coli clones unable to grow into colonies after transformation. In contrast, asRNA clones in which highly expressed genes are being targeted would

be able to grow into colonies and selected during the subsequent phenotypic (+IPTG) screens. This hypothesis is supported by data from DNA array-based E. coli gene expression profiling (Tao et al., 1999). For example, 53 of the 79 essential genes (67%) targeted by asRNA constructs (Table S1) are within the top 10% highly expressed genes among the 4290 ORFs examined when E. coli cells were grown exponentially in LB broth plus glucose (Tao et al., 1999). To increase the diversity of asRNA clones identified, possible technical improvements include replacing Ptrc with a more stringent promoter element on the cloning vector or employing a number of plasmid vectors each containing a promoter with different range of activities (Nakashima et al., 2006; Xu et al., 2010). The recovery of 18 asRNA constructs derived Alectinib cost from 10 nonessential genes which share operons with essential genes provides strong support for a hypothesis that expressed asRNAs silence gene function in E. coli at VX-809 molecular weight the operon level. The mechanism of asRNA inhibition in S. aureus was examined previously by Young and coworkers (Young et al., 2006) who demonstrated that asRNAs exert their inhibition by eliciting degradation of mRNAs upstream (5′) of the regions where the asRNAs bind, which lends support to

our hypothesis. If the hypothesis is confirmed, an asRNA construct or synthetic oligonucleotide could inhibit as many as 11 essential

genes simultaneously on the rplN operon (Fig. 2a), rendering it difficult for multiple resistant mutations to occur in multiple genes. If such multigene mechanism of gene silencing turns out to be prevalent among bacteria, it will facilitate design and development of antisense-based antimicrobial therapeutics which are ‘polypharmaceutical’ (Good & Stach, 2011) or ‘multitargeting’ (Silver, 2007): antibiotics (e.g. most of the successful antibiotics in clinical use) target or interact with two or more bacterial target proteins. In this study, two genomic libraries were constructed successfully and screened for inducible buy Decitabine growth inhibitory asRNA clones. The asRNA constructs discovered could knock-down or silence the expression of 79 E. coli essential genes. While the genes being targeted are not yet comprehensive, likely due to a leaky Ptrc promoter of pHN678, this communication represents a first published report to successfully apply regulated asRNA technology to discover E. coli asRNA clones at the genome level. Such conditional asRNA clones will not only stimulate studies of global functions of genes and operons in E. coli but also facilitate discovery and development of novel antimicrobial agents to combat multidrug-resistant pathogens. Funding for this project has been provided by NIH grant SC3GM083686 (to H.H.X.).