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Van Gelder K, Lindner SN, Hanson AD, Zhou J. Strangers in a foreign land: 'Yeastizing' plant enzymes. Microb Biotechnol 2024; 17:e14525. [PMID: 39222378 PMCID: PMC11368087 DOI: 10.1111/1751-7915.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/02/2024] [Indexed: 09/04/2024] Open
Abstract
Expressing plant metabolic pathways in microbial platforms is an efficient, cost-effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour-intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost-effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data-driven machine learning framework designed to extract 'yeastizing' rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design-build-test cycle.
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Affiliation(s)
- Kristen Van Gelder
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Steffen N. Lindner
- Department of Systems and Synthetic MetabolismMax Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Department of BiochemistryCharité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt‐UniversitätBerlinGermany
| | - Andrew D. Hanson
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Juannan Zhou
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
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2
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Uddin A. Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04091-x. [PMID: 38488980 DOI: 10.1007/s12035-024-04091-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
Codon usage bias (CUB) is the phenomenon of non-uniform usage of synonymous codons in which some codons are more used than others and it helps in understanding the molecular organization of genome. Bioinformatic approach was used to analyze the protein-coding sequences of genes associated with Parkinson's disease (PD) to explore compositional features and codon usage pattern as no details work was reported yet. The average improved effective number of codons (Nc) and Nc prime were 42.74 and 44.26 respectively, indicated that CUB was low in these genes. In most of the genes, the overall GC content was almost 50% and GC content at the 1st codon position was the highest while GC content at the 2nd codon position was lowest. Relative synonymous codon usage (RSCU) analysis elucidated over-represented (p > 1.6) and under-represented codons (p < 0.6). The GTG (Val) is the only codon over-represented in all genes. Over-represented codons except (GTG) were A or T ending while under-represented codons (except ACT) were G or C ending. The codons namely TTA (Leu), CTA (Leu), ATC (Ile), ATA (Ile), AGT (Ser), AAC (Asn), TGT (Cys), TGC (Cys), CGC (Arg), AGA (Arg), and AGG (Arg) were absent in SNCA1 to SNCA8 genes. The codon TCG (Ser) was absent in all genes except UCHL1 and PINK1. Correspondence analysis (COA) revealed that the pattern of codon usage differs among genes associated with PD. Neutrality plot analysis indicated some of the points are diagonal distribution suggested that mutation pressure influenced the CUB in genes associated with PD.
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Affiliation(s)
- Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi-788150, Assam, India.
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3
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Khandia R, Gurjar P, Kamal MA, Greig NH. Relative synonymous codon usage and codon pair analysis of depression associated genes. Sci Rep 2024; 14:3502. [PMID: 38346990 PMCID: PMC10861588 DOI: 10.1038/s41598-024-51909-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Depression negatively impacts mood, behavior, and mental and physical health. It is the third leading cause of suicides worldwide and leads to decreased quality of life. We examined 18 genes available at the genetic testing registry (GTR) from the National Center for Biotechnological Information to investigate molecular patterns present in depression-associated genes. Different genotypes and differential expression of the genes are responsible for ensuing depression. The present study, investigated codon pattern analysis, which might play imperative roles in modulating gene expression of depression-associated genes. Of the 18 genes, seven and two genes tended to up- and down-regulate, respectively, and, for the remaining genes, different genotypes, an outcome of SNPs were responsible alone or in combination with differential expression for different conditions associated with depression. Codon context analysis revealed the abundance of identical GTG-GTG and CTG-CTG pairs, and the rarity of methionine-initiated codon pairs. Information based on codon usage, preferred codons, rare, and codon context might be used in constructing a deliverable synthetic construct to correct the gene expression level of the human body, which is altered in the depressive state. Other molecular signatures also revealed the role of evolutionary forces in shaping codon usage.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, 462026, MP, India.
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamilnadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Mohammad Amjad Kamal
- Joint Laboratory of Artificial Intelligence in Healthcare, Institutes for Systems Genetics and West China School of Nursing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
- Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee place, Hebersham, NSW, 2770, Australia
| | - Nigel H Greig
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD, 21224, USA.
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4
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Zhao M, Ma J, Zhang L, Qi H. Engineering strategies for enhanced heterologous protein production by Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:32. [PMID: 38247006 PMCID: PMC10801990 DOI: 10.1186/s12934-024-02299-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Microbial proteins are promising substitutes for animal- and plant-based proteins. S. cerevisiae, a generally recognized as safe (GRAS) microorganism, has been frequently employed to generate heterologous proteins. However, constructing a universal yeast chassis for efficient protein production is still a challenge due to the varying properties of different proteins. With progress in synthetic biology, a multitude of molecular biology tools and metabolic engineering strategies have been employed to alleviate these issues. This review first analyses the advantages of protein production by S. cerevisiae. The most recent advances in improving heterologous protein yield are summarized and discussed in terms of protein hyperexpression systems, protein secretion engineering, glycosylation pathway engineering and systems metabolic engineering. Furthermore, the prospects for efficient and sustainable heterologous protein production by S. cerevisiae are also provided.
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Affiliation(s)
- Meirong Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Jianfan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Lei Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Haishan Qi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China.
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5
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Khandia R, Gurjar P, Romashchenko V, Al-Hussain SA, Alexiou A, Zouganelis G, Zaki MEA. In-silico Codon Context and Synonymous Usage Analysis of Genes for Molecular Mechanisms Inducing Autophagy and Apoptosis with Reference to Neurodegenerative Disorders. J Alzheimers Dis 2024; 99:927-939. [PMID: 38728191 DOI: 10.3233/jad-240158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Background Autophagy and apoptosis are cellular processes that maintain cellular homeostasis and remove damaged or aged organelles or aggregated and misfolded proteins. Stress factors initiate the signaling pathways common to autophagy and apoptosis. An imbalance in the autophagy and apoptosis, led by cascade of molecular mechanism prior to both processes culminate into neurodegeneration. Objective In present study, we urge to investigate the codon usage pattern of genes which are common before initiating autophagy and apoptosis. Methods In the present study, we took up eleven genes (DAPK1, BECN1, PIK3C3 (VPS34), BCL2, MAPK8, BNIP3 L (NIX), PMAIP1, BAD, BID, BBC3, MCL1) that are part of molecular signaling mechanism prior to autophagy and apoptosis. We analyzed dinucleotide odds ratio, codon bias, usage, context, and rare codon analysis. Results CpC and GpG dinucleotides were abundant, with the dominance of G/C ending codons as preferred codons. Clustering analysis revealed that MAPK8 had a distinct codon usage pattern compared to other envisaged genes. Both positive and negative contexts were observed, and GAG-GAG followed by CTG-GCC was the most abundant codon pair. Of the six synonymous arginine codons, two codons CGT and CGA were the rarest. Conclusions The information presented in the study may be used to manipulate the process of autophagy and apoptosis and to check the pathophysiology associated with their dysregulation.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, NSW, Australia
| | | | - Sami A Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, NSW, Australia
- University Centre for Research & Development, Chandigarh University, Chandigarh-Ludhiana Highway, Mohali, Punjab, India
- Department of Research & Development, Funogen, Athens, Greece
- Department of Research & Development, AFNP Med, Wienna, Austria
| | - George Zouganelis
- School of Human Sciences, College of Life and Natural Sciences, University of Derby, Kedleston Road, Derby, UK
| | - Magdi E A Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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6
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Pfeifer BA, Beitelshees M, Hill A, Bassett J, Jones CH. Harnessing synthetic biology for advancing RNA therapeutics and vaccine design. NPJ Syst Biol Appl 2023; 9:60. [PMID: 38036580 PMCID: PMC10689799 DOI: 10.1038/s41540-023-00323-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Recent global events have drawn into focus the diversity of options for combatting disease across a spectrum of prophylactic and therapeutic approaches. The recent success of the mRNA-based COVID-19 vaccines has paved the way for RNA-based treatments to revolutionize the pharmaceutical industry. However, historical treatment options are continuously updated and reimagined in the context of novel technical developments, such as those facilitated through the application of synthetic biology. When it comes to the development of genetic forms of therapies and vaccines, synthetic biology offers diverse tools and approaches to influence the content, dosage, and breadth of treatment with the prospect of economic advantage provided in time and cost benefits. This can be achieved by utilizing the broad tools within this discipline to enhance the functionality and efficacy of pharmaceutical agent sequences. This review will describe how synthetic biology principles can augment RNA-based treatments through optimizing not only the vaccine antigen, therapeutic construct, therapeutic activity, and delivery vector. The enhancement of RNA vaccine technology through implementing synthetic biology has the potential to shape the next generation of vaccines and therapeutics.
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Affiliation(s)
- Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | | | - Andrew Hill
- Pfizer, 66 Hudson Boulevard, New York, NY, 10001, USA
| | - Justin Bassett
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
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Alagar Boopathy LR, Beadle E, Garcia-Bueno Rico A, Vera M. Proteostasis regulation through ribosome quality control and no-go-decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1809. [PMID: 37488089 DOI: 10.1002/wrna.1809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/14/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Abstract
Cell functionality relies on the existing pool of proteins and their folding into functional conformations. This is achieved through the regulation of protein synthesis, which requires error-free mRNAs and ribosomes. Ribosomes are quality control hubs for mRNAs and proteins. Problems during translation elongation slow down the decoding rate, leading to ribosome halting and the eventual collision with the next ribosome. Collided ribosomes form a specific disome structure recognized and solved by ribosome quality control (RQC) mechanisms. RQC pathways orchestrate the degradation of the problematic mRNA by no-go decay and the truncated nascent peptide, the repression of translation initiation, and the recycling of the stalled ribosomes. All these events maintain protein homeostasis and return valuable ribosomes to translation. As such, cell homeostasis and function are maintained at the mRNA level by preventing the production of aberrant or unnecessary proteins. It is becoming evident that the crosstalk between RQC and the protein homeostasis network is vital for cell function, as the absence of RQC components leads to the activation of stress response and neurodegenerative diseases. Here, we review the molecular events of RQC discovered through well-designed stalling reporters. Given the impact of RQC in proteostasis, we discuss the relevance of identifying endogenous mRNA regulated by RQC and their preservation in stress conditions. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms Translation > Regulation.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
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8
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Alagar Boopathy L, Beadle E, Xiao A, Garcia-Bueno Rico A, Alecki C, Garcia de-Andres I, Edelmeier K, Lazzari L, Amiri M, Vera M. The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome. Nucleic Acids Res 2023; 51:6370-6388. [PMID: 37158240 PMCID: PMC10325905 DOI: 10.1093/nar/gkad338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
Cells survive harsh environmental conditions by potently upregulating molecular chaperones such as heat shock proteins (HSPs), particularly the inducible members of the HSP70 family. The life cycle of HSP70 mRNA in the cytoplasm is unique-it is translated during stress when most cellular mRNA translation is repressed and rapidly degraded upon recovery. Contrary to its 5' untranslated region's role in maximizing translation, we discovered that the HSP70 coding sequence (CDS) suppresses its translation via the ribosome quality control (RQC) mechanism. The CDS of the most inducible Saccharomyces cerevisiae HSP70 gene, SSA4, is uniquely enriched with low-frequency codons that promote ribosome stalling during heat stress. Stalled ribosomes are recognized by the RQC components Asc1p and Hel2p and two novel RQC components, the ribosomal proteins Rps28Ap and Rps19Bp. Surprisingly, RQC does not signal SSA4 mRNA degradation via No-Go-Decay. Instead, Asc1p destabilizes SSA4 mRNA during recovery from heat stress by a mechanism independent of ribosome binding and SSA4 codon optimality. Therefore, Asc1p operates in two pathways that converge to regulate the SSA4 mRNA life cycle during stress and recovery. Our research identifies Asc1p as a critical regulator of the stress response and RQC as the mechanism tuning HSP70 synthesis.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Alan RuoChen Xiao
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Celia Alecki
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Kyla Edelmeier
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Luca Lazzari
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Mehdi Amiri
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Maria Vera
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
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9
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Recent Advances on the Production of Itaconic Acid via the Fermentation and Metabolic Engineering. FERMENTATION 2023. [DOI: 10.3390/fermentation9010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Itaconic acid (ITA) is one of the top 12 platform chemicals. The global ITA market is expanding due to the rising demand for bio-based unsaturated polyester resin and its non-toxic qualities. Although bioconversion using microbes is the main approach in the current industrial production of ITA, ecological production of bio-based ITA faces several issues due to: low production efficiency, the difficulty to employ inexpensive raw materials, and high manufacturing costs. As metabolic engineering advances, the engineering of microorganisms offers a novel strategy for the promotion of ITA bio-production. In this review, the most recent developments in the production of ITA through fermentation and metabolic engineering are compiled from a variety of perspectives, including the identification of the ITA synthesis pathway, the metabolic engineering of natural ITA producers, the design and construction of the ITA synthesis pathway in model chassis, and the creation, as well as application, of new metabolic engineering strategies in ITA production. The challenges encountered in the bio-production of ITA in microbial cell factories are discussed, and some suggestions for future study are also proposed, which it is hoped offers insightful views to promote the cost-efficient and sustainable industrial production of ITA.
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10
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Perrin J, Besseau S, Papon N, Courdavault V. Boosting lignan-precursor synthesis in yeast cell factories through co-factor supply optimization. Front Bioeng Biotechnol 2022; 10:1079801. [DOI: 10.3389/fbioe.2022.1079801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
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Design of typical genes for heterologous gene expression. Sci Rep 2022; 12:9625. [PMID: 35688911 PMCID: PMC9187722 DOI: 10.1038/s41598-022-13089-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
Heterologous protein expression is an important method for analysing cellular functions of proteins, in genetic circuit engineering and in overexpressing proteins for biopharmaceutical applications and structural biology research. The degeneracy of the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, plays an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the influence of a profiled codon usage adaptation approach on protein expression levels in the eukaryotic model organism Saccharomyces cerevisiae. We selected green fluorescent protein (GFP) and human α-synuclein (αSyn) as representatives for stable and intrinsically disordered proteins and representing a benchmark and a challenging test case. A new approach was implemented to design typical genes resembling the codon usage of any subset of endogenous genes. Using this approach, synthetic genes for GFP and αSyn were generated, heterologously expressed and evaluated in yeast. We demonstrate that GFP is expressed at high levels, and that the toxic αSyn can be adapted to endogenous, low-level expression. The new software is publicly available as a web-application for performing host-specific protein adaptations to a set of the most commonly used model organisms ( https://odysseus.motorprotein.de ).
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12
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Biosynthesis and regulation of anthocyanin pathway genes. Appl Microbiol Biotechnol 2022; 106:1783-1798. [PMID: 35171341 DOI: 10.1007/s00253-022-11835-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 11/02/2022]
Abstract
Anthocyanins are the phenolic compounds responsible for coloring pigments in fruits and vegetables. Anthocyanins offer a wide range of health benefits to human health. Their scope has expanded dramatically in the past decade, making anthocyanin control, influx, and outflow regulation fascinating for many researchers. The main culprit is anthocyanin stability and concentration form, which demands novel ways because these are critical in the food industry. This review aims to examine anthocyanin synthesis via triggering transcription genes that code for anthocyanin-producing enzymes. The balance between production and breakdown determines anthocyanin accumulation. Thus, increasing the anthocyanin content in food requires the stability of molecules in the vacuolar lumen, the pigment fading process, and a better understanding of the mechanism. The promising option is biosynthesis by metabolically engineered microorganisms with a lot of success. This study aims to look into and evaluate the existing literature on anthocyanin production, namely the biosynthesis of anthocyanin pathway genes, production by microbial cell factories, and the regulatory factors that can modulate the production of anthocyanins. Understanding these mechanisms will provide new biotechnological approaches.Key points• Factors affecting the regulation of anthocyanins• Focus on degradation, biosynthesis pathway genes, and alternative systems for the production of anthocyanins• Microbial cell factories can be used to produce large amounts of anthocyanins.
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13
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Otto M, Liu D, Siewers V. Saccharomyces cerevisiae as a Heterologous Host for Natural Products. Methods Mol Biol 2022; 2489:333-367. [PMID: 35524059 DOI: 10.1007/978-1-0716-2273-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell factories can provide a sustainable supply of natural products with applications as pharmaceuticals, food-additives or biofuels. Besides being an important model organism for eukaryotic systems, Saccharomyces cerevisiae is used as a chassis for the heterologous production of natural products. Its success as a cell factory can be attributed to the vast knowledge accumulated over decades of research, its overall ease of engineering and its robustness. Many methods and toolkits have been developed by the yeast metabolic engineering community with the aim of simplifying and accelerating the engineering process.In this chapter, a range of methodologies are highlighted, which can be used to develop novel natural product cell factories or to improve titer, rate and yields of an existing cell factory with the goal of developing an industrially relevant strain. The addressed topics are applicable for different stages of a cell factory engineering project and include the choice of a natural product platform strain, expression cassette design for heterologous or native genes, basic and advanced genetic engineering strategies, and library screening methods using biosensors. The many engineering methods available and the examples of yeast cell factories underline the importance and future potential of this host for industrial production of natural products.
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Affiliation(s)
- Maximilian Otto
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Dany Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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14
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Wright G, Rodriguez A, Li J, Milenkovic T, Emrich SJ, Clark PL. CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern. Protein Sci 2022; 31:221-231. [PMID: 34738275 PMCID: PMC8740841 DOI: 10.1002/pro.4223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 01/03/2023]
Abstract
There is a growing appreciation that synonymous codon usage, although historically regarded as phenotypically silent, can instead alter a wide range of mechanisms related to functional protein production, a term we use here to describe the net effect of transcription (mRNA synthesis), mRNA half-life, translation (protein synthesis) and the probability of a protein folding correctly to its active, functional structure. In particular, recent discoveries have highlighted the important role that sub-optimal codons can play in modifying co-translational protein folding. These results have drawn increased attention to the patterns of synonymous codon usage within coding sequences, particularly in light of the discovery that these patterns can be conserved across evolution for homologous proteins. Because synonymous codon usage differs between organisms, for heterologous gene expression it can be desirable to make synonymous codon substitutions to match the codon usage pattern from the original organism in the heterologous expression host. Here we present CHARMING (for Codon HARMonizING), a robust and versatile algorithm to design mRNA sequences for heterologous gene expression and other related codon harmonization tasks. CHARMING can be run as a downloadable Python script or via a web portal at http://www.codons.org.
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Affiliation(s)
- Gabriel Wright
- Department of Computer Science & EngineeringUniversity of Notre DameNotre DameIndianaUSA,Present address:
Department of Electrical Engineering and Computer ScienceMilwaukee School of EngineeringMilwaukeeWIUSA
| | - Anabel Rodriguez
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jun Li
- Department of Applied and Computational Mathematics & StatisticsUniversity of Notre DameNotre DameIndianaUSA
| | - Tijana Milenkovic
- Department of Computer Science & EngineeringUniversity of Notre DameNotre DameIndianaUSA
| | - Scott J. Emrich
- Department of Electrical Engineering & Computer ScienceUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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15
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Xu G, Shi X, Gao Y, Wang J, Cheng H, Liu Y, Chen Y, Li J, Xu X, Zha J, Xia K, Linhardt RJ, Zhang X, Shi J, Koffas MA, Xu Z. Semi-rational evolution of pyruvate carboxylase from Rhizopus oryzae for elevated fumaric acid synthesis in Saccharomyces cerevisiae. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Huang Y, Lin T, Lu L, Cai F, Lin J, Jiang YE, Lin Y. Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris. Microb Cell Fact 2021; 20:209. [PMID: 34736476 PMCID: PMC8567542 DOI: 10.1186/s12934-021-01696-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022] Open
Abstract
Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by influencing both translational elongation rates and accuracy. Until now, it remains untested whether optimized genes based on codon pair bias results in higher protein expression levels compared to codon usage bias. Results In this study, an algorithm based on dynamic programming was introduced to develop codon pair optimization (CPO) which is a software tool to provide simple and efficient codon pair optimization for synthetic gene design in Pichia pastoris. Two reporters (MT1-MMP E2C6 and ADAM17 A9B8 scFvs) were employed to test the effects of codon pair bias and CPO optimization on their protein expression levels. Four variants of MT1-MMP E2C6 and ADAM17 A9B8 for each were generated, one variant with the best codon-pair context, one with the worst codon-pair context, one with unbiased codon-pair context, and another optimized based on codon usage. The expression levels of variants with the worst codon-pair context were almost undetectable by Western blot and the variants with the best codon-pair context were expressed well. The expression levels on MT1-MMP E2C6 and ADAM17 A9B8 were more than five times and seven times higher in the optimized sequences based on codon-pair context compared to that based on codon usage, respectively. The results indicated that the codon-pair context-based codon optimization is more effective in enhancing expression of protein in Pichia pastoris. Conclusions Codon-pair context plays an important role on the protein expression in Pichia pastoris. The codon pair optimization (CPO) software developed in this study efficiently improved the protein expression levels of exogenous genes in Pichia pastoris, suggesting gene design based on codon pair bias is an alternative strategy for high expression of recombinant proteins in Pichia pastoris. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01696-y.
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Affiliation(s)
- Yide Huang
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China. .,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China.
| | - Ting Lin
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Lingfang Lu
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Fan Cai
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Jie Lin
- College of Mathematics and Informatics, Fujian Normal University, Fuzhou, 350007, China
| | - Yu E Jiang
- College of Mathematics and Informatics, Fujian Normal University, Fuzhou, 350007, China.
| | - Yao Lin
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China. .,Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China.
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17
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Fox DM, Branson KM, Walker RC. mRNA codon optimization with quantum computers. PLoS One 2021; 16:e0259101. [PMID: 34714834 PMCID: PMC8555812 DOI: 10.1371/journal.pone.0259101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/12/2021] [Indexed: 11/19/2022] Open
Abstract
Reverse translation of polypeptide sequences to expressible mRNA constructs is a NP-hard combinatorial optimization problem. Each amino acid in the protein sequence can be represented by as many as six codons, and the process of selecting the combination that maximizes probability of expression is termed codon optimization. This work investigates the potential impact of leveraging quantum computing technology for codon optimization. A Quantum Annealer (QA) is compared to a standard genetic algorithm (GA) programmed with the same objective function. The QA is found to be competitive in identifying optimal solutions. The utility of gate-based systems is also evaluated using a simulator resulting in the finding that while current generations of devices lack the hardware requirements, in terms of both qubit count and connectivity, to solve realistic problems, future generation devices may be highly efficient.
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Affiliation(s)
- Dillion M. Fox
- Data and Computational Science, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Kim M. Branson
- Artificial Intelligence and Machine Learning, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Ross C. Walker
- Data and Computational Science, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, La Jolla, California, United States of America
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18
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den Haan R, Rose SH, Cripwell RA, Trollope KM, Myburgh MW, Viljoen-Bloom M, van Zyl WH. Heterologous production of cellulose- and starch-degrading hydrolases to expand Saccharomyces cerevisiae substrate utilization: Lessons learnt. Biotechnol Adv 2021; 53:107859. [PMID: 34678441 DOI: 10.1016/j.biotechadv.2021.107859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Selected strains of Saccharomyces cerevisiae are used for commercial bioethanol production from cellulose and starch, but the high cost of exogenous enzymes for substrate hydrolysis remains a challenge. This can be addressed through consolidated bioprocessing (CBP) where S. cerevisiae strains are engineered to express recombinant glycoside hydrolases during fermentation. Looking back at numerous strategies undertaken over the past four decades to improve recombinant protein production in S. cerevisiae, it is evident that various steps in the protein production "pipeline" can be manipulated depending on the protein of interest and its anticipated application. In this review, we briefly introduce some of the strategies and highlight lessons learned with regards to improved transcription, translation, post-translational modification and protein secretion of heterologous hydrolases. We examine how host strain selection and modification, as well as enzyme compatibility, are crucial determinants for overall success. Finally, we discuss how lessons from heterologous hydrolase expression can inform modern synthetic biology and genome editing tools to provide process-ready yeast strains in future. However, it is clear that the successful expression of any particular enzyme is still unpredictable and requires a trial-and-error approach.
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Affiliation(s)
- Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Kim M Trollope
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marthinus W Myburgh
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa.
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19
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Gatina DZ, Garanina EE, Zhuravleva MN, Synbulatova GE, Mullakhmetova AF, Solovyeva VV, Kiyasov AP, Rutland CS, Rizvanov AA, Salafutdinov II. Proangiogenic Effect of 2A-Peptide Based Multicistronic Recombinant Constructs Encoding VEGF and FGF2 Growth Factors. Int J Mol Sci 2021; 22:ijms22115922. [PMID: 34072943 PMCID: PMC8198600 DOI: 10.3390/ijms22115922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/16/2022] Open
Abstract
Coronary artery disease remains one of the primary healthcare problems due to the high cost of treatment, increased number of patients, poor clinical outcomes, and lack of effective therapy. Though pharmacological and surgical treatments positively affect symptoms and arrest the disease progression, they generally exhibit a limited effect on the disease outcome. The development of alternative therapeutic approaches towards ischemic disease treatment, especially of decompensated forms, is therefore relevant. Therapeutic angiogenesis, stimulated by various cytokines, chemokines, and growth factors, provides the possibility of restoring functional blood flow in ischemic tissues, thereby ensuring the regeneration of the damaged area. In the current study, based on the clinically approved plasmid vector pVax1, multigenic constructs were developed encoding vascular endothelial growth factor (VEGF), fibroblast growth factors (FGF2), and the DsRed fluorescent protein, integrated via picornaviruses' furin-2A peptide sequences. In vitro experiments demonstrated that genetically modified cells with engineered plasmid constructs expressed the target proteins. Overexpression of VEGF and FGF2 resulted in increased levels of the recombinant proteins. Concomitantly, these did not lead to a significant shift in the general secretory profile of modified HEK293T cells. Simultaneously, the secretome of genetically modified cells showed significant stimulating effects on the formation of capillary-like structures by HUVEC (endothelial cells) in vitro. Our results revealed that when the multicistronic multigene vectors encoding 2A peptide sequences are created, transient transgene co-expression is ensured. The results obtained indicated the mutual synergistic effects of the growth factors VEGF and FGF2 on the proliferation of endothelial cells in vitro. Thus, recombinant multicistronic multigenic constructs might serve as a promising approach for establishing safe and effective systems to treat ischemic diseases.
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Affiliation(s)
- Dilara Z. Gatina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
| | - Ekaterina E. Garanina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
| | - Margarita N. Zhuravleva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
| | - Gulnaz E. Synbulatova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
| | - Adelya F. Mullakhmetova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
| | - Valeriya V. Solovyeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
| | - Andrey P. Kiyasov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
| | - Catrin S. Rutland
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham LE12 5RD, UK;
| | - Albert A. Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
- Correspondence: (A.A.R.); (I.I.S.)
| | - Ilnur I. Salafutdinov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (D.Z.G.); (E.E.G.); (M.N.Z.); (G.E.S.); (A.F.M.); (V.V.S.); (A.P.K.)
- Correspondence: (A.A.R.); (I.I.S.)
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20
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Du C, Zhao X, Song W, He N, Jiang S, Zhou Y, Zhang G. Combined strategies to improve the expression of acidic mammalian chitinase in Pichia pastoris for the production of N, N'-diacetylchitobiose. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Yang BX, Xie CY, Xia ZY, Wu YJ, Li B, Tang YQ. The effect of xylose reductase genes on xylitol production by industrial Saccharomyces cerevisiae in fermentation of glucose and xylose. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.05.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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22
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Sampaio de Oliveira KB, Leite ML, Rodrigues GR, Duque HM, da Costa RA, Cunha VA, de Loiola Costa LS, da Cunha NB, Franco OL, Dias SC. Strategies for recombinant production of antimicrobial peptides with pharmacological potential. Expert Rev Clin Pharmacol 2020; 13:367-390. [PMID: 32357080 DOI: 10.1080/17512433.2020.1764347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION The need to develop new drugs for the control of pathogenic microorganisms has redoubled efforts to prospect for antimicrobial peptides (AMPs) from natural sources and to characterize its structure and function. These molecules present a broad spectrum of action against different microorganisms and frequently present promiscuous action, with anticancer and immunomodulatory activities. Furthermore, AMPs can be used as biopharmaceuticals in the treatment of hospital-acquired infections and other serious diseases with relevant social and economic impacts.Areas covered: The low yield and the therefore difficult extraction and purification process in AMPs are problems that limit their industrial application and scientific research. Thus, optimized heterologous expression systems were developed to significantly boost AMP yields, allow high efficiency in purification and structural optimization for the increase of therapeutic activity.Expert opinion: This review provides an update on recent developments in the recombinant production of ribosomal and non-ribosomal synthesis of AMPs and on strategies to increase the expression of genes encoding AMPs at the transcriptional and translational levels and regulation of the post-translational modifications. Moreover, there are detailed reports of AMPs that have already reached marketable status or are in the pipeline under advanced stages of preclinical testing.
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Affiliation(s)
- Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Michel Lopes Leite
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Gisele Regina Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Rosiane Andrade da Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Victor Albuquerque Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Lorena Sousa de Loiola Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Nicolau Brito da Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Octavio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Patologia Molecular, Campus Darcy Ribeiro , Brasília, Brazil.,S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco , Campo Grande, Mato Grosso do Sul, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Biologia Animal, Campus Darcy Ribeiro , Brasília, Brazil
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23
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He H, Wu S, Mei M, Ning J, Li C, Ma L, Zhang G, Yi L. A Combinational Strategy for Effective Heterologous Production of Functional Human Lysozyme in Pichia pastoris. Front Bioeng Biotechnol 2020; 8:118. [PMID: 32211388 PMCID: PMC7075855 DOI: 10.3389/fbioe.2020.00118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
Human lysozyme (hLYZ), known for its bacteriolytic activity, is widely applied in the food and pharmaceutical industries as an antimicrobial agent. However, its extensive application was limited by its low large-scale production efficiency. In this study, a combinational method of integrating codon optimization, multiple gene copies, and ER molecular chaperone co-expression was developed to improve the heterologous production of hLYZ in Pichia pastoris GS115. Our results showed that increasing the copy number of the optimized hLYZ gene in P. pastoris could enhance its secretory production level up to 1.57-fold. The recombinant opt-hLYZ-6C strain that contains six copies of opt-hLYZ gene exhibited the highest mRNA transcription levels, giving the highest production of 0.22 ± 0.02 mg/mL of hLYZ in the medium supernatant with a bacteriolytic activity of 14,680 ± 300 U/mL against Micrococcus lysodeikticus in the shaking flask experiment. Moreover, co-overexpression of ER retention molecular chaperones, such as Pdi1 or Ero1, in the recombinant opt-hLYZ-6C strain both presented positive effects on the secretory production of hLYZ. Our further characterization indicated that tandem co-expression of Ero1 and Pdi1 together presented an added-up effect. The secretory production of hLYZ in the medium supernatant reached 0.34 ± 0.02 mg/mL of the recombinant opt-hLYZ-6C-EP strain in the shaking flask experiment, with a bacteriolytic activity of 21,200 ± 400 U/mL. Compared to the recombinant opt-hLYZ-1C strain, these final improvements were calculated as 2.43-fold and 2.30-fold on secretory protein levels and antibacterial activity, respectively. Finally, the recombinant opt-hLYZ-6C-EP strain was applied for high-density cultivation in 5 L of fermenter, in which the secretory yield of hLYZ reached 2.34 ± 0.02 mg/mL in the medium supernatant, with a bacteriolytic activity of 1.76 ± 0.02 × 105 U/mL against M. lysodeikticus. All these numbers presented the highest heterologous production levels of hLYZ in microbial systems.
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Affiliation(s)
- Huahua He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Shijie Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Jiali Ning
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Chaoyin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
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24
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Thak EJ, Yoo SJ, Moon HY, Kang HA. Yeast synthetic biology for designed cell factories producing secretory recombinant proteins. FEMS Yeast Res 2020; 20:5721243. [DOI: 10.1093/femsyr/foaa009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Yeasts are prominent hosts for the production of recombinant proteins from industrial enzymes to therapeutic proteins. Particularly, the similarity of protein secretion pathways between these unicellular eukaryotic microorganisms and higher eukaryotic organisms has made them a preferential host to produce secretory recombinant proteins. However, there are several bottlenecks, in terms of quality and quantity, restricting their use as secretory recombinant protein production hosts. In this mini-review, we discuss recent developments in synthetic biology approaches to constructing yeast cell factories endowed with enhanced capacities of protein folding and secretion as well as designed targeted post-translational modification process functions. We focus on the new genetic tools for optimizing secretory protein expression, such as codon-optimized synthetic genes, combinatory synthetic signal peptides and copy number-controllable integration systems, and the advanced cellular engineering strategies, including endoplasmic reticulum and protein trafficking pathway engineering, synthetic glycosylation, and cell wall engineering, for improving the quality and yield of secretory recombinant proteins.
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Affiliation(s)
- Eun Jung Thak
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Su Jin Yoo
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hye Yun Moon
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
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25
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Abstract
Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided into basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.
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Ke J, Yoshikuni Y. Multi-chassis engineering for heterologous production of microbial natural products. Curr Opin Biotechnol 2019; 62:88-97. [PMID: 31639618 DOI: 10.1016/j.copbio.2019.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/30/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, heterologous expression of BGCs is of increasing interest in bioactive natural product (NP) discovery. However, this approach has had limited success because expression of BGCs relies heavily on the physiology of just a few commonly available host chassis. Expanding and diversifying the chassis portfolio for heterologous BGC expression may greatly increase the chances for successful NP production. In this review, we first discuss genetic and genome engineering technologies used to clone, modify, and transform BGCs into multiple strains and to engineer chassis strains. We then highlight studies that employed the multi-chassis approach successfully to optimize NP production, discover previously uncharacterized NPs, and better understand BGC function.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL 61801, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, 060-8589, Japan.
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27
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Zha J, Wu X, Gong G, Koffas MAG. Pathway enzyme engineering for flavonoid production in recombinant microbes. Metab Eng Commun 2019; 9:e00104. [PMID: 31720219 PMCID: PMC6838514 DOI: 10.1016/j.mec.2019.e00104] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 12/20/2022] Open
Abstract
Metabolic engineering of microbial strains for the production of flavonoids of industrial interest has attracted great attention due to its promising advantages over traditional extraction approaches, such as independence of plantation, facile downstream separation, and ease of process and quality control. However, most of the constructed microbial production systems suffer from low production titers, low yields and low productivities, restricting their commercial applications. One important reason of the inefficient production is that the expression conditions and the detailed functions of the flavonoid pathway enzymes are not well understood. In this review, we have collected the biochemical properties, structural details, and genetic information of the enzymes in the flavonoid biosynthetic pathway as a guide for the expression and analysis of these enzymes in microbial systems. Additionally, we have summarized the engineering approaches used in improving the performances of these enzymes in recombinant microorganisms. Major challenges and future directions on the flavonoid pathway are also discussed.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, 12180, NY, USA.,Department of Chemical and Biological Engineering, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, 12180, NY, USA
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Soleymani B, Mostafaie A. Analysis of Methods to Improve the Solubility of Recombinant Bovine Sex Determining Region Y Protein. Rep Biochem Mol Biol 2019; 8:227-235. [PMID: 32274394 PMCID: PMC7103077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 05/21/2019] [Indexed: 06/11/2023]
Abstract
BACKGROUND Inclusion body formation in E. coli is a significant problem in recombinant protein production.The aim of this study was to improve the solubility of recombinant bovine sex determining region Y protein(SRY) in BL21 (DE3) E. coli cells. METHODS In this research two recombinant bovine SRY (rbSRY) sequences were analyzed; these were wildtype SRY (wtbSRY) and codon-optimized SRY (cobSRY). Their expression in various culture conditions was examined; these differences included IPTG concentrations, temperatures, and media stabilizers. RESULTS IPTG and temperature significantly affected rbSRY solubility (P < 0.001). The optimum IPTG concentration and temperatures for wtbSRY and cobSRY induction were 0.3 mM at 27 and 32 °C,respectively. In addition, arginine and sorbitol concentrations significantly affected rbSRY solubility (P <0.01). Solubility of rbSRY protein was highest from the cobSRY construct in the presence 0.2 M arginine and 0.3 M sorbitol. The highest inclusion body production occurred with high glucose concentrations. CONCLUSION We found that modifications in temperature and IPTG and stabilizer concentrations affected rbSRY solubility.
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Affiliation(s)
- Bijan Soleymani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ali Mostafaie
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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29
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Liu D, Huang C, Guo J, Zhang P, Chen T, Wang Z, Zhao X. Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:197. [PMID: 31572493 PMCID: PMC6764132 DOI: 10.1186/s13068-019-1537-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in multiplex genome editing technologies. However, simultaneously modulating multiple genes on the chromosome remains challenging in Bacillus subtilis. Thus, developing an efficient and convenient method for B. subtilis multiplex genome editing is imperative. RESULTS Here, we developed a CRISPR/Cas9n-based multiplex genome editing system for iterative genome editing in B. subtilis. This system enabled us to introduce various types of genomic modifications with more satisfying efficiency than using CRISPR/Cas9, especially in multiplex gene editing. Our system achieved at least 80% efficiency for 1-8 kb gene deletions, at least 90% efficiency for 1-2 kb gene insertions, near 100% efficiency for site-directed mutagenesis, 23.6% efficiency for large DNA fragment deletion and near 50% efficiency for three simultaneous point mutations. The efficiency for multiplex gene editing was further improved by regulating the nick repair mechanism mediated by ligD gene, which finally led to roughly 65% efficiency for introducing three point mutations on the chromosome. To demonstrate its potential, we applied our system to simultaneously fine-tune three genes in the riboflavin operon and significantly improved the production of riboflavin in a single cycle. CONCLUSIONS We present not only the iterative CRISPR/Cas9n system for B. subtilis but also the highest efficiency for simultaneous modulation of multiple genes on the chromosome in B. subtilis reported to date. We anticipate this CRISPR/Cas9n mediated system to greatly enhance the optimization of diverse biological systems via metabolic engineering and synthetic biology.
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Affiliation(s)
- Dingyu Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Can Huang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Jiaxin Guo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Peiji Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Xueming Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
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An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana. Sci Rep 2019; 9:13777. [PMID: 31551463 PMCID: PMC6760150 DOI: 10.1038/s41598-019-50389-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/10/2019] [Indexed: 12/29/2022] Open
Abstract
Certain introns significantly increase mRNA accumulation by a poorly understood mechanism. These introns have no effect when located upstream, or more than ~1 Kb downstream, of the start of transcription. We tested the ability of a formerly non-stimulating intron containing 11 copies of the sequence TTNGATYTG, which is over-represented in promoter-proximal introns in Arabidopsis thaliana, to affect expression from various positions. The activity profile of this intron at different locations was similar to that of a natural intron from the UBQ10 gene, suggesting that the motif increases mRNA accumulation by the same mechanism. A series of introns with different numbers of this motif revealed that the effect on expression is linearly dependent on motif copy number up to at least 20, with each copy adding another 1.5-fold increase in mRNA accumulation. Furthermore, 6 copies of the motif stimulated mRNA accumulation to a similar degree from within an intron or when introduced into the 5'-UTR and coding sequences of an intronless construct, demonstrating that splicing is not required for this sequence to boost expression. The ability of this motif to substantially elevate expression from several hundred nucleotides downstream of the transcription start site reveals a novel type of eukaryotic gene regulation.
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Improved cellulase production in recombinant Saccharomyces cerevisiae by disrupting the cell wall protein-encoding gene CWP2. J Biosci Bioeng 2019; 129:165-171. [PMID: 31537451 DOI: 10.1016/j.jbiosc.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022]
Abstract
Budding yeast Saccharomyces cerevisiae has been widely used for heterologous protein production. However, low protein production titer and secretion levels continue to challenge its practical applications. The yeast cell wall plays important roles in yeast cell growth and environmental responses. Nevertheless, the effects of yeast cell wall proteins on heterologous protein production and secretion remain unclear. CWP2 encodes a mannoprotein that is the major component of the yeast cell wall. So far, studies on its function have been very limited. Here we show that CWP2 disruption improved extracellular cellobiohydrolase activity by 85.9%. A calcofluor white hypersensitivity assay revealed increased sensitivity of the mutant compared to the parental strain, indicating impaired cell wall integrity. However, no changes were observed in normal cell growth or growth stressed by tunicamycin and dithiothreitol, suggesting that the unfolded protein response pathway was not affected by the gene disruption. Comparative transcriptome analysis revealed changes in multiple genes involved in cell wall structure, biosynthesis, and cell wall integrity induced by CWP2 disruption, suggesting a pivotal role of Cwp2p in yeast cell wall organization. Notably, CWP2 disruption also led to elevated transcription of a large number of genes involved in ribosome biogenesis, which indicated that CWP2 is not only in yeast cell wall biosynthesis, but also in protein translation. This work reveals novel insights into the functions of CWP2 and also presents a new strategy to increase heterologous protein production in yeast strains by manipulating cell wall-related proteins.
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32
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Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design. J Mol Biol 2019; 431:2434-2441. [PMID: 31029701 DOI: 10.1016/j.jmb.2019.04.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/08/2023]
Abstract
Usage of sequential codon-pairs is non-random and unique to each species. Codon-pair bias is related to but clearly distinct from individual codon usage bias. Codon-pair bias is thought to affect translational fidelity and efficiency and is presumed to be under the selective pressure. It was suggested that changes in codon-pair utilization may affect human disease more significantly than changes in single codons. Although recombinant gene technologies often take codon-pair usage bias into account, codon-pair usage data/tables are not readily available, thus potentially impeding research efforts. The present computational resource (https://hive.biochemistry.gwu.edu/review/codon2) systematically addresses this issue. Building on our recent HIVE-Codon Usage Tables, we constructed a new database to include genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome, available in the GenBank. We believe that the growing understanding of the importance of codon-pair usage will make this resource an invaluable tool to many researchers in academia and pharmaceutical industry.
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Cripwell RA, Rose SH, Viljoen-Bloom M, van Zyl WH. Improved raw starch amylase production by Saccharomyces cerevisiae using codon optimisation strategies. FEMS Yeast Res 2019; 19:5237704. [PMID: 30535120 DOI: 10.1093/femsyr/foy127] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/07/2018] [Indexed: 11/12/2022] Open
Abstract
Amylases are used in a variety of industries that have a specific need for alternative enzymes capable of hydrolysing raw starch. Five α-amylase and five glucoamylase-encoding genes were expressed in the Saccharomyces cerevisiae Y294 laboratory strain to select for recombinant strains that best hydrolysed raw corn starch. Gene variants of four amylases were designed using codon optimisation and different secretion signals. The significant difference in activity levels among the gene variants confirms that codon optimisation of fungal genes for expression in S. cerevisiae does not guarantee improved recombinant protein production. The codon-optimised glucoamylase variant from Talaromyces emersonii (temG_Opt) yielded 3.3-fold higher extracellular activity relative to the native temG, whereas the codon-optimised T. emersonii α-amylase (temA_Opt) yielded 1.6-fold more extracellular activity than the native temA. The effect of four terminator sequences was also investigated using temG and temG_Opt as reporter genes, with the ALY2T terminator resulting in a 14% increase in glucoamylase activity relative to the gene cassettes containing the ENO1T terminator. This is the first report of engineered S. cerevisiae strains to express T. emersonii amylase variants, and these enzymes may have potential applications in the industrial conversion of raw starch under fermentation conditions.
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Affiliation(s)
- Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
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34
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Functional expression of porcine interferon-α using a combinational strategy in Pichia pastoris GS115. Enzyme Microb Technol 2019; 122:55-63. [DOI: 10.1016/j.enzmictec.2018.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/05/2018] [Accepted: 12/09/2018] [Indexed: 12/30/2022]
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Purification of Functional Human TRP Channels Recombinantly Produced in Yeast. Cells 2019; 8:cells8020148. [PMID: 30754715 PMCID: PMC6406451 DOI: 10.3390/cells8020148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/27/2019] [Accepted: 02/03/2019] [Indexed: 01/16/2023] Open
Abstract
(1) Background: Human transient receptor potential (TRP) channels constitute a large family of ion-conducting membrane proteins that allow the sensation of environmental cues. As the dysfunction of TRP channels contributes to the pathogenesis of many widespread diseases, including cardiac disorders, these proteins also represent important pharmacological targets. TRP channels are typically produced using expensive and laborious mammalian or insect cell-based systems. (2) Methods: We demonstrate an alternative platform exploiting the yeast Saccharomyces cerevisiae capable of delivering high yields of functional human TRP channels. We produce 11 full-length human TRP members originating from four different subfamilies, purify a selected subset of these to a high homogeneity and confirm retained functionality using TRPM8 as a model target. (3) Results: Our findings demonstrate the potential of the described production system for future functional, structural and pharmacological studies of human TRP channels.
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36
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Johnson JM, Hays FA. High-Throughput Protein Production of Membrane Proteins in Saccharomyces cerevisiae. Methods Mol Biol 2019; 2025:227-259. [PMID: 31267456 DOI: 10.1007/978-1-4939-9624-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This chapter outlines a protocol to assess viability for large-scale protein production and purification for selected targets from an initial medium-throughput cloning strategy. Thus, one can assess a broad number of potential candidate proteins, mutants, or expression variants using an empirically minimalistic approach. In addition, a key output from this protocol is utilization of Saccharomyces cerevisiae as a means for the efficient screening and production of purified proteins. The primary focus in this protocol is overexpression of polytopic integral membrane proteins though methods can be equally applied to soluble proteins. The protocol starts with outlining high-throughput (sans robotics) cloning of expression proteins into a dual-tag yeast expression plasmid. These membrane proteins are then screened for expression level, detergent solubilization, initial purity, and chromatography characteristics. Both small- and large-scale expression methods are discussed along with fermentation.
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Affiliation(s)
- Jennifer M Johnson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Franklin A Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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37
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Zhang Y, Zhang Y, Shang X, Wang B, Hu Q, Liu S, Wen T. Reconstruction of tricarboxylic acid cycle in Corynebacterium glutamicum with a genome-scale metabolic network model for trans-4-hydroxyproline production. Biotechnol Bioeng 2018; 116:99-109. [PMID: 30102770 DOI: 10.1002/bit.26818] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 07/25/2018] [Accepted: 08/08/2018] [Indexed: 11/09/2022]
Abstract
trans-4-Hydroxy- l-proline (Hyp) is an abundant component of mammalian collagen and functions as a chiral synthon for the syntheses of anti-inflammatory drugs in the pharmaceutical industry. Proline 4-hydroxylase (P4H) can catalyze the conversion of l-proline to Hyp; however, it is still challenging for the fermentative production of Hyp from glucose using P4H due to the low yield and productivity. Here, we report the metabolic engineering of Corynebacterium glutamicum for the fermentative production of Hyp by reconstructing tricarboxylic acid (TCA) cycle together with heterologously expressing the p4h gene from Dactylosporangium sp. strain RH1. In silico model-based simulation showed that α-ketoglutarate was redirected from the TCA cycle toward Hyp synthetic pathway driven by P4H when the carbon flux from succinyl-CoA to succinate descended to zero. The interruption of the TCA cycle by the deletion of sucCD-encoding the succinyl-CoA synthetase (SUCOAS) led to a 60% increase in Hyp production and had no obvious impact on the growth rate. Fine-tuning of plasmid-borne ProB* and P4H abundances led to a significant increase in the yield of Hyp on glucose. The final engineered Hyp-7 strain produced up to 21.72 g/L Hyp with a yield of 0.27 mol/mol (Hyp/glucose) and a volumetric productivity of 0.36 g·L -1 ·hr -1 in the shake flask fermentation. To our knowledge, this is the highest yield and productivity achieved by microbial fermentation in a glucose-minimal medium for Hyp production. This strategy provides new insights into engineering C. glutamicum by flux coupling for the fermentative production of Hyp and related products.
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Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bo Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qitiao Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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38
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Camiolo S, Toome-Heller M, Aime MC, Haridas S, Grigoriev IV, Porceddu A, Mannazzu I. An analysis of codon bias in six red yeast species. Yeast 2018; 36:53-64. [PMID: 30264407 DOI: 10.1002/yea.3359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/10/2018] [Accepted: 09/23/2018] [Indexed: 11/11/2022] Open
Abstract
Red yeasts, primarily species of Rhodotorula, Sporobolomyces, and other genera of Pucciniomycotina, are traditionally considered proficient systems for lipid and terpene production, and only recently have also gained consideration for the production of a wider range of molecules of biotechnological potential. Improvements of transgene delivery protocols and regulated gene expression systems have been proposed, but a dearth of information on compositional and/or structural features of genes has prevented transgene sequence optimization efforts for high expression levels. Here, the codon compositional features of genes in six red yeast species were characterized, and the impact that evolutionary forces may have played in shaping this compositional bias was dissected by using several computational approaches. Results obtained are compatible with the hypothesis that mutational bias, although playing a significant role, cannot alone explain synonymous codon usage bias of genes. Nevertheless, several lines of evidences indicated a role for translational selection in driving the synonymous codons that allow high expression efficiency. These optimal synonymous codons are identified for each of the six species analyzed. Moreover, the presence of intragenic patterns of codon usage, which are thought to facilitate polyribosome formation, was highlighted. The information presented should be taken into consideration for transgene design for optimal expression in red yeast species.
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Affiliation(s)
- Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Merje Toome-Heller
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Ilaria Mannazzu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
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Walker RSK, Pretorius IS. Applications of Yeast Synthetic Biology Geared towards the Production of Biopharmaceuticals. Genes (Basel) 2018; 9:E340. [PMID: 29986380 PMCID: PMC6070867 DOI: 10.3390/genes9070340] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/01/2018] [Accepted: 07/02/2018] [Indexed: 12/18/2022] Open
Abstract
Engineered yeast are an important production platform for the biosynthesis of high-value compounds with medical applications. Recent years have witnessed several new developments in this area, largely spurred by advances in the field of synthetic biology and the elucidation of natural metabolic pathways. This minireview presents an overview of synthetic biology applications for the heterologous biosynthesis of biopharmaceuticals in yeast and demonstrates the power and potential of yeast cell factories by highlighting several recent examples. In addition, an outline of emerging trends in this rapidly-developing area is discussed, hinting upon the potential state-of-the-art in the years ahead.
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Affiliation(s)
- Roy S K Walker
- Department of Molecular Sciences, Macquarie University, Sydney 2109, Australia.
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40
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Garcia-Ruiz E, HamediRad M, Zhao H. Pathway Design, Engineering, and Optimization. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:77-116. [PMID: 27629378 DOI: 10.1007/10_2016_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The microbial metabolic versatility found in nature has inspired scientists to create microorganisms capable of producing value-added compounds. Many endeavors have been made to transfer and/or combine pathways, existing or even engineered enzymes with new function to tractable microorganisms to generate new metabolic routes for drug, biofuel, and specialty chemical production. However, the success of these pathways can be impeded by different complications from an inherent failure of the pathway to cell perturbations. Pursuing ways to overcome these shortcomings, a wide variety of strategies have been developed. This chapter will review the computational algorithms and experimental tools used to design efficient metabolic routes, and construct and optimize biochemical pathways to produce chemicals of high interest.
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Affiliation(s)
- Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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41
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Mignon C, Mariano N, Stadthagen G, Lugari A, Lagoutte P, Donnat S, Chenavas S, Perot C, Sodoyer R, Werle B. Codon harmonization - going beyond the speed limit for protein expression. FEBS Lett 2018; 592:1554-1564. [PMID: 29624661 DOI: 10.1002/1873-3468.13046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 12/14/2022]
Abstract
Codon usage distribution has been soundly used by nature to fine tune protein biogenesis. Alteration of the mRNA structure or sequential scheduling of codons can profoundly affect translation, thus altering protein yield, functionality, solubility, and proper folding. Building on these observations, here, we present an evaluation of different recently designed algorithms of sequence adaptation based on Codon Adaptation Index (CAI) profiling. The first algorithm globally harmonizes synonymous codons in the original sequence in full respect to the heterologous expression host codon usage. The second recodes the sequence in accordance with the native sequence CAI profile. Our data, generated on three model proteins, highlights the importance to consider gene recoding as a parameter itself for recombinant protein expression improvement.
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Affiliation(s)
- Charlotte Mignon
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | - Natacha Mariano
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | | | - Adrien Lugari
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | | | - Stéphanie Donnat
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | | | | | | | - Bettina Werle
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
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42
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Gyulev IS, Willson BJ, Hennessy RC, Krabben P, Jenkinson ER, Thomas GH. Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia. ACS Synth Biol 2018; 7:311-327. [PMID: 29186949 DOI: 10.1021/acssynbio.7b00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solventogenic Clostridia are of interest to the chemical industry because of their natural ability to produce chemicals such as butanol, acetone and ethanol from diverse feedstocks. Their use as whole cell factories presents multiple metabolic engineering targets that could lead to improved sustainability and profitability of Clostridium industrial processes. However, engineering efforts have been held back by the scarcity of genetic and synthetic biology tools. Over the past decade, genetic tools to enable transformation and chromosomal modifications have been developed, but the lack of a broad palette of synthetic biology parts remains one of the last obstacles to the rapid engineered improvement of these species for bioproduction. We have systematically reviewed existing parts that have been used in the modification of solventogenic Clostridia, revealing a narrow range of empirically chosen and nonengineered parts that are in current use. The analysis uncovers elements, such as promoters, transcriptional terminators and ribosome binding sites where increased fundamental knowledge is needed for their reliable use in different applications. Together, the review provides the most comprehensive list of parts used and also presents areas where an improved toolbox is needed for full exploitation of these industrially important bacteria.
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Affiliation(s)
- Ivan S. Gyulev
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Benjamin J. Willson
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Rosanna C. Hennessy
- Department
of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Preben Krabben
- Green Biologics Limited, Milton Park, Abingdon, Oxfordshire OX14 4RU, United Kingdom
| | | | - Gavin H. Thomas
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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Besada-Lombana PB, McTaggart TL, Da Silva NA. Molecular tools for pathway engineering in Saccharomyces cerevisiae. Curr Opin Biotechnol 2017; 53:39-49. [PMID: 29274630 DOI: 10.1016/j.copbio.2017.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/26/2022]
Abstract
Molecular tools for the regulation of protein expression in Saccharomyces cerevisiae have contributed to rapid advances in pathway engineering for this yeast. This review considers new and enhanced additions to this toolbox, focusing on experimental approaches to modulate enzyme synthesis and enzyme fate. Methods for genome engineering, regulation of transcription, post-translational protein localization, and combinatorial screening and sensing in S. cerevisiae are highlighted, and promising new approaches are introduced.
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Affiliation(s)
- Pamela B Besada-Lombana
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Tami L McTaggart
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA.
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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: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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45
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Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression. Curr Genet 2017; 64:589-598. [PMID: 29098364 DOI: 10.1007/s00294-017-0774-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/30/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
Abstract
The tRNA population reflects the codon bias of the organism and affects the translation of heterologous target mRNA molecules. In this study, Saccharomyces cerevisiae strains with modified levels of rare tRNA were engineered, that allowed efficient generation of recombinant proteins with unfavorable codon usage. We established a novel synthetic tRNA expression cassette and verified functional nonsense suppressor tRNAGlnSCUA generation in a stop codon read-through assay with a modified β-galactosidase reporter gene. Correlation between altered tRNA and protein level was shown by survival of copper sensitive S. cerevisiae cells in the presence of copper ions by an increased transcription of tRNAArgCCG molecules, recognizing rare codons in a modified CUP1 gene. Genome integration of tRNA expression cassette led to the generation of arginine-tRNA-adapted S. cerevisiae strains, which showed elevated tRNA levels (tRNAArgCCG, tRNAArgGCG and tRNAArgUCG) pairing to rare codons. The modified strain MNY3 revealed a considerably improved monitoring of protein-protein interaction from Aspergillus fumigatus bait and prey sequences in yeast two-hybrid experiments. In future, this principle to overcome limited recombinant protein expression by tRNA adaption of expression strains instead of codon adaption might provide new designer yeast cells for an efficient protein production and for improved genome-wide protein-protein interaction analyses.
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46
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Strategies to Obtain Diverse and Specific Human Monoclonal Antibodies From Transgenic Animals. Transplantation 2017; 101:1770-1776. [DOI: 10.1097/tp.0000000000001702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Forman V, Callari R, Folly C, Heider H, Hamberger B. Production of Putative Diterpene Carboxylic Acid Intermediates of Triptolide in Yeast. Molecules 2017; 22:E981. [PMID: 28608823 PMCID: PMC6152743 DOI: 10.3390/molecules22060981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/07/2017] [Indexed: 11/16/2022] Open
Abstract
The development of medical applications exploiting the broad bioactivities of the diterpene therapeutic triptolide from Tripterygium wilfordii is limited by low extraction yields from the native plant. Furthermore, the extraordinarily high structural complexity prevents an economically attractive enantioselective total synthesis. An alternative production route of triptolide through engineered Saccharomyces cerevisiae (yeast) could provide a sustainable source of triptolide. A potential intermediate in the unknown biosynthetic route to triptolide is the diterpene dehydroabietic acid. Here, we report a biosynthetic route to dehydroabietic acid by transient expression of enzymes from T. wilfordii and Sitka spruce (Picea sitchensis) in Nicotiana benthamiana. The combination of diterpene synthases TwTPS9, TwTPS27, and cytochromes P450 PsCYP720B4 yielded dehydroabietic acid and a novel analog, tentatively identified as 'miltiradienic acid'. This biosynthetic pathway was reassembled in a yeast strain engineered for increased yields of the pathway intermediates, the diterpene olefins miltiradiene and dehydroabietadiene. Introduction in that strain of PsCYP720B4 in combination with two alternative NADPH-dependent cytochrome P450 reductases resulted in scalable in vivo production of dehydroabietic acid and its analog from glucose. Approaching future elucidation of the remaining biosynthetic steps to triptolide, our findings may provide an independent platform for testing of additional recombinant candidate genes, and ultimately pave the way to biotechnological production of the high value diterpenoid therapeutic.
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Affiliation(s)
- Victor Forman
- Evolva A/S, Lersø Park Allé 42-44, Copenhagen Ø DK-2100, Denmark.
- Evolva SA, Duggingerstrasse 23, Reinach CH-4153, Switzerland.
| | - Roberta Callari
- Evolva SA, Duggingerstrasse 23, Reinach CH-4153, Switzerland.
| | | | - Harald Heider
- Evolva SA, Duggingerstrasse 23, Reinach CH-4153, Switzerland.
| | - Björn Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.
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Rogers DW, Böttcher MA, Traulsen A, Greig D. Ribosome reinitiation can explain length-dependent translation of messenger RNA. PLoS Comput Biol 2017; 13:e1005592. [PMID: 28598992 PMCID: PMC5482490 DOI: 10.1371/journal.pcbi.1005592] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/23/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022] Open
Abstract
Models of mRNA translation usually presume that transcripts are linear; upon reaching the end of a transcript each terminating ribosome returns to the cytoplasmic pool before initiating anew on a different transcript. A consequence of linear models is that faster translation of a given mRNA is unlikely to generate more of the encoded protein, particularly at low ribosome availability. Recent evidence indicates that eukaryotic mRNAs are circularized, potentially allowing terminating ribosomes to preferentially reinitiate on the same transcript. Here we model the effect of ribosome reinitiation on translation and show that, at high levels of reinitiation, protein synthesis rates are dominated by the time required to translate a given transcript. Our model provides a simple mechanistic explanation for many previously enigmatic features of eukaryotic translation, including the negative correlation of both ribosome densities and protein abundance on transcript length, the importance of codon usage in determining protein synthesis rates, and the negative correlation between transcript length and both codon adaptation and 5' mRNA folding energies. In contrast to linear models where translation is largely limited by initiation rates, our model reveals that all three stages of translation-initiation, elongation, and termination/reinitiation-determine protein synthesis rates even at low ribosome availability.
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Affiliation(s)
- David W. Rogers
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| | - Marvin A. Böttcher
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Duncan Greig
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
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49
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Metabolic engineering strategies to bio-adipic acid production. Curr Opin Biotechnol 2017; 45:136-143. [PMID: 28365404 DOI: 10.1016/j.copbio.2017.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 11/21/2022]
Abstract
Adipic acid is the most industrially important dicarboxylic acid as it is a key monomer in the synthesis of nylon. Today, adipic acid is obtained via a chemical process that relies on petrochemical precursors and releases large quantities of greenhouse gases. In the last two years, significant progress has been made in engineering microbes for the production of adipic acid and its immediate precursors, muconic acid and glucaric acid. Not only have the microbial substrates expanded beyond glucose and glycerol to include lignin monomers and hemicellulose components, but the number of microbial chassis now goes further than Escherichia coli and Saccharomyces cerevisiae to include microbes proficient in aromatic degradation, cellulose secretion and degradation of multiple carbon sources. Here, we review the metabolic engineering and nascent protein engineering strategies undertaken in each of these chassis to convert different feedstocks to adipic, muconic and glucaric acid. We also highlight near term prospects and challenges for each of the metabolic routes discussed.
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Webster GR, Teh AYH, Ma JKC. Synthetic gene design-The rationale for codon optimization and implications for molecular pharming in plants. Biotechnol Bioeng 2016; 114:492-502. [PMID: 27618314 DOI: 10.1002/bit.26183] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 08/10/2016] [Accepted: 09/05/2016] [Indexed: 12/14/2022]
Abstract
Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as "silent" as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised. Multiple inter-linked factors affecting protein expression need to be taken into consideration when optimizing a gene sequence. Over the years, various computer programmes have been developed to aid in the gene sequence optimization process. However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the "optimal" gene sequence. In this review, codon usage bias and factors affecting codon selection will be discussed and the evidence for codon optimization impact will be reviewed for recombinant protein expression using plants as a case study. These developments will be relevant to all recombinant expression systems; however, molecular pharming in plants is an area which has consistently encountered difficulties with low levels of recombinant protein expression, and should benefit from an evidence based rational approach to synthetic gene design. Biotechnol. Bioeng. 2017;114: 492-502. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Gina R Webster
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
| | - Audrey Y-H Teh
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
| | - Julian K-C Ma
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
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