Bacterial RNAs

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-	Most of bacterial genomes is involved in protein coding, but a number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression both at DNA and RNA level.	+	[[Image:Bacterial_pae.jpg|300px|right|thumb|PAE-1 bacterial family secondary structure]]
-	These sequences often are able to fold as a stem-loop based structures (SLS) and this feature is indispensable to their biological functions.	+	Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures (SLS), essential to their functionality. SLSs have been found also in repetitive sequences in several bacterial genomes, even if only in few cases a clear biological function was assessed.
-	We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.	+
-	A second analysis revealed that 29 out of 40 analyzed genomes have a number of SLSs which can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set.	+
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-	SLSs selected in this way Regrouping of the selected sequences by sequence similarity, strand reciprocity and genomic location allowed to remove redundancies. HMM analysis was used to define a final set of 92 families. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.	+
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-	Conclusions	+
-	Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. Their predicted structure and genomic location suggest that even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at RNA level.	+
		+	Starting from this considerations we decided to perform a systematic analysis of these elements and to identify
		+	all the repeated sequence families able to share a common SLS. The project started with the identification of all the sequences able to fold in a SLS manner from a set of 40 wholly-sequenced genomes representative of the bacterial world. SLSs were extracted, annotated and stored in a relational database. A first result of this project was to demonstrate that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. It is therefore possible that there is a selective pressure in some microorganisms to preserve these sequences because of their biological functions.
		+	A second analysis based on clustering procedures revealed that most of analyzed genomes have SLSs that can be grouped by sequence similarity. Such SLSs, which correspond to a very little fraction of the starting population, have a substantially higher aptitude to fold into a stable secondary structure than the initial set.
		+	This procedure allowed to identify a large collection of families of repeated stem-loop containing sequences. Secondary structure analysis revealed for many of them the presence of a conserved secondary structure, possibly linked to their biological function.
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	* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]		* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]
	* COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.		* COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.
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Current revision

Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures (SLS), essential to their functionality. SLSs have been found also in repetitive sequences in several bacterial genomes, even if only in few cases a clear biological function was assessed.

Starting from this considerations we decided to perform a systematic analysis of these elements and to identify all the repeated sequence families able to share a common SLS. The project started with the identification of all the sequences able to fold in a SLS manner from a set of 40 wholly-sequenced genomes representative of the bacterial world. SLSs were extracted, annotated and stored in a relational database. A first result of this project was to demonstrate that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. It is therefore possible that there is a selective pressure in some microorganisms to preserve these sequences because of their biological functions. A second analysis based on clustering procedures revealed that most of analyzed genomes have SLSs that can be grouped by sequence similarity. Such SLSs, which correspond to a very little fraction of the starting population, have a substantially higher aptitude to fold into a stable secondary structure than the initial set. This procedure allowed to identify a large collection of families of repeated stem-loop containing sequences. Secondary structure analysis revealed for many of them the presence of a conserved secondary structure, possibly linked to their biological function.

[edit] References

• PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170
• COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.

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Bioinformatics: Research Activity: Eukaryotic CSTs - Bacterial RNAs - Image processing