Article
Biochemistry & Molecular Biology
Petra Vande Zande, Patricia J. Wittkopp
Summary: This study uses expression and fitness data from Saccharomyces cerevisiae gene deletion strains to show that cis-acting mutations tend to have lower pleiotropy and trans-acting mutations are more deleterious. These findings provide strong support for the role of pleiotropy in the preferential fixation of cis-regulatory alleles over evolutionary time.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Guokun Wang, Aline Tavares, Simone Schmitz, Lucas Franca, Hugo Almeida, Joao Cavalheiro, Ana Carolas, Suleyman Ozmerih, Lars M. Blank, Bruno S. Ferreira, Irina Borodina
Summary: This study developed an integrated process for manufacturing CCM from glucose by yeast fermentation, achieving high CCM yield and purity. The engineered strain ST10209 produced 1.4 g/L CCM in microplate assay and 22.5 g/L CCM in a 2 L fermenter, outperforming the previous strain ST8943. The CCM recovery yield reached 66.3% with 95.4% purity using a recovery and purification process involving activated carbon treatment.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Biology
Ching-Hua Shih, Justin Fay
Summary: The evolution of cis-regulatory sequences is influenced by their impact on gene expression. Studies have shown that allele-specific expression dynamics are affected by cis-acting variations within and between species, suggesting a key role of cis-regulatory sequences in tuning gene expression dynamics.
Article
Biochemical Research Methods
Natalia Kakko, Anssi Rantasalo, Tino Koponen, Virve Vidgren, Matti Kannisto, Natalia Maiorova, Heli Nygren, Dominik Mojzita, Merja Penttila, Paula Jouhten
Summary: We achieved inducible synthetic resource-use control overSaccharomyces cerevisiae by expressing a bacterial ClpXP proteasome from an inducible promoter. This control method efficiently repressed cell growth, improved product yields, and did not compromise biomass accumulation. The study provides a new approach to tackle uncertainties in strain optimization and address strain stability and low productivity challenges.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Chenyao Zhou, Mingjie Li, Surui Lu, Yanfei Cheng, Xuena Guo, Xiaoxian He, Zhaoyue Wang, Xiu-Ping He
Summary: This study utilized the Escherichia coli MAR operator cis-element marO to engineer promoters in Saccharomyces cerevisiae for metabolic flux control, resulting in increased production of squalene and lanosterol. The engineered promoters using marO were effective in reducing the accumulation of other metabolites, leading to higher yields of the target products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Seungsoo Kim, Joanna Wysocka
Summary: Uncovering the cis-regulatory code that governs gene transcription in a given genome and cellular state remains a central goal of biology. This review discusses the different layers of regulation that influence transcriptional outputs, including the binding of transcription factors to specific DNA sequences, the role of cofactors in facilitating their function, and the complex interplay within regulatory landscapes. The authors propose that a quantitative, mechanistically informed model of transcriptional regulation is essential for ultimately understanding the cis-regulatory code.
Article
Biochemistry & Molecular Biology
Jung-Hoon Yoon, Debashree Basu, Jayati Roy Choudhury, Satya Prakash, Louise Prakash
Summary: The study demonstrates the essential role of Pol lambda in inserting the correct nucleotide T opposite 1-MeA, while Pol zeta is responsible for extending synthesis. The ability of Pol lambda to accommodate 1-MeA in a syn confirmation and form Hoogsteen base pair with T during DNA synthesis is highlighted. This adds a novel aspect to Pol lambda's function in translesion synthesis, in addition to its role as a scaffolding component for Pol zeta.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Plant Sciences
Qi Gao, Ann E. Cleves, Xiao Wang, Yizhou Liu, Sean Bowen, Robert Thomas Williamson, Ajay N. Jain, Edward Sherer, Mikhail Reibarkh
Summary: This study presents the high-resolution 3D structure of the cis-Pro conformer of aureobasidin A for the first time, and validates the biological relevance of both the cis-Pro and trans-Pro conformers. This is important for a better understanding of the structure of aureobasidin A and the design of future therapeutic drugs.
JOURNAL OF NATURAL PRODUCTS
(2022)
Article
Biotechnology & Applied Microbiology
Emil D. Jensen, Francesca Ambri, Marie B. Bendtsen, Alex A. Javanpour, Chang C. Liu, Michael K. Jensen, Jay D. Keasling
Summary: Directed evolution optimizes proteins and metabolic reactions towards user-defined goals through iterative rounds of mutagenesis, selection, and amplification. A study demonstrated an integrated workflow for enzyme evolution using an orthogonal replication system and a transcription factor-based biosensor, resulting in significant improvement in product titers. The combination of synthetic biology tools presented an efficient approach to accelerate directed evolution of metabolic enzymes.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Tannia Uribe-Calvillo, Laetitia P. Maestroni, Marie-Claude Marsolier, Basheer P. Khadaroo, Christine Arbiol, Jonathan P. Schott, Bertrand Llorente
Summary: Break-induced replication (BIR) is a highly mutagenic DNA repair pathway that is most efficient near chromosome ends. The efficiency of ectopic BIR is affected by the length of DNA to replicate and is characterized by repeated cycles of strand invasion, elongation, and dissociation. The processivity of ectopic BIR is dependent on the length of DNA already synthesized. Additionally, the Srs2 helicase promotes ectopic BIR in diploid cells but only in telomere proximal sites in haploid cells.
Article
Biotechnology & Applied Microbiology
Oguz Ulas Yaman, Beste Avci, Pinar Calik
Summary: Designing promoter architectures in yeast relies on genomic and functional annotations. This study introduces a curated pipeline for predicting cis-acting DNA sequences/sites (cADSs) in Saccharomyces cerevisiae. Using this pipeline and a scanning algorithm, the researchers were able to predict master transcription factors (TFs) and cADSs in Pichia pastoris, a yeast lacking extensive functional annotation studies. The methodology presented in this study provides a valuable tool for understanding gene regulation in yeasts.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
