Computational analysis of LexA regulons in Proteus species

Abstract

To gain a general understanding of the SOS system in Proteus species, in this study LexA-binding sites and the LexA regulons in 23 Proteus genomes were first predicted by phylogenetic footprinting server, then with Proteus vulgaris as an example, the expression of LexA regulon in iron limitation was investigated by proteomic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) method. The results showed that LexA proteins were highly conserved in Proteus species, and were in a close phylogenetic relationship with those in Gram-negative bacteria; the core SOS response genes lexA and recA were found in all the 23 genomes, indicating that this system was widely distributed in this genus; besides that, putative LexA-binding sites were also found in the upstream sequences of some genes involved in other biological processes such as biosynthesis, drug resistance, and stress response. Proteomic and RT-qPCR analyses showed that under iron deficient condition, the expression of lexA, recA and sulA was transcriptionally upregulated (p < 0.05), lexA was also translationally upregulated but recA was on the contrary (p < 0.05), whereas another SOS response gene dinI was transcriptionally downregulated (p < 0.01). These results indicated that in response to iron deficiency, the members of LexA regulon were not regulated by the same way, suggesting the existence of a precise regulation mechanism of SOS response in P. vulgaris. In conclusion, this study provided a preliminary understanding of the SOS system in Proteus species, which laid the foundation for further investigation of its roles in SOS response and other biological processes.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  1. Adamczak R, Porollo A, Meller J (2005) Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 59(3):467–475. https://doi.org/10.1002/prot.20441

    CAS  Article  PubMed  Google Scholar 

  2. Bellio P, Mancini A, Di Pietro L, Cracchiolo S, Franceschini N, Reale S, de Angelis F, Perilli M, Amicosante G, Spyrakis F, Tondi D, Cendron L, Celenza G (2020) Inhibition of the transcriptional repressor LexA: withstanding drugresistance by inhibiting the bacterial mechanisms of adaptation to antimicrobials. Life Sci 241:117116. https://doi.org/10.1016/j.lfs.2019.117116

    CAS  Article  PubMed  Google Scholar 

  3. Berghuis BA, Raducanu VS, Elshenawy MM, Jergic S, Depken M, Dixon NE, Hamdan SM, Dekker NH (2018) What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments. Crit Rev Biochem Mol Biol 53(1):49–63. https://doi.org/10.1080/10409238.2017.1394264

    CAS  Article  PubMed  Google Scholar 

  4. Bielow C, Mastrobuoni G, Kempa S (2016) Proteomics quality control: quality control software for MaxQuant results. J Proteome Res 15:777–787. https://doi.org/10.1021/acs.jproteome.5b00780

    CAS  Article  PubMed  Google Scholar 

  5. Blázquez J, Rodríguez-Beltrán J, Matic I (2018) Antibiotic-induced genetic variation: how it arises and how it can be prevented. Annu Rev Microbiol 72:209–230. https://doi.org/10.1146/annurev-micro-090817-062139

    CAS  Article  PubMed  Google Scholar 

  6. Butala M, Zgur-Bertok D, Busby SJ (2009) The bacterial LexA transcriptional repressor. Cell Mol Life Sci 66(1):82–93. https://doi.org/10.1007/s00018-008-8378-6

    CAS  Article  PubMed  Google Scholar 

  7. Chen X, Hu Y, Yang B, Gong X, Zhang N, Niu L, Wu Y, Ge H (2015) Structure of lpg0406, a carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response from Legionella pneumophila. Protein Sci 24(12):2070–2075. https://doi.org/10.1002/pro.2811

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Chistyakov VA, Prazdnova EV, Mazanko MS, Churilov MN, Chmyhalo VK (2018) Increase in bacterial resistance to antibiotics after cancer therapy with platinum-based drugs. Mol Biol (Mosk) 52(2):270–276. https://doi.org/10.7868/S002689841S020106

    CAS  Article  Google Scholar 

  9. Dong J, Lai R, Nielsen K, Fekete CA, Qiu H, Hinnebusch AG (2004) The essential ATP-binding cassette protein RLI1 functions in translation by promoting preinitiation complex assembly. J Biol Chem 279(40):42157–42168. https://doi.org/10.1074/jbc.M404502200

    CAS  Article  PubMed  Google Scholar 

  10. Drzewiecka D (2016) Significance and roles of Proteus spp. bacteria in natural environments. Microb Ecol 72(4):741–758. https://doi.org/10.1007/s00248-015-0720-6

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Fraikin N, Goormaghtigh F, Van Melderen L (2020) Type II toxin-antitoxin systems: evolution and revolutions. J Bacteriol 202(7):e00763-e819. https://doi.org/10.1128/JB.00763-19

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. Galkin VE, Britt RL, Bane LB, Yu X, Cox MM, Egelman EH (2011) Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein. J Mol Biol 408(5):815–824. https://doi.org/10.1016/j.jmb.2011.03.046

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. Galli E, Ferat JL, Desfontaines JM, Val ME, Skovgaard O, Barre FX, Possoz C (2019) Replication termination without a replication fork trap. Sci Rep 9(1):8315. https://doi.org/10.1038/s41598-019-43795-2

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. Girlich D, Bonnin RA, Dortet L, Naas T (2020) Genetics of acquired antibiotic resistance genes in Proteus spp. Front Microbiol 11:256. https://doi.org/10.3389/fmicb.2020.00256

    Article  PubMed  PubMed Central  Google Scholar 

  15. Groban ES, Johnson MB, Banky P, Burnett PG, Calderon GL, Dwyer EC, Fuller SN, Gebre B, King LM, Sheren IN, Von Mutius LD, O’Gara TM, Lovett CM (2005) Binding of the Bacillus subtilis LexA protein to the SOS operator. Nucleic Acids Res 33(19):6287–6295. https://doi.org/10.1093/nar/gki939

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. Hamilton AL, Kamm MA, Ng SC, Morrison M (2018) Proteus spp. as putative gastrointestinal pathogens. Clin Microbiol Rev 31(3):e00085-17. https://doi.org/10.1128/CMR.00085-17

    Article  PubMed  PubMed Central  Google Scholar 

  17. Hizume K, Araki H (2019) Replication fork pausing at protein barriers on chromosomes. FEBS Lett 593(13):1449–1458. https://doi.org/10.1002/1873-3468.13481

    CAS  Article  PubMed  Google Scholar 

  18. Kizawa A, Kawahara A, Takashima K, Takimura Y, Nishiyama Y, Hihara Y (2017) The LexA transcription factor regulates fatty acid biosynthetic genes in the cyanobacterium Synechocystis sp. PCC 6803. Plant J 92(2):189–198. https://doi.org/10.1111/tpj.13644

    CAS  Article  PubMed  Google Scholar 

  19. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874. https://doi.org/10.1093/molbev/msw054

    CAS  Article  Google Scholar 

  20. Leaden L, Silva LG, Ribeiro RA, Dos Santos NM, Lorenzetti APR, Alegria TGP, Schulz ML, Medeiros MHG, Koide T, Marques MV (2018) Iron deficiency generates oxidative stress and activation of the sos response in Caulobacter crescentus. Front Microbiol 9:2014. https://doi.org/10.3389/fmicb.2018.02014

    Article  PubMed  PubMed Central  Google Scholar 

  21. Li S, Xu M, Su Z (2010) Computational analysis of LexA regulons in Cyanobacteria. BMC Genomics 11:527. https://doi.org/10.1186/1471-2164-11-527

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. Locher KP (2016) Mechanistic diversity in ATP-binding cassette (ABC) transporters. Nat Struct Mol Biol 23(6):487–493. https://doi.org/10.1038/nsmb.3216

    CAS  Article  PubMed  Google Scholar 

  23. Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ (2019) The SOS system: a complex and tightly regulated response to DNA damage. Environ Mol Mutagen 60(4):368–384. https://doi.org/10.1002/em.22267

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. Memar MY, Yekani M, Celenza G, Poortahmasebi V, Naghili B, Bellio P, Baghi HB (2020) The central role of the SOS DNA repair system in antibiotics resistance: a new target for a new infectious treatment strategy. Life Sci 262:118562. https://doi.org/10.1016/j.lfs.2020.118562

    CAS  Article  PubMed  Google Scholar 

  25. Meng Y, Sheen CR, Magon NJ, Hampton MB, Dobson RCJ (2020) Structure-function analyses of alkylhydroperoxidase D from Streptococcus pneumoniae reveal an unusual three-cysteine active site architecture. J Biol Chem 295(10):2984–2999. https://doi.org/10.1074/jbc.RA119.012226

    CAS  Article  PubMed  Google Scholar 

  26. Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM (2018) Inhibitors of lexa autoproteolysis and the bacterial SOS response discovered by an academic-industry partnership. ACS Infect Dis 4(3):349–359. https://doi.org/10.1021/acsinfecdis.7b00122

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D (2005) VirtualFootprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21(22):4187–4189. https://doi.org/10.1093/bioinformatics/bti635

    CAS  Article  PubMed  Google Scholar 

  28. Ohshima N, Yamashita S, Takahashi N, Kuroishi C, Shiro Y, Takio K (2008) Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (UgpQ) requires Mg2+, Co2+, or Mn2+ for its enzyme activity. J Bacteriol 190(4):1219–1223. https://doi.org/10.1128/JB.01223-07

    CAS  Article  PubMed  Google Scholar 

  29. Prasad R, Goffeau A (2012) Yeast ATP-binding cassette transporters conferring multidrug resistance. Annu Rev Microbiol 66:39–63. https://doi.org/10.1146/annurev-micro-092611-150111

    CAS  Article  PubMed  Google Scholar 

  30. Qin Z, Devine R, Hutchings MI, Wilkinson B (2019) A role for antibiotic biosynthesis monooxygenase domain proteins in fidelity control during aromatic polyketide biosynthesis. Nat Commun 10(1):3611. https://doi.org/10.1038/s41467-019-11538-6

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. Recacha E, Machuca J, Díaz de Alba P, Ramos-Güelfo M, Docobo-Pérez F, Rodriguez-Beltrán J, Blázquez J, Pascual A, Rodríguez-Martínez JM (2017) Quinolone resistance reversion by targeting the SOS response. MBio 8(5):e00971-17. https://doi.org/10.1128/mBio.00971-17

    Article  PubMed  PubMed Central  Google Scholar 

  32. Salikhova ZZ, Sokolova RB, Iusupova DV (2000) Biosynthesis of Proteus mirabilis nuclease. Mikrobiologiia 69(6):778–782

    CAS  PubMed  Google Scholar 

  33. Schaffer JN, Pearson MM (2015) Proteus mirabilis and urinary tract infections. Microbiol Spectr 3. https://doi.org/10.1128/microbiolspec.UTI-0017-2013

  34. Spiro S (2012) Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors. Philos Trans R Soc Lond B Biol Sci 367(1593):1213–1225. https://doi.org/10.1098/rstb.2011.0309

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. Taboada B, Estrada K, Ciria R, Merino E (2018) Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. Bioinformatics 34(23):4118–4120. https://doi.org/10.1093/bioinformatics/bty496

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Vedyaykin A, Rumyantseva N, Khodorkovskii M, Vishnyakov I (2020) SulA is able to block cell division in Escherichia coli by a mechanism different from sequestration. Biochem Biophys Res Commun 525(4):948–953. https://doi.org/10.1016/j.bbrc.2020.03.012

    CAS  Article  PubMed  Google Scholar 

  37. De Vries J, Genschel J, Urbanke C, Thole H, Wackernagel W (1994) The single-stranded-DNA-binding proteins (SSB) of Proteus mirabilis and Serratia marcescens. Eur J Biochem 224(2):613–622. https://doi.org/10.1111/j.1432-1033.1994.00613.x

    Article  PubMed  Google Scholar 

  38. West SC, Little JW (1984) P. mirabilis RecA protein catalyses cleavage of E. coli LexA protein and the lambda repressor in vitro. Mol Gen Genet 194(1–2):111–113. https://doi.org/10.1007/BF00383505

    CAS  Article  PubMed  Google Scholar 

  39. Wurihan, Gezi, Brambilla E, Wang S, Sun H, Fan L, Shi Y, Sclavi B, Morigen (2018) DnaA and LexA proteins regulate transcription of the uvrb gene in Escherichia coli: The role of DnaA in the control of the SOS regulon. Front Microbiol 9:1212. https://doi.org/10.3389/fmicb.2018.01212

  40. Yan Y, Huang SY (2020) Modeling protein–protein or protein–DNA/RNA complexes using the HDOCK webserver. Methods Mol Biol 2165:217–229. https://doi.org/10.1007/978-1-0716-0708-4_12

    Article  PubMed  Google Scholar 

  41. Yang J, Chen X, McDermaid A, Ma Q (2017) DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses. Bioinformatics 33(16):2586–2588. https://doi.org/10.1093/bioinformatics/btx223

    CAS  Article  PubMed  Google Scholar 

  42. Yin Y, Wang Z, Cheng D, Chen X, Chen Y, Ma Z (2018) The ATP-binding protein FgArb1 is essential for penetration, infectious and normal growth of Fusarium graminearum. New Phytol 19(4):1447–1466. https://doi.org/10.1111/nph.15261

    CAS  Article  Google Scholar 

Download references

Author information

Affiliations

Authors

Contributions

LYZ contributed to the study design and manuscript draft. CLY performed the experiments. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Yongzhong Lu.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest in the publication.

Ethical approval

No human or animal subjects were involved in the experiments, so an ethical approval was not required.

Informed consent

Informed consent was not required in this study.

Additional information

This work was supported by the Open Project Program of State Key Laboratory of Food Science and Technology, Jiangnan University (No. SKLF-KF-201921), and Shandong Provincial Key Research and Development Program, China (2019GHY112087).

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Lu, Y., Cheng, L. Computational analysis of LexA regulons in Proteus species. 3 Biotech 11, 131 (2021). https://doi.org/10.1007/s13205-021-02683-1

Download citation

Keywords

  • LexA
  • Phylogenetic footprinting
  • Proteus
  • RecA
  • SOS response