Regulation of the Bacillus subtilis Divergent yetL and yetM Genes by a Transcriptional Repressor, YetL, in Response to Flavonoids

Abstract

DNA microarray analysis revealed that transcription of the Bacillus subtilis yetM gene encoding a putative flavin adenine dinucleotide-dependent monooxygenase was triggered by certain flavonoids during culture and was derepressed by disruption of the yetL gene in the opposite orientation situated immediately upstream of yetM, which encodes a putative MarR family transcriptional regulator. In vitro analyses, including DNase I footprinting and gel retardation analysis, indicated that YetL binds specifically to corresponding single sites in the divergent yetL and yetM promoter regions, with higher affinity to the yetM region; the former region overlaps the Shine-Dalgarno sequence of yetL, and the latter region contains a perfect 18-bp palindromic sequence (TAGTTAGGCGCCTAACTA). In vitro gel retardation and in vivo lacZ fusion analyses indicated that some flavonoids (kaempferol, apigenin, and luteolin) effectively inhibit YetL binding to the yetM cis sequence, but quercetin, galangin, and chrysin do not inhibit this binding, implying that the 4-hydroxyl group on the B-ring of the flavone structure is indispensable for this inhibition and that the coexistence of the 3-hydroxyl groups on the B-and C-rings does not allow antagonism of YetL.

Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi

“…Binding of the aromatic ligand releases the repressor from the promoter and leads to the induction of the regulated gene(s). Structurally, the reported aromatic ligands range from salicylate (MarR) [18], 3-chlorobenzoate [19], 2-methylhydroquinone [20] to flavonoids [21]. The genes encoding MarR proteins are generally part of the gene cluster that they regulate and are divergently oriented to them.…”

Transcriptional response machineries of Bacillus subtilis conducive to plant growth promotion

“…As reported in our previous studies and described here, B. subtilis is the first Gram-positive bacterium that was demonstrated to possess multiple flavonoidresponsive transcriptional regulatory systems, 21,32) while it was also reported that, in addition to the NodD system, rhizobia that are classified as Gram-negative bacteria possess the other transcriptional regulatory systems in response to flavonoids. 33,34) The LmrA/QdoR system is first characterized in the genus Bacillus as the system that utilizes flavonoids as an effector molecule for the transcriptional induction of their regulon.…”

“…These DNA-binding motifs consist of the internal region of each subunit, and their N and C termini are intertwined with each other to form a core domain. As YetL dimerization in solution was confirmed by gel filtration, 32) it is assumed that YetL shares this structural feature.…”

“…We found that the fisetin addition significantly (over threefold) elevated the transcription of many genes such as the dhbACEBF, fhuBCG, ycl-NOPQ, and yfiZyfhA operons and the yusV and ycgT genes (http://www.genome.jp/kegg/expression), 32) which have been originally known to be under the control of Fur, an iron-sensing global transcriptional repressor. 49) Fur orthologs are found in many Gram-positive and Gram-negative bacteria and constitute a unique family with other metalloregulatory proteins such as Zur and PerR.…”

“…29) (TAGTTAGGCGCCTAACTA). An in vitro gel retardation assay with the YetL protein and the DNA probes corresponding to the yetL and yetM promoter regions and an in vivo reporter assay of the B. subtilis strains carrying the yetL or yetM promoter-lacZ fusion indicated that the DNA binding of YetL is inhibited effectively by flavonoids such as kaempferol, apigenin, and luteolin, and its weaker interruption by flavonoids such as quercetin and fisetin appears to be different from the case of LmrA/QdoR (the responsive property of YetL to flavonoids with different structural features is discussed in our previous report 32) ). After our publication of the YetL regulatory system, some bacterial transcriptional factors that recognize and respond to flavonoids have been additionally reported, including TetR members of Bradyrhizobium japonicum FrrA 33) and Sinorhizobium meliloti EmrR, 34) and LysR members of Lactobacillus brevis KaeR 35) and Herbaspirillum seropedicae strain SmR1 FdeR.…”