0–3.3-fold induction following BC treatment. The expression increase for asnS find more determined by QRT-PCR was also above twofold (Fig. 3). Of these genes, serS, asnS, tyrS and argS encode seryl-, asparaginyl-, tyrosyl- and arginyl-tRNA synthetase, respectively. Intriguingly, tRNAs synthesized by all of them except seryl-tRNA synthetase needed to be modified with queuosine. The level of queA that is involved in queuosine synthesis was also increased. In addition to queuosine

modification, modified nucleoside 2-thiocytidine (s2C) has so far been found in position 32 of Ser- and Arg-tRNA species (Jager et al., 2004). The synthesis of s2C32 in tRNA requires the product of ydaO, which was found to be upregulated by BC in the present study. The reason for these findings is still unclear. However, as the modifications in tRNAs with queuosine and s2C are both implicated in modulating Entinostat nmr the codon–anticodon interactions (Meier et al., 1985; Jager et al., 2004), it is possible that the mRNA-decoding process may be influenced. Besides

these tRNA modifications, modifications in the 23S rRNA gene by products of rumB and ygjO were also induced by BC. Most rRNA gene modifications are known to be clustered near the regions of the ribosome that are important for mRNA decoding, the binding of auxiliary factors, and subunit association (Madsen et al., 2003). Therefore, we propose that rumB and ygjO may also be required in the optimization of the decoding process. Alkaloids are photosensitive molecules that can induce the production of superoxide and singlet oxygen upon irradiation in the UVA region (Hudson & Towers, 1991; Brezova et al., 2004). Although artificial light sources emitting UVA were not used in our experiment, we found that a variety of superoxide-inducible genes were upregulated by BC (Table S2). In addition, both microarray and QRT-PCR assays revealed a significant increase in the expression of mutT, which is involved in preventing guanines from oxidization by singlet oxygen. Consequently,

GPX6 we suppose that the photochemical behavior of berberine may be initiated during certain experimental process, possibly during the preparation of drug solutions under exposure to the natural UVA from ambient sunlight. However, further study is necessary to confirm this hypothesis. In this study, we defined the expression profiles of S. flexneri in response to BC. Approximately 9% of the genes from the functional class of DNA replication and repair and 11% of the genes from the class of cell division and chromosome partitioning were significantly induced by BC. These results further support the previous findings that berberine is able to interact with DNA (Pilch et al., 1997) and suggest that BC may inhibit the initiation of replication and chromosome segregation, perhaps through interaction with oriC, which may be involved in the antibacterial mechanism of BC.