de/transcriptomics/transcriptomics-facility/sm14koli.html for details on content and layout of microarrays). Hybridization signals
to this website oligonucleotide probes corresponding to the intergenic regions were not analyzed further in this study. A total of 168 genes (2.7% of the 6206 ORFs predicted in the S. meliloti 1021 genome) displayed at least 2-fold changes in their mRNA levels (i.e. 1 ≤ M ≤ -1) and were catalogued as differentially expressed in both strains (see additional file 1: differentially accumulated transcripts in S. meliloti 1021 and 1021Δhfq derivative strain; the microarray data described in this work have been deposited AZD1152 in the ArrayExpress database under accession number A-MEXP-1760). Of these, 91 were found to
be down-regulated and 77 up-regulated in the 1021Δhfq mutant. Replicon distribution of the 168 Hfq-dependent genes revealed that 103 (61%) were chromosomal and 65 had plasmid location; 45 (27%) in pSymA and 20 (12%) in pSymB (Fig. 2, upper charts). Taking into account the gene content of S. meliloti 1021 with 54% genes annotated in the chromosome, 21% in pSymA and 24% located on pSymB, this distribution showed a replicon bias in Hfq activity with 1.3-fold more impact than expected on pSymA-encoded transcripts. The former observation is more evident when looking at the location of Compound C next genes scored as down-regulated in the 1021Δhfq mutant; as many as 34 (37%) of these 91 down-regulated genes were pSymA-borne which is almost 1.8-fold more than expected for the ORF content of this megaplasmid. Figure 2 Hfq-dependent alteration of the S. meliloti transcriptome and proteome. Differentially expressed transcripts (upper graphs) and proteins (lower graphs) in the S. meliloti hfq knock-out mutants.
Histograms show the number of differentially expressed genes and their distribution in the three S. meliloti replicons: chromosome (Chrom.), pSymA and pSymB. The distribution of annotated ORFs in the genome is indicated as reference. The adscription of these genes to functional categories according to the KEGG and S. meliloti databases is shown to the right in circle charts (see text for web pages of the referred databases). In brackets the number of genes belonging to each category. According to the S. meliloti 1021 genome sequence annotations (http://iant.toulouse.inra.fr/bacteria/annotation/cgi/rhime.cgi)and the KEGG database (http://www.genome.jp/kegg/) 137 (82%) out of the 168 genes with altered expression in 1021Δhfq could be assigned to particular functional categories, whereas 31 (18%) exhibited global or partial homology to database entries corresponding to putative genes with unknown function (Fig. 2, upper circle graph).