A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

<p>Abstract</p> <p>Background</p> <p>Non-coding RNAs (ncRNA) are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the <it>Prochlorococcus/Synechococcus </it>group of marine cyanobacteria.</p> <p>Results</p> <p>Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of <it>Prochlorococcus</it>, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'.</p> <p>Conclusion</p> <p>Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of <it>E. coli </it>and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.</p

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria-1

<p><b>Copyright information:</b></p><p>Taken from "A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/375</p><p>BMC Genomics 2007;8():375-375.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2190773.</p><p></p>last line. The perfectly conserved sequence motif within the unpaired region is given in capital, red letters

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria-3

<p><b>Copyright information:</b></p><p>Taken from "A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/375</p><p>BMC Genomics 2007;8():375-375.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2190773.</p><p></p>, sp. PCC 7120 (Nos. 7120), (Nos. punct.) and PCC 7421 (Gloe. 7421) was analyzed by staining a 10% polyacrylamide gel with ethidium bromide.. Northern blot hybridization with DNA oligonucleotides for the presence of Yfr1 (lower part) and, as a control, the 6S RNA (upper part)

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria-0

<p><b>Copyright information:</b></p><p>Taken from "A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/375</p><p>BMC Genomics 2007;8():375-375.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2190773.</p><p></p>respective strain numbers are prefixed "Pro" and "Syn" for and . B. Sequence/structure model for putative Yfr1 RNAs from 15 different and as shown in part A. Sequence is given in IUPAC-notation (R: A or G; Y: C or U; S: G or C; K: G or U; B: G, U or C; V: G, C or A; D: G, U or A; H: A, C or U). Base pair colors indicate the number of different base pairs which occur in the different sequences at this position (red = 1, yellow = 2, green = 3) and their shading resembles the frequency of base pairing, i.e. the number of sequences where this base pair is not present

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria-2

<p><b>Copyright information:</b></p><p>Taken from "A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/375</p><p>BMC Genomics 2007;8():375-375.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2190773.</p><p></p>). Base pair colors indicate the number of different base pairs which occur in the different sequences at this position (red = 1, yellow = 2, green = 3 and blue = 4) and their shading resembles the frequency of base pairing, i.e. the number of sequences where this base pair is not present. The unpaired sequence is given as a sequence logo prepared using WebLogo [23]

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria-5

<p><b>Copyright information:</b></p><p>Taken from "A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/375</p><p>BMC Genomics 2007;8():375-375.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2190773.</p><p></p>respective strain numbers are prefixed "Pro" and "Syn" for and . B. Sequence/structure model for putative Yfr1 RNAs from 15 different and as shown in part A. Sequence is given in IUPAC-notation (R: A or G; Y: C or U; S: G or C; K: G or U; B: G, U or C; V: G, C or A; D: G, U or A; H: A, C or U). Base pair colors indicate the number of different base pairs which occur in the different sequences at this position (red = 1, yellow = 2, green = 3) and their shading resembles the frequency of base pairing, i.e. the number of sequences where this base pair is not present

An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease

Cyanophage genomes frequently possess the psbA gene, encoding the D1 polypeptide of photosystem II. This protein is believed to maintain host photosynthetic capacity during infection and enhance phage fitness under high-light conditions. Although the first documented cyanophage-encoded psbA gene contained a group I intron, this feature has not been widely reported since, despite a plethora of new sequences becoming available. In this study, we show that in cyanophage S-PM2, this intron is spliced during the entire infection cycle. Furthermore, we report the widespread occurrence of psbA introns in marine metagenomic libraries, and with psbA often adjacent to a homing endonuclease (HE). Bioinformatic analysis of the intergenic region between psbA and the adjacent HE gene F-CphI in S-PM2 showed the presence of an antisense RNA (asRNA) connecting these two separate genetic elements. The asRNA is co-regulated with psbA and F-CphI, suggesting its involvement with their expression. Analysis of scaffolds from global ocean survey datasets shows this asRNA to be commonly associated with the 30 end of cyanophage psbA genes, implying that this potential mechanism of regulating marine 'viral' photosynthesis is evolutionarily conserved. Although antisense transcription is commonly found in eukaryotic and increasingly also in prokaryotic organisms, there has been no indication for asRNAs in lytic phages so far. We propose that this asRNA also provides a means of preventing the formation of mobile group I introns within cyanophage psbA genes. The ISME Journal (2010) 4, 1121-1135; doi: 10.1038/ismej.2010.43; published online 22 April 2010</p

An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease

Cyanophage genomes frequently possess the psbA gene, encoding the D1 polypeptide of photosystem II. This protein is believed to maintain host photosynthetic capacity during infection and enhance phage fitness under high-light conditions. Although the first documented cyanophage-encoded psbA gene contained a group I intron, this feature has not been widely reported since, despite a plethora of new sequences becoming available. In this study, we show that in cyanophage S-PM2, this intron is spliced during the entire infection cycle. Furthermore, we report the widespread occurrence of psbA introns in marine metagenomic libraries, and with psbA often adjacent to a homing endonuclease (HE). Bioinformatic analysis of the intergenic region between psbA and the adjacent HE gene F-CphI in S-PM2 showed the presence of an antisense RNA (asRNA) connecting these two separate genetic elements. The asRNA is co-regulated with psbA and F-CphI, suggesting its involvement with their expression. Analysis of scaffolds from global ocean survey datasets shows this asRNA to be commonly associated with the 3′ end of cyanophage psbA genes, implying that this potential mechanism of regulating marine ‘viral’ photosynthesis is evolutionarily conserved. Although antisense transcription is commonly found in eukaryotic and increasingly also in prokaryotic organisms, there has been no indication for asRNAs in lytic phages so far. We propose that this asRNA also provides a means of preventing the formation of mobile group I introns within cyanophage psbA genes