ABC Transporters are Hub Genes in Response of Resistant E. Coli ST131 to Ciprofloxacin

The worldwide spread of bacterial infection and the emergence of resistance to antibiotics have become two major problems in the field of medical sciences. As a serious threat, antibiotic resistance genes, in addition to pathogenic bacteria, have been found in bacteria that are generally recognized as safe. One of the common mechanisms of multidrug resistance (MDR) is due to overexpression of efflux pumps. ATP-binding cassette (ABC) transporters are one type of efflux pumps which have an important role in bacterial MDR. ABC transporters mediate the antibiotic expel from the bacterial cell by hydrolyzing ATP. In order to study antibiotic resistance caused by ABC transporters and to capture molecular/gene networks activated/inactivated by any antibiotic, a RNA-seq analysis is performed on Escherichia coli ST131 which is treated by ciprofloxacin. Based on gene expression analysis, 589 genes expressed differentially (FDR p-value <  0.05). Totally 22 significant networks were extracted from differentially expressed genes (PPI <  0.05) which 3 of them have ABC transporters as enriched function including malEFG, lolCDE, and glnHPQ and the genes malG, lolE, and glnP are their hubs respectively. Among them, malEFG has two distinct enriched functions, ABC transporters and two-component system coincidently which means it is more likely to actively cooperate in antibiotic resistance. Since malEFG is up and two other networks are down regulated, ciprofloxacin can play the role of an activator for the first network and an inactivator for the others.

1.        Dadgostar P. Antimicrobial resistance: implications and costs. Infect Drug Resist. 2019;12:3903-10.

2.        Rahimi T, Niazi A, Deihimi T, Taghavi SM, Ayatollahi S, Ebrahimie E. Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil. Funct Integr Genomics. 2018;18(5):533-43.

3.        Peterson E, Kaur P. Antibiotic resistance mechanisms in bacteria: relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front Microbiol. 2018;9:2928.

4.        Fasciana T, Giordano G, Di Carlo P, Colomba C, Mascarella C, Tricoli MR, et al. Virulence factors and antimicrobial resistance of ESCHERICHIA COLI ST131 in community-onset healthcare-associated infections in SICILY, Italy. Pharmacol Online. 2017;1:12-21.

5.        Nicolas-Chanoine MH, Bertrand X, Madec JY. Escherichia coli ST131, an intriguing clonal group. Clin Microbiol Rev. 2014;27(3):543-74.

6.        Ojkic N, Lilja E, Direito S, Dawson A, Allen RJ, Waclaw B. A roadblock-and-kill mechanism of action model for the DNA-targeting antibiotic ciprofloxacin. Antimicrob Agents Chemother. 2020;64(9):e02487-19.

7.        Du D, Wang-Kan X, Neuberger A, van Veen HW, Pos KM, Piddock LJ, et al. Multidrug efflux pumps: structure, function and regulation. Nat Rev Microbiol. 2018;16(9):523-39.

8.        Thomas C, Tampé R. Structural and mechanistic principles of ABC transporters. Annu Rev Biochem. 2020;89:605-36.

9.        Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.

10.      Orelle C, Mathieu K, Jault JM. Multidrug ABC transporters in bacteria. Res Microbiol. 2019;170(8):381-91.

11.      Moreira MA, Souza EC, Moraes CA. Multidrug efflux systems in Gram-negative bacteria. Braz J Microbiol. 2004;35(1-2):19-28.

12.      Linton KJ, Higgins CF. The Escherichia coli ATP‐binding cassette (ABC) proteins. Mol Microbiol. 1998;28(1):5-13.

13.      Van Veen HW, Venema K, Bolhuis H, Oussenko I, Kok J, Poolman B, et al. Multidrug resistance mediated by a bacterial homolog of the human multidrug transporter MDR1. Proc Natl Acad Sci. 1996;93(20):10668-72.

14.      Robey RW, Pluchino KM, Hall MD, Fojo AT, Bates SE, Gottesman MM. Revisiting the role of ABC transporters in multidrug-resistant cancer. Nat Rev Cancer. 2018;18(7):452-64.

15.      Klitgaard RN, Jana B, Guardabassi L, Nielsen KL, Løbner-Olesen A. DNA damage repair and drug efflux as potential targets for reversing low or intermediate ciprofloxacin resistance in E. coli K-12. Front Microbiol. 2018;9:1438.

16.      Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. Cytoscape StringApp: network analysis and visualization of proteomics data. J Proteome Res. 2018;18(2):623-32.

17.      Scardoni G, Petterlini M, Laudanna C. Analyzing biological network parameters with CentiScaPe. Bioinformatics. 2009;25(21):2857-9.

18.      Zhu Z, Jin Z, Deng Y, Wei L, Yuan X, Zhang M, et al. Co-expression network analysis identifies four hub genes associated with prognosis in soft tissue sarcoma. Front Genet. 2019;10:37.

19.      Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45(D1):D353-61.

20.      Gene Ontology Consortium. The gene ontology resource: 20 years and still GOing strong. Nucleic Acids Res. 2019;47(D1):D330-8.

21.      Chen H, Zhang Z, Jiang S, Li R, Li W, Zhao C, et al. New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. Brief Bioinform. 2020;21(4):1397-410.

22.      Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, et al. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2019;20(4):1085-93.

23.      Sharma S, Zhou R, Wan L, Feng S, Song K, Xu C, et al. Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins. Nat Commun. 2021;12(1):1-1.

24.      Bedouelle H, Schmeissner U, Hofnung M, Rosenberg M. Promoters of the malEFG and malK-lamB operons in Escherichia coli K12. J Mol Biol. 1982;161(4):519-31.

25.      Mächtel R, Narducci A, Griffith DA, Cordes T, Orelle C. An integrated transport mechanism of the maltose ABC importer. Res Microbiol. 2019;170(8):321-37.

26.      Mohany NA, Totti A, Naylor KR, Janovjak H. Microbial methionine transporters and biotechnological applications. Appl Microbiol Biotechnol. 2021;105:3919-29.

27.      Dong H, Zhang Z, Tang X, Paterson NG, Dong C. Structural and functional insights into the lipopolysaccharide ABC transporter LptB 2 FG. Nat Commun. 2017;8:222.

28.      Ruiz N, Gronenberg LS, Kahne D, Silhavy TJ. Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli. Proc Natl Acad Sci. 2008;105(14):5537-42.

29.      Thongbhubate K, Nakafuji Y, Matsuoka R, Kakegawa S, Suzuki H. Effect of Spermidine on Biofilm Formation in Escherichia coli K-12. J Bacteriol. 2021;203(10):e00652-20.

30.      Liu W, Tan M, Zhang C, Xu Z, Li L, Zhou R. Functional characterization of murB-potABCD operon for polyamine uptake and peptidoglycan synthesis in Streptococcus suis. Microbiol Res. 2018;207:177-87.

31.      Breland EJ, Eberly AR, Hadjifrangiskou M. An overview of two-component signal transduction systems implicated in extra-intestinal pathogenic E. coli infections. Front Cell Infect Microbiol. 2017;7:162.

32.      Eyers CE, editor. Histidine Phosphorylation: Methods and Protocols. Humana Press; 2020.

33.      Nickerson NN, Jao CC, Xu Y, Quinn J, Skippington E, Alexander MK, et al. A novel inhibitor of the LolCDE ABC transporter essential for lipoprotein trafficking in Gram-negative bacteria. Antimicrob Agents Chemother. 2018;62(4):e02151-17.

34.      Lorenz C, Dougherty TJ, Lory S. Transcriptional responses of Escherichia coli to a small-molecule inhibitor of LolCDE, an essential component of the lipoprotein transport pathway. J Bacteriol. 2016;198(23):3162-75.

35.      Nohno T, Saito T, Hong JS. Cloning and complete nucleotide sequence of the Escherichia coli glutamine permease operon (glnHPQ). Mol Gen Genet. 1986;205(2):260-9.

36.      Hosie AH, Poole PS. Bacterial ABC transporters of amino acids. Res Microbiol. 2001;152(3-4):259-70.

37.      Amawi H, Sim HM, Tiwari AK, Ambudkar SV, Shukla S. ABC transporter-mediated multidrug-resistant cancer. In: LIU, X. & PAN, G. (eds.) Drug Transporters in Drug Disposition, Effects and Toxicity. Singapore: Springer Singapore. 2019:549-80.

38.      Ahmad A, Majaz S, Nouroz F. Two-component systems regulate ABC transporters in antimicrobial peptide production, immunity and resistance. Microbiology. 2020;166(1):4-20.

39.      Richardson LA. Understanding and overcoming antibiotic resistance. PLoS biol. 2017;15(8):e2003775.

40.      Raymond B. Five rules for resistance management in the antibiotic apocalypse, a road map for integrated microbial management. Evol Appl. 2019;12(6):1079-91.

41.      Shi K, Cao M, Li C, Huang J, Zheng S, Wang G. Efflux proteins MacAB confer resistance to arsenite and penicillin/macrolide-type antibiotics in Agrobacterium tumefaciens 5A. World J Microbiol Biotechnol. 2019;35(8):1-0.

42.      Li XZ, Elkins CA, Zgurskaya HI, editors. Efflux-mediated antimicrobial resistance in bacteria: mechanisms, regulation and clinical implications. Springer; 2016.

43.      Laws M, Shaaban A, Rahman KM. Antibiotic resistance breakers: current approaches and future directions. FEMS Microbiol Rev. 2019;43(5):490-516.

44.      Douafer H, Andrieu V, Phanstiel IV O, Brunel JM. Antibiotic adjuvants: make antibiotics great again!. J Med Chem. 2019;62(19):8665-81.

45.      González-Bello C. Antibiotic adjuvants–A strategy to unlock bacterial resistance to antibiotics. Bioorg Med Chem Lett. 2017;27(18):4221-8.