Αr7 RNA explained

αr7 is a family of bacterial small non-coding RNAs with representatives in a broad group of Alphaproteobacterial species from the order Hyphomicrobiales. The first member of this family (Smr7C 150nt) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). Further homology and structure conservation analysis identified full-length homologs in several nitrogen-fixing symbiotic rhizobia (i.e. R. leguminosarum bv.viciae, R. leguminosarum bv. trifolii, R. etli, and several Mesorhizobium species), in the plant pathogens belonging to Agrobacterium species (i.e. A. tumefaciens, A. vitis, A. radiobacter, and Agrobacterium H13) as well as in a broad spectrum of Brucella species (B. ovis, B. canis, B. abortus and B. microtis, and several biobars of B. melitensis). αr7 RNA species are 134-159 nucleotides (nt) long (Table 1) and share a well defined common secondary structure (Figure 1, Figure 2). αr7 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the Alphaproteobacterial genomes (Figure 4).

Discovery and structure

Smr7C sRNA was described by del Val et al.[1] in the intergenic regions (IGRs) of the reference S. meliloti 1021 strain (Sinorhizobium meliloti 1021). Northern hybridization experiments detected two RNA species expressed from the smr7C locus, which accumulated differentially in free-living and endosymbiotic bacteria.TAP-based 5'-RACE experiments mapped the transcription start site (TSS) to two close G residues. From the six independent sequences obtained, five mapped to residue 201,681 in the chromosome and one to the upstream residue 201,679. Furthermore, an additional 5'-RACE product could be obtained from this transcript in both TAP- and mock-treated RNA samples. The sequence of this second RACE product mapped the processing site of Smr7C to residue 201,723 nt in the S. meliloti 1021 genome. The 3'-end was assumed to be located at the 201,828 nt position matching the last residue of the consecutive stretch of Us of a bona fide Rho-independent terminator. Parallel and later studies[2] [3] in which Smr7C transcript is referred to as sra03 or Sm13, independently confirmed the expression this sRNA in S. melilloti and in its closely related strain 2011. Recent deep sequencing-based characterization of the small RNA fraction (50-350 nt) of S. meliloti 2021 further also confirmed the expression of Smr7C (here referred to as SmelC023), and mapped the 5'- end of the full-length transcript to the same position in the S. meliloti 1021 genome, and the 3' end to position 201,825.[4]

The nucleotide sequence of Smr7C was initially used as query to search against the Rfam database (version 10.0;[5]). This homology search rendered no matches to known bacterial sRNA in this database. Smr7C was next BLASTed with default parameters against all the currently available bacterial genomes (1,615 sequences at 20 April 2011;[6]). The regions exhibiting significant homology to the query sequence (78-89% similarity) were extracted to create a Covariance Model (CM) from a seed alignment using Infernal (version1.0).[7] This CM was used in a further search for new members of the αr7 family in the existing bacterial genomic databases (Table 1) and to create the final CM model (Figure 1).

Table 1: αr7 homologs in other symbionts and pathogens
CM model Name GI accession number begin end strand %GC length Organism
class=cellinside αr7class=cellinside Smr7Cclass=cellinside gi|15963753|ref|NC_003047.1|class=cellinside 201679class=cellinside 201828class=cellinside +class=cellinside 64class=cellinside 150class=cellinside Sinorhizobium meliloti 1021
class=cellinside αr7class=cellinside Smedr7Cclass=cellinside gi|150395228|ref|NC_009636.1|class=cellinside 3585152class=cellinside 3585302class=cellinside +class=cellinside 60class=cellinside 151class=cellinside Sinorhizobium medicae WSM419 chromosome
class=cellinside αr7class=cellinside Sfr7Cclass=cellinside gi|227820587|ref|NC_012587.1|class=cellinside 3727302class=cellinside 3727450class=cellinside -class=cellinside 66class=cellinside 149class=cellinside Sinorhizobium fredii NGR234 chromosome
class=cellinside αr7class=cellinside Atr7Cclass=cellinside gi|159184118|ref|NC_003062.2|class=cellinside 112535class=cellinside 112678class=cellinside -class=cellinside 65class=cellinside 144class=cellinside Agrobacterium tumefaciens str. C58 chromosome circular
class=cellinside αr7class=cellinside AH13r7Cclass=cellinside gi|325291453|ref|NC_015183.1|class=cellinside 112523class=cellinside 112667class=cellinside -class=cellinside 63class=cellinside 145class=cellinside Agrobacterium sp. H13-3 chromosome
class=cellinside αr7class=cellinside ReCIATr7Cclass=cellinside gi|190889639|ref|NC_010994.1|class=cellinside 205678class=cellinside 205811class=cellinside -class=cellinside 61class=cellinside 134class=cellinside Rhizobium etli CIAT 652
class=cellinside αr7class=cellinside Arr7CIclass=cellinside gi|222084201|ref|NC_011985.1|class=cellinside 243240class=cellinside 243377class=cellinside -class=cellinside 62class=cellinside 138class=cellinside Agrobacterium radiobacter K84 chromosome 1
class=cellinside αr7class=cellinside Rlt2304r7Cclass=cellinside gi|209547612|ref|NC_011369.1|class=cellinside 4280520class=cellinside 4280653class=cellinside -class=cellinside 63class=cellinside 134class=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
class=cellinside αr7class=cellinside Avr7CIclass=cellinside gi|222147015|ref|NC_011989.1|class=cellinside 255869class=cellinside 256019class=cellinside +class=cellinside 60class=cellinside 151class=cellinside Agrobacterium vitis S4 chromosome 1
class=cellinside αr7class=cellinside Rlvr7Cclass=cellinside gi|116249766|ref|NC_008380.1|class=cellinside 192620class=cellinside 192753class=cellinside -class=cellinside 62class=cellinside 134class=cellinside Rhizobium leguminosarum bv. viciae 3841
class=cellinside αr7class=cellinside Rlt1325r7Cclass=cellinside gi|241202755|ref|NC_012850.1|class=cellinside 4553564class=cellinside 4553697class=cellinside -class=cellinside 62class=cellinside 134class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325
class=cellinside αr7class=cellinside ReCFNr7Cclass=cellinside gi|86355669|ref|NC_007761.1|class=cellinside 163762class=cellinside 163895class=cellinside -class=cellinside 60class=cellinside 134class=cellinside Rhizobium etli CFN 42
class=cellinside αr7class=cellinside Mlr7Cclass=cellinside gi|57165207|ref|NC_002678.2|class=cellinside 2648243class=cellinside 2648390class=cellinside -class=cellinside 65class=cellinside 148class=cellinside Mesorhizobium loti MAFF303099 chromosome
class=cellinside αr7class=cellinside MsBNCr7Cclass=cellinside gi|110632362|ref|NC_008254.1|class=cellinside 4251581class=cellinside 4251722class=cellinside +class=cellinside 60class=cellinside 142class=cellinside Mesorhizobium sp. BNC1
class=cellinside αr7class=cellinside Mcr7Cclass=cellinside gi|319779749|ref|NC_014923.1|class=cellinside 1781903class=cellinside 1782047class=cellinside +class=cellinside 68class=cellinside 145class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
class=cellinside αr7class=cellinside Bcr7CIclass=cellinside gi|161617991|ref|NC_010103.1|class=cellinside 134573class=cellinside 134715class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella canis ATCC 23365 chromosome I
class=cellinside αr7class=cellinside Bs23445r7CIclass=cellinside gi|163842277|ref|NC_010169.1|class=cellinside 134908class=cellinside 135050class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella suis ATCC 23445 chromosome I
class=cellinside αr7class=cellinside Bm16Mr7CIclass=cellinside gi|17986284|ref|NC_003317.1|class=cellinside 1868345class=cellinside 1868487class=cellinside +class=cellinside 62class=cellinside 143class=cellinside Brucella melitensis bv. 1 str. 16M chromosome I
class=cellinside αr7class=cellinside BaS19r7CIclass=cellinside gi|189023268|ref|NC_010742.1|class=cellinside 134335class=cellinside 134477class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella abortus S19 chromosome 1
class=cellinside αr7class=cellinside Bm23457r7CIclass=cellinside gi|225851546|ref|NC_012441.1|class=cellinside 134555class=cellinside 134697class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella melitensis ATCC 23457 chromosome I
class=cellinside αr7class=cellinside Bs1330r7CIclass=cellinside gi|56968325|ref|NC_004310.3|class=cellinside 134590class=cellinside 134732class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella suis 1330 chromosome I
class=cellinside αr7class=cellinside Ba19941r7CIclass=cellinside gi|62288991|ref|NC_006932.1|class=cellinside 135949class=cellinside 136091class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I
class=cellinside αr7class=cellinside Bmar7CIclass=cellinside gi|82698932|ref|NC_007618.1|class=cellinside 132316class=cellinside 132458class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I
class=cellinside αr7class=cellinside Bor7CIclass=cellinside gi|148558820|ref|NC_009505.1|class=cellinside 134888class=cellinside 135029class=cellinside -class=cellinside 63class=cellinside 142class=cellinside Brucella ovis ATCC 25840 chromosome I
class=cellinside αr7class=cellinside Bmir7CIclass=cellinside gi|256368465|ref|NC_013119.1|class=cellinside 136167class=cellinside 136309class=cellinside -class=cellinside 62class=cellinside 143class=cellinside Brucella microti CCM 4915 chromosome 1
class=cellinside αr7class=cellinside Oar7CIclass=cellinside gi|153007346|ref|NC_009667.1|class=cellinside 149814class=cellinside 149972class=cellinside -class=cellinside 58class=cellinside 159class=cellinside Brucella anthropi ATCC 49188 chromosome 1

The results were manually inspected to deduce a consensus secondary structure for the family (Figure1 and Figure2). The consensus structure was also independently predicted with the program locARNATE[8] with very similar predictions. The manual inspection of the sequences found with the CM using Infernal allowed finding 26 true homolog sequences, all of them present as single chromosomal copies in the Alphaproteobacterial genomes. The rhizobial species encoding the closer homologs to Smr7C were: S. medicae and S. fredii, two R. leguminosarum trifolii strains (WSM2304 and WSM1325), two R. etli strains CFN 42 and CIAT 652, the reference R. leguminosarum bv. viciae 3841 strain, and the Agrobacterium species A. vitis, A. tumefaciens, A. radiobacter and A. H13 and the Mesorhizobum species loti, M. ciceri and M. BNC. All these sequences showed significant Infernal E-values (3.66E-49 – 2.93E-12) and bit-scores. The rest of the sequences found with the model showed high E-values between (1.58E-10 and 2.88E-09) but lower bit-scores and are encoded by Brucella species (B. ovis, B. canis, B. abortus, B. microtis, several biobars of B. melitensis, and B. anthropi).

Expression information

Parallel studies assessed Smr7C expression in S. meliloti 1021 under different biological conditions; i.e. bacterial growth in TY, minimal medium (MM) and luteolin-MM broth and endosymbiotic bacteria (i.e. mature symbiotic alfalfa nodules). Expression of Smr7C in free-living bacteria was found to be growth-dependent, being the gene strongly down-regulated when bacteria entered the stationary phase.Expression of SmrC7 increased ~13-fold in nodules when compared with free-living bacteria (log phase TY or MM cultures), suggesting the induction of this sRNAs during bacterial infection and/or bacteroid differentiation. SmrC7 expression has also been proved in parallel studies.

Promoter analysis

All the promoter regions of the αr7 family members examined so far are very conserved in a sequence stretch extending up to 80 bp upstream of the transcription start site of the sRNA. All closest homologous loci have recognizable σ70-dependent promoters showing a -35/-10 consensus motif CTTAGAC-n17-CTATAT, which has been previously shown to be widely conserved among several other genera in the Alphaproteobacteria.[9] To identify binding sites for other known transcription factors we used the fasta sequences provided by RegPredict,[10] [11] and used those position weight matrices (PSWM) provided by RegulonDB.[12] [13] We built PSWM for each transcription factor from the RegPredict sequences using the Consensus/Patser program, choosing the best final matrix for motif lengths between 14 and 30 a threshold average E-value < 10E-10 for each matrix was established, (see "Thresholded consensus" in gps-tools2.its.yale.edu). Moreover, we searched for conserved unknown motifs using MEME[14] [15] and used relaxed regular expressions (i.e. pattern matching) over all promoters of the Smr7C homologs promoters.

This studies revealed a 20 bp conserved motif in ll promoter regions, marked in orange as MEME conserved motif, in (Figure 4), but no significant similarity to known transcription factor binding sites matrices could be established.

Genomic context

All identified members of the αr7 family are trans-encoded sRNAs transcribed from independent promoters in chromosomal IGRs. Most of the neighboring genes of the seed alignment's members were not annotated and thus were further manually curated.[16] [17] [18]

The αr7 sRNAs' genomic regions of the Sinorhizobium, Rhizobium and Agrobacterium group members exhibited a great degree of conservation with the upstream and downstream genes coding for a DNA polymerase, and a MarR family transcriptional regulator, respectively. Partial synteny of the αr7 genomic regions was observed in the Mesorhizobium and Brucella group, where instead of the MarR family transcriptional regulator gene, a peptidase encoding gene was found.

Table 2: Detailed Genomic context information of the α7 sRNA seed members.! Family !! Feature !! Name !! Strand !! Begin !! End !! Protein name !! Annotation !! Organism
class=cellinside αr7class=cellinside geneclass=cellinside Smed_3381class=cellinside Rclass=cellinside 3581962class=cellinside 3584976class=cellinside YP_001329037.1class=cellinside DNA polymeraseclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr7class=cellinside sRNAclass=cellinside Smedr7Cclass=cellinside Dclass=cellinside 3585152class=cellinside 3585302class=cellinside -class=cellinside -class=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr7class=cellinside geneclass=cellinside Smed_3382class=cellinside Dclass=cellinside 3585430class=cellinside 3585873class=cellinside YP_001329038.1class=cellinside MarR family transcriptional regulatorclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr7class=cellinside geneclass=cellinside SMc02850class=cellinside Rclass=cellinside 198469class=cellinside 201483class=cellinside NP_384281.1class=cellinside DNA polymeraseclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr7class=cellinside sRNAclass=cellinside Smr7Cclass=cellinside Dclass=cellinside 201679class=cellinside 201828class=cellinside -class=cellinside -class=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr7class=cellinside geneclass=cellinside SMc02851class=cellinside Dclass=cellinside 201956class=cellinside 202399class=cellinside NP_384282.1class=cellinside MarR family transcriptional regulatorclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr7class=cellinside geneclass=cellinside NGR_c35130class=cellinside Rclass=cellinside 3725266class=cellinside 3726657class=cellinside YP_002827990.1class=cellinside peptidase M2class=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr7class=cellinside sRNAclass=cellinside Sfr7Cclass=cellinside Rclass=cellinside 3727302class=cellinside 3727450class=cellinside -class=cellinside -class=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr7class=cellinside geneclass=cellinside NGR_c35150class=cellinside Dclass=cellinside 3727551class=cellinside 3730673class=cellinside YP_002827992.1class=cellinside DNA polymeraseclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr7class=cellinside geneclass=cellinside Atu0109class=cellinside Rclass=cellinside 112000class=cellinside 112446class=cellinside NP_353144.2class=cellinside MarR family transcriptional regulatorclass=cellinside Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
class=cellinside αr7class=cellinside sRNAclass=cellinside Atr7Cclass=cellinside Rclass=cellinside 112535class=cellinside 112678class=cellinside -class=cellinside -class=cellinside Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
class=cellinside αr7class=cellinside geneclass=cellinside Atu8081class=cellinside Rclass=cellinside 112724class=cellinside 113134class=cellinside NP_353145.1class=cellinside hypothetical proteinclass=cellinside Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
class=cellinside αr7class=cellinside geneclass=cellinside AGROH133_02963class=cellinside Rclass=cellinside 111988class=cellinside 112422class=cellinside YP_004277416.1class=cellinside MarR family transcriptional regulatorclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr7class=cellinside sRNAclass=cellinside AH13r7Cclass=cellinside Rclass=cellinside 112523class=cellinside 112667class=cellinside -class=cellinside -class=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr7class=cellinside geneclass=cellinside AGROH133_02965class=cellinside Dclass=cellinside 112837class=cellinside 115824class=cellinside YP_004277417.1class=cellinside DNA polymeraseclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr7class=cellinside geneclass=cellinside RHECIAT_CH0000189class=cellinside Rclass=cellinside 205143class=cellinside 205559class=cellinside YP_001976363.1class=cellinside MarR family transcriptional regulatorclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr7class=cellinside sRNAclass=cellinside ReCIATr7Cclass=cellinside Rclass=cellinside 205678class=cellinside 205811class=cellinside -class=cellinside -class=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr7class=cellinside geneclass=cellinside RHECIAT_CH0000190class=cellinside Dclass=cellinside 205998class=cellinside 208991class=cellinside YP_001976364.1class=cellinside DNA polymeraseclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr7class=cellinside geneclass=cellinside Arad_0270class=cellinside Rclass=cellinside 242680class=cellinside 243111class=cellinside YP_002542926.1class=cellinside MarR family transcriptional regulatorclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr7class=cellinside sRNAclass=cellinside Arr7CIclass=cellinside Rclass=cellinside 243240class=cellinside 243377class=cellinside -class=cellinside -class=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr7class=cellinside geneclass=cellinside Arad_0271class=cellinside Dclass=cellinside 243543class=cellinside 246545class=cellinside YP_002542927.1class=cellinside DNA polymeraseclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr7class=cellinside geneclass=cellinside Rleg2_4102class=cellinside Rclass=cellinside 4279984class=cellinside 4280400class=cellinside YP_002283590.1class=cellinside MarR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr7class=cellinside sRNAclass=cellinside Rlt2304r7Cclass=cellinside Rclass=cellinside 4280520class=cellinside 4280653class=cellinside -class=cellinside -class=cellinside Rhizobium leguminosarum bv trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr7class=cellinside geneclass=cellinside Rleg2_4103class=cellinside Dclass=cellinside 4280807class=cellinside 4283806class=cellinside YP_002283591.1class=cellinside DNA polymeraseclass=cellinside Rhizobium leguminosarum bv trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr7class=cellinside geneclass=cellinside Avi_0299class=cellinside Rclass=cellinside 252729class=cellinside 255707class=cellinside YP_002548197.1class=cellinside DNA polymeraseclass=cellinside Agrobacterium vitis S4 chromosome 1 (NC_011989)
class=cellinside αr7class=cellinside sRNAclass=cellinside Avr7CIclass=cellinside Dclass=cellinside 255869class=cellinside 256019class=cellinside -class=cellinside -class=cellinside Agrobacterium vitis S4 chromosome 1 (NC_011989)
class=cellinside αr7class=cellinside geneclass=cellinside Avi_0300class=cellinside Dclass=cellinside 256094class=cellinside 256543class=cellinside YP_002548198.1class=cellinside MarR family transcriptional regulatorclass=cellinside Agrobacterium vitis S4 chromosome 1 (NC_011989)
class=cellinside αr7class=cellinside geneclass=cellinside RL0159class=cellinside Rclass=cellinside 192083class=cellinside 192499class=cellinside YP_765764.1class=cellinside MarR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv viciae 3841 (NC_008380)
class=cellinside αr7class=cellinside sRNAclass=cellinside Rlvr7Cclass=cellinside Rclass=cellinside 192620class=cellinside 192753class=cellinside -class=cellinside -class=cellinside Rhizobium leguminosarum bv viciae 3841 (NC_008380)
class=cellinside αr7class=cellinside geneclass=cellinside RL0160class=cellinside Dclass=cellinside 192994class=cellinside 196044class=cellinside YP_765765.1class=cellinside DNA polymeraseclass=cellinside Rhizobium leguminosarum bv viciae 3841 (NC_008380)
class=cellinside αr7class=cellinside geneclass=cellinside Rleg_4422class=cellinside Rclass=cellinside 4553028class=cellinside 4553444class=cellinside YP_002978199.1class=cellinside MarR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr7class=cellinside sRNAclass=cellinside Rlt1325r7Cclass=cellinside Rclass=cellinside 4553564class=cellinside 4553697class=cellinside -class=cellinside -class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr7class=cellinside geneclass=cellinside Rleg_4423class=cellinside Dclass=cellinside 4553938class=cellinside 4556988class=cellinside YP_002978200.1class=cellinside DNA polymeraseclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr7class=cellinside geneclass=cellinside RHE_CH00150class=cellinside Rclass=cellinside 163227class=cellinside 163643class=cellinside YP_467702.1class=cellinside MarR family transcriptional regulatorclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr7class=cellinside sRNAclass=cellinside ReCFNr7Cclass=cellinside Rclass=cellinside 163762class=cellinside 163895class=cellinside -class=cellinside -class=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr7class=cellinside geneclass=cellinside RHE_CH00151class=cellinside Dclass=cellinside 164051class=cellinside 167050class=cellinside YP_467703.1class=cellinside DNA polymeraseclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr7class=cellinside geneclass=cellinside mll3297class=cellinside Rclass=cellinside 2646732class=cellinside 2648117class=cellinside NP_104434.1class=cellinside peptidase M2class=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr7class=cellinside sRNAclass=cellinside Mlr7Cclass=cellinside Rclass=cellinside 2648243class=cellinside 2648390class=cellinside -class=cellinside -class=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr7class=cellinside geneclass=cellinside mlr3298class=cellinside Dclass=cellinside 2648514class=cellinside 2651525class=cellinside NP_104435.1class=cellinside DNA polymeraseclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr7class=cellinside geneclass=cellinside Meso_3945class=cellinside Rclass=cellinside 4248490class=cellinside 4251426class=cellinside YP_676477.1class=cellinside DNA polymeraseclass=cellinside Mesorhizobium sp. BNC1 (NC_008254)
class=cellinside αr7class=cellinside sRNAclass=cellinside MsBNCr7Cclass=cellinside Dclass=cellinside 4251581class=cellinside 4251722class=cellinside -class=cellinside -class=cellinside Mesorhizobium sp. BNC1 (NC_008254)
class=cellinside αr7class=cellinside geneclass=cellinside Meso_3946class=cellinside Rclass=cellinside 4251731class=cellinside 4253149class=cellinside YP_676478.1class=cellinside 6-phosphogluconate dehydrogenaseclass=cellinside Mesorhizobium sp. BNC1 (NC_008254)
class=cellinside αr7class=cellinside geneclass=cellinside Mesci_1702class=cellinside Rclass=cellinside 1778784class=cellinside 1781777class=cellinside YP_004140907.1class=cellinside DNA polymeraseclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
class=cellinside αr7class=cellinside sRNAclass=cellinside Mcr7Cclass=cellinside Dclass=cellinside 1781903class=cellinside 1782047class=cellinside -class=cellinside -class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
class=cellinside αr7class=cellinside geneclass=cellinside Mesci_1703class=cellinside Dclass=cellinside 1782152class=cellinside 1783537class=cellinside YP_004140908.1class=cellinside peptidase M2class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
class=cellinside αr7class=cellinside geneclass=cellinside BCAN_A0124class=cellinside Rclass=cellinside 132964class=cellinside 134379class=cellinside YP_001591996.1class=cellinside peptidase M2class=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bcr7CIclass=cellinside Rclass=cellinside 134573class=cellinside 134715class=cellinside -class=cellinside -class=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr7class=cellinside geneclass=cellinside BCAN_A0126class=cellinside Dclass=cellinside 134940class=cellinside 137879class=cellinside YP_001591998.1class=cellinside DNA polymeraseclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr7class=cellinside geneclass=cellinside BSUIS_A0126class=cellinside Rclass=cellinside 133299class=cellinside 134714class=cellinside YP_001626800.1class=cellinside peptidase M2class=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bs23445r7CIclass=cellinside Rclass=cellinside 134908class=cellinside 135050class=cellinside -class=cellinside -class=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr7class=cellinside geneclass=cellinside BSUIS_A0128class=cellinside Dclass=cellinside 135275class=cellinside 138211class=cellinside YP_001626802.1class=cellinside DNA polymeraseclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr7class=cellinside geneclass=cellinside BMEI1825class=cellinside Rclass=cellinside 1865184class=cellinside 1868168class=cellinside NP_540742.1class=cellinside DNA polymeraseclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome I (NC_003317)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bm16Mr7CIclass=cellinside Dclass=cellinside 1868345class=cellinside 1868487class=cellinside -class=cellinside -class=cellinside Brucella melitensis bv. 1 str. 16M chromosome I (NC_003317)
class=cellinside αr7class=cellinside geneclass=cellinside BMEI1827class=cellinside Dclass=cellinside 1868645class=cellinside 1870096class=cellinside NP_540744.1class=cellinside peptidase M2class=cellinside Brucella melitensis bv. 1 str. 16M chromosome I (NC_003317)
class=cellinside αr7class=cellinside geneclass=cellinside BAbS19_I01130class=cellinside Rclass=cellinside 132726class=cellinside 134141class=cellinside YP_001934145.1class=cellinside peptidase M2class=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr7class=cellinside sRNAclass=cellinside BaS19r7CIclass=cellinside Rclass=cellinside 134335class=cellinside 134477class=cellinside -class=cellinside -class=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr7class=cellinside geneclass=cellinside BAbS19_I01140class=cellinside Dclass=cellinside 134702class=cellinside 137638class=cellinside YP_001934146.1class=cellinside DNA polymeraseclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr7class=cellinside geneclass=cellinside BMEA_A0128class=cellinside Rclass=cellinside 132946class=cellinside 134361class=cellinside YP_002731894.1class=cellinside peptidase M2class=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bm23457r7CIclass=cellinside Rclass=cellinside 134555class=cellinside 134697class=cellinside -class=cellinside -class=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr7class=cellinside geneclass=cellinside BMEA_A0130class=cellinside Dclass=cellinside 134922class=cellinside 137858class=cellinside YP_002731896.1class=cellinside DNA polymeraseclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr7class=cellinside geneclass=cellinside BR0121class=cellinside Rclass=cellinside 132981class=cellinside 134396class=cellinside NP_697162.1class=cellinside peptidase M2class=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bs1330r7CIclass=cellinside Rclass=cellinside 134590class=cellinside 134732class=cellinside -class=cellinside -class=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr7class=cellinside geneclass=cellinside BR0123class=cellinside Dclass=cellinside 134957class=cellinside 137896class=cellinside NP_697164.1class=cellinside DNA polymeraseclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr7class=cellinside geneclass=cellinside BruAb1_0118class=cellinside Rclass=cellinside 134340class=cellinside 135755class=cellinside YP_220895.1class=cellinside peptidase M2class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr7class=cellinside sRNAclass=cellinside Ba19941r7CIclass=cellinside Rclass=cellinside 135949class=cellinside 136091class=cellinside -class=cellinside -class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr7class=cellinside geneclass=cellinside BruAb1_0120class=cellinside Dclass=cellinside 136316class=cellinside 139252class=cellinside YP_220897.1class=cellinside DNA polymeraseclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr7class=cellinside geneclass=cellinside BAB1_0118class=cellinside Rclass=cellinside 130707class=cellinside 132122class=cellinside YP_413614.1class=cellinside peptidase M2class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bmar7CIclass=cellinside Rclass=cellinside 132316class=cellinside 132458class=cellinside -class=cellinside -class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr7class=cellinside geneclass=cellinside BAB1_0120class=cellinside Dclass=cellinside 132683class=cellinside 135619class=cellinside YP_413616.1class=cellinside DNA polymeraseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr7class=cellinside geneclass=cellinside BOV_0118class=cellinside Rclass=cellinside 133280class=cellinside 134695class=cellinside YP_001258159.1class=cellinside peptidase M2class=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bor7CIclass=cellinside Rclass=cellinside 134888class=cellinside 135029class=cellinside -class=cellinside -class=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr7class=cellinside geneclass=cellinside BOV_0119class=cellinside Dclass=cellinside 135254class=cellinside 138190class=cellinside YP_001258160.1class=cellinside DNA polymeraseclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr7class=cellinside geneclass=cellinside BMI_I124class=cellinside Rclass=cellinside 134558class=cellinside 135973class=cellinside YP_003106091.1class=cellinside peptidase M2class=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr7class=cellinside sRNAclass=cellinside Bmir7CIclass=cellinside Rclass=cellinside 136167class=cellinside 136309class=cellinside -class=cellinside -class=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr7class=cellinside geneclass=cellinside BMI_I126class=cellinside Dclass=cellinside 136534class=cellinside 139470class=cellinside YP_003106093.1class=cellinside DNA polymeraseclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr7class=cellinside geneclass=cellinside Oant_0136class=cellinside Rclass=cellinside 148306class=cellinside 149715class=cellinside YP_001368696.1class=cellinside peptidase M2class=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr7class=cellinside sRNAclass=cellinside Oar7CIclass=cellinside Rclass=cellinside 149814class=cellinside 149972class=cellinside -class=cellinside -class=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr7class=cellinside geneclass=cellinside Oant_0137class=cellinside Dclass=cellinside 150127class=cellinside 153057class=cellinside YP_001368697.1class=cellinside DNA polymeraseclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)

Data download

Covariance Model in stockholm format can be downloaded at gps-tools2.its.yale.edu.

Notes and References

  1. del Val C, Rivas E, Torres-Quesada O, Toro N, Jiménez-Zurdo JI . Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics . Mol Microbiol . 66. 5 . 1080–1091 . 2007 . 17971083. 10.1111/j.1365-2958.2007.05978.x . 2780559.
  2. Vincent M Ulvé . Emeric W Sevin . Angélique Chéron . Frédérique Barloy-Hubler . Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021. BMC Genomics. 8. 467. 467. 2007. 10.1186/1471-2164-8-467. 18093320. 2245857 . free .
  3. Claudio Valverde . Jonathan Livny . Jan-Philip Schlüter . Jan Reinkensmeier . Anke Becker . Gustavo Parisi. rediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011 . BMC Genomics. 9. 406. 2009. 10.1186/1471-2164-9-416. 18793445 . 2573895 . 416 . free .
  4. Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A . A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics. 11. 245. 2010. 10.1186/1471-2164-11-436. 20637113. 3091635. 436 . free .
  5. Web site: Sanger – Software . 14 May 2012.
  6. Web site: NCBI . 14 May 2012.
  7. Nawrocki EP, Kolbe DL, Eddy SR . Infernal 1.0: inference of RNA alignments. Bioinformatics. 25. 10. 1335–1337. 10.1093/bioinformatics/btp157. 2009. 19307242. 2732312.
  8. Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R . Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLOS Comput Biol. 4. 65. e65. 10.1371/journal.pcbi.0030065. 17432929. 1851984. 2007. 2007PLSCB...3...65W . free .
  9. MacLellan SR, MacLean AM, Finan TM . Promoter prediction in the rhizobia. 152. 6. Microbiology. 1751–1763. 2006. 10.1099/mic.0.28743-0. 16735738. free.
  10. Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I . RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Research. 38. Web Server issue. W299–W307. 2010. 10.1093/nar/gkq531. 20542910. 2896116.
  11. Web site: regpredict.lbl.gov . 14 May 2012 . dead . https://web.archive.org/web/20120323233555/http://regpredict.lbl.gov/regpredict/help.html . 23 March 2012 .
  12. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, Garcia-Sotelo JS, Lopez-Fuentes A, Porron-Sotelo L, Alquicira-Hernandez S, Medina-Rivera A, Martinez-Flores I, Alquicira-Hernandez K, Martinez-Adame R, Bonavides-Martinez C, Miranda-Rios J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J . RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Research. 39. Database issue. D98–D105. 2010. 10.1093/nar/gkq1110. 21051347. 3013702.
  13. Web site: regulondb.ccg.unam.mx . 14 May 2012.
  14. Bailey TL, Elkan C . Proceedings. International Conference on Intelligent Systems for Molecular Biology . Fitting a mixture model by expectation maximization to discover motifs in biopolymers. 28–36. 1994. 2 . 7584402 .
  15. Web site: meme.sdsc.edu/meme4_6_1/intro.html . 14 May 2012 . dead . https://web.archive.org/web/20110929030945/http://meme.sdsc.edu/meme4_6_1/intro.html . 29 September 2011 .
  16. Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, König R . GOPET: a tool for automated predictions of Gene Ontology terms . BMC Bioinformatics . 7. 171 . 2006 . 16549020. 10.1186/1471-2105-7-161 . 1434778 . free .
  17. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M . Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005. 21. 18. 3674–3676. 16081474. 10.1093/bioinformatics/bti610. free.
  18. del Val C, Ernst P, Falkenhahn M, Fladerer C, Glatting KH, Suhai S, Hotz-Wagenblatt A . ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. Nucleic Acids Res. 35. Web Server issue. W444–50. 17526514. 10.1093/nar/gkm364. 1933246. July 2007.

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Αr7 RNA".

Except where otherwise indicated, Everything.Explained.Today is © Copyright 2009-2024, A B Cryer, All Rights Reserved. Cookie policy.