REFERENCES
Anantharaman, V., and Aravind, L. (2003) Application of comparative
genomics in the identification and analysis of novel families of
membrane-associated receptors in bacteria. BMC Genomics4 : 34.
Andrews, E.S.V., and Patrick, W.M. (2022) The hypothesized role of YbeZ
in 16S rRNA maturation. Arch Microbiol 204 : 114.
Armitano, J., Redder, P., Guimarães, V.A., and Linder, P. (2016) An
Essential Factor for High Mg2+ Tolerance of Staphylococcus aureus.Front Microbiol 7 : 1888.
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M.,et al. (2006) Construction of Escherichia coli K-12 in-frame,
single-gene knockout mutants: the Keio collection. Mol Syst Biol2 : 2006.0008.
Babu, V.M.P., Sankari, S., Budnick, J.A., Caswell, C.C., and Walker,
G.C. (2020) Sinorhizobium meliloti YbeY is a zinc-dependent
single-strand specific endoribonuclease that plays an important role in
16S ribosomal RNA processing. Nucleic Acids Res 48 :
332–348.
Bobonis, J., Mitosch, K., Mateus, A., Karcher, N., Kritikos, G.,
Selkrig, J., et al. (2022) Bacterial retrons encode
phage-defending tripartite toxin–antitoxin systems. Nature609 : 144–150.
Butland, G., Peregrín-Alvarez, J.M., Li, J., Yang, W., Yang, X.,
Canadien, V., et al. (2005) Interaction network containing
conserved and essential protein complexes in Escherichia coli.Nature 433 : 531–537.
Caglar, M.U., Houser, J.R., Barnhart, C.S., Boutz, D.R., Carroll, S.M.,
Dasgupta, A., et al. (2017) The E. coli molecular phenotype under
different growth conditions. Sci Rep 7 : 45303.
Christensen, D.G., Orr, J.S., Rao, C.V., and Wolfe, A.J. (2017)
Increasing Growth Yield and Decreasing Acetylation in Escherichia coli
by Optimizing the Carbon-to-Magnesium Ratio in Peptide-Based Media.Applied and Environmental Microbiologyhttps://journals.asm.org/doi/abs/10.1128/AEM.03034-16. Accessed January
25, 2022.
Ciolli Mattioli, C., Eisner, K., Rosenbaum, A., Wang, M., Rivalta, A.,
Amir, A., et al. (2023) Physiological stress drives the emergence
of a Salmonella subpopulation through ribosomal RNA regulation.Current Biologyhttps://www.sciencedirect.com/science/article/pii/S0960982223013131.
Accessed October 25, 2023.
Cruz-Loya, M., Kang, T.M., Lozano, N.A., Watanabe, R., Tekin, E.,
Damoiseaux, R., et al. (2019) Stressor interaction networks
suggest antibiotic resistance co-opted from stress responses to
temperature. ISME J 13 : 12–23.
Datsenko, K.A., and Wanner, B.L. (2000) One-step inactivation of
chromosomal genes in Escherichia coli K-12 using PCR products.PNAS 97 : 6640–6645.
Davies, B.W., Köhrer, C., Jacob, A.I., Simmons, L.A., Zhu, J., Aleman,
L.M., et al. (2010) Role of Escherichia coli YbeY, a highly
conserved protein, in rRNA processing. Mol Microbiol 78 :
506–518.
Davis, J.H., and Williamson, J.R. (2017) Structure and dynamics of
bacterial ribosome biogenesis. Philosophical Transactions of the
Royal Society B: Biological Sciences 372 : 20160181.
D’Souza, A.R., Van Haute, L., Powell, C.A., Mutti, C.D., Páleníková, P.,
Rebelo-Guiomar, P., et al. (2021) YbeY is required for ribosome
small subunit assembly and tRNA processing in human mitochondria.Nucleic Acids Research https://doi.org/10.1093/nar/gkab404.
Accessed May 28, 2021.
Gibson, M.M., Bagga, D.A., Miller, C.G., and Maguire, M.E. (1991)
Magnesium transport in Salmonella typhimurium: the influence of new
mutations conferring Co2+ resistance on the CorA Mg2+ transport system.Mol Microbiol 5 : 2753–2762.
Green, M.R., and Sambrook, J. (2020) The Inoue Method for Preparation
and Transformation of Competent Escherichia coli: “Ultracompetent”
Cells. Cold Spring Harb Protoc 2020 : pdb.prot101196.
Jacob, A.I., Köhrer, C., Davies, B.W., RajBhandary, U.L., and Walker,
G.C. (2013) Conserved bacterial RNase YbeY plays key roles in 70S
ribosome quality control and 16S rRNA maturation. Mol Cell49 : 427–438.
Kasari, V., Mets, T., Tenson, T., and Kaldalu, N. (2013) Transcriptional
cross-activation between toxin-antitoxin systems of Escherichia coli.BMC Microbiology 13 : 45.
Kazakov, A.E., Vassieva, O., Gelfand, M.S., Osterman, A., and Overbeek,
R. (2003) Bioinformatics classification and functional analysis of PhoH
homologs. In Silico Biol 3 : 3–15.
Keseler, I.M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A.,
Gama-Castro, S., Bonavides-Martínez, C., et al. (2013) EcoCyc:
fusing model organism databases with systems biology. Nucleic
Acids Res 41 : D605-612.
Khan, A. ul M., Torelli, A., Wolf, I., and Gretz, N. (2018) AutoCellSeg:
robust automatic colony forming unit (CFU)/cell analysis using adaptive
image segmentation and easy-to-use post-editing techniques. Sci
Rep 8 : 7302.
Kim, S.K., Makino, K., Amemura, M., Shinagawa, H., and Nakata, A. (1993)
Molecular analysis of the phoH gene, belonging to the phosphate regulon
in Escherichia coli. Journal of Bacteriology 175 :
1316–1324.
Lee, D.D., Galera-Laporta, L., Bialecka-Fornal, M., Moon, E.C., Shen,
Z., Briggs, S.P., et al. (2019) Magnesium Flux Modulates
Ribosomes to Increase Bacterial Survival. Cell 177 :
352-360.e13.
Li, R., Jin, M., Du, J., Li, M., Chen, S., and Yang, S. (2020) The
Magnesium Concentration in Yeast Extracts Is a Major Determinant
Affecting Ethanol Fermentation Performance of Zymomonas mobilis.Front Bioeng Biotechnol 8 : 957.
Liao, Z., Schelcher, C., and Smirnov, A. (2021) YbeY, éminence grise of
ribosome biogenesis. Biochemical Society Transactions49 : 727–745.
Liu, J., Zhou, W., Liu, G., Yang, C., Sun, Y., Wu, W., et al.(2015) The Conserved Endoribonuclease YbeY Is Required for Chloroplast
Ribosomal RNA Processing in Arabidopsis1. Plant Physiol168 : 205–221.
McCarthy, B.J., Britten, R.J., and Roberts, R.B. (1962) The Synthesis of
Ribosomes in E. coli: III. Synthesis of Ribosomal RNA. Biophysical
Journal 2 : 57–82.
Neidhardt, F.C., Bloch, P.L., and Smith, D.F. (1974) Culture Medium for
Enterobacteria. J Bacteriol 119 : 736–747.
Nonaka, G., Blankschien, M., Herman, C., Gross, C.A., and Rhodius, V.A.
(2006) Regulon and promoter analysis of the E. coli heat-shock factor,
σ32, reveals a multifaceted cellular response to heat stress.Genes Dev 20 : 1776–1789.
Orelle, C., Carlson, E.D., Szal, T., Florin, T., Jewett, M.C., and
Mankin, A.S. (2015) Protein synthesis by ribosomes with tethered
subunits. Nature 524 : 119–124.
Otsuka, Y., Muto, A., Takeuchi, R., Okada, C., Ishikawa, M., Nakamura,
K., et al. (2015) GenoBase: comprehensive resource database of
Escherichia coli K-12. Nucleic Acids Research 43 :
D606–D617.
Piir, K., Paier, A., Liiv, A., Tenson, T., and Maiväli, Ü. (2011)
Ribosome degradation in growing bacteria. EMBO Rep 12 :
458–462.
Pontes, M.H., Yeom, J., and Groisman, E.A. (2016) Reducing Ribosome
Biosynthesis Promotes Translation during Low Mg2+ Stress.Molecular Cell 64 : 480–492.
Quan, J., and Tian, J. (2011) Circular polymerase extension cloning for
high-throughput cloning of complex and combinatorial DNA libraries.Nat Protoc 6 : 242–251.
R Core Team (2022) R: A Language and Environment for Statistical
Computing . R Foundation for Statistical Computing, Vienna, Austria.
https://www.R-project.org/.
Rajagopala, S.V., Yamamoto, N., Zweifel, A.E., Nakamichi, T., Huang,
H.-K., Mendez-Rios, J.D., et al. (2010) The Escherichia coli K-12
ORFeome: a resource for comparative molecular microbiology. BMC
Genomics 11 : 470.
Rampersad, S.N. (2012) Multiple Applications of Alamar Blue as an
Indicator of Metabolic Function and Cellular Health in Cell Viability
Bioassays. Sensors (Basel) 12 : 12347–12360.
Sambrook, J. (2001) Molecular cloning : a laboratory manual .
Third edition. Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory
Press, [2001] ©2001, .
https://search.library.wisc.edu/catalog/999897924602121.
Shajani, Z., Sykes, M.T., and Williamson, J.R. (2011) Assembly of
Bacterial Ribosomes. Annu Rev Biochem 80 : 501–526.
Siibak, T., Peil, L., Xiong, L., Mankin, A., Remme, J., and Tenson, T.
(2009) Erythromycin- and Chloramphenicol-Induced Ribosomal Assembly
Defects Are Secondary Effects of Protein Synthesis Inhibition.Antimicrobial Agents and Chemotherapyhttps://journals.asm.org/doi/abs/10.1128/AAC.00870-08. Accessed December
17, 2021.
Smith, B.A., Gupta, N., Denny, K., and Culver, G.M. (2018)
Characterization of 16S rRNA Processing with Pre-30S Subunit Assembly
Intermediates from E. coli. Journal of Molecular Biology430 : 1745–1759.
Smith, L.K., Gomez, M.J., Shatalin, K.Y., Lee, H., and Neyfakh, A.A.
(2007) Monitoring of gene knockouts: genome-wide profiling of
conditionally essential genes. Genome Biol 8 : R87.
Sprouffske, K., and Wagner, A. (2016) Growthcurver: an R package for
obtaining interpretable metrics from microbial growth curves. BMC
Bioinformatics 17 : 172.
Sueki, A., Stein, F., Savitski, M.M., Selkrig, J., and Typas, A. (2020)
Systematic Localization of Escherichia coli Membrane Proteins.mSystems 5 : e00808-19.
Umlauf, N., Klein, N., Simon, T., and Zeileis, A. (2021) bamlss: A Lego
Toolbox for Flexible Bayesian Regression (and Beyond). J Stat
Soft 100 : 1–53.
VanBogelen, R.A., and Neidhardt, F.C. (1990) Ribosomes as sensors of
heat and cold shock in Escherichia coli. Proceedings of the
National Academy of Sciences 87 : 5589–5593.
Vercruysse, M., Köhrer, C., Shen, Y., Proulx, S., Ghosal, A., Davies,
B.W., et al. (2016) Identification of YbeY-Protein Interactions
Involved in 16S rRNA Maturation and Stress Regulation in Escherichia
coli. mBio 7 .
Wickham, H. (2016) ggplot2: Elegant Graphics for Data Analysis .
2nd ed. 2016., Springer International Publishing : Imprint: Springer,
Cham.
Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L.D., François,
R., et al. (2019) Welcome to the Tidyverse. Journal of Open
Source Software 4 : 1686.
Wilson, D.N. (2014) Ribosome-targeting antibiotics and mechanisms of
bacterial resistance. Nat Rev Microbiol 12 : 35–48.
Xia, Y., Weng, Y., Xu, C., Wang, D., Pan, X., Tian, Z., et al.(2020) Endoribonuclease YbeY Is Essential for RNA Processing and
Virulence in Pseudomonas aeruginosa. mBio 11 .