 10 non-homologous CDSs. (A) Alignment of the multiple copies of a PMP in T. brennaborense. A highly conserved core can be observed in the region −120 to −5 upstream of the TLS of the downstream CDSs. Color blocks represent conserved residues. The location of the TLS is indicated. (B) Alignment of the CDSs downstream of the PMP. No sequence conservation is observed. (C) Location of the PMPs (black arrows) along the 3-Mb circular chromosome (Mb are marked as 1, 2 and 3 in the figure). The orientation of each gene is depicted according to the genome annotation.

Figure 3.

Alignment of a PMP present in four distant species. (A) Alignment of the promoter region of eight CDSs in Herpetosiphon aurantiacus ATCC23779, Carboxydothermus hydrogenoformans Z 2901, Thermotoga lettingae TMO and Deinococcus maricopensis DSM2121. Color blocks show nucleotide sequence conservation. A variable region of non-conserved sequence (29 to 93 nt long) was observed in all cases between the TLS and the PMP. (B) Alignment of the coding sequence of the eight downstream CDSs. No sequence conservation is observed.

Figure 4.

Quantification of PMP propagation in prokaryotic genomes. (A) Number of families per genome (total = 4074 families in 1043 genomes). (B) Number of promoters per family (total = 13 111 promoters in 4074 families); please note the logarithmic scale on the y-axis.

Figure 5.

Two-members families features (2771/4074 families). (A) Identity distribution (mean = 92%). (B) Alignment length distribution (mean = 66 nt).