Article
Biotechnology & Applied Microbiology
Xianzun Xiao, Liming Ouyang, Jie Qi, Ju Chu
Summary: Aspergillus niger lacks basic genetic elements for dynamic control, with the identification of the first hypoxia-inducible promoters providing new insights into the organism's adaptability to low oxygen conditions. Promoter truncation analysis revealed core regions determining hypoxia response.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Microbiology
Theopi Rados, Katherine Andre, Micaela Cerletti, Alex Bisson
Summary: This study developed a new xylose-inducible promoter, Pxyl, and characterized its function using msfGFP as a reporter gene. The results showed that the Pxyl promoter exhibited higher levels of gene expression in the presence of xylose compared to the previously described inducible promoter, PtnaA. Additionally, the study validated the inducibility of Pxyl by reproducing morphological phenotypes through the overexpression of FtsZ1 and FtsZ2 genes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Fatemeh Sadat Shariati, Malihe Keramati, Vahideh Valizadeh, Reza Ahangari Cohan, Dariush Norouzian
Summary: The IPTG-inducible promoter is costly and toxic, leading to the development of the Self-Inducible Expression (SILEX) system using Hsp70. While the Hsp27 system showed higher expression levels, inducible systems had the highest expression. SILEX systems demonstrated stable expression and lower variation compared to IPTG-inducible systems.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Anna O. Shemyakina, Elena G. Grechishnikova, Andrey D. Novikov, Andrey F. Asachenko, Tatyana Kalinina, Konstantin Lavrov, Alexander S. Yanenko
Summary: Rhodococcus bacteria, particularly the M33 strain, have the potential for superexpression of target enzymes and are suitable for biodegradation and biocatalysis applications. A set of recombinant promoters, including P-tuf, P-sod, P-cpi, and P(nh), have been studied for their activity levels and regulation possibilities in the M33 strain, providing valuable resources for constructing Rhodococcus strains with specific characteristics.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Peili Shen, Dandan Niu, Kugen Permaul, Kangming Tian, Suren Singh, Zhengxiang Wang
Summary: This study identified 1443 differently expressed genes in Bacillus licheniformiscultivated in media supplemented with ammonia, with 859 upregulated and 584 downregulated genes. Ammonia-inducible promoters were shown to mediate amyL expression, with P-plp yielding the highest enzyme expression level. B. licheniformis possesses glucose-independent ammonia-inducible promoters that can enhance enzyme yield in fermentations traditionally fed with ammonia.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Microbiology
Qiang Liu, Daiyu Li, Ning Wang, Gang Guo, Yun Shi, Quanming Zou, Xiaokai Zhang
Summary: This study identified highly expressed genes in Staphylococcus aureus and successfully cloned their promoter regions. By constructing shuttle vectors with these active promoters, the compatibility and activity of the vectors were evaluated. The vectors were also used to overexpress endogenous proteins and validate their physiological functions and phenotypes in S. aureus. These constructed vectors provide a versatile tool for the analysis of gene function in staphylococcal cells.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Forestry
Shichao Xin, Jinu Udayabhanu, Xuemei Dai, Yuwei Hua, Yueting Fan, Huasun Huang, Tiandai Huang
Summary: In this study, three Hevea polyubiquitin genes and their promoters were identified, which could potentially be used to drive transgene expression in Hevea genetic engineering.
Article
Biochemistry & Molecular Biology
Xue-Lian Wu, Xiao-Wei Liu, Yang Wang, Meng-Yun Guo, Jian-Ren Ye
Summary: By analyzing the transcriptome data of Burkholderia pyrrocinia JK-SH007, 54 highly expressed genes were identified and their promoter sequences were screened using genome-wide data and BPROM, resulting in 18 promoter sequences. A promoter trap system based on two reporter proteins was developed and successfully used to insert eight constitutive promoters into B. pyrrocinia JK-SH007. Five of these promoters showed higher activity than the control promoter PRPL, with P14 and P19 demonstrating stable high transcription levels at all time points.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Irene Robles-Rebollo, Sergi Cuartero, Adria Canellas-Socias, Sarah Wells, Mohammad M. Karimi, Elisabetta Mereu, Alexandra G. Chivu, Holger Heyn, Chad Whilding, Dirk Dormann, Samuel Marguerat, Inmaculada Rioja, Rab K. Prinjha, Michael P. H. Stumpf, Amanda G. Fisher, Matthias Merkenschlager
Summary: This study demonstrates that inducible genes and enhancers are mainly regulated by transcriptional burst frequency, which is coordinated in single cells and individual alleles. Cohesin is required for coupling burst frequencies of inducible enhancers and promoters, but not for regulating enhancer burst frequencies. The results also suggest that cohesin and BD2 may act on shared pathways in enhancer-mediated inducible gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Junfei Ma, Qianyu Ji, Shuying Wang, Jingxuan Qiu, Qing Liu
Summary: In this study, 21 promoters were identified from Listeria monocytogenes through RNA-seq analysis, among which 7 showed higher strength than a previously reported strong promoter. Additionally, 5 selected constitutive promoters exhibited higher UreB production activity, with P-18 showing the highest activity. This study provides a panel of strong constitutive promoters for Listeria monocytogenes and offers a theoretical basis for mining constitutive promoters in other organisms.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Andres Felipe Carrillo Rincon, Natalie G. Farny
Summary: In this study, the architecture of inducible bacterial promoters, such as lac and tet, were improved to enhance their strength, control, and portability. The improvement was achieved by targeting the consensus -10 and -35 sequences recognized by sigma(70), incorporating a strong ribosome binding site for Gram-negative bacteria, and independently controlling the transcriptional regulators. The improved promoters were successfully tested using the far-red fluorescent protein mCardinal and showed enhanced OFF state control and inducibility. The promoters were also found to be portable to other Gram-negative species. These findings have significant implications for protein production in biotechnology applications.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
Summary: The study analyzed the expression dynamics of thousands of genes with inducible promoters, revealing the impact of RNA polymerase and LacI repressor binding site strengths on gene expression. By fitting a statistical mechanics model, properties of theoretically optimal inducible promoters were accurately modeled. Through the examination of three alternative promoter architectures, the study showed how repositioning binding sites within promoters influences the combinatorial effects observed between promoter elements.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Hyun-Woo Je, Chang-Hun Ji, Jun-Yong Kim, Hahk-Soo Kang
Summary: The CRISPR/Cas9 system faces toxicity issues in Streptomyces genome engineering due to overexpression of the Cas9 protein. The CaExTun platform has been developed to optimize Cas9 expression for reduced toxicity while maintaining sufficient DSB activity. This tool enables rapid optimization of the CRISPR/Cas9 system in a species-specific manner, facilitating genome engineering efforts in Streptomyces.
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.
Article
Genetics & Heredity
Zhenchi Huang, Qingchun Xu, Xiaolan Fang, Zhihua Wu
Summary: The transcriptional properties of artificial promoters are closely related to the type and arrangement position of cis-elements. Through experimental analysis, it has been determined that the improved promoters have significant advantages in terms of expression activity and inducibility, which is important for the construction and optimization of transgenic plants.
Review
Audiology & Speech-Language Pathology
Julia Sidorova, Pablo Carbonell, Milena Cukic
Summary: The possibility of estimating glucose value from voice has the potential to revolutionize diabetes treatment by providing nonintrusive and instantaneous blood glucose estimation. This review provides a comprehensive overview of different approaches in this field and includes a transparency and reproducibility score to assess the biases in primary research. The discussion on future research pathways further highlights the importance of this topic.
Article
Biochemistry & Molecular Biology
Nicole G. H. Leferink, Andres M. Escorcia, Bodi R. Ouwersloot, Linus O. Johanissen, Sam Hay, Marc W. van der Kamp, Nigel S. Scrutton
Summary: The study identified the essential roles of key residues in bacterial monoterpene synthases, particularly the importance of Phe77 and other aromatic amino acids in monoterpenoid synthesis, as well as the critical roles of Phe295 and Ala301 in different synthetic pathways.
Review
Biochemistry & Molecular Biology
Jack A. Connolly, William R. Harcombe, Michael J. Smanski, Linda L. Kinkel, Eriko Takano, Rainer Breitling
Summary: Microbiomes consisting of diverse communities of organisms from across kingdoms can significantly impact plant growth and health through intercellular signals. Utilizing these signals to engineer microbiomes for beneficial interactions with crops represents a significant opportunity in advancing microbiome engineering. Achieving an optimized microbiome through the selection of synergistic consortia and genetic engineering of signal pathways is crucial for this goal.
NATURAL PRODUCT REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Mauro A. Rinaldi, Clara A. Ferraz, Nigel S. Scrutton
Summary: This review discusses strategies to increase terpenoid titres in Escherichia coli, including altering metabolic pathways and selecting suitable heterologous homologs for E. coli expression to increase titres and product diversity.
NATURAL PRODUCT REPORTS
(2022)
Review
Biotechnology & Applied Microbiology
Jonathan Tellechea-Luzardo, Irene Otero-Muras, Angel Goni-Moreno, Pablo Carbonell
Summary: Biofoundries are highly automated facilities that enable rapid and efficient processes in biomanufacturing and engineering biology. However, they can be costly and time-consuming to develop. By considering strategies early on and identifying bottlenecks, biofoundries can be optimized for efficiency. This article provides a survey of technological solutions and explores pathways towards the creation of a functional biofoundry.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Chemistry, Physical
Linus O. Johannissen, Aoife Taylor, Samantha J. O. Hardman, Derren J. Heyes, Nigel S. Scrutton, Sam Hay
Summary: This article proposes a complete mechanism for the photochemistry between protochlorophyllide (PChlide) and nicotinamide adenine dinucleotide phosphate (NADPH) based on computational calculations. The mechanism is consistent with recent experimental data and explains how photoexcitation facilitates hydride transfer, with implications for biological hydride transfer reactions.
Article
Chemistry, Physical
Tobias M. Hedison, Andreea I. Iorgu, Donato Calabrese, Derren J. Heyes, Muralidharan Shanmugam, Nigel S. Scrutton
Summary: This study investigates the structural, dynamical, and functional relationship of copper nitrite reductases (CuNiRs) through combining crystallographic techniques and solution-state approaches. The findings shed light on the catalytic mechanisms of these enzymes and suggest the involvement of protein dynamics. The importance of integrating high-resolution crystallographic techniques and low-resolution solution-state approaches in studying metalloenzymes is emphasized.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Hanan L. L. Messiha, Nigel S. S. Scrutton, David Leys
Summary: Biosynthetic routes for cost-efficient, eco-friendly, and sustainable production of compounds like styrene are urgently needed. The traditional biosynthesis of styrene from L-phenylalanine via trans-cinnamate is limited by styrene toxicity. This study demonstrates that using an E. coli consortium, whole-cell cascade biotransformation can efficiently convert L-phenylalanine to styrene, avoiding the issue of styrene toxicity and the need for enzyme purification.
Article
Biotechnology & Applied Microbiology
Helen Park, Helen S. Toogood, Guo-Qiang Chen, Nigel S. Scrutton
Summary: The engineered strain Halomonas bluephagenesis TD1.0 was able to produce propane, bioplastic PHB, and biochemicals mandelate and hydroxymandelate in a single fermentation process. Multi-product separation was achieved, showcasing the versatility of biotechnology. This achievement further establishes H. bluephagenesis as a valuable platform for industrial biotechnology.
MICROBIAL BIOTECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Jonathan Tellechea-Luzardo, Martin T. Stiebritz, Pablo Carbonell
Summary: Advances in synthetic biology and genetic engineering have led to the development of transcription factor (TF)-based biosensors, which are promising tools for detecting chemical compounds and eliciting specific responses. However, widespread use of these biosensors is hindered by challenges that can be addressed by increasing knowledge of metabolite-activated transcription factors, identifying new transcription factors, and improving the design workflow for biosensor circuits. These improvements are especially important in the bioproduction field, where better biosensor-based approaches are needed for screening and regulation. This work summarizes the current understanding of TF-based biosensors, discusses recent experimental and computational approaches for modification and improvement, and suggests future research directions for bioproduction screening and genetic circuit regulation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Jonathan Tellechea-Luzardo, Hector Martin Lazaro, Raul Moreno Lopez, Pablo Carbonell
Summary: Allosteric transcription factor (aTF) based biosensors are widely used in engineering genetic circuits. However, the scattered and incomplete knowledge about validated molecule-TF pairs and the limited number of known TF-compound interactions pose challenges in finding new TF-ligand pairs. In this study, we present Sensbio, a computational tool that utilizes a TF-ligand reference database to identify potential transcription factors activated by specific input molecules. Our tool includes algorithms, an online application, and a predictive model based on machine learning for discovering new matches.
BMC BIOINFORMATICS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Nigel S. S. Scrutton
Summary: The study of enzymes has a long history and continues to advance rapidly. Modern enzymology focuses on understanding the complex relationships between enzyme structures, catalytic mechanisms, and biological function. Topics of interest include the regulation of enzymes at the gene and post-translational levels, as well as how catalytic activity is influenced by interactions with small molecules, macromolecules, and the enzyme environment. Insights from enzymology research have practical applications in diagnostics, pharmaceuticals, and industrial processes. The FEBS Journal seeks to highlight the latest research and provide informative reviews to showcase the breadth and importance of contemporary molecular enzymology research.
Article
Chemistry, Physical
Magnus Speirs, Samantha J. O. Hardman, Andreea I. Iorgu, Linus O. Johannissen, Derren J. Heyes, Nigel S. Scrutton, Igor Sazanovich, Sam Hay
Summary: Recent reports have shown the use of ene-reductase flavoenzymes for non-natural photochemical reactions. These studies have focused on reduced flavoenzymes, but oxidized flavins have better light harvesting properties. In a binary complex of the oxidized ene-reductase with nonreactive nicotinamide coenzyme analogs, visible photoexcitation of flavin mononucleotide leads to electron transfer, but longer-lived excited states may be achieved through enzyme engineering and substrate choice.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemical Research Methods
Erik K. R. Hanko, Tariq A. Joosab Noor Mahomed, Ruth A. Stoney, Rainer Breitling
Summary: TFBMiner is a tool that identifies putative metabolite-responsive transcription factor-based biosensors (TFBs) through data mining and analysis. It utilizes a heuristic rule-based gene organization model to identify gene clusters involved in the catabolism of user-defined molecules and their associated transcriptional regulators, providing wet-lab scientists with a ranked list of candidates. The pipeline was validated by identifying known sensors and discovering a biosensor for S-mandelic acid.
ACS SYNTHETIC BIOLOGY
(2023)
Review
Chemistry, Physical
Joshua N. Whitehead, Nicole G. H. Leferink, Linus O. Johannissen, Sam Hay, Nigel S. Scrutton
Summary: This article reviews the important discoveries and advances in terpene synthase/cyclase (TS) biocatalysis, summarizes the recent literature, and explores the future prospects of TS rational design. The article highlights the catalytic motifs in TSs that control product outcome and examines the recent strategies for TS engineering, including machine learning and data-driven approaches. The ultimate goal is to achieve rational and predictive engineering of TSs for designer terpene synthases.
