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Castro-Gutierrez V, Fuller E, Garcillán-Barcia MP, Helgason T, Hassard F, Moir J. Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria. Microb Genom 2022; 8. [DOI: 10.1099/mgen.0.000881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bioremediation of metaldehyde from drinking water using metaldehyde-degrading strains has recently emerged as a promising alternative. Whole-genome sequencing was used to obtain full genomes for metaldehyde degraders
Acinetobacter calcoaceticus
E1 and
Sphingobium
CMET-H. For the former, the genetic context of the metaldehyde-degrading genes had not been explored, while for the latter, none of the degrading genes themselves had been identified. In
A. calcoaceticus
E1, IS91 and IS6-family insertion sequences (ISs) were found surrounding the metaldehyde-degrading gene cluster located in plasmid pAME76. This cluster was located in closely-related plasmids and associated to identical ISs in most metaldehyde-degrading β- and γ-Proteobacteria, indicating horizontal gene transfer (HGT). For
Sphingobium
CMET-H, sequence analysis suggested a phytanoyl-CoA family oxygenase as a metaldehyde-degrading gene candidate due to its close homology to a previously identified metaldehyde-degrading gene known as mahX. Heterologous gene expression in
Escherichia coli
alongside degradation tests verified its functional significance and the degrading gene homolog was henceforth called mahS. It was found that mahS is hosted within the conjugative plasmid pSM1 and its genetic context suggested a crossover between the metaldehyde and acetoin degradation pathways. Here, specific replicons and ISs responsible for maintaining and dispersing metaldehyde-degrading genes in α, β and γ-Proteobacteria through HGT were identified and described. In addition, a homologous gene implicated in the first step of metaldehyde utilisation in an α-Proteobacteria was uncovered. Insights into specific steps of this possible degradation pathway are provided.
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Affiliation(s)
- Víctor Castro-Gutierrez
- Environmental Pollution Research Center (CICA), University of Costa Rica, Montes de Oca, 11501, Costa Rica
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
- Department of Biology, University of York, Heslington, York, UK
| | - Edward Fuller
- Department of Biology, University of York, Heslington, York, UK
| | - María Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Cantabria, Spain
| | | | - Francis Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - James Moir
- Department of Biology, University of York, Heslington, York, UK
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Ji M, Liu Y, Wu H, Li S, Duan H, Shi J, Sun J. Engineering Bacillus subtilis ATCC 6051a for the production of recombinant catalases. J Ind Microbiol Biotechnol 2021; 48:6177681. [PMID: 33734388 PMCID: PMC9113483 DOI: 10.1093/jimb/kuab024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/13/2021] [Indexed: 11/14/2022]
Abstract
Catalases are a large group of enzymes that decompose hydrogen peroxide to oxygen and hydrogen, and have been applied widely in numerous areas. Bacillus subtilis ATCC 6051a is a well-known host strain for high level secretion of heterologous peptides. However, the application of 6051a was seriously hampered by insufficient transformation efficiency. In this study, D-xylose inducible comK was integrated into the genome of B. subtilis ATCC 6051a, generating 164S, a mutant owns a transformation efficiency of 1 000-fold higher than its parent strain, thus allowing gene replacement by double crossover recombination using linear dsDNAs. The efficiency of the flanking arms for homologous recombination was then analyzed. We found that 400 bp was the minimal length of homologous fragments required to initiate efficient recombination in the 164S strain. In addition, DNA cassettes encoding two mesophilic catalases (Orf 2-62 and Orf 2-63) from B. licheniformis were integrated onto 164S. The catalytic properties of recombinant Orf 2-62 and Orf 2-63 were analyzed, and were found to be predominantly secreted into the fermentation broth, although they obviously lack any known secretory signal peptide. This work demonstrated that B. subtilis 164S is an excellent cell tool, not only for its superior secretion capacity, but also for its convenience in genetic modification.
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Affiliation(s)
- Minghua Ji
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhui Liu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haiying Wu
- Materials and Physical Biology Division School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Sijie Li
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
| | - Haiyan Duan
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiping Shi
- Correspondence should be addressed to: Jiping Shi. Phone: +86-21-20325163. E-mail:
| | - Junsong Sun
- Correspondence should be addressed to: Junsong Sun. Phone: +86-21-20325163. E-mail:
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3
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Ye B, Li Y, Tao Q, Yao X, Cheng M, Yan X. Random Mutagenesis by Insertion of Error-Prone PCR Products to the Chromosome of Bacillus subtilis. Front Microbiol 2020; 11:570280. [PMID: 33281764 PMCID: PMC7691275 DOI: 10.3389/fmicb.2020.570280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis is an attractive host for the directed evolution of the enzymes whose substrates cannot be transported across cell membrane. However, the generation of a mutant library in B. subtilis suffers problems of small library size, plasmid instability, and heterozygosity. Here, a large library of random mutant was created by inserting error-prone PCR (epPCR) products to the chromosome of B. subtilis. Specifically, the epPCR product was fused with flanking regions and antibiotic resistant marker using a PCR-based multimerization method, generating insertion construct. The epPCR product was integrated into the chromosome via homologous recombination after the insertion construct was transformed into the supercompetent cells of B. subtilis strain SCK6. The transformation efficiency of the insertion construct was improved through co-expressing homologous recombination-promoting protein NgAgo, raising the number of competent cells, and increasing the length of flanking regions. A library containing 5.31 × 105 random mutants was constructed using per μg insertion construct, which is sufficient for directed evolution. The library generation process was accomplished within 1 day. The effectiveness of this method was confirmed by improving the activity of Methyl Parathion Hydrolase (MPH) toward chlorpyrifos and by enhancing the secretion level of MPH in B. subtilis. Taken together, the present work provides a fast and efficient method to integrate epPCR products into the chromosome of B. subtilis, facilitating directed evolution and expression optimization of target proteins.
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Affiliation(s)
| | | | | | | | | | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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4
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A novel method to optimise the utility of underused moulted plumulaceous feather samples for genetic analysis in bird conservation. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01117-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abstract
Non-invasive sampling methods are increasingly being used in conservation research as they reduce or eliminate the stress and disturbance resulting from invasive sampling of blood or tissue. Here we present a protocol optimised for obtaining usable genetic material from moulted plumulaceous feather samples. The combination of simple alterations to a ‘user-developed’ method, comprised of increased incubation time and modification of temperature and volume of DNA elution buffer, are outlined to increase DNA yield and significantly increase DNA concentration (W = 81, p < 0.01, Cohens’s d = 0.89). We also demonstrate that the use of a primerless polymerase chain reaction (PCR) technique increases DNA quality and amplification success when used prior to PCR reactions targeting avian mitochondrial DNA (mtDNA). A small amplicon strategy proved effective for mtDNA amplification using PCR, targeting three overlapping 314–359 bp regions of the cytochrome oxidase I barcoding region which, when combined, aligned with target-species reference sequences. We provide evidence that samples collected non-invasively in the field and kept in non-optimal conditions for DNA extraction can be used effectively to sequence a 650 bp region of mtDNA for genetic analysis.
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5
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Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
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6
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Kim S, Min IM, Ren S, Spector A, Jin MM, Lis JT. Development of temperature-sensitive mutants of the Drosophila melanogaster P-TEFb (Cyclin T/CDK9) heterodimer using yeast two-hybrid screening. Biochem Biophys Res Commun 2013; 433:243-8. [PMID: 23500466 DOI: 10.1016/j.bbrc.2013.02.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
Abstract
P-TEFb complex, a heterodimer of the kinase CDK9 and Cyclin T, is a critical factor that stimulates the process of transcription elongation. Here, we explored a fast and large-scale screening method to induce a temperature-dependent conditional disruption of the CDK9/Cyclin T interaction and developed an assay to validate their mutant phenotypes in a biological context. First, we used the yeast two-hybrid system to screen Drosophila melanogaster Cyclin T mutants at a large scale for temperature or cold sensitive (TS or CS) CDK9 interaction phenotypes. The isolated P-TEFb TS mutants were then expressed in Drosophila cells and were investigated for their effects on Drosophila hsp70 transcriptional activity. Our results showed that these P-TEFb TS mutants had a reduced level of hsp70 transcription at restrictive temperatures. A model structure of the Cyclin T and CDK9 complex suggested that the key TS mutations were found within the α2- and α3-helices at the interface of the complex, which may disrupt the binding of Cyclin T to CDK9 directly or indirectly by affecting the conformation of Cyclin T. The yeast two-hybrid-based screening strategy described here for isolating TS or CS interaction phenotypes can be directly applicable to other complexes in higher organisms. The use of TS or CS mutants will enable a 'real-time and reversible perturbation' restricted to specific protein-protein interactions, providing a mechanistic insight into the biological process mediated by a target complex.
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Affiliation(s)
- Soyoun Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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7
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Wen S, Yang J, Tan T. Full-length single-stranded PCR product mediated chromosomal integration in intact Bacillus subtilis. J Microbiol Methods 2013. [DOI: 10.1016/j.mimet.2012.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Wang Y, Weng J, Waseem R, Yin X, Zhang R, Shen Q. Bacillus subtilis genome editing using ssDNA with short homology regions. Nucleic Acids Res 2012; 40:e91. [PMID: 22422839 PMCID: PMC3384351 DOI: 10.1093/nar/gks248] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, we developed a simple and efficient Bacillus subtilis genome editing method in which targeted gene(s) could be inactivated by single-stranded PCR product(s) flanked by short homology regions and in-frame deletion could be achieved by incubating the transformants at 42°C. In this process, homologous recombination (HR) was promoted by the lambda beta protein synthesized under the control of promoter PRM in the lambda cI857 PRM–PR promoter system on a temperature sensitive plasmid pWY121. Promoter PR drove the expression of the recombinase gene cre at 42°C for excising the floxed (lox sites flanked) disruption cassette that contained a bleomycin resistance marker and a heat inducible counter-selectable marker (hewl, encoding hen egg white lysozyme). Then, we amplified the single-stranded disruption cassette using the primers that carried 70 nt homology extensions corresponding to the regions flanking the target gene. By transforming the respective PCR products into the B. subtilis that harbored pWY121 and incubating the resultant mutants at 42°C, we knocked out multiple genes in the same genetic background with no marker left. This process is simple and efficient and can be widely applied to large-scale genome analysis of recalcitrant Bacillus species.
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Affiliation(s)
- Yang Wang
- Department of Plant Nutrition, College of Resource and Environmental Sciences, Nanjing Agricultural University, No.1 Weigang Road, Nanjing 210095, Jiangsu Province, PR China
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9
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de Berardinis V, Durot M, Weissenbach J, Salanoubat M. Acinetobacter baylyi ADP1 as a model for metabolic system biology. Curr Opin Microbiol 2009; 12:568-76. [PMID: 19709925 DOI: 10.1016/j.mib.2009.07.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 07/15/2009] [Indexed: 01/20/2023]
Abstract
Information produced by the annotation of an 'average bacterial genome' can be separated into three parts. One-third represents what we know, another third what we think we know, and the last third what we know we do not know. Knowledge of metabolism is also described by this three thirds rule. Understanding how a cell operates will require a better knowledge of the two ignored thirds of its parts. Moreover, metabolism needs to be further investigated using organisms whose life styles are different from those of model organisms. In this short review, we present Acinetobacter baylyi ADP1 as an environmental model especially suitable for large-scale genetic manipulation. Resources have been constructed in the past few years that can form the basis for diverse metabolic studies: the genome sequence, a single gene mutant collection, and a genome-scale metabolic model.
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10
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Huang WE, Singer AC, Spiers AJ, Preston GM, Whiteley AS. Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1. Environ Microbiol 2008; 10:1668-80. [DOI: 10.1111/j.1462-2920.2008.01583.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Zhang L, Li Y, Wang Z, Xia Y, Chen W, Tang K. Recent developments and future prospects of Vitreoscilla hemoglobin application in metabolic engineering. Biotechnol Adv 2007; 25:123-36. [PMID: 17184955 DOI: 10.1016/j.biotechadv.2006.11.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Revised: 11/02/2006] [Accepted: 11/02/2006] [Indexed: 11/27/2022]
Abstract
In hypoxic conditions, bacteria express a kind of hemoglobin, which is proposed to enhance respiration and energy metabolism by promoting oxygen delivery. Bacteria hemoglobin from Vitreoscilla stercoraria - Vitreoscilla hemoglobin (VHb), when expressed in various hosts in oxygen-limited conditions, has been shown to improve growth, protein secretion, metabolite productivity and stress resistance of hosts, thus rendering the protein promising in metabolic engineering, especially in plant metabolism optimization. In this review, many well-studies areas are presented to illustrate the potential of VHb application in biotechnology industry, to discuss the cellular mechanisms of VHb function and to show the wide variety of approaches taken within the field.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan-SJTU-Nottingham Plant Biotechnology R and D Center, Fudan University, Shanghai 200433, PR China
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12
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Abstract
This chapter focuses on protein engineering strategies that aim to increase the chances of obtaining crystals suitable for X-ray diffraction. The chapter is divided into three main parts: one dealing with protein engineering through a bioinformatics approach, the second focusing on DNA modifications via random mutagenesis, and the third describing a nonexhaustive number of in vitro modifications based on site-directed mutagenesis.
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Affiliation(s)
- Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Universités Aix-Marseille I et II, Marseille, France
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13
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Young DM, Parke D, Ornston LN. OPPORTUNITIES FOR GENETIC INVESTIGATION AFFORDED BYACINETOBACTER BAYLYI, A NUTRITIONALLY VERSATILE BACTERIAL SPECIES THAT IS HIGHLY COMPETENT FOR NATURAL TRANSFORMATION. Annu Rev Microbiol 2005; 59:519-51. [PMID: 16153178 DOI: 10.1146/annurev.micro.59.051905.105823] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genetic and physiological properties of Acinetobacter baylyi strain ADP1 make it an inviting subject for investigation of the properties underlying its nutritional versatility. The organism possesses a relatively small genome in which genes for most catabolic functions are clustered in several genetic islands that, unlike pathogenicity islands, give little evidence of horizontal transfer. Coupling mutagenic polymerase chain reaction to natural transformation provides insight into how structure influences function in transporters, transcriptional regulators, and enzymes. With appropriate selection, mutants in which such molecules have acquired novel function may be obtained. The extraordinary competence of A. baylyi for natural transformation and the ease with which it expresses heterologous genes make it a promising platform for construction of novel metabolic systems. Steps toward this goal should take into account the complexity of existing pathways in which transmembrane trafficking plays a significant role.
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Affiliation(s)
- David M Young
- 1Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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14
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Parke D, Ornston LN. Toxicity caused by hydroxycinnamoyl-coenzyme A thioester accumulation in mutants of Acinetobacter sp. strain ADP1. Appl Environ Microbiol 2004; 70:2974-83. [PMID: 15128559 PMCID: PMC404445 DOI: 10.1128/aem.70.5.2974-2983.2004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydroxycinnamates, aromatic compounds that play diverse roles in plants, are dissimilated by enzymes encoded by the hca genes in the nutritionally versatile, naturally transformable bacterium Acinetobacter sp. strain ADP1. A key step in the hca-encoded pathway is activation of the natural substrates caffeate, p-coumarate, and ferulate by an acyl:coenzyme A (acyl:CoA) ligase encoded by hcaC. As described in this paper, Acinetobacter cells with a knockout of the next enzyme in the pathway, hydroxycinnamoyl-CoA hydratase/lyase (HcaA), are extremely sensitive to the presence of the three natural hydroxycinnamate substrates; Escherichia coli cells carrying a subclone with the hcaC gene are hydroxycinnamate sensitive as well. When the hcaA mutation was combined with a mutation in the repressor HcaR, exposure of the doubly mutated Acinetobacter cells to caffeate, p-coumarate, or ferulate at 10(-6) M totally inhibited the growth of cells. The toxicity of p-coumarate and ferulate to a DeltahcaA strain was found to be a bacteriostatic effect. Although not toxic to wild-type cells initially, the diphenolic caffeate was itself converted to a toxin over time in the absence of cells; the converted toxin was bactericidal. In an Acinetobacter strain blocked in hcaA, a secondary mutation in the ligase (HcaC) suppresses the toxic effect. Analysis of suppression due to the mutation of hcaC led to the development of a positive-selection strategy that targets mutations blocking HcaC. An hcaC mutation from one isolate was characterized and was found to result in the substitution of an amino acid that is conserved in a functionally characterized homolog of HcaC.
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Affiliation(s)
- Donna Parke
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
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15
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Singh MV, Bland CE, Weil PA. Molecular and genetic characterization of a Taf1p domain essential for yeast TFIID assembly. Mol Cell Biol 2004; 24:4929-42. [PMID: 15143185 PMCID: PMC416396 DOI: 10.1128/mcb.24.11.4929-4942.2004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast Taf1p is an integral component of the multiprotein transcription factor TFIID. By using coimmunoprecipitation assays, coupled with a comprehensive set of deletion mutants encompassing the entire open reading frame of TAF1, we have discovered an essential role of a small portion of yeast Taf1p. This domain of Taf1p, termed region 4, consisting of amino acids 200 to 303, contributes critically to the assembly and stability of the 15-subunit TFIID holocomplex. Region 4 of Taf1p is mutationally sensitive, can assemble several Tafps into a partial TFIID complex, and interacts directly with Taf4p and Taf6p. Mutations in Taf1p-region 4 induce temperature-conditional growth of yeast cells. At the nonpermissive temperature these mutations have drastic effects on both TFIID integrity and mRNA synthesis. These data are consistent with the hypothesis that Taf1p subserves a critical scaffold function within the TFIID complex. The significance of these data with regard to TFIID structure and function is discussed.
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Affiliation(s)
- Madhu V Singh
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232-0615, USA
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16
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Parke D, Ornston LN. Hydroxycinnamate (hca) catabolic genes from Acinetobacter sp. strain ADP1 are repressed by HcaR and are induced by hydroxycinnamoyl-coenzyme A thioesters. Appl Environ Microbiol 2003; 69:5398-409. [PMID: 12957928 PMCID: PMC194952 DOI: 10.1128/aem.69.9.5398-5409.2003] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydroxycinnamates are plant products catabolized through the diphenol protocatechuate in the naturally transformable bacterium Acinetobacter sp. strain ADP1. Genes for protocatechuate catabolism are central to the dca-pca-qui-pob-hca chromosomal island, for which gene designations corresponding to catabolic function are dca (dicarboxylic acid), pca (protocatechuate), qui (quinate), pob (p-hydroxybenzoate), and hca (hydroxycinnamate). Acinetobacter hcaC had been cloned and shown to encode a hydroxycinnamate:coenzyme A (CoA) SH ligase that acts upon caffeate, p-coumarate, and ferulate, but genes for conversion of hydroxycinnamoyl-CoA to protocatechuate had not been characterized. In this investigation, DNA from pobS to an XbaI site 5.3 kb beyond hcaC was captured in the plasmid pZR8200 by a strategy that involved in vivo integration of a cloning vector near the hca region of the chromosome. pZR8200 enabled Escherichia coli to convert p-coumarate to protocatechuate in vivo. Sequence analysis of the newly cloned DNA identified five open reading frames designated hcaA, hcaB, hcaK, hcaR, and ORF1. An Acinetobacter strain with a knockout of HcaA, a homolog of hydroxycinnamoyl-CoA hydratase/lyases, was unable to grow at the expense of hydroxycinnamates, whereas a strain mutated in HcaB, homologous to aldehyde dehydrogenases, grew poorly with ferulate and caffeate but well with p-coumarate. A chromosomal fusion of lacZ to the hcaE gene was used to monitor expression of the hcaABCDE promoter. LacZ was induced over 100-fold by growth in the presence of caffeate, p-coumarate, or ferulate. The protein deduced to be encoded by hcaR shares 28% identity with the aligned E. coli repressor, MarR. A knockout of hcaR produced a constitutive phenotype, as assessed in the hcaE::lacZ-Km(r) genetic background, revealing HcaR to be a repressor as well. Expression of hcaE::lacZ in strains with knockouts in hcaA, hcaB, or hcaC revealed unambiguously that hydroxycinnamoyl-CoA thioesters relieve repression of the hcaABCDE genes by HcaR.
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Affiliation(s)
- Donna Parke
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
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17
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Kim SY, Sohn JH, Bae JH, Pyun YR, Agaphonov MO, Ter-Avanesyan MD, Choi ES. Efficient library construction by in vivo recombination with a telomere-originated autonomously replicating sequence of Hansenula polymorpha. Appl Environ Microbiol 2003; 69:4448-54. [PMID: 12902228 PMCID: PMC169078 DOI: 10.1128/aem.69.8.4448-4454.2003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high frequency of transformation and an equal gene dosage between transformants are generally required for activity-based selection of mutants from a library obtained by directed evolution. An efficient library construction method was developed by using in vivo recombination in Hansenula polymorpha. Various linear sets of vectors and insert fragments were transformed and analyzed to optimize the in vivo recombination system. A telomere-originated autonomously replicating sequence (ARS) of H. polymorpha, reported as a recombination hot spot, facilitates in vivo recombination between the linear transforming DNA and chromosomes. In vivo recombination of two linear DNA fragments containing the telomeric ARS drastically increases the transforming frequency, up to 10-fold, compared to the frequency of circular plasmids. Direct integration of the one-end-recombined linear fragment into chromosomes produced transformants with single-copy gene integration, resulting in the same expression level for the reporter protein between transformants. This newly developed in vivo recombination system of H. polymorpha provides a suitable library for activity-based selection of mutants after directed evolution.
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Affiliation(s)
- So-Young Kim
- Laboratory of Microbial Functions, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong, Taejon 305-333, Russia
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18
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Fabret C, Poncet S, Danielsen S, Borchert TV, Ehrlich SD, Jannière L. Efficient gene targeted random mutagenesis in genetically stable Escherichia coli strains. Nucleic Acids Res 2000; 28:E95. [PMID: 11058145 PMCID: PMC113164 DOI: 10.1093/nar/28.21.e95] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe a method to generate in vivo collections of mutants orders of magnitude larger than previously possible. The method favors accumulation of mutations in the target gene, rather than in the host chromosome. This is achieved by propagating the target gene on a plasmid, in Escherichia coli cells, within the region preferentially replicated by DNA polymerase I (Pol I), which replicates only a minor fraction of the chromosome. Mutagenesis is enhanced by a conjunction of a Pol I variant that has a low replication fidelity and the absence of the mutHLS system that corrects replication errors. The method was tested with two reporter genes, encoding lactose repressor or lipase. The proportion of mutants in the collection was estimated to reach 1% after one cycle of growth and 10% upon prolonged cell cultivation, resulting in collections of 10(12)-10(13) mutants per liter of cell culture. The extended cultivation did not affect growth properties of the cells. We suggest that our method is well suited for generating protein variants too rare to be present in the collections established by methods used previously and for isolating the genes that encode such variants by submitting the cells of the collections to appropriate selection protocols.
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Affiliation(s)
- C Fabret
- Unité de Génétique Microbienne, Domaine de Vilvert INRA, 78352 Jouy-en-Josas, France
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Nielsen KM, Smalla K, van Elsas JD. Natural transformation of Acinetobacter sp. strain BD413 with cell lysates of Acinetobacter sp., Pseudomonas fluorescens, and Burkholderia cepacia in soil microcosms. Appl Environ Microbiol 2000; 66:206-12. [PMID: 10618225 PMCID: PMC91807 DOI: 10.1128/aem.66.1.206-212.2000] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/1999] [Accepted: 10/20/1999] [Indexed: 11/20/2022] Open
Abstract
To elucidate the biological significance of dead bacterial cells in soil to the intra- and interspecies transfer of gene fragments by natural transformation, we have exposed the kanamycin-sensitive recipient Acinetobacter sp. strain BD413(pFG4) to lysates of the kanamycin-resistant donor bacteria Acinetobacter spp., Pseudomonas fluorescens, and Burkholderia cepacia. Detection of gene transfer was facilitated by the recombinational repair of a partially (317 bp) deleted kanamycin resistance gene in the recipient bacterium. The investigation revealed a significant potential of these DNA sources to transform Acinetobacter spp. residing both in sterile and in nonsterile silt loam soil. Heat-treated (80 degrees C, 15 min) cell lysates were capable of transforming strain BD413 after 4 days of incubation in sterile soil and for up to 8 h in nonsterile soil. Transformation efficiencies obtained in vitro and in situ with the various lysates were similar to or exceeded those obtained with conventionally purified DNA. The presence of cell debris did not inhibit transformation in soil, and the debris may protect DNA from rapid biological inactivation. Natural transformation thus provides Acinetobacter spp. with an efficient mechanism to access genetic information from different bacterial species in soil. The relatively short-term biological activity (e.g., transforming activity) of chromosomal DNA in soil contrasts the earlier reported long-term physical stability of DNA, where fractions have been found to persist for several weeks in soil. Thus, there seems to be a clear difference between the physical and the functional significance of chromosomal DNA in soil.
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Affiliation(s)
- K M Nielsen
- Unigen and Department of Botany, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
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