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Onstead J, Zhang Z, Huo J, Ord JW, Smith S, Saier MH. Investigating How Genomic Contexts Impact IS5 Transposition Within the Escherichia coli Genome. Microorganisms 2024; 12:2600. [PMID: 39770802 PMCID: PMC11677980 DOI: 10.3390/microorganisms12122600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 12/06/2024] [Accepted: 12/12/2024] [Indexed: 01/11/2025] Open
Abstract
Insertions of the transposable element IS5 into its target sites in response to stressful environmental conditions, DNA structures, and DNA-binding proteins are well studied, but how the genomic contexts near IS5's native loci impact its transpositions is largely unknown. Here, by examining the roles of all 11 copies of IS5 within the genome of E. coli strain BW25113 in transposition, we reveal that the most significant copy of IS5 is one nested within and oriented in the same direction as the nmpC gene, while two other copies of IS5 harboring point mutations are hardly transposed. Transposition activity is heavily reliant on the upstream nmpC promoter that drives IS5 transposase gene ins5A, with more transpositions resulting from greater promoter activity. The IS5 element at nmpC but not at other loci transcribed detectable amounts of ins5A mRNA. By increasing expression of the ins5CB operon harbored in IS5, we demonstrate that Ins5B and Ins5C appear to exert a stimulatory role in IS5 transposition, suggesting that the downstream genomic regions near the native loci are involved in overall IS5 transposition as well. Using a strain that carries IS5 only at the nmpC locus, we confirm that IS5 primarily uses a copy/paste mechanism for transposition, although we cannot rule out the cut/paste mechanism.
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Affiliation(s)
| | - Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.O.); (J.H.); (J.W.O.); (S.S.)
| | | | | | | | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.O.); (J.H.); (J.W.O.); (S.S.)
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2
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Korenskaia AE, Shishkina OD, Klimenko AI, Andreenkova OV, Bobrovskikh MA, Shatskaya NV, Vasiliev GV, Gruntenko NE. New Wolbachia pipientis Genotype Increasing Heat Stress Resistance of Drosophila melanogaster Host Is Characterized by a Large Chromosomal Inversion. Int J Mol Sci 2022; 23:16212. [PMID: 36555851 PMCID: PMC9786649 DOI: 10.3390/ijms232416212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
The maternally transmitted endocellular bacteria Wolbachia is a well-known symbiont of insects, demonstrating both negative and positive effects on host fitness. The previously found Wolbachia strain wMelPlus is characterized by a positive effect on the stress-resistance of its host Drosophila melanogaster, under heat stress conditions. This investigation is dedicated to studying the genomic underpinnings of such an effect. We sequenced two closely related Wolbachia strains, wMelPlus and wMelCS112, assembled their complete genomes, and performed comparative genomic analysis engaging available Wolbachia genomes from the wMel and wMelCS groups. Despite the two strains under study sharing very close gene-composition, we discovered a large (>1/6 of total genome) chromosomal inversion in wMelPlus, spanning through the region that includes the area of the inversion earlier found in the wMel group of Wolbachia genotypes. A number of genes in unique inversion blocks of wMelPlus were identified that might be involved in the induction of a stress-resistant phenotype in the host. We hypothesize that such an inversion could rearrange established genetic regulatory-networks, causing the observed effects of such a complex fly phenotype as a modulation of heat stress resistance. Based on our findings, we propose that wMelPlus be distinguished as a separate genotype of the wMelCS group, named wMelCS3.
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Affiliation(s)
- Aleksandra E. Korenskaia
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova St. 1, 630090 Novosibirsk, Russia
| | - Olga D. Shishkina
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova St. 1, 630090 Novosibirsk, Russia
| | - Alexandra I. Klimenko
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
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3
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Antibiotic treatment enhances the genome-wide mutation rate of target cells. Proc Natl Acad Sci U S A 2016; 113:E2498-505. [PMID: 27091991 DOI: 10.1073/pnas.1601208113] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although it is well known that microbial populations can respond adaptively to challenges from antibiotics, empirical difficulties in distinguishing the roles of de novo mutation and natural selection have left several issues unresolved. Here, we explore the mutational properties of Escherichia coli exposed to long-term sublethal levels of the antibiotic norfloxacin, using a mutation accumulation design combined with whole-genome sequencing of replicate lines. The genome-wide mutation rate significantly increases with norfloxacin concentration. This response is associated with enhanced expression of error-prone DNA polymerases and may also involve indirect effects of norfloxacin on DNA mismatch and oxidative-damage repair. Moreover, we find that acquisition of antibiotic resistance can be enhanced solely by accelerated mutagenesis, i.e., without direct involvement of selection. Our results suggest that antibiotics may generally enhance the mutation rates of target cells, thereby accelerating the rate of adaptation not only to the antibiotic itself but to additional challenges faced by invasive pathogens.
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4
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IS5 inserts upstream of the master motility operon flhDC in a quasi-Lamarckian way. ISME JOURNAL 2011; 5:1517-25. [PMID: 21390082 DOI: 10.1038/ismej.2011.27] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mutation rates may be influenced by the environment. Here, we demonstrate that insertion sequence IS5 in Escherichia coli inserts into the upstream region of the flhDC operon in a manner that depends on whether the environment permits motility; this operon encodes the master regulator of cell motility, FlhDC, and the IS5 insertion increases motility. IS5 inserts upstream of flhD(+) when cells are grown on soft-agar plates that permit swimming motility, but does not insert upstream of this locus on hard-agar plates that do not permit swimming motility or in planktonic cultures. Furthermore, there was only one IS5 insertion event on soft-agar plates, indicating insertion of IS5 into flhDC is not due to general elevated IS5 transposition throughout the whole genome. We also show that the highly motile cells with IS5 upstream of flhD(+) have greater biofilm formation, although there is a growth cost due to the energetic burden of the enhanced motility as these highly motile cells have a lower yield in rich medium and reduced growth rate. Functional flagella are required for IS5 insertion upstream of flhD(+) as there was no IS5 insertion upstream of flhD(+) for flhD, flgK and motA mutants, and the mutation is stable. Additionally, the IS5 mutation occurs during biofilm formation, which creates genetic and phenotypic diversity. Hence, the cells appear to 'sense' whether motility is feasible before a sub-population undergoes a mutation to become hypermotile; this sensing appears related to the master transcription regulator, FlhDC.
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5
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Precise excision of IS5 from the intergenic region between the fucPIK and the fucAO operons and mutational control of fucPIK operon expression in Escherichia coli. J Bacteriol 2010; 192:2013-9. [PMID: 20097855 DOI: 10.1128/jb.01085-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Excision of transposable genetic elements from host DNA occurs at low frequencies and is usually imprecise. A common insertion sequence element in Escherichia coli, IS5, has been shown to provide various benefits to its host by inserting into specific sites. Precise excision of this element had not previously been demonstrated. Using a unique system, the fucose (fuc) regulon, in which IS5 insertion and excision result in two distinct selectable phenotypes, we have demonstrated that IS5 can precisely excise from its insertion site, restoring the wild-type phenotype. In addition to precise excision, several "suppressor" insertion, deletion, and point mutations restore the wild-type Fuc(+) phenotype to various degrees without IS5 excision. The possible bases for these observations are discussed.
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6
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Le Gac M, Doebeli M. Environmental viscosity does not affect the evolution of cooperation during experimental evolution of colicigenic bacteria. Evolution 2009; 64:522-33. [PMID: 19674096 DOI: 10.1111/j.1558-5646.2009.00814.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cooperation should be favored under environmental conditions allowing the preferential interaction of cooperators among themselves and limiting interactions with defectors. Bacteria cooperating to kill competitors by secreting a toxin evolved during several hundred generations in two environments: a viscous environment that should promote cooperator assortment, and a nonviscous environment that should not allow such preferential interaction. A quantitative decrease in cooperation was observed in all populations, but as expected, cooperation was maintained at a higher level in the viscous environment. Mutants that are resistant against but not producing the toxin were identified at a low frequency in a few populations from the viscous environment and at a high frequency in all the populations from the nonviscous environment. The underlying mutations were identified. Relative fitness of the cooperator and mutant genotypes were obtained with bacteria that were isogenic, except for the identified mutations. Competition experiments indicated that cooperation is not favored by environmental viscosity as imposed in our system and suggested that when it comes to cooperation, environmental viscosity should be considered not only in terms of individual movement, but also in terms of the distribution of the public good.
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Affiliation(s)
- Mickael Le Gac
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver BC V6T 1Z4, Canada.
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Yu WL, Chen SC, Hung SW, Chuang YC, Chung JG, Chen IC, Wu LT. Genetic association of blaSHV-5 with transposable elements IS26 and IS5 in Klebsiella pneumoniae from Taiwan. Clin Microbiol Infect 2006; 12:806-9. [PMID: 16842580 DOI: 10.1111/j.1469-0691.2006.01488.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A cloned 5,248-bp EcoRI fragment from the Klebsiella pneumoniae transferable plasmid pKP53 (> 70 kb) containing bla(SHV-5) was sequenced. Insertion sequences IS26 and IS5 were found downstream from bla(SHV-5). The DNA sequences of the genetic environment surrounding bla(SHV-5) were homologous to plasmid p1658/97 from Escherichia coli, containing a truncated recF gene and a truncated deoR gene upstream and downstream from bla(SHV-5), respectively. RecF may be involved in bla(SHV-5) translocation to the plasmid by RecF-dependent recombination. This novel genetic environment may be associated with the successful proliferation and/or expression of SHV-5 in K. pneumoniae strains from Taiwan.
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Affiliation(s)
- W L Yu
- Department of Critical Care Medicine, Chi-Mei Medical Center, Tainan, Taiwan
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8
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Sawers RG. Expression of fnr is constrained by an upstream IS5 insertion in certain Escherichia coli K-12 strains. J Bacteriol 2005; 187:2609-17. [PMID: 15805507 PMCID: PMC1070394 DOI: 10.1128/jb.187.8.2609-2617.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FNR is a global transcriptional regulator that controls anaerobic gene expression in Escherichia coli. Through the use of a number of approaches it was shown that fnr gene expression is reduced approximately three- to fourfold in E. coli strain MC4100 compared with the results seen with strain MG1655. This reduction in fnr expression is due to the insertion of IS5 (is5F) in the regulatory region of the gene at position -41 relative to the transcription initiation site. Transcription of the fnr gene nevertheless occurs from its own promoter in strain MC4100, but transcript levels are reduced approximately fourfold compared with those seen with strain MG1655. Remarkably, in strains bearing is5F the presence of Hfq prevents IS5-dependent transcriptional silencing of fnr expression. Thus, an hfq mutant of MC4100 is devoid of FNR protein and has the phenotype of an fnr mutant. In strain MG1655, or a derivative of MC4100 lacking is5F, mutation of hfq had no effect on fnr transcript levels. This finding indicates that IS5 mediates the effect of Hfq on fnr expression in MC4100. Western blot analysis revealed that cellular levels of FNR were reduced threefold in strain MC4100 compared with strain MG1655 results. A selection of FNR-dependent genes fused to lacZ were analyzed for the effects of reduced FNR levels on anaerobic gene expression. Expression of some operons, e.g., focA-pfl and fdnGHJI, was unaffected by reduction in the level of FNR, while the expression of other genes such as ndh and nikA was clearly affected.
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Affiliation(s)
- R Gary Sawers
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.
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9
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Sawers RG. Transcript analysis ofEscherichia coliK-12 insertion element IS5. FEMS Microbiol Lett 2005; 244:397-401. [PMID: 15766797 DOI: 10.1016/j.femsle.2005.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 02/14/2005] [Accepted: 02/15/2005] [Indexed: 10/25/2022] Open
Abstract
The mobile insertion element IS5 is a relatively small but genetically compact DNA sequence of 1195bp found in variable copy number in the genome of Escherichia coli strains. This study presents a detailed transcript analysis of the population of IS5 elements present in E. coli strains MC4100 and MG1655. The findings indicate that the ins5A gene comprising 978bp is transcribed from its own promoter, which is located close to the right-hand end of the element. The two divergently transcribed genes ins5C and in5B form an operon, and this transcript is fully contained within the borders of the ins5A transcript. Although transcription out of IS5 from element-internal promoters was negligible, in the case of MG1655 a major transcript was found to extend into the insertion element. This suggests that IS5-specific transcription can be influenced by the specific location of the element in the chromosome, the orientation it adopts and the gene it interrupts.
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Affiliation(s)
- R Gary Sawers
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom.
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10
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Hesslinger C, Sawers G. The tdcE gene in Escherichia coli strain W3110 is separated from the rest of the tdc operon by insertion of IS5 elements. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1999; 9:183-8. [PMID: 10520749 DOI: 10.3109/10425179809072194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Unlike other Escherichia coli K-12 strains, W3110 contains multiple copies of the insertion sequence IS5. Some of these IS5 elements have been involved in tandem duplication of a portion of the chromosome which includes, amonst others, the tdcABC-DEFG operon genes. The nucleotide sequence and insertion site of one of these elements, IS5P, was determined. It was shown that IS5P has inserted within the coding sequence of the tdcA gene and is flanked, not by the remaining portion of the tdcA gene, but by the extreme 3' end of the tdcD gene. In other E. coli K-12 strains the tdcD gene and three other genes, tdcE, tdcF and tdcG, all form part of the tdc operon. Our results demonstrate that during the duplication event the tdcABCgenes have been amplified and separated from the remaining genes tdcE, tdcF and tdcG of the operon, which are each present in single copy.
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Affiliation(s)
- C Hesslinger
- Lehrstuhl für Mikrobiologie, der Universität München, Munich, Germany
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11
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Abstract
We determined the genomic organization of 14 clinical strains of Bordetella pertussis isolated over an 18-month period in Alberta, Canada. The maps of these 14 strains, while demonstrating general similarity of gene order, display a number of examples of genomic rearrangements in the form of large chromosomal inversions.
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Affiliation(s)
- S Stibitz
- Division of Bacterial Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA.
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12
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Abstract
A physical map, EcoMap10, of the now completely sequenced Escherichia coli chromosome is presented. Calculated genomic positions for the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII are depicted. Both sequenced and unsequenced Kohara/Isono miniset clones are aligned to this calculated restriction map. DNA sequence searches identify the precise locations of insertion sequence elements and repetitive extragenic palindrome clusters. EcoGene10, a revised set of genes and functionally uncharacterized open reading frames (ORFs), is also depicted on EcoMap10. The complete set of unnamed ORFs in EcoGene10 are assigned provisional names beginning with the letter "y" by using a systematic nomenclature.
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Affiliation(s)
- K E Rudd
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33101-6129, USA.
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13
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Kotani H, Tabata S. LESSONS FROM SEQUENCING OF THE GENOME OF A UNICELLULAR CYANOBACTERIUM, SYNECHOCYSTIS SP. PCC6803. ACTA ACUST UNITED AC 1998; 49:151-171. [PMID: 15012231 DOI: 10.1146/annurev.arplant.49.1.151] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nucleotide sequence of the entire genome of the unicellular cyanobacterium, Synechocystis sp. PCC6803, has been determined. The length of the circular genome was 3,573,480 bp, and a total of 3168 protein-coding genes were assigned to the genome by a computer-assisted analysis. The functions of approximately 45% of the genes were deduced based on sequence similarity to known genes. Here are distinctive features of genetic information carried by the cyanobacteria, which have a phylogenetic relationship to both bacteria and plants.
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Affiliation(s)
- H. Kotani
- Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Chiba 292, Japan; e-mail:
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14
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Abstract
Gene amplification is a common feature of the genome of prokaryotic organisms. In this review, we analyze different instances of gene amplification in a variety of prokaryotes, including their mechanisms of generation and biological role. Growing evidence supports the concept that gene amplification be considered not as a mutation but rather as a dynamic genomic state related to the adaptation of bacterial populations to changing environmental conditions or biological interactions. In this context, the potentially amplifiable DNA regions impose a defined dynamic structure on the genome. If such structure has indeed been selected during evolution, it is a particularly challenging hypothesis.
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Affiliation(s)
- D Romero
- Department of Molecular Genetics, National University of Mexico, Cuernavaca, Morelos, Mexico.
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15
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Brooke JS, Valvano MA. Biosynthesis of inner core lipopolysaccharide in enteric bacteria identification and characterization of a conserved phosphoheptose isomerase. J Biol Chem 1996; 271:3608-14. [PMID: 8631969 DOI: 10.1074/jbc.271.7.3608] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The lpcA locus has been identified in Escherichia coli K12 novobiocin-supersensitive mutants that produce a short lipopolysaccharide (LPS) core which lacks glyceromannoheptose and terminal hexoses. We have characterized lpcA as a single gene mapping around 5.3 min (246 kilobases) on the E. coli K12 chromosome and encoding a 22.6-kDa cytosolic protein. Recombinant plasmids containing only lpcA restored a complete core LPS in the E. coli strain chi711. We show that this strain has an IS5-mediated chromosomal deletion of 35 kilobases that eliminates lpcA. The LpcA protein showed discrete similarities with a family of aldose/ketose isomerases and other proteins of unknown function. The isomerization of sedoheptulose 7-phosphate, into a phosphosugar presumed to be D-glycero-D-mannoheptose 7-phosphate, was detected in enzyme reactions with cell extracts of E. coli lpcA+ and of lpcA mutants containing the recombinant lpcA gene. We concluded that LpcA is the phosphoheptose isomerase used in the first step of glyceromannoheptose synthesis. We also demonstrated that lpcA is conserved among enteric bacteria, all of which contain glyceromannoheptose in the inner core LPS, indicating that LpcA is an essential component in a conserved biosynthetic pathway of inner core LPS.
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Affiliation(s)
- J S Brooke
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, N6A 5C1 Canada
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16
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Affiliation(s)
- F Ohtsubo
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan
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17
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Hill CW, Feulner G, Brody MS, Zhao S, Sadosky AB, Sandt CH. Correlation of Rhs elements with Escherichia coli population structure. Genetics 1995; 141:15-24. [PMID: 8536964 PMCID: PMC1206714 DOI: 10.1093/genetics/141.1.15] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The Rhs family of composite genetic elements was assessed for variation among independent Escherichia coli strains of the ECOR reference collection. The location and content of the RhsA-B-C-F subfamily correlates highly with the clonal structure of the ECOR collection. This correlation exists at several levels: the presence of Rhs core homology in the strain, the location of the Rhs elements present, and the identity of the Rhs core-extensions associated with each element. A provocative finding was that an identical 1518-bp segment, covering core-extension-b1 and its associated downstream open reading frame, is present in two distinct clonal groups, but in association with different Rhs elements. The sequence identity of this segment when contrasted with the divergence of other chromosomal segments suggests that shuffling of Rhs core extensions has been a relatively recent variation. Nevertheless the copies of core-extension-b1 were placed within the respective Rhs elements before the emergence of the clonal groups. In the course of this analysis, two new Rhs elements absent from E. coli K-12 were discovered: RhsF, a fourth member of the RhsA-B-C-F subfamily, and RhsG, the prototype of a third Rhs subfamily.
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Affiliation(s)
- C W Hill
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey 17033, USA
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18
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Kamath AV, Gish K, Yanofsky C. A copy of insertion element IS5 is present within tnaB in the Kohara library of Escherichia coli W3110. J Bacteriol 1994; 176:1546-7. [PMID: 8113202 PMCID: PMC205229 DOI: 10.1128/jb.176.5.1546-1547.1994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- A V Kamath
- Department of Biological Sciences, Stanford University, California 94305-5020
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19
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Abstract
From a historical perspective, the study of both the biochemistry and the genetics of lipopolysaccharide (LPS) synthesis began with the enteric bacteria. These organisms have again come to the forefront as the blocks of genes involved in LPS synthesis have been sequenced and analyzed. A number of new and unanticipated genes were found in these clusters, indicating a complexity of the biochemical pathways which was not predicted from the older studies. One of the most dramatic areas of LPS research has been the elucidation of the lipid A biosynthetic pathway. Four of the genes in this pathway have now been identified and sequenced, and three of them are located in a complex operon which also contains genes involved in DNA and phospholipid synthesis. The rfa gene cluster, which contains many of the genes for LPS core synthesis, includes at least 17 genes. One of the remarkable findings in this cluster is a group of several genes which appear to be involved in the synthesis of alternate rough core species which are modified so that they cannot be acceptors for O-specific polysaccharides. The rfb gene clusters which encode O-antigen synthesis have been sequenced from a number of serotypes and exhibit the genetic polymorphism anticipated on the basis of the chemical complexity of the O antigens. These clusters appear to have originated by the exchange of blocks of genes among ancestral organisms. Among the large number of LPS genes which have now been sequenced from these rfa and rfb clusters, there are none which encode proteins that appear to be secreted across the cytoplasmic membrane and surprisingly few which encode integral membrane proteins or proteins with extensive hydrophobic domains. These data, together with sequence comparison and complementation experiments across strain and species lines, suggest that the LPS biosynthetic enzymes may be organized into clusters on the inner surface of the cytoplasmic membrane which are organized around a few key membrane proteins.
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Affiliation(s)
- C A Schnaitman
- Department of Microbiology, Arizona State University, Tempe 85287-2701
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20
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Kasai H, Isono S, Kitakawa M, Mineno J, Akiyama H, Kurnit DM, Berg DE, Isono K. Efficient large-scale sequencing of the Escherichia coli genome: implementation of a transposon- and PCR-based strategy for the analysis of ordered lambda phage clones. Nucleic Acids Res 1992; 20:6509-15. [PMID: 1336178 PMCID: PMC334565 DOI: 10.1093/nar/20.24.6509] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have developed a strategy for efficient sequence analysis of the genome of E. coli K-12 using insertions of a Tn5-derived mini-transposon into overlapping ordered lambda phage clones to provide universal primer-binding sites, and PCR amplification of DNA segments adjacent to the insertions. Transposon-containing clones were selected by blue plaque formation on a dnaBamber lacZamber E. coli strain. Insertion points every 0.5-1 kb were identified by 'analytical PCR' and segments between the transposon inserts and phage arms were amplified by 'preparative PCR' using one biotinylated and one non-biotinylated primer. Single strands of amplified DNA fragments were coupled to Streptoavidin-coated paramagnetic beads (Dynabeads M280) through their biotin tails, purified magnetically, and used as templates for fluorescence-based automatic nucleotide sequencing.
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Affiliation(s)
- H Kasai
- Postgraduate School, Faculty of Science, Kobe University, Japan
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21
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Knight AI, Ni H, Cartwright KA, McFadden JJ. Identification and characterization of a novel insertion sequence, IS1106, downstream of the porA gene in B15 Neisseria meningitidis. Mol Microbiol 1992; 6:1565-73. [PMID: 1320728 DOI: 10.1111/j.1365-2958.1992.tb00878.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Examination of Neisseria meningitidis strains associated with endemic meningococcal disease demonstrated differences in the number of copies of a repetitive sequence. Characterization of a copy of this repetitive sequence present in B15 strains has revealed the presence of a novel insertion sequence (IS1106) located within a complex repetitive region downstream of the gene for the major surface antigen (porA). IS1106 has a length of 1137 bp and is flanked by 36bp inverted repeats. Two open reading frames (ORF1 and ORF2) are present in opposite strands in codon-codon register with ORF2 entirely located within ORF1. The predicted protein from ORF1 demonstrates homology with the 5A protein of IS5 (Kroger and Hobom, 1982). Strains from two independent outbreaks of B15 meningococcal disease in the UK were found to contain the same genomic deletion removing a copy of IS1106 downstream of the porA gene.
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Affiliation(s)
- A I Knight
- School of Biological Sciences, University of Surrey, Guildford, UK
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22
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Affiliation(s)
- W Hendrickson
- Department of Microbiology/Immunology, University of Illinois, Chicago 60612
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23
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Schnetz K, Rak B. IS5: a mobile enhancer of transcription in Escherichia coli. Proc Natl Acad Sci U S A 1992; 89:1244-8. [PMID: 1311089 PMCID: PMC48425 DOI: 10.1073/pnas.89.4.1244] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The cryptic bgl operon of Escherichia coli is activated by the spontaneous insertion of mobile DNA elements. Screening of a collection of such mutations revealed insertion of the 1195-base-pair element IS5 into various positions both upstream and downstream of the bgl promoter P0. Activation of the operon was in all cases attributable to enhancement of P0 activity. Introduction of internal deletions into IS5 almost completely abolished P0 enhancement, demonstrating that enhancement is not simply the result of mutational inactivation of some inhibitory sequences. Intact copies of IS5 in trans restored the enhancing activity of the deletion derivatives. The trans-activator is encoded by IS5 gene ins5A, an essential transposition function. Activation of gene expression by means of interaction of a defective mobile element in cis with functions encoded by a nondefective element in trans has so far been described only for a maize controlling element.
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Affiliation(s)
- K Schnetz
- Institut für Biologie III, Universität, Freiburg, Federal Republic of Germany
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24
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Komine Y, Inokuchi H. Precise mapping of the rnpB gene encoding the RNA component of RNase P in Escherichia coli K-12. J Bacteriol 1991; 173:1813-6. [PMID: 1705543 PMCID: PMC207335 DOI: 10.1128/jb.173.5.1813-1816.1991] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In Kohara's library derived from Escherichia coli K-12 W3110 (Y. Kohara, K. Akiyama, and K. Isono, Cell 50:495-508, 1987), multiple copies of chromosomal sequence are found at 68 and at 64 to 65 min (M. Umeda and E. Ohtsubo, J. Mol. Biol. 213:229-237, 1990). We have determined that the rnpB gene (previously mapped at 70 min [B. J. Bachmann, Microbiol. Rev. 54:130-197, 1990]) is located within these segments of repeated sequences as five separate copies, together with tdcA, B, C, and R (mapped at 68 min [Bachmann, 1990]) and six unidentified open reading frames. Since close linkage of rnpB and tdc is found in various strains of E. coli K-12, the rnpB gene should be mapped at 68 min rather than 70 min.
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Affiliation(s)
- Y Komine
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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25
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Rudd KE, Miller W, Werner C, Ostell J, Tolstoshev C, Satterfield SG. Mapping sequenced E.coli genes by computer: software, strategies and examples. Nucleic Acids Res 1991; 19:637-47. [PMID: 2011534 PMCID: PMC333660 DOI: 10.1093/nar/19.3.637] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Methods are presented for organizing and integrating DNA sequence data, restriction maps, and genetic maps for the same organism but from a variety of sources (databases, publications, personal communications). Proper software tools are essential for successful organization of such diverse data into an ordered, cohesive body of information, and a suite of novel software to support this endeavor is described. Though these tools automate much of the task, a variety of strategies is needed to cope with recalcitrant cases. We describe such strategies and illustrate their application with numerous examples. These strategies have allowed us to order, analyze, and display over one megabase of E. coli DNA sequence information. The integration task often exposes inconsistencies in the available data, perhaps caused by strain polymorphisms or human oversight, necessitating the application of sound biological judgment. The examples illustrate both the level of expertise required of the database curator and the knowledge gained as apparent inconsistencies are resolved. The software and mapping methods are applicable to the study of any genome for which a high resolution restriction map is available. They were developed to support a weakly coordinated sequencing effort involving many laboratories, but would also be useful for highly orchestrated sequencing projects.
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Affiliation(s)
- K E Rudd
- Laboratory of Bacterial Toxins, Food and Drug Administration, Bethesda, MD 20892
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26
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Umeda M, Ohtsubo E. Four types of IS1 with differences in nucleotide sequence reside in the Escherichia coli K-12 chromosome. Gene 1991; 98:1-5. [PMID: 1849492 DOI: 10.1016/0378-1119(91)90096-t] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Escherichia coli K-12 chromosome contains six copies of insertion element IS1 at loci is1A-is1F. We determined their nucleotide (nt) sequences and found that they were classified into four types. Two copies of IS1 which flank a chromosomal segment containing the argF gene (IS1B and IS1C) have identical nt sequences. Another identical pair are IS1A and IS1E. Comparison of their nt sequences with the IS1 in plasmid R100 revealed seven nt mismatches for IS1A (or IS1E), two for IS1B (or IS1C), four for IS1D, and 75 for IS1F. The fact that the IS1s flanking the argF segment are identical supports the idea that the segment, together with the particular pair of IS1s, has constituted a composite transposon and transposed after genetic transfer from another bacterial species into E. coli K-12. Duplicated sequences were not observed in the regions flanking each of four copies of IS1, indicating that rearrangements have occurred in these chromosomal regions after IS1 elements had been inserted into several target sites. The four types of IS1 present in the E. coli K-12 chromosome were essentially similar to IS1s in plasmid R100 and in the chromosomes of Shigella strains. This and the above results suggest that they have been transferred horizontally from other Enterobacteriaceae, including Shigella, into E. coli K-12.
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Affiliation(s)
- M Umeda
- Institute of Applied Microbiology, University of Tokyo, Japan
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27
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Abstract
Recent progress in studies on the bacterial chromosome is summarized. Although the greatest amount of information comes from studies on Escherichia coli, reports on studies of many other bacteria are also included. A compilation of the sizes of chromosomal DNAs as determined by pulsed-field electrophoresis is given, as well as a discussion of factors that affect gene dosage, including redundancy of chromosomes on the one hand and inactivation of chromosomes on the other hand. The distinction between a large plasmid and a second chromosome is discussed. Recent information on repeated sequences and chromosomal rearrangements is presented. The growing understanding of limitations on the rearrangements that can be tolerated by bacteria and those that cannot is summarized, and the sensitive region flanking the terminator loci is described. Sources and types of genetic variation in bacteria are listed, from simple single nucleotide mutations to intragenic and intergenic recombinations. A model depicting the dynamics of the evolution and genetic activity of the bacterial chromosome is described which entails acquisition by recombination of clonal segments within the chromosome. The model is consistent with the existence of only a few genetic types of E. coli worldwide. Finally, there is a summary of recent reports on lateral genetic exchange across great taxonomic distances, yet another source of genetic variation and innovation.
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Affiliation(s)
- S Krawiec
- Department of Biology, Lehigh University, Bethlehem, Pennsylvania 18015
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28
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Sharples GJ, Lloyd RG. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res 1990; 18:6503-8. [PMID: 2251112 PMCID: PMC332602 DOI: 10.1093/nar/18.22.6503] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of a novel group of highly conserved DNA sequences located within the intergenic regions of the chromosomes of Escherichia coli, Salmonella typhimurium and other bacteria. These intergenic repeat units (IRUs) are 124-127 nucleotides long and have the potential to form stable stem-loop structures. The location of these sequences within the intergenic regions is variable with respect to known or putative signals for transcription and translation of the flanking genes. Some of the IRU sequences are transcribed, others are probably not. The structure and possible functions of these sequences are discussed in relation to palindromic units and other repeated DNA sequences in bacteria.
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Affiliation(s)
- G J Sharples
- Department of Genetics, University of Nottingham, Medical School, Queens Medical Centre, UK
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29
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Umeda M, Ohtsubo E. Mapping of insertion element IS30 in the Escherichia coli K12 chromosome. MOLECULAR & GENERAL GENETICS : MGG 1990; 222:317-22. [PMID: 1980336 DOI: 10.1007/bf00633835] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We identified seven phage clones containing the insertion element IS30 in a lambda phage library mini-set, which includes 476 clones carrying chromosomal segments that cover almost the entire chromosome of Escherichia coli K12 W3110 (Kohara et al. 1987). We could assign locations and orientations to four copies of IS30 (named is30A to is30D) on the W3110 chromosome by restriction analysis of phage DNAs containing them. These IS30s were present at the same locations in chromosomes of both W3110 and another E. coli K12 strain JE5519, and thus are assumed to be present in other E. coli K12 derivatives, including early isolates. Among the IS30 copies found, one (is30B) contained a large deletion and possessed only a 181 bp stretch of the right terminal region of IS30.
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Affiliation(s)
- M Umeda
- Institute of Applied Microbiology, University of Tokyo, Japan
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