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Selas Castiñeiras T, Williams SG, Hitchcock AG, Smith DC. E. coli strain engineering for the production of advanced biopharmaceutical products. FEMS Microbiol Lett 2018; 365:5049002. [DOI: 10.1093/femsle/fny162] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/02/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Steven G Williams
- Cobra Biologics, Stephenson Building, The Science Park, Keele ST5 5SP, UK
| | - Antony G Hitchcock
- Cobra Biologics, Stephenson Building, The Science Park, Keele ST5 5SP, UK
| | - Daniel C Smith
- Cobra Biologics, Stephenson Building, The Science Park, Keele ST5 5SP, UK
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2
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Movement protein of Apple chlorotic leaf spot virus is genetically unstable and negatively regulated by Ribonuclease E in E. coli. Sci Rep 2017; 7:2133. [PMID: 28522867 PMCID: PMC5437062 DOI: 10.1038/s41598-017-02375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/10/2017] [Indexed: 12/03/2022] Open
Abstract
Movement protein (MP) of Apple chlorotic leaf spot virus (ACLSV) belongs to “30 K” superfamily of proteins and members of this family are known to show a wide array of functions. In the present study this gene was found to be genetically unstable in E. coli when transformed DH5α cells were grown at 28 °C and 37 °C. However, genetic instability was not encountered at 20 °C. Heterologous over expression failed despite the use of different transcriptional promoters and translational fusion constructs. Total cell lysate when subjected to western blotting using anti-ACLSV MP antibodies, showed degradation/cleavage of the expressed full-length protein. This degradation pointed at severe proteolysis or instability of the corresponding mRNA. Predicted secondary structure analysis of the transcript revealed a potential cleavage site for an endoribonuclease (RNase E) of E. coli. The negating effect of RNase E on transcript stability and expression was confirmed by northern blotting and quantitative RT-PCR of the RNA extracted from RNase E temperature sensitive mutant (strain N3431). The five fold accumulation of transcripts at non-permissive temperature (43 °C) suggests the direct role of RNase E in regulating the expression of ACLSV MP in E. coli.
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3
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Al-Allaf FA, Tolmachov OE, Zambetti LP, Tchetchelnitski V, Mehmet H. Remarkable stability of an instability-prone lentiviral vector plasmid in Escherichia coli Stbl3. 3 Biotech 2013; 3:61-70. [PMID: 28324350 PMCID: PMC3563744 DOI: 10.1007/s13205-012-0070-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 05/19/2012] [Indexed: 12/01/2022] Open
Abstract
Large-scale production of plasmid DNA to prepare therapeutic gene vectors or DNA-based vaccines requires a suitable bacterial host, which can stably maintain the plasmid DNA during industrial cultivation. Plasmid loss during bacterial cell divisions and structural changes in the plasmid DNA can dramatically reduce the yield of the desired recombinant plasmid DNA. While generating an HIV-based gene vector containing a bicistronic expression cassette 5′-Olig2cDNA-IRES-dsRed2-3′, we encountered plasmid DNA instability, which occurred in homologous recombination deficient recA1 Escherichia coli strain Stbl2 specifically during large-scale bacterial cultivation. Unexpectedly, the new recombinant plasmid was structurally changed or completely lost in 0.5 L liquid cultures but not in the preceding 5 mL cultures. Neither the employment of an array of alternative recA1 E. coli plasmid hosts, nor the lowering of the culture incubation temperature prevented the instability. However, after the introduction of this instability-prone plasmid into the recA13E. coli strain Stbl3, the transformed bacteria grew without being overrun by plasmid-free cells, reduction in the plasmid DNA yield or structural changes in plasmid DNA. Thus, E. coli strain Stbl3 conferred structural and maintenance stability to the otherwise instability-prone lentivirus-based recombinant plasmid, suggesting that this strain can be used for the faithful maintenance of similar stability-compromised plasmids in large-scale bacterial cultivations. In contrast to Stbl2, which is derived wholly from the wild type isolate E. coli K12, E. coli Stbl3 is a hybrid strain of mixed E. coli K12 and E. coli B parentage. Therefore, we speculate that genetic determinants for the benevolent properties of E. coli Stbl3 for safe plasmid propagation originate from its E. coli B ancestor.
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Affiliation(s)
- Faisal A Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Al-Abedia Campus, P. O. Box 715, Makkah, 21955, Saudi Arabia.
- Division of Clinical Sciences, Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK.
| | - Oleg E Tolmachov
- Faculty of Medicine, National Heart and Lung Institute, Sir Alexander Fleming Building, Imperial College London, London, SW7 2AZ, UK
| | - Lia Paola Zambetti
- Division of Clinical Sciences, Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Viktoria Tchetchelnitski
- Division of Clinical Sciences, Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Huseyin Mehmet
- Division of Clinical Sciences, Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
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4
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Speranskaya AS, Krinitsina AA, Kudryavtseva AV, Poltronieri P, Santino A, Oparina NY, Dmitriev AA, Belenikin MS, Guseva MA, Shevelev AB. Impact of recombination on polymorphism of genes encoding Kunitz-type protease inhibitors in the genus Solanum. Biochimie 2012; 94:1687-96. [DOI: 10.1016/j.biochi.2012.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 03/11/2012] [Indexed: 11/29/2022]
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5
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Bacterial artificial chromosome libraries of pulse crops: characteristics and applications. J Biomed Biotechnol 2011; 2012:493186. [PMID: 21811383 PMCID: PMC3144660 DOI: 10.1155/2012/493186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 05/29/2011] [Accepted: 05/30/2011] [Indexed: 12/01/2022] Open
Abstract
Pulse crops are considered minor on a global scale despite their nutritional value for human consumption. Therefore, they are relatively less extensively studied in comparison with the major crops. The need to improve pulse crop production and quality will increase with the increasing global demand for food security and people's awareness of nutritious food. The improvement of pulse crops will require fully utilizing all their genetic resources. Bacterial artificial chromosome (BAC) libraries of pulse crops are essential genomic resources that have the potential to accelerate gene discovery and enhance molecular breeding in these crops. Here, we review the availability, characteristics, applications, and potential applications of the BAC libraries of pulse crops.
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6
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d'Avenia M, Rosati A, Belisario MA, Torino M, Torino G, Turco MC, Pascale M. The expression of the pro-apoptotic gene Air is inducible in human pancreatic adenocarcinoma cells. J Cell Physiol 2011; 226:2207-12. [DOI: 10.1002/jcp.22736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Blakesley RW, Hansen NF, Gupta J, McDowell JC, Maskeri B, Barnabas BB, Brooks SY, Coleman H, Haghighi P, Ho SL, Schandler K, Stantripop S, Vogt JL, Thomas PJ, Bouffard GG, Green ED. Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates. BMC Genomics 2010; 11:21. [PMID: 20064230 PMCID: PMC2827409 DOI: 10.1186/1471-2164-11-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 01/11/2010] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage. RESULTS To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain. CONCLUSION Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.
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Affiliation(s)
- Robert W Blakesley
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Wahls WP, Davidson MK. Low-copy episomal vector pFY20 and high-saturation coverage genomic libraries for the fission yeast Schizosaccharomyces pombe. Yeast 2008; 25:643-50. [PMID: 18613214 DOI: 10.1002/yea.1605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In fission yeast, as in many organisms, episomally replicating plasmid DNA molecules can be used for a wide variety of applications. However, replicating plasmids described previously are each propagated at a high copy number per cell. Plasmid fission yeast twenty (pFY20) contains the ura4(+) gene for positive and negative selection, an origin of replication (ars1) and a stability element (stb). Although this plasmid does not have a centromere, it is propagated with a copy number of about two plasmids per haploid genome equivalent and it is transmitted with relatively high fidelity in mitosis and meiosis. This low-copy vector is useful for screens and mutational studies where overexpression (e.g. from high copy plasmids) is undesirable. We therefore constructed multiple partial-digest, size-fractionated, fission yeast genomic DNA libraries in pFY20 and in the cloning vector pBluescript KS(+). These libraries have sufficient complexity (average of 2100 genome equivalents each) for saturation screening by complementation, plasmid shuffle or hybridization.
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Affiliation(s)
- Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205-7199, USA
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9
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Simões-Barbosa A, Argañaraz ER, Barros AM, Rosa ADC, Alves NP, Louvandini P, D'Souza-Ault MR, Nitz N, Sturm NR, Nascimento RJ, Teixeira ARL. Hitchhiking Trypanosoma cruzi minicircle DNA affects gene expression in human host cells via LINE-1 retrotransposon. Mem Inst Oswaldo Cruz 2007; 101:833-43. [PMID: 17293976 DOI: 10.1590/s0074-02762006000800003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Accepted: 09/19/2006] [Indexed: 11/22/2022] Open
Abstract
The horizontal transfer of Trypanosoma cruzi mitochondrial minicircle DNA to the genomes of naturally infected humans may play an important role in the pathogenesis of Chagas disease. Minicircle integrations within LINE-1 elements create the potential for foreign DNA mobility within the host genome via the machinery associated with this retrotransposon. Here we document integration of minicircle DNA fragments in clonal human macrophage cell lines and their mobilization over time. The movement of an integration event in a clonal transfected cell line was tracked at three months and three years post-infection. The minicircle sequence integrated into a LINE-1 retrotransposon; one such foreign fragment subsequently relocated to another genomic location in association with associated LINE-1 elements. The p15 locus was altered at three years as a direct effect of minicircle/LINE-1 acquisition, resulting in elimination of p15 mRNA. Here we show for the first time a molecular pathology stemming from mobilization of a kDNA/LINE-1 mutation. These genomic changes and detected transcript variations are consistent with our hypothesis that minicircle integration is a causal component of parasite-independent, autoimmune-driven lesions seen in the heart and other target tissues associated with Chagas disease.
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Affiliation(s)
- Augusto Simões-Barbosa
- Laboratório Multidisciplinar de Pesquisa em Doença de Chagas, Universidade de Brasília, 70919-970 Brasília, DF, Brasil
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Egorov IK. Mouse models of efficient and inefficient anti-tumor immunity, with emphasis on minimal residual disease and tumor escape. Cancer Immunol Immunother 2006; 55:1-22. [PMID: 16091932 PMCID: PMC11030122 DOI: 10.1007/s00262-005-0007-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 03/25/2005] [Indexed: 10/25/2022]
Abstract
Tumor escape from the host immune response remains the major problem holding the development of immunotherapies for cancer. In this review, congenic mouse lines are discussed that differ dramatically in their ability to respond to tumors tested and, thereby, to survive or to succumb to the tumor and/or its metastases. This ability is under the control of either MHC class I or nontrivial MHC class II beta genes expressed in a small subpopulation of antigen-presenting cells. Two hypotheses can explain the results obtained so far: (1) emergence of tumor cell variants that escape the host immune response in morbid mice but are eliminated in survivors, and (2) tumor-induced immunosuppression, which is either efficient or not, depending on the congenic line used. It is argued that further experimentation on these congenics will allow to choose the correct hypothesis, and to characterize the mechanism(s) of elimination of minimal residual disease and prevention of tumor escape by the immune system of survivors as well as the reason(s) for its failure in morbid mice. It is also argued that the use of these models will substantially increase the chance to resolve the controversy of poor correlation of immunotherapy testing in mice with clinical results.
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Affiliation(s)
- Igor K Egorov
- The Jackson Laboratory, Bar Harbor, ME 04609-1500, USA,
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11
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Ammiraju JSS, Yu Y, Luo M, Kudrna D, Kim H, Goicoechea JL, Katayose Y, Matsumoto T, Wu J, Sasaki T, Wing RA. Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1596-607. [PMID: 16200416 DOI: 10.1007/s00122-005-0091-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 08/15/2005] [Indexed: 05/04/2023]
Abstract
The International Rice Genome Sequencing Project has recently announced the high-quality finished sequence that covers nearly 95% of the japonica rice genome representing 370 Mbp. Nevertheless, the current physical map of japonica rice contains 62 physical gaps corresponding to approximately 5% of the genome, that have not been identified/represented in the comprehensive array of publicly available BAC, PAC and other genomic library resources. Without finishing these gaps, it is impossible to identify the complete complement of genes encoded by rice genome and will also leave us ignorant of some 5% of the genome and its unknown functions. In this article, we report the construction and characterization of a tenfold redundant, 40 kbp insert fosmid library generated by random mechanical shearing. We demonstrated its utility in refining the physical map of rice by identifying and in silico mapping 22 gap-specific fosmid clones with particular emphasis on chromosomes 1, 2, 6, 7, 8, 9 and 10. Further sequencing of 12 of the gap-specific fosmid clones uncovered unique rice genome sequence that was not previously reported in the finished IRGSP sequence and emphasizes the need to complete finishing of the rice genome.
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Affiliation(s)
- Jetty S S Ammiraju
- Department of Plant Sciences and BIO5 Institute, Arizona Genomics Institute, The University of Arizona, Tucson, AZ 85721, USA
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12
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Al-Allaf FA, Tolmachov O, Themis M, Coutelle C. Coupled analysis of bacterial transformants and ligation mixture by duplex PCR enables detection of fatal instability of a nascent recombinant plasmid. ACTA ACUST UNITED AC 2005; 64:142-6. [PMID: 16054701 DOI: 10.1016/j.jbbm.2005.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 04/26/2005] [Accepted: 04/26/2005] [Indexed: 10/25/2022]
Abstract
When a DNA cloning experiment fails, it is often difficult to distinguish between an inadequate cloning protocol and instability of the new recombinant plasmid. The identification of plasmid instability is particularly challenging when the instability is fatal and no DNA of the expected construct can be isolated. We have effectively addressed this problem by employment of duplex PCR (insert-insert, vector-insert) to analyse both the ligation mixture and the resultant bacterial transformants. Using this approach we found a fatal maintenance instability of one of the plasmids generated during subcloning of the cDNA for human LDLR in Escherichia coli STBL2. The described duplex PCR screening method allows monitoring of the fate of nascent recombinant plasmid from ligation, through the initial bacterial colony and the subsequent overnight culture.
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Affiliation(s)
- Faisal A Al-Allaf
- Section of Cell and Molecular Biology, Faculty of Medicine, 2nd floor, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK.
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Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, Maskeri B, Young AC, Benjamin B, Brooks SY, Coleman BI, Gupta J, Ho SL, Karlins EM, Maduro QL, Stantripop S, Tsurgeon C, Vogt JL, Walker MA, Masiello CA, Guan X, Bouffard GG, Green ED. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res 2004; 14:2235-44. [PMID: 15479945 PMCID: PMC525681 DOI: 10.1101/gr.2648404] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 08/16/2004] [Indexed: 11/25/2022]
Abstract
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of "sequence finishing" remains expensive. Near-perfect finished sequence is an appropriate goal for the human genome and a small set of reference genomes; however, such a high-quality product cannot be cost-justified for large numbers of additional genomes, at least for the foreseeable future. Here we describe the generation and quality of an intermediate grade of finished genomic sequence (termed comparative-grade finished sequence), which is tailored for use in multispecies sequence comparisons. Our analyses indicate that this sequence is very high quality (with the residual gaps and errors mostly falling within repetitive elements) and reflects 99% of the total sequence. Importantly, comparative-grade sequence finishing requires approximately 40-fold less reagents and approximately 10-fold less personnel effort compared to the generation of near-perfect finished sequence, such as that produced for the human genome. Although applied here to finishing sequence derived from individual bacterial artificial chromosome (BAC) clones, one could envision establishing routines for refining sequences emanating from whole-genome shotgun sequencing projects to a similar quality level. Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses.
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Affiliation(s)
- Robert W Blakesley
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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14
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Keith JM, Cochran DAE, Lala GH, Adams P, Bryant D, Mitchelson KR. Unlocking hidden genomic sequence. Nucleic Acids Res 2004; 32:e35. [PMID: 14973330 PMCID: PMC373418 DOI: 10.1093/nar/gnh022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs.
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Affiliation(s)
- Jonathan M Keith
- Department of Mathematics, University of Queensland, St Lucia, Queensland 4072, Australia.
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15
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Leem SH, Kouprina N, Grimwood J, Kim JH, Mullokandov M, Yoon YH, Chae JY, Morgan J, Lucas S, Richardson P, Detter C, Glavina T, Rubin E, Barrett JC, Larionov V. Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements. Genome Res 2004; 14:239-46. [PMID: 14718380 PMCID: PMC327099 DOI: 10.1101/gr.1929904] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2003] [Accepted: 11/24/2003] [Indexed: 12/18/2022]
Abstract
The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to approximately 1% of euchromatic regions of the human genome. Gap filling is a laborious process because it relies on analysis of random clones of numerous genomic BAC or cosmid libraries. In this work we demonstrate that closing the gaps can be accelerated by a selective recombinational capture of missing chromosomal segments in yeast. The use of both methodologies allowed us to close the four remaining gaps on the human chromosome 19. Analysis of the gap sequences revealed that they contain several abnormalities that could result in instability of the sequences in microbe hosts, including large blocks of micro- and minisatellites and a high density of Alu repeats. Sequencing of the gap regions, in both BAC and YAC forms, allowed us to generate a complete sequence of four genes, including the neuronal cell signaling gene SCK1/SLI. The SCK1/SLI gene contains a record number of minisatellites, most of which are polymorphic and transmitted through meiosis following a Mendelian inheritance. In conclusion, the use of the alternative recombinational cloning system in yeast may greatly accelerate work on closing the remaining gaps in the human genome (as well as in other complex genomes) to achieve the goal of annotation of all human genes.
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Affiliation(s)
- Sun-Hee Leem
- Laboratory of Biosystems and Cancer, Center for Cancer Research, National Cancer Institute (NCI, NIH), Bethesda, Maryland 20892, USA
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16
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Kouprina N, Larionov V. Exploiting the yeast Saccharomyces cerevisiae for the study of the organization and evolution of complex genomes. FEMS Microbiol Rev 2004; 27:629-49. [PMID: 14638416 DOI: 10.1016/s0168-6445(03)00070-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Yeast artificial chromosome (YAC) cloning systems have advanced the analysis of complex genomes considerably. They permit the cloning of larger fragments than do bacterial artificial chromosome systems, and the cloned material is more easily modified. We recently developed a novel YAC cloning system called transformation-associated recombination (TAR) cloning. Using in vivo recombination in yeast, TAR cloning selectively isolates, as circular YACs, desired chromosome segments or entire genes from complex genomes. The ability to do that without constructing a representative genomic library of random clones greatly facilitates analysis of gene function and its role in disease. In this review, we summarize how recombinational cloning techniques have advanced the study of complex genome organization, gene expression, and comparative genomics.
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Affiliation(s)
- Natalay Kouprina
- National Cancer Institute, NIH, Bldg. 37, Room 5032, 90000 Rockville Pike, Bethesda, MD 20892, USA
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17
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Kouprina N, Leem SH, Solomon G, Ly A, Koriabine M, Otstot J, Pak E, Dutra A, Zhao S, Barrett JC, Larionov V. Segments missing from the draft human genome sequence can be isolated by transformation-associated recombination cloning in yeast. EMBO Rep 2003; 4:257-62. [PMID: 12634842 PMCID: PMC1315894 DOI: 10.1038/sj.embor.embor766] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2002] [Revised: 12/05/2002] [Accepted: 12/18/2002] [Indexed: 11/09/2022] Open
Abstract
The reported draft human genome sequence includes many contigs that are separated by gaps of unknown sequence. These gaps may be due to chromosomal regions that are not present in the Escherichia coli libraries used for DNA sequencing because they cannot be cloned efficiently, if at all, in bacteria. Using a yeast artificial chromosome (YAC)/ bacterial artificial chromosome (BAC) library generated in yeast, we found that approximately 6% of human DNA sequences tested transformed E. coli cells less efficiently than yeast cells, and were less stable in E. coli than in yeast. When the ends of several YAC/BAC isolates cloned in yeast were sequenced and compared with the reported draft sequence, major inconsistencies were found with the sequences of those YAC/BAC isolates that transformed E. coli cells inefficiently. Two human genomic fragments were re-isolated from human DNA by transformation-associated recombination (TAR) cloning. Re-sequencing of these regions showed that the errors in the draft are the results of both missassembly and loss of specific DNA sequences during cloning in E. coli. These results show that TAR cloning might be a valuable method that could be widely used during the final stages of the Human Genome Project.
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Affiliation(s)
- Natalay Kouprina
- Laboratory of Biosystems and Cancer, National Cancer Institute, Building 37, Room 5031, Bethesda, Maryland 20892, USA.
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18
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Völker J, Makube N, Plum GE, Klump HH, Breslauer KJ. Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: implications for triplet expansion diseases. Proc Natl Acad Sci U S A 2002; 99:14700-5. [PMID: 12417759 PMCID: PMC137482 DOI: 10.1073/pnas.222519799] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have embedded the hexameric triplet repeats (CAG)(6) and (CTG)(6) between two (GC)(3) domains to produce two 30-mer hairpins with the sequences d[(GC)(3)(CAG)(6)(GC)(3)] and d[(GC)(3)(CTG)(6)(GC)(3)]. This construct reduces the conformational space available to these repetitive DNA sequences. We find that the (CAG)(6) and (CTG)(6) repeats form stable, ordered, single-stranded structures. These structures are stabilized at 62 degrees C by an average enthalpy per base of 1.38 kcal.mol(-1) for the CAG triplet and 2.87 kcal.mol(-1) for the CTG triplet, while being entropically destabilized by 3.50 cal.K(-1).mol(-1) for the CAG triplet and 7.6 cal.K(-1).mol(-1) for the CTG triplet. Remarkably, these values correspond, respectively, to 1/3 (for CAG) and 2/3 (for CTG) of the enthalpy and entropy per base values associated with Watson-Crick base pairs. We show that the presence of the loop structure kinetically inhibits duplex formation from the two complementary 30-mer hairpins, even though the duplex is the thermodynamically more stable state. Duplex formation, however, does occur at elevated temperatures. We propose that this thermally induced formation of a more stable duplex results from thermal disruption of the single-stranded order, thereby allowing the complementary domains to associate (perhaps via "kissing hairpins"). Our melting profiles show that, once duplex formation has occurred, the hairpin intermediate state cannot be reformed, consistent with our interpretation of kinetically trapped hairpin structures. The duplex formed by the two complementary oligonucleotides does not have any unusual optical or thermodynamic properties. By contrast, the very stable structures formed by the individual single-stranded triplet repeat sequences are thermally and thermodynamically unusual. We discuss this stable, triplet repeat, single-stranded structure and its interconversion with duplex in terms of triplet expansion diseases.
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Affiliation(s)
- J Völker
- Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, 610 Taylor Road, Piscataway 08854, USA
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Lubjuhn T, Sramkova A, Masello JF, Quillfeldt P, Epplen JT. Truly hypervariable DNA fingerprints due to exceptionally high mutation rates. Electrophoresis 2002; 23:517-9. [PMID: 11870758 DOI: 10.1002/1522-2683(200202)23:4<517::aid-elps517>3.0.co;2-3] [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] [Indexed: 11/06/2022]
Abstract
The power of DNA fingerprinting is due to comparatively high mutation rates of minisatellite and microsatellite DNA sequences. Studying the mating system of a parrot species (Burrowing Parrots, Cyanoliseus patagonus) using oligonucleotide probes, we observed mutation rates that are several orders of magnitude higher than those described anywhere in the literature. Most plausibly, the respective values are based on 3-4 loci with mutation rates of up to 100%.
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Affiliation(s)
- Thomas Lubjuhn
- Institute for Evolutionary Biology and Ecology, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany.
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Organization, Replication, Transposition, and Repair of DNA. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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