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The Coding and Noncoding Architecture of the Caulobacter crescentus Genome

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Transcription start site and RNA-seq-derived transcript architecture reveals mRNA complexity.

A. Metagene plot of the normalized RNA-seq reads centered on the 5′ PPP sites identified by 5′ global RACE (Zhou et al. [unpublished data]). RNA-seq reads are mapped to the 5′ nucleotide with an enriched peak resulting from partial shearing of the RNA [70]. B. Global distribution of 5′ UTR lengths for all C. crescentus mRNAs with identified 5′ ends shown in blue with Y-axis scale on the left. Cumulative distribution of 5′ UTRs less than 200 nt shown in red with Y-axis scale the right. C. Leaderless dnaQ mRNA, where transcription is initiated at the 5′ nucleotide of the initiating ATG. D. Long 5′ UTR (150 nt) of the dnaA mRNA. E. TSS selection yields alternative translation products: A full length CDS is translated in the +1 reading frame measuring 804 nt. An internally initiated transcript encodes a 360 nt CDS that is translated in the +2 reading frame highlighted in red. LC-MS peptides corresponding to both CDSs are shown in yellow. F. Alternative transcripts drive two different start codons for ftsW with the position of each translation start site (initiating ATG codon) marked below. ATG 2 is in the same reading frame as ATG 1. Shown on the left is a low agar swarmer plate assay for motility and cell division defects, with the cell division inhibitor sidA as a positive control and the ileS leader CDS (CCNA_03934) as a negative control. Shown in the middle is a cell length distribution from cells containing a xylose inducible high-copy plasmid (pBXSPA) with ftsWs or no insert. Shown on the right is the localization of ftsWs-YFP expressed from a low copy plasmid pftsWs-YFP where the promoter for ftsW has been replaced by two transcription terminators.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1004463.g004