Commands of Synthetic Biology to Modernize and Re-design the Biological Systems

Hina Ilyas, Aimen Afzal, Zaheer Abbas, Sabahat Noor, Irfan Ullah, Raja Sheraz Rafique, Zeeshan Abbas, Muhammad Umer Bin Muhammad Ishaq

Abstract


The scope of synthetic biology continues to expand and has encompassed a huge number of biological features. Its scope starts from scratch, enabling the de novo synthesis of biological systems. It has re-designed the biological systems and empowered the production of synthetic genes, RNA, DNA and proteins by undertaking the control of pathways involved in genetic regulation. It has increased the production of nano-scale RNA architectures and synthetic biological circuits which either have therapeutic or other productive uses. Furthermore, advancements in synthetic biology have enabled the generation of diversity through methods such as epPCR and site-directed mutagenesis, allowing for the creation of complex genetic variations. Additionally, synthetic biology intersects with computer engineering to design functional biological devices and circuits, utilizing computational analysis to guide the design process. Moreover, ethical and regulatory considerations are paramount in synthetic biology, with careful examination required to address dual-use concerns, environmental impacts, and issues of social justice and equitable access to benefits. As synthetic biology continues to advance, it presents opportunities to address pressing challenges in fields ranging from medicine and agriculture to environmental conservation and beyond. Thus, the fusion of synthetic biology with other scientific disciplines holds promise for transformative innovation and societal benefit. The present discussion enlightened the core of generating complex biological systems and has given a brief overview on the fusion of synthetic biology with other fields of science.

Keywords: Biological Systems; Genetic Regulation; Synthetic biology circuits   


Full Text:

PDF

References


Goodwin DA, Meares CF. Advances in pretargeting biotechnology. Biotechnology advances, (2001); 19(6): 435-450.

Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD. GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome research, (2006); 16(4): 550-556.

Zhao L, Lu W. Mirror image proteins. Current opinion in chemical biology, (2014); 2256-61.

Jacobsen MT, Erickson PW, Kay MS. Aligator: A Computational Tool for Optimizing Total Chemical Synthesis of Large Proteins. Bioorganic & Medicinal Chemistry, (2017).

Luo D, Saltzman WM. Synthetic DNA delivery systems. Nature biotechnology, (2000); 18(1): 33-37.

Wiegrebe L. An autocorrelation model of bat sonar. Biological Cybernetics, (2008); 98(6): 587-595.

MUNTAHA ST, AHMED A, AHMED K, MUKHTAR N, NAUREEN U, et al. APPLICATIONS AND FUTURE PROSPECTS OF GENETIC ENGINEERING: A NEW GLOBAL PERSPECTIVE. FUUAST Journal of Biology, (2016); 6(2).

Patra S, Andrew AA. Human, Social, and Environmental Impacts of Human Genetic Engineering. Biomedical Sciences, (2015).

Mepham TB. The role of food ethics in food policy. Proceedings of the Nutrition Society, (2000); 59(4): 609-618.

Wood AJ, Lo T-W, Zeitler B, Pickle CS, Ralston EJ, et al. Targeted genome editing across species using ZFNs and TALENs. Science, (2011); 333(6040): 307-307.

Narancic T, O'Connor KE. Microbial biotechnology addressing the plastic waste disaster. Microbial biotechnology, (2017); 10(5): 1232-1235.

Andrianantoandro E, Basu S, Karig DK, Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Molecular systems biology, (2006); 2(1).

Peisajovich SG. Evolutionary synthetic biology. ACS synthetic biology, (2012); 1(6): 199-210.

Libis V, Delépine B, Faulon J-L. Expanding biosensing abilities through computer-aided design of metabolic pathways. ACS synthetic biology, (2016); 5(10): 1076-1085.

Weber W, Fussenegger M. Emerging biomedical applications of synthetic biology. Nature Reviews Genetics, (2012); 13(1): 21-35.

Fung E, Wong WW, Suen JK, Bulter T, Lee S-g, et al. A synthetic gene–metabolic oscillator. Nature, (2005); 435(7038): 118-122.

Ausländer S, Ausländer D, Fussenegger M. Synthetic biology—the synthesis of biology. Angewandte Chemie International Edition, (2017); 56(23): 6396-6419.

Zorina ZA, Obozova TA. New data on the brain and cognitive abilities of birds. Zoologichesky Zhurnal, (2011); 90(7): 784-802.

Kajimura S, Saito M. A new era in brown adipose tissue biology: molecular control of brown fat development and energy homeostasis. Annual review of physiology, (2014); 76225-249.

Hughes RA, Ellington AD. Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology. Cold Spring Harbor perspectives in biology, (2017); 9(1): a023812.

Juhas M, Ajioka JW. High molecular weight DNA assembly in vivo for synthetic biology applications. Critical reviews in biotechnology, (2017); 37(3): 277-286.

Gurvitz M, Burns KM, Brindis R, Broberg CS, Daniels CJ, et al. Emerging Research Directions in Adult Congenital Heart Disease. Journal of the American College of Cardiology, (2016); 67(16): 1956-1964.

Fraser PD, Enfissi EM, Bramley PM. Genetic engineering of carotenoid formation in tomato fruit and the potential application of systems and synthetic biology approaches. Archives of Biochemistry and Biophysics, (2009); 483(2): 196-204.

Strzyz P. Synthetic biology: Designer cells tackle diabetes. Nature Reviews Molecular Cell Biology, (2017); 18(2): 69-69.

Madhavan A, Jose AA, Parameswaran B, RAVEENDRAN S, PANDEY A, et al. Synthetic biology and metabolic engineering approaches and its impact on non-conventional Yeast and Biofuel production. Frontiers in Energy Research, (2017); 58.

Wei C, Liu J, Yu Z, Zhang B, Gao G, et al. TALEN or Cas9–rapid, efficient and specific choices for genome modifications. Journal of Genetics and Genomics, (2013); 40(6): 281-289.

Clift D, McEwan WA, Labzin LI, Konieczny V, Mogessie B, et al. A Method for the Acute and Rapid Degradation of Endogenous Proteins. Cell, (2017).

Burma S, Chen BP, Chen DJ. Role of non-homologous end joining (NHEJ) in maintaining genomic integrity. DNA repair, (2006); 5(9): 1042-1048.

van Attikum H, Bundock P, Hooykaas PJ. Non‐homologous end‐joining proteins are required for Agrobacterium T‐DNA integration. The EMBO journal, (2001); 20(22): 6550-6558.

Rémy S, Tesson L, Ménoret S, Usal C, Scharenberg AM, et al. Zinc-finger nucleases: a powerful tool for genetic engineering of animals. Transgenic research, (2010); 19(3): 363-371.

Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, et al. Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Molecular cell, (2008); 31(2): 294-301.

Liu J, Li C, Yu Z, Huang P, Wu H, et al. Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy. Journal of genetics and genomics, (2012); 39(5): 209-215.

Nielsen ML, Isbrandt T, Rasmussen KB, Thrane U, Hoof JB, et al. Genes linked to production of secondary metabolites in Talaromyces atroroseus revealed using CRISPR-Cas9. PloS one, (2017); 12(1): e0169712.

Turanli-Yildiz B, Alkim C, Cakar ZP (2012) Protein engineering methods and applications. Protein Engineering: InTech.

Bassalo MC, Liu R, Gill RT. Directed evolution and synthetic biology applications to microbial systems. Current opinion in biotechnology, (2016); 39126-133.

Cirino PC, Mayer KM, Umeno D. Generating mutant libraries using error-prone PCR. Directed Evolution Library Creation: Methods and Protocols, (2003); 3-9.

Williams TC, Pretorius IS, Paulsen IT. Synthetic evolution of metabolic productivity using biosensors. Trends in biotechnology, (2016); 34(5): 371-381.

Williams TC, Xu X, Ostrowski M, Pretorius IS, Paulsen IT. Positive-feedback, ratiometric biosensor expression improves high-throughput metabolite-producer screening efficiency in yeast. Synthetic Biology, (2017); 2(1).

Michener JK, Thodey K, Liang JC, Smolke CD. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metabolic engineering, (2012); 14(3): 212-222.

Cheng AA, Lu TK. Synthetic biology: an emerging engineering discipline. Annual review of biomedical engineering, (2012); 14155-178.

Alon U. Biological networks: the tinkerer as an engineer. Science, (2003); 301(5641): 1866-1867.

Cameron DE, Bashor CJ, Collins JJ. A brief history of synthetic biology. Nature Reviews Microbiology, (2014); 12(5): 381-390.

Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nature biotechnology, (2004); 22(7): 841-847.

Zorina ZA. Animal intelligence: Laboratory experiments and observations in nature. Zoologichesky Zhurnal, (2005); 84(1): 134-148.

Khalil AS, Collins JJ. Synthetic biology: applications come of age. Nature Reviews Genetics, (2010); 11(5): 367-379.

Saito H, Inoue T. RNA and RNP as new molecular parts in synthetic biology. Journal of biotechnology, (2007); 132(1): 1-7.

Bray D. Protein molecules as computational elements in living cells. Nature, (1995); 376(6538): 307-312.

Gordley RM, Bugaj LJ, Lim WA. Modular engineering of cellular signaling proteins and networks. Current opinion in structural biology, (2016); 39106-114.

Whaley SR, English D, Hu EL, Barbara PF, Belcher AM. Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature, (2000); 405(6787): 665-668.

Tamerler C, Sarikaya M. Molecular biomimetics: building materials nature's way, one molecule at a time. Nanofabrication Towards Biomedical Applications: Techniques, Tools, Applications, and Impact, (2005); 119-134.

Sarikaya M, Tamerler C, Jen AK-Y, Schulten K, Baneyx F. Molecular biomimetics: nanotechnology through biology. Nature materials, (2003); 2(9): 577-585.

Domaille DW, Que EL, Chang CJ. Synthetic fluorescent sensors for studying the cell biology of metals. Nature chemical biology, (2008); 4(3): 168-175.

Nolan EM, Lippard SJ. Small-molecule fluorescent sensors for investigating zinc metalloneurochemistry. Accounts of chemical research, (2008); 42(1): 193-203.

Rurack K. Flipping the light switch ‘ON’–the design of sensor molecules that show cation-induced fluorescence enhancement with heavy and transition metal ions. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, (2001); 57(11): 2161-2195.

Purnick PE, Weiss R. The second wave of synthetic biology: from modules to systems. Nature reviews Molecular cell biology, (2009); 10(6): 410-422.

Council NR. Science and security in a post 9/11 world: A report based on regional discussions between the science and security communities. (2007).

Baulcombe D, Crute I, Davies B, Dunwell J, Gale M, et al. Reaping the benefits: science and the sustainable intensification of global agriculture. Chapter: Book Name. 2009 of publication; The Royal Society.

Mikami K (2011) Human Genetic Biobanks in Asia: Politics of trust and scientific advancement. JSTOR.

Hopkins MM, Martin PA, Nightingale P, Kraft A, Mahdi S. The myth of the biotech revolution: An assessment of technological, clinical and organisational change. Research policy, (2007); 36(4): 566-589.

National Academies of Sciences E, Medicine. Biodefense in the age of synthetic biology. (2018).

Council NR, Policy, Affairs G, Development S, Cooperation, et al. Biotechnology research in an age of terrorism. Chapter: Book Name. 2004 of publication; National Academies Press.




DOI: http://dx.doi.org/10.62940/als.v11i3.2658

Refbacks

  • There are currently no refbacks.