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Falchi FA. Analyzing the Function of Essential Genes by Plasmid Shuffling. Methods Mol Biol 2022; 2548:37-49. [PMID: 36151490 DOI: 10.1007/978-1-0716-2581-1_3] [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] [Indexed: 06/16/2023]
Abstract
Investigations on gene essentiality have important implications in several fields of basic and applied research. A variety of strategies have been developed over the years to identify essential genes. Here, we describe an implemented plasmid shuffling method useful to assess the essentiality of overlapped genes under very stringent conditions. A host strain harboring the chromosomal deletion of the genes of interest is complemented by a thermosensitive plasmid carrying the copy of gene 1, gene 2, and rpsL allele, conferring streptomycin sensitivity to an otherwise resistant strain. A compatible plasmid harboring a different selectable marker and the copy of gene 2 only is transformed into the host strain, resulting in the coexistence of two plasmids. These cells are grown at high temperatures in a medium containing streptomycin. Under such conditions, viable cells are expected to contain only the incoming plasmid and to carry suppressor mutation(s) that bypass the loss of the essential gene 1. The system may thus represent a valuable tool to identify interactions between essential proteins and cell pathways.
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2
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A Shift to Human Body Temperature (37°C) Rapidly Reprograms Multiple Adaptive Responses in Escherichia coli That Would Facilitate Niche Survival and Colonization. J Bacteriol 2021; 203:e0036321. [PMID: 34516284 PMCID: PMC8544407 DOI: 10.1128/jb.00363-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
One of the first environmental cues sensed by a microbe as it enters a human host is an upshift in temperature to 37°C. In this dynamic time point analysis, we demonstrate that this environmental transition rapidly signals a multitude of gene expression changes in Escherichia coli. Bacteria grown at 23°C under aerobic conditions were shifted to 37°C, and mRNA expression was measured at time points after the shift to 37°C (t = 0.5, 1, and 4 h). The first hour is characterized by a transient shift to anaerobic respiration strategies and stress responses, particularly acid resistance, indicating that temperature serves as a sentinel cue to predict and prepare for various niches within the host. The temperature effects on a subset of stress response genes were shown to be mediated by RpoS and directly correlated with RpoS, DsrA, and RprA levels, and increased acid resistance was observed that was dependent on 23°C growth and RpoS. By 4 h, gene expression shifted to aerobic respiration pathways and decreased stress responses, coupled with increases in genes associated with biosynthesis (amino acid and nucleotides), iron uptake, and host defense. ompT, a gene that confers resistance to antimicrobial peptides, was highly thermoregulated, with a pattern conserved in enteropathogenic and uropathogenic E. coli strains. An immediate decrease in curli gene expression concomitant with an increase in flagellar gene expression implicates temperature in this developmental decision. Together, our studies demonstrate that temperature signals a reprogramming of gene expression immediately upon an upshift that may predict, prepare, and benefit the survival of the bacterium within the host. IMPORTANCE As one of the first cues sensed by the microbe upon entry into a human host, understanding how bacteria like E. coli modulate gene expression in response to temperature improves our understanding of how bacteria immediately initiate responses beneficial for survival and colonization. For pathogens, understanding the various pathways of thermal regulation could yield valuable targets for anti-infective chemotherapeutic drugs or disinfection measures. In addition, our data provide a dynamic examination of the RpoS stress response, providing genome-wide support for how temperature impacts RpoS through changes in RpoS stability and modulation by small regulatory RNAs.
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Abstract
The outer membrane of Gram-negative bacteria is essential for their survival in harsh environments and provides intrinsic resistance to many antibiotics. This membrane is remarkable; it is a highly asymmetric lipid bilayer. The inner leaflet of the outer membrane contains phospholipids, whereas the fatty acyl chains attached to lipopolysaccharide (LPS) comprise the hydrophobic portion of the outer leaflet. This lipid asymmetry, and in particular the exclusion of phospholipids from the outer leaflet, is key to creating an almost impenetrable barrier to hydrophobic molecules that can otherwise pass through phospholipid bilayers. It has long been known that these lipids are not made in the outer membrane. It is now believed that conserved multisubunit protein machines extract these lipids after their synthesis is completed at the inner membrane and transport them to the outer membrane. A longstanding question is how the cell builds and maintains this asymmetric lipid bilayer in coordination with the assembly of the other components of the cell envelope. This Review describes the trans-envelope lipid transport systems that have been identified to participate in outer-membrane biogenesis: LPS transport via the Lpt machine, and phospholipid transport via the Mla pathway and several recently proposed transporters.
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Affiliation(s)
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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4
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Stargardt P, Striedner G, Mairhofer J. Tunable expression rate control of a growth-decoupled T7 expression system by L-arabinose only. Microb Cell Fact 2021; 20:27. [PMID: 33522916 PMCID: PMC7852362 DOI: 10.1186/s12934-021-01512-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Precise regulation of gene expression is of utmost importance for the production of complex membrane proteins (MP), enzymes or other proteins toxic to the host cell. In this article we show that genes under control of a normally Isopropyl β-D-1-thiogalactopyranoside (IPTG)-inducible PT7-lacO promoter can be induced solely with L-arabinose in a newly constructed Escherichia coli expression host BL21-AI<gp2>, a strain based on the recently published approach of bacteriophage inspired growth-decoupled recombinant protein production. RESULTS Here, we show that BL21-AI<gp2> is able to precisely regulate protein production rates on a cellular level in an L-arabinose concentration-dependent manner and simultaneously allows for reallocation of metabolic resources due to L-arabinose induced growth decoupling by the phage derived inhibitor peptide Gp2. We have successfully characterized the system under relevant fed-batch like conditions in microscale cultivation (800 µL) and generated data proofing a relevant increase in specific yields for 6 different Escherichia coli derived MP-GFP fusion proteins by using online-GFP signals, FACS analysis, SDS-PAGE and western blotting. CONCLUSIONS In all cases tested, BL21-AI<gp2> outperformed the parental strain BL21-AI, operated in growth-associated production mode. Specific MP-GFP fusion proteins yields have been improved up to 2.7-fold. Therefore, this approach allows for fine tuning of MP production or expression of multi-enzyme pathways where e.g. particular stoichiometries have to be met to optimize product flux.
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Affiliation(s)
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
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5
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Benedet M, Falchi FA, Puccio S, Di Benedetto C, Peano C, Polissi A, Dehò G. The Lack of the Essential LptC Protein in the Trans-Envelope Lipopolysaccharide Transport Machine Is Circumvented by Suppressor Mutations in LptF, an Inner Membrane Component of the Escherichia coli Transporter. PLoS One 2016; 11:e0161354. [PMID: 27529623 PMCID: PMC4986956 DOI: 10.1371/journal.pone.0161354] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/03/2016] [Indexed: 12/29/2022] Open
Abstract
The lipopolysaccharide (LPS) transport (Lpt) system is responsible for transferring LPS from the periplasmic surface of the inner membrane (IM) to the outer leaflet of the outer membrane (OM), where it plays a crucial role in OM selective permeability. In E. coli seven essential proteins are assembled in an Lpt trans-envelope complex, which is conserved in γ-Proteobacteria. LptBFG constitute the IM ABC transporter, LptDE form the OM translocon for final LPS delivery, whereas LptC, an IM-anchored protein with a periplasmic domain, interacts with the IM ABC transporter, the periplasmic protein LptA, and LPS. Although essential, LptC can tolerate several mutations and its role in LPS transport is unclear. To get insights into the functional role of LptC in the Lpt machine we searched for viable mutants lacking LptC by applying a strong double selection for lptC deletion mutants. Genome sequencing of viable ΔlptC mutants revealed single amino acid substitutions at a unique position in the predicted large periplasmic domain of the IM component LptF (LptFSupC). In complementation tests, lptFSupC mutants suppress lethality of both ΔlptC and lptC conditional expression mutants. Our data show that mutations in a specific residue of the predicted LptF periplasmic domain can compensate the lack of the essential protein LptC, implicate such LptF domain in the formation of the periplasmic bridge between the IM and OM complexes, and suggest that LptC may have evolved to improve the performance of an ancestral six-component Lpt machine.
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Affiliation(s)
- Mattia Benedet
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Federica A. Falchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Simone Puccio
- Scuola di Dottorato in Medicina Molecolare e Traslazionale, Università degli Studi di Milano, Segrate, Italy
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milan, Italy
| | | | - Clelia Peano
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
- * E-mail:
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6
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Functional Interaction between the Cytoplasmic ABC Protein LptB and the Inner Membrane LptC Protein, Components of the Lipopolysaccharide Transport Machinery in Escherichia coli. J Bacteriol 2016; 198:2192-203. [PMID: 27246575 DOI: 10.1128/jb.00329-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/24/2016] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED The assembly of lipopolysaccharide (LPS) in the outer leaflet of the outer membrane (OM) requires the transenvelope Lpt (lipopolysaccharide transport) complex, made in Escherichia coli of seven essential proteins located in the inner membrane (IM) (LptBCFG), periplasm (LptA), and OM (LptDE). At the IM, LptBFG constitute an unusual ATP binding cassette (ABC) transporter, composed by the transmembrane LptFG proteins and the cytoplasmic LptB ATPase, which is thought to extract LPS from the IM and to provide the energy for its export across the periplasm to the cell surface. LptC is a small IM bitopic protein that binds to LptBFG and recruits LptA via its N- and C-terminal regions, and its role in LPS export is not completely understood. Here, we show that the expression level of lptB is a critical factor for suppressing lethality of deletions in the C-terminal region of LptC and the functioning of a hybrid Lpt machinery that carries Pa-LptC, the highly divergent LptC orthologue from Pseudomonas aeruginosa We found that LptB overexpression stabilizes C-terminally truncated LptC mutant proteins, thereby allowing the formation of a sufficient amount of stable IM complexes to support growth. Moreover, the LptB level seems also critical for the assembly of IM complexes carrying Pa-LptC which is otherwise defective in interactions with the E. coli LptFG components. Overall, our data suggest that LptB and LptC functionally interact and support a model whereby LptB plays a key role in the assembly of the Lpt machinery. IMPORTANCE The asymmetric outer membrane (OM) of Gram-negative bacteria contains in its outer leaflet an unusual glycolipid, the lipopolysaccharide (LPS). LPS largely contributes to the peculiar permeability barrier properties of the OM that prevent the entry of many antibiotics, thus making Gram-negative pathogens difficult to treat. In Escherichia coli the LPS transporter (the Lpt machine) is made of seven essential proteins (LptABCDEFG) that form a transenvelope complex. Here, we show that increased expression of the membrane-associated ABC protein LptB can suppress defects of LptC, which participates in the formation of the periplasmic bridge. This reveals functional interactions between these two components and supports a role of LptB in the assembly of the Lpt machine.
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7
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Simpson BW, May JM, Sherman DJ, Kahne D, Ruiz N. Lipopolysaccharide transport to the cell surface: biosynthesis and extraction from the inner membrane. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0029. [PMID: 26370941 DOI: 10.1098/rstb.2015.0029] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The cell surface of most Gram-negative bacteria is covered with lipopolysaccharide (LPS). The network of charges and sugars provided by the dense packing of LPS molecules in the outer leaflet of the outer membrane interferes with the entry of hydrophobic compounds into the cell, including many antibiotics. In addition, LPS can be recognized by the immune system and plays a crucial role in many interactions between bacteria and their animal hosts. LPS is synthesized in the inner membrane of Gram-negative bacteria, so it must be transported across their cell envelope to assemble at the cell surface. Over the past two decades, much of the research on LPS biogenesis has focused on the discovery and understanding of Lpt, a multi-protein complex that spans the cell envelope and functions to transport LPS from the inner membrane to the outer membrane. This paper focuses on the early steps of the transport of LPS by the Lpt machinery: the extraction of LPS from the inner membrane. The accompanying paper (May JM, Sherman DJ, Simpson BW, Ruiz N, Kahne D. 2015 Phil. Trans. R. Soc. B 370, 20150027. (doi:10.1098/rstb.2015.0027)) describes the subsequent steps as LPS travels through the periplasm and the outer membrane to its final destination at the cell surface.
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Affiliation(s)
- Brent W Simpson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Janine M May
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - David J Sherman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA Department of Molecular and Cellular Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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8
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Thiaville PC, El Yacoubi B, Köhrer C, Thiaville JJ, Deutsch C, Iwata-Reuyl D, Bacusmo JM, Armengaud J, Bessho Y, Wetzel C, Cao X, Limbach PA, RajBhandary UL, de Crécy-Lagard V. Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria. Mol Microbiol 2015; 98:1199-221. [PMID: 26337258 DOI: 10.1111/mmi.13209] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 02/06/2023]
Abstract
Threonylcarbamoyladenosine (t(6)A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t(6)A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t(6)A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNA(Ile)-lysidine synthetase. We confirm that t(6)A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t(6)A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t(6)A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t(6)A(-) D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t(6)A in tRNAs. Thus, although t(6)A is universally conserved in tRNAs, its role in translation might vary greatly between organisms.
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Affiliation(s)
- Patrick C Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, 32610, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.,Institut de Génétique et Microbiologie, Université of Paris-Sud, Orsay, France
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jennifer J Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Chris Deutsch
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', Bagnols-sur-Cèze, F-30200, France
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Institute of Physics, Academia Sinica, 128 Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Uttam L RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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9
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Bollati M, Villa R, Gourlay LJ, Benedet M, Dehò G, Polissi A, Barbiroli A, Martorana AM, Sperandeo P, Bolognesi M, Nardini M. Crystal structure of LptH, the periplasmic component of the lipopolysaccharide transport machinery from Pseudomonas aeruginosa. FEBS J 2015; 282:1980-97. [PMID: 25735820 DOI: 10.1111/febs.13254] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 02/19/2015] [Accepted: 03/02/2015] [Indexed: 01/26/2023]
Abstract
UNLABELLED Lipopolysaccharide (LPS) is the main glycolipid present in the outer leaflet of the outer membrane (OM) of Gram-negative bacteria, where it modulates OM permeability, therefore preventing many toxic compounds from entering the cell. LPS biogenesis is an essential process in Gram-negative bacteria and thus is an ideal target pathway for the development of novel specific antimicrobials. The lipopolysaccharide transport (Lpt) system is responsible for transporting LPS from the periplasmic surface of the inner membrane, where it is assembled, to the cell surface where it is then inserted in the OM. The Lpt system has been widely studied in Escherichia coli, where it consists of seven essential proteins located in the inner membrane (LptBCFG), in the periplasm (LptA) and in the OM (LptDE). In the present study, we focus our attention on the Pseudomonas aeruginosa PAO1 Lpt system. We identified an LptA orthologue, named LptH, and solved its crystal structure at a resolution of 2.75 Å. Using interspecies complementation and site-directed mutagenesis of a conserved glycine residue, we demonstrate that P. aeruginosa LptH is the genetic and functional homologue of E. coli LptA, with whom it shares the β-jellyroll fold identified also in other members of the canonical E. coli Lpt model system. Furthermore, we modeled the N-terminal β-jellyroll domain of P. aeruginosa LptD, based on the crystal structure of its homologue from Shigella flexneri, aiming to provide more general insight into the mechanism of LPS binding and transport in P. aeruginosa. Both LptH and LptD may represent new targets for the discovery of next generation antibacterial drugs, targeting specific opportunistic pathogens such as P. aeruginosa. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank under accession number PDB 4uu4.
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Affiliation(s)
- Michela Bollati
- Department of Biosciences, University of Milano, Italy.,CNR-IBF, University of Milano, Italy
| | | | | | | | - Gianni Dehò
- Department of Biosciences, University of Milano, Italy
| | - Alessandra Polissi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutrition Sciences, University of Milano, Italy
| | - Alessandra M Martorana
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Paola Sperandeo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Italy.,CNR-IBF, University of Milano, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
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10
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Abstract
The increasing emergence of antimicrobial multiresistant bacteria is of great concern to public health. While these bacteria are becoming an ever more prominent cause of nosocomial and community-acquired infections worldwide, the antibiotic discovery pipeline has been stalled in the last few years with very few efforts in the research and development of novel antibacterial therapies. Some of the root causes that have hampered current antibiotic drug development are the lack of understanding of the mode of action (MOA) of novel antibiotic molecules and the poor characterization of the bacterial physiological response to antibiotics that ultimately causes resistance. Here, we review how bacterial genetic tools can be applied at the genomic level with the goal of profiling resistance to antibiotics and elucidating antibiotic MOAs. Specifically, we highlight how chemical genomic detection of the MOA of novel antibiotic molecules and antibiotic profiling by next-generation sequencing are leveraging basic antibiotic research to unprecedented levels with great opportunities for knowledge translation.
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Affiliation(s)
- Silvia T Cardona
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and.,b Department of Medical Microbiology & Infectious Disease , University of Manitoba , Winnipeg , Canada
| | - Carrie Selin
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and
| | - April S Gislason
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and
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11
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Subashchandrabose S, Smith SN, Spurbeck RR, Kole MM, Mobley HLT. Genome-wide detection of fitness genes in uropathogenic Escherichia coli during systemic infection. PLoS Pathog 2013; 9:e1003788. [PMID: 24339777 PMCID: PMC3855560 DOI: 10.1371/journal.ppat.1003788] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/10/2013] [Indexed: 12/16/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is a leading etiological agent of bacteremia in humans. Virulence mechanisms of UPEC in the context of urinary tract infections have been subjected to extensive research. However, understanding of the fitness mechanisms used by UPEC during bacteremia and systemic infection is limited. A forward genetic screen was utilized to detect transposon insertion mutants with fitness defects during colonization of mouse spleens. An inoculum comprised of 360,000 transposon mutants in the UPEC strain CFT073, cultured from the blood of a patient with pyelonephritis, was used to inoculate mice intravenously. Transposon insertion sites in the inoculum (input) and bacteria colonizing the spleen (output) were identified using high-throughput sequencing of transposon-chromosome junctions. Using frequencies of representation of each insertion mutant in the input and output samples, 242 candidate fitness genes were identified. Co-infection experiments with each of 11 defined mutants and the wild-type strain demonstrated that 82% (9 of 11) of the tested candidate fitness genes were required for optimal fitness in a mouse model of systemic infection. Genes involved in biosynthesis of poly-N-acetyl glucosamine (pgaABCD), major and minor pilin of a type IV pilus (c2394 and c2395), oligopeptide uptake periplasmic-binding protein (oppA), sensitive to antimicrobial peptides (sapABCDF), putative outer membrane receptor (yddB), zinc metallopeptidase (pqqL), a shikimate pathway gene (c1220) and autotransporter serine proteases (pic and vat) were further characterized. Here, we report the first genome-wide identification of genes that contribute to fitness in UPEC during systemic infection in a mammalian host. These fitness factors may represent targets for developing novel therapeutics against UPEC. Uropathogenic E. coli is a major cause of bacterial bloodstream infections in humans. Dissemination of E. coli into the bloodstream during urinary tract infections may lead to potentially fatal complications. This pathogen is becoming increasingly resistant to currently used antibiotics. To develop additional tools to treat such infections, a thorough understanding of the mechanism of pathogenesis is required. Here, we report major progress towards that goal by identifying bacterial genes that are critical for the ability of this pathogen to cause bloodstream infections using a mouse model of infection. This study sheds light on the conditions encountered by E. coli during systemic infection. Further research on the genes identified in this study may reveal bacterial targets that can be used to develop novel therapeutics against bloodstream infections caused by E. coli.
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Affiliation(s)
- Sargurunathan Subashchandrabose
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sara N. Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Rachel R. Spurbeck
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Monica M. Kole
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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12
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On the essentiality of lipopolysaccharide to Gram-negative bacteria. Curr Opin Microbiol 2013; 16:779-85. [PMID: 24148302 DOI: 10.1016/j.mib.2013.09.007] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/23/2013] [Indexed: 01/26/2023]
Abstract
Lipopolysaccharide is a highly acylated saccharolipid located on the outer leaflet of the outer membrane of Gram-negative bacteria. Lipopolysaccharide is critical to maintaining the barrier function preventing the passive diffusion of hydrophobic solutes such as antibiotics and detergents into the cell. Lipopolysaccharide has been considered an essential component for outer membrane biogenesis and cell viability based on pioneering studies in the model Gram-negative organisms Escherichia coli and Salmonella. With the isolation of lipopolysaccharide-null mutants in Neisseria meningitidis, Moraxella catarrhalis, and most recently in Acinetobacter baumannii, it has become increasingly apparent that lipopolysaccharide is not an essential outer membrane building block in all organisms. We suggest the accumulation of toxic intermediates, misassembly of essential outer membrane porins, and outer membrane stress response pathways that are activated by mislocalized lipopolysaccharide may collectively contribute to the observed strain-dependent essentiality of lipopolysaccharide.
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13
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Experimental evolution of a facultative thermophile from a mesophilic ancestor. Appl Environ Microbiol 2011; 78:144-55. [PMID: 22020511 DOI: 10.1128/aem.05773-11] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Experimental evolution via continuous culture is a powerful approach to the alteration of complex phenotypes, such as optimal/maximal growth temperatures. The benefit of this approach is that phenotypic selection is tied to growth rate, allowing the production of optimized strains. Herein, we demonstrate the use of a recently described long-term culture apparatus called the Evolugator for the generation of a thermophilic descendant from a mesophilic ancestor (Escherichia coli MG1655). In addition, we used whole-genome sequencing of sequentially isolated strains throughout the thermal adaptation process to characterize the evolutionary history of the resultant genotype, identifying 31 genetic alterations that may contribute to thermotolerance, although some of these mutations may be adaptive for off-target environmental parameters, such as rich medium. We undertook preliminary phenotypic analysis of mutations identified in the glpF and fabA genes. Deletion of glpF in a mesophilic wild-type background conferred significantly improved growth rates in the 43-to-48°C temperature range and altered optimal growth temperature from 37°C to 43°C. In addition, transforming our evolved thermotolerant strain (EVG1064) with a wild-type allele of glpF reduced fitness at high temperatures. On the other hand, the mutation in fabA predictably increased the degree of saturation in membrane lipids, which is a known adaptation to elevated temperature. However, transforming EVG1064 with a wild-type fabA allele had only modest effects on fitness at intermediate temperatures. The Evolugator is fully automated and demonstrates the potential to accelerate the selection for complex traits by experimental evolution and significantly decrease development time for new industrial strains.
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Forti F, Mauri V, Dehò G, Ghisotti D. Isolation of conditional expression mutants in Mycobacterium tuberculosis by transposon mutagenesis. Tuberculosis (Edinb) 2011; 91:569-78. [PMID: 21840262 DOI: 10.1016/j.tube.2011.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/28/2011] [Accepted: 07/17/2011] [Indexed: 12/22/2022]
Abstract
In Mycobacterium tuberculosis identification of essential genes has been hampered by the scarcity of suitable genetic tools for genome wide screenings. We constructed two Himar1 transposon derivatives in which the Streptomyces pristinamycin I-inducible ptr promoter was inserted at one transposon end in outward orientation. These transposons, Tn-pip/pptr (which harbours the promoter and its repressor pip gene) and Tn-pptr (which depends on a host expressing the pip gene), were inserted in the thermosensitive mycobacteriophage phAE87. After transduction into M. tuberculosis H37Rv, hygromycin resistant clones were selected in the presence of pristinamycin, screened for inducer dependent growth, and the transposon insertion point mapped by sequencing. Out of 3530 Hyg(R) mutants tested, we obtained 14 (0.4%) single insertion conditional mutants. In three (leuA, mazE6, rne) pptr was located upstream of genes whose function had been assessed by experimental evidence, whereas in seven the transposon targeted genes (ftsK, glf, infB, metC, pyrD, secY, and tuf) whose function had been assigned by similarity with homologous genes and four ORFs of unknown function (Rv0883c, Rv1478, Rv2050 and Rv2204c). These results validate our mutagenesis system and provide previously unavailable conditional expression mutants in genes of known, putative and unknown functions for genetic and physiological studies.
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Affiliation(s)
- Francesca Forti
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery. J Bacteriol 2010; 192:6418-27. [PMID: 20935093 DOI: 10.1128/jb.00621-10] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Random transposon mutagenesis is the strategy of choice for associating a phenotype with its unknown genetic determinants. It is generally performed by mobilization of a conditionally replicating vector delivering transposons to recipient cells using broad-host-range RP4 conjugative machinery carried by the donor strain. In the present study, we demonstrate that bacteriophage Mu, which was deliberately introduced during the original construction of the widely used donor strains SM10 λpir and S17-1 λpir, is silently transferred to Escherichia coli recipient cells at high frequency, both by hfr and by release of Mu particles by the donor strain. Our findings suggest that bacteriophage Mu could have contaminated many random-mutagenesis experiments performed on Mu-sensitive species with these popular donor strains, leading to potential misinterpretation of the transposon mutant phenotype and therefore perturbing analysis of mutant screens. To circumvent this problem, we precisely mapped Mu insertions in SM10 λpir and S17-1 λpir and constructed a new Mu-free donor strain, MFDpir, harboring stable hfr-deficient RP4 conjugative functions and sustaining replication of Π-dependent suicide vectors. This strain can therefore be used with most of the available transposon-delivering plasmids and should enable more efficient and easy-to-analyze mutant hunts in E. coli and other Mu-sensitive RP4 host bacteria.
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Transport of lipopolysaccharide across the cell envelope: the long road of discovery. Nat Rev Microbiol 2009; 7:677-83. [PMID: 19633680 DOI: 10.1038/nrmicro2184] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Intracellular lipid transport is poorly understood. Genetic studies to identify lipid-transport factors are complicated by the essentiality of many lipids, whereas biochemical and cell biology approaches aiming to determine localization and mechanisms of lipid transport are often challenged by the lack of adequate technology. Here, we review the epic history of how different approaches, technological advances and ingenuity contributed to the recent discovery of a multi-protein pathway that transports lipopolysaccharide across the envelope of Gram-negative bacteria.
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El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crécy-Lagard V. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res 2009; 37:2894-909. [PMID: 19287007 PMCID: PMC2685093 DOI: 10.1093/nar/gkp152] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. Using a combination of bioinformatic, genetic, structural and biochemical approaches, the universal protein family YrdC/Sua5 (COG0009) was shown to be involved in the biosynthesis of this hypermodified base. Contradictory reports on the essentiality of both the yrdC wild-type gene of Escherichia coli and the SUA5 wild-type gene of Saccharomyces cerevisiae led us to reconstruct null alleles for both genes and prove that yrdC is essential in E. coli, whereas SUA5 is dispensable in yeast but results in severe growth phenotypes. Structural and biochemical analyses revealed that the E. coli YrdC protein binds ATP and preferentially binds RNAThr lacking only the t6A modification. This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo.
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Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology, University of Florida, Gainesville, FL 32611-0700, USA
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Sperandeo P, Dehò G, Polissi A. The lipopolysaccharide transport system of Gram-negative bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:594-602. [PMID: 19416651 DOI: 10.1016/j.bbalip.2009.01.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 01/16/2009] [Accepted: 01/16/2009] [Indexed: 02/06/2023]
Abstract
The cell envelope of Gram-negative bacteria consists of two distinct membranes, the inner (IM) and the outer membrane (OM) separated by the periplasm. The OM contains in the outer leaflet the lipopolysaccharide (LPS), a complex lipid with important biological activities. In the host it elicits the innate immune response whereas in the bacterium it is responsible for the peculiar permeability barrier properties exhibited by the OM. The chemical structure of LPS and its biosynthetic pathways have been fully elucidated. By contrast only recently details of the transport and assembly of LPS into the OM have emerged. LPS is synthesized in the cytoplasm and at the inner leaflet of the IM and needs to cross two different compartments, the IM and the periplasm, to reach its final destination at the OM. This review focuses on recent studies that led to our present understanding of the protein machine implicated in LPS transport and in assembly at the cell surface.
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Affiliation(s)
- Paola Sperandeo
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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19
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Domenech P, Kobayashi H, LeVier K, Walker GC, Barry CE. BacA, an ABC transporter involved in maintenance of chronic murine infections with Mycobacterium tuberculosis. J Bacteriol 2009; 191:477-85. [PMID: 18996991 PMCID: PMC2620812 DOI: 10.1128/jb.01132-08] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 10/31/2008] [Indexed: 11/20/2022] Open
Abstract
BacA is an inner membrane protein associated with maintenance of chronic infections in several diverse host-pathogen interactions. To understand the function of the bacA gene in Mycobacterium tuberculosis (Rv1819c), we insertionally inactivated this gene and analyzed the resulting mutant for a variety of phenotypes. BacA deficiency in M. tuberculosis did not affect sensitivity to detergents, acidic pH, and zinc, indicating that there was no global compromise in membrane integrity, and a comprehensive evaluation of the major lipid constituents of the cell envelope failed to reveal any significant differences. Infection of mice with this mutant revealed no impact on establishment of infection but a profound effect on maintenance of extended chronic infection and ultimate outcome. As in alphaproteobacteria, deletion of BacA in M. tuberculosis led to increased bleomycin resistance, and heterologous expression of the M. tuberculosis BacA homolog in Escherichia coli conferred sensitivity to antimicrobial peptides. These results suggest a striking conservation of function for BacA-related proteins in transport of a critical molecule that determines the outcome of the host-pathogen interaction.
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Affiliation(s)
- Pilar Domenech
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Disease, 33 North Drive, Bethesda, Maryland 20892, USA
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Lee JY, Sung BH, Yu BJ, Lee JH, Lee SH, Kim MS, Koob MD, Kim SC. Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli. Nucleic Acids Res 2008; 36:e102. [PMID: 18641039 PMCID: PMC2532725 DOI: 10.1093/nar/gkn449] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Now that many genomes have been sequenced and the products of newly identified genes have been annotated, the next goal is to engineer the desired phenotypes in organisms of interest. For the phenotypic engineering of microorganisms, we have developed novel artificial transcription factors (ATFs) capable of reprogramming innate gene expression circuits in Escherichia coli. These ATFs are composed of zinc finger (ZF) DNA-binding proteins, with distinct specificities, fused to an E. coli cyclic AMP receptor protein (CRP). By randomly assembling 40 different types of ZFs, we have constructed more than 6.4 × 104 ATFs that consist of 3 ZF DNA-binding domains and a CRP effector domain. Using these ATFs, we induced various phenotypic changes in E. coli and selected for industrially important traits, such as resistance to heat shock, osmotic pressure and cold shock. Genes associated with the heat-shock resistance phenotype were then characterized. These results and the general applicability of this platform clearly indicate that novel ATFs are powerful tools for the phenotypic engineering of microorganisms and can facilitate microbial functional genomic studies.
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Affiliation(s)
- Ju Young Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bong Hyun Sung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Byung Jo Yu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jun Hyoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sang Hee Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mi Sun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael D. Koob
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Biomass Team, Korea Institute of Energy Research, Daejeon, Korea and Department of Laboratory Medicine and Pathology, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
- *To whom correspondence should be addressed. Tel: +82 42 869 2619; Fax: +82 42 869 2610;
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Leduc I, Banks KE, Fortney KR, Patterson KB, Billings SD, Katz BP, Spinola SM, Elkins C. Evaluation of the repertoire of the TonB-dependent receptors of Haemophilus ducreyi for their role in virulence in humans. J Infect Dis 2008; 197:1103-9. [PMID: 18462159 DOI: 10.1086/586901] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Haemophilus ducreyi contains 3 TonB-dependent receptors: the hemoglobin receptor HgbA, which is required for virulence in humans; the heme receptor TdhA; and an uncharacterized conserved hypothetical protein TdX (HD0646). A double tdX/tdhA mutant (FX527) was constructed on the background of a human-passaged variant of strain 35000 (35000HP). Six volunteers were infected with 35000HP at 3 sites on one arm and with FX527 at 3 sites on the other. The pustule formation rate was 55.6% (95% confidence interval [CI], 35.7%-75.4%) at 18 parent-strain sites and 44.4% (95% CI, 15.0%-73.9%) at 18 mutant-strain sites (P = .51). Similar amounts of 35000HP and FX527 were recovered from pustules in semiquantitative culture. Thus, TdX and TdhA are not necessary for virulence, whereas HgbA is both necessary and sufficient for virulence in humans. The data suggest that hemoglobin is the sole source of heme/iron used by H. ducreyi in vivo and has implications for the potential of HgbA as a vaccine.
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Affiliation(s)
- Isabelle Leduc
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill 27599, USA
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22
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White-Ziegler CA, Malhowski AJ, Young S. Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12. J Bacteriol 2007; 189:5429-40. [PMID: 17526711 PMCID: PMC1951813 DOI: 10.1128/jb.01929-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using DNA microarrays, we identified 126 genes in Escherichia coli K-12 whose expression is increased at human body temperature (37 degrees C) compared to growth at 23 degrees C. Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. Using quantitative real-time PCR, we investigated the thermoregulatory response for representative genes in each of these three categories (hisJ, cysP, srlE, garP, fes, and cirA), along with the fimbrial gene papB. Increased expression at 37 degrees C compared to 23 degrees C was retained in both exponential and stationary phases for all of the genes and in most of the various media tested, supporting the relative importance of this cue in adapting to changing environments. Because iron acquisition is important for both growth and virulence, we analyzed the regulation of the iron utilization genes cirA and fes and found that growth in iron-depleted medium abrogated the thermoregulatory effect, with high-level expression at both temperatures, contrasting with papB thermoregulation, which was not greatly altered by limiting iron levels. A positive role for the environmental regulator H-NS was found for fes, cirA, hisJ, and srlE transcription, whereas it had a primarily negative effect on cysP and garP expression. Together, these studies indicate that temperature is a broadly used cue for regulating gene expression in E. coli and that H-NS regulates iron, carbohydrate, and amino acid utilization gene expression.
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Nogales J, Macchi R, Franchi F, Barzaghi D, Fernández C, García JL, Bertoni G, Díaz E. Characterization of the last step of the aerobic phenylacetic acid degradation pathway. MICROBIOLOGY-SGM 2007; 153:357-365. [PMID: 17259607 DOI: 10.1099/mic.0.2006/002444-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Phenylacetic acid (PA) degradation in bacteria involves an aerobic hybrid pathway encoded by the paa gene cluster. It is shown here that succinyl-CoA is one of the final products of this pathway in Pseudomonas putida and Escherichia coli. Moreover, in vivo and in vitro studies revealed that the paaE gene encodes the beta-ketoadipyl-CoA thiolase that catalyses the last step of the PA catabolic pathway, i.e. the thiolytic cleavage of beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA. Succinyl-CoA is suggested as a common final product of aerobic hybrid pathways devoted to the catabolism of aromatic compounds.
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Affiliation(s)
- Juan Nogales
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Raffaella Macchi
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Federico Franchi
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Dagania Barzaghi
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Cristina Fernández
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José L García
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Giovanni Bertoni
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Eduardo Díaz
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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E. coli metabolomics: capturing the complexity of a “simple” model. TOPICS IN CURRENT GENETICS 2007. [DOI: 10.1007/4735_2007_0221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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25
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Rengby O, Arnér ESJ. Titration and conditional knockdown of the prfB gene in Escherichia coli: effects on growth and overproduction of the recombinant mammalian selenoprotein thioredoxin reductase. Appl Environ Microbiol 2006; 73:432-41. [PMID: 17085697 PMCID: PMC1796992 DOI: 10.1128/aem.02019-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Release factor 2 (RF2), encoded by the prfB gene in Escherichia coli, catalyzes translational termination at UGA and UAA codons. Termination at UGA competes with selenocysteine (Sec) incorporation at Sec-dedicated UGA codons, and RF2 thereby counteracts expression of selenoproteins. prfB is an essential gene in E. coli and can therefore not be removed in order to increase yield of recombinant selenoproteins. We therefore constructed an E. coli strain with the endogenous chromosomal promoter of prfB replaced with the titratable P(BAD) promoter. Knockdown of prfB expression gave a bacteriostatic effect, while two- to sevenfold overexpression of RF2 resulted in a slightly lowered growth rate in late exponential phase. In a turbidostatic fermentor system the simultaneous impact of prfB knockdown on growth and recombinant selenoprotein expression was subsequently studied, using production of mammalian thioredoxin reductase as model system. This showed that lowering the levels of RF2 correlated directly with increasing Sec incorporation specificity, while also affecting total selenoprotein yield concomitant with a lower growth rate. This study thus demonstrates that expression of prfB can be titrated through targeted exchange of the native promoter with a P(BAD)-promoter and that knockdown of RF2 can result in almost full efficiency of Sec incorporation at the cost of lower total selenoprotein yield.
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Affiliation(s)
- Olle Rengby
- Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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Köstner M, Schmidt B, Bertram R, Hillen W. Generating tetracycline-inducible auxotrophy in Escherichia coli and Salmonella enterica serovar Typhimurium by using an insertion element and a hyperactive transposase. Appl Environ Microbiol 2006; 72:4717-25. [PMID: 16820464 PMCID: PMC1489314 DOI: 10.1128/aem.00492-06] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the construction and application of a novel insertion element for transposase-mediated mutagenesis in gram-negative bacteria. Besides Km(r) as a selectable marker, the insertion element InsTet(G-)1 carries the anhydrotetracycline (atc)-regulated outward-directed PA promoter so that atc-dependent conditional gene knockouts or knockdowns are generated. The complex formed between the purified hyperactive transposase and InsTet(G-)1 was electroporated into Escherichia coli or Salmonella enterica serovar Typhimurium, and mutant pools were collected. We used E. coli strains with either TetR or the reverse variant revTetR(r2), while only TetR was employed in Salmonella. Screening of the InsTet(G-)1 insertion mutant pools revealed 15 atc-regulatable auxotrophic mutants for E. coli and 4 atc-regulatable auxotrophic mutants for Salmonella. We have also screened one Salmonella mutant pool in murine macrophage-like J774-A.1 cells using ampicillin enrichment. Two mutants with the InsTet(G-)1 insertion in the gene pyrE or argA survived this procedure, indicating a reduced intracellular growth rate in J774-A.1 cells. The nature of the mutants and the modes of their regulation are discussed.
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Affiliation(s)
- Martin Köstner
- Lehrstuhl für Mikrobiologie, Friedrich Alexander Universität Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
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Sperandeo P, Pozzi C, Dehò G, Polissi A. Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG–yhbG locus. Res Microbiol 2006; 157:547-58. [PMID: 16765569 DOI: 10.1016/j.resmic.2005.11.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Revised: 11/22/2005] [Accepted: 11/30/2005] [Indexed: 11/27/2022]
Abstract
In Escherichia coli and most Gram-negative bacteria, KDO (3-deoxy-D-manno-octulosonate), a component of the lipopolysaccharide inner core, is essential for outer membrane biogenesis and cell viability. Two recently identified genes involved in KDO biosynthesis, kdsD and kdsC, belong to the yrbG-yhbG locus where four additional ORFs (yrbG, yrbK, yhbN and yhbG) with unknown function are located. We have constructed six conditional expression mutants in which the arabinose-inducible araBp promoter is respectively located upstream of each gene of the locus. Complementation analysis of these mutants indicates that the locus is organized in at least three operons and that the three distal genes (yrbK, yhbN and yhbG) are essential for E. coli viability. Surprisingly, kdsD and kdsC (encoding a D-arabinose 5-phosphate isomerase and a KDO 8-phosphate phosphatase, respectively) were shown to be non-essential, indicating genetic redundancy for these two functions. A preliminary characterization of the arabinose-dependent mutants under permissive conditions and upon depletion revealed increased sensitivity to hydrophobic toxic chemicals, suggesting that the mutants have a defective outer membrane. These genes may thus be implicated in cell envelope integrity.
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Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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Cardona ST, Mueller CL, Valvano MA. Identification of essential operons with a rhamnose-inducible promoter in Burkholderia cenocepacia. Appl Environ Microbiol 2006; 72:2547-55. [PMID: 16597956 PMCID: PMC1448982 DOI: 10.1128/aem.72.4.2547-2555.2006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Scanning of bacterial genomes to identify essential genes is of biological interest, for understanding the basic functions required for life, and of practical interest, for the identification of novel targets for new antimicrobial therapies. In particular, the lack of efficacious antimicrobial treatments for infections caused by the Burkholderia cepacia complex is causing high morbidity and mortality of cystic fibrosis patients and of patients with nosocomial infections. Here, we present a method based on delivery of the tightly regulated rhamnose-inducible promoter P(rhaB) for identifying essential genes and operons in Burkholderia cenocepacia. We demonstrate that different levels of gene expression can be achieved by using two vectors that deliver P(rhaB) at two different distances from the site of insertion. One of these vectors places P(rhaB) at the site of transposon insertion, while the other incorporates the enhanced green fluorescent protein gene (e-gfp) downstream from P(rhaB). This system allows us to identify essential genes and operons in B. cenocepacia and provides a new tool for systematically identifying and functionally characterizing essential genes at the genomic level.
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Affiliation(s)
- Silvia T Cardona
- Department of Microbiology and Immunology, Dental Sciences Building, Room 3014, The University of Western Ontario, London, Ontario, Canada N6A 5C1
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Atkins HS, Dassa E, Walker NJ, Griffin KF, Harland DN, Taylor RR, Duffield ML, Titball RW. The identification and evaluation of ATP binding cassette systems in the intracellular bacterium Francisella tularensis. Res Microbiol 2006; 157:593-604. [PMID: 16503121 DOI: 10.1016/j.resmic.2005.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 11/29/2005] [Accepted: 12/08/2005] [Indexed: 11/22/2022]
Abstract
Francisella tularensis is a facultative intracellular bacterium responsible for the disease tularemia. Analysis of the fully sequenced genome of the virulent F. tularensis strain SCHU S4 has led to the identification of twenty ATP binding cassette (ABC) systems, of which five appear to be non-functional. The fifteen complete systems comprise three importers, five exporters, four systems involved in non-transport processes, and three systems of unknown or ill-defined function. The number and classification of the ABC systems in F. tularensis is similar to that observed in other intracellular bacteria, indicating that some of these systems may be important for the intracellular lifestyle of these organisms. Among the ABC systems identified in the genome are systems that may be involved in the virulence of F. tularensis SCHU S4. Six ABC system proteins were evaluated as candidate vaccine antigens against tularemia, although none provided significant protection against F. tularensis. However, a greater understanding of these systems may lead to the development of countermeasures against F. tularensis.
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Affiliation(s)
- Helen S Atkins
- Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
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