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Huang X, Jiao Y, Guo J, Wang Y, Chu G, Wang M. Analysis of codon usage patterns in Haloxylon ammodendron based on genomic and transcriptomic data. Gene X 2022; 845:146842. [PMID: 36038027 DOI: 10.1016/j.gene.2022.146842] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
Haloxylon ammodendron, a xero-halophytic shrub of Chenopodiaceae, is a dominant species in deserts, which has a strong drought and salt tolerance and plays an important role in sand fixation. However, the codon usage bias (CUB) in H. ammodendron is still unclear at present. In this study, the codon usage patterns of 38,657 coding sequences (CDSs) in the newly released whole-genome sequence data of H. ammodendron and 3,948 CDSs in the previously obtained transcriptome sequencing data were compared and analyzed. The results showed that the CDSs with the total guanineandcytosine(GC)content in the range of 40% ∼ 45% was the most in the genome and transcriptome. Among which, the GC1, GC2, and GC3 contents of genomic CDSs were 50.83%, 40.56%, and 40.23%, respectively, and those of CDSs in the transcriptome were 47.16%, 39.02%, and 39.59%, respectively. Therefore, the bases in H. ammodendron were rich in adenine and thymine, and the overallcodonusage was biasedtoward A- and U-ending codons. The analysis of neutrality plot, effective number of codon (ENC) plot, and parity rule 2 (PR2) bias plot showed that both natural selection and mutation pressure had great influences on the CUB of H. ammodendron, but natural selection was the most important determinant. Besides, gene expression level and the function and protein length of some specific genes also had influences on the codon usage pattern. Finally, a total of 25 common optimal codons were found in the genomic and transcriptomic data, and AU/GC-ending codons ratio was 24:1. It should be noted that the salt-tolerant unigenes had similar codon usage, and the highly expressed genes had higher usage frequency of optimal codons and lower GC content than the lowly expressed genes. In addition, there was no difference in the ENC values of salt-tolerant unigenes in H. ammodendron, and the expression level of the genes had no correlation with CAI. This study will help to elucidate the formation mechanism of H. ammodendron codon usage bias, and make contributions to the identification of new genes and the genetic engineering study on H. ammodendron.
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Affiliation(s)
- Xiang Huang
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Yalin Jiao
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Jiaxing Guo
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Ying Wang
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Guangming Chu
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China
| | - Mei Wang
- College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, P.R. China.
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Gomes C, Ferreira D, Carvalho JPF, Barreto CAV, Fernandes J, Gouveia M, Ribeiro F, Duque AS, Vieira SI. Current genetic engineering strategies for the production of antihypertensive ACEI peptides. Biotechnol Bioeng 2020; 117:2610-2628. [PMID: 32369185 DOI: 10.1002/bit.27373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/16/2020] [Accepted: 05/02/2020] [Indexed: 12/16/2022]
Abstract
Hypertension is a major and highly prevalent risk factor for various diseases. Among the most frequently prescribed antihypertensive first-line drugs are synthetic angiotensin I-converting enzyme inhibitors (ACEI). However, since their use in hypertension therapy has been linked to various side effects, interest in the application of food-derived ACEI peptides (ACEIp) as antihypertensive agents is rapidly growing. Although promising, the industrial production of ACEIp through conventional methods such as chemical synthesis or enzymatic hydrolysis of food proteins has been proven troublesome. We here provide an overview of current antihypertensive therapeutics, focusing on ACEI, and illustrate how biotechnology and bioengineering can overcome the limitations of ACEIp large-scale production. Latest advances in ACEIp research and current genetic engineering-based strategies for heterologous production of ACEIp (and precursors) are also presented. Cloning approaches include tandem repeats of single ACEIp, ACEIp fusion to proteins/polypeptides, joining multivariate ACEIp into bioactive polypeptides, and producing ACEIp-containing modified plant storage proteins. Although bacteria have been privileged ACEIp heterologous hosts, particularly when testing for new genetic engineering strategies, plants and microalgae-based platforms are now emerging. Besides being generally safer, cost-effective and scalable, these "pharming" platforms can perform therelevant posttranslational modifications and produce (and eventually deliver) biologically active protein/peptide-based antihypertensive medicines.
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Affiliation(s)
- Carolina Gomes
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland.,Plant Cell Biotechnology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Green-it Unit, Oeiras, Portugal
| | - Diana Ferreira
- Department of Medical Sciences (DCM), Institute of Biomedicine (iBiMED), Universidade de Aveiro, Aveiro, Portugal
| | - João P F Carvalho
- Department of Medical Sciences (DCM), Institute of Biomedicine (iBiMED), Universidade de Aveiro, Aveiro, Portugal
| | - Carlos A V Barreto
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Joana Fernandes
- Department of Medical Sciences (DCM), Institute of Biomedicine (iBiMED), Universidade de Aveiro, Aveiro, Portugal
| | - Marisol Gouveia
- Department of Medical Sciences (DCM), Institute of Biomedicine (iBiMED), Universidade de Aveiro, Aveiro, Portugal
| | - Fernando Ribeiro
- School of Health Sciences (ESSUA), Institute of Biomedicine (iBiMED), Universidade de Aveiro, Aveiro, Portugal
| | - Ana S Duque
- Plant Cell Biotechnology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Green-it Unit, Oeiras, Portugal
| | - Sandra I Vieira
- Department of Medical Sciences (DCM), Institute of Biomedicine (iBiMED), Universidade de Aveiro, Aveiro, Portugal
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Ulagesan S, Choi JW, Nam TJ, Choi YH. Peptidyl-prolyl isomerase and the biological activities of recombinant protein cyclophilin from Pyropia yezoensis (PyCyp). Protein Expr Purif 2020; 172:105636. [PMID: 32272150 DOI: 10.1016/j.pep.2020.105636] [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: 01/13/2020] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023]
Abstract
Cyclophilins are highly conserved proteins associated with peptidyl-prolyl cis-trans isomerase activity (PPIase). The present study was designed to analyze the biological activity of recombinant cyclophilin from the marine red algae Pyropia yezoensis (PyCyp). The cyclophilin gene from P. yezoensis was cloned into the pPROEX-HTA expression vector. The plasmid was transformed into BL21 Escherichia coli by high efficiency transformation. Recombinant protein was expressed using 0.1 mM IPTG and the fusion protein was purified by affinity column chromatography. The His-tag was removed by TEV protease. The recombinant protein was further purified on a HiPrep Sephacryl S-200 HR column and by reversed-phase high performance liquid chromatography with a Sep-pak plus C18 column. Purified cyclophilin was characterized by a variety of analytical methods and analyzed for its peptidyl-prolyl isomerase activity. Our recombinant PyCyp was shown to catalyze cis-trans isomerization. PyCyp was also evaluated for antimicrobial activity against both Gram-positive and Gram-negative bacteria cultures and showed significant antibacterial activity against tested pathogens. PyCyp was shown to permeabilize bacterial membranes as evidenced by increased fluorescence intensity in SYTOX Green uptake assays with Staphylococcus aureus. The radical scavenging activity of PyCyp increased in a dose-dependent manner, indicating significant antioxidant activity. This study provides information for the development of therapeutic proteins from marine algae.
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Affiliation(s)
- Selvakumari Ulagesan
- Institute of Fisheries Sciences, Pukyong National University, Busan, 46041, Republic of Korea
| | - Jeong-Wook Choi
- Institute of Fisheries Sciences, Pukyong National University, Busan, 46041, Republic of Korea
| | - Taek-Jeong Nam
- Institute of Fisheries Sciences, Pukyong National University, Busan, 46041, Republic of Korea
| | - Youn-Hee Choi
- Institute of Fisheries Sciences, Pukyong National University, Busan, 46041, Republic of Korea; Department of Marine Bio-materials & Aquaculture, Pukyong National University, 45, Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea.
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4
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Leaf-Encapsulated Vaccines: Agroinfiltration and Transient Expression of the Antigen Staphylococcal Endotoxin B in Radish Leaves. J Immunol Res 2018; 2018:3710961. [PMID: 29577048 PMCID: PMC5821973 DOI: 10.1155/2018/3710961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/24/2017] [Accepted: 10/10/2017] [Indexed: 01/08/2023] Open
Abstract
Transgene introgression is a major concern associated with transgenic plant-based vaccines. Agroinfiltration can be used to selectively transform nonreproductive organs and avoid introgression. Here, we introduce a new vaccine modality in which Staphylococcal enterotoxin B (SEB) genes are agroinfiltrated into radishes (Raphanw sativus L.), resulting in transient expression and accumulation of SEB in planta. This approach can simultaneously express multiple antigens in a single leaf. Furthermore, the potential of high-throughput vaccine production was demonstrated by simultaneously agroinfiltrating multiple radish leaves using a multichannel pipette. The expression of SEB was detectable in two leaf cell types (epidermal and guard cells) in agroinfiltrated leaves. ICR mice intranasally immunized with homogenized leaves agroinfiltrated with SEB elicited detectable antibody to SEB and displayed protection against SEB-induced interferon-gamma (IFN-γ) production. The concept of encapsulating antigens in leaves rather than purifying them for immunization may facilitate rapid vaccine production during an epidemic disease.
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Al-Hawash AB, Zhang X, Ma F. Strategies of codon optimization for high-level heterologous protein expression in microbial expression systems. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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6
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Specht EA, Karunanithi PS, Gimpel JA, Ansari WS, Mayfield SP. Host Organisms: Algae. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Elizabeth A. Specht
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
| | - Prema S. Karunanithi
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
| | - Javier A. Gimpel
- Centre for Biotechnology and Bioengineering; Department of Chemical Engineering and Biotechnology, Universidad de Chile; 851 Beaucheff Santiago USA
| | - William S. Ansari
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
| | - Stephen P. Mayfield
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
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7
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Cisgenesis and intragenesis in microalgae: promising advancements towards sustainable metabolites production. Appl Microbiol Biotechnol 2016; 100:10225-10235. [DOI: 10.1007/s00253-016-7948-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 11/26/2022]
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8
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Patra KP, Li F, Carter D, Gregory JA, Baga S, Reed SG, Mayfield SP, Vinetz JM. Alga-produced malaria transmission-blocking vaccine candidate Pfs25 formulated with a human use-compatible potent adjuvant induces high-affinity antibodies that block Plasmodium falciparum infection of mosquitoes. Infect Immun 2015; 83:1799-808. [PMID: 25690099 PMCID: PMC4399074 DOI: 10.1128/iai.02980-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/08/2015] [Indexed: 01/21/2023] Open
Abstract
A vaccine to prevent the transmission of malaria parasites from infected humans to mosquitoes is an important component for the elimination of malaria in the 21st century, yet it remains neglected as a priority of malaria vaccine development. The lead candidate for Plasmodium falciparum transmission-blocking vaccine development, Pfs25, is a sexual stage surface protein that has been produced for vaccine testing in a variety of heterologous expression systems. Any realistic malaria vaccine will need to optimize proper folding balanced against cost of production, yield, and potentially reactogenic contaminants. Here Chlamydomonas reinhardtii microalga-produced recombinant Pfs25 protein was formulated with four different human-compatible adjuvants (alum, Toll-like receptor 4 [TLR-4] agonist glucopyranosal lipid A [GLA] plus alum, squalene-oil-in-water emulsion, and GLA plus squalene-oil-in-water emulsion) and compared for their ability to induce malaria transmission-blocking antibodies. Alga-produced recombinant Pfs25 plus GLA plus squalene-oil-in-water adjuvant induced the highest titer and avidity in IgG antibodies, measured using alga-produced recombinant Pfs25 as the enzyme-linked immunosorbent assay (ELISA) antigen. These antibodies specifically reacted with the surface of P. falciparum macrogametes and zygotes and effectively prevented parasites from developing within the mosquito vector in standard membrane feeding assays. Alga-produced Pfs25 in combination with a human-compatible adjuvant composed of a TLR-4 agonist in a squalene-oil-in-water emulsion is an attractive new vaccine candidate that merits head-to-head comparison with other modalities of vaccine production and administration.
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MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Animals
- Antibodies, Protozoan/blood
- Antibody Affinity
- Chlamydomonas reinhardtii/genetics
- Chlamydomonas reinhardtii/metabolism
- Culicidae/parasitology
- Enzyme-Linked Immunosorbent Assay
- Female
- Humans
- Immunoglobulin G/blood
- Malaria Vaccines/administration & dosage
- Malaria Vaccines/genetics
- Malaria Vaccines/immunology
- Malaria Vaccines/isolation & purification
- Mice, Inbred BALB C
- Plasmodium falciparum/immunology
- Plasmodium falciparum/isolation & purification
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Protozoan Proteins/isolation & purification
- Treatment Outcome
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Vaccines, Subunit/isolation & purification
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/isolation & purification
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Affiliation(s)
- Kailash P Patra
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Fengwu Li
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Darrick Carter
- Infectious Disease Research Institute, Seattle, Washington, USA
| | - James A Gregory
- Infectious Disease Research Institute, Seattle, Washington, USA
| | - Sheyenne Baga
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Steven G Reed
- Infectious Disease Research Institute, Seattle, Washington, USA
| | - Stephen P Mayfield
- Division of Biological Science and the San Diego Center for Algae Biotechnology, University of California San Diego, La Jolla, California, USA
| | - Joseph M Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA
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9
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Abstract
Chlamydomonas reinhardtii has many advantages as a photosynthetic model organism. One of these is facile, targeted chloroplast transformation by particle bombardment. Functional recombinant proteins can be expressed to significant levels in this system, potentially outperforming higher plants in speed of scaling, cost, and space requirements. Several strategies and regulatory regions can be used for achieving transgene expression. Here we present two of those strategies: one makes use of the psbD promoter for expressing moderate levels of the recombinant protein in a photosynthetic background. The other strategy is based on the strong psbA promoter for obtaining high yields of the recombinant product in a non-photosynthetic strain. We herein describe the vectors, transformation procedures, and screening methods associated with these two strategies.
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10
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Production and purification of recombinant hypocholesterolemic peptides. Biotechnol Lett 2014; 37:41-54. [DOI: 10.1007/s10529-014-1657-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/29/2014] [Indexed: 01/03/2023]
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11
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Heidari HR, Bandehpour M, Vahidi H, Barar J, Kazemi B, Naderi-Manesh H. Improvement in the stability and functionality of Nicotiana tabacum produced recombinant TRAIL through employment of endoplasmic reticulum expression and ascorbate buffer mediated extraction strategies. ACTA ACUST UNITED AC 2014; 4:123-32. [PMID: 25337465 PMCID: PMC4204037 DOI: 10.15171/bi.2014.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/15/2014] [Accepted: 03/31/2014] [Indexed: 02/04/2023]
Abstract
Introduction: In order to employ Nicotiana tabacum cells as a profitable natural bioreactor for production of bio-functional "Soluble human TRAIL" (ShTRAIL), endoplasmic reticulum (ER) targeted expression and innovative extraction procedures were exploited.
Methods: At first, the ShTRAIL encoding gene was sub-cloned into designed H2 helper vector to equip it with potent TMV omega leader sequences, ER sorting signal peptide, poly-histidine tag and ER retention signal peptide (KDEL). Then, the ER targeted ShTRAIL cassette was sequentially sub-cloned into "CaMV-35S" helper and "pGreen-0179" final expression vectors. Afterward, Agrobacterium mediated transformation method was adopted to express the ShTRAIL in the ER of N. tabacum . Next, the ShTRAIL protein was extracted through both phosphate and innovative ascorbate extraction buffers. Subsequently, oligomerization state of the ShTRAIL was evaluated through cross-linking assay and western blot analysis. Then, semi-quantitative western blot analysis was performed to estimate the ShTRAIL production. Finally, biological activity of the ShTRAIL was evaluated through MTT assay.
Results: The phosphate buffer extracted ShTRAIL was produced in dimmer form, whereas the ShTRAIL extracted with ascorbate buffer generated trimer form. The ER targeted ShTRAIL strategy increased the ShTRAIL’s production level up to about 20 μg/g of fresh weight of N. tabacum . MTT assay indicated that ascorbate buffer extracted ShTRAIL could prohibit proliferation of A549 cell line.
Conclusion: Endoplasmic reticulum expression and reductive ascorbate buffer extraction procedure can be employed to enhance the stability and overall production level of bio-functional recombinant ShTRAIL from transgenic N. tabacum cells.
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Affiliation(s)
- Hamid Reza Heidari
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran ; Student s Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran ; Department of Biotechnology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Vahidi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran ; Department of Biotechnology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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12
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Chen HC, Melis A. Marker-free genetic engineering of the chloroplast in the green microalga Chlamydomonas reinhardtii. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:818-28. [PMID: 23647698 DOI: 10.1111/pbi.12073] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/05/2013] [Accepted: 03/20/2013] [Indexed: 05/11/2023]
Abstract
The work applied a transgene expression method based on the replacement of an inactive rbcL gene as the selection marker in Chlamydomonas reinhardtii chloroplasts. The native rbcL gene in strain CC2653 has a point mutation that causes early translation termination, thus resulting in a photosynthesis mutant. Recovery of rbcL function for selection is offered along with the heterologous expression of the alcohol dehydrogenase ADH1 gene from Saccharomyces cerevisiae in the Chlamydomonas chloroplast. The CrCpADH1 gene was inserted via double homologous recombination in the psaB-rbcL chloroplast intergenic region of recipient strain CC2653, using the psaB and rbcL gene sequences for the double homologous recombination. This transformation conferred a functional rbcL gene and expression of the CrCpADH1 transgene in the recipient strain. This method alleviated the need to use antibiotics for selection, resulting in a negligible number of false positives during screening, and attaining a transformation efficiency greater than 90%. The approach also ensured segregation of chloroplast DNA copies, so as to achieve homoplasmy of the transformant chloroplast DNA, with a concomitant elimination of recipient strain Cp DNA. High levels of steady-state CrCpADH1 transcripts were detected in the homoplasmic transformants. However, CrCpADH1 protein levels were attenuated under continuous illumination growth conditions due to oxygen accumulation in the cells. Under conditions of low oxygen partial pressure, or anoxia, accumulation of CrCpADH1 protein in the cells and ethanol in the growth medium was observed. A metabolic pathway for ethanol production is proposed in Chlamydomonas, mediated by the chloroplast-localized CrCpADH1 transgenic enzyme.
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Affiliation(s)
- Hsu-Ching Chen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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13
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Behura SK, Singh BK, Severson DW. Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications. Evol Appl 2013; 6:1079-89. [PMID: 24187589 PMCID: PMC3804240 DOI: 10.1111/eva.12088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/14/2013] [Indexed: 12/17/2022] Open
Abstract
Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vectorborne diseases such as malaria, dengue, West Nile, and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the covariance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other nonmosquito insects. By applying a maximum likelihood-based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny-dependent manner, but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame Notre Dame, IN, USA
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14
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Behura SK, Severson DW. Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes. Biol Rev Camb Philos Soc 2012; 88:49-61. [PMID: 22889422 DOI: 10.1111/j.1469-185x.2012.00242.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.
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Affiliation(s)
- Susanta K Behura
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
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15
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Franz AWE, Jasinskiene N, Sanchez-Vargas I, Isaacs AT, Smith MR, Khoo CCH, Heersink MS, James AA, Olson KE. Comparison of transgene expression in Aedes aegypti generated by mariner Mos1 transposition and ΦC31 site-directed recombination. INSECT MOLECULAR BIOLOGY 2011; 20:587-98. [PMID: 21699593 PMCID: PMC3556457 DOI: 10.1111/j.1365-2583.2011.01089.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Transgenic mosquitoes generated by transposable elements (TEs) often poorly express transgenes owing to position effects. To avoid these effects, the ΦC31 site-directed recombination system was used to insert transgenes into a locus favourable for gene expression in Aedes aegypti. We describe phenotypes of mariner Mos1 TE and ΦC31 transgenic mosquitoes expressing the enhanced green fluorescent protein (EGFP) reporter in midguts of blood-fed females. Mosquitoes of nine TE-generated lines [estimated transformation frequency (TF): 9.3%] clearly expressed the eye-specific selection marker but only 2/9 lines robustly expressed the EGFP reporter. The piggyBac TE-generated ΦC31 docking strain, attP26, supported recombination with attB site containing donors at an estimated TF of 1.7-4.9%. Using a codon-optimized ΦC31 integrase mutant instead of the 'wild-type' enzyme did not affect TF. Site-directed recombination of line attP26 with an attB-containing donor expressing EGFP from the Ae. aegypti carboxypeptidase promoter produced one transgenic line with blood-fed females expressing the reporter in midgut tissue. Docking strain attP26 also supported robust expression of Flock House virus B2 from the Ae. aegypti polyubiquitin promoter. Our data confirm that eye-specific selection marker expression alone is not a reliable indicator for robust gene-of-interest expression in Ae. aegypti and that the ΦC31 system can ensure predictable transgene expression in this mosquito species.
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Affiliation(s)
- Alexander W E Franz
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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Coragliotti AT, Beligni MV, Franklin SE, Mayfield SP. Molecular factors affecting the accumulation of recombinant proteins in the Chlamydomonas reinhardtii chloroplast. Mol Biotechnol 2011; 48:60-75. [PMID: 21113690 PMCID: PMC3068253 DOI: 10.1007/s12033-010-9348-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an effort to develop microalgae as a robust system for the production of valuable proteins, we analyzed some of the factors affecting recombinant protein expression in the chloroplast of the green alga Chlamydomonas reinhardtii. We monitored mRNA accumulation, protein synthesis, and protein turnover for three codon-optimized transgenes including GFP, bacterial luciferase, and a large single chain antibody. GFP and luciferase proteins were quite stable, while the antibody was less so. Measurements of protein synthesis, in contrast, clearly showed that translation of the three chimeric mRNAs was greatly reduced when compared to endogenous mRNAs under control of the same atpA promoter/UTR. Only in a few conditions this could be explained by limited mRNA availability since, in most cases, recombinant mRNAs accumulated quite well when compared to the atpA mRNA. In vitro toeprint and in vivo polysome analyses suggest that reduced ribosome association might contribute to limited translational efficiency. However, when recombinant polysome levels and protein synthesis are analyzed as a whole, it becomes clear that other steps, such as inefficient protein elongation, are likely to have a considerable impact. Taken together, our results point to translation as the main step limiting the expression of heterologous proteins in the C. reinhardtii chloroplast.
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Affiliation(s)
- Anna T Coragliotti
- The Department of Cell Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
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Liu PF, Nakatsuji T, Zhu W, Gallo RL, Huang CM. Passive immunoprotection targeting a secreted CAMP factor of Propionibacterium acnes as a novel immunotherapeutic for acne vulgaris. Vaccine 2011; 29:3230-8. [PMID: 21354482 DOI: 10.1016/j.vaccine.2011.02.036] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 01/31/2011] [Accepted: 02/12/2011] [Indexed: 02/07/2023]
Abstract
Propionibacterium acnes (P. acnes) bacteria play a key role in the pathogenesis of acne vulgaris. Although our previous studies have demonstrated that vaccines targeting a surface sialidase or bacterial particles exhibit a preventive effect against P. acnes, the lack of therapeutic activities and incapability of neutralizing secretory virulence factors motivate us to generate novel immunotherapeutics. In this study, we develop an immunotherapeutic antibody to secretory Christie-Atkins-Munch-Peterson (CAMP) factor of P. acnes. Via agroinfiltration, P. acnes CAMP factor was encapsulated into the leaves of radishes. ICR mice intranasally immunized with whole leaves expressing CAMP factor successfully produced neutralizing antibodies that efficiently attenuated P. acnes-induced ear swelling and production of macrophage-inflammatory protein-2. Passive neutralization of CAMP factor enhanced immunity to eradicate P. acnes at the infection site without influencing bacterial growth elsewhere. We propose that CAMP factor is a novel therapeutic target for the treatment of various P. acnes-associated diseases and highlight the concept of neutralizing P. acnes virulence without disturbing the bacterial commensalism in human microbiome.
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Affiliation(s)
- Pei-Feng Liu
- Department of Medicine, Division of Dermatology, University of California, San Diego, San Diego, CA 92121, USA
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Specht E, Miyake-Stoner S, Mayfield S. Micro-algae come of age as a platform for recombinant protein production. Biotechnol Lett 2010; 32:1373-83. [PMID: 20556634 PMCID: PMC2941057 DOI: 10.1007/s10529-010-0326-5] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 06/07/2010] [Indexed: 12/03/2022]
Abstract
A complete set of genetic tools is still being developed for the micro-alga Chlamydomonas reinhardtii. Yet even with this incomplete set, this photosynthetic single-celled plant has demonstrated significant promise as a platform for recombinant protein expression. In recent years, techniques have been developed that allow for robust expression of genes from both the nuclear and plastid genome. With these advances, many research groups have examined the pliability of this and other micro-algae as biological machines capable of producing recombinant peptides and proteins. This review describes recent successes in recombinant protein production in Chlamydomonas, including production of complex mammalian therapeutic proteins and monoclonal antibodies at levels sufficient for production at economic parity with existing production platforms. These advances have also shed light on the details of algal protein production at the molecular level, and provide insight into the next steps for optimizing micro-algae as a useful platform for the production of therapeutic and industrially relevant recombinant proteins.
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Affiliation(s)
- Elizabeth Specht
- San Diego Center for Algae Biotechnology, Department of Biological Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0368 USA
| | - Shigeki Miyake-Stoner
- San Diego Center for Algae Biotechnology, Department of Biological Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0368 USA
| | - Stephen Mayfield
- San Diego Center for Algae Biotechnology, Department of Biological Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0368 USA
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Franconi R, Demurtas OC, Massa S. Plant-derived vaccines and other therapeutics produced in contained systems. Expert Rev Vaccines 2010; 9:877-92. [PMID: 20673011 DOI: 10.1586/erv.10.91] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The use of contained plant systems for the production of biopharmaceuticals represents a powerful alternative to current methods, combining the benefits of whole-plant systems and cell cultures. In vitro contained production systems include plant cell suspensions, hairy root cultures, novel plants grown in contained conditions and microalgae. These systems show intrinsic advantages, such as control over growth conditions, production in compliance with good manufacturing practice and avoidance of political resistance to the release of genetically modified field crops. At present, one of the two plant-produced vaccine-related products that have gone all the way through production and regulatory hurdles derives from tobacco cell suspensions, and the second is a human therapeutic enzyme, which is expected to reach commercial development soon and derives from carrot suspension cells. In the future, several other products from contained systems are expected to reach the clinical trial stage.
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Affiliation(s)
- Rosella Franconi
- Italian National Agency for New Technologies, UTBIORAD, CR Casaccia, Rome, Italy.
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Lapidot M, Shrestha RP, Weinstein Y, Arad S. Red Microalgae: From Basic Know-How to Biotechnology. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3795-4_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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