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Pan H, Guo X, Pan Z, Wang R, Tian B, Li H. Fork PCR: a universal and efficient genome-walking tool. Front Microbiol 2023; 14:1265580. [PMID: 37808312 PMCID: PMC10556450 DOI: 10.3389/fmicb.2023.1265580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
The reported genome-walking methods still suffer from some deficiencies, such as cumbersome experimental steps, short target amplicon, or deep background. Here, a simple and practical fork PCR was proposed for genome-walking. The fork PCR employs a fork primer set of three random oligomers to implement walking task. In primary fork PCR, the low-stringency amplification cycle mediates the random binding of primary fork primer to some places on genome, producing a batch of single-stranded DNAs. In the subsequent high-stringency amplification, the target single-strand is processed into double-strand by the site-specific primer, but a non-target single-stranded DNA cannot be processed by any primer. As a result, only the target DNA can be exponentially amplified in the remaining high-stringency cycles. Secondary/tertiary nested fork PCR(s) further magnifies the amplification difference between the both DNAs by selectively enriching target DNA. The applicability of fork PCR was validated by walking several gene loci. The fork PCR could be a perspective substitution for the existing genome-walking schemes.
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Affiliation(s)
- Hao Pan
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, China
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Xinyue Guo
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Zhenkang Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Rongrong Wang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Bingkun Tian
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Haixing Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
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Trinh Q, Shi H, Xu W, Hao J, Luo Y, Huang K. Loop-linker PCR: an advanced PCR technique for genome walking. IUBMB Life 2012; 64:841-5. [PMID: 23008115 DOI: 10.1002/iub.1069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this article, we developed a novel PCR method, termed loop-linker PCR, to isolate flanking sequences in transgenic crops. The novelty of this approach is its use of a stem-loop structure to design a loop-linker adapter. The adapter is designed to form a nick site when ligated with restricted DNA. This modification not only can prevent the self-ligation of adapters but also promotes the elongation of the 3' end of the loop-linker adapter to generate a stem-loop structure in the ligation products. Moreover, the suppressive effect of the stem-loop structure decreases nonspecific amplification and increases the success rate of the approach; all extension products will suppress exponential amplification except from the ligation product that contains the specific primer binding site. Using this method, 442, 1830, 107, and 512 bp left border flanking sequences were obtained from the transgenic maizes LY038, DAS-59122-7, Event 3272, and the transgenic soybean MON89788, respectively. The experimental results demonstrated that loop-linker PCR is an efficient, reliable, and cost-effective method for identifying flanking sequences in transgenic crops and could be applied for other genome walking applications.
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Affiliation(s)
- Quoclinh Trinh
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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Trinh Q, Xu W, Shi H, Luo Y, Huang K. An A-T linker adapter polymerase chain reaction method for chromosome walking without restriction site cloning bias. Anal Biochem 2012; 425:62-7. [PMID: 22406246 DOI: 10.1016/j.ab.2012.02.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 02/19/2012] [Accepted: 02/22/2012] [Indexed: 11/29/2022]
Abstract
A-T linker adapter polymerase chain reaction (PCR) was modified and employed for the isolation of genomic fragments adjacent to a known DNA sequence. The improvements in the method focus on two points. The first is the modification of the PO(4) and NH(2) groups in the adapter to inhibit the self-ligation of the adapter or the generation of nonspecific products. The second improvement is the use of the capacity of rTaq DNA polymerase to add an adenosine overhang at the 3' ends of digested DNA to suppress self-ligation in the digested DNA and simultaneously resolve restriction site clone bias. The combination of modifications in the adapter and in the digested DNA leads to T/A-specific ligation, which enhances the flexibility of this method and makes it feasible to use many different restriction enzymes with a single adapter. This novel A-T linker adapter PCR overcomes the inherent limitations of the original ligation-mediated PCR method such as low specificity and a lack of restriction enzyme choice. Moreover, this method also offers higher amplification efficiency, greater flexibility, and easier manipulation compared with other PCR methods for chromosome walking. Experimental results from 143 Arabidopsis mutants illustrate that this method is reliable and efficient in high-throughput experiments.
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Affiliation(s)
- Quoclinh Trinh
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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Glanz S, Jacobs J, Kock V, Mishra A, Kück U. Raa4 is a trans-splicing factor that specifically binds chloroplast tscA intron RNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:421-431. [PMID: 21954961 DOI: 10.1111/j.1365-313x.2011.04801.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
During trans-splicing of discontinuous organellar introns, independently transcribed coding sequences are joined together to generate a continuous mRNA. The chloroplast psaA gene from Chlamydomonas reinhardtii encoding the P(700) core protein of photosystem I (PSI) is split into three exons and two group IIB introns, which are both spliced in trans. Using forward genetics, we isolated a novel PSI mutant, raa4, with a defect in trans-splicing of the first intron. Complementation analysis identified the affected gene encoding the 112.4 kDa Raa4 protein, which shares no strong sequence identity with other known proteins. The chloroplast localization of the protein was confirmed by confocal fluorescence microscopy, using a GFP-tagged Raa4 fusion protein. RNA-binding studies showed that Raa4 binds specifically to domains D2 and D3, but not to other conserved domains of the tripartite group II intron. Raa4 may play a role in stabilizing folding intermediates or functionally active structures of the split intron RNA.
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Affiliation(s)
- Stephanie Glanz
- Department for General and Molecular Botany, Ruhr-University Bochum, D-44780 Bochum, Germany
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Jacobs J, Glanz S, Bunse-Grassmann A, Kruse O, Kück U. RNA trans-splicing: identification of components of a putative chloroplast spliceosome. Eur J Cell Biol 2010; 89:932-9. [PMID: 20705358 DOI: 10.1016/j.ejcb.2010.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Group II introns with highly complex RNA structures have been discovered in both prokaryotes and eukaryotic organelles. Usually, excision of non-coding group II intron sequences occurs by cis-splicing, the intramolecular ligation of exons in the same precursor RNA, but some group II introns are excised by intermolecular ligation. This process is called trans-splicing, and genome sequencing predicted that this type of RNA processing occurs in more than 180 organelle genomes from eukaryotes. A well characterised trans-spliced intron RNA is represented by the chloroplast psaA gene of the model alga Chlamydomonas reinhardtii. The psaA gene is split into three exons, which are widely distributed over the plastome and transcribed independently. PsaA exons are flanked by sequences typical for group II introns and joined by trans-splicing via two transesterification reactions. Although it is known that some group II introns are able to splice autocatalytically, trans-splicing of the psaA RNA depends on several nucleus and chloroplast encoded factors. The phylogenetic relationship between group II introns and nuclear spliceosomal RNA led to the hypothesis that these factors are part of large multiprotein and ribonucleoprotein complexes akin to the nuclear spliceosome. Here, we give a concise overview of experimental strategies to identify novel factors involved in trans-splicing of psaA RNA and review recent results that have elucidated the composition and function of a putative chloroplast spliceosome involved in processing of chloroplast precursor RNAs.
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Affiliation(s)
- Jessica Jacobs
- Department for General and Molecular Biology, Ruhr-University Bochum, 44780 Bochum, Germany
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Tang X, Jin Y, Cande WZ. Bqt2p is essential for initiating telomere clustering upon pheromone sensing in fission yeast. ACTA ACUST UNITED AC 2006; 173:845-51. [PMID: 16769823 PMCID: PMC2063910 DOI: 10.1083/jcb.200602152] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The telomere bouquet, i.e., telomere clustering on the nuclear envelope (NE) during meiotic prophase, is thought to promote homologous chromosome pairing. Using a visual screen, we identified bqt2/im295, a mutant that disrupts telomere clustering in fission yeast. Bqt2p is required for linking telomeres to the meiotic spindle pole body (SPB) but not for attachment of telomeres or the SPB to the NE. Bqt2p is expressed upon pheromone sensing and colocalizes thereafter to Sad1p, an SPB protein. This localization only depends on Bqt1p, not on other identified proteins required for telomere clustering. Upon pheromone sensing, generation of Sad1p foci next to telomeres depends on Bqt2p. However, depletion of Bqt2p from the SPB is dispensable for dissolving the telomere bouquet at the end of meiotic prophase. Therefore, telomere bouquet formation requires Bqt2p as a linking component and is finely regulated during meiotic progression.
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Affiliation(s)
- Xie Tang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Jeung JU, Cho SK, Shin JS. A partial-complementary adapter for an improved and simplified ligation-mediated suppression PCR technique. ACTA ACUST UNITED AC 2005; 64:110-20. [PMID: 16005075 DOI: 10.1016/j.jbbm.2005.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 04/18/2005] [Accepted: 06/06/2005] [Indexed: 11/20/2022]
Abstract
Ligation-mediated suppression PCR (LMS-PCR) is a powerful tool for walking in unknown genomic DNA regions from known adjacent sequences. This approach has made it feasible to obtain promoter sequences and to enable researchers to identify full-length gene sequences or isoforms of multigene families. However, the advantages of LMS-PCR can be obviated by the presence of incomplete base modifications on the suppression adapters. We propose here that a 'partial-complementary adapter' is a more reliable suppression adapter, demanding only 5'-end phosphorylation. We also describe a simplified procedure for the easier preparation of PCR templates with very small quantities of DNA and a fast and direct characterization of the suppression-PCR products. A set of practical guidelines is proposed for pre-checking the efficiency of the adapter modification using two model systems: bacteriophage lambda (lambda) and Arabidopsis.
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Affiliation(s)
- Ji-Ung Jeung
- IRRI-Korea Office, NICS, RDA, Suwon 441-854, Korea
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Schönfeld C, Wobbe L, Borgstädt R, Kienast A, Nixon PJ, Kruse O. The nucleus-encoded protein MOC1 is essential for mitochondrial light acclimation in Chlamydomonas reinhardtii. J Biol Chem 2004; 279:50366-74. [PMID: 15448140 DOI: 10.1074/jbc.m408477200] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial respiration plays an important role in optimizing photosynthetic efficiency in plants. As yet, the mechanisms by which plant mitochondria sense and respond to changes in the environment are unclear, particularly when exposed to light. Here we describe the characterization of the Chlamydomonas reinhardtii mutant stm6, which was identified on the basis of impaired state transitions, a mechanism that regulates light harvesting in the chloroplast. The gene disrupted in stm6, termed Moc1, encodes a homologue of the human mitochondrial transcription termination factor (mTERF). MOC1 is targeted to the mitochondrion, and its expression is up-regulated in response to light. Loss of MOC1 causes a high light-sensitive phenotype and disrupts the transcription and expression profiles of the mitochondrial respiratory complexes causing, as compared with wild type, light-mediated changes in the expression levels of nuclear and mitochondrial encoded cytochrome c oxidase subunits and ubiquinone-NAD subunits. The absence of MOC1 leads to a reduction in the levels of cytochrome c oxidase and of rotenone-insensitive external NADPH dehydrogenase activities of the mitochondrial respiratory electron transfer chain. Overall, we have identified a novel mitochondrial factor that regulates the composition of the mitochondrial respiratory chain in the light so that it can act as an effective sink for reductant produced by the chloroplast.
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Affiliation(s)
- Christine Schönfeld
- Molecular Cell Physiology Group, Department of Biology, University of Bielefeld, 33501 Bielefeld, Germany
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Stauber EJ, Fink A, Markert C, Kruse O, Johanningmeier U, Hippler M. Proteomics of Chlamydomonas reinhardtii light-harvesting proteins. EUKARYOTIC CELL 2004; 2:978-94. [PMID: 14555480 PMCID: PMC219354 DOI: 10.1128/ec.2.5.978-994.2003] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
With the recent development of techniques for analyzing transmembrane thylakoid proteins by two-dimensional gel electrophoresis, systematic approaches for proteomic analyses of membrane proteins became feasible. In this study, we established detailed two-dimensional protein maps of Chlamydomonas reinhardtii light-harvesting proteins (Lhca and Lhcb) by extensive tandem mass spectrometric analysis. We predicted eight distinct Lhcb proteins. Although the major Lhcb proteins were highly similar, we identified peptides which were unique for specific lhcbm gene products. Interestingly, lhcbm6 gene products were resolved as multiple spots with different masses and isoelectric points. Gene tagging experiments confirmed the presence of differentially N-terminally processed Lhcbm6 proteins. The mass spectrometric data also revealed differentially N-terminally processed forms of Lhcbm3 and phosphorylation of a threonine residue in the N terminus. The N-terminal processing of Lhcbm3 leads to the removal of the phosphorylation site, indicating a potential novel regulatory mechanism. At least nine different lhca-related gene products were predicted by comparison of the mass spectrometric data against Chlamydomonas expressed sequence tag and genomic databases, demonstrating the extensive variability of the C. reinhardtii Lhca antenna system. Out of these nine, three were identified for the first time at the protein level. This proteomic study demonstrates the complexity of the light-harvesting proteins at the protein level in C. reinhardtii and will be an important basis of future functional studies addressing this diversity.
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Affiliation(s)
- Einar J Stauber
- Lehrstuhl für Pflanzenphysiologie, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
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Hanikenne M. Chlamydomonas reinhardtii as a eukaryotic photosynthetic model for studies of heavy metal homeostasis and tolerance. THE NEW PHYTOLOGIST 2003; 159:331-340. [PMID: 33873346 DOI: 10.1046/j.1469-8137.2003.00788.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a useful model of a photosynthetic cell. This unicellular eukaryote has been intensively used for studies of a number of physiological processes such as photosynthesis, respiration, nitrogen assimilation, flagella motility and basal body function. Its easy-to-manipulate and short life cycle make this organism a powerful tool for genetic analysis. Over the past 15 yr, a dramatically increased number of molecular technologies (including nuclear and organellar transformation systems, cosmid, yeast artificial chromosome (YAC) and bacterial artificial chromosome (BAC) libraries, reporter genes, RNA interference, DNA microarrays, etc.) have been applied to Chlamydomonas. Moreover, as parts of the Chlamydomonas genome project, molecular mapping, as well as whole genome and extended expressed sequence tag (EST) sequencing programs, are currently underway. These developments have allowed Chlamydomonas to become an extremely valuable model for molecular approaches to heavy metal homeostasis and tolerance in photosynthetic organisms.
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Affiliation(s)
- M Hanikenne
- Genetics of Microorganisms, Department of Life Sciences, B22, University of Liège, B4000 Liège, Belgium
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