However, this site overlaps the MEME predicted σ54 site, prompting the authors to screen for alternative σ54 binding regions. Subsequent analysis of the promoter using the PromScan algorithm, with a cut off

score of 0.70, identified a second σ54 consensus site at nucleotide MCC 950 position 356. The proximal location of this site to the proposed GGAGG Shine Dalgarno ribosome binding sequence at nucleotide position 455 was more consistent with conventional σ54 promoter architecture, Figure 5(b). Primer extension analysis of RNA extracts from phenylacetic acid grown P. putida CA-3 confirmed the transcriptional start site at nucleotide 381, upon sequencing of the 5′ RACE PCR product, Figure 5(b) and 5(c). Figure 5 Analysis HDAC inhibitor drugs of the paaL promoter region. (a) Promoter structure of the archetypal σ54 factor dependent promoter employed by GenomeMatScan to predict the P. putida KT2440 sigmulon. The upstream activating sequence UAS is indicated, flanked by distal/proximal enhancer binding protein sites displaying diverse spatial positioning upstream of σ54-RNA polymerase promoter C188-9 manufacturer complex formation. Schematic originally proposed by Cases et al, [38]. (b) Annotated nucleotide sequence of the 456 bp intergenic region between the paaG stop codon, (X), and the paaL start codon (M) in P. putida CA-3. Nucleotide positions are indicated in italics. An imperfect integration host factor (IHF) binding site is highlighted in

bold italics with a tetrameric palindrome indicated by directional arrows. Both consensus GG-N10-GC σ54 factor binding sites are highlighted in grey, with the primer extension mapped transcriptional start site indicated numerically (+1). (c) RACE directed RT-PCR amplification of the paaL transcriptional start site. Lanes; 1 = 465 bp RACE product, 2 = negative control, (adapter ligated RNA), and M = Hyperladder II DNA marker (Bioline).

Relative sequence identities of paaL genes and promoters from diverse Pseudomonas species Clustal W analysis was performed with paaL genes and promoters from available PACoA catabolon host genomes, (P. entomophila Urocanase L48, P. fluorescens Pf5, P. putida F1, P. putida KT2440, P. putida W619 and P. putida GB-1), and styrene degradation associated paaL genes from P. putida CA-3, Y2 and P. fluorescens ST, (Table 1). The analysis revealed greater diversity occurred in promoter sequences than in gene sequences. This is clearly demonstrated among the paaL genes from the styrene degraders P. fluorescens ST, P. putida CA-3 and Pseudomonas sp. Y2, which all share > 80% sequence identity with KT2440 paaL sequence, but less than 16% identity at the respective promoter level, Table 1. Among the three styrene degrading strains the authors note that the paaL promoters are 100% identical, while the catabolic genes share ~97% sequence identity, Table 1. Table 1 Clustal W alignment of microbial paaL genes and promoters. Percentage Sequence Identity – CA-3 F1 GB1 KT2440 L48 Pf5 ST W619 Y2 paaL Genes CA-3 – 81.