Figure 1. Schematic of the corA leader mRNA

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Figure 1. Schematic of the corA leader mRNA Figure 1. Schematic of the corA leader mRNA. The Salmonella corA leader can adopt two mutually exclusive conformations, stem-loops A+B or C+D, that control transcription elongation into the corA coding region by modulating accessibility of a rut site (3). Stem-loop A may not form in vivo due to translation of the overlapping ORF corL (dashed black box denotes corL start and stop codons) (3). Major sites of in vitro RNAP pausing (green) and Rho-dependent termination (blue) are denoted. In this work, we identify an additional RNA structure, stem-loop E (orange), whose formation may be independent of stem-loops B versus C+D. Stem-loops C+D suppress RNAP pausing at U240 (red star). Stem-loop E prevents Rho from triggering transcription termination at U192 (green star). From: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader Nucleic Acids Res. 2016;45(2):631-642. doi:10.1093/nar/gkw889 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 2. Mapping of RNAP pause sites in the corA leader Figure 2. Mapping of RNAP pause sites in the corA leader. (A) Schematic of DNA templates used for in vitro transcription assays, modified from (20). Inclusion of a 26 nt C-less initial transcribed sequence (ITS) facilitates synchronization of transcription (30). (B) A 6% denaturing gel showing RNA sequencing (left), transcription termination (center) and pausing assays (right) performed using a wild-type corA leader template generated from pMK100 as described in Materials and Methods. All panels are from the same gel and were re-ordered for clarity. RNAP pauses frequently within the corA leader, including at the sites of Rho-dependent termination (blue bars). The major pause site, U192 (green star) is not a site of Rho-dependent termination. The results are representative of at least three independent experiments and only the relevant portion of the gel is shown. From: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader Nucleic Acids Res. 2016;45(2):631-642. doi:10.1093/nar/gkw889 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 3. The same RNA conformation that sequesters the rut site (stem-loops C+D) reduces efficiency of RNAP pausing at U240. (A and B) A 6% denaturing gel of RNAP pausing assays performed using DNA templates generated from plasmid pMK100 or derivatives containing mutations in (A) stem-loop C or (B) stem-loop D (Figure 1). A red star indicates the position of the U240 pause, which is within the corA start codon. Pause efficiency and half-life were calculated as described in Materials and Methods. The results are representative of at least three independent experiments and only the relevant portion of the gel is shown. Data shown in (A) are from the same gel; solid line denotes where intervening lanes were omitted for clarity. From: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader Nucleic Acids Res. 2016;45(2):631-642. doi:10.1093/nar/gkw889 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 4. Rho can utilize YC dinucleotides downstream of C140 Figure 4. Rho can utilize YC dinucleotides downstream of C140. (A) A 6% denaturing gel of transcription termination assays performed using DNA templates generated from plasmid pMK100 or derivatives harboring mutations in YC dinucleotides between positions 152–196 (Figure 1), in the presence of purified Rho protein. Reactions were performed in triplicate and only the relevant portion of the gel is shown. The results are representative of at least three independent experiments. Green star indicates the position of the U192 pause. (B) The accumulation of free phosphate was monitored to quantify Rho ATPase activity. Purified Rho protein was incubated with RNA corresponding to the wild-type corA leader mRNA or variants harboring mutations YC dinucleotides between positions 152–196 (Figure 1). Data shown correspond to mean values and standard deviation of technical duplicates and are representative of three independent experiments. From: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader Nucleic Acids Res. 2016;45(2):631-642. doi:10.1093/nar/gkw889 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 5. Stem-loop E prevents Rho from terminating transcription at a major RNAP pause site, U192, in a rut site-independent manner. (A) A 6% denaturing gel of transcription termination assays performed using templates generated from plasmid pMK100 or derivatives containing mutations in stem-loop E (Figure 1). Green star indicates the position of the U192 pause. Calculation of termination efficiency was performed as described in Materials and Methods. Reactions were performed in triplicate and only the relevant portion of the gel is shown. The results are representative of at least three independent experiments. (B) A 6% denaturing gel of RNAP pausing assays performed using DNA templates generated from plasmid pMK100 or derivatives containing mutations in stem-loop E (Figure 1). The results are representative of at least three independent experiments and only the relevant portion of the gel is shown. Green star indicates the position of the U192 pause. (C) A 6% denaturing gel of transcription termination assays performed using templates generated from plasmid pMK100 or derivatives containing mutations that disrupt stem-loop E and/or remove YC nucleotides predicted to participate in stem-loop E base-pairing (Figure 1). Reactions were performed in triplicate and only the relevant portion of the gel is shown. The results are representative of at least three independent experiments. Green star indicates the position of the U192 pause. The data shown are from the same gel; the panels were re-ordered and intervening lanes were omitted for clarity. From: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader Nucleic Acids Res. 2016;45(2):631-642. doi:10.1093/nar/gkw889 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 6. Stem-loop E promotes Rho activity in a rut site-independent manner. (A) The accumulation of free phosphate was monitored to quantify Rho ATPase activity. Purified Rho protein was incubated with RNA corresponding to the wild-type corA leader mRNA or variants harboring mutations in stem-loop E (Figure 1). Data shown correspond to mean values and standard deviation of technical duplicates and are representative of three independent experiments. (B) β-galactosidase activity (Miller units) from wild-type Salmonella (14028s) harboring plasmid pYS1040 or derivatives harboring mutations that disrupt or restore stem-loop E base-pairing potential (Figure 1). Data shown indicate mean values and standard deviations from an experiment performed in biological duplicate that is representative of three independent experiments. (C) The accumulation of free phosphate was monitored to quantify Rho ATPase activity. Purified Rho protein was incubated with RNA corresponding to the wild-type corA leader mRNA or variants harboring mutations in stem-loop E and/or the C-rich region at position 175–177 (Figure 1). Data shown correspond to mean values and standard deviation of technical duplicates and are representative of three independent experiments. (D) Percentage of 5΄ radiolabeled RNA bound by Rho and retained following vacuum filtration. RNAs correspond to the wild-type corA leader (black) or mutant derivatives containing mutations in stem-loop E (yellow, orange), stem-loop C (red, positive control) or the rut site (blue, negative control). Data shown are from a single experiment that is representative of three independent experiments. From: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader Nucleic Acids Res. 2016;45(2):631-642. doi:10.1093/nar/gkw889 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 7. The corA leader RNA controls three steps of Rho-dependent transcription termination. Once RNAP (light blue) begins transcribing the corA gene, cytoplasmic signal(s) can influence whether the corA leader RNA adopts the stem-loop B conformation or the stem-loops C+D conformatiion. The stem-loop B conformation presents an accessible rut site (dark blue), whereas stem-loops C+D sequester nucleotides specifically recognized by Rho (yellow). Stem-loops C+D also reduce the efficiency of RNAP pausing at U240 (red star). Stem-loop E (orange), whose formation is independent of stem-loops B versus C+D, prevents Rho from accessing RNAP complexes paused at U192 (green star), thus promoting termination at downstream sites. Black lines represent RNA and grey lines represent DNA. From: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader Nucleic Acids Res. 2016;45(2):631-642. doi:10.1093/nar/gkw889 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com