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Nascent Chain-Monitored Remodeling of the Sec Machinery for Salinity Correction MICROBIOLOGY Correction for “Nascent chain-monitored remodeling of the Sec USA (112:E5513–E5522; first published September 21, 2015; 10.1073/ machinery for salinity adaptation of marine bacteria,” by Eiji pnas.1513001112). Ishii, Shinobu Chiba, Narimasa Hashimoto, Seiji Kojima, Michio The authors note that Fig. 6 appeared incorrectly. The cor- Homma, Koreaki Ito, Yoshinori Akiyama, and Hiroyuki Mori, rected figure and its legend appear below. which appeared in issue 40, October 6, 2015, of Proc Natl Acad Sci A Fig. 6. Regulatory importance of the vemP-secD2-secF2 operon arrangement. (A) Predicted secondary structure of mRNA at the vemP-secD2VA intergenic re- gion. The RNA sequence from the fifth last codon of vemP to the third codon of secD2VA are shown with the secondary structure predicted by CentroidHomfold. The putative SD sequence and the start codon of secD2VA are indicated by box and underline, respectively. The P site and the A site of the VemP-stalled ribo- some (Fig. 4C) are shown schematically. To separate the VemP arrest point and CORRECTION the secondary structure-forming region, we inserted one or two copies of the 18 B C nucleotides encoding the last five amino acid residues of VemP followed by the termination codon, shown at the bottom. (B) Separation of the arrest point and the stem-loop-forming region impairs the regulation. E. coli cells carrying in- dicated vemP-secDF2VA plasmids (with or without the insertion mutations shown in A) were induced with IPTG for 15 min at 37 °C and treated with (+) or without (−)3mMNaN3 for 5 min. Cells were then pulse-labeled for 1 min. Cell extracts of equivalent radioactivities were subjected to anti-VemP (upper gel) and anti-V. SecD2 (lower gel) immunoprecipitation. In the upper gel, “p” indicates the signal peptide unprocessed form of VemP, which included the polypeptide part of the elongation arrested VemP, whereas “m” indicates the signal peptide-processed mature form. Relative intensities of V.SecD2 are shown in the bottom graph, taking the value of lane 1 as unity (n = 3). Gray and black bars represent results obtained without and with NaN3 treatment, respectively. (C) The insertion mu- tations do not affect translation arrest of VemP. E. coli cells carrying pBAD24-Δss- vemP-V.secDF2 with or without the insertion mutations were induced with 0.02% arabinose for 1 h at 37 °C. The same amounts of proteins were separated D by 10% wide-range gel electrophoresis, followed by immunodetection of VemP. (D)ThesecD2VA-secF2VA interval. The nucleotide sequence from the fourth last codon of secD2VA to the fifth codon of secF2VA is shown. The predicted SD se- quence of secF2VA is underlined. www.pnas.org/cgi/doi/10.1073/pnas.1522482112 www.pnas.org PNAS | December 22, 2015 | vol. 112 | no. 51 | E7157 Downloaded by guest on September 27, 2021 Nascent chain-monitored remodeling of the Sec PNAS PLUS machinery for salinity adaptation of marine bacteria Eiji Ishiia, Shinobu Chibab, Narimasa Hashimotoa, Seiji Kojimac, Michio Hommac, Koreaki Itob, Yoshinori Akiyamaa, and Hiroyuki Moria,1 aInstitute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; bFaculty of Life Sciences, Kyoto Sangyou University, Kita-ku, Kyoto 603-8555, Japan; and cGraduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan Edited by Linda L. Randall, University of Missouri, Columbia, MO, and approved August 26, 2015 (received for review July 2, 2015) SecDF interacts with the SecYEG translocon in bacteria and enhances Therefore, it is conceivable that these bacteria are equipped with protein export in a proton-motive-force-dependent manner. Vibrio mechanisms that allow them to cope with changing concentrations alginolyticus, a marine-estuarine bacterium, contains two SecDF of sodium, a major solute of seawater. paralogs, V.SecDF1 and V.SecDF2. Here, we show that the export- These bacteria have two circular chromosomes, large (chro- + + enhancing function of V.SecDF1 requires Na instead of H ,whereas mosome 1) and small (chromosome 2), both of which are in- + + V.SecDF2 is Na -independent, presumably requiring H .Inaccord dispensable for viability (11). Whereas chromosome 1 carries with the cation-preference difference, V.SecDF2 was only expressed many essential genes involved in protein synthesis and house- + under limited Na concentrations whereas V.SecDF1 was constitu- keeping, chromosome 2 contains a number of genes encoding + tive. However, it is not the decreased concentration of Na per se transporters and transcription regulators involved in environ- that the bacterium senses to up-regulate the V.SecDF2 expression, mental adaptation (12). The genomic information reveals that because marked up-regulation of the V.SecDF2 synthesis was ob- Vibrio secA, secY, secE + species possess a single copy of the ,and served irrespective of Na concentrations under certain genetic/ secG genes on chromosome 1. Because each of the SecA (13), physiological conditions: (i) when the secDF1VA gene was deleted SecY (14), and SecE (15) homologs of Vibrio can function when and (ii) whenever the Sec export machinery was inhibited. VemP introduced into E. coli cells, the fundamental makeup of the Sec (Vibrio export monitoring polypeptide), a secretory polypeptide machinery may be common among these bacterial species. How- encoded by the upstream ORF of secDF2VA, plays the primary role ever, protein translocation into the Vibrio membrane vesicles in MICROBIOLOGY in this regulation by undergoing regulated translational elongation + – vitro was enhanced by the Na -motive force, instead of the pro- arrest, which leads to unfolding of the Shine Dalgarno sequence for ton-motive force (16). Furthermore, protein export in E. coli cells translation of secDF2 . Genetic analysis of V. alginolyticus estab- VA expressing the V. alginolyticus SecDF1 (V.SecDF1) protein (dis- lished that the VemP-mediated regulation of SecDF2 is essential for + cussed below) was enhanced by Na (5). Whereas the sodium the survival of this marine bacterium in low-salinity environments. dependence of the Vibrio SecDF is in accord with their marine These results reveal that a class of marine bacteria exploits nascent- origin, V. alginolyticus and other Vibrio species actually have two chain ribosome interactions to optimize their protein export path- secDF secDF1 secDF2 ways to propagate efficiently under different ionic environments sets of genes, which we designate and ,on that they face in their life cycles. chromosomes 1 and 2, respectively. The present study addresses whether these SecDF homologs play different roles in the bacte- protein export | proton-motive force | ribosome | SecD | translation arrest rial physiology and how their expression is regulated. A remarkable mechanism is known about regulation of protein targeting/translocation machineries, in which specific monitoring ells must export specific proteins to their surfaces for growth, substrates directly monitor the activities of the respective systems; Creproduction, and interaction with the environment. In bac- SecM monitors the Sec protein export activity in E. coli (17, 18) teria, the SecA ATPase and the SecYEG translocon play central roles in translocation of secretory proteins across the cytoplasmic membrane (1, 2). In addition, efficient operation of protein export Significance in bacteria requires SecDF, a membrane protein complex having 12 transmembrane segments and large periplasmic domains of Bacteria living in seawater must cope with low-sodium environ- functional importance (3). SecDF is encoded either by the sepa- ments that they may encounter. Here we show an unexpected rate secD and secF genes (4) or as a single polypeptide (5). The finding that remodeling of the Sec protein export machinery crystal structures of Thermus thermophilus SecDF (TSecDF) and plays a pivotal role in this adaptation. Vibrio alginolyticus pos- structure-instructed functional studies of the Escherichia coli sesses alternative SecDF1 and SecDF2 homologs that use the + + ortholog suggest that SecDF drives polypeptide translocation by transmembrane gradient of Na andthatofH , respectively, to enhance protein export by cooperating with the SecYEG trans- capturing a substrate that is emerging from the translocon into the + periplasmic space and undergoing proton-motive-force-dependent locon. The synthesis of SecDF2 is induced in low-Na environ- cycles of conformational changes (5, 6). ments, and this induction is essential for the bacterium to survive In the present study, we address the functions and expression low salinity. Remarkably, the Vibrio species use a nascent poly- regulation of the two SecDF paralogs in a halophilic, marine- peptide, VemP, to monitor the functional state of the Sec path- estuarine bacterium, Vibrio alginolyticus.TheVibrio group of gram- way and to up-regulate translation of SecDF2 when activity of negative bacteria such as Vibrio parahaemolyticus are important for the SecDF1-containing Sec machinery declines. human health because many of them cause severe foodborne illness V. alginolyticus Author contributions: E.I., S.C., K.I., Y.A., and H.M. designed research; E.I., S.C., N.H., S.K., and wound infections (7, 8). wasreportedtobein- M.H., and H.M. performed research; E.I., S.C., K.I., Y.A., and H.M. analyzed data; and K.I. volved in toxin production in infected sea animals (9). These bac- and H.M. wrote the paper. teria living in seawater, including estuary areas, encounter, migrate The authors declare no conflict of interest. into,
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