page_title: Αr14 RNA
section_title: Genomic Context
hierarchical_section_title: Αr14 RNA / Genomic Context
caption_attribution_description: English: Figure 8: Group IV according to the genomic context of the αr14 family.. The αr14 RNA genes are represented by red arrows and the flanking ORFs by arrows on different colors depending on their product function (legend). Numbers indicate the αr14 RNA gene's and flanking ORFs coordinates in each organism genome database. The gene strand is represented with the file direction. On the left of the figure identification names are used which correspond to a certain organism: αr14_Bcr14CI1 = Brucella canis ATCC 23365 chromosome I (NC_010103), αr14_Bs23445r14CI1 = Brucella suis ATCC 23445 chromosome I (NC_010169), αr14_BaS19r14CI1 = Brucella abortus S19 chromosome 1 (NC_010742), αr14_Bs1330r14CI1 = Brucella suis 1330 chromosome I (NC_004310), αr14_Ba19941r14CI1 = Brucella abortus bv str 9-94chromosome I (NC_006932), αr14_Bor14CI1 = Brucella ovis ATCC 25840 chromosome I (NC_009505), αr14_Bmir14CI1 = Brucella microti CCM 4915 chromosome 1 (NC_013119).
context_page_description: αr14 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria. The first member of this family was found in a Sinorhizobium meliloti 1021 locus located in the chromosome. It was later renamed NfeR1 and shown to be highly expressed in salt stress and during the symbiotic interaction on legume roots. Further homology and structure conservation analysis identified 2 other chromosomal copies and 3 plasmidic ones. Moreover, full-length Smr14C homologs have been identified in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. αr14C RNA species are 115-125 nt long and share a well defined common secondary structure. Most of the αr14 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions of the α-proteobacterial genomes.
context_section_description: Most of the members of the αr14 family are trans-encoded sRNAs transcribed from independent promoters in chromosomal IGRs. Many of the neighboring genes of the seed alignment’s members were not annotated and thus were further manually curated.  
  The tandem copies in the Sinorhizobium group’s genomes (Smr14C2, Smr14C3, Smedr14C1, Smedr14C2, Sfr14C1, Sfr14C2) presented a conserved genomic context. The gene upstream coded for an unknown protein containing the domain DUF1127 and the gene downstream coded for a trigger factor.
  Partially conserved genomic context, DUF1127 protein upstream and 5-keto-4-deoxyuronate isomerase downstream, was found for the plasmidic copies of the Rhizobium group Rlt1325r14p02, Rlvr14p11, Rlt2304r14p02, and ReCIATr14A.
  A similar case of partial genomic conservation, DUF1127 protein upstream and tRNA (uracil-5-)-methyltransferase downstream, was found in the case of the Mesorhizobium species, which also presented tandem copies M. loti (Mlr14C1, Mlr14C2) and M. ciceri (Mcr14C1, Mcr14C2). The same context was found for the second copy in the chromosome II of Ochrobactrum anthropii (Oar14CII2) and the second copy in chromosome I in the Brucella group  (Bor14CI2, Bcr14CI2, Bmir14CI2, Bs1330r14CI2, Bm16Mr14CI1, BaS19r14CI2, Bm23457r14CI1, BMEA_A0934, BruAb1_0906, Ba19941r14CI2). In all these cases the sRNAs did appear as single copy in their IGR. Bs23445r14CI2, Bmar14CI2, and Rlvr14C2 shared the gene coding for tRNA (uracil-5-)-methyltransferase downstream, but did not shared the genes coding upstream.
  The results showed two other well-conserved genomic contexts. One with a gene coding for nicotinic acid mononucleotide adenylyltransferase upstream and a gene coding for a molybdenum ABC transporter downstream, which is shared by the third copy of ar14 family in the A. radiobacter genome (Arr14CI3) and in the Rhizobium group genomes (ReCFNr14C3, Rlt1325r14C3, Rlvr14C3, Rlt2304r14C3). The second group is formed by the first copy in the Chromosome I in the Brucellas genomes that share the gene upstream coding for an LrgB membrane protein and the gene downstream a coding for an alpha/beta hydrolase.
  Additional files:
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caption: Figure 8: Group IV according to the genomic context of the αr14 family.. The αr14 RNA genes are represented by red arrows and the flanking ORFs by arrows on different colors depending on their product function (legend). Numbers indicate the αr14 RNA gene's and flanking ORFs coordinates in each organism genome database. The gene strand is represented with the file direction. On the left of the figure identification names are used which correspond to a certain organism: αr14_Bcr14CI1 = Brucella canis ATCC 23365 chromosome I (NC_010103), αr14_Bs23445r14CI1 = Brucella suis ATCC 23445 chromosome I (NC_010169), αr14_BaS19r14CI1 = Brucella abortus S19 chromosome 1 (NC_010742), αr14_Bs1330r14CI1 = Brucella suis 1330 chromosome I (NC_004310), αr14_Ba19941r14CI1 = Brucella abortus bv str 9-94chromosome I (NC_006932), αr14_Bor14CI1 = Brucella ovis ATCC 25840 chromosome I (NC_009505), αr14_Bmir14CI1 = Brucella microti CCM 4915 chromosome 1 (NC_013119).
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