Gene and Protein Network Analysis of AmpC β Lactamase

Cell Biochemistry and Biophysics

Volumn 71, Issue 3, 2015, Pages 1553-1567

  Anitha, P ^a   Bag, Susmita ^a   Anbarasu, Anand ^a   Ramaiah, Sudha ^a  

^a VIT UNIVERSITY   (India)

Author keywords

AmpC lactamases; Gene regulatory networks; Molecular sequence annotation

Indexed keywords

BACTERIA (MICROORGANISMS);

AMPC BETA-LACTAMASES; BACTERIAL PROTEIN; BETA LACTAMASE;

BIOLOGY; DNA SEQUENCE; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PROTEIN ANALYSIS;

BACTERIAL PROTEINS; BETA-LACTAMASES; COMPUTATIONAL BIOLOGY; GENE ONTOLOGY; GENE REGULATORY NETWORKS; PROTEIN INTERACTION MAPPING; SEQUENCE ANALYSIS, DNA;

EID: 84930086272     PISSN: 10859195     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12013-014-0379-5     Document Type: Article

References (62)

1. Taneja, N., Rao, P., Arora, J., & Dogra, A. (2008). Occurrence of ESBL & Amp-C beta-lactamases & susceptibility to newer antimicrobial agents in complicated UTI. Indian Journal of Medical Research,127(1), 85–88.
2. Wilke, M. S., Lovering, A. L., & Strynadka, N. C. (2005). Beta-lactam antibiotic resistance: A current structural perspective. Current Opinion in Microbiology,8(5), 525–533.
3. Majiduddin, F. K., Materon, I. C., & Palzkill, T. G. (2002). Molecular analysis of beta-lactamase structure and function. International Journal of Medical Microbiology,292(2), 127–137.
4. Abraham, E. P., & Chain, E. (1940). An enzyme from bacteria able to destroy penicillin. Nature,146, 837.
5. Balasubramanian, D., Schneper, L., Merighi, M., Smith, R., Narasimhan, G., Lory, S., et al. (2012). The regulatory repertoire of Pseudomonas aeruginosa AmpC ß-lactamase regulator AmpR includes virulence genes. PLoS One,7(3), 34067–34088.
6. Bush, K., Jacoby, G. A., & Medeiros, A. A. (1995). A functional classification scheme for β-lactamases and its correlation with molecular structure. Antimicrobial Agents and Chemotherapy,39(6), 1211–1233.
7. Jacoby, G. A. (2009). AmpC beta-lactamases. Clinical Microbiology Reviews,22(1), 161–182.
8. Moya, B., Juan, C., Alberti, S., Perez, J. L., & Oliver, A. (2008). Benefit of having multiple ampD genes for acquiring beta-lactam resistance without losing fitness and virulence in Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy,52(10), 3694–3700.
9. Philippon, A., Arlet, G., & Jacoby, G. A. (2002). Plasmid-determined AmpC-type beta-lactamases. Antimicrobial Agents and Chemotherapy,46(1), 1–11.
10. Singhal, S., Mathur, T., Khan, S., Upadhyay, D. J., Chugh, S., Gaind, R., et al. (2005). Evaluation of methods for AmpC beta-lactamase in Gram negative clinical isolates from tertiary care hospitals. Indian Journal of Medical Microbiology,23(2), 120–124.
11. Thomson, K. S. (2001). Controversies about extended spectrum and AmpC beta-lactamases. Emerging Infectious Diseases,7(2), 333–336.
12. Barnaud, G., Arlet, G., Verdet, C., Gaillot, O., Lagrange, P. H., & Philippon, A. (1998). Salmonella enteritidis: AmpC plasmid-mediated inducible β-lactamases (DHA-1) with an ampR gene from Morganella morganii. Antimicrobial Agents and Chemotherapy,42(9), 2352–2358.
13. Bagge, N., Ciofu, O., Hentzer, M., Campbell, J. I., Givskov, M., & Hoiby, N. (2002). Constitutive high expression of chromosomal β-lactamase in Pseudomonas aeruginosa caused by a new insertion sequence (IS1669) located in ampD. Antimicrobial Agents and Chemotherapy,46(11), 3406–3411.
14. Lodge, J. M., & Piddock, L. J. (1991). The control of class I beta-lactamase expression in Enterobacteriaceae and Pseudomonas aeruginosa. Journal of Antimicrobial Chemotherapy,28(2), 167–172.
15. Moya, B., Dotsch, A., Juan, C., Blázquez, J., Zamorano, L., Haussler, S., et al. (2009). Beta-lactam resistance response triggered by inactivation of a nonessential penicillin-binding protein. PLoS Pathogens,5(3), 1000353–1000363.
16. Bartowsky, E., & Normark, S. (1993). Interactions of wild-type and mutant AmpR of Citrobacter freundii with target DNA. Molecular Microbiology,10(3), 555–565.
17. Lodge, J. M., Busby, S. J. W., & Piddock, L. J. (1993). Investigation of the Pseudomonas aeruginosa ampR gene and its role at the chromosomal ampC beta-lactamase promoter. FEMS Microbiology Letters,111, 315–320.
18. Lister, P. D., Wolter, D. J., & Hanson, N. D. (2009). Antibacterial-resistant Pseudomonas aeruginosa: Clinical impact and complex regulation of chromosomally encoded resistance mechanisms. Clinical Microbiology Reviews,22(4), 582–610.
19. Natarajan, J., Berrar, D., Dubitzky, W., Hack, C., Zhang, Y., DeSesa, C., et al. (2006). Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. BMC Bioinformatics,7, 373–389.
20. Selga, E., Oleaga, C., Ramirez, S., De Almagro, M. C., Noe, V., & Ciudad, C. J. (2009). Networking of differentially expressed genes in human cancer cells resistant to methotrexate. Genome Medicine,1(9), 83–99.
21. Snel, B., Lehmann, G., Bork, P., & Huynen, M. A. (2000). STRING: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Research,28(18), 3442–3444.
22. Von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., & Snel, B. (2003). STRING: A database of predicted functional associations between proteins. Nucleic Acids Research,31(1), 258–261.
23. Von Mering, C., Jensen, L. J., Snel, B., Hooper, S. D., Krupp, M., Foglierini, M., et al. (2005). STRING: Known and predicted protein–protein associations integrated and transferred across organisms. Nucleic Acids Research,33, 433–437.
24. Von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., et al. (2007). STRING 7: Recent developments in the integration and prediction of protein interactions. Nucleic Acids Research,35, 358–362.
25. Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., et al. (2009). STRING 8: A global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research,37, 412–416.
26. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., et al. (2011). The STRING database in 2011: Functional interaction networks of proteins globally integrated and scored. Nucleic Acids Research,39(1), 561–568.
27. Franceschini, A., Szklarczyk, D., Frankild, S. M., Kuhn, M., Simonovic, A., Roth, J., et al. (2013). STRING v9.1: Protein–protein interaction networks, with increased coverage and integration. Nucleic Acids Research,41, 808–815.
28. Kanehisa, M. (1997). A database for post-genome analysis. Trends in Genetics,13(9), 375–376.
29. Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., et al. (2004). UniProt: The universal protein knowledge base. Nucleic Acids Research,32(1), 115–119.
30. UniProt-Consortium. (2010). The universal protein resource (UniProt) in 2010. Nucleic Acids Research,38, 142–148.
31. Jain, E., Bairoch, A., Duvaud, S., Phan, I., Redaschi, N., Suzek, B. E., et al. (2009). Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics,10, 136–154.
32. Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution,24, 1596–1599.
33. Kumar, S., Stecher, G., Peterson, D., & Tamura, K. (2012). MEGA-CC: Computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics,28, 2685–2686.
34. De Castro, E., Sigrist, C. J., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., et al. (2006). ScanPROSITE: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research,34, 362–365.
35. Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C. J., Hofmann, K., et al. (2002). The PROSITE database, its status in 2002. Nucleic Acids Research,30(1), 235–238.
36. Sigrist, C. J. A., De Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., et al. (2013). New and continuing developments at PROSITE. Nucleic Acids Research,41, 344–347.
37. Corpet, F., Gouzy, J., & Kahn, D. (1999). Recent improvements of the ProDom database of protein domain families. Nucleic Acids Research,27, 263–267.
38. Sonnhammer, E. L., & Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Science,3, 482–492.
39. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., et al. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research,13(11), 2498–2504.
40. Raman, K. (2010). Construction and analysis of protein–protein interaction networks. Automated experimentation,2, 2–11.
41. Lindberg, F., Lindquist, S., & Normark, S. (1987). Inactivation of the ampD gene causes semiconstitutive overproduction of the inducible Citrobacter freundii beta-lactamase. Journal of Bacteriology,169(5), 1923–1928.
42. Lindquist, S., Lindberg, F., & Normark, S. (1989). Binding of the Citrobacter freundii AmpR regulator to a single DNA site provides both autoregulation and activation of the inducible ampC beta-lactamase gene. Journal of Bacteriology,171(7), 3746–3753.
43. Dietz, H., Pfeifle, D., & Wiedemann, B. (1996). Location of N-acetylmuramyl-l-alanyl-d-glutamylmesodiaminopimelic acid, presumed signal molecule for beta-lactamase induction, in the bacterial cell. Antimicrobial Agents and Chemotherapy,40(9), 2173–2177.
44. Schmidtke, A. J., & Hanson, N. D. (2008). Role of ampD homologs in overproduction of AmpC in clinical isolates of Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy,52(11), 3922–3927.
45. Tans-Kersten, J., Gay, J., & Allen, C. (2000). Ralstonia solanacearum AmpD is required for wild type bacterial wilt virulence. Molecular Plant Pathology,1(3), 179–185.
46. Zamorano, L., Reeve, T. M., Juan, C., Moya, B., Cabot, G., Vocadlo, D. J., et al. (2011). AmpG inactivation restores susceptibility of pan-beta-lactam-resistant Pseudomonas aeruginosa clinical strains. Antimicrobial Agents and Chemotherapy,55(5), 1990–1996.
47. Jacobs, C., Frere, J. M., & Normark, S. (1997). Cytosolic intermediates for cell wall biosynthesis and degradation control inducible beta-lactam resistance in Gram-negative bacteria. Cell,88(6), 823–832.
48. Normark, S. (1995). Beta-Lactamase induction in gram-negative bacteria is intimately linked to peptidoglycan recycling. Microbial Drug Resistance,1(2), 111–114.
49. Ni, M., & Zhang, D. (2005). Analysis of AmpC beta-lactamase gene in Pseudomonas aeruginosa. Journal of Huazhong University of Science and Technology,25(1), 17–19.
50. Jones, R. N. (1998). Important and emerging β-lactamase-mediated resistances in hospital-based pathogens: The Amp C enzymes. Diagnostic Microbiology and Infectious Disease,31(3), 461–466.
51. Balcewich, M. D., Reeve, T. M., Orlikow, E. A., Donald, L. J., Vocadlo, D. J., & Mark, B. L. (2010). Crystal structure of the AmpR effector binding domain provides insight into the molecular regulation of inducible ampC beta-lactamase. Journal of Molecular Biology,400(5), 998–1010.
52. Everett, M., Walsh, T., Guay, G., & Bennett, P. (1995). GcvA, a LysR-type transcriptional regulator protein, activates expression of the cloned Citrobacter freundiiampC beta-lactamase gene in Escherichia coli: Cross-talk between DNA-binding proteins. Microbiology,141(2), 419–430.
53. Lindberg, F., Westman, L., & Normark, S. (1985). Regulatory components in Citrobacter freundii ampC beta-lactamase induction. Proceedings of the National Academy of Sciences of the United States of America,82(14), 4620–4624.
54. Grundstrom, T., & Jaurin, B. (1982). Overlap between ampC and frd operons on the Escherichia coli chromosome. Proceedings of the National Academy of Sciences of the United States of America,79(4), 1111–1115.
55. Mizuno, T. (1998). His-Asp phosphotransfer signal transduction. Journal of Biochemistry,123(4), 555–563.
56. Hoch, J. A., & Varughese, K. I. (2001). Keeping signals straight in phosphorelay signal transduction. Journal of Bacteriology,183(17), 4941–4949.
57. Hirakawa, H., Nishino, K., Yamada, J., Hirata, T., & Yamaguchi, A. (2003). Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli. Journal of Antimicrobial Chemotherapy,52(4), 576–582.
58. Zeng, X., & Lin, J. (2013). Beta-lactamase induction and cell wall metabolism in Gram-negative bacteria. Frontiers in Microbiology,4, 128–137.
59. Johnson, J. W., Fisher, J. F., & Mobashery, S. (2013). Bacterial cell-wall recycling. Annals of the New York Academy of Sciences,1277, 54–75.
60. Martín, J. F., Casqueiro, J., Kosalková, K., Marcos, A. T., & Gutiérrez, S. (1999). Penicillin and cephalosporin biosynthesis: mechanism of carbon catabolite regulation of penicillin production. Antonie van Leeuwenhoek,75(1–2), 21–31.
61. Anitha, P., Anbarasu, A., & Ramaiah, S. (2014). Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii. Computers in Biology and Medicine,48, 17–27.
62. Singh, R., Saxena, A., & Singh, H. (2009). Identification of group specific motifs in beta-lactamase family of proteins. Journal of Biomedical Science,16(1), 109–116.