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Article ; Online: Plant synthetic biology: exploring the frontiers of sustainable agriculture and fundamental plant biology.

Yang, Jae-Seong / Reyna-Llorens, Ivan

2023 Volume 74, Issue 13, Page(s) 3787–3790

MeSH term(s)	Synthetic Biology ; Plants/genetics ; Genetic Engineering ; Agriculture
Language	English
Publishing date	2023-07-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erad220
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Article ; Online: OASIS portable: User-friendly offline suite for secure survival analysis.

Han, Seong Kyu / Kwon, Hyunwoo C / Yang, Jae-Seong / Kim, Sanguk / Lee, Seung-Jae V

Molecules and cells

2024 Volume 47, Issue 2, Page(s) 100011

Abstract: Online application for survival analysis (OASIS) and its update, OASIS 2, have been widely used for survival analysis in biological and medical sciences. Here, we provide a portable version of OASIS, an all-in-one offline suite, to facilitate secure ... ...

Abstract	Online application for survival analysis (OASIS) and its update, OASIS 2, have been widely used for survival analysis in biological and medical sciences. Here, we provide a portable version of OASIS, an all-in-one offline suite, to facilitate secure survival analysis without uploading the data to online servers. OASIS portable provides a virtualized and isolated instance of the OASIS 2 webserver, operating on the users' personal computers, and enables user-friendly survival analysis without internet connection and security issues.
MeSH term(s)	Survival Analysis ; Internet
Language	English
Publishing date	2024-01-17
Publishing country	United States
Document type	Letter
ZDB-ID	1148964-9
ISSN	0219-1032 ; 1016-8478
ISSN (online)	0219-1032
ISSN	1016-8478
DOI	10.1016/j.mocell.2024.100011
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Article ; Online: Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii.

Milito, Alfonsina / Aschern, Moritz / McQuillan, Josie L / Yang, Jae-Seong

Journal of experimental botany

2023 Volume 74, Issue 13, Page(s) 3833–3850

Abstract: Microalgae hold enormous potential to provide a safe and sustainable source of high-value compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly progressing climate change. Bioengineering microalgal strains will be key to ... ...

Abstract	Microalgae hold enormous potential to provide a safe and sustainable source of high-value compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly progressing climate change. Bioengineering microalgal strains will be key to optimizing and modifying their metabolic outputs, and to render them competitive with established industrial biotechnology hosts, such as bacteria or yeast. To achieve this, precise and tuneable control over transgene expression will be essential, which would require the development and rational design of synthetic promoters as a key strategy. Among green microalgae, Chlamydomonas reinhardtii represents the reference species for bioengineering and synthetic biology; however, the repertoire of functional synthetic promoters for this species, and for microalgae generally, is limited in comparison to other commercial chassis, emphasizing the need to expand the current microalgal gene expression toolbox. Here, we discuss state-of-the-art promoter analyses, and highlight areas of research required to advance synthetic promoter development in C. reinhardtii. In particular, we exemplify high-throughput studies performed in other model systems that could be applicable to microalgae, and propose novel approaches to interrogating algal promoters. We lastly outline the major limitations hindering microalgal promoter development, while providing novel suggestions and perspectives for how to overcome them.
MeSH term(s)	Chlamydomonas reinhardtii/genetics ; Chlamydomonas reinhardtii/metabolism ; Microalgae/genetics ; Microalgae/metabolism ; Biotechnology ; Promoter Regions, Genetic/genetics ; Synthetic Biology
Language	English
Publishing date	2023-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erad100
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Article ; Online: Riboswitch-guided chalcone synthase engineering and metabolic flux optimization for enhanced production of flavonoids.

Hwang, Hyun Gyu / Milito, Alfonsina / Yang, Jae-Seong / Jang, Sungho / Jung, Gyoo Yeol

Metabolic engineering

2022 Volume 75, Page(s) 143–152

Abstract: Flavonoids are a group of secondary metabolites from plants that have received attention as high value-added pharmacological substances. Recently, a robust and efficient bioprocess using recombinant microbes has emerged as a promising approach to supply ... ...

Abstract	Flavonoids are a group of secondary metabolites from plants that have received attention as high value-added pharmacological substances. Recently, a robust and efficient bioprocess using recombinant microbes has emerged as a promising approach to supply flavonoids. In the flavonoid biosynthetic pathway, the rate of chalcone synthesis, the first committed step, is a major bottleneck. However, chalcone synthase (CHS) engineering was difficult because of high-level conservation and the absence of effective screening tools, which are limited to overexpression or homolog-based combinatorial strategies. Furthermore, it is necessary to precisely regulate the metabolic flux for the optimum availability of malonyl-CoA, a substrate of chalcone synthesis. In this study, we engineered CHS and optimized malonyl-CoA availability to establish a platform strain for naringenin production, a key molecular scaffold for various flavonoids. First, we engineered CHS through synthetic riboswitch-based high-throughput screening of rationally designed mutant libraries. Consequently, the catalytic efficiency (k
MeSH term(s)	Flavonoids/genetics ; Riboswitch ; Chalcones ; Glycerol ; Flavanones/genetics ; Malonyl Coenzyme A/genetics ; Malonyl Coenzyme A/metabolism ; Metabolic Engineering
Chemical Substances	Flavonoids ; flavanone synthetase (EC 2.3.1.74) ; Riboswitch ; Chalcones ; Glycerol (PDC6A3C0OX) ; Flavanones ; Malonyl Coenzyme A (524-14-1)
Language	English
Publishing date	2022-12-20
Publishing country	Belgium
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2022.12.006
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Article ; Online: Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production.

Kang, Chae Won / Lim, Hyun Gyu / Won, Jaehyuk / Cha, Sanghak / Shin, Giyoung / Yang, Jae-Seong / Sung, Jaeyoung / Jung, Gyoo Yeol

Nature communications

2022 Volume 13, Issue 1, Page(s) 6506

Abstract: Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we ... ...

Abstract	Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named "Population guider", in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.
MeSH term(s)	Microbial Consortia/genetics ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Acclimatization ; Ampicillin/metabolism ; Alginates/metabolism
Chemical Substances	Ampicillin (7C782967RD) ; Alginates
Language	English
Publishing date	2022-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-34190-z
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Article ; Online: Kinetic compartmentalization by unnatural reaction for itaconate production.

Ye, Dae-Yeol / Noh, Myung Hyun / Moon, Jo Hyun / Milito, Alfonsina / Kim, Minsun / Lee, Jeong Wook / Yang, Jae-Seong / Jung, Gyoo Yeol

Nature communications

2022 Volume 13, Issue 1, Page(s) 5353

Abstract: Physical compartmentalization of metabolism using membranous organelles in eukaryotes is helpful for chemical biosynthesis to ensure the availability of substrates from competitive metabolic reactions. Bacterial hosts lack such a membranous system, which ...

Abstract	Physical compartmentalization of metabolism using membranous organelles in eukaryotes is helpful for chemical biosynthesis to ensure the availability of substrates from competitive metabolic reactions. Bacterial hosts lack such a membranous system, which is one of the major limitations for efficient metabolic engineering. Here, we employ kinetic compartmentalization with the introduction of an unnatural enzymatic reaction by an engineered enzyme as an alternative strategy to enable substrate availability from competitive reactions through kinetic isolation of metabolic pathways. As a proof of concept, we kinetically isolate the itaconate synthetic pathway from the tricarboxylic acid cycle in Escherichia coli, which is natively separated by mitochondrial membranes in Aspergillus terreus. Specifically, 2-methylcitrate dehydratase is engineered to alternatively catalyze citrate and kinetically secure cis-aconitate for efficient production using a high-throughput screening system. Itaconate production can be significantly improved with kinetic compartmentalization and its strategy has the potential to be widely applicable.
MeSH term(s)	Escherichia coli/metabolism ; Metabolic Engineering ; Metabolic Networks and Pathways ; Succinates/metabolism
Chemical Substances	Succinates ; itaconic acid (Q4516562YH)
Language	English
Publishing date	2022-09-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-33033-1
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Article ; Online: Impact of C-terminal amino acid composition on protein expression in bacteria.

Weber, Marc / Burgos, Raul / Yus, Eva / Yang, Jae-Seong / Lluch-Senar, Maria / Serrano, Luis

Molecular systems biology

2020 Volume 16, Issue 5, Page(s) e9208

Abstract: The C-terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C-terminal sequence and levels of protein expression remains ... ...

Abstract	The C-terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C-terminal sequence and levels of protein expression remains unknown. Here, we identified C-terminal amino acid biases that are ubiquitous across the bacterial taxonomy (1,582 genomes). We showed that the frequency is higher for positively charged amino acids (lysine, arginine), while hydrophobic amino acids and threonine are lower. We then studied the impact of C-terminal composition on protein levels in a library of Mycoplasma pneumoniae mutants, covering all possible combinations of the two last codons. We found that charged and polar residues, in particular lysine, led to higher expression, while hydrophobic and aromatic residues led to lower expression, with a difference in protein levels up to fourfold. We further showed that modulation of protein degradation rate could be one of the main mechanisms driving these differences. Our results demonstrate that the identity of the last amino acids has a strong influence on protein expression levels.
MeSH term(s)	Amino Acid Sequence ; Amino Acids/chemistry ; Amino Acids/metabolism ; Amino Acids, Aromatic/chemistry ; Amino Acids, Aromatic/metabolism ; Arginine/chemistry ; Arginine/metabolism ; Bacteria/chemistry ; Bacteria/genetics ; Bacteria/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/classification ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cluster Analysis ; Codon Usage/genetics ; Codon, Terminator/genetics ; Computational Biology ; Evolution, Molecular ; Genes, Bacterial ; Hydrophobic and Hydrophilic Interactions ; Lysine/chemistry ; Lysine/metabolism ; Mycoplasma pneumoniae/chemistry ; Mycoplasma pneumoniae/genetics ; Mycoplasma pneumoniae/metabolism ; Phylogeny ; Protein Domains ; Protein Processing, Post-Translational/genetics
Chemical Substances	Amino Acids ; Amino Acids, Aromatic ; Bacterial Proteins ; Codon, Terminator ; Arginine (94ZLA3W45F) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2020-05-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193510-5
ISSN	1744-4292 ; 1744-4292
ISSN (online)	1744-4292
ISSN	1744-4292
DOI	10.15252/msb.20199208
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Article ; Online: Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward a specific metabolite.

Seok, Joo Yeon / Han, Yong Hee / Yang, Jae-Seong / Yang, Jina / Lim, Hyun Gyu / Kim, Seong Gyeong / Seo, Sang Woo / Jung, Gyoo Yeol

Cell reports

2021 Volume 36, Issue 8, Page(s) 109589

Abstract: Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic ... ...

Abstract	Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolve cells under the selective condition toward the acquisition of genotypes that optimally reallocate cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determine that mutations in the conserved regions of proteins involved in global transcriptional regulation alter the expression of several genes associated with central carbon metabolism. These changes rewire central carbon flux toward the 3-HP production pathway, increasing 3-HP yield and reducing acetate accumulation by alleviating overflow metabolism. Our study provides a perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.
MeSH term(s)	Biosensing Techniques/methods ; Carbohydrate Metabolism ; Directed Molecular Evolution ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Glycerol/metabolism ; Lactic Acid/analogs & derivatives ; Lactic Acid/metabolism ; Metabolic Engineering/methods ; Metabolic Networks and Pathways ; Mutation ; Synthetic Biology
Chemical Substances	Escherichia coli Proteins ; Lactic Acid (33X04XA5AT) ; hydracrylic acid (C4ZF6XLD2X) ; Glycerol (PDC6A3C0OX)
Language	English
Publishing date	2021-08-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.109589
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Article ; Online: Catalytic RNA, ribozyme, and its applications in synthetic biology.

Park, Soyeon V / Yang, Jae-Seong / Jo, Hyesung / Kang, Byunghwa / Oh, Seung Soo / Jung, Gyoo Yeol

Biotechnology advances

2019 Volume 37, Issue 8, Page(s) 107452

Abstract: Ribozymes are functional RNA molecules that can catalyze biochemical reactions. Since the discovery of the first catalytic RNA, various functional ribozymes (e.g., self-cleaving ribozymes, splicing ribozymes, RNase P, etc.) have been uncovered, and their ...

Abstract	Ribozymes are functional RNA molecules that can catalyze biochemical reactions. Since the discovery of the first catalytic RNA, various functional ribozymes (e.g., self-cleaving ribozymes, splicing ribozymes, RNase P, etc.) have been uncovered, and their structures and mechanisms have been identified. Ribozymes have the advantage of possessing features of "RNA" molecules; hence, they are highly applicable for manipulating various biological systems. To fully employ ribozymes in a broad range of biological applications in synthetic biology, a variety of ribozymes have been developed and engineered. Here, we summarize the main features of ribozymes and the methods used for engineering their functions. We also describe the past and recent efforts towards exploiting ribozymes for effective and novel applications in synthetic biology. Based on studies on their significance in biological applications till date, ribozymes are expected to advance technologies in artificial biological systems.
MeSH term(s)	Catalysis ; Nucleic Acid Conformation ; RNA, Catalytic ; Synthetic Biology
Chemical Substances	RNA, Catalytic
Language	English
Publishing date	2019-10-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	47165-3
ISSN	1873-1899 ; 0734-9750
ISSN (online)	1873-1899
ISSN	0734-9750
DOI	10.1016/j.biotechadv.2019.107452
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Article ; Online: rec-Y3H screening allows the detection of simultaneous RNA-protein interface mutations.

Garriga-Canut, Mireia / Yang, Jae-Seong / Preusser, Friedrich / Speroni, Silvia / Gili, Maria / Maurer, Sebastian P

Methods (San Diego, Calif.)

2019 Volume 178, Page(s) 19–32

Abstract: Understanding which proteins and RNAs directly interact is crucial for revealing cellular mechanisms of gene regulation. Efficient methods allowing to detect RNA-protein interactions and dissect the underlying molecular origin for RNA-binding protein ( ... ...

Abstract	Understanding which proteins and RNAs directly interact is crucial for revealing cellular mechanisms of gene regulation. Efficient methods allowing to detect RNA-protein interactions and dissect the underlying molecular origin for RNA-binding protein (RBP) specificity are in high demand. The recently developed recombination-Y3H screening (rec-Y3H) enabled many-by-many detection of interactions between pools of proteins and RNA fragments for the first time. Here, we test different conditions for protein-RNA interaction selection during rec-Y3H screening and provide information on the screen performance in several selection media. We further show that rec-Y3H can detect the nucleotide and amino acid sequence determinants of protein-RNA interactions by mutating residues of interacting proteins and RNAs simultaneously. We envision that systematic RNA-protein interface mutation screening will be useful to understand the molecular origin of RBP selectivity and to engineer RBPs with targeted specificities in the future.
MeSH term(s)	Binding Sites/genetics ; Gene Expression Regulation/genetics ; High-Throughput Screening Assays/methods ; Humans ; Mutation/genetics ; RNA/genetics ; RNA/isolation & purification ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/isolation & purification
Chemical Substances	RNA-Binding Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2019-09-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2019.09.002
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