sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.

Small non-coding RNAs (sRNAs) carry out a variety of biological functions and affect protein synthesis and protein activities in prokaryotes. Recently, numerous sRNAs and their targets were identified in Escherichia coli and in other bacteria. It is crucial to have a comprehensive resource concerning the annotation of small non-coding RNAs in microbial genomes. This work presents an integrated database, namely sRNAMap, to collect the sRNA genes, the transcriptional regulators of sRNAs and the sRNA target genes by integrating a variety of biological databases and by surveying literature. In this resource, we collected 397 sRNAs, 62 regulators/sRNAs and 60 sRNAs/targets in 70 microbial genomes. Additionally, more valuable information of the sRNAs, such as the secondary structure of sRNAs, the expressed conditions of sRNAs, the expression profiles of sRNAs, the transcriptional start sites of sRNAs and the cross-links to other biological databases, are provided for further investigation. Besides, various textual and graphical interfaces were designed and implemented to facilitate the data access in sRNAMap. sRNAMap is available at http://sRNAMap.mbc.nctu.edu.tw/.

INTRODUCTION

Small non-coding RNAs (sRNAs), which are discovered in many organisms ranging from bacteria to mammals, play important regulatory roles in cell physiology including regulation of cell development, cell death and chromosome silencing (1). Many of them regulate gene expression at a posttranscriptional level, either by acting as antisense RNAs, by binding to complementary sequences of target transcripts, or by interacting with proteins (2). Figure 1 depicts the synthesis and the functions of small non-coding RNAs. The transcription of sRNAs is regulated by transcription factors. Furthermore, sRNAs can play regulatory roles in translation repression, translation activation, mRNA degradation and mRNA stability.

Figure 1.

The synthesis and functions of small non-coding RNAs collected in sRNAMap.

EcoCyc (3) and RegulonDB (4) integrate biological knowledge of the transcriptional regulation in Escherichia coli, as well as knowledge on the organization of the genes and regulatory signals into operons in the chromosome. ASAP (5) is developed to store genome sequences in conjunction with associated annotations and functional characterization data. NONCODE (6) is an integrated knowledge database dedicated to non-coding RNAs. In addition, Storz et al. (7) used northern blotting analysis to document a total of 79 small RNAs in E. coli.

The increased investigations of important regulatory roles for sRNAs encoded far from their targets, acting on multiple targets, or both, has expanded interest in how to find such regulatory RNAs and how they work (8). Therefore, a resource collects the comprehensive annotation of small non-coding RNAs is crucial. We present an integrated database, sRNAMap, to collect the annotations of the sRNAs and the regulatory relationship between transcriptional regulator and sRNA, and between sRNA and its target genes. The design concept of the sRNAMap is illustrated in Figure 1. Additionally, more valuable information of sRNAs, such as the secondary structure of sRNAs, the expressed conditions of sRNAs, the expression profiles of sRNAs, the transcriptional start sites of sRNAs and the cross-links to other biological databases, are provided for further investigation. Besides, various textual and graphical interfaces were designed and implemented to facilitate the data access in sRNAMap.

DATABASE STATISTICS

The sRNAMap currently collects 397 sRNA genes, 62 regulator/sRNA regulations and 60 sRNA/target regulations in seventy microbial genomes. The detailed list of genome is given in Table S4. As given in Table 1, for instance, the number of experimentally validated sRNA genes in E. coli, Shigella boydii, Shigella flexneri and Yersinia pestis are 87, 35, 40 and 24, respectively. Table 2 gives the length distribution of the total known sRNA genes. Moreover, the sRNAMap analysed the transcriptional start sites of sRNA genes. Figure S3 (see Supplementary Materials) is the schematic diagram for the classification of transcription start sites of sRNA. In E. coli K-12 MG1655, 30 sRNAs have transcription start sites and 33 sRNAs have 49 putative transcription start sites, as given in Table S5.

Table 1.

The briefly statistics of small non-coding RNAs in sRNAMap

Species names	No. of experimentally verified sRNAs
Escherichia coli	87
EnterobacteriaPhage VT2-Sakai genomic DNA	1
Enterobacter intermedius	1
Enterobacter cloacae	1
Enterobacter aerogenes	1
Yersinia pseudotuberculosis	21
Yersinia pestis	24
Yersinia mollaretii ATCC 43 969	1
Yersinia intermedia ATCC 29 909	1
Yersinia frederiksenii ATCC 33 641	1
Yersinia enterocolitica	23
Yersinia bercovieri ATCC 43 970	1
Shigella sonnei 046	38
Shigella flexneri	40
Shigella dysenteriae	33
Shigella boydii	35
Serratia proteamaculans 568	2
Salmonella typhimurium	15
Salmonella enteritidis	2
Salmonella typhi	10
Salmonella paratyphi A ATCC 9150	30
Salmonella enterica Subsp. Arizonae	1
Salmonella choleraesuis SC-B67	4
Photorhabdus luminescens TTO1	1
Pectobacterium carotovorum	2
Pectobacterium atrosepticum SCRI1043	15
Klebsiella pneumoniae	4
Klebsiella oxytoca	2

Table 2.

Nucleotide length distribution of sRNA genes

	<100	100 ∼ 200	200 ∼ 300	300 ∼ 400	400 ∼ 500
No. of sRNAs	334	436	68	58	12

DATA GENERATION

The data generation flow of sRNAMap database is depicted in Figure 2. The data generation flow comprises two major parts: (i) integration of external data sources and (ii) integration of annotated tools. We collect the sRNA information from a variety of biological databases, such as RegulonDB, ASAP and NONCODE. Information of sRNAs including the accessions, names, genomic location, species, descriptions and sequences were obtained. Furthermore, the regulator/sRNA regulations and sRNA/target regulations were obtained from RegulonDB and NPInter (9). In addition to collecting data from external databases, we gather the sRNA information by surveying literatures. Besides, RNA secondary structures, cross-species comparisons and 37 expression profiles of sRNAs were integrated into the database. 308 computationally identified sRNAs (10,11) and 114 computationally identified regulator/sRNA regulations and sRNA/target regulations (12,13) were obtained.

Figure 2.

The data generation flow of sRNAMap.

Gene Expression Omnibus (GEO) (14) is a database repository of high-throughput gene expression data and hybridization arrays, chips, microarrays. The expression profiles related to sRNA were obtained and integrated. Besides, UCSC Archaeal Genome Browser (15), which is a popular web-based tool for quickly displaying a requested portion of a genome at any scale, was integrated to provide the sequence conservation of sRNAs. RNAfold (16) was applied to fold the RNA secondary structures of sRNAs. Moreover, RNALogo (17), which presents a graphical representation of the patterns in an aligned RNA sequence family with a consensus structure, was integrated for presenting the sRNA families. The cross-links to other biological databases are provided for each sRNA in the database. The integrated external data sources, the linked external data sources and the integrated annotated tools are listed in Table S1, Table S2 and Table S3 (see Supplementary Materials), respectively.

INTERFACE

The sRNAMap provides a variety of interfaces and graphical visualization to present the plentiful information of sRNAs. Users can submit keywords or sequences to search the database. For each sRNA gene, the database provides the sequence, the genomic location, promoter information, secondary structures, literatures, annotations, expression profiles, sequence conservation and its transcriptional regulatory network. Additionally, the sRNAMap has the regulator/sRNA page and the sRNA/target page which provide the experimental conditions and the regulator/sRNA regulations and sRNA/target regulations. Figure S1 shows the interface of sRNA genes in sRNAMap.

sRNAMap also provides several browsing functions, such as the genome browser, the network browser, the expression profile browser, the computational sRNAs browser and the literature record browser (Figure S2, see Supplementary Materials).

DISCUSSIONS

sRNAMap is an integrated and comprehensive database comprising plentiful information about sRNA. Table 3 gives the comparison of sRNAMap with other databases related to sRNA including RegulonDB, ASAP, NONCODE, NPInter and Rfam (18). sRNAMAp aims on the annotation of small non-coding RNAs in microbial genomes, while Rfam mainly aims on the collection of non-coding RNA families and a variety of regulatory RNA structural motifs. Rfam currently collects 53 sRNA families. Our proposed sRNAMap collects 87 E. coli sRNAs and totally 397 sRNAs from 70 species. Moreover, sRNAMap also collects computational sRNA and supports information about RNA secondary structures, transcriptional start sites of sRNA and especially the expression profiles of sRNA. Consequently, we would like to say that sRNAMap provides more plentiful and effective information than Rfam and other databases in the aspect of sRNAs.

Table 3.

Comparing sRNAMap with other resources

	RegulonDB	ASAP	NONCODE	NPInter	Rfam	sRNAMap
No. of sRNAs	79	72	134	103	53	397
No. of relations
Regulators/sRNAs	16	–	–	50	–	62
sRNAs/targets	26	–	–	43	–	60
No. of species supported	1 (E. coli)	59 (Microbial genomes)	21 (Microbial genomes)	1 (E. coli)	248	70 (Microbial genomes)
Computational sRNAs supported	–	–	–	–	–	Yes
Secondary structure of sRNAs	–	–	–	–	Yes	Yes
Transcription start site of sRNAs	1 typea	–	–	–	–	5 typesa
Expression profiles supported	–	–	–	–	–	Yes
Transcriptional regulatory network	Regulators/sRNAs sRNAs/targets	–	–	–	–	Regulators/sRNAs sRNAs/targets
Sequence homology search	–	–	–	–	Yes	Yes

aThe classification of transcriptional start sites of sRNA is described in Figure S1 (See Supplementary Materials).

AVAILABILITY

The sRNAMap database will be continuously maintained and updated. The database is now freely available at http://sRNAMap.mbc.nctu.edu.tw/.

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online.

FUNDING

The National Science Council of the Republic of China (Contract No. NSC 96-3112-E-009-002, NSC 95-2311-B-009-004-MY3 and 97-2627-B-009-007); National Research Program for Genomic Medicine (NRPGM), Taiwan; MOE ATU (Partial). Funding for the open access publication charge: National Science Council of the Republic of China and MOE ATU.

Conflict of Interest statement: None declared.