Review
Biotechnology & Applied Microbiology
Alan Costello, Ahmed H. Badran
Summary: Researchers aim to control cellular behavior by reducing or eliminating unwanted interactions, in order to achieve reliable and predictable gene circuits and develop context-independent biological activities. Current focus is on biological orthogonalization, isolating researcher-specified bioactivities from host processes, with the potential to create an orthogonal central dogma and novel cellular functions.
TRENDS IN BIOTECHNOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Christian S. Diercks, David A. Dik, Peter G. Schultz
Summary: The maturation of chemical synthesis during the 20th century elevated chemistry from largely empirical to a rational science, allowing chemists to purposefully craft matter at the molecular level and contribute to progress in neighboring natural sciences. The recent major advance in the field involves the interdisciplinary use of chemical and biological synthetic methods to alter biological macromolecules in ways previously unimaginable, expanding upon the defining characteristics of living organisms at the molecular level. One successful case study is the addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.
Review
Immunology
Andreacarola Urso, Alice Prince
Summary: Host and pathogen metabolism play a significant role in the outcome of infection, with immunometabolites influencing the pathogenesis and adaptation of bacteria.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jacopo De Capitani, Hannes Mutschler
Summary: The construction of a self-replicating biochemical system is an important goal in bottom-up synthetic biology. In vitro cell-free systems have provided valuable insights into the requirements for a minimal self-replicating system. The main limitations of current systems lie in their macromolecular composition and the utilization of small molecules for RNA and protein synthesis. This Perspective discusses recent advancements in generating a minimal cell-free system capable of regenerating its own macromolecular components and maintaining a homeostatic balance.
Article
Biochemistry & Molecular Biology
Yuanqing Feng, Hongzhan Xu, Jinghao Liu, Ning Xie, Lei Gao, Yanyun He, Yuan Yao, Fengxiang Lv, Yan Zhang, Jian Lu, Wei Zhang, Chuan-Yun Li, Xinli Hu, Ziheng Yang, Rui-Ping Xiao
Summary: Cis-regulatory elements play crucial roles in tissue-specific gene expression and phenotype evolution. Mutations in promoters and enhancers may drive species adaptations to environments. TRIM72, a highly conserved protein involved in energy metabolism, shows varying levels of expression in primate hearts, with mutations in the promoter being responsible for these differences. Accelerated rates of evolution in the TRIM72 promoter suggest positive selection influenced by changes in cardiac physiology after species divergence. Mutations in the TRIM72 promoter account for differential expression in human and rhesus macaque hearts, affecting genes involved in oxidative phosphorylation, mitochondrial respiration, and cardiac energy capacity. Phylogenetic regression analyses indicate a correlation between high cardiac TRIM72 expression and heart rate in mammals.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Immunology
Rui-kun Zhang, Kun Yan, Hai-feng Chen, Yang Zhang, Gui-jin Li, Xiao-gang Chen, Lin-pu Ge, Feng Cheng, Zhi-neng Chen, Xin-miao Yao
Summary: This study investigated the effect of traditional Chinese medicine (TCM) intervention on the structure and function of the gut microbiota (GM) in patients with osteoporosis (OP). After three months of treatment, patients in the TCM group showed improved bone mineral density (BMD) compared to the control group. The GM composition and metabolites also underwent significant changes. This suggests that TCM may promote the rehabilitation of OP patients through modulation of the GM.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Oncology
Ke Liu, Jun Huang, Jiao Liu, Changfeng Li, Guido Kroemer, Daolin Tang, Rui Kang
Summary: This study uncovers the HSP90-centric, iron-modulated mechanism that confers immunosuppression, potentially providing therapeutic targets for overcoming acquired resistance to anticancer immunotherapies. The upregulation of immune checkpoints induced by IFN gamma requires increased protein stability of STAT1, mediated by the HSP90-SUGT1 chaperone complex. In addition, the upregulation of IDO1 in cancer cells acts as an immunosuppressive feedback mechanism. Combination therapies involving anti-PD-1 immunotherapy, iron chelation, HSP90 inhibition, or IDO1 inhibition show effectiveness and safety in preclinical models of pancreatic cancer.
Article
Environmental Sciences
Cong Zhou, Mei-jie Yang, Zhi Hu, Pu Shi, Yong-ren Li, Yong-jun Guo, Tao Zhang, Hao Song
Summary: This study investigates the adaptive evolutionary characteristics in euryhaline bivalves through comparative genomics analyses. The results reveal positive selection in genes related to solute transport, antioxidant response, energy metabolism, and membrane lipids adjustments. These findings enhance our understanding of the molecular mechanisms underlying the remarkable salinity adaption of euryhaline bivalves.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Microbiology
Madeleine Bouzon, Volker Doring, Ivan Dubois, Anne Berger, Gabriele M. M. Stoffel, Liliana Calzadiaz Ramirez, Sophia N. Meyer, Marion Foure, David Roche, Alain Perret, Tobias J. Erb, Arren Bar-Even, Steffen N. Lindner
Summary: This study explores the potential and limits of evolving enzyme cofactor specificity within the cellular context. By using adaptive evolution experiments in an NADPH-auxotrophic strain of E. coli, mutations were found in malic enzyme and dihydrolipoamide dehydrogenase that altered their cofactor preference. However, the study also reveals that biochemical constraints, such as unfavorable thermodynamics, limit the evolution of central metabolism oxidoreductases toward reducing NADP(+).
Review
Virology
Putu Prathiwi Primadharsini, Shigeo Nagashima, Hiroaki Okamoto
Summary: Hepatitis E virus is the leading cause of acute hepatitis worldwide, with transmission routes varying between developing and industrialized countries. Zoonotic transmission poses a risk for HEV infection, but the exact mechanism and determinants are not fully understood.
Article
Multidisciplinary Sciences
S. A. Mullaeva, Ya. A. Delegan, R. A. Streletskii, O. I. Sazonova, K. V. Petrikov, A. A. Ivanova, I. A. Dyatlov, I. G. Shemyakin, A. G. Bogun, A. A. Vetrova
Summary: Pollution of the environment by crude oil and oil products poses a global problem. The strain Pseudomonas veronii 7-41 can degrade medium-chain n-alkanes and polycyclic aromatic hydrocarbons. A natural plasmid carrying operons for the degradation of two different classes of hydrocarbons was identified. The strain showed different degradation abilities in single-substrate and double-substrate systems.
SCIENTIFIC REPORTS
(2022)
Article
Immunology
Nada El Mahmoudi, Guillaume Rastoldo, Emna Marouane, David Pericat, Isabelle Watabe, Alain Tonetto, Charlotte Hautefort, Christian Chabbert, Francesca Sargolini, Brahim Tighilet
Summary: Corticosteroids are commonly used for their anti-inflammatory properties in treating brain injuries and inflammatory diseases. However, the efficacy of acute corticotherapy is being questioned, especially in cases of acute peripheral vestibulopathies. A study using a rodent model of unilateral vestibular neurectomy compared the effects of acute corticosteroid treatment and placebo on vestibular syndrome.
JOURNAL OF NEUROINFLAMMATION
(2021)
Article
Biochemistry & Molecular Biology
Dan Tan, Srihari Konduri, Meric Erikci Ertunc, Pan Zhang, Justin Wang, Tina Chang, Antonio F. M. Pinto, Andrea Rocha, Cynthia J. Donaldson, Joan M. Vaughan, Raissa G. Ludwig, Elizabeth Willey, Manasi Iyer, Peter C. Gray, Pamela Maher, Nicola J. Allen, J. Bradley Zuchero, Andrew Dillin, Marcelo A. Mori, Steven G. Kohama, Dionicio Siegel, Alan Saghatelian
Summary: Lipids play important roles in the structure, development, and function of healthy brains. Dysregulated lipid metabolism is linked to diseased brains. This study examined the brain lipidome of mice and found a decrease in 3-sulfogalactosyl diacylglycerols (SGDGs) in the central nervous system with aging, which is associated with myelination. Additionally, SGDG was found to suppress inflammation by acting on the NF-kappa B pathway.
NATURE CHEMICAL BIOLOGY
(2023)
Review
Microbiology
Bo Zhang, Jiangyue Wu, Fanping Meng
Summary: Adaptive laboratory evolution (ALE) experiments are a feasible method for enhancing the phenotype, performance, and stability of microalgae to obtain strains with beneficial mutations. Improving the efficiency of ALE and verifying the stability of resulting strains are the primary challenges that need to be addressed in future research.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Jonaid Ahmad Malik, Sakeel Ahmed, Zahid Yaseen, Muteb Alanazi, Tareq Nafea Alharby, Hisham Abdulaziz Alshammari, Sirajudheen Anwar
Summary: SARS-CoV-2, the virus responsible for COVID-19, primarily affects the lungs but also impacts other organs. Elderly and comorbid patients with preexisting polypharmacy experience worsened complications. Changes in the gut microbiota contribute to the severity of the disease.
Article
Biochemical Research Methods
Huseyin Tas, Angel Goni-Moreno, Victor de Lorenzo
Summary: A collection of NOT gates from E. coli was reconstructed and transferred to broad host range plasmids, providing a toolbox for genetic circuit design in various Gram-negative species. Characterization and comparison of gates in Pseudomonas putida with E. coli data allowed evaluation of gate portability.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Microbiology
Alejandro Arce-Rodriguez, Pablo Nikel, Belen Calles, Max Chavarria, Raul Platero, Tino Krell, Victor de Lorenzo
Summary: The soil bacterium Pseudomonas putida KT2440 has low intracellular levels of 3',5'-cyclic adenosine monophosphate (cAMP) due to stringent regulation of its synthesis, efflux, and degradation. Despite this, the low levels of cAMP sustain activation of certain promoters dependent on the cAMP-receptor protein (CRP) through unusual binding parameters of cAMP to CRP. This suggests that altering interaction parameters can enable genetic devices to take over different domains of the functional landscape while retaining the same regulatory parts and logic.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Danilo Perez-Pantoja, Pablo I. Nikel, Max Chavarria, Victor de Lorenzo
Summary: The dnt pathway of Burkholderia sp. R34 is evolving from its ancestral substrate naphthalene to a new xenobiotic one, 2,4-dinitrotoluene (DNT). The gene cluster encoding the leading multicomponent ring dioxygenase DntA has activity on both old and new substrates, and is induced by a transcription factor dntR upon the addition of salicylate. The induction of dnt genes by salicylate is amplified upon exposure to true DntA substrates naphthalene or DNT.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Jillian Silbert, Victor de Lorenzo, Tomas Aparicio
Summary: In this study, the conjugation machinery of the RP4 plasmid was recruited into a synthetic construct using yeast assembly, enabling the transfer of chromosomal segments between P. putida KT2440 and other Gram-negative bacteria. This new device expands the molecular toolbox for P. putida and allows for genomic manipulations previously only possible with laboratory strains and species.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jonathan Tellechea-Luzardo, Leanne Hobbs, Elena Velazquez, Lenka Pelechova, Simon Woods, Victor de Lorenzo, Natalio Krasnogor
Summary: The advance in gene synthesis and editing techniques, along with integration of life science research with informatics, IoT, and automation, are bringing full-stack biotechnology platforms for cell line programming closer to reality. These platforms will increase the speed of biological product production and consumption, making traceability, transparency, and trustworthiness essential for engineered cell lines and their processes.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Victor de Lorenzo
Summary: Our current era is marked by awareness of climate change, environmental deterioration, global pandemics, and inequalities between developed and underdeveloped countries, with a recognition of the crucial role of microorganisms in the functioning of the biosphere. To address these challenges, it is important to engage in multi-faceted discussions involving politics, technology, and science, utilizing advanced microbial biotechnology tools.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Pablo Nikel, Ilaria Benedetti, Nicolas T. Wirth, Victor de Lorenzo, Belen Calles
Summary: The potential of regulatory nodes from different bacteria as parts for expression cargoes was examined. The performance of these expression devices, assembled within the same plasmid backbone, was analyzed in Escherichia coli. The study revealed differences in their capacity, expression noise, inducibility, and ON/OFF ratios due to the arrangement of functional DNA segments. This research resulted in a collection of formatted expression cargoes without cross talk, providing choices for users and improving interoperability of specific constructs.
MICROBIAL BIOTECHNOLOGY
(2022)
Review
Biology
Victor de Lorenzo
Summary: Contemporary synthetic biology and biotechnologies provide tools and strategies for addressing climate change, but the challenge lies in delivering these technologies to various dimensions of time and space. Environmental Galenics (EG) refers to the science and technology of releasing designed biological agents into deteriorated ecosystems to achieve safe and effective recovery. EG also involves using microorganism carriers and horizontal gene transfer channels to spread beneficial activities.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Elena Velazquez, Beatriz Alvarez, Luis Angel Fernandez, Victor de Lorenzo
Summary: This study exploited the ability of T7 RNA polymerase fusions with cytosine deaminases to induce C -> T changes in specific DNA segments of Pseudomonas putida KT2440. By introducing CdA-RNAP(T7) fusions into test strains, the researchers achieved specific mutagenesis of DNA segments. It was found that the absence of uracil-DNA glycosylase significantly increased mutagenic rates, and the most active variant, pmCDA1, caused extensive mutations.
MICROBIAL BIOTECHNOLOGY
(2022)
Editorial Material
Microbiology
Victor de Lorenzo
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Pavel Dvorak, Teca Calcagno Galvao, Katharina Pflueger-Grau, Alice M. Banks, Victor de Lorenzo, Jose I. Jimenez
Summary: The biodegradative capacity of bacteria is influenced by water availability. The activity and specificity of the transcriptional regulator XylR in the biodegradation of m-xylene were examined when water potential was manipulated. Water limitation led to increased effector specificity, which could be counteracted by external addition of glycine betaine. XylR variants were unaffected by water potential and the conformational changes in the A domain and effector-binding pocket were suggested by AlphaFold prediction.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Juhyun Kim, Victor de Lorenzo, Angel Goni-Moreno
Summary: Experimental evidence shows that the differential pressure experienced by cells in the middle versus the periphery of a colony affects their growth rate and spatial direction, ultimately shaping the colony's form.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Biochemical Research Methods
Angeles Hueso-Gil, Belen Calles, Viïctor de Lorenzo
Summary: The inner physicochemical heterogeneity of bacterial cells leads to three-dimensional variations of resources, which has been exploited in adjusting parameters for optogenetic control of biofilm formation in Pseudomonas putida. A superactive variant of PleD diguanylate cyclase was inserted into the chromosome of wild-type and biofilm-deficient P. putida. Random chromosomal insertions enable sampling the intracellular milieu for optimal resources that deliver a preset phenotypic specification.
ACS SYNTHETIC BIOLOGY
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Victor de Lorenzo, Kenneth Timmis
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Huseyin Tas, Lewis Grozinger, Angel Goni-Moreno, Victor de Lorenzo
Summary: The study successfully assembled a NOR gate in Pseudomonas putida using components tailored for E. coli with the help of the circuit design tool CELLO. By leveraging the functional parameters of genetic inverters and specific inducible promoters, the library was expanded to increase compatibility between different bacterial hosts. This demonstrates the potential for reusing genetic modules optimized for one host to construct functional genetic circuits in a new bacterial chassis.
