Transcription–replication interactions reveal bacterial genome regulation
Bervoets, I. & Charlier, D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol. Rev. 43, 304–339 (2019).
Vilar, J. M. G., Guet, C. C. & Leibler, S. Modeling network dynamics: the lac operon, a case study. J. Cell Biol. 161, 471–476 (2003).
Narula, J., Devi, S. N., Fujita, M. & Igoshin, O. A. Ultrasensitivity of the Bacillus subtilis sporulation decision. Proc. Natl Acad. Sci. USA 109, E3513–E3522 (2012).
Homberger, C., Hayward, R. J., Barquist, L. & Vogel, J. Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads. mBio 14, e0355722 (2023).
Balakrishnan, R. et al. Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria. Science 378, eabk2066 (2022).
Cooper, S. & Helmstetter, C. E. Chromosome replication and the division cycle of Escherichia coli B/r. J. Mol. Biol. 31, 519–540 (1968).
Schaechter, M., Bentzon, M. W. & Maaloe, O. Synthesis of deoxyribonucleic acid during the division cycle of bacteria. Nature 183, 1207–1208 (1959).
Wang, M., Zhang, J., Xu, H. & Golding, I. Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality. Nat. Microbiol. 4, 2118–2127 (2019).
Narula, J. et al. Chromosomal arrangement of phosphorelay genes couples sporulation and DNA replication. Cell 162, 328–337 (2015).
Slager, J. & Veening, J.-W. Hard-wired control of bacterial processes by chromosomal gene location. Trends Microbiol. 24, 788–800 (2016).
Peterson, J. R., Cole, J. A., Fei, J., Ha, T. & Luthey-Schulten, Z. A. Effects of DNA replication on mRNA noise. Proc. Natl Acad. Sci. USA 112, 15886–15891 (2015).
Laub, M. T., McAdams, H. H., Feldblyum, T., Fraser, C. M. & Shapiro, L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290, 2144–2148 (2000).
Fang, G. et al. Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution. BMC Genom. 14, 450 (2013).
Zhou, B. et al. The global regulatory architecture of transcription during the Caulobacter cell cycle. PLoS Genet. 11, e1004831 (2015).
De Nisco, N. J., Abo, R. P., Wu, C. M., Penterman, J. & Walker, G. C. Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti. Proc. Natl Acad. Sci. USA 111, 3217–3224 (2014).
Bandekar, A. C., Subedi, S., Ioerger, T. R. & Sassetti, C. M. Cell-cycle-associated expression patterns predict gene function in Mycobacteria. Curr. Biol. 30, 3961–3971.e6 (2020).
Cooper, S. The synchronization manifesto: a critique of whole-culture synchronization. FEBS J. 286, 4650–4656 (2019).
Blattman, S. B., Jiang, W., Oikonomou, P. & Tavazoie, S. Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nat. Microbiol. 5, 1192–1201 (2020).
Kuchina, A. et al. Microbial single-cell RNA sequencing by split-pool barcoding. Science 371, eaba5257 (2021).
Imdahl, F., Vafadarnejad, E., Homberger, C., Saliba, A.-E. & Vogel, J. Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria. Nat. Microbiol. 5, 1202–1206 (2020).
Homberger, C., Barquist, L. & Vogel, J. Ushering in a new era of single-cell transcriptomics in bacteria. microLife 3, uqac020 (2022).
Lopez, R., Regier, J., Cole, M. B., Jordan, M. I. & Yosef, N. Deep generative modeling for single-cell transcriptomics. Nat. Methods 15, 1053–1058 (2018).
Bremer, H. & Dennis, P. P. Modulation of chemical composition and other parameters of the cell at different exponential growth rates. EcoSal Plus 3, https://doi.org/10.1128/ecosal.5.2.3 (2008).
Michelsen, O., Teixeira de Mattos, M. J., Jensen, P. R. & Hansen, F. G. Precise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r. Microbiology 149, 1001–1010 (2003).
Wang, X., Lesterlin, C., Reyes-Lamothe, R., Ball, G. & Sherratt, D. J. Replication and segregation of an Escherichia coli chromosome with two replication origins. Proc. Natl Acad. Sci. USA 108, E243–E250 (2011).
Dimude, J. U. et al. Origins left, right, and centre: increasing the number of initiation sites in the chromosome. Genes 9, 376 (2018).
Ivanova, D. et al. Shaping the landscape of the Escherichia coli chromosome: replication-transcription encounters in cells with an ectopic replication origin. Nucleic Acids Res. 43, 7865–7877 (2015).
Khodursky, A. B. et al. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc. Natl Acad. Sci. USA 97, 9419–9424 (2000).
Pham, T. M. et al. A single-molecule approach to DNA replication in Escherichia coli cells demonstrated that DNA polymerase III is a major determinant of fork speed. Mol. Microbiol. 90, 584–596 (2013).
Kjeldgaard, N. O., Maaloe, O. & Schaechter, M. The transition between different physiological states during balanced growth of Salmonella typhimurium. J. Gen. Microbiol. 19, 607–616 (1958).
Skinner, S. O., Sepúlveda, L. A., Xu, H. & Golding, I. Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization. Nat. Protoc. 8, 1100–1113 (2013).
Proshkin, S., Rahmouni, A. R., Mironov, A. & Nudler, E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 328, 504–508 (2010).
Pomerantz, R. T. & O’Donnell, M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456, 762–766 (2008).
de la Fuente, A., Palacios, P. & Vicente, M. Transcription of the Escherichia coli dcw cluster: evidence for distal upstream transcripts being involved in the expression of the downstream ftsZ gene. Biochimie 83, 109–115 (2001).
Flärdh, K., Palacios, P. & Vicente, M. Cell division genes ftsQAZ in Escherichia coli require distant cis-acting signals upstream of ddlB for full expression. Mol. Microbiol. 30, 305–315 (1998).
Lutkenhaus, J. F., Wolf-Watz, H. & Donachie, W. D. Organization of genes in the ftsA–envA region of the Escherichia coli genetic map and identification of a new fts locus (ftsZ). J. Bacteriol. 142, 615–620 (1980).
Zaslaver, A., Mayo, A., Ronen, M. & Alon, U. Optimal gene partition into operons correlates with gene functional order. Phys. Biol. 3, 183–189 (2006).
Zhu, M., Mu, H., Han, F., Wang, Q. & Dai, X. Quantitative analysis of asynchronous transcription–translation and transcription processivity in under various growth conditions. iScience 24, 103333 (2021).
Zhu, M., Mori, M., Hwa, T. & Dai, X. Disruption of transcription–translation coordination in Escherichia coli leads to premature transcriptional termination. Nat. Microbiol. 4, 2347–2356 (2019).
Sharpe, M. E., Hauser, P. M., Sharpe, R. G. & Errington, J. Bacillus subtilis cell cycle as studied by fluorescence microscopy: constancy of cell length at initiation of DNA replication and evidence for active nucleoid partitioning. J. Bacteriol. 180, 547–555 (1998).
Golding, I. Revisiting replication-induced transcription in Escherichia coli. Bioessays 42, e1900193 (2020).
Guptasarma, P. Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? Bioessays 17, 987–997 (1995).
Ray, A., Edmonds, K. A., Palmer, L. D., Skaar, E. P. & Giedroc, D. P. Glucose-induced biofilm accessory protein A (GbaA) is a monothiol-dependent electrophile sensor. Biochemistry 59, 2882–2895 (2020).
Van Loi, V. et al. The two-Cys-type TetR repressor GbaA confers resistance under disulfide and electrophile stress in Staphylococcus aureus. Free Radic. Biol. Med. 177, 120–131 (2021).
Campbell, J. L. & Kleckner, N. E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork. Cell 62, 967–979 (1990).
Theisen, P. W., Grimwade, J. E., Leonard, A. C., Bogan, J. A. & Helmstetter, C. E. Correlation of gene transcription with the time of initiation of chromosome replication in Escherichia coli. Mol. Microbiol. 10, 575–584 (1993).
Buettner, F. et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 33, 155–160 (2015).
Cooper, S. The Escherichia coli cell cycle. Res. Microbiol. 141, 17–29 (1990).
Garrido, T., Sánchez, M., Palacios, P., Aldea, M. & Vicente, M. Transcription of ftsZ oscillates during the cell cycle of Escherichia coli. EMBO J. 12, 3957–3965 (1993).
Zhou, P. & Helmstetter, C. E. Relationship between ftsZ gene expression and chromosome replication in Escherichia coli. J. Bacteriol. 176, 6100–6106 (1994).
Lin, J. & Amir, A. Homeostasis of protein and mRNA concentrations in growing cells. Nat. Commun. 9, 4496 (2018).
Rosenfeld, N., Elowitz, M. B. & Alon, U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323, 785–793 (2002).
Ma, P. et al. Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states. Cell 186, 877–891.e14 (2023).
Brennan, M. A. & Rosenthal, A. Z. Single-Cell RNA sequencing elucidates the structure and organization of microbial communities. Front. Microbiol. 12, 713128 (2021).
Xu, Z. et al. Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq. Nat. Commun. 14, 5130 (2023).
Luecken, M. D. & Theis, F. J. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol. Syst. Biol. 15, e8746 (2019).
Jun, S., Si, F., Pugatch, R. & Scott, M. Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review. Rep. Prog. Phys. 81, 056601 (2018).
La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).
Bergen, V., Soldatov, R. A., Kharchenko, P. V. & Theis, F. J. RNA velocity-current challenges and future perspectives. Mol. Syst. Biol. 17, e10282 (2021).
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Arndt, D. et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44, W16–W21 (2016).
Levin, M. et al. The mid-developmental transition and the evolution of animal body plans. Nature 531, 637–641 (2016).
Zalts, H. & Yanai, I. Developmental constraints shape the evolution of the nematode mid-developmental transition. Nat. Ecol. Evol. 1, 113 (2017).
Keseler, I. M. et al. The EcoCyc database in 2021. Front. Microbiol. 12, 711077 (2021).
Karp, P. D. et al. The BioCyc collection of microbial genomes and metabolic pathways. Brief. Bioinform. 20, 1085–1093 (2019).
Fuchs, S. et al. AureoWiki—the repository of the Staphylococcus aureus research and annotation community. Int. J. Med. Microbiol. 308, 558–568 (2018).
Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Chen, J., Yoong, P., Ram, G., Torres, V. J. & Novick, R. P. Single-copy vectors for integration at the SaPI1 attachment site for Staphylococcus aureus. Plasmid 76, 1–7 (2014).
Benson, M. A. et al. Staphylococcus aureus regulates the expression and production of the staphylococcal superantigen-like secreted proteins in a Rot-dependent manner. Mol. Microbiol. 81, 659–675 (2011).
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