Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices
Abstract
:1. Introduction
2. Materials and Methods
2.1. Homolog Identification, Primer Design, PCR, RT-PCR, and Cloning
2.2. Growth Analysis
2.3. Codon Adaptation Index, Codon Usage, and Codon Optimization
2.4. Mevalonate Production Cultures and HPLC Analysis
3. Results and Discussion
3.1. Codon Usage and Preferences of P. indianae Are Strongly AT-Biased
3.2. E.coli Are Not Well Equipped to Express the AT-rich Genes of P. indianae
3.3. Strains with Additional tRNAs for Rare Codons Do Not Effectively Relieve the Burden of Expressing P. indianae Genes
3.4. Codon Optimization Alleviates the Growth Deficiencies Seen When the P. indianae atoB Is Expressed in E. coli
3.5. Expression of Unoptimized Genes Hinders Biosynthesis from P. indianae Genes
3.6. Codon Optimization Allows Heterologous Production of Mevalonate from P. indianae Enzymes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Hillman, E.T.; Frazier, E.M.; Shank, E.K.; Ortiz-Velez, A.N.; Englaender, J.A.; Solomon, K.V. Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices. Microorganisms 2021, 9, 1986. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091986
Hillman ET, Frazier EM, Shank EK, Ortiz-Velez AN, Englaender JA, Solomon KV. Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices. Microorganisms. 2021; 9(9):1986. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091986
Chicago/Turabian StyleHillman, Ethan T., Elizabeth M. Frazier, Evan K. Shank, Adrian N. Ortiz-Velez, Jacob A. Englaender, and Kevin V. Solomon. 2021. "Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices" Microorganisms 9, no. 9: 1986. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091986