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Zimoń B, Psujek M, Matczak J, Guziński A, Wójcik E, Dastych J. Novel multiplex-PCR test for Escherichia coli detection. Microbiol Spectr 2024; 12:e0377323. [PMID: 38687052 PMCID: PMC11237426 DOI: 10.1128/spectrum.03773-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Escherichia coli is a diverse and ubiquitous strain of both commensal and pathogenic bacteria. In this study, we propose the use of multiplex polymerase chain reaction (PCR), using amplification of three genes (cydA, lacY, and ydiV), as a method for determining the affiliation of the tested strains to the E. coli species. The novelty of the method lies in the small number of steps needed to perform the diagnosis and, consequently, in the small amount of time needed to obtain it. This method, like any other, has some limitations, but its advantage is fast, cheap, and reliable identification of the presence of E. coli. Sequences of the indicated genes from 1,171 complete E. coli genomes in the NCBI database were used to prepare the primers. The developed multiplex PCR was tested on 47,370 different Enterobacteriaceae genomes using in silico PCR. The sensitivity and specificity of the developed test were 95.76% and 99.49%, respectively. Wet laboratory analyses confirmed the high specificity, repeatability, reproducibility, and reliability of the proposed test. Because of the detection of three genes, this method is very cost and labor-effective, yet still highly accurate, specific, and sensitive in comparison to similar methods. IMPORTANCE Detection of E. coli from environmental or clinical samples is important due to the common occurrence of this species of bacteria in all human and animal environments. As commonly known, these bacteria strains can be commensal and pathogenic, causing numerous infections of clinical importance, including infections of the digestive system, urinary, respiratory, and even meninges, particularly dangerous for newborns. The developed multiplex polymerase chain reaction test, confirming the presence of E. coli in samples, can be used in many laboratories. The test provides new opportunities for quick and cheap analyses, detecting E. coli using only three pairs of primers (analysis of the presence of three genes) responsible for metabolism and distinguishing E. coli from other pathogens from the Enterobacteriaceae family. Compared to other tests previously described in the literature, our method is characterized by high specificity and sensitivity.
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Affiliation(s)
- Bogumił Zimoń
- Bioinformatics and Genetics Department, Proteon Pharmaceuticals, Lodz, Lodzkie, Poland
| | - Michał Psujek
- Diagnostics and Monitoring Department, Proteon Pharmaceuticals, Lodz, Lodzkie, Poland
| | - Justyna Matczak
- Diagnostics and Monitoring Department, Proteon Pharmaceuticals, Lodz, Lodzkie, Poland
| | - Arkadiusz Guziński
- Bioinformatics and Genetics Department, Proteon Pharmaceuticals, Lodz, Lodzkie, Poland
| | - Ewelina Wójcik
- Proteon Pharmaceuticals, Supervisor, Lodz, Lodzkie, Poland
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2
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Azis K, Zerva I, Melidis P, Caceres C, Bourtzis K, Ntougias S. Biochemical and nutritional characterization of the medfly gut symbiont Enterobacter sp. AA26 for its use as probiotics in sterile insect technique applications. BMC Biotechnol 2019; 19:90. [PMID: 31847833 PMCID: PMC6918548 DOI: 10.1186/s12896-019-0584-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Enterobacter sp. AA26 was recently isolated from the midgut of Ceratitis capitata (Wiedemann) and it was shown to have positive effects in rearing efficiency when used as larval probiotics. In this study, biomass production was carried out in bench-scale bioreactors to elucidate the biokinetic properties of Enterobacter sp. AA26 and its nutritional value. Results Strain AA26 is a psychrotolerant, halotolerant, facultatively anaerobic bacterium with broad pH range for growth (pH 4 to 10.2), which possessed the typical biochemical profile of Enterobacter spp. The specific oxygen uptake rate (SOUR) was calculated as 63.2 ± 1.26 and 121 ± 1.73 mg O2 g− 1 VSS h− 1, with the yield coefficients in acetate and glucose being equal to 0.62 ± 0.03 and 0.67 ± 0.003 g biomass produced/g substrate consumed, respectively. The maximum specific growth rate (μmax) of strain AA26 grown in fill-and-draw bioreactors at 20 °C and 35 °C was 0.035 and 0.069 h− 1, respectively. Strain AA26 grew effectively in agro-industrial wastewaters, i.e. cheese whey wastewater (CWW), as alternative substrate for replacing yeast-based media. Biomass of strain AA26 could provide all the essential amino acids and vitamins for the artificial rearing of C. capitata. Greater intracellular α- and β-glucosidase activities were observed during growth of strain AA26 in CWW than in yeast-based substrate, although the opposite pattern was observed for the respective extracellular activities (p < 0.01). Low protease activity was exhibited in cells grown in yeast-based medium, while no lipase activities were detected. Conclusions The ability of strain AA26 to grow in agro-industrial wastes and to provide all the essential nutrients can minimize the cost of commercial media used for mass rearing and large scale sterile insect technique applications.
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Affiliation(s)
- Konstantinos Azis
- Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, 67100, Xanthi, Greece
| | - Ioanna Zerva
- Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, 67100, Xanthi, Greece
| | - Paraschos Melidis
- Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, 67100, Xanthi, Greece
| | - Carlos Caceres
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, A-1400, Vienna, Austria
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, A-1400, Vienna, Austria
| | - Spyridon Ntougias
- Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, 67100, Xanthi, Greece.
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Evidence for the transport of maltose by the sucrose permease, CscB, of Escherichia coli. J Membr Biol 2009; 228:79-88. [PMID: 19294451 DOI: 10.1007/s00232-009-9161-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 02/16/2009] [Indexed: 10/21/2022]
Abstract
The purpose of this study was to examine the sugar recognition and transport properties of the sucrose permease (CscB), a secondary active transporter from Escherichia coli. We tested the hypothesis that maltose transport is conferred by the wild-type CscB transporter. Cells of E. coli HS4006 harboring pSP72/cscB were red on maltose MacConkey agar indicator plates. We were able to measure "downhill" maltose transport and establish definitive kinetic behavior for maltose entry in such cells. Maltose was an effective competitor of sucrose transport in cells with CscB, suggesting that the respective maltose and sucrose binding sites and translocation pathways through the CscB channel overlap. Accumulation ("uphill" transport) of maltose by cells with CscB was profound, demonstrating active transport of maltose by CscB. Sequencing of cscB encoded on plasmid pSP72/cscB used in cells for transport studies indicate an unaltered primary CscB structure, ruling out the possibility that mutation conferred maltose transport by CscB. We conclude that maltose is a bona fide substrate for the sucrose permease of E. coli. Thus, future studies of sugar binding, transport, and permease structure should consider maltose, as well as sucrose.
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Tavoulari S, Frillingos S. Substrate Selectivity of the Melibiose Permease (MelY) from Enterobacter cloacae. J Mol Biol 2008; 376:681-93. [DOI: 10.1016/j.jmb.2007.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Revised: 12/01/2007] [Accepted: 12/07/2007] [Indexed: 10/22/2022]
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5
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Amino acids that confer transport of raffinose and maltose sugars in the raffinose permease (RafB) of Escherichia coli as implicated by spontaneous mutations at Val-35, Ser-138, Ser-139, Gly-389 and Ile-391. J Membr Biol 2007; 220:87-95. [PMID: 18008022 DOI: 10.1007/s00232-007-9077-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 10/01/2007] [Indexed: 10/22/2022]
Abstract
In order to identify amino acid residues in the Escherichia coli raffinose-H(+) permease (RafB) that play a role in sugar selection and transport, we first incubated E. coli HS4006 containing plasmid pRU600 (expresses inducible raffinose permease and alpha-galactosidase) on maltose MacConkey indicator plates overnight. Initially, all colonies were white, indicating no fermentation of maltose. Upon further incubation, 100 mutants appeared red. pRU600 DNA was prepared from 55 mutants. Five mutants transferred the phenotype for fermentation of maltose (red). Plasmid DNA from five maltose-positive phenotype transformants was prepared and sequenced, revealing three distinct types of mutations. Two mutants exhibited Val-35-->Ala (MT1); one mutant had Ile-391-->Ser (MT2); and two mutants had Ser-138-->Asp, Ser-139-->Leu and Gly-389-->Ala (MT3). Transport studies of [(3)H]-maltose showed that cells harboring MT1, MT2 and MT3 had greater uptake (P <or= 0.05) than cells harboring wild-type RafB. However, [(14)C]-raffinose uptake was reduced in all mutant cells (P <or= 0.05) with MT1, MT2 and MT3 mutants compared to cells harboring wild-type RafB. Kinetic analysis showed enhanced apparent K (m) values for maltose and reduced V (max)/ K (m) ratios for raffinose compared to wild-type values. The apparent K (i) value of maltose for RafB indicates a competitive relationship between maltose and raffinose. Maltose "uphill" accumulation was greater for mutants (P <or= 0.05) than for cells with wild-type RafB. Thus, we implicate residues in RafB that are responsible for raffinose transport and suggest that the substituted residues in RafB dictate structures that enhance transport of maltose.
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6
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Shinnick SG, Perez SA, Varela MF. Altered substrate selection of the melibiose transporter (MelY) of Enterobacter cloacae involving point mutations in Leu-88, Leu-91, and Ala-182 that confer enhanced maltose transport. J Bacteriol 2003; 185:3672-7. [PMID: 12775706 PMCID: PMC156228 DOI: 10.1128/jb.185.12.3672-3677.2003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated mutants of Escherichia coli HS4006 containing the melibiose-H(+) symporter (MelY) from Enterobacter cloacae that had enhanced fermentation on 1% maltose MacConkey plates. DNA sequencing revealed three site classes of mutations: L-88-P, L-91-P, and A-182-P. The mutants L-88-P and L-91-P had 3.6- and 5.1-fold greater maltose uptake than the wild type and enhanced apparent affinities for maltose. Energy-coupled transport was defective for melibiose accumulation, but detectable maltose accumulation for the mutants indicated that active transport is dependent upon the substrate transported through the carrier. We conclude that the residues Leu-88, Leu-91 (transmembrane segment 3 [TMS-3]), and Ala-182 (TMS-6) of MelY mediate sugar selection. These data represent the first MelY mutations that confer changes in sugar selection.
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Affiliation(s)
- Steven G Shinnick
- Department of Biology, Eastern New Mexico University, Portales, New Mexico 88130, USA
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7
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Frillingos S, Sahin-Tóth M, Wu J, Kaback HR. Cys-scanning mutagenesis: a novel approach to structure function relationships in polytopic membrane proteins. FASEB J 1998; 12:1281-99. [PMID: 9761772 DOI: 10.1096/fasebj.12.13.1281] [Citation(s) in RCA: 311] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The entire lactose permease of Escherichia coli, a polytopic membrane transport protein that catalyzes beta-galactoside/H+ symport, has been subjected to Cys-scanning mutagenesis in order to determine which residues play an obligatory role in the mechanism and to create a library of mutants with a single-Cys residue at each position of the molecule for structure/function studies. Analysis of the mutants has led to the following: 1) only six amino acid side chains play an irreplaceable role in the transport mechanism; 2) positions where the reactivity of the Cys replacement is increased upon ligand binding are identified; 3) positions where the reactivity of the Cys replacement is decreased by ligand binding are identified; 4) helix packing, helix tilt, and ligand-induced conformational changes are determined by using the library of mutants in conjunction with a battery of site-directed techniques; 5) the permease is a highly flexible molecule; and 6) a working model that explains coupling between beta-galactoside and H+ translocation. structure-function relationships in polytopic membrane proteins.
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Affiliation(s)
- S Frillingos
- Howard Hughes Medical Institute, Departments of Physiology and Microbiology and Molecular Genetics, Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90024
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8
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Okazaki N, Jue XX, Miyake H, Kuroda M, Shimamoto T, Tsuchiya T. Sequence of a melibiose transporter gene of Enterobacter cloacae. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1354:7-12. [PMID: 9375783 DOI: 10.1016/s0167-4781(97)00113-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We cloned a fragment of the chromosomal DNA of Enterobacter cloacae, which enabled a melibiose-negative Escherichia coli mutant lacking melB to grow on melibiose as the sole source of carbon. Transformed cells harboring the hybrid plasmid carrying the cloned DNA showed melibiose transport activity. The nucleotide sequence of the DNA region was determined. One complete open reading frame (ORF) and a part of another ORF were found in the region, and the amino acid sequences were deduced. The complete ORF was found to encode a melibiose transporter which consisted of 425 amino acid residues. Hydropathy analysis revealed that there are about 12 hydrophobic domains in this transporter. The incomplete ORF which exists in the upstream region of the transporter gene seemed to encode an alpha-galactosidase.
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Affiliation(s)
- N Okazaki
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima, Japan
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9
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Sun J, Frillingos S, Kaback HR. Binding of monoclonal antibody 4B1 to homologs of the lactose permease of Escherichia coli. Protein Sci 1997; 6:1503-10. [PMID: 9232651 PMCID: PMC2143751 DOI: 10.1002/pro.5560060714] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The conformationally sensitive epitope for monoclonal antibody (mAb) 4B1, which uncouples lactose from H+ translocation in the lactose permease of Escherichia coli, is localized in the periplasmic loop between helices VII and VIII (loop VII/VIII) on one face of a short helical segment (Sun J, et al., 1996, Biochemistry 35;990-998). Comparison of sequences in the region corresponding to loop VII/VIII in members of Cluster 5 of the Major Facilitator Superfamily (MFS), which includes five homologous oligosaccharide/H+ symporters, reveals interesting variations. 4B1 binds to the Citrobacter freundii lactose permease or E. coli raffinose permease with resultant inhibition of transport activity. Because E. coli raffinose permease contains a Pro residue at position 254 rather than Gly, it is unlikely that the mAb recognizes the peptide backbone at this position. Consistently, E. coli lactose permease with Pro in place of Gly254 also binds 4B1. In contrast, 4B1 binding is not observed with either Klebsiella pneumoniae lactose permease or E. coli sucrose permease. When the epitope is transferred from E. coli lactose permease (residues 245-259) to the sucrose permease, the modified protein binds 4B1, but the mAb has no significant effect on sucrose transport. The studies provide further evidence that the 4B1 epitope is restricted to loop VII/VIII, and that 4B1 binding induces a highly specific conformational change that uncouples substrate and H+ translocation.
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Affiliation(s)
- J Sun
- Howard Hughes Medical Institute, Department of Physiology, University of California Los Angeles 90095-1662, USA
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10
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Okazaki N, Jue XX, Miyake H, Kuroda M, Shimamoto T, Tsuchiya T. A melibiose transporter and an operon containing its gene in Enterobacter cloacae. J Bacteriol 1997; 179:4443-5. [PMID: 9209070 PMCID: PMC179276 DOI: 10.1128/jb.179.13.4443-4445.1997] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We detected inducible melibiose transport activity in cells of Enterobacter cloacae IID977. H+, but not Na+, was found to be the coupling cation for this transporter. We cloned and sequenced the gene encoding the melibiose transporter. A homology search of a protein sequence database revealed that this melibiose transporter has high sequence similarity with the lactose transporter (LacY) and the raffinose transporter (RafB) and has some similarity with the melibiose transporter (MelB) of Escherichia coli.
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Affiliation(s)
- N Okazaki
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima, Japan
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11
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Frillingos S, Ujwal ML, Sun J, Kaback HR. The role of helix VIII in the lactose permease of Escherichia coli: I. Cys-scanning mutagenesis. Protein Sci 1997; 6:431-7. [PMID: 9041646 PMCID: PMC2143654 DOI: 10.1002/pro.5560060220] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Using a functional lactose permease mutant devoid of Cys residues (C-less permease), each amino acid residue in transmembrane domain VIII and flanking hydrophilic loops (from Gln 256 to Lys 289) was replaced individually with Cys. Of the 34 single-Cys mutants, 26 accumulate lactose to > 70% of the steady state observed with C-less permease, and an additional 7 mutants (Gly 262-->Cys, Gly 268-->Cys, Asn 272-->Cys, Pro 280-->Cys, Asn 284-->Cys, Gly 287-->Cys, and Gly 288-->Cys) exhibit lower but significant levels of accumulation (30-50% of C-less). As expected (Ujwal ML, Sahin-Tóth M, Persson B, Kaback HR, 1994, Mol Membr Biol 1:9-16), Cys replacement for Glu 269 abolishes lactose transport. Immunoblot analysis reveals that the mutants are inserted into the membrane at concentrations comparable to C-less permease, with the exceptions of mutants Pro 280-->Cys, Gly 287-->Cys, and Lys 289-->Cys, which are expressed at reduced levels. The transport activity of the mutants is inhibited by N-ethylmaleimide (NEM) in a highly specific manner. Most of the mutants are insensitive, but Cys replacements render the permease sensitive to inactivation by NEM at positions that cluster in manner indicating that they are on one face of an alpha-helix (Gly 262-->Cys, Val 264-->Cys, Thr 265-->Cys, Gly 268-->Cys. Asn 272-->Cys, Ala 273-->Cys, Met 276-->Cys, Phe 277-->Cys, and Ala 279-->Cys). The results indicate that transmembrane domain VIII is in alpha-helical conformation and demonstrate that, although only a single residue in this region of the permease is essential for activity (Glu 269), one face of the helix plays an important role in the transport mechanism. More direct evidence for the latter conclusion is provided in the companion paper (Frillingos S. Kaback HR, 1997, Protein Sci 6:438-443) by using site-directed sulfhydryl modification of the Cys-replacement mutants in situ.
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Affiliation(s)
- S Frillingos
- Howard Hughes Medical Institute, University of California Los Angeles 90095-1662, USA
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12
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Varela MF, Wilson TH. Molecular biology of the lactose carrier of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1276:21-34. [PMID: 8764889 DOI: 10.1016/0005-2728(96)00030-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- M F Varela
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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13
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Parish JH, Bentley J. Relationships between bacterial drug resistance pumps and other transport proteins. J Mol Evol 1996; 42:281-93. [PMID: 8919880 DOI: 10.1007/bf02198855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have used three reference sequences representative of bacterial drug resistance pumps and sugar transport proteins to collect the 91 most closely related sequences from a composite, nonredundant protein sequence database. Having eliminated certain very close relatives, the remainder were subjected to analysis and alignment by using two different similarity matrices: one of these was a matrix based on structural conservation of amino acid residues in proteins of known conformation and the other was based on the more familiar mutational matrix. Unrooted similarity trees for these proteins were constructed for each matrix and compared. A systematic analysis of the differences between these trees was undertaken and the sequences were analyzed for the presence or absence of certain sequence motifs. The results show that the clades created by the two methods are broadly comparable but that there are some clusters of sequences that are significantly different. Further analysis confirmed that (1) the sequences collected by this objective method are all known or putative 12-helix (in some cases reported as 14-helix) transmembrane proteins, (2) there is evidence for few cases of an origin based on gene duplication, (3) the bacterial drug resistance pumps are distributed in more than one clade and cannot be regarded as a definitive subset of these proteins, and that (4) the diversity is such that there is no evidence of a single ancestral protein. The possible extension of the methods to other cases of divergent protein sequences is discussed.
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Affiliation(s)
- J H Parish
- Department of Biochemistry and Molecular Biology, University of Leeds, United Kingdom
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Rodríguez M, Holcík M, Iyer VN. Lethality and survival of Klebsiella oxytoca evoked by conjugative IncN group plasmids. J Bacteriol 1995; 177:6352-61. [PMID: 7592409 PMCID: PMC177484 DOI: 10.1128/jb.177.22.6352-6361.1995] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The transmission of plasmid pCU1 (or other IncN group plasmid) into a population of Klebsiella oxytoca cells reduces the viability of the population. A 2,400-bp region adjacent to traA is responsible for this phenotype and includes two regions, called kikA and kikC. Klebsiella cells which received this region and survived were found to acquire a chromosomal mutation which renders them immune to killing even after the plasmid is cured from the cells. To obtain insight into the mode of this apparent lethality, an appropriate pCU1lacZ derivative was constructed. It could be introduced with high efficiency into Klebsiella cells. Analyses of the resultant colonies indicate that the loss of viability is not a consequence of the death of plasmid-free segregants. On the contrary and unlike postsegregational killing by plasmids, cells survived by losing the plasmid or by acquiring, secondarily, a chromosomal mutation which confers immunity to killing.
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Affiliation(s)
- M Rodríguez
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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15
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Frillingos S, Sahin-Tóth M, Lengeler JW, Kaback HR. Helix packing in the sucrose permease of Escherichia coli: properties of engineered charge pairs between helices VII and XI. Biochemistry 1995; 34:9368-73. [PMID: 7626606 DOI: 10.1021/bi00029a012] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Of four putative intramembrane charge pairs in lactose permease, only three are conserved in the homologous sucrose permease of Escherichia coli [Bockmann, J., Heuel, H., & Lengeler, J. W. (1992) Mol. Gen. Genet. 235, 22-32]. The missing charge pair was introduced into wild-type sucrose permease by site-directed mutagenesis of Asn234 (helix VII) and Ser356 (helix XI). Individual replacement of either residue with a charged amino acid abolishes active sucrose transport with the exception of the Asn234-->Asp mutant. However, simultaneous replacement of Asn234 with Asp or Glu and Ser356 with Arg or Lys results in high activity. Thus, an acidic residue at position 234 rescues the activity of the Ser356-->Arg or Ser356-->Lys mutant, and a basic residue at position 356 rescues the activity of the Asn234-->Glu mutant. Furthermore, when expressed at a relatively low rate, the double mutant Asn234-->Asp/Ser356-->Arg is present in the membrane in a significantly greater amount than wild-type, suggesting that the charge pair improves insertion of sucrose permease into the membrane. The results indicate that helices VII and XI of sucrose permease are in close proximity and that a charge pair interaction can be established between residues 234 (helix VII) and 356 (helix XI). However, interchange of the acidic residue at position 234 with the basic residue at position 356 abolishes sucrose transport.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S Frillingos
- Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles 90095-1662, USA
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Frillingos S, Sahin-Tóth M, Persson B, Kaback HR. Cysteine-scanning mutagenesis of putative helix VII in the lactose permease of Escherichia coli. Biochemistry 1994; 33:8074-81. [PMID: 8025113 DOI: 10.1021/bi00192a012] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using a functional lactose permease mutant devoid of Cys residues (C-less permease), each amino acid residue in putative transmembrane helix VII and the flanking cytoplasmic and periplasmic regions (from Leu212 to Glu255) was replaced individually with Cys. Of the 44 single-Cys mutants, 40 exhibit high transport activity, accumulating lactose to > 50% of the steady-state observed with C-less permease. In contrast, permease with Cys in place of Ala213 or Tyr236 exhibits low but significant activity, and Cys substitution for Asp237 or Asp240 yields permease molecules with little or no activity due to disruption of charge-neutralizing interactions between Asp237 and Lys358 or Asp240 and Lys319, respectively. Immunological analysis reveals that membrane levels of the mutant proteins are comparable to that of C-less permease with the exception of Tyr228-->Cys, which exhibits reduced but significant levels of permease. Finally, the effect of N-ethylmaleimide (NEM) was tested on each mutant, and the results indicate that the transport activity of the great majority of the mutants is not affected by the alkylating agent. Remarkably, the six positions where Cys replacements render the permease highly sensitive to inactivation by NEM are confined to the C-terminal half of helix VII, a region that is strongly conserved among transport proteins homologous to lactose permease. The results demonstrate that although no residue per se in the region scanned is essential, structural features of the C terminus of helix VII may be important for transport activity.
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Affiliation(s)
- S Frillingos
- Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles 90024-1662
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Zhang H, Obias V, Gonyer K, Dennis D. Production of polyhydroxyalkanoates in sucrose-utilizing recombinant Escherichia coli and Klebsiella strains. Appl Environ Microbiol 1994; 60:1198-205. [PMID: 8017916 PMCID: PMC201459 DOI: 10.1128/aem.60.4.1198-1205.1994] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The cloned poly-3-hydroxybutyrate (PHB) synthesis pathway from Alcaligenes eutrophus has been introduced into sucrose-utilizing strains of Escherichia coli, Klebsiella aerogenes, and Klebsiella oxytoca. The plasmid-borne genes were well expressed in these environments and were able to mediate the production of significant amounts of PHB when the bacteria were grown with sucrose as the sole carbon source. The molecular weight of the PHB polymer made in K. aerogenes and E. coli was approximately 1 x 10(6) to 2 x 10(6). Sucrose uptake in K. aerogenes was measured and found to be similar to that found for other Klebsiella strains, but sucrose uptake in the E. coli strain was not detectable. K. aerogenes is able to utilize sugarcane molasses as the sole carbon source to accumulate PHB at the rate of approximately 1 g of PHB per liter of culture fluid per h. A K. oxytoca fadR strain was able to incorporate 3-hydroxyvalerate into a poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-co-V) polymer to levels as high as 56 mol% when grown in a medium containing propionate. Total PHB-co-V levels could be enhanced by adding propionate at the beginning of stationary phase rather than at the time of inoculation.
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Affiliation(s)
- H Zhang
- Department of Biology, James Madison University, Harrisonburg, Virginia 22807
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18
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Ujwal ML, Sahin-Tóth M, Persson B, Kaback HR. Role of glutamate-269 in the lactose permease of Escherichia coli. Mol Membr Biol 1994; 11:9-16. [PMID: 7912610 DOI: 10.3109/09687689409161024] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glu-269, which is located on the hydrophilic face of putative helix VIII in the lactose permease of Escherichia coli, has been replaced with Asp, Gln or Cys by oligonucleotide-directed, site specific mutagenesis. Cells expressing Asp-269 permease exhibit no lactose accumulation or lactose-induced H+ translocation, but retain some ability to mediate lactose influx down a concentration gradient at high substrate concentrations. Furthermore, right-side-out membrane vesicles containing Asp-269 permease do not catalyse active lactose transport, facilitated lactose efflux or equilibrium exchange. Remarkably, however, Asp-269 permease accumulates beta, D-galactopyranosyl 1-thio-beta,D-galactopyranoside in a partially uncoupled fashion, whereas no transport of methyl-beta,D-thiogalactopyranoside, sucrose or maltose is detectable. Mutant permeases containing neutral replacements (Gln or Cys) or Glu-269 are completely devoid of activity, although the proteins are present in the membrane at concentrations comparable with wild-type or Asp-269 permease. The observations demonstrate that a carboxylate at position 269 is essential for transport activity, and Glu-269 is important for substrate binding and/or recognition.
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Affiliation(s)
- M L Ujwal
- Howard Hughes Medical Institute, Department of Physiology, University of California at Los Angeles 90024
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19
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Titgemeyer F, Mason RE, Saier MH. Regulation of the raffinose permease of Escherichia coli by the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system. J Bacteriol 1994; 176:543-6. [PMID: 8288553 PMCID: PMC205084 DOI: 10.1128/jb.176.2.543-546.1994] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In enteric bacteria, chromosomally encoded permeases specific for lactose, maltose, and melibiose are allosterically regulated by the glucose-specific enzyme IIA of the phosphotransferase system. We here demonstrate that the plasmid-encoded raffinose permease of enteric bacteria is similarly subject to this type of inhibition.
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Affiliation(s)
- F Titgemeyer
- Department of Biology, University of California at San Diego, La Jolla 92093-0116
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20
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Lee J, Hwang P, Wilson T. Lysine 319 interacts with both glutamic acid 269 and aspartic acid 240 in the lactose carrier of Escherichia coli. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80687-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Baldwin SA. Mammalian passive glucose transporters: members of an ubiquitous family of active and passive transport proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1154:17-49. [PMID: 8507645 DOI: 10.1016/0304-4157(93)90015-g] [Citation(s) in RCA: 225] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- S A Baldwin
- Department of Biochemistry and Molecular Biology, University of Leeds, UK
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22
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Sahin-Tóth M, Kaback HR. Cysteine scanning mutagenesis of putative transmembrane helices IX and X in the lactose permease of Escherichia coli. Protein Sci 1993; 2:1024-33. [PMID: 8318887 PMCID: PMC2142399 DOI: 10.1002/pro.5560020615] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Using a functional lactose permease mutant devoid of Cys residues (C-less permease), each amino-acid residue in putative transmembrane helices IX and X and the short intervening loop was systematically replaced with Cys (from Asn-290 to Lys-335). Thirty-four of 46 mutants accumulate lactose to high levels (70-100% or more of C-less), and an additional 7 mutants exhibit lower but highly significant lactose accumulation. As expected (see Kaback, H.R., 1992, Int. Rev. Cytol. 137A, 97-125), Cys substitution for Arg-302, His-322, or Glu-325 results in inactive permease molecules. Although Cys replacement for Lys-319 or Phe-334 also inactivates lactose accumulation, Lys-319 is not essential for active lactose transport (Sahin-Tóth, M., Dunten, R.L., Gonzalez, A., & Kaback, H.R., 1992, Proc. Natl. Acad. Sci. USA 89, 10547-10551), and replacement of Phe-334 with leucine yields permease with considerable activity. All single-Cys mutants except Gly-296 --> Cys are present in the membrane in amounts comparable to C-less permease, as judged by immunological techniques. In contrast, mutant Gly-296 --> Cys is hardly detectable when expressed at a relatively low rate from the lac promoter/operator but present in the membrane in stable form when expressed at a high rate from T7 promoter. Finally, studies with N-ethylmaleimide (NEM) show that only a few mutants are inactivated significantly. Remarkably, the rate of inactivation of Val-315 --> Cys permease is enhanced at least 10-fold in the presence of beta-galactopyranosyl 1-thio-beta-D-galactopyranoside (TDG) or an H+ electrochemical gradient (delta mu-H+). The results demonstrate that only three residues in this region of the permease -Arg-302, His-322, and Glu-325-are essential for active lactose transport. Furthermore, the enhanced reactivity of the Val-315 --> Cys mutant toward NEM in the presence of TDG or delta mu-H+ probably reflects a conformational alteration induced by either substrate binding or delta mu-H+.
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Affiliation(s)
- M Sahin-Tóth
- Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles 90024-1574
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23
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Bockmann J, Heuel H, Lengeler JW. Characterization of a chromosomally encoded, non-PTS metabolic pathway for sucrose utilization in Escherichia coli EC3132. MOLECULAR & GENERAL GENETICS : MGG 1992; 235:22-32. [PMID: 1435727 DOI: 10.1007/bf00286177] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A wild-type isolate, EC3132, of Escherichia coli, that is able to grow on sucrose was isolated and its csc genes (mnemonic for chromosomally coded sucrose genes) transferred to strains of E. coli K12. EC3132 and all sucrose-positive exconjugants and transductants invariably showed a D-serine deaminase (Dsd)-negative phenotype. The csc locus maps adjacent to dsdA, the structural gene for the D-serine deaminase, and contains an inducible regulon, controlled by a sucrose-specific repressor CscR, together with structural genes for a sucrose hydrolase (invertase) CscA, for a D-fructokinase CscK, and for a transport system CscB. Based on DNA sequencing studies, this last codes for a hydrophobic protein of 415 amino acids. CscB is closely related to the beta-galactoside transport system LacY (31.2% identical residues) and a raffinose transport system RafB (32.3% identical residues) of the enteric bacteria, both of the proton symport type. A two-dimensional model common to the three transport proteins, which is based on the integrated consensus sequence, will be discussed.
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Affiliation(s)
- J Bockmann
- Universität Osnabrück, Fachbereich Biologie/Chemie, FRG
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24
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Hama H, Wilson T. Primary structure and characteristics of the melibiose carrier of Klebsiella pneumoniae. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)36971-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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25
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van Iwaarden PR, Driessen AJ, Konings WN. What we can learn from the effects of thiol reagents on transport proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1113:161-70. [PMID: 1510995 DOI: 10.1016/0304-4157(92)90037-b] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many secondary membrane transport systems contain reactive sulfhydryl groups. In this review the applications of SH reagents for analyzing the role of sulfhydryl groups in membrane transport systems will be discussed. First an overview will be given of the more important reagents, that have been used to study SH-groups in membrane transport systems, and examples will be given of transport proteins in which the role of cysteines have been analyzed. An important application of SH-reagents to label transport proteins using various SH-reagents modified with fluorescent- or spin-label moieties will be discussed. Two general models are shown which have been proposed to explain the role of sulfhydryl groups in some membrane transport systems.
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Affiliation(s)
- P R van Iwaarden
- Department of Microbiology, University of Groningen, Haren, Netherlands
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26
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Poolman B, Modderman R, Reizer J. Lactose transport system of Streptococcus thermophilus. The role of histidine residues. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50402-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Chapter 6 Mechanisms of active and passive transport in a family of homologous sugar transporters found in both prokaryotes and eukaryotes. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/s0167-7306(08)60068-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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28
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Sugar—Cation Symport Systems in Bacteria. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/s0074-7696(08)62676-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
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29
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Hinkle PC, Hinkle PV, Kaback HR. Information content of amino acid residues in putative helix VIII of the lac permease from Escherichia coli. Biochemistry 1990; 29:10989-94. [PMID: 2271693 DOI: 10.1021/bi00501a017] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mutants in putative helix VIII of lactose permease that retain the ability to accumulate lactose were created by cassette mutagenesis. A mutagenic insert encoding amino acid residues 259-278 was synthesized chemically by using reagents contaminated with 1% each of the other three bases and ligated into a KpnI/BclI site in the lacY gene in plasmid pGEM-4. Mutants that retain transport activity were selected by transforming a strain of Escherichia coli containing a wild-type lacZ gene, but deleted in lacY, with the mutant library and identifying colonies that transport lactose on indicator plates. Sequencing of the mutated region in lacY in 129 positive colonies reveals 43 single amino acid mutations at 26 sites and 26 multiple mutations. The variable amino acid positions are largely on one side of the putative alpha-helix, a stripe opposite Glu269. This mutable stripe of low information content is probably in contact with the membrane phospholipids.
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Affiliation(s)
- P C Hinkle
- Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110
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30
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Abstract
The cell membranes of various bacteria contain proton-linked transport systems for D-xylose, L-arabinose, D-galactose, D-glucose, L-rhamnose, L-fucose, lactose, and melibiose. The melibiose transporter of E. coli is linked to both Na+ and H+ translocation. The substrate and inhibitor specificities of the monosaccharide transporters are described. By locating, cloning, and sequencing the genes encoding the sugar/H+ transporters in E. coli, the primary sequences of the transport proteins have been deduced. Those for xylose/H+, arabinose/H+, and galactose/H+ transport are homologous to each other. Furthermore, they are just as similar to the primary sequences of the following: glucose transport proteins found in a Cyanobacterium, yeast, alga, rat, mouse, and man; proteins for transport of galactose, lactose, or maltose in species of yeast; and to a developmentally regulated protein of Leishmania for which a function is not yet established. Some of these proteins catalyze facilitated diffusion of the sugar without cation transport. From the alignments of the homologous amino acid sequences, predictions of common structural features can be made: there are likely to be twelve membrane-spanning alpha-helices, possibly in two groups of six; there is a central hydrophilic region, probably comprised largely of alpha-helix; the highly conserved amino acid residues (40-50 out of 472-522 total) form discrete patterns or motifs throughout the proteins that are presumably critical for substrate recognition and the molecular mechanism of transport. Some of these features are found also in other transport proteins for citrate, tetracycline, lactose, or melibiose, the primary sequences of which are not similar to each other or to the homologous series of transporters. The glucose/Na+ transporter of rabbit and man is different in primary sequence to all the other sugar transporters characterized, but it is homologous to the proline/Na+ transporter of E. coli, and there is evidence for its structural similarity to glucose/H+ transporters in Plants. In vivo and in vitro mutagenesis of the lactose/H+ and melibiose/Na+ (H+) transporters of E. coli has identified individual amino acid residues alterations of which affect sugar and/or cation recognition and parameters of transport. Most of the bacterial transport proteins have been identified and the lactose/H+ transporter has been purified. The directions of future investigations are discussed.
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Affiliation(s)
- P J Henderson
- Department of Biochemistry, University of Cambridge, United Kingdom
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31
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Roepe PD, Consler TG, Menezes ME, Kaback HR. The lac permease of Escherichia coli: site-directed mutagenesis studies on the mechanism of beta-galactoside/H+ symport. Res Microbiol 1990; 141:290-308. [PMID: 2177909 DOI: 10.1016/0923-2508(90)90003-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this communication, we summarize site-directed mutagenesis studies of the lac permease from Escherichia coli, a prototypic H(+)-coupled active transport protein. We classify mutant permeases by phenotype, and suggest possible roles for some individual residues in the mechanism of H+/lactose symport. Although high-resolution structural information is not presently available, kinetic analysis of the partial reactions catalysed by the mutant permeases, as well as biophysical studies, suggest an evolving model for the mechanism of H+/lactose symport.
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Affiliation(s)
- P D Roepe
- Department of Physiology, Howard Hughes Medical Institute, University of California, Los Angeles 90024-1570
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32
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The lac permease of Escherichia coli: a prototype transport protein. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/b978-0-444-81125-7.50024-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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33
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Hitchin FE, Reeve EC. Clonal analysis of the lac operons from Klebsiella M5al and the Lac plasmid (pRE2) from Klebsiella V9A. Genet Res (Camb) 1989; 54:85-91. [PMID: 2515112 DOI: 10.1017/s0016672300028457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The chromosomal lac region of the coliform bacterium Klebsiella M5al was cloned into the multicopy plasmid pBR322 to give pHE7 and pHE8. pHE8 contains 12.6 kb of M5al DNA, including its complete lac operon, and pHE7 contains 2.5 kb of M5al DNA and includes the complete lac Y gene and a small segment of lacZ. The M5al operon has the same gene order as the Escherichia coli lac operon. The lac genes of the Lac plasmid of Klebsiella V9A were cloned into pBR322 to give pHE1 and pHE2, of approximately 39 and 43 kb. Both plasmids were unstable in an E. coli RecA-strain, in contrast to the stability of pHE8. Polyacrylamide gel electrophoresis tests suggested that the M5al beta-galactosidase monomer is about 5% longer, i.e. has about 50 more amino acids, than that of the E. coli Z gene. Tests made on the enzymes coded by the lac operons of M5al, another Klebsiella strain (V9A) and its resident Lac plasmid, and several Lac+ Enterobacteria, led to the conclusion that only Escherichia coli among the Enterobacteria contains an active lacA gene.
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