Figure 1. RNA-binding proteins stabilize antiterminator structures. Alternative stem-loop structures in transcribed leader regions from representative operons are shown. Terminator stem regions that participate in alternative structures are in blue, whereas antiterminator regions are in red. (A) NasR-responsive nasF operon leader in termination conformation. Dots indicate the critical residues A1 and G4 in the P1 and P2 loops. (B) Each ANTAR monomer is hypothesized to bind one of the loops, P1 and P2. Stabilizing the P2 antiterminator structure permits transcription readthrough [6] by shortening the terminator stem and separating it from the poly-U tract [2]. (C) LicT-responsive bglP operon leader in termination conformation. RAT is the ribonucleic antiterminator. (D) Each CAT (co-antiterminator) monomer binds to the antiterminator stem. Unusual base- pairing within the antiterminator stem is depicted schematically [25]. Stablilizing the antiterminator structure permits transcription readthrough [22] by shortening the terminator stem and separating it from the poly-U tract. doi:10.1371/journal.pgen.1002773.g001 with aspects of nitrogen metabolism pro- vokes intriguing questions about their physiology and evolution. Comparison to CAT Domain Antitermination Proteins of the BglG-LicT-SacY family, present in both gram-negative and gram- positive lineages, control genes for sugar catabolism. These homodimeric proteins contain PRD domains (PTS regulation domain) that place them under control of the phosphotransferase system for sugar uptake [21]. The carboxyl-terminal CAT (co-antiterminator) domain interacts with the RAT (ribonucleic antiterminator) ele- ment in the transcribed leader region. The CAT-stabilized antiterminator is mutually exclusive with the terminator structure [22] (Figure 1C and 1D). The CAT domain is a homodimer of four-stranded b-sheets [23]. Phosphoryla- tion results in massive structural changes [24] that bring the two CAT monomers into proper alignment to interact with a distorted minor grove in the antitermina- PLoS Genetics | www.plosgenetics.org 2 June 2012 | Volume 8 | Issue 6 | e1002773