Computational elucidation of regulatory network 1 responding to acid stress in Lactococcus lactis MG1363

predict and validate regulons related to acid stress response in Lactococcus lactis 33 MG1363. A total of 51 regulons were identified, and 14 of them have computational 34 verified significance. Among these 14 regulons, five of them were computationally 35 predicted to be connected with acid stress response with (i) known transcriptional 36 factors in MEME suite database successfully mapped in Lactococcus lactis MG1363; 37 and (ii) differentially expressed genes between pH values of 6.5 (control) and 5.1 38 (treatment). Validated by 36 literature confirmed acid stress response related proteins 39 and genes, 33 genes in Lactococcus lactis MG1363 were found having orthologous 40 genes using BLAST, associated to six regulons. An acid response related regulatory 41 network was constructed, involving two trans-membrane proteins, eight regulons 42 ( llrA , llrC , hllA , ccpA , NHP6A, rcfB , regulons #8 and #39), nine functional modules, 43 and 33 genes with orthologous genes known to be associated to acid stress. Our 44 RECTA pipeline provides an effective way to construct a reliable gene regulatory 45 network based on regulon elucidation. The predicted resistance pathways could serve 46 as promising candidates for better acid tolerance engineering in Lactococcus lactis . It 47 has a strong application power and can be effectively applied to other bacterial 48 genomes, where the elucidation of the transcriptional regulation network is needed. 49

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