Pub Date : 2008-01-01DOI: 10.1016/S1387-2656(08)00006-9
Xiangjun Zhou, Joyce Van Eck, Li Li
Carotenoids are a group of pigments that are essential to human diets. An increasing interest in carotenoids as a nutritional source of vitamin A and health-promoting compounds has prompted the recent progress in metabolic engineering of carotenogenesis in food crops. Current strategies have been mainly focused on manipulating genes encoding carotenogeic enzymes. In many cases, it is difficult to reach the desired levels of carotenoid enhancement. In this chapter, we briefly summarize the recent progress on our understanding of carotenoid biosynthesis. We describe the isolation of a novel gene, the Or gene, from a high-beta-carotene orange cauliflower mutant. The Or gene encodes a plastid-targeted protein containing a cysteine-rich zinc finger domain and appears to be plant-specific. The insertion of a copia-like LTR retrotransponson in the Or gene confers high levels of carotenoid accumulation in the normally low-pigmented tissues. Rather than directly regulating carotenoid biosynthesis, the Or gene controls carotenoid accumulation by inducing the formation of chromoplasts, which provide a metabolic sink to sequester and deposit carotenoids. Examination of the Or transgenic potato tubers confirms that the Or-induced carotenoid accumulation is associated with the formation of a metabolic sink. Thus, the Or gene offers a new molecular tool to complement current approaches for nutritional enhancement in agriculturally important crops.
{"title":"Use of the cauliflower Or gene for improving crop nutritional quality.","authors":"Xiangjun Zhou, Joyce Van Eck, Li Li","doi":"10.1016/S1387-2656(08)00006-9","DOIUrl":"https://doi.org/10.1016/S1387-2656(08)00006-9","url":null,"abstract":"<p><p>Carotenoids are a group of pigments that are essential to human diets. An increasing interest in carotenoids as a nutritional source of vitamin A and health-promoting compounds has prompted the recent progress in metabolic engineering of carotenogenesis in food crops. Current strategies have been mainly focused on manipulating genes encoding carotenogeic enzymes. In many cases, it is difficult to reach the desired levels of carotenoid enhancement. In this chapter, we briefly summarize the recent progress on our understanding of carotenoid biosynthesis. We describe the isolation of a novel gene, the Or gene, from a high-beta-carotene orange cauliflower mutant. The Or gene encodes a plastid-targeted protein containing a cysteine-rich zinc finger domain and appears to be plant-specific. The insertion of a copia-like LTR retrotransponson in the Or gene confers high levels of carotenoid accumulation in the normally low-pigmented tissues. Rather than directly regulating carotenoid biosynthesis, the Or gene controls carotenoid accumulation by inducing the formation of chromoplasts, which provide a metabolic sink to sequester and deposit carotenoids. Examination of the Or transgenic potato tubers confirms that the Or-induced carotenoid accumulation is associated with the formation of a metabolic sink. Thus, the Or gene offers a new molecular tool to complement current approaches for nutritional enhancement in agriculturally important crops.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(08)00006-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37434220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2008-01-01DOI: 10.1016/S1387-2656(08)00007-0
Huub Schellekens
Therapeutic proteins in general induce an immune response, especially when administered as multiple doses over prolonged periods. Non-human therapeutic proteins such as asparaginase and streptokinase induce antibodies by the classical immune reaction and their primary immunogenic factor is the degree of non-self. Human therapeutic proteins such as the interferons and GM-CSF breakdown immune tolerance and protein aggregation is their main factor inducing antibodies. Many other factors influence the level of immunogenicity of proteins, such as storage conditions,contaminants or impurities in the preparation, downstream processing, dose and length of treatment, as well as route of administration, appropriate formulation and disease status and concomitant treatment of patients. Clinical manifestations of antibodies directed against the protein include loss of efficacy, cross neutralization of endogenous proteins and general immune system effects, such as anaphylaxis or serum sickness.
{"title":"How to predict and prevent the immunogenicity of therapeutic proteins.","authors":"Huub Schellekens","doi":"10.1016/S1387-2656(08)00007-0","DOIUrl":"https://doi.org/10.1016/S1387-2656(08)00007-0","url":null,"abstract":"<p><p>Therapeutic proteins in general induce an immune response, especially when administered as multiple doses over prolonged periods. Non-human therapeutic proteins such as asparaginase and streptokinase induce antibodies by the classical immune reaction and their primary immunogenic factor is the degree of non-self. Human therapeutic proteins such as the interferons and GM-CSF breakdown immune tolerance and protein aggregation is their main factor inducing antibodies. Many other factors influence the level of immunogenicity of proteins, such as storage conditions,contaminants or impurities in the preparation, downstream processing, dose and length of treatment, as well as route of administration, appropriate formulation and disease status and concomitant treatment of patients. Clinical manifestations of antibodies directed against the protein include loss of efficacy, cross neutralization of endogenous proteins and general immune system effects, such as anaphylaxis or serum sickness.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(08)00007-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37434221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2008-01-01DOI: 10.1016/S1387-2656(08)00004-5
Joji M Otaki, Tomonori Gotoh, Haruhiko Yamamoto
Three-dimensional structure of a protein molecule is primarily determined by its amino acid sequence, and thus the elucidation of general rules embedded in amino acid sequences is of great importance in protein science and engineering. To extract valuable information from sequences, we propose an analytical method in which a protein sequence is considered to be constructed by serial superimpositions of short amino acid sequences of n amino acid sets, especially triplets (3-aa sets). Using the comprehensive nonredundant protein database, we first examined "availability" of all possible combinatorial sets of 8,000 triplet species. Availability score was mathematically defined as an indicator for the relative "preference" or "avoidance" for a given short constituent sequence to be used in protein chain. Availability scores of real proteins were clearly biased against those of randomly generated proteins. We found many triplet species that occurred in the database more than expected or less than expected. Such bias was extended to longer sets, and we found that some species of pentats (5-aa sets) that occurred reasonably frequently in the randomly generated protein population did not occur at all in any real proteins known today. Availability score was dependent on species, potentially serving as a phylogenetic indicator. Furthermore, we suggest possibilities of various biotechnological applications of characteristic short sequences such as human-specific and pathogen-specific short sequences obtained from availability analysis. Availability score was also dependent on secondary structures, potentially serving as a structural indicator. Availability analysis on triplets may be combined with a comprehensive data collection on the varphi and psi peptide-bond angles of the amino acid at the center of each triplet, i.e., a collection of Ramachandran plots for each triplet. These triplet characters, together with other physicochemical data, will provide us with basic information between protein sequence and structure, by which structure prediction and engineering may be greatly facilitated. Availability analysis may also be useful in identifying word processing units in amino acid sequences based on an analogy to natural languages. Together with other approaches, availability analysis will elucidate general rules hidden in the primary sequences and eventually contributes to rebuilding the paradigm of protein science.
{"title":"Potential implications of availability of short amino acid sequences in proteins: an old and new approach to protein decoding and design.","authors":"Joji M Otaki, Tomonori Gotoh, Haruhiko Yamamoto","doi":"10.1016/S1387-2656(08)00004-5","DOIUrl":"https://doi.org/10.1016/S1387-2656(08)00004-5","url":null,"abstract":"<p><p>Three-dimensional structure of a protein molecule is primarily determined by its amino acid sequence, and thus the elucidation of general rules embedded in amino acid sequences is of great importance in protein science and engineering. To extract valuable information from sequences, we propose an analytical method in which a protein sequence is considered to be constructed by serial superimpositions of short amino acid sequences of n amino acid sets, especially triplets (3-aa sets). Using the comprehensive nonredundant protein database, we first examined \"availability\" of all possible combinatorial sets of 8,000 triplet species. Availability score was mathematically defined as an indicator for the relative \"preference\" or \"avoidance\" for a given short constituent sequence to be used in protein chain. Availability scores of real proteins were clearly biased against those of randomly generated proteins. We found many triplet species that occurred in the database more than expected or less than expected. Such bias was extended to longer sets, and we found that some species of pentats (5-aa sets) that occurred reasonably frequently in the randomly generated protein population did not occur at all in any real proteins known today. Availability score was dependent on species, potentially serving as a phylogenetic indicator. Furthermore, we suggest possibilities of various biotechnological applications of characteristic short sequences such as human-specific and pathogen-specific short sequences obtained from availability analysis. Availability score was also dependent on secondary structures, potentially serving as a structural indicator. Availability analysis on triplets may be combined with a comprehensive data collection on the varphi and psi peptide-bond angles of the amino acid at the center of each triplet, i.e., a collection of Ramachandran plots for each triplet. These triplet characters, together with other physicochemical data, will provide us with basic information between protein sequence and structure, by which structure prediction and engineering may be greatly facilitated. Availability analysis may also be useful in identifying word processing units in amino acid sequences based on an analogy to natural languages. Together with other approaches, availability analysis will elucidate general rules hidden in the primary sequences and eventually contributes to rebuilding the paradigm of protein science.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(08)00004-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37434218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2008-01-01DOI: 10.1016/S1387-2656(08)00001-X
Sebastian Charbonnier, Oriol Gallego, Anne-Claude Gavin
Proteins very rarely act in isolation. Biomolecular interactions are central to all biological functions. In human, for example, interference with biomolecular networks often lead to disease. Protein-protein and protein-metabolite interactions have traditionally been studied one by one. Recently, significant progresses have been made in adapting suitable tools for the global analysis of biomolecular interactions. Here we review this suite of powerful technologies that enable an exponentially growing number of large-scale interaction datasets. These new technologies have already contributed to a more comprehensive cartography of several pathways relevant to human pathologies, offering a broader choice for therapeutic targets. Genome-wide scale analyses in model organisms reveal general organizational principles of eukaryotic proteomes. We also review the biochemical approaches that have been used in the past on a smaller scale for the quantification of the binding constant and the thermodynamics parameters governing biomolecular interaction. The adaptation of these technologies to the large-scale measurement of biomolecular interactions in (semi-)quantitative terms represents an important challenge.
{"title":"The social network of a cell: recent advances in interactome mapping.","authors":"Sebastian Charbonnier, Oriol Gallego, Anne-Claude Gavin","doi":"10.1016/S1387-2656(08)00001-X","DOIUrl":"https://doi.org/10.1016/S1387-2656(08)00001-X","url":null,"abstract":"<p><p>Proteins very rarely act in isolation. Biomolecular interactions are central to all biological functions. In human, for example, interference with biomolecular networks often lead to disease. Protein-protein and protein-metabolite interactions have traditionally been studied one by one. Recently, significant progresses have been made in adapting suitable tools for the global analysis of biomolecular interactions. Here we review this suite of powerful technologies that enable an exponentially growing number of large-scale interaction datasets. These new technologies have already contributed to a more comprehensive cartography of several pathways relevant to human pathologies, offering a broader choice for therapeutic targets. Genome-wide scale analyses in model organisms reveal general organizational principles of eukaryotic proteomes. We also review the biochemical approaches that have been used in the past on a smaller scale for the quantification of the binding constant and the thermodynamics parameters governing biomolecular interaction. The adaptation of these technologies to the large-scale measurement of biomolecular interactions in (semi-)quantitative terms represents an important challenge.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(08)00001-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37433789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2008-01-01DOI: 10.1016/S1387-2656(08)00019-7
Evelyn Mae Tecson Mendoza, Antonio C Laurena, José Ramón Botella
Papaya with resistance to papaya ringspot virus (PRSV) is the first genetically modified tree and fruit crop and also the first transgenic crop developed by a public institution that has been commercialized. This chapter reviews the different transformation systems used for papaya and recent advances in the use of transgenic technology to introduce important quality and horticultural traits in papaya. These include the development of the following traits in papaya: resistance to PRSV, mites and Phytophthora, delayed ripening trait or long shelf life by inhibiting ethylene production or reducing loss of firmness, and tolerance or resistance to herbicide and aluminum toxicity. The use of papaya to produce vaccine against tuberculosis and cysticercosis, an infectious animal disease, has also been explored. Because of the economic importance of papaya, there are several collaborative and independent efforts to develop PRSV transgenic papaya technology in 14 countries. This chapter further reviews the strategies and constraints in the adoption of the technology and biosafety to the environment and food safety. Constraints to adoption include public perception, strict and expensive regulatory procedures and intellectual property issues.
{"title":"Recent advances in the development of transgenic papaya technology.","authors":"Evelyn Mae Tecson Mendoza, Antonio C Laurena, José Ramón Botella","doi":"10.1016/S1387-2656(08)00019-7","DOIUrl":"https://doi.org/10.1016/S1387-2656(08)00019-7","url":null,"abstract":"<p><p>Papaya with resistance to papaya ringspot virus (PRSV) is the first genetically modified tree and fruit crop and also the first transgenic crop developed by a public institution that has been commercialized. This chapter reviews the different transformation systems used for papaya and recent advances in the use of transgenic technology to introduce important quality and horticultural traits in papaya. These include the development of the following traits in papaya: resistance to PRSV, mites and Phytophthora, delayed ripening trait or long shelf life by inhibiting ethylene production or reducing loss of firmness, and tolerance or resistance to herbicide and aluminum toxicity. The use of papaya to produce vaccine against tuberculosis and cysticercosis, an infectious animal disease, has also been explored. Because of the economic importance of papaya, there are several collaborative and independent efforts to develop PRSV transgenic papaya technology in 14 countries. This chapter further reviews the strategies and constraints in the adoption of the technology and biosafety to the environment and food safety. Constraints to adoption include public perception, strict and expensive regulatory procedures and intellectual property issues.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(08)00019-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37434158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2008-01-01DOI: 10.1016/S1387-2656(08)00008-2
John M Aletta, John C Hu
Protein arginine methylation is a rapidly growing field of biomedical research that holds great promise for extending our understanding of developmental and pathological processes. Less than ten years ago, fewer than two dozen proteins were verified to contain methylarginine. Currently, however, hundreds of methylarginine proteins have been detected and many have been confirmed by mass spectrometry and other proteomic and molecular techniques. Several of these proteins are products of disease genes or are implicated in disease processes by recent experimental or clinical observations. The purpose of this chapter is twofold; (1) to re-examine the role of protein arginine methylation placed within the context of cell growth and differentiation, as well as within the rich variety of cellular metabolic methylation pathways and (2) to review the implications of recent advances in protein methylarginine detection and the analysis of protein methylarginine function for our understanding of human disease.
{"title":"Protein arginine methylation in health and disease.","authors":"John M Aletta, John C Hu","doi":"10.1016/S1387-2656(08)00008-2","DOIUrl":"https://doi.org/10.1016/S1387-2656(08)00008-2","url":null,"abstract":"<p><p>Protein arginine methylation is a rapidly growing field of biomedical research that holds great promise for extending our understanding of developmental and pathological processes. Less than ten years ago, fewer than two dozen proteins were verified to contain methylarginine. Currently, however, hundreds of methylarginine proteins have been detected and many have been confirmed by mass spectrometry and other proteomic and molecular techniques. Several of these proteins are products of disease genes or are implicated in disease processes by recent experimental or clinical observations. The purpose of this chapter is twofold; (1) to re-examine the role of protein arginine methylation placed within the context of cell growth and differentiation, as well as within the rich variety of cellular metabolic methylation pathways and (2) to review the implications of recent advances in protein methylarginine detection and the analysis of protein methylarginine function for our understanding of human disease.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(08)00008-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37434222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-01-01DOI: 10.1016/S1387-2656(07)13002-7
G Wesley Hatfield, David A Roth
Translation Engineering combined with synthetic biology (gene synthesis) techniques makes it possible to deliberately alter the presumed translation kinetics of genes without altering the amino acid sequence. Here, we describe proprietary technologies that design and assemble synthetic genes for high expression and enhanced protein production, and offers new insights and methodologies for affecting protein structure and function. We have patented Translation Engineering technologies to manage the complexity of gene design to account for codon pair usage, translational pausing signals, RNA secondary structure and user-defined sequences such as restriction sites. Failure to optimize for codon pair-encoded translation pauses often results in the relatively common occurrence of a slowly translated codon pair that slows the rate of protein elongation and decreases total protein production. Translation Engineering technology improves heterologous expression by tuning the gene sequence for translation in any well-characterized host, including cell-free expression techniques characterized by "broken"Escherichia coli systems used in kits for today's molecular tools market. In addition, we have patented a novel gene assembly method (Computationally Optimized DNA Assembly; CODA) that uses the degeneracy of the genetic code to design oligonucleotides with thermodynamic properties for self-assembly into a single, linear DNA product. Fast translational kinetics and robust protein expression are optimized in synthetic "Hot Rod" genes that are guaranteed to express in E. coli at high levels. These genes are optimized for codon usage and other properties known to aid protein expression, and importantly, they are engineered to be devoid of mRNA secondary structures that might impede transcription, and over-represented codon pairs that might impede translation. Hot Rod genes allow translating ribosomes and E. coli RNA polymerases to maintain coupled translation and transcription at maximal rates. As a result, the nascent mRNA is produced at a high level and is sequestered in polysomes where it is protected from degradation, even further enhancing protein production. In this review we demonstrate that codon context can profoundly influence translation kinetics, and that over-represented codon pairs are often present at protein domain boundaries and appear to control independent protein folding in several popular expression systems. Finally, we consider that over-represented codon pairs (pause sites) may be essential to solving problems of protein expression, solubility, folding and activity encountered when genes are introduced into heterologous expression systems, where the specific set of codon pairs controlling ribosome pausing are different. Thus, Translation Engineering combined with synthetic biology (gene synthesis) techniques may allow us to manipulate the translation kinetics of genes to restore or enhance function in a variety of traditional and nove
翻译工程与合成生物学(基因合成)技术相结合,可以在不改变氨基酸序列的情况下故意改变基因的假定翻译动力学。在这里,我们描述了设计和组装高表达和增强蛋白质生产的合成基因的专有技术,并为影响蛋白质结构和功能提供了新的见解和方法。我们拥有翻译工程专利技术,以管理基因设计的复杂性,以解释密码子对的使用,翻译暂停信号,RNA二级结构和用户定义的序列,如限制位点。密码子对编码翻译停顿的优化失败通常会导致相对常见的密码子对翻译缓慢,从而减慢蛋白质延伸率并降低总蛋白质产量。翻译工程技术通过调整基因序列来改善异种表达,以便在任何具有良好特征的宿主中进行翻译,包括以“破碎”大肠杆菌系统为特征的无细胞表达技术,这些技术用于当今分子工具市场的试剂盒中。此外,我们还获得了一种新的基因组装方法(computational Optimized DNA assembly;CODA),利用遗传密码的退化来设计具有热力学性质的寡核苷酸,以便自组装成单一的线性DNA产物。在合成的“Hot Rod”基因中优化了快速翻译动力学和稳健的蛋白表达,保证了在大肠杆菌中高水平表达。这些基因对密码子的使用和其他已知的有助于蛋白质表达的特性进行了优化,重要的是,它们被设计成缺乏可能阻碍转录的mRNA二级结构,以及可能阻碍翻译的过度代表的密码子对。热杆基因允许翻译核糖体和大肠杆菌RNA聚合酶保持最大速率的耦合翻译和转录。因此,新生的mRNA在高水平上产生,并被隔离在多聚体中,在那里它被保护不被降解,甚至进一步提高了蛋白质的产生。在这篇综述中,我们证明密码子上下文可以深刻地影响翻译动力学,并且在几种流行的表达系统中,过度代表的密码子对通常存在于蛋白质结构域边界并似乎控制独立的蛋白质折叠。最后,我们认为过度代表的密码子对(暂停位点)可能对解决当基因被引入异种表达系统时遇到的蛋白质表达、溶解度、折叠和活性问题至关重要,在异种表达系统中,控制核糖体暂停的特定密码子对集是不同的。因此,翻译工程与合成生物学(基因合成)技术相结合,可能使我们能够操纵基因的翻译动力学,以恢复或增强各种传统和新型表达系统的功能。
{"title":"Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translation Engineering.","authors":"G Wesley Hatfield, David A Roth","doi":"10.1016/S1387-2656(07)13002-7","DOIUrl":"https://doi.org/10.1016/S1387-2656(07)13002-7","url":null,"abstract":"<p><p>Translation Engineering combined with synthetic biology (gene synthesis) techniques makes it possible to deliberately alter the presumed translation kinetics of genes without altering the amino acid sequence. Here, we describe proprietary technologies that design and assemble synthetic genes for high expression and enhanced protein production, and offers new insights and methodologies for affecting protein structure and function. We have patented Translation Engineering technologies to manage the complexity of gene design to account for codon pair usage, translational pausing signals, RNA secondary structure and user-defined sequences such as restriction sites. Failure to optimize for codon pair-encoded translation pauses often results in the relatively common occurrence of a slowly translated codon pair that slows the rate of protein elongation and decreases total protein production. Translation Engineering technology improves heterologous expression by tuning the gene sequence for translation in any well-characterized host, including cell-free expression techniques characterized by \"broken\"Escherichia coli systems used in kits for today's molecular tools market. In addition, we have patented a novel gene assembly method (Computationally Optimized DNA Assembly; CODA) that uses the degeneracy of the genetic code to design oligonucleotides with thermodynamic properties for self-assembly into a single, linear DNA product. Fast translational kinetics and robust protein expression are optimized in synthetic \"Hot Rod\" genes that are guaranteed to express in E. coli at high levels. These genes are optimized for codon usage and other properties known to aid protein expression, and importantly, they are engineered to be devoid of mRNA secondary structures that might impede transcription, and over-represented codon pairs that might impede translation. Hot Rod genes allow translating ribosomes and E. coli RNA polymerases to maintain coupled translation and transcription at maximal rates. As a result, the nascent mRNA is produced at a high level and is sequestered in polysomes where it is protected from degradation, even further enhancing protein production. In this review we demonstrate that codon context can profoundly influence translation kinetics, and that over-represented codon pairs are often present at protein domain boundaries and appear to control independent protein folding in several popular expression systems. Finally, we consider that over-represented codon pairs (pause sites) may be essential to solving problems of protein expression, solubility, folding and activity encountered when genes are introduced into heterologous expression systems, where the specific set of codon pairs controlling ribosome pausing are different. Thus, Translation Engineering combined with synthetic biology (gene synthesis) techniques may allow us to manipulate the translation kinetics of genes to restore or enhance function in a variety of traditional and nove","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(07)13002-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40977675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-01-01DOI: 10.1016/S1387-2656(07)13006-4
David Liénard, Christophe Sourrouille, Véronique Gomord, Loïc Faye
Plant represented the essence of pharmacopoeia until the beginning of the 19th century when plant-derived pharmaceuticals were partly supplanted by drugs produced by the industrial methods of chemical synthesis. In the last decades, genetic engineering has offered an alternative to chemical synthesis, using bacteria, yeasts and animal cells as factories for the production of therapeutic proteins. More recently, molecular farming has rapidly pushed towards plants among the major players in recombinant protein production systems. Indeed, therapeutic protein production is safe and extremely cost-effective in plants. Unlike microbial fermentation, plants are capable of carrying out post-translational modifications and, unlike production systems based on mammalian cell cultures, plants are devoid of human infective viruses and prions. Furthermore, a large panel of strategies and new plant expression systems are currently developed to improve the plant-made pharmaceutical's yields and quality. Recent advances in the control of post-translational maturations in transgenic plants will allow them, in the near future, to perform human-like maturations on recombinant proteins and, hence, make plant expression systems suitable alternatives to animal cell factories.
{"title":"Pharming and transgenic plants.","authors":"David Liénard, Christophe Sourrouille, Véronique Gomord, Loïc Faye","doi":"10.1016/S1387-2656(07)13006-4","DOIUrl":"https://doi.org/10.1016/S1387-2656(07)13006-4","url":null,"abstract":"<p><p>Plant represented the essence of pharmacopoeia until the beginning of the 19th century when plant-derived pharmaceuticals were partly supplanted by drugs produced by the industrial methods of chemical synthesis. In the last decades, genetic engineering has offered an alternative to chemical synthesis, using bacteria, yeasts and animal cells as factories for the production of therapeutic proteins. More recently, molecular farming has rapidly pushed towards plants among the major players in recombinant protein production systems. Indeed, therapeutic protein production is safe and extremely cost-effective in plants. Unlike microbial fermentation, plants are capable of carrying out post-translational modifications and, unlike production systems based on mammalian cell cultures, plants are devoid of human infective viruses and prions. Furthermore, a large panel of strategies and new plant expression systems are currently developed to improve the plant-made pharmaceutical's yields and quality. Recent advances in the control of post-translational maturations in transgenic plants will allow them, in the near future, to perform human-like maturations on recombinant proteins and, hence, make plant expression systems suitable alternatives to animal cell factories.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(07)13006-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40979844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-01-01DOI: 10.1016/S1387-2656(07)13004-0
Eric Soler, Louis-Marie Houdebine
Vaccination is one of the most efficient ways to eradicate some infectious diseases in humans and animals. The material traditionally used as vaccines is attenuated or inactivated pathogens. This approach is sometimes limited by the fact that the material for vaccination is not efficient, not available, or generating deleterious side effects. A possible theoretical alternative is the use of recombinant proteins from the pathogens. This implies that the proteins having the capacity to vaccinate have been identified and that they can be produced in sufficient quantity at a low cost. Genetically modified organisms harboring pathogen genes can fulfil these conditions. Microorganisms, animal cells as well as transgenic plants and animals can be the source of recombinant vaccines. Each of these systems that are all getting improved has advantages and limits. Adjuvants must generally be added to the recombinant proteins to enhance their vaccinating capacity. This implies that the proteins used to vaccinate have been purified to avoid any immunization against the contaminants. The efficiency of a recombinant vaccine is poorly predictable. Multiple proteins and various modes of administration must therefore be empirically evaluated on a case-by-case basis. The structure of the recombinant proteins, the composition of the adjuvants and the mode of administration of the vaccines have a strong and not fully predictable impact on the immune response as well as the protection level against pathogens. Recombinant proteins can theoretically also be used as carriers for epitopes from other pathogens. The increasing knowledge of pathogen genomes and the availability of efficient systems to prepare large amounts of recombinant proteins greatly facilitate the potential use of recombinant proteins as vaccines. The present review is a critical analysis of the state of the art in this field.
{"title":"Preparation of recombinant vaccines.","authors":"Eric Soler, Louis-Marie Houdebine","doi":"10.1016/S1387-2656(07)13004-0","DOIUrl":"https://doi.org/10.1016/S1387-2656(07)13004-0","url":null,"abstract":"<p><p>Vaccination is one of the most efficient ways to eradicate some infectious diseases in humans and animals. The material traditionally used as vaccines is attenuated or inactivated pathogens. This approach is sometimes limited by the fact that the material for vaccination is not efficient, not available, or generating deleterious side effects. A possible theoretical alternative is the use of recombinant proteins from the pathogens. This implies that the proteins having the capacity to vaccinate have been identified and that they can be produced in sufficient quantity at a low cost. Genetically modified organisms harboring pathogen genes can fulfil these conditions. Microorganisms, animal cells as well as transgenic plants and animals can be the source of recombinant vaccines. Each of these systems that are all getting improved has advantages and limits. Adjuvants must generally be added to the recombinant proteins to enhance their vaccinating capacity. This implies that the proteins used to vaccinate have been purified to avoid any immunization against the contaminants. The efficiency of a recombinant vaccine is poorly predictable. Multiple proteins and various modes of administration must therefore be empirically evaluated on a case-by-case basis. The structure of the recombinant proteins, the composition of the adjuvants and the mode of administration of the vaccines have a strong and not fully predictable impact on the immune response as well as the protection level against pathogens. Recombinant proteins can theoretically also be used as carriers for epitopes from other pathogens. The increasing knowledge of pathogen genomes and the availability of efficient systems to prepare large amounts of recombinant proteins greatly facilitate the potential use of recombinant proteins as vaccines. The present review is a critical analysis of the state of the art in this field.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(07)13004-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40979843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-01-01DOI: 10.1016/S1387-2656(07)13012-X
MaryAnn Foote
Nanotechnology refers to the use of very small pieces of matter, typically < or =200 nm in diameter. Nanoparticle albumin-bound (nab) paclitaxel, a soluble form of the cytotoxin paclitaxel that has demonstrated utility in the setting of cancer chemotherapy, is produced by nab technology using the protein albumin. nab-Paclitaxel targets tumors, enhances tumor penetration by the novel mechanism of albumin receptor-mediated (gp60) endothelial transcytosis, and avoids the use of surfactants and solvents such as Cremophor and Tween. nab-Paclitaxel minimizes the toxicities associated with Cremophor and eliminates the need for premedication for hypersensitivity reactions caused by Cremophor. The albumin coating that surrounds the active drug assists in the transport of the nanoparticles to the interior of the tumor cell that preferentially takes in albumin as a nutrient through the gp60 pathway. In nonclinical studies, nab-paclitaxel achieved higher intratumoral concentrations compared with solvent-based paclitaxel and increased the bioavailability of paclitaxel by eliminating the entrapment of paclitaxel in the plasma. Compared with solvent-based paclitaxel, at equitoxic doses, the nab-paclitaxel produced more complete regressions, longer time to recurrence, longer doubling times, and prolonged survival. nab-Paclitaxel has been shown to have superior efficacy compared with solvent-based paclitaxel without the need for premedication in clinical trials of patients with advanced solid tumors. nab-Paclitaxel has been effective in patients for whom previous chemotherapy has not been helpful. nab Technology has the potential to be applied to other insoluble drugs.
{"title":"Using nanotechnology to improve the characteristics of antineoplastic drugs: improved characteristics of nab-paclitaxel compared with solvent-based paclitaxel.","authors":"MaryAnn Foote","doi":"10.1016/S1387-2656(07)13012-X","DOIUrl":"https://doi.org/10.1016/S1387-2656(07)13012-X","url":null,"abstract":"<p><p>Nanotechnology refers to the use of very small pieces of matter, typically < or =200 nm in diameter. Nanoparticle albumin-bound (nab) paclitaxel, a soluble form of the cytotoxin paclitaxel that has demonstrated utility in the setting of cancer chemotherapy, is produced by nab technology using the protein albumin. nab-Paclitaxel targets tumors, enhances tumor penetration by the novel mechanism of albumin receptor-mediated (gp60) endothelial transcytosis, and avoids the use of surfactants and solvents such as Cremophor and Tween. nab-Paclitaxel minimizes the toxicities associated with Cremophor and eliminates the need for premedication for hypersensitivity reactions caused by Cremophor. The albumin coating that surrounds the active drug assists in the transport of the nanoparticles to the interior of the tumor cell that preferentially takes in albumin as a nutrient through the gp60 pathway. In nonclinical studies, nab-paclitaxel achieved higher intratumoral concentrations compared with solvent-based paclitaxel and increased the bioavailability of paclitaxel by eliminating the entrapment of paclitaxel in the plasma. Compared with solvent-based paclitaxel, at equitoxic doses, the nab-paclitaxel produced more complete regressions, longer time to recurrence, longer doubling times, and prolonged survival. nab-Paclitaxel has been shown to have superior efficacy compared with solvent-based paclitaxel without the need for premedication in clinical trials of patients with advanced solid tumors. nab-Paclitaxel has been effective in patients for whom previous chemotherapy has not been helpful. nab Technology has the potential to be applied to other insoluble drugs.</p>","PeriodicalId":79566,"journal":{"name":"Biotechnology annual review","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1387-2656(07)13012-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40978610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}