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Gschwind R, Petitjean M, Fournier C, Lao J, Clermont O, Nordmann P, Mellmann A, Denamur E, Poirel L, Ruppé E. Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event. Antimicrob Agents Chemother 2024; 68:e0145923. [PMID: 38441061 PMCID: PMC10989005 DOI: 10.1128/aac.01459-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Beta-lactamase-mediated degradation of beta-lactams is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase-encoding genes can be transferred between closely related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) have never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Pseudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Münster (Germany). Its genome was sequenced. The ESBL-encoding gene (named blaMUN-1) was cloned, and the corresponding enzyme was characterized. The distribution of the gene among bacteria was investigated using the RefSeq Genomes database. The frequency and relative abundance of its closest homolog in the global microbial gene catalog (GMGC) were analyzed. The E. coli strain exhibited two distinct morphotypes. Each morphotype possessed two chromosomal copies of the blaMUN-1 gene, with one morphotype having two additional copies located on a phage-plasmid p0111. Each copy was located within a 7.6-kb genomic island associated with mobility. blaMUN-1 encoded for an extended-spectrum Ambler subclass A2 beta-lactamase with 43.0% amino acid identity to TLA-1. blaMUN-1 was found in species among the Bacteroidales order and in Sutterella wadsworthensis (Pseudomonadota). Its closest homolog in GMGC was detected frequently in human fecal samples. This is, to our knowledge, the first reported instance of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. Although the gene was frequently detected in the human gut, inter-phylum transfer was rare, indicating that inter-phylum barriers are effective in impeding the spread of ESBL-encoding genes, but not entirely impenetrable.
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Affiliation(s)
- Rémi Gschwind
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
| | - Marie Petitjean
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Claudine Fournier
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
- INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland
| | - Julie Lao
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
| | - Olivier Clermont
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
| | - Patrice Nordmann
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
- INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland
- University of Lausanne, University Hospital Center, Lausanne, Switzerland
| | | | - Erick Denamur
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
- INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland
- University of Lausanne, University Hospital Center, Lausanne, Switzerland
| | - Etienne Ruppé
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
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2
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Jacquier H, Assao B, Chau F, Guindo O, Condamine B, Magnan M, Bridier-Nahmias A, Sayingoza-Makombe N, Moumouni A, Page AL, Langendorf C, Coldiron ME, Denamur E, de Lastours V. Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger. J Infect 2023; 87:199-209. [PMID: 37369264 DOI: 10.1016/j.jinf.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 06/29/2023]
Abstract
OBJECTIVE Whole genome sequencing (WGS) of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESBL-E. coli faecal isolates in rural Southern Niger. METHODS Stools of 383 healthy participants were collected among which 92.4% were ESBL-Enterobacterales carriers. A subset of 90 ESBL-E. coli containing stools (109 ESBL-E. coli isolates) were further analysed by WGS, using short- and long-reads. RESULTS Most isolates belonged to the commensalism-adapted phylogroup A (83.5%), with high clonal diversity. The blaCTX-M-15 gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, blaCTX-M-15 was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of blaCTX-M-15 in closely related strains argued for mobilisation between plasmids or from plasmid to chromosome. CONCLUSIONS Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger due to the spread of highly diverse A phylogroup commensalism-adapted clones, with frequent chromosomal integration of blaCTX-M-15. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.
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Affiliation(s)
- Hervé Jacquier
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, 94000 Créteil, France.
| | - Bachir Assao
- Epicentre, Médecins Sans Frontières, Maradi, Niger
| | - Françoise Chau
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France
| | | | | | - Mélanie Magnan
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France
| | | | | | | | | | | | | | - Erick Denamur
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Laboratoire de Génétique Moléculaire, Hôpital Universitaire Bichat, 75018 Paris, France
| | - Victoire de Lastours
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Service de Médecine Interne, Hôpital Universitaire Beaujon, 92110 Clichy, France
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3
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Ramadevi S, Shelin R, Shanmugaraja M. Comprehensive Analysis of the Physiological Characterization of Escherichia coli Nissle 1917. Curr Microbiol 2023; 80:150. [PMID: 36976334 DOI: 10.1007/s00284-023-03253-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/05/2023] [Indexed: 03/29/2023]
Abstract
Escherichia coli Nissle 1917 (EcN) is one of the probiotics that has drawn more attention from researchers in recent days as it extends many host beneficial effects. EcN is being used as a treatment regimen especially for gastrointestinal disorders for more than 100 years. Apart from its clinical applications in its original form, EcN is being genetically engineered to meet the therapeutic requirements which ultimately led to the gradual transformation of EcN from being a mere food supplement to a complex therapeutic agent. However, comprehensive analysis of physiological characterization of EcN is inadequate. In this study, we have systematically studied various physiological parameters and found that EcN grows very well at the normal as well as at stressful conditions such as temperature (30, 37 and 42 °C), nutritional (minimal and LB), pH (ranging from 3 to 7) and osmotic stress (0.4 M NaCl, 0.4 M KCl, 0.4 M Sucrose and salt conditions). However, EcN shows nearly onefold reduction in viability at extreme acidic conditions (pH 3 and 4). It produces biofilm and curlin very efficiently compared to the laboratory strain MG1655. Through genetic analysis we have also shown that EcN exhibits high level of transformation efficiency and greater ability to retain heterogenous plasmid. Very interestingly, we have found that EcN is highly resistant to P1 phage infection. Since, EcN is being exploited largely for its clinical and therapeutic applications, the results that we have reported here would add more value and further expand its scope in clinical and biotechnological research.
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Affiliation(s)
- S Ramadevi
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Chennai, Tamil Nadu, India
| | - Ruby Shelin
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Chennai, Tamil Nadu, India
| | - Meenakshi Shanmugaraja
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Chennai, Tamil Nadu, India.
- Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, 626005, Tamil Nadu, India.
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Protein-Ligand Interactions in Scarcity: The Stringent Response from Bacteria to Metazoa, and the Unanswered Questions. Int J Mol Sci 2023; 24:ijms24043999. [PMID: 36835415 PMCID: PMC9965611 DOI: 10.3390/ijms24043999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
The stringent response, originally identified in Escherichia coli as a signal that leads to reprogramming of gene expression under starvation or nutrient deprivation, is now recognized as ubiquitous in all bacteria, and also as part of a broader survival strategy in diverse, other stress conditions. Much of our insight into this phenomenon derives from the role of hyperphosphorylated guanosine derivatives (pppGpp, ppGpp, pGpp; guanosine penta-, tetra- and tri-phosphate, respectively) that are synthesized on starvation cues and act as messengers or alarmones. These molecules, collectively referred to here as (p)ppGpp, orchestrate a complex network of biochemical steps that eventually lead to the repression of stable RNA synthesis, growth, and cell division, while promoting amino acid biosynthesis, survival, persistence, and virulence. In this analytical review, we summarize the mechanism of the major signaling pathways in the stringent response, consisting of the synthesis of the (p)ppGpp, their interaction with RNA polymerase, and diverse factors of macromolecular biosynthesis, leading to differential inhibition and activation of specific promoters. We also briefly touch upon the recently reported stringent-like response in a few eukaryotes, which is a very disparate mechanism involving MESH1 (Metazoan SpoT Homolog 1), a cytosolic NADPH phosphatase. Lastly, using ppGpp as an example, we speculate on possible pathways of simultaneous evolution of alarmones and their multiple targets.
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Yuan LG, Liu NN, Xi XG. Biochemical and functional characterization of an exonuclease from Chaetomium thermophilum. Biochem Biophys Res Commun 2022; 636:17-24. [DOI: 10.1016/j.bbrc.2022.10.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022]
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6
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Pozdeev G, Mogre A, Dorman CJ. Consequences of producing DNA gyrase from a synthetic gyrBA operon in Salmonella enterica serovar Typhimurium. Mol Microbiol 2021; 115:1410-1429. [PMID: 33539568 PMCID: PMC8359277 DOI: 10.1111/mmi.14689] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022]
Abstract
DNA gyrase is an essential type II topoisomerase that is composed of two subunits, GyrA and GyrB, and has an A2B2 structure. Although the A and B subunits are required in equal proportions to form DNA gyrase, the gyrA and gyrB genes that encode them in Salmonella (and in many other bacteria) are at separate locations on the chromosome, are under separate transcriptional control, and are present in different copy numbers in rapidly growing bacteria. In wild‐type Salmonella, gyrA is near the chromosome's replication terminus, while gyrB is near the origin. We generated a synthetic gyrBA operon at the oriC‐proximal location of gyrB to test the significance of the gyrase gene position for Salmonella physiology. Although the strain producing gyrase from an operon had a modest alteration to its DNA supercoiling set points, most housekeeping functions were unaffected. However, its SPI‐2 virulence genes were expressed at a reduced level and its survival was reduced in macrophage. Our data reveal that the horizontally acquired SPI‐2 genes have a greater sensitivity to disturbance of DNA topology than the core genome and we discuss its significance in the context of Salmonella genome evolution and the gyrA and gyrB gene arrangements found in other bacteria.
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Affiliation(s)
- German Pozdeev
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Aalap Mogre
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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Kugarajah V, Dharmalingam S. Sulphonated polyhedral oligomeric silsesquioxane/sulphonated poly ether ether ketone nanocomposite membranes for microbial fuel cell: Insights to the miniatures involved. CHEMOSPHERE 2020; 260:127593. [PMID: 32679377 DOI: 10.1016/j.chemosphere.2020.127593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
In this study we demonstrate Sulphonated Polyhedral oligomeric silsesquioxane (S-POSS) incorporated Sulphonated Poly Ether Ether Ketone (SPEEK) as an effective cation exchange membrane (CEM) for improving performance and sustainability in a fabricated tubular Microbial Fuel Cell (MFC). The organic-inorganic caged frame of S-POSS enables several ion conducting channels thereby resulting in better proton conductivity and water uptake in addition to hydroxide ions native in POSS. Among the membranes, SPEEK+ 5 wt% S-POSS exhibits a highest maximum performance of 162 ± 1.4 mW m-2 with the highest IEC of 1.8 ± 0.05 meq g-1. Microbial community analysis reveals the predominance of several bacterial strains contributing to wide range of mechanisms. Three phyla including Betaproteobacteria, Gammaproteobacteria and Firmicutes showed maximum predominance. In addition to a novel nanocomposite membrane, the present research introduces perceptions of two metabolic mechanisms of the microbial community available which opens pathway for future insights on how other miniatures involve in electron transfer mechanisms.
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Affiliation(s)
- Vaidhegi Kugarajah
- Department of Mechanical Engineering, Anna University, Chennai, 600 025, India
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8
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Asaad M, Abo-kadoum M, NZUNGIZE L, UAE M, NZAOU SA, Xie J. Methylation in Mycobacterium-host interaction and implications for novel control measures. INFECTION GENETICS AND EVOLUTION 2020; 83:104350. [DOI: 10.1016/j.meegid.2020.104350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/16/2020] [Accepted: 05/01/2020] [Indexed: 12/12/2022]
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9
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Karthik M, Meenakshi S, Munavar M. Unveiling the molecular basis for pleiotropy in selected rif mutants of Escherichia coli: Possible role for Tyrosine in the Rif binding pocket and fast movement of RNA polymerase. Gene 2019; 713:143951. [DOI: 10.1016/j.gene.2019.143951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 10/26/2022]
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10
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Oetermann S, Jongsma R, Coenen A, Keller J, Steinbüchel A. LcpRVH2 - regulating the expression of latex-clearing proteins in Gordonia polyisoprenivorans VH2. MICROBIOLOGY-SGM 2019; 165:343-354. [PMID: 30628882 DOI: 10.1099/mic.0.000755] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Gordonia polyisoprenivorans VH2 harbours two latex clearing proteins, which are responsible for the cleavage of poly(cis-1,4-isoprene) into oligoisoprenes, thereby allowing growth in presence of, e.g. natural rubber. A gene coding for a putative regulator of the TetR-family (lcpRVH2) is located 131 bp upstream of lcp1VH2. We heterologously expressed lcpRVH2 in Escherichia coli, and purified and characterized the protein with respect to its ability to bind to the operator region of lcp1VH2. LcpRVH2 forms a dimer in its native state. The size of the dimer was determined to be 52.7 kDa by size exclusion chromatography, whereas the calculated size of a monomer was 24.1 kDa. Electrophoretic mobility shift assays (EMSAs) with the purified protein revealed a shift upon binding to the intergenic region between lcpRVH2 and lcp1VH2. Within this region, an inverted repeat was identified in silico, probably being the binding site of LcpRVH2. This binding sequence was confirmed by a DNase I footprinting assay. A shift also occurred in EMSAs with this 44 bp sequence only. Interestingly, no regulator was detected upstream of the second lcp (lcp2VH2). Therefore, we performed EMSA studies with LcpRVH2 and the putative operator region upstream of lcp2VH2, and discovered by DNase I footprinting another binding sequence upstream of lcp2VH2. Hence, we concluded that LcpRVH2 binds the operator region of both lcps and, most likely, regulates their expression in G. polyisoprenivorans VH2.
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Affiliation(s)
- Sylvia Oetermann
- 1Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Rense Jongsma
- 1Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Anna Coenen
- 1Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jeanne Keller
- 1Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- 2Department of Environmental Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,1Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
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11
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Meenakshi S, Karthik M, Munavar MH. A putative curved DNA region upstream of rcsA in Escherichia coli plays a key role in transcriptional regulation by H-NS. FEBS Open Bio 2018; 8:1209-1218. [PMID: 30087827 PMCID: PMC6070653 DOI: 10.1002/2211-5463.12348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/31/2017] [Accepted: 11/07/2017] [Indexed: 11/24/2022] Open
Abstract
It is well established that in Escherichia coli, the histone‐like nucleoid structuring (H‐NS) protein also functions as negative regulator of rcsA transcription. However, the exact mode of regulation of rcsA transcription by H‐NS has not been studied extensively. Here, we report the multicopy effect of dominant‐negative hns alleles on the transcription of rcsA based on expression of cps‐lac transcriptional fusion in ∆lon, ∆lon rpoB12, ∆lon rpoB77 and lon+ strains. Our results indicate that H‐NS defective in recognizing curved DNA fails to repress rcsA transcription significantly, while nonoligomeric H‐NS molecules still retain the repressor activity to an appreciable extent. Together with bioinformatics analysis, our study envisages a critical role for the putative curved DNA region present upstream of rcsA promoter in the transcriptional regulation of rcsA by H‐NS.
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Affiliation(s)
- Shanmugaraja Meenakshi
- Department of Molecular Biology School of Biological Sciences Centre for Advanced Studies in Functional and Organismal Genomics Madurai Kamaraj University [University with Potential for Excellence] Madurai India
| | - Maruthan Karthik
- Department of Molecular Biology School of Biological Sciences Centre for Advanced Studies in Functional and Organismal Genomics Madurai Kamaraj University [University with Potential for Excellence] Madurai India
| | - M Hussain Munavar
- Department of Molecular Biology School of Biological Sciences Centre for Advanced Studies in Functional and Organismal Genomics Madurai Kamaraj University [University with Potential for Excellence] Madurai India
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12
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Evidence for up and down regulation of 450 genes by rpoB12 (rif) mutation and their implications in complexity of transcription modulation in Escherichia coli. Microbiol Res 2018; 212-213:80-93. [PMID: 29853171 DOI: 10.1016/j.micres.2018.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/20/2018] [Accepted: 04/28/2018] [Indexed: 11/22/2022]
Abstract
Analyses of mutations in rpoB subunit of Escherichia coli that lead to resistance to rifampicin have been invaluable in providing insight into events during transcription continue to be discovered. Earlier we reported that rpoB12 suppresses over-expression of cps genes in Δlon mutant of E. coli, by interfering with the transcription of rcsA. Here we report Microarray based Transcriptome profile of Δlon and Δlon rpoB12 strains. The data analyses clearly reveal that rpoB12 mutation results in the differential expression of ∼450 genes. The transcription profiles of some of the genes namely, rcsA, gadE, csgD, bolA, ypdI, dnaJ, clpP, csrA and hdeA are significantly altered, particularly the genes implicated in virulence. Some of the phenotypic traits namely, biofilm formation, motility, curli synthesis and ability to withstand acidic stress in a lon+rpoB12 strain were assessed. The results clearly indicate that rpoB12 up-regulates biofilm formation and curli synthesis while it makes the cells sensitive for growth in acidic medium and inhibits motility almost completely. Furthermore, rpoB12 modulates the expression profile of a significant number of genes involved in stress responses, genes encoding small RNAs. Thus, this study reveals the versatile role of the rpoB12 mutation, especially its impact on the regulation of genes related to virulence and highlights its medical importance.
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13
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Ashmore D, Chaudhari A, Barlow B, Barlow B, Harper T, Vig K, Miller M, Singh S, Nelson E, Pillai S. Evaluation of E. coli inhibition by plain and polymer-coated silver nanoparticles. Rev Inst Med Trop Sao Paulo 2018; 60:e18. [PMID: 29694600 PMCID: PMC5956551 DOI: 10.1590/s1678-9946201860018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/15/2018] [Indexed: 11/22/2022] Open
Abstract
Escherichia coli causes various ailments such as septicemia, enteritis, foodborne illnesses, and urinary tract infections which are of concern in the public health field due to antibiotic resistance. Silver nanoparticles (AgNP) are known for their biocompatibility and antibacterial activity, and may prove to be an alternative method of treatment, especially as wound dressings. In this study, we compared the antibacterial efficacy of two polymer-coated silver nanoparticles either containing 10% Ag (Ag 10% + Polymer), or 99% Ag (AgPVP) in relation to plain uncoated silver nanoparticles (AgNP). Atomic force microscopy was used to characterize the nanoparticles, and their antibacterial efficacy was compared by the minimum inhibitory concentration (MIC) and bacterial growth curve assays, followed by molecular studies using scanning electron microscopy (SEM) and (qRT- PCR). AgNP inhibited the growth of E. coli only at 0.621 mg/mL, which was double the concentration required for both coated nanoparticles (0.312 mg/mL). Similarly, bacterial growth was impeded as early as 8 h at 0.156 mg/mL of both coated nanoparticles as compared to 0.312 mg/mL for plain AgNP. SEM data showed that nanoparticles damaged the cell membrane, resulting in bacterial cell lysis, expulsion of cellular contents, and complete disintegration of some cells. The expression of genes associated with the TCA cycle (aceF and frdB) and amino acid metabolism (gadB, metL, argC) were substantially downregulated in E. coli treated with nanoparticles. The reduction in the silver ion (Ag+) concentration of polymer-coated AgNP did not affect their antibacterial efficacy against E. coli.
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Affiliation(s)
- D'Andrea Ashmore
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | | | - Brandi Barlow
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Brett Barlow
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Talia Harper
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Komal Vig
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Michael Miller
- AU Research Instrumentation Facility, Harrison School of Pharmacy, Auburn University, Auburn, Alabama, USA
| | - Shree Singh
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | | | - Shreekumar Pillai
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
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14
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Ashwin Sri Bala S, Madhumathi I, Vinodha S, Munavar MH. Glu 571 of PheT plays a pivotal role in the thermal stability of Escherichia coli PheRS enzyme. J Basic Microbiol 2018; 58:475-491. [PMID: 29660847 DOI: 10.1002/jobm.201700645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/19/2018] [Accepted: 03/05/2018] [Indexed: 11/08/2022]
Abstract
As of date the two temperature sensitive mutations isolated in pheST operon include pheS5 (G293 →A293 ) and pheT354. Recently, we reported that G673 of pheS defines a hot spot for intragenic suppressors of pheS5. In this investigation, in 13 independent experiments, a collection of temperature sensitive mutants were isolated by localized mutagenesis. Complementation using clones bearing pheS+ , pheT+ , and pheS+ T+ indicated that 34 mutants could harbor lesion(s) in pheS and four could be in pheT and one mutant might be a double mutant. Surprisingly, all the 34 pheS mutants harbored the very same (G293 →A293 ) transition mutation as present in the classical pheS5 mutant. Most unexpectedly, the four pheT mutants isolated harbored the same G1711 →A1711 transition, a mutation which is hitherto unreported. Since all the four pheT mutants were defined by the same G1711 →A1711 base change, we believe that getting other mutations could be hard hitting and therefore it is proposed that G1711 itself could be a "hot spot" for emergence of Ts mutations in pheT and similarly G293 itself could be a "hot spot" for Ts lesions in pheS. These results clearly imply a vital role for Glutamic acid571 (Glu571 ) of PheT and reinforce criticality of Glycine98 (Gly98 ) of PheS in the thermal stability of PheRS enzyme.
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Affiliation(s)
- Sridar Ashwin Sri Bala
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional and Organismal Genomics, Madurai Kamaraj University (University with Potential for Excellence), Madurai, India
| | - Irulappan Madhumathi
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional and Organismal Genomics, Madurai Kamaraj University (University with Potential for Excellence), Madurai, India
| | - Sengottuvel Vinodha
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional and Organismal Genomics, Madurai Kamaraj University (University with Potential for Excellence), Madurai, India
| | - M Hussain Munavar
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional and Organismal Genomics, Madurai Kamaraj University (University with Potential for Excellence), Madurai, India
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15
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Maddamsetti R, Lenski RE. Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection. PLoS Genet 2018; 14:e1007199. [PMID: 29385126 PMCID: PMC5809092 DOI: 10.1371/journal.pgen.1007199] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/12/2018] [Accepted: 01/15/2018] [Indexed: 12/23/2022] Open
Abstract
Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls. However, the resolution in that previous work was limited to only a few genetic markers. We sought to clarify and understand these puzzling results by sequencing complete genomes from each population. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors' origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage.
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Affiliation(s)
- Rohan Maddamsetti
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
| | - Richard E. Lenski
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
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16
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Oligo(cis-1,4-isoprene) aldehyde-oxidizing dehydrogenases of the rubber-degrading bacterium Gordonia polyisoprenivorans VH2. Appl Microbiol Biotechnol 2017; 101:7945-7960. [PMID: 28956111 DOI: 10.1007/s00253-017-8508-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/16/2017] [Accepted: 09/01/2017] [Indexed: 12/23/2022]
Abstract
The actinomycete Gordonia polyisoprenivorans strain VH2 is well-known for its ability to efficiently degrade and catabolize natural rubber [poly(cis-1,4-isoprene)]. Recently, a pathway for the catabolism of rubber by strain VH2 was postulated based on genomic data and the analysis of mutants (Hiessl et al. in Appl Environ Microbiol 78:2874-2887, 2012). To further elucidate the degradation pathway of poly(cis-1,4-isoprene), 2-dimensional-polyacrylamide gel electrophoresis was performed. The analysis of the identified protein spots by matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry confirmed the postulated intracellular pathway suggesting a degradation of rubber via β-oxidation. In addition, other valuable information on rubber catabolism of G. polyisoprenivorans strain VH2 (e.g. oxidative stress response) was provided. Identified proteins, which were more abundant in cells grown with rubber than in cells grown with propionate, implied a putative long-chain acyl-CoA-dehydrogenase, a 3-ketoacyl-CoA-thiolase, and an aldehyde dehydrogenase. The amino acid sequence of the latter showed a high similarity towards geranial dehydrogenases. The expression of the corresponding gene was upregulated > 10-fold under poly(cis-1,4-isoprene)-degrading conditions. The putative geranial dehydrogenase and a homolog were purified and used for enzyme assays. Deletion mutants for five aldehyde dehydrogenases were generated, and growth with poly(cis-1,4-isoprene) was investigated. While none of the mutants had an altered phenotype regarding growth with poly(cis-1,4-isoprene) as sole carbon and energy source, purified aldehyde dehydrogenases were able to catalyze the oxidation of oligoisoprene aldehydes indicating an involvement in rubber degradation.
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Stuart MK, Hudman DA, Nachtrab SN, Hiatt JL, Seo J, Pullen SJ, Sargentini NJ. Fine Epitope Mapping of Monoclonal Antibodies to the DNA Repair Protein, RadA. Monoclon Antib Immunodiagn Immunother 2017; 36:83-94. [PMID: 28581365 DOI: 10.1089/mab.2017.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Repair of DNA damage is vital to the health and survival of all organisms. In Escherichia coli, a protein known as RadA (or Sms) participates in recombinational repair, a process that uses an undamaged DNA strand in one DNA duplex to fill a gap in a homologous DNA strand in a sister DNA duplex. In a prior report, we described the production of monoclonal antibodies (MAbs) specific for RadA. Here, we investigated the epitopes recognized by two of the antibodies, MAbs 6F5 and 2A2. Premature stop codons (ochre mutations) were introduced into the radA gene at selected sites, and the truncated RadA proteins were probed by western blotting. Deletion of as few as four amino acids (457-460) from the C-terminus of RadA significantly increased the sensitivity of E. coli to ultraviolet (UV) radiation and abolished recognition of RadA by MAb 6F5. Single alanine substitutions made between positions 443-460 also adversely affected the ability of MAb 6F5 to bind to RadA, further supporting the idea that MAb 6F5 is specific for the RadA C-terminus. An ochre mutation at position 258 abolished the recognition of RadA by MAb 2A2, whereas an ochre mutation at position 279 did not, suggesting that MAb 2A2 binds to an epitope between residues 258 and 279. MAb 2A2 recognition of RadA was destroyed by endoproteinase glu-C cleavage of RadA at position 266, and by a single alanine substitution at position 265. In a competitive enzyme-linked immunosorbent assay (ELISA), a synthetic peptide comprising residues 263-273 of RadA blocked MAb 2A2 recognition of immobilized full-length RadA by more than 97%. We infer from our results that MAb 6F5 binds to the extreme C-terminus of RadA and that MAb 2A2 is specific for an epitope within positions 263-273.
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Affiliation(s)
- Melissa K Stuart
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Deborah A Hudman
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Stephanie N Nachtrab
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Jacob L Hiatt
- 2 Lakeland Regional Medical Center , Saint Joseph, Michigan
| | - Jin Seo
- 3 Truman State University , Kirksville, Missouri
| | | | - Neil J Sargentini
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
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18
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The Legacy of Genetic Analysis Advances Contemporary Research with Escherichia coli K-12 and Salmonella enterica serovar Typhimurium LT2. EcoSal Plus 2017; 7. [PMID: 28443537 DOI: 10.1128/ecosalplus.esp-0014-2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Escherichia coli K-12 and Salmonella enterica serovar Typhimurium LT2 became standard organisms for genetic analysis during the Truman administration. Half a century later, genetic analysis with these strains had become an art form, interpreted through 23 articles in the ambitious two-volume masterpiece edited by the late Fred Neidhardt and colleagues. These legacy articles now are available through EcoSal Plus, so as to inform and inspire contemporary genetic analyses in these standard organisms and their relatives.
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Wei XB, Zhang B, Bazeille N, Yu Y, Liu NN, René B, Mauffret O, Xi XG. A 3'-5' exonuclease activity embedded in the helicase core domain of Candida albicans Pif1 helicase. Sci Rep 2017; 7:42865. [PMID: 28216645 PMCID: PMC5316945 DOI: 10.1038/srep42865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/18/2017] [Indexed: 11/11/2022] Open
Abstract
3′-5′ exonucleases are frequently found to be associated to polymerases or helicases domains in the same enzyme or could function as autonomous entities. Here we uncovered that Candida albicans Pif1 (CaPif1) displays a 3′-5′ exonuclease activity besides its main helicase activity. These two latter activities appear to reside on the same polypeptide and the new exonuclease activity could be mapped to the helicase core domain. We clearly show that CaPif1 displays exclusively exonuclease activity and unambiguously establish the directionality of the exonuclease activity as the 3′-to-5′ polarity. The enzyme appears to follow the two-metal-ion driven hydrolyzing activity exhibited by most of the nucleases, as shown by its dependence of magnesium and also by the identification of aspartic residues. Interestingly, an excellent correlation could be found between the presence of the conserved residues and the exonuclease activity when testing activities on Pif1 enzymes from eight fungal organisms. In contrast to others proteins endowed with the double helicase/exonuclease functionality, CaPif1 differs in the fact that the two activities are embedded in the same helicase domain and not located on separated domains. Our findings may suggest a biochemical basis for mechanistic studies of Pif1 family helicases.
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Affiliation(s)
- Xiao-Bin Wei
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bo Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nicolas Bazeille
- LBPA, ENS-Cachan, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235 Cachan, France
| | - Ying Yu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Brigitte René
- LBPA, ENS-Cachan, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235 Cachan, France
| | - Olivier Mauffret
- LBPA, ENS-Cachan, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235 Cachan, France
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.,LBPA, ENS-Cachan, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235 Cachan, France
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20
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Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing. Proc Natl Acad Sci U S A 2016; 113:E829-38. [PMID: 26831095 DOI: 10.1073/pnas.1520560113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the importance of the nonuniform progression of elongation in translation is well recognized, there have been few attempts to explore this process by directly profiling nascent polypeptides, the relevant intermediates of translation. Such approaches will be essential to complement other approaches, including ribosome profiling, which is extremely powerful but indirect with respect to the actual translation processes. Here, we use the nascent polypeptide's chemical trait of having a covalently attached tRNA moiety to detect translation intermediates. In a case study, Escherichia coli SecA was shown to undergo nascent polypeptide-dependent translational pauses. We then carried out integrated in vivo and in vitro nascent chain profiling (iNP) to characterize 1,038 proteome members of E. coli that were encoded by the first quarter of the chromosome with respect to their propensities to accumulate polypeptidyl-tRNA intermediates. A majority of them indeed undergo single or multiple pauses, some occurring only in vitro, some occurring only in vivo, and some occurring both in vivo and in vitro. Thus, translational pausing can be intrinsically robust, subject to in vivo alleviation, or require in vivo reinforcement. Cytosolic and membrane proteins tend to experience different classes of pauses; membrane proteins often pause multiple times in vivo. We also note that the solubility of cytosolic proteins correlates with certain categories of pausing. Translational pausing is widespread and diverse in nature.
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Abstract
This review focuses on the steps unique to methionine biosynthesis, namely the conversion of homoserine to methionine. The past decade has provided a wealth of information concerning the details of methionine metabolism and the review focuses on providing a comprehensive overview of the field, emphasizing more recent findings. Details of methionine biosynthesis are addressed along with key cellular aspects, including regulation, uptake, utilization, AdoMet, the methyl cycle, and growing evidence that inhibition of methionine biosynthesis occurs under stressful cellular conditions. The first unique step in methionine biosynthesis is catalyzed by the metA gene product, homoserine transsuccinylase (HTS, or homoserine O-succinyltransferase). Recent experiments suggest that transcription of these genes is indeed regulated by MetJ, although the repressor-binding sites have not yet been verified. Methionine also serves as the precursor of S-adenosylmethionine, which is an essential molecule employed in numerous biological processes. S-adenosylhomocysteine is produced as a consequence of the numerous AdoMet-dependent methyl transfer reactions that occur within the cell. In E. coli and Salmonella, this molecule is recycled in two discrete steps to complete the methyl cycle. Cultures challenged by oxidative stress appear to experience a growth limitation that depends on methionine levels. E. coli that are deficient for the manganese and iron superoxide dismutases (the sodA and sodB gene products, respectively) require the addition of methionine or cysteine for aerobic growth. Modulation of methionine levels in response to stressful conditions further increases the complexity of its regulation.
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Abstract
The F1F0-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of Escherichia coli and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α3β3γδεab2c10. Traditionally they were divided into two physically separable units: an F1 that catalyzes ATP hydrolysis (α3β3γδε) and a membrane-bound F0 sector that transports protons (ab2c10). In terms of rotary function, the subunits can be divided into rotor subunits (γεc10) and stator subunits (α3β3δab2). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and b subunits, and part of the proton channel in subunit a. Among the rotor subunits, the c subunits form a ring in the membrane, and interact with subunit a to form the proton channel. Subunits γ and ε bind to the c-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.
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23
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Meenakshi S, Munavar MH. Suppression of capsule expression in Δlon strains of Escherichia coli by two novel rpoB mutations in concert with HNS: possible role for DNA bending at rcsA promoter. Microbiologyopen 2015; 4:712-29. [PMID: 26403574 PMCID: PMC4618605 DOI: 10.1002/mbo3.268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/23/2015] [Accepted: 05/04/2015] [Indexed: 11/29/2022] Open
Abstract
Analyses of mutations in genes coding for subunits of RNA polymerase always throw more light on the intricate events that regulate the expression of gene(s). Lon protease of Escherichia coli is implicated in the turnover of RcsA (positive regulator of genes involved in capsular polysaccharide synthesis) and SulA (cell division inhibitor induced upon DNA damage). Failure to degrade RcsA and SulA makes lon mutant cells to overproduce capsular polysaccharides and to become sensitive to DNA damaging agents. Earlier reports on suppressors for these characteristic lon phenotypes related the role of cochaperon DnaJ and tmRNA. Here, we report the isolation and characterization of two novel mutations in rpoB gene capable of modulating the expression of cps genes in Δlon strains of E. coli in concert with HNS. clpA, clpB, clpY, and clpQ mutations do not affect this capsule expression suppressor (Ces) phenotype. These mutant RNA polymerases affect rcsA transcription, but per se are not defective either at rcsA or at cps promoters. The results combined with bioinformatics analyses indicate that the weaker interaction between the enzyme and DNA::RNA hybrid during transcription might play a vital role in the lower level expression of rcsA. These results might have relevance to pathogenesis in related bacteria.
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Affiliation(s)
- Shanmugaraja Meenakshi
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional and Organismal Genomics, Madurai Kamaraj University [University with Potential for Excellence], Madurai, Tamil Nadu, 625 021, India
| | - M Hussain Munavar
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional and Organismal Genomics, Madurai Kamaraj University [University with Potential for Excellence], Madurai, Tamil Nadu, 625 021, India
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24
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Nord S, Bhatt MJ, Tükenmez H, Farabaugh PJ, Wikström PM. Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor. RNA (NEW YORK, N.Y.) 2015; 21:1454-1468. [PMID: 26089326 PMCID: PMC4509935 DOI: 10.1261/rna.051383.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/04/2015] [Indexed: 06/04/2023]
Abstract
The in vivo assembly of ribosomal subunits requires assistance by maturation proteins that are not part of mature ribosomes. One such protein, RbfA, associates with the 30S ribosomal subunits. Loss of RbfA causes cold sensitivity and defects of the 30S subunit biogenesis and its overexpression partially suppresses the dominant cold sensitivity caused by a C23U mutation in the central pseudoknot of 16S rRNA, a structure essential for ribosome function. We have isolated suppressor mutations that restore partially the growth of an RbfA-lacking strain. Most of the strongest suppressor mutations alter one out of three distinct positions in the carboxy-terminal domain of ribosomal protein S5 (S5) in direct contact with helix 1 and helix 2 of the central pseudoknot. Their effect is to increase the translational capacity of the RbfA-lacking strain as evidenced by an increase in polysomes in the suppressed strains. Overexpression of RimP, a protein factor that along with RbfA regulates formation of the ribosome's central pseudoknot, was lethal to the RbfA-lacking strain but not to a wild-type strain and this lethality was suppressed by the alterations in S5. The S5 mutants alter translational fidelity but these changes do not explain consistently their effect on the RbfA-lacking strain. Our genetic results support a role for the region of S5 modified in the suppressors in the formation of the central pseudoknot in 16S rRNA.
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Affiliation(s)
- Stefan Nord
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Monika J Bhatt
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21228, USA
| | - Hasan Tükenmez
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Philip J Farabaugh
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21228, USA
| | - P Mikael Wikström
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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25
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Kracke F, Vassilev I, Krömer JO. Microbial electron transport and energy conservation - the foundation for optimizing bioelectrochemical systems. Front Microbiol 2015; 6:575. [PMID: 26124754 PMCID: PMC4463002 DOI: 10.3389/fmicb.2015.00575] [Citation(s) in RCA: 291] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/25/2015] [Indexed: 12/23/2022] Open
Abstract
Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical techniques.
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Affiliation(s)
- Frauke Kracke
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
| | - Igor Vassilev
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
| | - Jens O Krömer
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
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27
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A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise. Mol Cell 2015; 58:393-405. [DOI: 10.1016/j.molcel.2015.03.013] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 02/13/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
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28
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Agrawal A, Mohanty BK, Kushner SR. Processing of the seven valine tRNAs in Escherichia coli involves novel features of RNase P. Nucleic Acids Res 2014; 42:11166-79. [PMID: 25183518 PMCID: PMC4176162 DOI: 10.1093/nar/gku758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here we report that RNase P is required for the initial separation of all seven valine tRNAs from three distinct polycistronic transcripts (valV valW, valU valX valY lysY and lysT valT lysW valZ lysY lysZ lysQ). Particularly significant is the mechanism by which RNase P processes the valU and lysT polycistronic transcripts. Specifically, the enzyme initiates processing by first removing the Rho-independent transcription terminators from the primary valU and lysT transcripts. Subsequently, it proceeds in the 3′ → 5′ direction generating one pre-tRNA at a time. Based on the absolute requirement for RNase P processing of all three primary transcripts, inactivation of the enzyme leads to a >4-fold decrease in the levels of both type I and type II valine tRNAs. The ability of RNase P to initiate tRNA processing at the 3′ ends of long primary transcripts by endonucleolytically removing the Rho-independent transcription terminator represents a previously unidentified function for the enzyme, which is responsible for generating the mature 5’ termini of all 86 E. coli tRNAs. RNase E only plays a very minor role in the processing of all three valine polycistronic transcripts.
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Affiliation(s)
- Ankit Agrawal
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Bijoy K Mohanty
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Sidney R Kushner
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA Department of Genetics, University of Georgia, Athens, GA 30602, USA
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29
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Weng X, Xiao J. Spatial organization of transcription in bacterial cells. Trends Genet 2014; 30:287-97. [PMID: 24862529 DOI: 10.1016/j.tig.2014.04.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/28/2014] [Accepted: 04/29/2014] [Indexed: 11/27/2022]
Abstract
Prokaryotic transcription has been extensively studied over the past half a century. However, there often exists a gap between the structural, mechanistic description of transcription obtained from in vitro biochemical studies, and the cellular, phenomenological observations from in vivo genetic studies. It is now accepted that a living bacterial cell is a complex entity; the heterogeneous cellular environment is drastically different from the homogenous, well-mixed situation in vitro. Where molecules are inside a cell may be important for their function; hence, the spatial organization of different molecular components may provide a new means of transcription regulation in vivo, possibly bridging this gap. In this review, we survey current evidence for the spatial organization of four major components of transcription [genes, transcription factors, RNA polymerase (RNAP) and RNAs] and critically analyze their biological significance.
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Affiliation(s)
- Xiaoli Weng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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30
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Ponmani T, Munavar MH. G673 could be a novel mutational hot spot for intragenic suppressors of pheS5 lesion in Escherichia coli. Microbiologyopen 2014; 3:369-82. [PMID: 24811065 PMCID: PMC4082710 DOI: 10.1002/mbo3.161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 12/12/2013] [Accepted: 01/02/2014] [Indexed: 11/08/2022] Open
Abstract
The pheS5 Ts mutant of Escherichia coli defined by a G293 → A293 transition, which is responsible for thermosensitive Phenylalanyl-tRNA synthetase has been well studied at both biochemical and molecular level but genetic analyses pertaining to suppressors of pheS5 were hard to come by. Here we have systematically analyzed a spectrum of Temperature-insensitive derivatives isolated from pheS5 Ts mutant and identified two intragenic suppressors affecting the same base pair coordinate G673 (pheS19 defines G673 → T673 ; Gly225 → Cys225 and pheS28 defines G673 → C673 ; Gly225 → Arg225). In fact in the third derivative, the intragenic suppressor originally named pheS43 (G673 → C673 transversion) is virtually same as pheS28. In the fourth case, the very pheS5 lesion itself has got changed from A293 → T293 (named pheS40). Cloning of pheS(+), pheS5, pheS5-pheS19, pheS5-pheS28 alleles into pBR322 and introduction of these clones into pheS5 mutant revealed that excess of double mutant protein is not at all good for the survival of cells at 42°C. These results clearly indicate a pivotal role for Gly225 in the structural/functional integrity of alpha subunit of E. coli PheRS enzyme and it is proposed that G673 might define a hot spot for intragenic suppressors of pheS5.
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Affiliation(s)
- Thangaraj Ponmani
- Department of Molecular Biology, School of Biological Sciences, Centre for Excellence in Genomic Sciences, Centre for Advanced Studies in functional and organismal Genomics, Madurai Kamaraj University [University with Potential for Excellence], Madurai, 625 021, India
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A ΔdinB mutation that sensitizes Escherichia coli to the lethal effects of UV- and X-radiation. Mutat Res 2014; 763-764:19-27. [PMID: 24657250 DOI: 10.1016/j.mrfmmm.2014.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 03/09/2014] [Accepted: 03/12/2014] [Indexed: 11/23/2022]
Abstract
The DinB (PolIV) protein of Escherichia coli participates in several cellular functions. We investigated a dinB mutation, Δ(dinB-yafN)883(::kan) [referred to as ΔdinB883], which strongly sensitized E. coli cells to both UV- and X-radiation killing. Earlier reports indicated dinB mutations had no obvious effect on UV radiation sensitivity which we confirmed by showing that normal UV radiation sensitivity is conferred by the ΔdinB749 allele. Compared to a wild-type strain, the ΔdinB883 mutant was most sensitive (160-fold) in early to mid-logarithmic growth phase and much less sensitive (twofold) in late log or stationary phases, thus showing a growth phase-dependence for UV radiation sensitivity. This sensitizing effect of ΔdinB883 is assumed to be completely dependent upon the presence of UmuDC protein; since the ΔdinB883 mutation did not sensitize the ΔumuDC strain to UV radiation killing throughout log phase and early stationary phase growth. The DNA damage checkpoint activity of UmuDC was clearly affected by ΔdinB883 as shown by testing a umuC104 ΔdinB883 double-mutant. The sensitivities of the ΔumuDC strain and the ΔdinB883 ΔumuDC double-mutant strain were significantly greater than for the ΔdinB883 strain, suggesting that the ΔdinB883 allele only partially suppresses UmuDC activity. The ΔdinB883 mutation partially sensitized (fivefold) uvrA and uvrB strains to UV radiation, but did not sensitize a ΔrecA strain. A comparison of the DNA sequences of the ΔdinB883 allele with the sequences of the Δ(dinB-yafN)882(::kan) and ΔdinB749 alleles, which do not sensitize cells to UV radiation, revealed ΔdinB883 is likely a "gain-of-function" mutation. The ΔdinB883 allele encodes the first 54 amino acids of wild-type DinB followed by 29 predicted residues resulting from the continuation of the dinB reading frame into an adjacent insertion fragment. The resulting polypeptide is proposed to interfere directly or indirectly with UmuDC function(s) involved in protecting cells against the lethal effects of radiation.
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Hudman DA, Sargentini NJ. Resazurin-based assay for screening bacteria for radiation sensitivity. SPRINGERPLUS 2013; 2:55. [PMID: 23483236 PMCID: PMC3586403 DOI: 10.1186/2193-1801-2-55] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 02/13/2013] [Indexed: 12/02/2022]
Abstract
We report a simple and efficient colorimetric method to screen large numbers of bacterial strains for UV- and X-radiation sensitivity. We used reference radiation-sensitive and control strains of Escherichia coli K-12 to compare our colorimetric method to a standard clonogenic plating method. Our colorimetric method was as accurate as the standard method and was superior in terms of savings in supplies and man-hours.
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Affiliation(s)
- Deborah A Hudman
- Department of Microbiology and Immunology, AT Still University of Health Sciences, Kirksville, MO USA
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Abstract
Colicins are the only proteins imported by Escherichia coli and thus serve as tools to study the protein import mechanism. Most of the colicins studied degrade DNA, 16S RNA or tRNA in the cytoplasm, or form pores in the cytoplasmic membrane. Two bacteriocins, Cma (colicin M) and Pst (pesticin), affect the murein structure in the periplasm. These two bacteriocins must be imported only across the outer membrane and therefore represent the simplest system for studying protein import. Cma can be reversibly translocated across the outer membrane. Cma and Pst unfold during import. The crystal structure of Pst reveals a phage T4L (T4 lysozyme) fold of the activity domain. Both bacteriocins require energy for import which is translocated from the cytoplasmic membrane into the outer membrane by the Ton system. Cma kills cells only when the periplasmic FkpA PPIase (peptidylprolyl cis–trans isomerase)/chaperone is present.
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Smith RM, Jacklin AJ, Marshall JJT, Sobott F, Halford SE. Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA. Nucleic Acids Res 2012; 41:405-17. [PMID: 23147004 PMCID: PMC3592466 DOI: 10.1093/nar/gks1000] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Type IIB restriction–modification protein BcgI contains A and B subunits in a
2:1 ratio: A has the active sites for both endonuclease and methyltransferase functions
while B recognizes the DNA. Like almost all Type IIB systems, BcgI needs two unmethylated
sites for nuclease activity; it cuts both sites upstream and downstream of the recognition
sequence, hydrolyzing eight phosphodiester bonds in a single synaptic complex. This
complex may incorporate four A2B protomers to give the eight catalytic centres
(one per A subunit) needed to cut all eight bonds. The BcgI recognition sequence contains
one adenine in each strand that can be N6-methylated. Although most DNA
methyltransferases operate at both unmethylated and hemi-methylated sites, BcgI
methyltransferase is only effective at hemi-methylated sites, where the nuclease component
is inactive. Unlike the nuclease, the methyltransferase acts at solitary sites,
functioning catalytically rather than stoichiometrically. Though it transfers one methyl
group at a time, presumably through a single A subunit, BcgI methyltransferase can be
activated by adding extra A subunits, either individually or as part of A2B
protomers, which indicates that it requires an assembly containing at least two
A2B units.
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Affiliation(s)
- Rachel M Smith
- The DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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35
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Wang RY, Shi ZY, Chen JC, Chen GQ. Cloning large gene clusters from E. coli using in vitro single-strand overlapping annealing. ACS Synth Biol 2012; 1:291-5. [PMID: 23651252 DOI: 10.1021/sb300025d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite recent advances in genomic sequencing and DNA chemical synthesis, construction of large gene clusters containing DNA fragments is still a difficult and expensive task. To tackle this problem, we developed a gene cluster extraction method based on in vitro single-strand overlapping annealing (SSOA). It starts with digesting the target gene cluster in an existing genome, followed by recovering digested chromosome fragments. Subsequently, the single-strand DNA overhangs formed from the digestion process would be specifically annealed and covalently joined together with a circular and a linear vector, respectively. The SSOA method was successfully applied to clone a 18 kb DNA fragment encoding NADH:ubiquinone oxidoreductase. Genomic DNA fragments of different sizes including 11.86, 18.33, 28.67, 34.56, and 55.99 kb were used to test the cloning efficiency. Combined with genetic information from KEGG and the KEIO strain collection, this method will be useful to clone any specific region of an E. coli genome at sizes less than ~28 kb. The method provides a cost-effective way for genome assembly, alternative to chemically synthesized gene clusters.
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Affiliation(s)
- Rui-Yan Wang
- MOE Key
Lab of Bioinformatics and Systems Biology, Department
of Biological Science and Biotechnology, School of Life Sciences,
Tsinghua-Peking Center for Life Sciences and ‡Center for Nano and Micro Mechanics, Tsinghua University, Beijing 100084,
China
| | - Zhen-Yu Shi
- MOE Key
Lab of Bioinformatics and Systems Biology, Department
of Biological Science and Biotechnology, School of Life Sciences,
Tsinghua-Peking Center for Life Sciences and ‡Center for Nano and Micro Mechanics, Tsinghua University, Beijing 100084,
China
| | - Jin-Chun Chen
- MOE Key
Lab of Bioinformatics and Systems Biology, Department
of Biological Science and Biotechnology, School of Life Sciences,
Tsinghua-Peking Center for Life Sciences and ‡Center for Nano and Micro Mechanics, Tsinghua University, Beijing 100084,
China
| | - Guo-Qiang Chen
- MOE Key
Lab of Bioinformatics and Systems Biology, Department
of Biological Science and Biotechnology, School of Life Sciences,
Tsinghua-Peking Center for Life Sciences and ‡Center for Nano and Micro Mechanics, Tsinghua University, Beijing 100084,
China
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Richardson NC, Sargentini NJ, Singh VK, Stuart MK. Monoclonal antibodies against the Escherichia coli DNA repair protein RadA/Sms. Hybridoma (Larchmt) 2012; 31:25-31. [PMID: 22316482 DOI: 10.1089/hyb.2011.0075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The RadA/Sms protein facilitates DNA repair in Escherichia coli cells damaged by UV radiation, X-rays, and chemical agents. However, the precise mechanism by which RadA/Sms aids DNA repair is unknown. Here we report the production of monoclonal antibodies (MAbs) specific for RadA/Sms for use in biochemical and physiological investigations. Histidine-tagged RadA/Sms (RadA-6xHis) was overproduced in E. coli BL21 cells transformed with the radA/sms coding region in plasmid pRSET A and purified by nickel affinity chromatography. Splenocytes from female BALB/c mice hyperimmunized with the purified protein were fused to SP2/0-Ag14 myeloma cells, and the resultant hybridomas were selected in HAT medium. MAbs were detected in hybridoma culture supernatants by indirect ELISA and Western blot analysis against purified RadA-6xHis. MAbs from four cell lines were further evaluated by Western blotting against peptide maps generated by endoproteinase Glu-C digestion of RadA-6xHis. Each of the four MAbs recognized a unique epitope on the fusion protein. Two of the MAbs (6F5 and 2A2) also detected wild-type (tagless) RadA/Sms produced from the pJS003 plasmid in E. coli K-12 cells. We anticipate that these antibodies will prove useful for the detection, isolation, and functional analysis of RadA/Sms.
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Affiliation(s)
- Nastassia C Richardson
- Department of Microbiology/Immunology, A.T. Still University, Kirksville College of Osteopathic Medicine, 800 W. Jefferson Street, Kirksville, MO 63501, USA
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Anupama K, Leela JK, Gowrishankar J. Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol Microbiol 2011; 82:1330-48. [PMID: 22026368 DOI: 10.1111/j.1365-2958.2011.07895.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The endonuclease RNase E of Escherichia coli is essential for viability, but deletion of its C-terminal half (CTH) is not lethal. RNase E preferentially acts on 5'-monophosphorylated RNA whose generation from primary transcripts is catalysed by RppH, but ΔRppH strains are viable. Here we show that the RNase E-ΔCTH ΔRppH combination is lethal, and that the lethality is suppressed by rho or nusG mutations impairing Rho-dependent transcription termination. Lethality was correlated with defects in bulk mRNA decay and tRNA processing, which were reversed by the rho suppressor. Lethality suppression was dependent on RNase H1 or the helicase UvsW of phage T4, both of which act to remove RNA-DNA hybrids (R-loops). The rho and nusG mutations also rescued inviability of a double alteration R169Q (that abolishes 5'-sensing) with ΔCTH in RNase E, as also that of conditional RNase E deficiency. We suggest that the ΔCTH alteration leads to loss of a second 5'-end-independent pathway of RNase E action. We further propose that an increased abundance of R-loops in the rho and nusG mutants, although ordinarily inimical to growth, contributes to rescue the lethality associated with loss of the two RNase E cleavage pathways by providing an alternative means of RNA degradation.
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Affiliation(s)
- K Anupama
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
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Marbaniang CN, Gowrishankar J. Role of ArgP (IciA) in lysine-mediated repression in Escherichia coli. J Bacteriol 2011; 193:5985-96. [PMID: 21890697 PMCID: PMC3194910 DOI: 10.1128/jb.05869-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 08/24/2011] [Indexed: 11/20/2022] Open
Abstract
Initially identified as an inhibitor of oriC-initiated DNA replication in vitro, the ArgP or IciA protein of Escherichia coli has subsequently been described as a nucleoid-associated protein and also as a transcriptional regulator of genes involved in DNA replication (dnaA and nrdA) and amino acid metabolism (argO, dapB, and gdhA [the last in Klebsiella pneumoniae]). ArgP mediates lysine (Lys) repression of argO, dapB, and gdhA in vivo, for which two alternative mechanisms have been identified: at the dapB and gdhA regulatory regions, ArgP binding is reduced upon the addition of Lys, whereas at argO, RNA polymerase is trapped at the step of promoter clearance by Lys-bound ArgP. In this study, we have examined promoter-lac fusions in strains that were argP(+) or ΔargP or that were carrying dominant argP mutations in order to identify several new genes that are ArgP-regulated in vivo, including lysP, lysC, lysA, dapD, and asd (in addition to argO, dapB, and gdhA). All were repressed upon Lys supplementation, and in vitro studies demonstrated that ArgP binds to the corresponding regulatory regions in a Lys-sensitive manner (with the exception of argO, whose binding to ArgP was Lys insensitive). Neither dnaA nor nrdA was ArgP regulated in vivo, although their regulatory regions exhibited low-affinity binding to ArgP. Our results suggest that ArgP is a transcriptional regulator for Lys repression of genes in E. coli but that it is noncanonical in that it also exhibits low-affinity binding, without apparent direct regulatory effect, to a number of additional sites in the genome.
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Affiliation(s)
- Carmelita N. Marbaniang
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
| | - J. Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
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Compromised factor-dependent transcription termination in a nusA mutant of Escherichia coli: spectrum of termination efficiencies generated by perturbations of Rho, NusG, NusA, and H-NS family proteins. J Bacteriol 2011; 193:3842-50. [PMID: 21602355 DOI: 10.1128/jb.00221-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The proteins NusA and NusG, which are essential for the viability of wild-type Escherichia coli, participate in various postinitiation steps of transcription including elongation, antitermination, and termination. NusG is required, along with the essential Rho protein, for factor-dependent transcription termination (also referred to as polarity), but the role of NusA is less clear, with conflicting reports that it both promotes and inhibits the process. In this study, we found that a recessive missense nusA mutant [nusA(R258C)] exhibits a transcription termination-defective (that is, polarity-relieved) phenotype, much like missense mutants in rho or nusG, but is unaffected for either the rate of transcription elongation or antitermination in λ phage. Various combinations of the rho, nusG, and nusA mutations were synthetically lethal, and the lethality was suppressed by expression of the N-terminal half of nucleoid protein H-NS. Our results suggest that NusA function is indeed needed for factor-dependent transcription termination and that an entire spectrum of termination efficiencies can be generated by perturbations of the Rho, NusG, NusA, and H-NS family of proteins, with the corresponding phenotypes extending from polarity through polarity relief to lethality.
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40
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Modulation of Rho-dependent transcription termination in Escherichia coli by the H-NS family of proteins. J Bacteriol 2011; 193:3832-41. [PMID: 21602341 DOI: 10.1128/jb.00220-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nascent transcripts in Escherichia coli that fail to be simultaneously translated are subject to a factor-dependent mechanism of termination (also termed a polarity) that involves the proteins Rho and NusG. In this study, we found that overexpression of YdgT suppressed the polarity relief phenotypes and restored the efficiency of termination in rho or nusG mutants. YdgT and Hha belong to the H-NS and StpA family of proteins that repress a large number of genes in Gram-negative bacteria. Variants of H-NS defective in one or the other of its two dimerization domains, but not those defective in DNA binding alone, also conferred a similar suppression phenotype in rho and nusG mutants. YdgT overexpression was associated with derepression of proU, a prototypical H-NS-silenced locus. Polarity relief conferred by rho or nusG was unaffected in a derivative completely deficient for both H-NS and StpA, although the suppression effects of YdgT or the oligomerization-defective H-NS variants were abolished in this background. Transcription elongation rates in vivo were unaffected in any of the suppressor-bearing strains. Finally, the polarity defects of rho and nusG mutants were exacerbated by Hha and YdgT deficiency. A model is proposed that invokes a novel role for the polymeric architectural scaffold formed on DNA by H-NS and StpA independent of the gene-silencing functions of these nucleoid proteins, in modulating Rho-dependent transcription termination such that interruption of the scaffold (as obtained by expression either of the H-NS oligomerization variants or of YdgT) is associated with improved termination efficiency in the rho and nusG mutants.
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41
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A reliable method for storage of tailed phages. J Microbiol Methods 2011; 84:486-9. [DOI: 10.1016/j.mimet.2011.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 01/03/2011] [Accepted: 01/11/2011] [Indexed: 11/19/2022]
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Chern EC, Siefring S, Paar J, Doolittle M, Haugland RA. Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes. Lett Appl Microbiol 2011; 52:298-306. [PMID: 21204885 DOI: 10.1111/j.1472-765x.2010.03001.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Compare specificity and sensitivity of quantitative PCR (qPCR) assays targeting single and multi-copy gene regions of Escherichia coli. METHODS AND RESULTS A previously reported assay targeting the uidA gene (uidA405) was used as the basis for comparing the taxonomic specificity and sensitivity of qPCR assays targeting the rodA gene (rodA984) and two regions of the multi-copy 23S ribosomal RNA gene (EC23S and EC23S857). Experimental analyses of 28 culture collection strains representing E. coli and 21 related non-target species indicated that the uidA405 and rodA984 assays were both 100% specific for E. coli while the EC23S assay was only 29% specific. The EC23S857 assay was only 95% specific due to detection of E. fergusonii. The uidA405, rodA984, EC23S and EC23S857 assays were 85%, 85%, 100% and 86% sensitive, respectively, in detecting 175 presumptive E. coli culture isolates from fresh, marine and waste water samples. In analyses of DNA extracts from 32 fresh, marine and waste water samples, the rodA984, EC23S and EC23S857 assays detected mean densities of target sequences at ratios of approximately 1:1, 243:1 and 6:1 compared with the mean densities detected by the uidA405 assay. CONCLUSIONS The EC23S assay was less specific for E. coli, whereas the rodA984 and EC23S857 assay taxonomic specificities and sensitivities were similar to those of the uidA405 gene assay. SIGNIFICANCE AND IMPACT The EC23S857 assay has a lower limit of detection for E. coli cells than the uidA405 and rodA984 assays due to its multi-copy gene target and therefore provides greater analytical sensitivity in monitoring for these faecal pollution indicators in environmental waters by qPCR methods.
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Affiliation(s)
- E C Chern
- US Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH 45268, USA
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43
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O'Connor M, Gregory ST. Inactivation of the RluD pseudouridine synthase has minimal effects on growth and ribosome function in wild-type Escherichia coli and Salmonella enterica. J Bacteriol 2011; 193:154-62. [PMID: 21037010 PMCID: PMC3019933 DOI: 10.1128/jb.00970-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 10/18/2010] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the pseudouridine (Ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion of rluD in K-12 strains of E. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50S ribosomal subunit assembly and 30S-50S subunit association. Suppressor mutations in the prfB and prfC genes encoding release factor 2 (RF2) and RF3 that restore the wild type-growth rate and also correct the ribosomal defects have now been isolated. These suppressors link helix 69 Ψ residues with the termination phase of protein synthesis. However, further genetic analysis reported here also reveals that the slow growth and other defects associated with inactivation of rluD in E. coli K-12 strains are due to a defective RF2 protein, with a threonine at position 246, which is present in all K-12 strains. This is in contrast to the more typical alanine found at this position in most bacterial RF2s, including those of other E. coli strains. Inactivation of rluD in E. coli strains containing the prfB allele from E. coli B or in Salmonella enterica, both carrying an RF2 with Ala246, has negligible effects on growth, termination, or ribosome function. The results indicate that, in contrast to those in wild bacteria, termination functions in E. coli K-12 strains carrying a partially defective RF2 protein are especially susceptible to perturbation of ribosome-RF interactions, such as that caused by loss of h69 Ψ modifications.
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Affiliation(s)
- Michael O'Connor
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City, Missouri 64110, USA.
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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45
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Evidence that the supE44 mutation of Escherichia coli is an amber suppressor allele of glnX and that it also suppresses ochre and opal nonsense mutations. J Bacteriol 2010; 192:6039-44. [PMID: 20833812 DOI: 10.1128/jb.00474-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Translational readthrough of nonsense codons is seen not only in organisms possessing one or more tRNA suppressors but also in strains lacking suppressors. Amber suppressor tRNAs have been reported to suppress only amber nonsense mutations, unlike ochre suppressors, which can suppress both amber and ochre mutations, essentially due to wobble base pairing. In an Escherichia coli strain carrying the lacZU118 episome (an ochre mutation in the lacZ gene) and harboring the supE44 allele, suppression of the ochre mutation was observed after 7 days of incubation. The presence of the supE44 lesion in the relevant strains was confirmed by sequencing, and it was found to be in the duplicate copy of the glnV tRNA gene, glnX. To investigate this further, an in vivo luciferase assay developed by D. W. Schultz and M. Yarus (J. Bacteriol. 172:595-602, 1990) was employed to evaluate the efficiency of suppression of amber (UAG), ochre (UAA), and opal (UGA) mutations by supE44. We have shown here that supE44 suppresses ochre as well as opal nonsense mutations, with comparable efficiencies. The readthrough of nonsense mutations in a wild-type E. coli strain was much lower than that in a supE44 strain when measured by the luciferase assay. Increased suppression of nonsense mutations, especially ochre and opal, by supE44 was found to be growth phase dependent, as this phenomenon was only observed in stationary phase and not in logarithmic phase. These results have implications for the decoding accuracy of the translational machinery, particularly in stationary growth phase.
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Kapoor S, Das G, Varshney U. Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNA(fMet) selection on the ribosomal P-site in Escherichia coli. Nucleic Acids Res 2010; 39:202-12. [PMID: 20798174 PMCID: PMC3017606 DOI: 10.1093/nar/gkq760] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The accuracy of the initiator tRNA (tRNAfMet) selection in the ribosomal P-site is central to the fidelity of protein synthesis. A highly conserved occurrence of three consecutive G–C base pairs in the anticodon stem of tRNAfMet contributes to its preferential selection in the P-site. In a genetic screen, using a plasmid borne copy of an inactive tRNAfMet mutant wherein the three G–C base pairs were changed, we isolated Escherichia coli strains that allow efficient initiation with the tRNAfMet mutant. Here, extensive characterization of two such strains revealed novel mutations in the metZWV promoter severely compromising tRNAfMet levels. Low cellular abundance of the chromosomally encoded tRNAfMet allows efficient initiation with the tRNAfMet mutant and an elongator tRNAGln, revealing that a high abundance of the cellular tRNAfMet is crucial for the fidelity of initiator tRNA selection on the ribosomal P-site in E. coli. We discuss possible implications of the changes in the cellular tRNAfMet abundance in proteome remodeling.
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Affiliation(s)
- Suman Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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47
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Role for CysJ flavin reductase in molybdenum cofactor-dependent resistance of Escherichia coli to 6-N-hydroxylaminopurine. J Bacteriol 2010; 192:2026-33. [PMID: 20118259 DOI: 10.1128/jb.01438-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We have previously described a novel Escherichia coli detoxification system for the removal of toxic and mutagenic N-hydroxylated nucleobases and related compounds that requires the molybdenum cofactor. Two subpathways (ycbX and yiiM) were identified, each employing a novel molybdo activity capable of inactivating N-hydroxylated compounds by reduction to the corresponding amine. In the present study, we identify the cysJ gene product as one additional component of this system. While the CysJ protein has been identified as the NADPH:flavin oxidoreductase component of the CysJI sulfite reductase complex (CysJ(8)I(4)), we show that the role of CysJ in base analog detoxification is unique and independent of CysI and sulfite reductase. We further show that CysJ functions as a specific partner of the YcbX molybdoenzyme. We postulate that the function of CysJ in this pathway is to provide, via its NADPH:flavin reductase activity, the reducing equivalents needed for the detoxification reaction at the YcbX molybdocenter. In support of the proposed interaction of the CysJ and YcbX proteins, we show that an apparent CysJ-YcbX "hybrid" protein from two Vibrio species is capable of compensating for a double cysJ ycbX defect in E. coli.
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Silkie SS, Nelson KL. Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. WATER RESEARCH 2009; 43:4860-4871. [PMID: 19765792 DOI: 10.1016/j.watres.2009.08.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/05/2009] [Accepted: 08/08/2009] [Indexed: 05/28/2023]
Abstract
We measured the concentrations of four host-specific (human, dog, cow, and horse Bacteroidales), four generic fecal (16S total Bacteroidales and Escherichia coli, 23S Enterococcus and uidA E. coli,) and two universal bacterial (16S universal and rpoB universal) DNA targets by qPCR in raw sewage and pooled fecal samples from dogs, cows, horses, and Canada Geese. A spiking protocol using the non-fecal bacterium Pseudomonas syringae pph 6 was developed to estimate the recovery of DNA from fecal and environmental samples. The measured fecal marker concentrations were used to calculate baseline ratios and variability of host-specific to generic indicators for each host type. The host-specific markers were found in high concentrations (8-9 log(10)copies/g dry wt.) in their respective hosts' samples, which were equal to or greater than the concentrations of generic E. coli and Enterococcus markers, lending support to the use of host-specific and generic Bacteroidales as sensitive indicators of fecal pollution. The host-specific markers formed a consistent percentage of total Bacteroidales in target host feces and raw sewage, with human-specific comprising 82%, dog-specific 6%, cow-specific 4% and horse-specific 2%. Based on this limited data set, the measurement of host-specific indicators by qPCR has several promising applications. These applications include determining the percentage of total Bacteroidales contributed by a specific host type, using the ratios of host-specific markers to E. coli or Enterococcus to estimate the contribution of each source to these regulated fecal indicator bacteria, and estimating the mass of feces from each host type in environmental samples.
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Affiliation(s)
- Sarah S Silkie
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720-1710, USA
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Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm. Amino Acids 2009; 37:443-58. [PMID: 19198978 DOI: 10.1007/s00726-009-0241-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 01/12/2009] [Indexed: 02/07/2023]
Abstract
Adaptive signal transduction within microbial cells involves a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile two-component systems (TCS), arisen early in bacterial evolution. In Escherichia coli, cross-talk between the AtoS histidine kinase and the AtoC response regulator, forming the AtoSC TCS, through His --> Asp phosphotransfer, activates AtoC directly to induce atoDAEB operon expression, thus modulating diverse fundamental cellular processes such as short-chain fatty acid catabolism, poly-(R)-3-hydroxybutyrate biosynthesis and chemotaxis. Among the inducers hitherto identified, acetoacetate is the classical activator. The AtoSC TCS functional modulation by polyamines, histamine and Ca(2+), as well as the role of AtoC as transcriptional regulator, add new promising perspectives in the physiological significance and potential pharmacological exploitation of this TCS in cell proliferation, bacteria-host interactions, chemotaxis, and adaptation.
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Abstract
Lactoferrin, an iron-binding glycoprotein, is a cell-secreted mediator that bridges innate and adaptive immune function in mammals. It is a pleiotropic molecule that directly assists in the influence of presenting cells for the development of T-helper cell polarization. The aim of this review is to provide an overview of research regarding the role of lactoferrin in maintaining immune homeostasis, in particular as a mediator of immune responses to infectious assault, trauma and injury. These findings are critically relevant in the development of both prophylactic and therapeutic interventions in humans. Understanding these particular effects of lactoferrin will provide a logical framework for determining its role in health and disease.
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Affiliation(s)
- Jeffrey K Actor
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at Houston, TX 77030, USA.
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