Article
Multidisciplinary Sciences
Tianchi Chen, M. Ali Al-Radhawi, Christopher A. Voigt, Eduardo D. Sontag
Summary: A design for genetically encoded counters using repressor-based circuits is proposed, allowing for scalable computation and bypassing limitations on maximal circuit genes per cell. The design utilizes distributed computation with specialized cell types and connector modules for interconnecting single-bit counters to achieve an N-bit counter. An optimization framework is used to determine gate parameters and guide the construction of novel gates, moving towards circuits capable of finite automaton computation akin to central processing units.
Review
Biology
Almando Geraldi, Fatiha Khairunnisa, Nadya Farah, Le Minh Bui, Ziaur Rahman
Summary: Biotechnology uses biological synthesis to create high-value products, with metabolic engineering adjusting cellular pathways to enhance production. Biological scaffolds anchor enzymes and substrates to improve production by fixing them in the right location and orientation, serving as a strategy to address challenges in achieving efficient metabolic activities.
Article
Biotechnology & Applied Microbiology
Irene Otero-Muras, Pablo Carbonell
Summary: Metabolic engineering involves optimizing processes from single-cell to fermentation to increase production of valuable chemicals. A systems approach has accelerated scaling from rapid prototyping to industrial production, with automated DNA assembly reducing time from conception to production. The success of metabolic engineering often relies on retrobiosynthetic protocols and dynamic regulation strategies assembled as genetic circuits in host strains.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Sean F. Sullivan, Anuj Shetty, Tharun Bharadwaj, Naveen Krishna, Vikas D. Trivedi, Venkatesh Endalur Gopinarayanan, Todd C. Chappell, Daniel M. Sellers, R. Pravin Kumar, Nikhil U. Nair
Summary: Engineering the utilization of non-native substrates in industrial microbes provides a way to use renewable sources for bioprocesses. Previous research has shown that activating the GAL regulon in Saccharomyces cerevisiae during growth on the non-native substrate xylose enhances gene expression and growth compared to constitutive overexpression of the same pathway. However, this method was not easily adaptable to other non-native substrates. In this study, a variant of Gal3p called Gal3pMC was constructed, which can activate the GAL regulon with diverse substrates and mimic the dynamics of the native system. Testing this regulon approach with non-native lignocellulosic sugars resulted in higher growth rates and final cell densities compared to constitutive overexpression. The co-utilization of multiple non-native substrates suggests that this regulon approach could be universally beneficial for engineering synthetic heterotrophy.
METABOLIC ENGINEERING
(2023)
Review
Biochemistry & Molecular Biology
Dongsoo Yang, Hyunmin Eun, Cindy Pricilia Surya Prabowo
Summary: Polyketides, a type of natural products, have versatile applications such as pharmaceuticals, nutraceuticals, and cosmetics. Aromatic polyketides, including type II and III polyketides, are important chemicals for human health, such as antibiotics and anticancer agents. However, they are mainly produced from challenging sources like soil bacteria or plants. To address this issue, metabolic engineering and synthetic biology have been used to efficiently engineer model microorganisms for enhanced production of aromatic polyketides. This review discusses the recent advancements and future prospects of metabolic engineering and synthetic biology strategies in the production of type II and type III polyketides in model microorganisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Fang Ba, Yushi Liu, Wan-Qiu Liu, Xintong Tian, Jian Li
Summary: Serine integrases are powerful tools in synthetic biology, and this study introduces a versatile method called SYMBIOSIS that can manipulate DNA parts both in vivo and in vitro. By proposing a 'keys match locks' model, the researchers demonstrate the ability of three orthogonal serine integrases to accurately switch on synthetic biobricks. They also show that purified integrases can facilitate plasmid assembly in vitro, leading to the creation of colored Escherichia coli.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Luna Rizik, Loai Danial, Mouna Habib, Ron Weiss, Ramez Daniel
Summary: Researchers have utilized the perceptgene technology to create synthetic gene circuits based on the computational properties of neuronal networks. These circuits can perform non-binary logic computation and signal processing, and can be modified for different tasks by adjusting parameters.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Bouchra Ezzamouri, Saeed Shoaie, Rodrigo Ledesma-Amaro
Summary: The microbial communities of the human body play a crucial role in human health, with potential for novel therapeutic and diagnostic interventions. The integration of systems biology approaches and synthetic biology can enhance the quality and impact of future studies on the human microbiome, highlighting important avenues for future research.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Plant Sciences
Tawni Bull, Arjun Khakhar
Summary: Synthetic control systems have advanced the study and engineering of unicellular organisms, but applying these tools to multicellular organisms like plants has been challenging. Predictable engineering of plants can help alleviate global problems.
PLANT CELL REPORTS
(2023)
Review
Biotechnology & Applied Microbiology
Govinda R. Navale, Mahesh S. Dharne, Sandip S. Shinde
Summary: Isoprenoids, also known as terpenoids, are diverse organic compounds found abundantly in nature, with various applications in pharmaceutical, nutraceutical, and chemical industries. Recent advancements in metabolic engineering have enabled the production of isoprenoids in heterologous host systems like Escherichia coli and Saccharomyces cerevisiae. Challenges and strategies for scale-up and engineering of isoprenoids in heterologous host systems have been discussed in detail.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Review
Biochemical Research Methods
Shixiu Cui, Xueqin Lv, Xianhao Xu, Taichi Chen, Hongzhi Zhang, Yanfeng Liu, Jianghua Li, Guocheng Du, Rodrigo Ledesma-Amaro, Long Liu
Summary: Dynamic regulation of metabolic pathways involves complex genetic circuits to process various signals and control metabolic flux for optimal synthesis of target molecules.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Plant Sciences
Revuru Bharadwaj, Sarma R. Kumar, Ashutosh Sharma, Ramalingam Sathishkumar
Summary: Gene clusters responsible for specialized metabolites in plants offer a potential untapped source for highly useful biomolecules. These clusters evolve through gene duplications and neofunctionalization, tightly regulated at nucleosome level. Further research is needed to explore the significance and regulatory mechanisms of these gene clusters in plant biosynthesis.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Revuru Bharadwaj, Sarma R. Kumar, Ashutosh Sharma, Ramalingam Sathishkumar
Summary: Plants contain gene clusters encoding enzymes for the biosynthesis of specialized metabolites, which have evolved through gene duplications and neofunctionalization and are tightly regulated at nucleosome level. The prevalence of these gene clusters presents an attractive possibility of untapped source of highly useful biomolecules in plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Vimalraj Mani, Soyoung Park, Jin A. Kim, Soo In Lee, Kijong Lee
Summary: Terpenoids, with vast structural diversity, are high-value specialized metabolites widely used in cosmetics, foods, and pharmaceuticals. Recent advancements in heterologous production platforms and metabolic engineering technologies have overcome challenges related to the bioavailability of terpenoids in natural sources. Studies have shown that subcellular localization of precursor pool and introduced enzymes are crucial for increasing targeted terpenoid production in plants.
Editorial Material
Biochemical Research Methods
Michael B. Sheets, Joshua T. Atkinson, Mark P. Styczynski, Emily R. Aurand
Summary: As engineering biology continues to have increasing impacts, it is crucial to introduce the field early on in an accessible manner. However, teaching engineering biology faces challenges such as limited representation in widely used scientific textbooks or curricula, as well as its interdisciplinary nature. To address this, we have developed an adaptable curriculum module that provides a versatile slide deck designed by engineering biology experts to cover the fundamental principles and applications of the field. Free and accessible through a public website, this module can be used independently or integrated into existing curricula, aiming to enhance the ease of teaching current engineering biology topics and promote public engagement with the field.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Microbiology
Kevin C. Ma, Magnus Unemo, Samo Jeverica, Robert D. Kirkcaldy, Hideyuki Takahashi, Makoto Ohnishi, Yonatan H. Grad
JOURNAL OF CLINICAL MICROBIOLOGY
(2017)
Article
Genetics & Heredity
Chris Hadjineophytou, Jan Haug Anonsen, Nelson Wang, Kevin C. Ma, Raimonda Viburiene, Ashild Vik, Odile B. Harrison, Martin C. J. Maiden, Yonatan H. Grad, Michael Koomey
Article
Biology
Allison L. Hicks, Stephen M. Kissler, Tatum D. Mortimer, Kevin C. Ma, George Taiaroa, Melinda Ashcroft, Deborah A. Williamson, Marc Lipsitch, Yonatan H. Grad
Letter
Microbiology
Kevin C. Ma, Tatum D. Mortimer, Yonatan H. Grad
Article
Multidisciplinary Sciences
Kevin C. Ma, Tatum D. Mortimer, Marissa A. Duckett, Allison L. Hicks, Nicole E. Wheeler, Leonor Sanchez-Buso, Yonatan H. Grad
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Kevin C. Ma, Tatum D. Mortimer, Allison L. Hicks, Nicole E. Wheeler, Leonor Sanchez-Buso, Daniel Golparian, George Taiaroa, Daniel H. F. Rubin, Yi Wang, Deborah A. Williamson, Magnus Unemo, Simon R. Harris, Yonatan H. Grad
NATURE COMMUNICATIONS
(2020)
Article
Biology
Kevin C. Ma, Tigist F. Menkir, Stephen Kissler, Yonatan H. Grad, Marc Lipsitch
Summary: This study fitted structured compartmental models to seroprevalence data from New York State and found that minority populations have higher infection risk and experience unequal epidemic trajectories in the spread of SARS-CoV-2.
Article
Immunology
Kevin C. Ma, Jaime E. Hale, Yonatan H. Grad, Galit Alter, Katherine Luzuriaga, Roger B. Eaton, Stephanie Fischinger, Devinder Kaur, Robin Brody, Sameed M. Siddiqui, Dylan Leach, Catherine M. Brown, R. Monina Klevens, Lawrence Madoff, Anne Marie Comeau
Summary: Using newborn screening specimens as a source of maternal antibodies, this study estimated statewide seroprevalence of SARS-CoV-2 in Massachusetts during the COVID-19 pandemic, revealing longitudinal trends and associations between seroprevalence and community demographics.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)
