Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element - PubMed (original) (raw)

Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element

Alexey G Vitreschak et al. RNA. 2003 Sep.

Abstract

Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B(12) biosynthesis and be transported by a posttranscriptional regulatory mechanism, which involves direct binding of Ado-CBL to 5'untranslated gene regions (5'UTR). Using comparative analysis of genes and regulatory regions, we identified a highly conserved RNA structure, the B12-element, which is widely distributed in 5'UTRs of vitamin B(12)-related genes in eubacteria. Multiple alignment of approximately 200 B12-elements from 66 bacterial genomes reveals their common secondary structure and several extended regions of sequence conservation, including the previously known B12-box motif. In analogy to the model of regulation of the riboflavin and thiamin biosynthesis, we suggest Ado-CBL-mediated regulation based on formation of alternative RNA structures including the B12-element. In Gram-negative proteobacteria, as well as in cyanobacteria, actinobacteria, and the CFB group, the cobalamin biosynthesis and vitamin B(12) transport genes are predicted to be regulated by inhibition of translation initiation, whereas in the Bacillus/Clostridium group of Gram-positive bacteria, these genes seem to be regulated by transcriptional antitermination. Phylogenetic analysis of the B12-elements reveals a large number of likely duplications of B12-elements in several bacterial genomes. These lineage-specific duplications of RNA regulatory elements seem to be a major evolutionary mechanism for expansion of the vitamin B(12) regulon.

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Figures

FIGURE 1.

FIGURE 1.

Alignment of _B12_-element sequences. The first column contains the genome abbreviations (listed in Table 3 ▶) and the names of the proximal downstream genes. The second column contains the position of the first base relative to the start codon. The complementary stems of the RNA secondary structure are shown by arrows in the upper line. Base-paired positions are highlighted in matching colors. Conserved positions are set in red; degenerate conserved positions, in green; nonconserved positions, in black; nonconsensus nucleotides in conserved positions, in blue. The lengths of the additional and variable stem–loops are given.

FIGURE 1.

FIGURE 1.

Alignment of _B12_-element sequences. The first column contains the genome abbreviations (listed in Table 3 ▶) and the names of the proximal downstream genes. The second column contains the position of the first base relative to the start codon. The complementary stems of the RNA secondary structure are shown by arrows in the upper line. Base-paired positions are highlighted in matching colors. Conserved positions are set in red; degenerate conserved positions, in green; nonconserved positions, in black; nonconsensus nucleotides in conserved positions, in blue. The lengths of the additional and variable stem–loops are given.

FIGURE 1.

FIGURE 1.

Alignment of _B12_-element sequences. The first column contains the genome abbreviations (listed in Table 3 ▶) and the names of the proximal downstream genes. The second column contains the position of the first base relative to the start codon. The complementary stems of the RNA secondary structure are shown by arrows in the upper line. Base-paired positions are highlighted in matching colors. Conserved positions are set in red; degenerate conserved positions, in green; nonconserved positions, in black; nonconsensus nucleotides in conserved positions, in blue. The lengths of the additional and variable stem–loops are given.

FIGURE 2.

FIGURE 2.

Conserved structure of the _B12_-element. Capital letters indicate invariant positions. Lowercase letters indicate strongly conserved positions. Degenerate positions: R = A or G; Y = C or U; K = G or U; M = A or C; H = not G; D = not C; N = any nucleotide. Dashes and black dots indicate obligatory and facultative base pairs, respectively. The conserved helices are numbered P0 to P6. Stem–loops of variable and constant lengths are shown by broken and sold lines, respectively. Additional stem–loops are designated Add-I and Add-II. The sequence of the conserved B12-box motif is shaded in gray. The variable structure VS separates two conserved parts of the _B12_-element, BI and BII. Taxonomic variations of the VS topology are shown in the inset.

FIGURE 3.

FIGURE 3.

Predicted RNA secondary structure of the _B12_-elements upstream of btuB from E. coli and cbiA from S. typhimurium genes. Chemical modifications of the B12-loop region of the btuB (A) and cbiA (B) 5′UTRs are shown by filled triangles (Ravnum and Andersson 2001; Nahvi et al. 2002).

FIGURE 4.

FIGURE 4.

Multiple alignment of the btuB upstream regions from enterobacteria (A) and some α-proteobacteria (B). Gray background denotes the P0 and P3 stems of the _B12_-element and the proposed RBS sequestors. Bold black denotes the main stem of the antisequestor. Arrows show the complementary stems of RNA secondary structures. Candidate pseudoknots are underlined and designated Pkn. RBSs and start codons are shown in bold letters.

FIGURE 5.

FIGURE 5.

Conserved RNA elements upstream of some _B12_-regulated genes. The P0 and P3 stems of the _B12_-element are highlighted in green. Proposed regulatory hairpins (sequestors in proteobacteria and actinobacteria; terminators in the Bacillus/Clostridium group) are highlighted in blue. Red denotes the base stem of the antiterminator/antisequestor. Arrows in the upper line show the complementary stems of RNA secondary structures. Candidate pseudoknots that overlap the P3 loop and the antiterminator/antisequestor are underlined. RBSs and the start codons are set in blue.

FIGURE 6.

FIGURE 6.

Predicted mechanism of the _B12_-mediated regulation of CBL genes: (A) transcriptional attenuation; (B) translational attenuation (inhibition of translation initiation).

FIGURE 7.

FIGURE 7.

Phylogenetic tree of _B12_-elements. The names of the proximal genes of the _B12_-regulated operons are given. The genome abbreviations are listed in Table 3 ▶. _B12_-elements without the BII part are set in bold and shaded in gray. Groups of genome-specific _B12_-elements are circled by dotted lines.

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