?
Nitrogen fixation and molecular oxygen: Comparative genomic reconstruction of transcription regulation in Alphaproteobacteria
Frontiers in Microbiology. 2016. Vol. 7. P. 1–14.
Tsoy O. V., Ravcheev D. A., Čuklina J., Gelfand M. S.
Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of Bacteria and Archaea. The transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class Alphaproteobacteria. This regulatory network includes the activator of nitrogen fixation NifA, working in tandem with the alternative sigma-factor RpoN as well as oxygen-responsive regulatory systems, one-component regulators FnrN/FixK and two-component system FixLJ. Here we used a comparative genomics approach for in silico study of the transcriptional regulatory network in 50 genomes of Alphaproteobacteria. We extended the known regulons and proposed the scenario for the evolution of the nitrogen fixation transcriptional network. The reconstructed network substantially expands the existing knowledge of transcriptional regulation in nitrogen-fixing microorganisms and can be used for genetic experiments, metabolic reconstruction, and evolutionary analysis. © 2016 Tsoy, Ravcheev, Čuklina and Gelfand.
Margarita Chetyrkina, Umriukhin P., Ershova E. et al., Biomaterials Translational 2025 Vol. 6 No. 3 P. 359–370
Fullerenes are one of the most popular nanomaterials, and C70 fullerene is the second most common fullerene after C60 buckminsterfullerene. Minor modification of fullerenes derivatives can change their biological effects and antioxidant properties. A plethora of water-soluble derivatives can be synthesised based on buckminsterfullerenes. In the present study, we synthesised three water-soluble C70 fullerene derivatives ...
Added: February 12, 2026
Pavel Latyshev, Fedor Pavlov, Herbert A. et al., Frontiers in Big Data 2023 Vol. 6 Article 1140663
Due to advances in NGS technologies whole-genome maps of various functional genomic elements were generated for a dozen of species, however experiments are still expensive and are not available for many species of interest. Deep learning methods became the state-of-the-art computational methods to analyze the available data, but the focus is often only on the ...
Added: June 8, 2023
Poloznikov A., Nikulin S., Hushpulian D. et al., Antioxidants 2022 Vol. 11 No. 2 Article 220
To evaluate the differences in action of commercially available 2-oxoglutarate mimetics and “branched-tail” oxyquinoline inhibitors of hypoxia-inducible factor prolyl hydroxylase (HIF PHD), the inhibitors’ IC50 values in the activation of HIF1 ODD-luciferase reporter were selected for comparative transcriptomics. Structure–activity relationship and computer modeling for the oxyquinoline series of inhibitors led to the identification of novel ...
Added: February 3, 2023
German A. Ashniev, Sernova N., Shevkoplias A. et al., BMC Genomics 2022 Vol. 23 Article 558
The histidine metabolism and transport (his) genes are controlled by a variety of RNA-dependent regulatory systems among diverse taxonomic groups of bacteria including T-box riboswitches in Firmicutes and Actinobacteria and RNA attenuators in Proteobacteria. Using a comparative genomic approach, we previously identified a novel DNA-binding transcription factor (named HisR) that controls the histidine metabolism genes ...
Added: January 31, 2023
Philip V.Toukach, Egorova K. S., Computational and Structural Biotechnology Journal 2022 Vol. 20 P. 5466–5476
In this paper, we present the results of a systematic statistical analysis of the fungal glycome in comparison with the prokaryotic and protistal glycomes as described in the scientific literature and presented in the Carbohydrate Structure Database (CSDB). The monomeric and dimeric compositions of glycans, their non-carbohydrate modifications, glycosidic linkages, sizes of structures, branching degree ...
Added: October 24, 2022
Lohan S., Mandal D., Choi W. et al., Journal of Medicinal Chemistry 2022 Vol. 65 No. 1 P. 665–687
We report the synthesis and antibacterial activities of a series of amphiphilic membrane-active peptides composed, in part, of various non-genetically coded hydrophobic amino acids. Lead cyclic peptides, 8C and 9C, showed broad-spectrum activity against drug-resistant Gram-positive (MIC=1.5-6.2 µg/mL) and Gram-negative (MIC=12.5-25 µg/mL) bacteria. Cytotoxicity study showed the predominant lethal action of the peptides against bacteria ...
Added: February 1, 2022
Garushyants S., Beliavskaia A., Malko D. et al., Frontiers in Microbiology 2018 Vol. 9 Article 738
While most endosymbiotic bacteria are transmitted only vertically, Holospora spp., an alphaproteobacterium from the Rickettsiales order, can desert its host and invade a new one. All bacteria from the genus Holospora are intranuclear symbionts of ciliates Paramecium spp. with strict species and nuclear specificity. Comparative metabolic reconstruction based on the newly sequenced genome of Holospora ...
Added: December 16, 2021
Arnold S., Cortland J., Maltseva D. et al., Journal of Cancer Research and Clinical Oncology 2021 Vol. 148 No. 6 P. 1525–1542
Purpose:
The transcription factor Fra-2 affects the invasive potential of breast cancer cells by dysregulating adhesion molecules in vitro. Previous results suggested that it upregulates the expression of E- and P-selectin ligands. Such selectin ligands are important members of the leukocyte adhesion cascade, which govern the adhesion and transmigration of cancer cells into the stroma of ...
Added: October 23, 2021
Landrette S. F., Madera D., He F. et al., Leukemia 2011 Vol. 25 No. 4 P. 655–662
Cytokine signaling pathways are frequent targets of oncogenic mutations in acute myeloid leukemia (AML), promoting proliferation and survival. We have previously shown that the transcription factor PLAGL2 promotes proliferation and cooperates with the leukemia fusion protein Cbfβ-SMMHC in AML development. Here, we show that PLAGL2 upregulates expression of the thrombopoietin receptor Mpl, using two consensus ...
Added: April 21, 2021
Jordan K., Conley A., Antonov I. et al., Journal of Bacteriology 2011 Vol. 193 No. 20 P. 5879–5880
We report the first whole-genome sequences for five strains, two carried and three pathogenic, of the emerging pathogen Haemophilus haemolyticus. Preliminary analyses indicate that these genome sequences encode markers that distinguish H. haemolyticus from its closest Haemophilus relatives and provide clues to the identity of its virulence factors. ...
Added: March 19, 2021
Gelfand M. S., Scientific Reports 2018 Vol. 8 No. 1 P. 1–12
Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, transporter, and transcription factor. The ...
Added: March 17, 2019
Gelfand M. S., Kaznadzey А., Shelyakin P., Biology Direct 2017 Vol. 12 No. 2 P. 1–14
BACKGROUND:
Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. This study focuses on ...
Added: February 7, 2018
Bondarenko V., Gelfand M. S., Plos One 2016 Vol. 11 No. 9 P. 1–16
A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) possess only ultra-short introns, around ...
Added: March 13, 2017
Zhang B., Gelfand M. S., Khaitovich P. et al., Genome Biology and Evolution 2016 Vol. 8 No. 3 P. 840–850
Small nuclear and nucleolar RNAs (snRNAs and snoRNAs) are known to be functionally and evolutionarily conserved elements of transcript processing machinery. Here, we investigated the expression evolution of snRNAs and snoRNAs by measuring their abundance in the frontal cortex of humans, chimpanzees, rhesus monkeys, and mice. Although snRNA expression is largely conserved, 44% of the ...
Added: March 13, 2017