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Wellner SM, Alobaidallah MSA, Fei X, Herrero-Fresno A, Olsen JE. Genome-wide identification of fitness-genes in aminoglycoside-resistant Escherichia coli during antibiotic stress. Sci Rep 2024; 14:4163. [PMID: 38378700 PMCID: PMC10879529 DOI: 10.1038/s41598-024-54169-8] [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: 12/07/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
Resistance against aminoglycosides is widespread in bacteria. This study aimed to identify genes that are important for growth of E. coli during aminoglycoside exposure, since such genes may be targeted to re-sensitize resistant E. coli to treatment. We constructed three transposon mutant libraries each containing > 230.000 mutants in E. coli MG1655 strains harboring streptomycin (aph(3″)-Ib/aph(6)-Id), gentamicin (aac(3)-IV), or neomycin (aph(3″)-Ia) resistance gene(s). Transposon Directed Insertion-site Sequencing (TraDIS), a combination of transposon mutagenesis and high-throughput sequencing, identified 56 genes which were deemed important for growth during streptomycin, 39 during gentamicin and 32 during neomycin exposure. Most of these fitness-genes were membrane-located (n = 55) and involved in either cell division, ATP-synthesis or stress response in the streptomycin and gentamicin exposed libraries, and enterobacterial common antigen biosynthesis or magnesium sensing/transport in the neomycin exposed library. For validation, eight selected fitness-genes/gene-clusters were deleted (minCDE, hflCK, clsA and cpxR associated with streptomycin and gentamicin resistance, and phoPQ, wecA, lpp and pal associated with neomycin resistance), and all mutants were shown to be growth attenuated upon exposure to the corresponding antibiotics. In summary, we identified genes that are advantageous in aminoglycoside-resistant E. coli during antibiotic stress. In addition, we increased the understanding of how aminoglycoside-resistant E. coli respond to antibiotic exposure.
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Affiliation(s)
- Sandra Marina Wellner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Mosaed Saleh A Alobaidallah
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, 21423, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, 22384, Jeddah, Saudi Arabia
| | - Xiao Fei
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Universidade da Santiago de Compostela (USC), Campus Terra, 27002, Lugo, Spain.
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark.
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Alobaidallah MSA, García V, Wellner SM, Thomsen LE, Herrero-Fresno A, Olsen JE. Enhancing the Efficacy of Chloramphenicol Therapy for Escherichia coli by Targeting the Secondary Resistome. Antibiotics (Basel) 2024; 13:73. [PMID: 38247632 PMCID: PMC10812820 DOI: 10.3390/antibiotics13010073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
The increasing prevalence of antimicrobial resistance and the limited availability of new antimicrobial agents have created an urgent need for new approaches to combat these issues. One such approach involves reevaluating the use of old antibiotics to ensure their appropriate usage and maximize their effectiveness, as older antibiotics could help alleviate the burden on newer agents. An example of such an antibiotic is chloramphenicol (CHL), which is rarely used due to its hematological toxicity. In the current study, we employed a previously published transposon mutant library in MG1655/pTF2::blaCTX-M-1, containing over 315,000 unique transposon insertions, to identify the genetic factors that play an important role during growth in the presence of CHL. The list of conditionally essential genes, collectively referred to as the secondary resistome (SR), included 67 genes. To validate our findings, we conducted gene knockout experiments on six genes: arcA, hfq, acrZ, cls, mdfA, and nlpI. Deleting these genes resulted in increased susceptibility to CHL as demonstrated by MIC estimations and growth experiments, suggesting that targeting the products encoded from these genes may reduce the dose of CHL needed for treatment and hence reduce the toxicity associated with CHL treatment. Thus, the gene products are indicated as targets for antibiotic adjuvants to favor the use of CHL in modern medicine.
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Affiliation(s)
- Mosaed Saleh A. Alobaidallah
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (M.S.A.A.); (V.G.); (S.M.W.); (L.E.T.)
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (M.S.A.A.); (V.G.); (S.M.W.); (L.E.T.)
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade da Santiago de Compostela (USC), 27002 Lugo, Spain
| | - Sandra M. Wellner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (M.S.A.A.); (V.G.); (S.M.W.); (L.E.T.)
| | - Line E. Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (M.S.A.A.); (V.G.); (S.M.W.); (L.E.T.)
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (M.S.A.A.); (V.G.); (S.M.W.); (L.E.T.)
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Campus Terra, Universidade da Santiago de Compostela (USC), 27002 Lugo, Spain
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (M.S.A.A.); (V.G.); (S.M.W.); (L.E.T.)
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Rcs Phosphorelay Activation in Cardiolipin-Deficient Escherichia coli Reduces Biofilm Formation. J Bacteriol 2019; 201:JB.00804-18. [PMID: 30782633 DOI: 10.1128/jb.00804-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 02/07/2019] [Indexed: 11/20/2022] Open
Abstract
Biofilm formation is a complex process that requires a number of transcriptional, proteomic, and physiological changes to enable bacterial survival. The lipid membrane presents a barrier to communication between the machinery within bacteria and the physical and chemical features of their extracellular environment, and yet little is known about how the membrane influences biofilm development. We found that depleting the anionic phospholipid cardiolipin reduces biofilm formation in Escherichia coli cells by as much as 50%. The absence of cardiolipin activates the regulation of colanic acid synthesis (Rcs) envelope stress response, which represses the production of flagella, disrupts initial biofilm attachment, and reduces biofilm growth. We demonstrate that a reduction in the concentration of cardiolipin impairs translocation of proteins across the inner membrane, which we hypothesize activates the Rcs pathway through the outer membrane lipoprotein RcsF. Our study demonstrates a molecular connection between the composition of membrane phospholipids and biofilm formation in E. coli and suggests that altering lipid biosynthesis may be a viable approach for altering biofilm formation and possibly other multicellular phenotypes related to bacterial adaptation and survival.IMPORTANCE There is a growing interest in the role of lipid membrane composition in the physiology and adaptation of bacteria. We demonstrate that a reduction in the anionic phospholipid cardiolipin impairs biofilm formation in Escherichia coli cells. Depleting cardiolipin reduced protein translocation across the inner membrane and activated the Rcs envelope stress response. Consequently, cardiolipin depletion produced cells lacking assembled flagella, which impacted their ability to attach to surfaces and seed the earliest stage in biofilm formation. This study provides empirical evidence for the role of anionic phospholipid homeostasis in protein translocation and its effect on biofilm development and highlights modulation of the membrane composition as a potential method of altering bacterial phenotypes related to adaptation and survival.
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Mutations That Enhance the Ciprofloxacin Resistance of Escherichia coli with qnrA1. Antimicrob Agents Chemother 2015; 60:1537-45. [PMID: 26711751 DOI: 10.1128/aac.02167-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/13/2015] [Indexed: 01/20/2023] Open
Abstract
Plasmid-mediated qnr genes provide only a modest decrease in quinolone susceptibility but facilitate the selection of higher-level resistance. In Escherichia coli strain J53 without qnr, ciprofloxacin resistance often involves mutations in the GyrA subunit of DNA gyrase. Mutations in gyrA were absent, however, when 43 mutants with decreased ciprofloxacin susceptibility were selected from J53(pMG252) with qnrA1. Instead, in 13 mutants, individual and whole-genome sequencing identified mutations in marR and soxR associated with increased expression of marA and soxS and, through them, increased expression of the AcrAB pump, which effluxes quinolones. Nine mutants had increased expression of the MdtE efflux pump, and six demonstrated increased expression of the ydhE pump gene. Many efflux mutants also had increased resistance to novobiocin, another pump substrate, but other mutants were novobiocin hypersusceptible. Mutations in rfaD and rfaE in the pathway for inner core lipopolysaccharide (LPS) biosynthesis were identified in five such strains. Many of the pump and LPS mutants had decreased expression of OmpF, the major porin channel for ciprofloxacin entry. Three mutants had increased expression of qnrA that persisted when pMG252 from these strains was outcrossed. gyrA mutations were also rare when mutants with decreased ciprofloxacin susceptibility were selected from E. coli J53 with aac(6')-Ib-cr or qepA. We suggest that multiple genes conferring low-level resistance contribute to enhanced ciprofloxacin resistance selected from an E. coli strain carrying qnrA1, aac(6')-Ib-cr, or qepA because these determinants decrease the effective ciprofloxacin concentration and allow more common but lower-resistance mutations than those in gyrA to predominate.
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Abstract
The pathways in Escherichia coli and (largely by analogy) S. enterica remain the paradigm of bacterial lipid synthetic pathways, although recently considerable diversity among bacteria in the specific areas of lipid synthesis has been demonstrated. The structural biology of the fatty acid synthetic proteins is essentially complete. However, the membrane-bound enzymes of phospholipid synthesis remain recalcitrant to structural analyses. Recent advances in genetic technology have allowed the essentialgenes of lipid synthesis to be tested with rigor, and as expected most genes are essential under standard growth conditions. Conditionally lethal mutants are available in numerous genes, which facilitates physiological analyses. The array of genetic constructs facilitates analysis of the functions of genes from other organisms. Advances in mass spectroscopy have allowed very accurate and detailed analyses of lipid compositions as well as detection of the interactions of lipid biosynthetic proteins with one another and with proteins outside the lipid pathway. The combination of these advances has resulted in use of E. coli and S. enterica for discovery of new antimicrobials targeted to lipid synthesis and in deciphering the molecular actions of known antimicrobials. Finally,roles for bacterial fatty acids other than as membrane lipid structural components have been uncovered. For example, fatty acid synthesis plays major roles in the synthesis of the essential enzyme cofactors, biotin and lipoic acid. Although other roles for bacterial fatty acids, such as synthesis of acyl-homoserine quorum-sensing molecules, are not native to E. coli introduction of the relevant gene(s) synthesis of these foreign molecules readily proceeds and the sophisticated tools available can used to decipher the mechanisms of synthesis of these molecules.
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An artificial pathway to 3,4-dihydroxybenzoic acid allows generation of new aminocoumarin antibiotic recognized by catechol transporters of E. coli. ACTA ACUST UNITED AC 2011; 18:304-13. [PMID: 21439475 DOI: 10.1016/j.chembiol.2010.12.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/01/2010] [Accepted: 12/02/2010] [Indexed: 11/22/2022]
Abstract
An artificial operon was synthesized, consisting of the genes for chorismate pyruvate-lyase of E. coli and for 4-hydroxybenzoate 3-hydroxylase of Corynebacterium cyclohexanicum. This operon, directing the biosynthesis of 3,4-dihdroxybenzoate, was expressed in the heterologous expression host Streptomyces coelicolor M512, together with a modified biosynthetic gene cluster for the aminocoumarin antibiotic clorobiocin. The resulting strain produced a clorobiocin derivative containing a 3,4-dihdroxybenzoyl moiety. Its structure was confirmed by MS and NMR analysis, and it was found to be a potent inhibitor of the gyrases from Escherichia coli and Staphylococcus aureus. Bioassays against different E. coli mutants suggested that this compound is actively imported by catechol siderophore transporters in the cell envelope. This study provides an example of the structure of a natural product that can be rationally modified by synthetic biology.
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Quigley BR, Tropp BE. E. coli cardiolipin synthase: function of N-terminal conserved residues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2107-13. [PMID: 19341704 DOI: 10.1016/j.bbamem.2009.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 02/24/2009] [Accepted: 03/20/2009] [Indexed: 11/17/2022]
Abstract
The E. coli cls open reading frame (ORF) predicts a 54.8 kDa polypeptide, whereas mature cardiolipin (CL) synthase is 46 kDa. The N-terminal region extending to residue 60 contains several conserved residues but is not essential for enzyme activity. A deletion mutant that is missing residues 2-60 produces a fully active protein. These findings raise the question of why several residues in a region that is not required for enzyme activity are conserved. Recombinant DNA technology was used to introduce an EYMPE epitope (EE) tag into the interior of CL synthase. The EE tagged polypeptide retained the biological properties of wild type CL synthase, including full enzymatic activity. Site-directed mutagenesis was used to alter conserved residues in the N-terminal region. An EE tagged CL synthase in which Leu-7 and Val-8 were both replaced by Ser residues retains in vitro activity but loses most of its in vivo activity. Furthermore, the mutant protein has a higher apparent molecular mass than its parent protein. Taken together, these findings suggest that conserved residues L7 and V8 play a role in polypeptide processing, topology, or both.
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Affiliation(s)
- Bernard R Quigley
- The Graduate Center, City University of New York, New York, NY 10016, USA
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9
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Abstract
Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.
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Affiliation(s)
- Athanasios Lykidis
- Genome Biology Program, DOE-Joint Genome Institute, Walnut Creek, CA 94598, USA.
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10
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O'Connell CM, Nicks KM. A plasmid-cured Chlamydia muridarum strain displays altered plaque morphology and reduced infectivity in cell culture. MICROBIOLOGY-SGM 2006; 152:1601-1607. [PMID: 16735724 DOI: 10.1099/mic.0.28658-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A highly conserved cryptic plasmid is present in Chlamydia trachomatis yet naturally occurring plasmid-deficient isolates are very rare. This paper describes the isolation and characterization of a plasmid-deficient strain of C. muridarum, using novobiocin as a curing agent. Plasmid-deficient derivatives of C. muridarum strain Nigg were generated at high efficiencies (4-30%). Phenotypic characterization revealed that the cured derivative was unable to accumulate glycogen within intracytoplasmic inclusions. In addition, this strain formed small plaques at a reduced efficiency compared to the wild-type parent.
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Affiliation(s)
- Catherine M O'Connell
- Department of Microbiology and Immunology, UAMS, 4301 West Markham, Little Rock, AR 72205, USA
| | - Kristy M Nicks
- Department of Microbiology and Immunology, UAMS, 4301 West Markham, Little Rock, AR 72205, USA
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11
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Tsatskis Y, Khambati J, Dobson M, Bogdanov M, Dowhan W, Wood JM. The osmotic activation of transporter ProP is tuned by both its C-terminal coiled-coil and osmotically induced changes in phospholipid composition. J Biol Chem 2005; 280:41387-94. [PMID: 16239220 DOI: 10.1074/jbc.m508362200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transporter ProP of Escherichia coli (ProPEc) senses extracellular osmolality and mediates osmoprotectant uptake when it is rising or high. A replica of the ProPEc C terminus (Asp468-Arg497) forms an intermolecular alpha-helical coiled-coil. This structure is implicated in the osmoregulation of intact ProPEc, in vivo. Like that from Corynebacterium glutamicum (ProPCg), the ProP orthologue from Agrobacterium tumefaciens (ProPAt) sensed and responded to extracellular osmolality after expression in E. coli. The osmotic activation profiles of all three orthologues depended on the osmolality of the bacterial growth medium, the osmolality required for activation rising as the growth osmolality approached 0.7 mol/kg. Thus, each could undergo osmotic adaptation. The proportion of cardiolipin in a polar lipid extract from E. coli increased with extracellular osmolality so that the osmolality activating ProPEc was a direct function of membrane cardiolipin content. Group A ProP orthologues (ProPEc, ProPAt) share the C-terminal coiled-coil domain and were activated at low osmolalities. Like variant ProPEc-R488I, in which the C-terminal coiled-coil is disrupted, ProPEc derivatives that lack the coiled-coil and Group B orthologue ProPCg required a higher osmolality to activate. The amplitude of ProPEc activation was reduced 10-fold in its deletion derivatives. The coiled-coil structure is not essential for osmotic activation of ProP per se. However, it tunes Group A orthologues to osmoregulate over a low osmolality range. Coiled-coil lesions may impair both coiled-coil formation and interaction of ProPEc with amplifier protein ProQ. Cardiolipin may contribute to ProP adaptation by altering bulk membrane properties or by acting as a ProP ligand.
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Affiliation(s)
- Yonit Tsatskis
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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12
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Bogdanov M, Zhang W, Xie J, Dowhan W. Transmembrane protein topology mapping by the substituted cysteine accessibility method (SCAM(TM)): application to lipid-specific membrane protein topogenesis. Methods 2005; 36:148-71. [PMID: 15894490 PMCID: PMC4104023 DOI: 10.1016/j.ymeth.2004.11.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 11/15/2004] [Accepted: 11/15/2004] [Indexed: 01/03/2023] Open
Abstract
We provide an overview of lipid-dependent polytopic membrane protein topogenesis, with particular emphasis on Escherichia coli strains genetically altered in their lipid composition and strategies for experimentally determining the transmembrane organization of proteins. A variety of reagents and experimental strategies are described including the use of lipid mutants and thiol-specific chemical reagents to study lipid-dependent and host-specific membrane protein topogenesis by substituted cysteine site-directed chemical labeling. Employing strains in which lipid composition can be controlled temporally during membrane protein synthesis and assembly provides a means to observe dynamic changes in protein topology as a function of membrane lipid composition.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas-Houston, Medical School, Houston, TX 77030, USA
| | - Wei Zhang
- Department of Biochemistry and Molecular Biology, University of Texas-Houston, Medical School, Houston, TX 77030, USA
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, University of Texas-Houston, Medical School, Houston, TX 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas-Houston, Medical School, Houston, TX 77030, USA
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Zhong S, Khodursky A, Dykhuizen DE, Dean AM. Evolutionary genomics of ecological specialization. Proc Natl Acad Sci U S A 2004; 101:11719-24. [PMID: 15289609 PMCID: PMC511043 DOI: 10.1073/pnas.0404397101] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Indexed: 11/18/2022] Open
Abstract
We used a combination of genomic techniques to monitor chromosomal evolution across hundreds of generations as Escherichia coli adapted to growth-limiting concentrations of either lactulose, methyl-galactoside, or a 72:28 mixture of the two. DNA microarrays identified 8 unique duplications and 16 unique deletions among 42 evolvants from 23 chemostat experiments. Each mutation was confirmed by sequencing PCR-amplified flanking genomic DNA and, except for one deletion, an insertion sequence was found at the break point. vPCR of insertion sequences identified these same mutations and 16 additional insertions (all confirmed by sequencing). The pattern of genomic evolution is highly reproducible. Statistical analyses show that duplications at lac and mutations in mgl are adaptations specific to lactulose and to methyl-galactoside, respectively. Adaptation to mixed sugars is characterized by similar mutations, but lac duplications and mgl mutations usually arise in different backgrounds, producing ecological specialists for each sugar. This suggests that an antagonistic pleiotropic tradeoff between duplications at lac and mutations in mgl retards the evolution of generalists. Other mutations that repeatedly appear in replicate experiments are adaptations to the chemostat environment and are not specific to one or the other sugar.
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Affiliation(s)
- Shaobin Zhong
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
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Abstract
Phospholipids play multiple roles in bacterial cells. These are the establishment of the permeability barrier, provision of the environment for many enzyme and transporter proteins, and they influence membrane-related processes such as protein export and DNA replication. The lipid synthetic pathway also provides precursors for protein modification and for the synthesis of other molecules. This review concentrates on the phospholipid synthetic pathway and discusses recent data on the synthesis and function of phospholipids mainly in the bacterium Escherichia coli.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801, USA.
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15
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Cooper VS. Long-term experimental evolution in Escherichia coli. X. Quantifying the fundamental and realized niche. BMC Evol Biol 2002; 2:12. [PMID: 12199912 PMCID: PMC122090 DOI: 10.1186/1471-2148-2-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2002] [Accepted: 08/22/2002] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Twelve populations of the bacterium, Escherichia coli, adapted to a simple, glucose-limited, laboratory environment over 10,000 generations. As a consequence, these populations tended to lose functionality on alternative resources. I examined whether these populations in turn became inferior competitors in four alternative environments. These experiments are among the first to quantify and compare dimensions of the fundamental and realized niches. RESULTS Three clones were isolated from each of the twelve populations after 10,000 generations of evolution. Direct competition between these clones and the ancestor in the selective environment revealed average fitness improvements of approximately 50%. When grown in the wells of Biolog plates, however, evolved clones grew 25% worse on average than the ancestor on a variety of different carbon sources. Next, I competed each evolved population versus the ancestor in four foreign environments (10-fold higher and lower glucose concentration, added bile salts, and dilute LB media). Surprisingly, nearly all populations were more fit than the ancestor in each foreign environment, though the margin of improvement was least in the most different environment. Most populations also evolved increased sensitivity to novobiocin. CONCLUSIONS Reduced functionality on numerous carbon sources suggested that the fundamental niche of twelve E. coli populations had narrowed after adapting to a specific laboratory environment. However, in spite of these results, the same populations were competitively superior in four novel environments. These findings suggest that adaptation to certain dimensions of the environment may compensate for other functional losses and apparently enhance the realized niche.
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Affiliation(s)
- Vaughn S Cooper
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Ungar D, Barth A, Haase W, Kaunzinger A, Lewitzki E, Ruiz T, Reiländer H, Michel H. Analysis of a putative voltage-gated prokaryotic potassium channel. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5386-96. [PMID: 11606201 DOI: 10.1046/j.0014-2956.2001.02477.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Most of the completely sequenced prokaryotic genomes contain genes of potassium channel homologues, but there is still not much known about the role of these proteins in prokaryotes. Here we describe the large-scale overproduction and purification of a prokaryotic voltage-gated potassium channel homologue, Kch, from Escherichia coli. After successful overproduction of the protein, a specific increase in the potassium permeability of the cells was found. Kch could be purified in large amounts using classical purification methods to prevent aggregation of the protein. The physiological state of the protein was revealed to be a homotetramer and the protein was shown to be localized to the cytoplasmic membrane of the cells. In the course of the localization studies, we found a specific increase in the density of the cytoplasmic membrane on Kch production. This was linked to the observed increase in the protein to lipid ratio in the membranes. Another observed change in the membrane composition was an increase in the cardiolipin to phosphatidylglycerol ratio, which may indicate a specific cardiolipin requirement of Kch. On the basis of some of our results, we discuss a function for Kch in the maintenance of the membrane potential in E. coli.
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Affiliation(s)
- D Ungar
- Department of Molecular Membrane Biology, Max-Planck-Institute of Biophysics, Frankfurt/Main, Germany
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17
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Affiliation(s)
- M Schlame
- Department of Anesthesiology, Hospital for Special Surgery, Cornell University Medical College, 555 E. 70th St., New York, NY 10021, USA
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18
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Guo D, Tropp BE. A second Escherichia coli protein with CL synthase activity. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1483:263-74. [PMID: 10634942 DOI: 10.1016/s1388-1981(99)00193-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Escherichia coli open reading frame f413, which has the potential to code for a polypeptide homologous to cardiolipin (CL) synthase, has been cloned. Its polypeptide product has a molecular mass of 48 kDa, is membrane-bound, and catalyzes CL formation but does not hydrolyze CL. A comparison of the sequences predicted for the polypeptides encoded by f413 and cls indicates that the N-terminal residues specified by cls may be unnecessary for CL synthase activity. Construction of a truncated cls gene and characterization of its polypeptide product have confirmed this conclusion.
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Affiliation(s)
- D Guo
- Queens College CUNY, Department of Chemistry and Biochemistry, 65-30 Kissena Boulevard, Flushing, NY 11367, USA
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Jovanovic M, Lilic M, Janjusevic R, Jovanovic G, Savic DJ, Milija J. tRNA synthetase mutants of Escherichia coli K-12 are resistant to the gyrase inhibitor novobiocin. J Bacteriol 1999; 181:2979-83. [PMID: 10217798 PMCID: PMC93749 DOI: 10.1128/jb.181.9.2979-2983.1999] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In previous studies we demonstrated that mutations in the genes cysB, cysE, and cls (nov) affect resistance of Escherichia coli to novobiocin (J. Rakonjac, M. Milic, and D. J. Savic, Mol. Gen. Genet. 228:307-311, 1991; R. Ivanisevic, M. Milic, D. Ajdic, J. Rakonjac, and D. J. Savic, J. Bacteriol. 177:1766-1771, 1995). In this work we expand this list with mutations in rpoN (the gene for RNA polymerase subunit sigma54) and the tRNA synthetase genes alaS, argS, ileS, and leuS. Similarly to resistance to the penicillin antibiotic mecillinam, resistance to novobiocin of tRNA synthetase mutants appears to depend upon the RelA-mediated stringent response. However, at this point the overlapping pathways of mecillinam and novobiocin resistance diverge. Under conditions of stringent response induction, either by the presence of tRNA synthetase mutations or by constitutive production of RelA protein, inactivation of the cls gene diminishes resistance to novobiocin but not to mecillinam.
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Affiliation(s)
- M Jovanovic
- Institute of Molecular Genetics and Genetic Engineering, 11001 Belgrade, Yugoslavia
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Rudolph AE, Stuckey JA, Zhao Y, Matthews HR, Patton WA, Moss J, Dixon JE. Expression, characterization, and mutagenesis of the Yersinia pestis murine toxin, a phospholipase D superfamily member. J Biol Chem 1999; 274:11824-31. [PMID: 10207000 DOI: 10.1074/jbc.274.17.11824] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A phospholipase D (PLD) superfamily was recently identified that contains proteins of highly diverse functions with the conserved motif HXKX4DX6G(G/S). The superfamily includes a bacterial nuclease, human and plant PLD enzymes, cardiolipin synthases, phosphatidylserine synthases, and the murine toxin from Yersinia pestis (Ymt). Ymt is particularly effective as a prototype for family members containing two conserved motifs, because it is smaller than many other two-domain superfamily enzymes, and it can be overexpressed. Large quantities of pure recombinant Ymt allowed the formation of diffraction-quality crystals for x-ray structure determination. Dimeric Ymt was shown to have PLD-like activity as demonstrated by the hydrolysis of phosphatidylcholine. Ymt also used bis(para-nitrophenol) phosphate as a substrate. Using these substrates, the amino acids essential for Ymt function were determined. Specifically, substitution of histidine or lysine in the conserved motifs reduced the turnover rate of bis(para-nitrophenol) phosphate by a factor of 10(4) and phospholipid turnover to an undetectable level. The role of the conserved residues in catalysis was further defined by the isolation of a radiolabeled phosphoenzyme intermediate, which identified a conserved histidine residue as the nucleophile in the catalytic reaction. Based on these data, a unifying two-step catalytic mechanism is proposed for this diverse family of enzymes.
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Affiliation(s)
- A E Rudolph
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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21
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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Chang SC, Heacock PN, Mileykovskaya E, Voelker DR, Dowhan W. Isolation and characterization of the gene (CLS1) encoding cardiolipin synthase in Saccharomyces cerevisiae. J Biol Chem 1998; 273:14933-41. [PMID: 9614098 DOI: 10.1074/jbc.273.24.14933] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In eukaryotic cells, cardiolipin (CL) synthase catalyzes the final step in the synthesis of CL from phosphatidylglycerol and CDP-diacylglycerol. CL and its synthesis are localized predominantly to the mitochondrial inner membrane, and CL is generally thought to be an essential component of many mitochondrial processes. By using homology searches for genes potentially encoding phospholipid biosynthetic enzymes, we have cloned the gene (CLS1) encoding CL synthase in Saccharomyces cerevisiae. Overexpression of the CLS1 gene under its endogenous promoter or the inducible GAL1 promoter in yeast and expression of CLS1 in baculovirus-infected insect cells resulted in elevated CL synthase activity. Disruption of the CLS1 gene in a haploid yeast strain resulted in the loss of CL synthase activity, no detectable CL, a 5-fold elevation in phosphatidylglycerol levels, and lack of staining of mitochondria by a dye with high affinity for CL. The cls1::TRP1 null mutant grew on both fermentable and non-fermentable carbon sources but more poorly on the latter. The level and activity of cytochrome c oxidase was normal, and a dye whose accumulation is dependent on membrane proton electrochemical potential effectively stained the mitochondria. These results definitively identify the gene encoding the CL synthase of yeast.
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Affiliation(s)
- S C Chang
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77225, USA
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Guo D, Tropp BE. Cloning of the Bacillus firmus OF4 cls gene and characterization of its gene product. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1389:34-42. [PMID: 9443601 DOI: 10.1016/s0005-2760(97)00086-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The gene that codes for cardiolipin (CL) synthase and an adjacent gene that codes for a MecA homolog in the alkaliphilic bacteria Bacillus firmus OF4 have been cloned and sequenced (GenBank accession number U88888). The cls gene contains 1509 nucleotides, corresponding to a polypeptide of 57.9 kDa. The predicted amino acid sequence has 129 identities and 100 similarities with the Escherichia coli CL synthase. Homologies were also noted with polypeptide sequences from putative cls genes from Bacillus subtilis and Pseudomonas putida. Conserved histidine, tyrosine, and serine residues may be part of the active site and participate in phosphatidyl group transfer. The B. firmus OF4 cls gene product was inserted into plasmid pET3 to form a recombinant plasmid pDG2, which overproduces CL synthase in E. coli. A membrane fraction containing the overproduced enzyme converts phosphatidylglycerol to CL and glycerol. The B. firmus enzyme is stimulated by potassium phosphate, inhibited by CL and phosphatidate, and has a slightly higher pH optimum than the E. coli enzyme.
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Affiliation(s)
- D Guo
- Queens College CUNY, Department of Chemistry and Biochemistry, Flushing, NY 11367, USA
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Abstract
Escherichia coli cardiolipin synthase catalyzes reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) and glycerol. The enzyme is specified by the cls gene, located at min 28.02 of the E. coli genetic map. Cells with mutations in cls have longer doubling times, tend to lose viability in the stationary phase, are more resistant to 3,4-dihydroxybutyl-1-phosphonate, and have an altered sensitivity to novobiocin. Although cls null mutants appear to lack CL synthase activity, they are still able to form trace quantities of CL. The enzyme appears to be regulated at both the genetic and enzymatic levels. CL synthase's molecular mass is 45-46 kDa, or about 8 kDa less than the polypeptide predicted by the gene sequence, suggesting that posttranslational processing occurs. CL synthase can use various polyols such as mannitol and arabitol to convert CL to the corresponding phosphatidylglycerol analog. When the amino acid sequences of four bacterial CL synthases are compared, three highly conserved regions are apparent. One of these regions contains a conserved pentapeptide sequence, RN(Q)HRK, and another has a conserved HXK sequence. These two sequences may be part of the active site. E. coli CL synthase has been studied by using a mixed micelle assay. The enzyme is inhibited by CL, the product of the reaction, and by phosphatidate. Phosphatidylethanolamine partially offsets inhibition caused by CL but not by phosphatidate. CDP-diacylglycerol does not appear to affect the activity of the purified enzyme but does stimulate the activity associated with crude membrane preparations.
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Affiliation(s)
- B E Tropp
- Queens College CUNY, Department of Chemistry and Biochemistry, Flushing, NY 11367, USA. btr$
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25
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Koonin EV. A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins. Trends Biochem Sci 1996. [DOI: 10.1016/s0968-0004(96)30024-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ponting CP, Kerr ID. A novel family of phospholipase D homologues that includes phospholipid synthases and putative endonucleases: identification of duplicated repeats and potential active site residues. Protein Sci 1996; 5:914-22. [PMID: 8732763 PMCID: PMC2143407 DOI: 10.1002/pro.5560050513] [Citation(s) in RCA: 259] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phosphatidylcholine-specific phospholipase D (PLD) enzymes catalyze hydrolysis of phospholipid phosphodiester bonds, and also transphosphatidylation of phospholipids to acceptor alcohols. Bacterial and plant PLD enzymes have not been shown previously to be homologues or to be homologous to any other protein. Here we show, using sequence analysis methods, that bacterial and plant PLDs show significant sequence similarities both to each other, and to two other classes of phospholipid-specific enzymes, bacterial cardiolipin synthases, and eukaryotic and bacterial phosphatidylserine synthases, indicating that these enzymes form an homologous family. This family is suggested also to include two Poxviridae proteins of unknown function (p37K and protein K4), a bacterial endonuclease (nuc), an Escherichia coli putative protein (o338) containing an N-terminal domain showing similarities with helicase motifs V and VI, and a Synechocystis sp. putative protein with a C-terminal domain likely to possess a DNA-binding function. Surprisingly, four regions of sequence similarity that occur once in nuc and o338, appear twice in all other homologues, indicating that the latter molecules are bi-lobed, having evolved from an ancestor or ancestors that underwent a gene duplication and fusion event. It is suggested that, for each of these enzymes, conserved histidine, lysine, aspartic acid, and/or asparagine residues may be involved in a two-step ping pong mechanism involving an enzyme-substrate intermediate.
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Affiliation(s)
- C P Ponting
- Fibrinolysis Research Unit, University of Oxford, United Kingdom.
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Lee S, Robb J, Nazar R. Truncated phenylalanine ammonia-lyase expression in tomato (Lycopersicon esculentum). J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)49773-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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