ArcZ, a cleaved sRNA that is highly conserved in its 3′ part. (A) Alignment of ArcZ sequence from Pantoea ananatis (NZ_CM012203), Escherichia coli (NC_000913.3), Salmonella typhimurium (NC_003197.2), Klebsiella pneumoniae (NC_009648), Photorhabdus laumondii (CP024901.1), Xenorhabdus nematophila (CP060401.1), Dickeya dadantii (CP002038.1), Pectobacterium carotovorum (CP051652.1), Yersinia enterocolitica (CP107102.1), Serratia marcescens (CP139958.1), Proteus mirabilis (CP045257.1), Erwinia amylovora (FN666575.1), Providencia alcalifaciens (CP084296.1), Edwardsiella tarda (CP084506.1), Shigella sonnei (CP026802.1), Citrobacter freundii (CP049015.1), Enterobacter cloacae (CP001918.1), and Cronobacter sakazakii (CP011047.1). Conservation score is plotted below, and the conserved region is colored in red. This alignment was carried out using ClustalW and Jalview (Thompson et al. 2003; Clamp et al. 2004; Troshin et al. 2011). The red squares correspond to known transcription starts. (B) Synteny analysis of chromosomal regions surrounding ArcZ was performed using AnnoView (Wei et al. 2024). The same genome accession numbers as A were used. (C) Model of ArcZ maturation in E. coli. The stem–loop represents the Rho-independent transcriptional termination site of arcZ. The 3′ region of ArcZ is recognized by Hfq through binding. RNase E cleaves ArcZ at a consensus sequence, producing a mature processed form of ArcZ that binds to target mRNA.
