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Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123090. [PMID: 37413921 DOI: 10.1016/j.saa.2023.123090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.
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Affiliation(s)
- Ana Sarić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Jovana Rajić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Anja Tolić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Tanja Dučić
- ALBA CELLS Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Valles, 08290 Barcelona, Spain.
| | - Melita Vidaković
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
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2
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Razin SV, Zhegalova IV, Kantidze OL. Domain Model of Eukaryotic Genome Organization: From DNA Loops Fixed on the Nuclear Matrix to TADs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:667-680. [PMID: 36154886 DOI: 10.1134/s0006297922070082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 06/16/2023]
Abstract
The article reviews the development of ideas on the domain organization of eukaryotic genome, with special attention on the studies of DNA loops anchored to the nuclear matrix and their role in the emergence of the modern model of eukaryotic genome spatial organization. Critical analysis of results demonstrating that topologically associated chromatin domains are structural-functional blocks of the genome supports the notion that these blocks are fundamentally different from domains whose existence was proposed by the domain hypothesis of eukaryotic genome organization formulated in the 1980s. Based on the discussed evidence, it is concluded that the model postulating that eukaryotic genome is built from uniformly organized structural-functional blocks has proven to be untenable.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Zhegalova
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Kharkevich Institute for Information Transmission Problems, Moscow, 127051, Russia
| | - Omar L Kantidze
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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3
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Barranco I, Salas-Huetos A, Berlanga A, Spinaci M, Yeste M, Ribas-Maynou J. Involvement of extracellular vesicle-encapsulated miRNAs in human reproductive disorders: a systematic review. Reprod Fertil Dev 2022; 34:751-775. [PMID: 35527383 DOI: 10.1071/rd21301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
In recent years, extracellular vesicles (EVs) have emerged as essential players in cell-to-cell communication, particularly having an active regulating role in biological systems. Because reproductive-associated processes are not exempt of this communication, multiple studies have been devoted to this realm, focusing on gamete maturation, embryo implantation or fetal development. The aim of the present review was to comprehensively and systematically collect evidence about the function of the microRNA (miRNA) encapsulated in EVs isolated from different reproductive tissues or fluids in reproductive-related diseases. Following PRISMA guidelines, we conducted a systematic search of the literature published in MEDLINE-PubMed until the end of February 2021. After selection, 32 studies were included in the qualitative review comparing the miRNA expression profile in EVs between different pathological disorders. Most reports showed the potential of the miRNAs carried by EVs to be used as putative biomarkers of reproductive disorders, including pregnancy affections, disease progression and quality of preimplantation embryos. The most relevant miRNAs were found to be highly heterogeneous among studies, with some conflicting results. Further research is thus warranted to address whether cofounding factors, such as the methods to isolate EVs and miRNAs, the subset of EVs, the criteria of patient selection, the timing of sample retrieval, or any other factor, may explain the inconsistencies between studies.
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Affiliation(s)
- Isabel Barranco
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Albert Salas-Huetos
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain; and Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain; and Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Angel Berlanga
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain; and Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain
| | - Marcella Spinaci
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain; and Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain
| | - Jordi Ribas-Maynou
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain; and Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain
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4
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Razin SV, Kantidze OL. The twisted path of the 3D genome: where does it lead? Trends Biochem Sci 2022; 47:736-744. [DOI: 10.1016/j.tibs.2022.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/19/2022] [Accepted: 04/11/2022] [Indexed: 01/01/2023]
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5
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Dynamics of nuclear matrix attachment regions during 5 th instar posterior silk gland development in Bombyx mori. BMC Genomics 2022; 23:247. [PMID: 35361117 PMCID: PMC8973518 DOI: 10.1186/s12864-022-08446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/06/2022] [Indexed: 12/02/2022] Open
Abstract
Background Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression of genes in the organism. In this study, we set out to elucidate how MARs temporally regulate the expression of the fibroin heavy chain (FIBH) gene during development. We addressed this by identifying MARs and studying their distribution and differentiation, in the posterior silk glands of Bombyx mori during 5th instar development. Results Of the MARs identified on three different days, 7.15% MARs were common to all 3 days, whereas, 1.41, 19.27 and 52.47% MARs were unique to day 1, day 5, and day 7, respectively highlighting the dynamic nature of the matrix associated DNA. The average chromatin loop length based on the chromosome wise distribution of MARs and the distances between these MAR regions decreased from day 1 (253.91 kb) to day 5 (73.54 kb) to day 7 (39.19 kb). Further significant changes in the MARs in the vicinity of the FIBH gene were found during different days of 5th instar development which implied their role in the regulation and expression of the FIBH gene. Conclusions The presence of MARs in the flanking regions of genes found to exhibit differential expression during 5th instar development indicates their possible role in the regulation of their expression. This reiterates the importance of MARs in the genomic functioning as regulators of the molecular mechanisms in the nucleus. This is the first study that takes into account the tissue specific genome-wide MAR association and the potential role of these MARs in developmentally regulated gene expression. The current study lays a foundation to understand the genome wide regulation of chromatin during development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08446-3.
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Ribas-Maynou J, Garcia-Bonavila E, Hidalgo CO, Catalán J, Miró J, Yeste M. Species-Specific Differences in Sperm Chromatin Decondensation Between Eutherian Mammals Underlie Distinct Lysis Requirements. Front Cell Dev Biol 2021; 9:669182. [PMID: 33996825 PMCID: PMC8120241 DOI: 10.3389/fcell.2021.669182] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
Sperm present a highly particular DNA condensation that is acquired during their differentiation. Protamines are key elements for DNA condensation. However, whereas the presence of protamine 1 (P1) is conserved across mammalian species, that of protamine 2 (P2) has evolved differentially, existing only few species that use both protamines for sperm DNA condensation. In addition, altered P1/P2 ratios and alterations in the expression of P1 have previously been associated to infertility and DNA damage disorders. On the other hand, different methods evaluating DNA integrity, such as Sperm Chromatin Dispersion (SCD) and Comet tests, need a previous complete DNA decondensation to properly assess DNA breaks. Related with this, the present study aims to analyze the resilience of sperm DNA to decodensation in different eutherian mammals. Sperm samples from humans, horses, cattle, pigs and donkeys were used. Samples were embedded in low melting point agarose and treated with lysis solutions to induce DNA decondensation and formation of sperm haloes. The treatment consisted of three steps: (1) incubation in SDS + DTT for 30 min; (2) incubation in DTT + NaCl for 30 min; and (3) incubation in DTT + NaCl with or without proteinase K for a variable time of 0, 30, or 180 min. How incubation with the third lysis solution (with or without proteinase K) for 0, 30, and 180 min affected DNA decondensation was tested through analyzing core and halo diameters in 50 sperm per sample. Halo/core length ratio was used as an indicator of complete chromatin decondensation. While incubation time with the third lysis solution had no impact on halo/core length ratios in species having P1 and P2 (human, equine and donkey), DNA decondensation of pig and cattle sperm, which only present P1, significantly (P < 0.05) increased following incubation with the third lysis solution for 180 min. In addition, the inclusion of proteinase K was found to accelerate DNA decondensation. In conclusion, longer incubations in lysis solution including proteinase K lead to higher DNA decondensation in porcine and bovine sperm. This suggests that tests intended to analyze DNA damage, such as halo or Comet assays, require complete chromatin deprotamination to achieve high sensitivity in the detection of DNA breaks.
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Affiliation(s)
- Jordi Ribas-Maynou
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain.,Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain
| | - Estela Garcia-Bonavila
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain.,Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain
| | - Carlos O Hidalgo
- Department of Animal Selection and Reproduction, Regional Agrifood Research and Development Service of Asturias (SERIDA), Gijón, Spain
| | - Jaime Catalán
- Equine Reproduction Service, Department of Animal Medicine and Surgery, Faculty of Veterinary Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Jordi Miró
- Equine Reproduction Service, Department of Animal Medicine and Surgery, Faculty of Veterinary Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain.,Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain
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7
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Dusek J, Plchova H, Cerovska N, Poborilova Z, Navratil O, Kratochvilova K, Gunter C, Jacobs R, Hitzeroth II, Rybicki EP, Moravec T. Extended Set of GoldenBraid Compatible Vectors for Fast Assembly of Multigenic Constructs and Their Use to Create Geminiviral Expression Vectors. FRONTIERS IN PLANT SCIENCE 2020; 11:522059. [PMID: 33193468 PMCID: PMC7641900 DOI: 10.3389/fpls.2020.522059] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Methods for simple and fast assembly of exchangeable standard DNA parts using Type II S restriction enzymes are becoming more and more popular in plant synthetic and molecular biology. These methods enable routine construction of large and complex multigene DNA structures. Two available frameworks emphasize either high cloning capacity (Modular Cloning, MoClo) or simplicity (GoldenBraid, GB). Here we present a set of novel α-level plasmids compatible with the GB convention that extend the ability of GB to rapidly assemble more complex genetic constructs, while maintaining compatibility with all existing GB parts as well as most MoClo parts and GB modules. With the use of our new plasmids, standard GB parts can be assembled into complex assemblies containing 1, 5, 10 and up to theoretically 50 units in each successive level of infinite loop assembly. Assembled DNA constructs can be also combined with conventional binary GB-assemblies (1, 2, 4, 8… units). We demonstrate the usefulness of our framework on single tube assembly of replicating plant expression constructs based on the geminivirus Bean yellow dwarf virus (BeYDV).
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Affiliation(s)
- Jakub Dusek
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Helena Plchova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Noemi Cerovska
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Zuzana Poborilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Oldrich Navratil
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Kratochvilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Cornelius Gunter
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Raygaana Jacobs
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Inga I. Hitzeroth
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Edward P. Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Tomas Moravec
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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8
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Jia YL, Guo X, Ni TJ, Lu JT, Wang XY, Wang TY. Novel short synthetic matrix attachment region for enhancing transgenic expression in recombinant Chinese hamster ovary cells. J Cell Biochem 2019; 120:18478-18486. [PMID: 31168866 DOI: 10.1002/jcb.29165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/18/2019] [Accepted: 05/23/2019] [Indexed: 01/17/2023]
Abstract
Matrix attachment regions (MARs) are DNA fragments with specific motifs that enhance transgenic expression; however, the characteristics and functions of these elements remain unclear. In this study, we designed and synthesized three short chimeric MARs, namely, SM4, SM5, and SM6, with different numbers and orders of motifs on the basis of the features and motifs of previously reported MARs, namely, SM1, SM2, and SM3, respectively. Expression vectors with six synthetic MARs flanking the down or upstream of the expression cassette for enhanced green fluorescence protein (EGFP) were constructed and introduced into Chinese hamster ovary (CHO) cells. Results indicated that the EGFP expression of the CHO cells with transfection bySM4, SM5, or SM6-containing vectors was higher than that of those containing SM1, SM2, or SM3 regardless of the MAR insertion position. The improving effect of SM5 was particularly pronounced. Transgenic expression was further enhanced with the increasing SM5 copy number. Bioinformatics analysis indicated that several arrangements of the DNA-binding motifs for CEBP, FAST, Hox, glutathione, and NMP4 may help increase transgenic expression levels and the average population of highly expressed cells. Our findings on novel synthetic MARs will help establish stable expression systems in mammalian cells.
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Affiliation(s)
- Yan-Long Jia
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiao Guo
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tian-Jun Ni
- School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jiang-Tao Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiao-Yin Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tian-Yun Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan, China
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9
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Dolgova AS, Dolgov SV. Matrix attachment regions as a tool to influence plant transgene expression. 3 Biotech 2019; 9:176. [PMID: 30997313 DOI: 10.1007/s13205-019-1709-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/08/2019] [Indexed: 12/29/2022] Open
Abstract
The inclusion of special regulatory sequences known as matrix attachment regions (MARs) in transgene constructs has been suggested as a possible approach to stabilise the expression of foreign heterological genes. The present review provides a brief summary regarding the MARs that have been used in investigations studying their influence on plant transgene expression in different plants with different promoters and reporter genes, and the comparison of these investigations.
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Affiliation(s)
- Anna Sergeevna Dolgova
- 1Central Research Institute of Epidemiology, Moscow, Russia
- 2Saint-Petersburg Pasteur Institute, St. Petersburg, Russia
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10
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Diamos AG, Mason HS. Chimeric 3' flanking regions strongly enhance gene expression in plants. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1971-1982. [PMID: 29637682 PMCID: PMC6230951 DOI: 10.1111/pbi.12931] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/07/2018] [Accepted: 03/30/2018] [Indexed: 05/24/2023]
Abstract
Plants represent a promising platform for the highly scalable production of recombinant proteins. Previously, we identified the tobacco extensin terminator lacking its intron as an element that reduced transcript read-through and improved recombinant protein production in a plant-based system. In this study, we systematically compared nonreplicating plant expression vectors containing over 20 commonly used or newly identified terminators from diverse sources. We found that eight gene terminators enhance reporter gene expression significantly more than the commonly used 35S and NOS terminators. The intronless extensin terminator provided a 13.6-fold increase compared with the NOS terminator. Combining terminators in tandem produced large synergistic effects, with many combinations providing a >25-fold increase in expression. Addition of the tobacco Rb7 or TM6 matrix attachment region (MAR) strongly enhanced protein production when added to most terminators, with the Rb7 MAR providing the greatest enhancement. Using deletion analysis, the full activity of the 1193 bp Rb7 MAR was found to require only a 463-bp region at its 3' end. Combined terminators and MAR together provided a >60-fold increase compared with the NOS terminator alone. These combinations were then placed in a replicating geminiviral vector, providing a total of >150-fold enhancement over the original NOS vector, corresponding to an estimated yield of 3-5 g recombinant protein per kg leaf fresh weight or around 50% of the leaf total soluble protein. These results demonstrate the importance of 3' flanking regions in optimizing gene expression and show great potential for 3' flanking regions to improve DNA-based recombinant protein production systems.
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Affiliation(s)
- Andrew G. Diamos
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
| | - Hugh S. Mason
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
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11
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Slootweg E, Koropacka K, Roosien J, Dees R, Overmars H, Lankhorst RK, van Schaik C, Pomp R, Bouwman L, Helder J, Schots A, Bakker J, Smant G, Goverse A. Sequence Exchange between Homologous NB-LRR Genes Converts Virus Resistance into Nematode Resistance, and Vice Versa. PLANT PHYSIOLOGY 2017; 175:498-510. [PMID: 28747428 PMCID: PMC5580749 DOI: 10.1104/pp.17.00485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/20/2017] [Indexed: 05/24/2023]
Abstract
Plants have evolved a limited repertoire of NB-LRR disease resistance (R) genes to protect themselves against myriad pathogens. This limitation is thought to be counterbalanced by the rapid evolution of NB-LRR proteins, as only a few sequence changes have been shown to be sufficient to alter resistance specificities toward novel strains of a pathogen. However, little is known about the flexibility of NB-LRR R genes to switch resistance specificities between phylogenetically unrelated pathogens. To investigate this, we created domain swaps between the close homologs Gpa2 and Rx1, which confer resistance in potato (Solanum tuberosum) to the cyst nematode Globodera pallida and Potato virus X, respectively. The genetic fusion of the CC-NB-ARC of Gpa2 with the LRR of Rx1 (Gpa2CN/Rx1L) results in autoactivity, but lowering the protein levels restored its specific activation response, including extreme resistance to Potato virus X in potato shoots. The reciprocal chimera (Rx1CN/Gpa2L) shows a loss-of-function phenotype, but exchange of the first three LRRs of Gpa2 by the corresponding region of Rx1 was sufficient to regain a wild-type resistance response to G. pallida in the roots. These data demonstrate that exchanging the recognition moiety in the LRR is sufficient to convert extreme virus resistance in the leaves into mild nematode resistance in the roots, and vice versa. In addition, we show that the CC-NB-ARC can operate independently of the recognition specificities defined by the LRR domain, either aboveground or belowground. These data show the versatility of NB-LRR genes to generate resistance to unrelated pathogens with completely different lifestyles and routes of invasion.
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Affiliation(s)
- Erik Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Kamila Koropacka
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Jan Roosien
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Robert Dees
- Laboratory of Molecular Recognition and Antigen Technology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Hein Overmars
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Rene Klein Lankhorst
- Plant Research International, Centre for Biosystems Genomics, 6708 PD Wageningen, The Netherlands
| | - Casper van Schaik
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Rikus Pomp
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Liesbeth Bouwman
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Arjen Schots
- Laboratory of Molecular Recognition and Antigen Technology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Jaap Bakker
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
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12
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Diamos AG, Rosenthal SH, Mason HS. 5' and 3' Untranslated Regions Strongly Enhance Performance of Geminiviral Replicons in Nicotiana benthamiana Leaves. FRONTIERS IN PLANT SCIENCE 2016; 7:200. [PMID: 26941764 PMCID: PMC4764687 DOI: 10.3389/fpls.2016.00200] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/05/2016] [Indexed: 05/24/2023]
Abstract
We previously reported a recombinant protein production system based on a geminivirus replicon that yields high levels of vaccine antigens and monoclonal antibodies in plants. The bean yellow dwarf virus (BeYDV) replicon generates massive amounts of DNA copies, which engage the plant transcription machinery. However, we noticed a disparity between transcript level and protein production, suggesting that mRNAs could be more efficiently utilized. In this study, we systematically evaluated genetic elements from human, viral, and plant sources for their potential to improve the BeYDV system. The tobacco extensin terminator enhanced transcript accumulation and protein production compared to other commonly used terminators, indicating that efficient transcript processing plays an important role in recombinant protein production. Evaluation of human-derived 5' untranslated regions (UTRs) indicated that many provided high levels of protein production, supporting their cross-kingdom function. Among the viral 5' UTRs tested, we found the greatest enhancement with the tobacco mosaic virus omega leader. An analysis of the 5' UTRs from the Arabidopsis thaliana and Nicotinana benthamiana photosystem I K genes found that they were highly active when truncated to include only the near upstream region, providing a dramatic enhancement of transgene production that exceeded that of the tobacco mosaic virus omega leader. The tobacco Rb7 matrix attachment region inserted downstream from the gene of interest provided significant enhancement, which was correlated with a reduction in plant cell death. Evaluation of Agrobacterium strains found that EHA105 enhanced protein production and reduced cell death compared to LBA4301 and GV3101. We used these improvements to produce Norwalk virus capsid protein at >20% total soluble protein, corresponding to 1.8 mg/g leaf fresh weight, more than twice the highest level ever reported in a plant system. We also produced the monoclonal antibody rituximab at 1 mg/g leaf fresh weight.
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Lee K, Kim JH, Kwon H. The Actin-Related Protein BAF53 Is Essential for Chromosomal Subdomain Integrity. Mol Cells 2015; 38:789-95. [PMID: 26242195 PMCID: PMC4588722 DOI: 10.14348/molcells.2015.0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 01/09/2023] Open
Abstract
A chromosome territory is composed of chromosomal subdomains. The internal structure of chromosomal subdomains provides a structural framework for many genomic activities such as replication and DNA repair, and thus is key to determining the basis of their mechanisms. However, the internal structure and regulating proteins of a chromosomal subdomain remains elusive. Previously, we showed that the chromosome territory expanded after BAF53 knockdown. Because the integrity of chromosomal subdomains is a deciding factor of the volume of a chromosome territory, we examined here the effect of BAF53 knockdown on chromosomal subdomains. We found that BAF53 knockdown led to the disintegration of histone H2B-GFP-visualized chromosomal subdomains and BrdU-labeled replication foci. In addition, the size of DNA loops measured by the maximum fluorescent halo technique increased and became irregular after BAF53 knockdown, indicating DNA loops were released from the residual nuclear structure. These data can be accounted for by the model that BAF53 is prerequisite for maintaining the structural integrity of chromosomal subdomains.
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Affiliation(s)
- Kiwon Lee
- Department of Bioscience and Biotechnology and Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yongin 449-791,
Korea
| | - Ji Hye Kim
- Department of Bioscience and Biotechnology and Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yongin 449-791,
Korea
| | - Hyockman Kwon
- Department of Bioscience and Biotechnology and Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yongin 449-791,
Korea
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Distance effect of matrix attachment regions on transgene expression in stably transfected Chinese hamster ovary cells. Biotechnol Lett 2014; 36:1937-43. [PMID: 24930099 DOI: 10.1007/s10529-014-1563-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/19/2014] [Indexed: 02/06/2023]
Abstract
The β-globin matrix attachment regions (MARs) were inserted into the 5'-site of the eukaryotic expression vector cassette and DNA fragments 350 and 750 bp in length were inserted into the site to generate expression vectors with varying distances between the expression cassette and MAR. The vectors containing MARs increased chloramphenicol acetyltransferase (CAT) expression levels compared to the negative control vector lacking the MAR; the highest expression increase was 3.8-fold. A greater MAR-transgene distance (750 bp) correlated with a greater increase in transgene expression when compared to the control vector that lacked separation between the MAR and transgene. CAT gene copy numbers were higher in cells transformed with the vector possessing a smaller MAR-transgene distance (350 bp) than in cells belonging to the other three groups. However, MAR-induced transgene expression levels did not exhibit a direct relationship with gene copy number.
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