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Zhang Q, Liu Y, Zhang C, Zhou D. Easily biodegradable substrates are crucial for enhancing antibiotic risk reduction: Low-carbon discharging policies need to be more specified. WATER RESEARCH 2022; 210:117972. [PMID: 34952454 DOI: 10.1016/j.watres.2021.117972] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Governments have formulated stricter wastewater treatment plant (WWTP) discharge standards to address water pollution; however, with the cost of aggravating the refractory of the discharges. These policies are not in line with the classic co-metabolism theory; thus, we evaluated the effects of an easily biodegradable substrate on the removal efficiency of antibiotics and antibiotic resistance genes (ARGs) in the receiving water. In this study, reactor with 8 d of hydraulic retention time (HRT) was constructed to simulate a receiving river, and several antibiotics (0.30 mg/L each) were continuously discharged to the reactor (tetracycline, ciprofloxacin, amoxicillin, chloramphenicol, and sulfamethoxazole). Sodium acetate (NaAc) was used as a representative easily biodegradable substrate, and treatment protocols with and without a co-substrate were compared. The attenuation of the antibiotics in the simulated river and the production and dissemination of ARGs were analyzed. The results showed that 50 mg/L NaAc activated non-specific enzymes (a log2-fold change of 3.1-8.8 compared with 0 mg/L NaAc). The removal rate of the antibiotics was increased by 4-32%, and the toxicity of the downstream water was reduced by 35%. The upregulation of antioxidant enzymes caused the intracellular reactive oxygen species (ROSs) decreased by up to 47%, inhibiting horizontal gene transfer and reducing mobile genetic element-mediated ARGs (mARGs) by 18-56%. Furthermore, NaAc also increased the alpha diversity of the microbial community by 5-15% (Shannon-Wiener Index) and reduced the abundance of human bacterial pathogens by 22-36%. In summary, easily biodegradable substrates in the receiving water are crucial for reducing antibiotic risk.
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Affiliation(s)
- Qifeng Zhang
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Yang Liu
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Chongjun Zhang
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China.
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Akhova A, Nesterova L, Shumkov M, Tkachenko A. Cadaverine biosynthesis contributes to decreased Escherichia coli susceptibility to antibiotics. Res Microbiol 2021; 172:103881. [PMID: 34543694 DOI: 10.1016/j.resmic.2021.103881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022]
Abstract
Some bacterial stress responses are involved in survival under antibiotic treatment and contribute to less susceptible microbial forms selection. Here, we tested the role of cadaverine, one of the biogenic polyamines considered as universal adaptogens, in the processes. The expression of ldcC and cadA genes, encoding cadaverine-producing lysine decarboxylase, increased in Escherichia coli cells exposed to β-lactams and fluoroquinolones but not aminoglycosides. The transcriptional regulators RpoS and SoxS controlled the expression of ldcC and cadA, respectively, in response to antibiotics. Exogenous cadaverine had little effect on E. coli antibiotic susceptibility, whereas non-antibiotic-induced endogenous cadaverine contributed to its tolerance to β-lactams, fluoroquinolones, and aminoglycosides. Antibiotic-induced cadaverine synthesis promoted bacterial survival under fluoroquinolone exposure, as well as could contribute to low-resistant bacterial forms development. Selection under the fluoroquinolone levofloxacin exposure toward bacteria with an increased ability to synthesize cadaverine and negative correlation between LdcC activity and fluoroquinolone susceptibility in the selected forms were demonstrated. The same correlation in a special group of low-level resistant clinical E. coli isolates was revealed. So, cadaverine biosynthesis appeared to be a significant player in decreased E. coli antibiotic susceptibility development.
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Affiliation(s)
- Anna Akhova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Brunch of the Russian Academy of Sciences, 13, Golev st, Perm, 614081, Russia; Perm State University, 15, Bukirev st, 614068, Perm, Russia.
| | - Larisa Nesterova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Brunch of the Russian Academy of Sciences, 13, Golev st, Perm, 614081, Russia; Perm State University, 15, Bukirev st, 614068, Perm, Russia.
| | - Mikhail Shumkov
- Group of Microbial Genomes Editing, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, Leninsky prospect, 119071, Moscow, Russia.
| | - Alexander Tkachenko
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Brunch of the Russian Academy of Sciences, 13, Golev st, Perm, 614081, Russia; Perm State University, 15, Bukirev st, 614068, Perm, Russia.
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Kandiah E, Carriel D, Garcia PS, Felix J, Banzhaf M, Kritikos G, Bacia-Verloop M, Brochier-Armanet C, Elsen S, Gutsche I. Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA. Structure 2019; 27:1842-1854.e4. [PMID: 31653338 DOI: 10.1016/j.str.2019.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/09/2019] [Accepted: 10/01/2019] [Indexed: 11/28/2022]
Abstract
The only enzyme responsible for cadaverine production in the major multidrug-resistant human pathogen Pseudomonas aeruginosa is the lysine decarboxylase LdcA. This enzyme modulates the general polyamine homeostasis, promotes growth, and reduces bacterial persistence during carbenicillin treatment. Here we present a 3.7-Å resolution cryoelectron microscopy structure of LdcA. We introduce an original approach correlating phylogenetic signal with structural information and reveal possible recombination among LdcA and arginine decarboxylase subfamilies within structural domain boundaries. We show that LdcA is involved in full virulence in an insect pathogenesis model. Furthermore, unlike its enterobacterial counterparts, LdcA is regulated neither by the stringent response alarmone ppGpp nor by the AAA+ ATPase RavA. Instead, the P. aeruginosa ravA gene seems to play a defensive role. Altogether, our study identifies LdcA as an important player in P. aeruginosa physiology and virulence and as a potential drug target.
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Affiliation(s)
- Eaazhisai Kandiah
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Diego Carriel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Pierre Simon Garcia
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Jan Felix
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Manuel Banzhaf
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - George Kritikos
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Sylvie Elsen
- Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Irina Gutsche
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
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Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA. Sci Rep 2016; 6:24601. [PMID: 27080013 PMCID: PMC4832331 DOI: 10.1038/srep24601] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress
response enzyme whereas LdcC is its close paralogue thought to play mainly a
metabolic role. A unique macromolecular cage formed by two decamers of the
Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown
to counteract acid stress under starvation. Previously, we proposed a pseudoatomic
model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal
structures of an inactive LdcI decamer and a RavA monomer. We now present
cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and
an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for
their enzymatic activity. Comparison with each other and with available structures
uncovers differences between LdcI and LdcC explaining why only the acid stress
response enzyme is capable of binding RavA. We identify interdomain movements
associated with the pH-dependent enzyme activation and with the RavA binding.
Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain
enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the
cage-like assembly with RavA, implying that this complex may have an important
function under particular stress conditions.
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Singhal N, Sharma P, Kumar M, Joshi B, Bisht D. Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates. Proteome Sci 2012; 10:14. [PMID: 22375954 PMCID: PMC3310783 DOI: 10.1186/1477-5956-10-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 03/01/2012] [Indexed: 01/01/2023] Open
Abstract
Background Tuberculosis (TB) is the most threatening infectious disease globally. Although progress has been made to reduce global incidence of TB, emergence of multidrug resistant (MDR) TB threatens to undermine these advances. To combat the disease, novel intervention strategies effective against drug resistant and sensitive subpopulations of M. tuberculosis are urgently required as adducts in the present treatment regimen. Using THP-1 cells we have analyzed and compared the global protein expression profile of broth-cultured and intraphagosomally grown drug resistant and sensitive M.tuberculosis clinical isolates. Results On comparing the two dimensional (2-DE) gels, many proteins were found to be upregulated/expressed during intracellular state which were identified by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Four proteins (adenosylhomocysteinase, aspartate carbomyltransferase, putatitive thiosulfate sulfurtransferase and universal stress protein) were present in both intracellular MDR and sensitive isolates and three of these belonged to intermediary metabolism and respiration category. Two proteins (alanine dehydrogenase and adenosine kinase) of intracellular MDR isolate and two (glucose-6-phosphate isomerase and ATP synthase epsilon chain) of intracellular sensitive isolate belonged to intermediary metabolism and respiration category. One protein (Peroxidase/Catalase) of intracellular MDR and three (HSPX, 14 kDa antigen and 10 kDa chaperonin) of sensitive isolate belonged to virulence, detoxification and adaptation category. ESAT-6 of intracellular MDR belonged to cell wall and cell processes category. Two proteins (Antigen 85-C and Antigen 85-A) of intracellular sensitive isolate were involved in lipid metabolism while probable peptidyl-prolyl cis-trans isomerase A was involved in information pathways. Four (Rv0635, Rv1827, Rv0036c and Rv2032) of intracellular MDR and two proteins (Rv2896c and Rv2558c) of sensitive isolate were hypothetical proteins which were functionally characterized using bioinformatic tools. Bioinformatic findings revealed that the proteins encoded by Rv0036, Rv2032c, Rv0635, Rv1827 and Rv2896c genes are involved in cellular metabolism and help in intracellular survival. Conclusions Mass spectrometry and bioinformatic analysis of both MDR and sensitive isolates of M. tuberculosis during intraphagosomal growth showed that majority of commonly upregulated/expressed proteins belonged to the cellular metabolism and respiration category. Inhibitors of the metabolic enzymes/intermediate can therefore serve as suitable drug targets against drug-resistant and sensitive subpopulations of M. tuberculosis.
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Affiliation(s)
- Neelja Singhal
- Department of Biochemistry, National JALMA Institute for Leprosy and other Mycobacterial Diseases, Tajganj, Agra 282001, India.
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