Article
Biochemical Research Methods
Alexander R. Bricco, Iliya Miralavy, Shaowei Bo, Or Perlman, David E. Korenchan, Christian T. Farrar, Michael T. McMahon, Wolfgang Banzhaf, Assaf A. Gilad
Summary: We have developed a mechanism for protein optimization using genetic programming, known as Protein Optimization Engineering Tool (POET). By using this tool, we were able to develop proteins that produce four times more MRI contrast than the state-of-the-art. The peptides generated with POET were significantly different from existing CEST producing peptides, challenging previous understandings of their functionality. Unlike existing protein engineering algorithms that rely on divergent evolution, POET relies on convergent evolution, allowing the discovery of peptides with completely different sequences but the same or even better efficiency. Therefore, this novel approach can be applied beyond imaging agents and widely used in protein engineering.
ACS SYNTHETIC BIOLOGY
(2023)
Review
Agronomy
Ahamed Khan, Noohi Nasim, Baveesh Pudhuvai, Bhupendra Koul, Santosh Kumar Upadhyay, Lini Sethi, Nrisingha Dey
Summary: This review discusses the application of synthetic promoters in plants to overcome the limitations of native promoters in terms of size, distribution, and induction, which ultimately leads to insufficient transcriptional activity. It emphasizes the basic structure and function of the promoter, with a focus on the role of Cis-elements in gene expression regulation. The importance of synthetic promoters in the field of plant biology is highlighted, along with information on two major approaches: conventional methods and advancements in gene editing technology. The efficiency of synthetic promoters and the expression level of transgenes are crucial for successful plant genetic manipulation, making the development of synthetic promoters highly promising for genetic engineering-mediated crop improvement.
Review
Genetics & Heredity
Liliana Villao-Uzho, Tatiana Chavez-Navarrete, Ricardo Pacheco-Coello, Eduardo Sanchez-Timm, Efren Santos-Ordonez
Summary: One strategy to overcome crop diseases or abiotic stress is through the use of improved varieties achieved by genetic improvement methods such as conventional breeding, induced mutation, genetic transformation, or gene editing. Promoters, which regulate gene expression, are crucial for transgenic crops to improve specific traits. Many techniques, including RT-PCR, genetic libraries, cloning, and sequencing, are used to identify and isolate promoters for biotechnological crops. Promoter analysis through plant genetic transformation allows for understanding gene regulation and development, highlighting the importance of promoters in ensuring correct gene expression in biotechnological processes.
Article
Plant Sciences
Yuan Lin, Hainan Zhao, Magdalena Kotlarz, Jiming Jiang
Summary: Gene expression is regulated by interactions between cis-regulatory DNA elements (CREs) and regulatory proteins. Enhancers play a crucial role in this process, especially in eukaryotes, but little is known about the molecular mechanisms involved in plants. Researchers identified a distal enhancer, CRE beta, which regulates gene expression in response to osmotic pressure, and established a forward genetic screen pipeline to identify trans-regulatory factors associated with CRE beta function and the regulation of the endogenous gene AtDGK7.
Article
Biochemistry & Molecular Biology
Kaili Fan, Jill E. Moore, Xiao-ou Zhang, Zhiping Weng
Summary: Gene expression is controlled by regulatory elements within accessible chromatin, with certain elements accessible in multiple cell and tissue types and enriched with transcription factor motifs. These elements are highly conserved between human and mouse, associated with essential genes, and enriched in genes implicated in Mendelian diseases impacting various cell types.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Joan Calle Garcia, Anna Guadagno, Andreu Paytuvi-Gallart, Alfonso Saera-Vila, Ciro Gianmaria Amoroso, Daniela D'Esposito, Giuseppe Andolfo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria Raffaella Ercolano
Summary: The PRGdb database has been significantly expanded and upgraded, providing more data and tools, with a new section dedicated to collecting plant resistance transcriptomic experimental data. Additionally, the DRAGO3 tool has been improved in accuracy and sensitivity, leading to more reliable predictions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Barbara Pfister, Jessica M. Shields, Tobias Kockmann, Jonas Grossmann, Melanie R. Abt, Martha Stadler, Samuel C. Zeeman
Summary: This study used Saccharomyces cerevisiae as a testbed to investigate the functions of plant starch biosynthetic enzymes and create diverse starch-like polymers. The results revealed unexpected effects of glucan biosynthesis on protein abundances and demonstrated that different enzyme ratios influenced glucan structure and solubility.
Article
Plant Sciences
Xianpu Wang, Lili Xu, Xiuxia Liu, Li Xin, Shujing Wu, Xuesen Chen
Summary: The transient expression system developed for apple protoplasts shows that the AtUBQ10 and MdUBQ10 promoters are more efficient in driving gene expression compared to the CaMV 35S promoter. Using this system, it was demonstrated that active AtMKK7ac could activate signaling cascades and regulate phosphorylation and stability of MdWRKY33 in apple. The system also allowed for the reconstitution of ligand-induced interactions and regulation of AvrRpt2 stability involving auxin and the immune regulator RIN4.
HORTICULTURE RESEARCH
(2021)
Review
Chemistry, Multidisciplinary
Yong Yan, Xiaojun Zhu, Yue Yu, Chao Li, Zhaoliang Zhang, Feng Wang
Summary: Plant genetic engineering plays a crucial role in sustainable agriculture by improving crop yield, quality, and resistance to stresses. Nanotechnology-based gene delivery systems show promising potential in plant genetic transformation, with high efficiency and good compatibility. However, challenges still exist for the broad application of nanomaterial-mediated gene delivery in plants.
ADVANCED MATERIALS
(2022)
Article
Biology
Saqer S. Alotaibi
Summary: The study identified two B. distachyon promoters that actively function in N. benthamiana leaves, successfully regulating gene expression specifically in leaf tissues. Exploring these active promoters could potentially provide new genetic tools for transgene expression in plants or leaves to genetically manipulate photosynthesis for yield improvement.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Biochemical Research Methods
Y. -M Cai, S. Witham, N. J. Patron
Summary: This article presents a luminescence-based microplate assay for comparing the interactions between transcription factors and short DNA probes, and demonstrates how these data can be utilized to design synthetic plant promoters with varying response levels.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Alexandra J. Dickinson, Jingyuan Zhang, Michael Luciano, Guy Wachsman, Evan Sandoval, Martin Schnermann, Jose R. Dinneny, Philip N. Benfey
Summary: Research has shown that retinal binding occurs before lateral root formation and helps to promote root clock oscillations. The Arabidopsis protein TIL oscillates in the region of retinal binding, shares homology with vertebrate retinoid-binding proteins, and plays a role in lateral root organogenesis.
Article
Microbiology
Gloria Munoz-Fernandez, Javier-Fernando Montero-Bullon, Jose Luis Revuelta, Alberto Jimenez
Summary: Ashbya gossypii is a filamentous fungus used for industrial production of riboflavin and as a valuable biocatalyst for producing various metabolites. The study identified 10 new promoters in A. gossypii, including three strong promoters and seven medium/weak promoters, which significantly improved gene expression platforms. The functionality of the promoters was evaluated by overexpression and underexpression of the MSN2 gene, leading to significant changes in sporulation ability of the mutant strains.
Article
Plant Sciences
Kummari Divya, Sudhakar Reddy Palakolanu, Polavarapu Kavi Kishor, Aishwarya Shankhapal Rajesh, Vincent Vadez, Kiran K. Sharma, Pooja Bhatnagar Mathur
Summary: LEA genes in pearl millet respond differently to abiotic stresses, with PgLEA7 being significantly expressed under high VPD. The promoter regions of PgLEA contain stress-specific cis-acting elements, suggesting a role in abiotic stress tolerance in plants.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Plant Sciences
Konstantin Kanofsky, Jendrik Rusche, Lea Eilert, Fabian Machens, Reinhard Hehl
Summary: The study reveals that WRKY50 in A. thaliana requires specific WT-boxes for activation and binding at target gene promoters, demonstrating high flexibility of WRKY50 binding site recognition beyond the classic W-box TTGACC/T.
PLANT CELL REPORTS
(2021)