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MazF activation causes ACA sequence-independent and selective alterations in RNA levels in Escherichia coli

Archives of Microbiology volume 202, pages 105–114 (2020)Cite this article

Abstract

Escherichia coli MazF is a toxin protein that cleaves RNA at ACA sequences. Its activation has been thought to cause growth inhibition, primarily through indiscriminate cleavage of RNA. To investigate responses following MazF activation, transcriptomic profiles of mazF-overexpressing and non-overexpressing E. coli K12 cells were compared. Analyses of differentially expressed genes demonstrated that the presence and the number of ACA trimers in RNA was unrelated to cellular RNA levels. Mapping differentially expressed genes onto the chromosome identified two chromosomal segments in which upregulated genes formed clusters, and these segments were absent in the chromosomes of E. coli strains other than K12. These results suggest that MazF regulates selective, rather than indiscriminate, categories of genes, and is involved in the regulation of horizontally acquired genes. We conclude that the primary role of MazF is not only cleaving RNA indiscriminately but also generating a specific cellular state.

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References

  • Aakre CD, Phung TN, Huang D, Laub MT (2013) A bacterial toxin inhibits DNA replication elongation through a direct interaction with the β sliding clamp. Mol Cell 52:617–628

    CAS  PubMed  PubMed Central  Google Scholar 

  • Aiba H, Adhya S, de Crombrugghe B (1981) Evidence for two functional gal promoters in intact Escherichia coli cells. J Biol Chem 256:11905–11910

    CAS  PubMed  Google Scholar 

  • Amitai S, Kolodkin-Gal I, Hananya-Meltabashi M, Sacher A (2009) Engelberg-Kulka H (2009) Escherichia coli MazF leads to the simultaneous selective synthesis of both "death proteins" and "survival proteins". PLoS Genet 5:e1000390

    PubMed  PubMed Central  Google Scholar 

  • Blumer C, Kleefeld A, Lehnen D, Heintz M, Dobrindt U, Nagy G, Michaelis K, Emödy L, Polen T, Rachel R, Wendisch VF, Unden G (2005) Regulation of type 1 fimbriae synthesis and biofilm formation by the transcriptional regulator LrhA of Escherichia coli. Microbiology 151:3287–3298

    CAS  PubMed  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bustamante P, Tello M, Orellana O (2014) Toxin–antitoxin systems in the mobile genome of Acidithiobacillus ferrooxidans. PLoS ONE 9:e112226

    PubMed  PubMed Central  Google Scholar 

  • Cavalier-Smith T (2005) Economy, speed and size matter: evolutionary forces driving nuclear genome miniaturization and expansion. Ann Bot 95:147–175

    CAS  PubMed  PubMed Central  Google Scholar 

  • Culviner PH, Laub MT (2018) Global analysis of the E. coli toxin MazF reveals widespread cleavage of mRNA and the inhibition of rRNA maturation and ribosome biogenesis. Mol Cell 70:868–880

    CAS  PubMed  Google Scholar 

  • Deutscher MP (2006) Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Res 34:659–666

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ellrott K, Yang C, Sladek FM, Jiang T (2002) Identifying transcription factor binding sites through Markov chain optimizations. Bioinformatics 18(Suppl 2):S100–S109

    PubMed  Google Scholar 

  • Ferenci T, Zhou Z, Betteridge T, Ren Y, Liu Y, Feng L, Reeves PR, Wang L (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J Bacteriol 191:4025–4029

    CAS  PubMed  PubMed Central  Google Scholar 

  • Giovannoni SJ, Thrash JC, Temperton B (2014) Implications of streamlining theory for microbial ecology. ISME J 8:1553–1565

    PubMed  PubMed Central  Google Scholar 

  • Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57

    CAS  Google Scholar 

  • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40(Database issue):D109–D114

    CAS  PubMed  Google Scholar 

  • Karcagi I, Draskovits G, Umenhoffer K, Fekete G, Kovács K, Méhi O, Balikó G, Szappanos B, Györfy Z, Fehér T, Bogos B, Blattner FR, Pál C, Pósfai G, Papp B (2016) Indispensability of horizontally transferred genes and its impact on bacterial genome streamlining. Mol Biol Evol 33:1257–1269

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kasari V, Mets T, Tenson T, Kaldalu N (2013) Transcriptional cross-activation between toxin–antitoxin systems of Escherichia coli. BMC Microbiol 13:45

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kim Y, Wang X, Ma Q, Zhang XS, Wood TK (2009) Toxin–antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae. J Bacteriol 191:1258–1267

    CAS  PubMed  Google Scholar 

  • Kim Y, Wang X, Zhang XS, Grigoriu S, Page R, Peti W, Wood TK (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ Microbiol 12:1105–1121

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H (2009) A differential effect of E. coli toxin–antitoxin systems on cell death in liquid media and biofilm formation. PLoS ONE 4:e6785

    PubMed  PubMed Central  Google Scholar 

  • Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res 13:1589–1594

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kushner SR (2002) mRNA decay in Escherichia coli comes of age. J Bacteriol 184:4658–4665

    CAS  PubMed  PubMed Central  Google Scholar 

  • Magoc T, Wood D, Salzberg SL (2013) EDGE-pro: estimated degree of gene expression in prokaryotic genomes. Evol Bioinform Online 9:127–136

    PubMed  PubMed Central  Google Scholar 

  • Marianovsky I, Aizenman E, Engelberg-Kulka H, Glaser G (2001) The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome. J Biol Chem 276:5975–5984

    CAS  PubMed  Google Scholar 

  • Masuda H, Tan Q, Awano N, Wu KP, Inouye M (2012) YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Mol Microbiol 84:979–989

    CAS  PubMed  Google Scholar 

  • McCarthy JD, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-seq experiments with respect to biological variation. Nucleic Acids Res 40:4288–4297

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mets T, Kasvandik S, Saarma M, Maiväli Ü, Tenson T, Kaldalu N (2019) Fragmentation of Escherichia coli mRNA by MazF and MqsR. Biochimie 156:79–91

    CAS  PubMed  Google Scholar 

  • Mok WW, Park JO, Rabinowitz JD, Brynildsen MP (2015) RNA futile cycling in model persisters derived from MazF accumulation. mBio 6:e01588-15

    PubMed  PubMed Central  Google Scholar 

  • Moll I, Engelberg-Kulka H (2012) Selective translation during stress in Escherichia coli. Trends Biochem Sci 37:493–498

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mruk I, Kobayashi I (2014) To be or not to be: regulation of restriction–modification systems and other toxin–antitoxin systems. Nucleic Acids Res 42:70–86

    CAS  PubMed  Google Scholar 

  • Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006) Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress. Genes Dev 20:1776–1789

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ramisetty BC, Santhosh RS (2016) Horizontal gene transfer of chromosomal Type II toxin–antitoxin systems of Escherichia coli. FEMS Microbiol Lett 363:fnv238

    PubMed  Google Scholar 

  • Sauert M, Wolfinger MT, Vesper O, Müller C, Byrgazov K, Moll I (2016) The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli. Nucleic Acids Res 44:6660–6675

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shimazu T, Degenhardt K, Nur-E-Kamal A, Zhang J, Yoshida T, Zhang Y, Mathew R, White E, Inouye M (2007) NBK/BIK antagonizes MCL-1 and BCL-XL and activates BAK-mediated apoptosis in response to protein synthesis inhibition. Genes Dev 21:929–941

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539

    CAS  PubMed  Google Scholar 

  • Suzuki M, Roy R, Zheng H, Woychik N, Inouye M (2006) Bacterial bioreactors for high yield production of recombinant protein. J Biol Chem 281:37559–37565

    CAS  PubMed  Google Scholar 

  • Tripathi A, Dewan PC, Siddique SA, Varadarajan R (2014) MazF-induced growth inhibition and persister generation in Escherichia coli. J Biol Chem 289:4191–4205

    CAS  PubMed  Google Scholar 

  • Van Melderen L, Saavedra De Bast M (2009) Bacterial toxin–antitoxin systems: more than selfish entities? PLoS Genet 5:e1000437

    PubMed  PubMed Central  Google Scholar 

  • Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin AP (2017) Programming mRNA decay to modulate synthetic circuit resource allocation. Nat Commun 8:15128

    PubMed  PubMed Central  Google Scholar 

  • Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I (2011) Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell 147:147–157

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, Kim Y, Ma Q, Hong SH, Pokusaeva K, Sturino JM, Wood TK (2010) Cryptic prophages help bacteria cope with adverse environments. Nat Commun 1:147

    PubMed  PubMed Central  Google Scholar 

  • Wang X, Lord DM, Cheng HY, Osbourne DO, Hong SH, Sanchez-Torres V, Quiroga C, Zheng K, Herrmann T, Peti W, Benedik MJ, Page R, Wood TK (2012) A new type V toxin–antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat Chem Biol 8:855–861

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yamaguchi Y, Inouye M (2011) Regulation of growth and death in Escherichia coli by toxin–antitoxin systems. Nat Rev Microbiol 19:779–790

    Google Scholar 

  • Yamazaki Y, Niki Y, Kato J (2008) Profiling of Escherichia coli chromosome database. Methods Mol Biol 416:385–389

    CAS  PubMed  Google Scholar 

  • Zhang Y, Zhang J, Hoeflich KP, Ikura M, Qing G, Inouye M (2003) MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell 12:913–923

    CAS  PubMed  Google Scholar 

  • Zhang J, Zhang Y, Zhu L, Suzuki M, Inouye M (2004) Interference of mRNA function by sequence-specific endoribonuclease PemK. J Biol Chem 279:20678–20684

    CAS  PubMed  Google Scholar 

  • Zhu L, Phadtare S, Nariya H, Ouyang M, Husson RN, Inouye M (2008) The mRNA interferases, MazF-mt3 and MazF-mt7 from Mycobacterium tuberculosis target unique pentad sequences in single-stranded RNA. Mol Microbiol 69:559–569

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zorzini V, Mernik A, Lah J, Sterckx YG, De Jonge N, Garcia-Pino A, De Greve H, Versées W, Loris R (2016) Substrate recognition and activity regulation of the Escherichia coli mRNA endonuclease MazF. J Biol Chem 291:10950–10960

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We would like to thank to the rest of iGEM team Tokyo_Tech 2016 team members for collaboration on the early stages of this work. We are grateful to Ms. Tomoko Narisawa and Ms. Masako Sato for technical assistance. This work was supported by the Japan Society for the Promotion of Science (Grant number 17K07714).

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Affiliations

  1. iGEM Team Tokyo_Tech 2016, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan

    Kentaro Akiyama, Kazuki Fujisawa, Hiro Kondo, Yuya Netsu, Koji Nishikawa & Yoshio Takata

  2. School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan

    Yuya Nakamura, Yuta Kino, Nobuhiro Hayashi, Yoh-ichi Tagawa & Nobutaka Nakashima

  3. Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi 2-jyo, Toyohira-ku, Sapporo, 062-8517, Japan

    Shotaro Ayukawa & Nobutaka Nakashima

  4. School of Computing, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan

    Masayuki Yamamura

  5. Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan

    Nobutaka Nakashima

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  1. Kentaro Akiyama
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Correspondence to Nobutaka Nakashima.

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Akiyama, K., Fujisawa, K., Kondo, H. et al. MazF activation causes ACA sequence-independent and selective alterations in RNA levels in Escherichia coli. Arch Microbiol 202, 105–114 (2020). https://doi.org/10.1007/s00203-019-01726-9

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  • DOI: https://doi.org/10.1007/s00203-019-01726-9

Keywords

  • Horizontal gene transfer
  • MazF
  • Metatranscriptome
  • RNA-interferase
  • RNA-seq
  • Toxin-antitoxin