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Tan R, Jin M, Shao Y, Yin J, Li H, Chen T, Shi D, Zhou S, Li J, Yang D. High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota. Gut Microbes 2022; 14:2022442. [PMID: 35030982 PMCID: PMC8765071 DOI: 10.1080/19490976.2021.2022442] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Diet can not only provide nutrition for intestinal microbiota, it can also remodel them. However, is unclear whether and how diet affects the spread of antibiotic resistance genes (ARGs) in the intestinal microbiota. Therefore, we employed selected high-sugar, high-fat, high-protein, and normal diets to explore the effect. The results showed that high-sugar, high-fat, and high-protein diets promoted the amplification and transfer of exogenous ARGs among intestinal microbiota, and up-regulated the expression of trfAp and trbBp while significantly altered the intestinal microbiota and its metabolites. Inflammation-related products were strongly correlated with the spread of ARGs, suggesting the intestinal microenvironment after diet remodeling might be conducive to the spreading of ARGs. This may be attributed to changes in bacterial membrane permeability, the SOS response, and bacterial composition and diversity caused by diet-induced inflammation. In addition, acceptor bacteria (zygotes) screened by flow cytometry were mostly Proteobacteria, Firmicutes and Actinobacteria, and most were derived from dominant intestinal bacteria remodeled by diet, indicating that the transfer of ARGs was closely linked to diet, and had some selectivity. Metagenomic results showed that the gut resistance genome could be affected not only by diet, but by exogenous antibiotic resistant bacteria (ARB). Many ARG markers coincided with bacterial markers in diet groups. Therefore, dominant bacteria in different diets are important hosts of ARGs in specific dietary environments, but the many pathogenic bacteria present may cause serious harm to human health.
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Affiliation(s)
- Rong Tan
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China,Dong Yang Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin300050, China
| | - Min Jin
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China,Dong Yang Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin300050, China
| | - Yifan Shao
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China
| | - Jing Yin
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China
| | - Haibei Li
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China
| | - Tianjiao Chen
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China
| | - Danyang Shi
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China
| | - Shuqing Zhou
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China
| | - Junwen Li
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China,CONTACT Junwen Li Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin300050, China
| | - Dong Yang
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, P. R. China,Dong Yang Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin300050, China
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Kolatka K, Kubik S, Rajewska M, Konieczny I. Replication and partitioning of the broad-host-range plasmid RK2. Plasmid 2010; 64:119-34. [DOI: 10.1016/j.plasmid.2010.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/08/2010] [Accepted: 06/21/2010] [Indexed: 11/27/2022]
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König B, Müller JJ, Lanka E, Heinemann U. Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation. Nucleic Acids Res 2009; 37:1915-24. [PMID: 19190096 PMCID: PMC2665229 DOI: 10.1093/nar/gkp044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjugative transfer and stable inheritance. The structure of KorA bound to an 18-bp DNA duplex that contains the symmetric operator sequence and incorporates 5-bromo-deoxyuridine nucleosides has been determined by multiple-wavelength anomalous diffraction phasing at 1.96-Å resolution. KorA is present as a symmetric dimer and contacts DNA via a helix–turn–helix motif. Each half-site of the symmetric operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based on two KorA side chains forming hydrogen bonds to four bases within each operator half-site. KorA has a unique dimerization module shared by the RP4 proteins TrbA and KlcB. We propose that these proteins cooperate with the global RP4 repressor KorB in a similar manner via this dimerization module and thus regulate RP4 inheritance.
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Affiliation(s)
- Bettina König
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
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Bingle LEH, Rajasekar KV, Muntaha ST, Nadella V, Hyde EI, Thomas CM. A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB. Mol Microbiol 2008; 70:1502-14. [PMID: 19019158 PMCID: PMC2680271 DOI: 10.1111/j.1365-2958.2008.06498.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2008] [Indexed: 01/08/2023]
Abstract
A central feature of broad host range IncP-1 plasmids is the set of regulatory circuits that tightly control plasmid core functions under steady-state conditions. Cooperativity between KorB and either KorA or TrbA repressor proteins is a key element of these circuits and deletion analysis has implicated the conserved C-terminal domain of KorA and TrbA in this interaction. By NMR we show that KorA and KorB interact directly and identify KorA amino acids that are affected on KorB binding. Studies on mutants showed that tyrosine 84 (or phenylalanine, in some alleles) is dispensable for repressor activity but critical for the specific interaction with KorB in both in vivo reporter gene assays and in vitro electrophoretic mobility shift and co-purification assays. This confirms that direct and specific protein-protein interactions are responsible for the cooperativity observed between KorB and its corepressors and lays the basis for determining the biological importance of this cooperativity.
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Affiliation(s)
| | | | - Sidra tul Muntaha
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Vinod Nadella
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
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Gstalder ME, Faelen M, Mine N, Top EM, Mergeay M, Couturier M. Replication functions of new broad host range plasmids isolated from polluted soils. Res Microbiol 2003; 154:499-509. [PMID: 14499936 DOI: 10.1016/s0923-2508(03)00143-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nucleotide sequencing of replicons isolated from three new broad host range plasmids, pMOL98, pEMT8, and pEMT3, originating from polluted soils, showed a typical organization of iteron replicons replicating by the theta mode. In the pMOL98 replicon, the origin region and the rep gene were identified in complementation experiments. Sequence comparisons showed that the regions bearing these features are highly identical to regions in pIP02T and pSB102 and that the Rep proteins (but not the origin regions) of these three plasmids show some identity to the Rep proteins of the IncW group of plasmids. This suggests that pMOL98, pIPO2T, and pSB102 constitute a new Inc/Rep family, distantly related to the IncW group, but having an incompatibility phenotype different from the IncW phenotype. The pEMT8 replicon displayed an orf whose conceptually translated product is related to the Rep proteins of four plasmids, pSD20, pSW500, pMLb, and pALC1, not yet classified into any known incompatibility group. The vegetative origins of these plasmids were not similar, suggesting that the five plasmids could belong to a new family with similar Rep proteins but different incompatibility phenotypes. The pEMT3 replicon is clearly related to IncP replicons (sequence similarities and incompatibility phenotype), although sequence comparisons revealed some divergence with respect to the two well-documented subgroups IncPalpha and IncPbeta. This suggests that in these plasmids, despite the existence of a powerful system of centralized control over replication, maintenance, and transfer functions, plasticity and evolution of these functions are at work. Our analysis confirms the extreme genetic flexibility of plasmids and the absolute necessity of using multiple techniques (PCR, DNA sequencing, DNA chips, and databases) to analyze the role of broad host range plasmids in the capture, recombination and spread of genetic traits among bacteria.
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Affiliation(s)
- Marie-Eve Gstalder
- Laboratoire de Génétique des Procaryotes, IBMM, Université Libre de Bruxelles, rue des Prof. Jeener et Brachet, 12, 6104 Gosselies, Belgium.
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Kostelidou K, Thomas CM. DNA recognition by the KorA proteins of IncP-1 plasmids RK2 and R751. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1576:110-8. [PMID: 12031490 DOI: 10.1016/s0167-4781(02)00306-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The KorA repressor proteins of IncP-1 plasmids belong to a growing family of plasmid-encoded repressors that regulate partitioning genes, and in the IncP-1 plasmids coordinate these with expression of replication and transfer genes as well. Both KorA(RK2) (IncP-1 alpha) and KorA(R751) (IncP-1 beta) recognise the 5'-GTTTAGCTAAAC-3' palindrome. Reporter gene assays showed that KorA proteins from these two main subgroups of IncP-1 plasmids show specificity for their own promoter/operators and this preference was confirmed with in vitro binding studies using gel mobility shift assays on one representative promoter. Class I (high affinity) operators for KorA(RK2) are flanked by an A-A-A/T sequence in the upstream half; the T base was shown to greatly influence strong repression. A C-A-G triplet was present in the same region in the R751 O(A) sequences and the G base was accordingly found to be important for strong KorA(R751) repression. An obvious difference between the two KorA proteins is a histidine to serine change at the C-proximal end of the putative recognition helix of the HTH motif (aa 56). An IncP-1 alpha KorAH56S mutant protein had higher affinity for all operators but had improved more on R751 operators than on RK2 operators. This indicates that KorA of RK2 is not maximised for DNA binding activity and that the aa difference at position 56 may play a role in differentiation between alpha and beta KorA operators.
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Affiliation(s)
- Kalliopi Kostelidou
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Bhattacharyya A, Figurski DH. A small protein-protein interaction domain common to KlcB and global regulators KorA and TrbA of promiscuous IncP plasmids. J Mol Biol 2001; 310:51-67. [PMID: 11419936 DOI: 10.1006/jmbi.2001.4729] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The kor regulon of broad host-range, incompatibility group P (IncP) plasmids uses the KorA, KorB, and KorC repressors to regulate expression of genes for replication, conjugation, segregation, and host range. One operon, kilC, encodes the KorC repressor and two genes of unknown function (klcA and klcB). The predicted sequences of the 51.1 kDa KlcB protein, the 11.3 kDa KorA repressor, and another small (13.5 kDa) regulatory protein, TrbA, show a highly related 35 amino acid residue segment (V-L-P domain). We found that induction of the klcB gene is toxic to Escherichia coli host cells harboring an IncP plasmid. We confirmed a model in which the V-L-P domain of KlcB interacts directly with the V-L-P domain of KorA to derepress KorA-regulated operons, thereby allowing expression of toxic genes. First, a lacZ reporter fused to the kleA promoter, which is regulated by KorA and KorC, revealed that klcB induction specifically releases KorA-repression but has no effect on KorC repression. Second, induced expression of the V-L-P domains from KorA or KlcB is sufficient to release KorA-repression at the kleA promoter. Third, purified GST-KlcB fusion protein interacts specifically with His-tagged KorA. Fourth, fusion of the V-L-P domains of KorA and TrbA and full-length KlcB polypeptide to the DNA-binding domain of bacteriophage lambda repressor leads to the formation of functional, dimeric repressors, and mutations that alter conserved residues of the V-L-P domain adversely affect dimerization. Fifth, crosslinking experiments demonstrated that the V-L-P domain of KorA is able to dimerize in solution and form heterodimers in mixtures with full-length KorA polypeptide. These findings show that the V-L-P domain is a protein-protein interaction module that is likely to be responsible for dimerization of KorA and TrbA, and important for KlcB dimerization. We speculate on the possible significance of KlcB-KorA heterodimers in IncP plasmid maintenance.
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Affiliation(s)
- A Bhattacharyya
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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Kostelidou K, Thomas CM. The hierarchy of KorB binding at its 12 binding sites on the broad-host-range plasmid RK2 and modulation of this binding by IncC1 protein. J Mol Biol 2000; 295:411-22. [PMID: 10623535 DOI: 10.1006/jmbi.1999.3359] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
IncC and KorB proteins of broad-host-range plasmid RK2 are members of the ParA-ParB families of proteins needed for stable partitioning of bacterial chromosomes and plasmids. KorB also functions as a global regulator of expression of RK2 genes. It recognises and binds to a palindromic operator, O(B), found 12 times on RK2 DNA (O(B)1-O(B)12). We performed detailed studies on the binding of KorB to the 12 operators and showed that they fall into three groups (A, B, C) based on the binding strength of KorB. The highest affinity site is O(B)10, which occurs in the promoter transcribing genes for replication, trfAp. Purified IncC1 potentiated KorB binding to all O(B) sites except O(B)3, a site involved in partitioning. Using O(B)10 as a test system, we showed that IncC1 increases the stability of the KorB-DNA complex. The 5 bp sequences flanking the 13mer O(B) site were found to affect KorB binding and IncC1 potentiation activity. Study of hybrid operators indicated that flanking sequences on one side only were sufficient to specify the difference between O(B)10 and O(B)3. Replacement of adenine by guanine at positions -8 and -10 from the O(B)10 centre of symmetry was needed to convert it from the highest-affinity group (A) to the medium-affinity group (B) on the basis of KorB binding. These changes also eliminated potentiation by IncC1. The -8 and -10 positions from the centre of O(B)3 symmetry are occupied by guanines and this may provide part of the specificity of IncC1 behaviour on KorB binding. Studies on a series of synthetic operators suggested that KorB contacts O(B) flanking sequences, and that IncC1 may alter the conformation of multimeric KorB so that it is better able to make these contacts, thus stabilising the complexes once formed.
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Affiliation(s)
- K Kostelidou
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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Wang J, Chen R, Julin DA. Use of a translationally coupled reporter gene to eliminate nonsense mutations in a random mutagenesis study. Anal Biochem 1999; 273:310-3. [PMID: 10469504 DOI: 10.1006/abio.1999.4236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- J Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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Kostelidou K, Jones AC, Thomas CM. Conserved C-terminal region of global repressor KorA of broad-host-range plasmid RK2 is required for co-operativity between KorA and a second RK2 global regulator, KorB. J Mol Biol 1999; 289:211-21. [PMID: 10366500 DOI: 10.1006/jmbi.1999.2761] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
KorA and KorB proteins of IncP1 plasmid RK2 are encoded in the central control region (ccr) of the plasmid and act as global regulators of plasmid genes for replication, transfer and stable inheritance. KorA represses seven promoters on RK2, by binding to a defined operator site, OA, which always occurs in promoter regions. KorB recognises another operator, OB, which is found 12 times on the RK2 genome, but not always in promoter regions. At five of the KorA-regulated promoters, an OBsequence is also present. The presence of both KorA and KorB leads to severely decreased promoter activity. By measuring repression at different levels of KorA and KorB alone and in combination, we showed that there is at least 3. 4-fold co-operativity between them at korApin vivo. Testing the ability of previously isolated KorA mutants to act in a co-operative way in the presence of KorB in vivo or in vitro showed that the C-terminal part of KorA between amino acid positions 68 and 83 is required for this co-operativity. This region is part of a segment that is highly conserved between KorA and two other RK2 proteins, TrbA and KlcB. We propose that this conserved region may provide the basis for co-operativity with KorB either indirectly, by modulating DNA structure near the KorB binding site, or directly by serving as the "recognition" patch of each protein by KorB. It may thus serve as a key domain in allowing a sensitive response of the global circuits to changes in repressor concentration and thus modulation of replication, transfer and maintenance.
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Affiliation(s)
- K Kostelidou
- School of Biological Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
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Jagura-Burdzy G, Kostelidou K, Pole J, Khare D, Jones A, Williams DR, Thomas CM. IncC of broad-host-range plasmid RK2 modulates KorB transcriptional repressor activity In vivo and operator binding in vitro. J Bacteriol 1999; 181:2807-15. [PMID: 10217772 PMCID: PMC93723 DOI: 10.1128/jb.181.9.2807-2815.1999] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The korAB operon of broad-host-range plasmid RK2 encodes five genes, two of which, incC and korB, belong to the parA and parB families, respectively, of genome partitioning functions. Both korB and a third gene, korA, are responsible for coordinate regulation of operons encoding replication, transfer, and stable inheritance functions. Overexpression of incC alone caused rapid displacement of RK2. Using two different reporter systems, we show that incC modulates the action of KorB. Using promoter fusions to the reporter gene xylE, we show that incC potentiates the repression of transcription by korB. This modulation of korB activity was only observed with incC1, which encodes the full-length IncC (364 amino acids [aa]), whereas no effect was observed with incC2, which encodes a polypeptide of 259 aa that lacks the N-terminal 105 aa. Using bacterial extracts with IncC1 and IncC2 or IncC1 purified through the use of a His6 tail and Ni-agarose chromatography, we showed that IncC1 potentiates the binding of KorB to DNA at representative KorB operators. The ability of IncC to stabilize KorB-DNA complexes suggests that these two proteins work together in the global regulation of many operons on the IncP-1 genomes, as well in plasmid partitioning.
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Affiliation(s)
- G Jagura-Burdzy
- School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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