Article
Microbiology
Jiajia Li, Tania Chroumpi, Sandra Garrigues, Roland S. Kun, Jiali Meng, Sonia Salazar-Cerezo, Maria Victoria Aguilar-Pontes, Yu Zhang, Sravanthi Tejomurthula, Anna Lipzen, Vivian Ng, Chaevien S. Clendinen, Nikola Tolic, Igor Grigoriev, Adrian Tsang, Miia R. Makela, Berend Snel, Mao Peng, Ronald P. de Vries
Summary: Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. This study mapped the sugar metabolic network of Aspergillus niger to other fungi species and found that the diversity of sugar metabolism is correlated with taxonomic distance. Integrative analysis of transcriptome, proteome, and metabolome confirmed these results and provided a valuable resource for rational metabolic engineering.
Article
Biochemistry & Molecular Biology
Heankel Lyons, Reshma T. Veettil, Prashant Pradhan, Christy Fornero, Nancy De La Cruz, Keiichi Ito, Mikayla Eppert, Robert G. Roeder, Benjamin R. Sabari
Summary: Components of transcriptional machinery are selectively partitioned into specific condensates, often mediated by protein disorder, to regulate biochemical pathways. In this study, it was found that condensates composed of the intrinsically disordered region (IDR) of MED1 can selectively partition RNA polymerase II and its positive allosteric regulators, while excluding negative regulators. This selective compartmentalization is necessary for gene activation during a cell-state transition and is achieved through alternating blocks of charged amino acids in the IDRs of partitioned proteins.
Article
Biochemistry & Molecular Biology
Renata Novakova, Erik Mingyar, Lubomira Feckova, Dagmar Homerova, Dominika Csolleiova, Bronislava Rezuchova, Beatrica Sevcikova, Rachel Javorova, Jan Kormanec
Summary: This study identified the aur1 biosynthetic gene cluster and its regulators, Aur1P and Aur1O, in Streptomyces lavendulae. It demonstrated that Aur1P is a key positive regulator of auricin production, and Aur1O acts as a specific coactivator of Aur1P. Furthermore, it revealed that Aur1O belongs to a new family of transcriptional coactivators involved in the regulation of secondary metabolite biosynthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Microbiology
Fanny Nazaret, Genevieve Alloing, Karine Mandon, Pierre Frendo
Summary: The relationship between plants and associated soil microorganisms plays a crucial role in ecosystem functioning. This review focuses on MarR-like transcriptional regulators and their mechanisms of plant-signal perception, including how they help bacteria cope with the rhizosphere and plant endosphere, regulate the beneficial functions of Plant-Growth-Promoting Bacteria, and regulate the virulence of phytopathogenic bacteria.
Article
Biochemistry & Molecular Biology
Ulrike Johnsen, Marius Ortjohann, Andreas Reinhardt, Jonathan M. Turner, Caleb Stratton, Katherine R. Weber, Karol M. Sanchez, Julie Maupin-Furlow, Christopher Davies, Peter Schoenheit
Summary: In this study, a novel transcriptional regulator called GfcR was identified, which acts as an activator in the degradation of both D-glucose and D-fructose. GfcR activates multiple enzymes involved in the catabolism of these sugars and directly binds to the promoters of regulated genes. Furthermore, specific intermediates of the degradation pathways were found to induce the activity of GfcR.
MOLECULAR MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Cristian M. Pis Diez, Maria Juliana Juncos, Matias Villarruel Dujovne, Daiana A. Capdevila
Summary: The movement of bacteria in different niches during their life cycle requires a rapid response to environmental cues. This response is primarily driven by transcriptional regulators, which sense and respond to a wide range of chemical species, ultimately regulating gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has been a focus of research in recent decades. This review summarizes the state-of-the-art techniques used to understand these mechanisms and provides a roadmap for experimental design based on the desired answers and initial information about the system of study. The review also highlights recent research on allosteric mechanisms of sensing and regulation, discussing the use of multiple strategies and novel experimental techniques. The aim of these experiments is to gain a molecular-level understanding of how bacteria adapt to environmental threats.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yating Wang, Zhiai Xi, Xiuhong Wang, Yuyu Zhang, Yongguo Liu, Shuai Yuan, Shirui Zhao, Jiping Sheng, Demei Meng
Summary: In this study, 10 putative bHLH transcription factors were identified in the edible mushroom A. bisporus, and their role in postharvest development was investigated. The results suggest that these bHLH proteins play a crucial role in the regulation of arginine catabolism and control of postharvest mushroom development.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Genetics & Heredity
Pradeep Kumar, Mathilde Courtes, Celine Lemmers, Anne Le Digarcher, Ilda Coku, Arnaud Monteil, Charles Hong, Annie Varrault, Runhua Liu, Lizhong Wang, Tristan Bouschet
Summary: MicroRNAs are small non-coding RNAs that control gene expression. This study investigates the transcriptional regulation of two microRNAs, miR-335 and miR-3662, by targeting their candidate promoters using CRISPRa and CRISPRi. The results show that miR-335 expression depends on the promoter activity of its host gene, while miR-3662 can be activated by both the host gene promoter and an intronic sequence.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Xueyang Dong, Ben G. H. Guthrie, Margaret Alexander, Cecilia Noecker, Lorenzo Ramirez, Nathaniel R. Glasser, Peter J. Turnbaugh, Emily P. Balskus
Summary: This study develops genetic tools for the direct manipulation of Eggerthella lenta and other Coriobacteriia, including shuttle vectors, transformation methods, and genome editing systems. Using these tools, the researchers characterize endogenous promoters and inducible expression systems in Eggerthella lenta, and uncover a novel family of transcriptional regulators in gut Coriobacteriia. Furthermore, they utilize these genetic tools to study the effects of Eggerthella lenta genes on host biology.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Marketa Soltysova, Irena Sieglova, Milan Fabry, Jiri Brynda, Jana Skerlova, Pavlina Rezacova
Summary: The SorC/DeoR family is a large family of bacterial transcription regulators involved in carbohydrate metabolism and quorum sensing. Structural studies of two members from Bacillus subtilis revealed the structural basis of DNA recognition and proposed a common mode of DNA recognition likely shared by other family members.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Plant Sciences
Ravindra Kumar Chandan, Rahul Kumar, Durga Madhab Swain, Srayan Ghosh, Prakash Kumar Bhagat, Sunita Patel, Ganesh Bagler, Alok Krishna Sinha, Gopaljee Jha
Summary: AtRAV1, a transcription factor, is involved in the basal defense response in Arabidopsis thaliana. Overexpression of AtRAV1 confers disease resistance against fungal pathogens, while atrv1 mutants are hyper-susceptible to these pathogens. AtRAV1 is phosphorylated by AtMPK3 and this phosphorylation is important for the defense response in A. thaliana. RAV1 homologs can be used to enhance disease resistance in agriculturally important crop plants.
Review
Biochemistry & Molecular Biology
Katja Rust, Andreas Wodarz
Summary: Cell polarity, essential for various cellular and tissue functions, is mainly controlled by protein complexes along the apical-basal axis. However, gene expression regulation plays a significant role in influencing cell polarity, which is often overlooked.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Genetics & Heredity
Md. Sifatul Islam, Ajit Ghosh
Summary: Aldehyde dehydrogenases (ALDHs) play an important role in plants by serving as scavengers for reactive aldehydes and responding to stress. Both animals and plants have multiple ALDH families, with plants having 14 families. The expansion of ALDH isoforms in plants allows for diverse functions. Studies have shown that ALDH is crucial for plant development and environmental stress adaptability.
Article
Plant Sciences
Xiuting Hua, Qiaochu Shen, Yihan Li, Dong Zhou, Zhe Zhang, Sehrish Akbar, Zhengchao Wang, Jisen Zhang
Summary: A regulatory network module for SsSWEET13c was proposed in the developmental gradient of leaf and circadian rhythm in S. spontaneum. These results provide a novel understanding of the function and regulation of SWEET13c during the sugar transport and biomass production in S. spontaneum.
Article
Microbiology
Sieze Douwenga, Berdien van Olst, Sjef Boeren, Yanzhang Luo, Xin Lai, Bas Teusink, Jacques Vervoort, Michiel Kleerebezem, Herwig Bachmann
Summary: Bacteria like Lactococcus cremoris have a hierarchical sugar catabolism system, where they consistently prioritize the catabolization of higher-quality sugars for optimal growth rate, but also have some proteins always present for consuming certain lower-quality sugars.
MICROBIOLOGY SPECTRUM
(2023)
Article
Ecology
Miriam N. Ojima, Lin Jiang, Aleksandr A. Arzamasov, Keisuke Yoshida, Toshitaka Odamaki, Jinzhong Xiao, Aruto Nakajima, Motomitsu Kitaoka, Junko Hirose, Tadasu Urashima, Toshihiko Katoh, Aina Gotoh, Douwe van Sinderen, Dmitry A. Rodionov, Andrei L. Osterman, Mikiyasu Sakanaka, Takane Katayama
Summary: This study applied assembly theory to investigate the formation of bifidobacterial communities in the infant gut. The results showed that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis dominated through inhibitory priority effects, while Bifidobacterium breve benefited from facilitative priority effects and utilized a specific degradant to dominate. This study highlights the importance of initial community assembly and its impact on the maturation trajectory of the infant gut microbiota.
Article
Biochemistry & Molecular Biology
Maria S. Frolova, Inna A. Suvorova, Stanislav N. Iablokov, Sergei N. Petrov, Dmitry A. Rodionov
Summary: This study reconstructed the synthesis pathways of short-chain fatty acids (SCFAs) in the human gut microbiota and evaluated the SCFA production potential in HGM samples through the analysis of genomic and phenotypic data. The findings contribute to the predictive metabolic phenotype profiling of HGM datasets and enhance the in vitro methodology for studying cross-feeding interactions in gut microbiomes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Gennady Ponomarev, Bulat Fatykhov, Vladimir A. Nazarov, Ruslan Abasov, Evgeny Shvarov, Nina-Vicky Landik, Alexandra A. Denisova, Almira A. Chervova, Mikhail S. Gelfand, Marat D. Kazanov
Summary: In human cancers, APOBEC mutagenesis is not enriched in certain DNA secondary structures and is positively associated with inverted repeats. The APOBEC-induced mutational density is lower in G-quadruplex compared to four-stranded G-quadruplex and B-DNA. UV and APOBEC mutagenesis are absent in Z-DNA regions.
Article
Biotechnology & Applied Microbiology
James R. Crosby, Tunyaboon Laemthong, Ryan G. Bing, Ke Zhang, Tania N. N. Tanwee, Gina L. Lipscomb, Dmitry A. Rodionov, Ying Zhang, Michael W. W. Adams, Robert M. Kelly
Summary: This study characterizes the utilization of hemicellulose by the extreme thermophile Caldicellulosiruptor bescii by integrating genomic reconstruction, transcriptomic data, operon structures, and biochemical characteristics of key enzymes. The comparative genomics of the genus also reveals conserved and divergent mechanisms for hemicellulose utilization across the 15 sequenced species. These findings are essential for understanding lignocellulose degradation and can contribute to enhancing lignocellulose conversion for biofuel and chemical production through metabolic engineering efforts.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
German A. Ashniev, Natalia Sernova, Aleksei E. Shevkoplias, Ivan D. Rodionov, Irina A. Rodionova, Alexey G. Vitreschak, Mikhail S. Gelfand, Dmitry A. Rodionov
Summary: Using a comparative genomic approach, this study identified a novel DNA-binding transcription factor (HisR) and RNA regulatory elements (T-box riboswitches and RNA attenuators) involved in the regulation of histidine metabolism and transport genes in various bacterial taxa. The distribution of HisR and these regulatory mechanisms across over 600 species of Firmicutes were discussed from functional and evolutionary perspectives.
Article
Biochemistry & Molecular Biology
Gabriele Minazzato, Massimiliano Gasparrini, Annie Heroux, Natalia V. Sernova, Dmitry A. Rodionov, Michele Cianci, Leonardo Sorci, Nadia Raffaelli
Summary: Nicotinamide-adenine dinucleotide (NAD) plays a central role in metabolic reactions and its biosynthesis in bacteria is controlled by transcription factors. NadQ, a protein found in proteobacteria, acts as a repressor of de novo NAD biosynthesis. This study used comparative genomics to reconstruct NadQ regulons in bacterial genomes, and validated the DNA binding activity and structure of NadQ, providing a model for its regulation mechanism.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Microbiology
Kendall Kling, Sonya A. Trinh, Semen A. Leyn, Dmitry A. Rodionov, Ivan D. Rodionov, Alfa Herrera, Kasey Cervantes, George Pankey, Deborah Ashcraft, Egon A. Ozer, Adam Godzik, Karla J. F. Satchell
Summary: Our study demonstrated that phylogenetic lineage and multifunctional autoprocessing repeats-in-toxin (MARTX) toxinotype do not predict severity of Vibrio vulnificus infection. Strains capable of causing severe human disease are genetically diverse and not concentrated in one specific lineage. Therefore, food surveillance based on lineage type or toxinotype may not be an appropriate intervention measure for controlling this rare but serious infection.
Article
Microbiology
Aleksandr A. Arzamasov, Aruto Nakajima, Mikiyasu Sakanaka, Miriam N. Ojima, Takane Katayama, Dmitry A. Rodionov, Andrei L. Osterman
Summary: This study describes the NagR-mediated transcriptional regulation of WI and LNnT utilization in Bifidobacterium longum subsp. infantis. The elucidated regulatory network appears optimally adapted to simultaneous utilization of multiple HMOs, providing a rationale to add HMO mixtures (rather than individual components) to infant formulas. The study also provides insights into the evolutionary trajectories of complex regulatory networks controlling carbohydrate metabolism in bifidobacteria.
Article
Multidisciplinary Sciences
Ivan N. Semenkov, Pavel Shelyakin, Daria D. Nikolaeva, Maria N. Tutukina, Anna Sharapova, Sergey A. Lednev, Yuliya Sarana, Mikhail S. Gelfand, Pavel P. Krechetov, Tatiana Koroleva
Summary: This article presents original data on the impact of jet-fuel spillage on topsoil properties. The data set includes information on kerosene concentration over time, as well as physicochemical and biological properties of the soil. Additionally, sequencing data on microbial communities are provided.
Article
Biotechnology & Applied Microbiology
Jason L. Vailionis, Weishu Zhao, Ke Zhang, Dmitry A. Rodionov, Gina L. Lipscomb, Tania N. N. Tanwee, Hailey C. O'Quinn, Ryan G. Bing, Robert M. Kelly, Michael W. W. Adams, Ying Zhang
Summary: A genome-scale metabolic model was developed for the growth of Pyrococcus furiosus, an archaeon that ferments carbohydrates and peptides at 100 degrees C. The model investigates the energy balance of P. furiosus and reveals the importance of acetate production and the coupling of ATP synthase and hydrogenase in generating a sodium gradient. The model is used to guide genetic engineering designs for ethanol production and provides valuable insights for bio-based chemical and fuel production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Aleksandra Borkovskaia, Sofia Bogacheva, Tatiana Konyukhova, Elina Dadakhanova, Marina Gaskova, Olga Soldatkina, Maria Dubrovina, Alexander Popov, Ekaterina Mikhailova, Evgenia Inushkina, Marat Kazanov, Evgeniy Matveev, Galina Novichkova, Michael Maschan, Alexey Maschan, Yulia Olshanskaya, Elena Zerkalenkova
Summary: The pathogenesis of acute promyelocytic leukemia (APL) is based on RARA gene translocations, which are important for diagnosis and therapy selection. However, some cases of acute myeloid leukemia (AML) present APL-like morphological features without RARA gene translocations. In this study, genetic analysis revealed various gene fusions and mutations in AML cases with atypical promyelocytes accumulation, highlighting the genetic diversity of AML with APL-like morphology and its importance in therapy.
Article
Microbiology
Christine Tara Peterson, Josue Perez-Santiago, Stanislav N. Iablokov, Dmitry A. Rodionov, Scott N. Peterson
Summary: This study examined the impact of prebiotics and medicinal herbs on gut microbiota composition and host physiology using in vitro cultivation and 16S rRNA sequencing. By analyzing the relationship between sugar composition and microbiota composition, the study found that restructuring microbial communities with glycan substrates can alter community metabolism and influence host physiological changes. The combination of genome-wide metabolic reconstruction and 16S rRNA sequence-based community profiles provides valuable insights into community metabolism.
Article
Biochemistry & Molecular Biology
Evgenii V. Matveev, Vyacheslav V. Safronov, Gennady V. Ponomarev, Marat D. Kazanov
Summary: The importance of 3D protein structure in proteolytic processing is well known. We developed a method that utilizes the structural features of potential substrates to predict proteolytic sites, taking into consideration factors such as solvent accessibility, secondary structure, and temperature factor. By carefully curating the training set, selecting an appropriate machine learning method, and determining the optimal positive-to-negative class size ratio, we demonstrated that our method outperforms existing bioinformatics methods for predicting proteolytic sites. This method may also have applications in predicting other post-translational modifications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Kathleen M. Hudson, Leszek J. Klimczak, Joan F. Sterling, Adam B. Burkholder, Marat D. Kazanov, Natalie Saini, Piotr A. Mieczkowski, Dmitry A. Gordenin
Summary: By studying the hypermutation spectra in ssDNA, we found that mutagens often prefer specific nucleotides or oligonucleotide motifs. We used a yeast model to investigate mutagenesis by glycidamide, a simple endogenously formed epoxide in humans. Glycidamide predominantly caused ssDNA hypermutation in cytosines and adenines, with the most frequent mutations occurring in the nAt → nGt trinucleotide motif. This mutational motif was also observed in glycidamide-treated mouse cells and human cancers.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Christine Tara Peterson, Stanislav N. Iablokov, Dmitry A. Rodionov, Scott N. Peterson
Summary: Parkinson's disease is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Research indicates that initial dysregulation may occur in the gastrointestinal tract and gut barrier defects may accompany it. A study evaluated the effect of Ayurvedic herbs on fecal microbiota from Parkinson's disease patients and found that each participant showed unique changes, suggesting personalized response and potential for selecting individualized medicinal herbs.