Transcriptome profiling of Lactococcus lactis subsp. cremoris CECT 8666 in response to agmatine.

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The AGDI cluster of L. lactis is composed by five genes aguR, aguB, aguD, aguA and aguC. The last four genes are co-transcribed as a single policistronic mRNA forming the catabolic operon aguBDAC, which encodes the proteins necessary for agmatine uptake and its conversion into putrescine [1], [2]. The first gene of the cluster, aguR, encodes a transmembrane protein that functions as a one-component signal transduction system that senses the agmatine concentration of the medium and accordingly regulates the transcription of aguBDAC[2]. The catabolic operon aguBDAC is transcriptionally activated by agmatine [2] and transcriptionally regulated by carbon catabolite repression (CCR) via glucose, but not by other sugars such as lactose or galactose [1], [3]. On the contrary, the transcription of the aguR regulatory gene is not subject to CCR regulation [1], [3] nor is regulated by agmatine [2]. In this study we report the transcriptional profiling of L. lactis subsp. cremoris CECT 8666 grown in M17 medium with galactose (GalM17) as carbon source and supplemented with agmatine, compared to that of the strain grown in the same culture medium without agmatine. The transcriptional profiling data of agmatine-regulated genes were deposited in the Gene Expression Omnibus (GEO) database under Accession no. GSE74808.", "claims": [{"id": "claim-data-access", "statement": "Microarray data are accessible in the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74808.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981381", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Microarray data are accessible in the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74808."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Agmatine strongly upregulated the four AGDI catalytic genes aguB, aguD, aguA, and aguC, while aguR expression was unaffected; overall, 85 genes were downregulated and 179 upregulated. Differential expression was defined using a p value below 0.05 and an expression fold-change threshold greater than |0.5|, and the underlying microarray data are available through GEO accession GSE74808 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74808.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981381", "locator": "sections[11] \"Results and discussion\" paragraph 2", "quote": "The genes aguB, aguD, aguA and aguC coding for the proteins needed for the biosynthesis of putrescine through the AGDI pathway were highly upregulated in the L. lactis CECT 8666 strain grown with agmatine."}, {"asset": "source:pmid:26981381", "locator": "sections[11] \"Results and discussion\" paragraph 2", "quote": "The microarray analysis also revealed that the expression of the transcription regulator gene aguR was not affected by agmatine, as we previously demonstrated by RT-qPCR analysis [2]."}, {"asset": "source:pmid:26981381", "locator": "sections[11] \"Results and discussion\" paragraph 2", "quote": "In addition, other 85 genes were downregulated and 179 upregulated in the L. lactis CECT 8666 strain grown in GalM17 medium supplemented with agmatine compared to the strain grown without agmatine."}, {"asset": "source:pmid:26981381", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The transcriptional profiling data of agmatine-regulated genes were deposited in the Gene Expression Omnibus (GEO) database under Accession no. 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