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Genetic interaction network has a very limited impact on the evolutionary trajectories in continuous culture‑grown populations of yeast
Get PDFBackground
The impact of genetic interaction networks on evolution is a fundamental issue. Previous studies have demonstrated that the topology of the network is determined by the properties of the cellular machinery. Functionally related genes frequently interact with one another, and they establish modules, e.g., modules of protein complexes and biochemical pathways. In this study, we experimentally tested the hypothesis that compensatory evolutionary modifications, such as mutations and transcriptional changes, occur frequently in genes from perturbed modules of interacting genes.
Results
Using Saccharomyces cerevisiae haploid deletion mutants as a model, we investigated two modules lacking COG7 or NUP133, which are evolutionarily conserved genes with many interactions. We performed laboratory evolution experiments with these strains in two genetic backgrounds (with or without additional deletion of MSH2), subjecting them to continuous culture in a non-limiting minimal medium. Next, the evolved yeast populations were characterized through whole-genome sequencing and transcriptome analyses. No obvious compensatory changes resulting from inactivation of genes already included in modules were identified. The supposedly compensatory inactivation of genes in the evolved strains was only rarely observed to be in accordance with the established fitness effect of the genetic interaction network. In fact, a substantial majority of the gene inactivations were predicted to be neutral in the experimental conditions used to determine the interaction network. Similarly, transcriptome changes during continuous culture mostly signified adaptation to growth conditions rather than compensation of the absence of the COG7, NUP133 or MSH2 genes. However, we noticed that for genes whose inactivation was deleterious an upregulation of transcription was more common than downregulation.
Conclusions
Our findings demonstrate that the genetic interactions and the modular structure of the network described by others have very limited effects on the evolutionary trajectory following gene deletion of module elements in our experimental conditions and has no significant impact on short-term compensatory evolution. However, we observed likely compensatory evolution in functionally related (albeit non-interacting) genes
The Influence of Shadow Effects on the Spectral Characteristics of Glacial Meltwater
Get PDFThe phenomenon of shadows due to glaciers is investigated in Antarctica. The observed shadow effect disrupts analyses conducted by remote sensing and is a challenge in the assessment of sediment meltwater plumes in polar marine environments. A DJI Inspire 2 drone equipped with a
Zenmuse x5s camera was used to generate a digital surface model (DSM) of 6 King George Island glaciers: Ecology, Dera, Zalewski, Ladies, Krak, and Vieville. On this basis, shaded areas of coves near glaciers were traced. For the first time, spectral characteristics of shaded meltwater were observed with the simultaneous use of a Sequoia+ spectral camera mounted on a Parrot Bluegrass drone and in Landsat 8 satellite images. In total, 44 drone flights were made, and 399 satellite images were analyzed. Among them, four drone spectral images and four satellite images were selected,
meeting the condition of a visible shadow. For homogeneous waters (deep, low turbidity, without ice phenomena), the spectral properties tend to change during the approach to an obstacle casting a shadow especially during low shortwave downward radiation. In this case, in the shade, the amount
of radiation reflected in the green spectral band decreases by 50% far from the obstacle and by 43% near the obstacle, while in near infrared (NIR), it decreases by 42% and 21%, respectively. With highly turbid, shallow water and ice phenomena, this tendency does not occur. It was found that the green spectral band had the highest contrast in the amount of reflected radiation between nonshaded and shaded areas, but due to its high sensitivity, the analysis could have been overestimated. The spectral properties of shaded meltwater differ depending on the distance from the glacier front, which is related to the saturation of the water with sediment particles. We discovered that the pixel aggregation of uniform areas caused the loss of detailed information, while pixel aggregation of nonuniform, shallow areas with ice phenomena caused changes and the loss of original information. During the aggregation of the original pixel resolution (15 cm) up to 30 m, the smallest error occurred
in the area with a homogeneous water surface, while the greatest error (over 100%) was identified in the places where the water was strongly cloudy or there were ice phenomena
The LysR-Type Transcriptional Regulator BsrA (PA2121) Controls Vital Metabolic Pathways in Pseudomonas aeruginosa
Get PDFPseudomonas aeruginosa, a facultative human pathogen causing nosocomial
infections, has complex regulatory systems involving many transcriptional
regulators. LTTR (LysR-Type Transcriptional Regulator) family proteins are involved in
the regulation of various processes, including stress responses, motility, virulence,
and amino acid metabolism. The aim of this study was to characterize the LysR-type
protein BsrA (PA2121), previously described as a negative regulator of biofilm formation
in P. aeruginosa. Genome wide identification of BsrA binding sites using chromatin
immunoprecipitation and sequencing analysis revealed 765 BsrA-bound regions
in the P. aeruginosa PAO1161 genome, including 367 sites in intergenic regions. The
motif T-N11-A was identified within sequences bound by BsrA. Transcriptomic analysis
showed altered expression of 157 genes in response to BsrA excess; of these, 35
had a BsrA binding site within their promoter regions, suggesting a direct influence
of BsrA on the transcription of these genes. BsrA-repressed loci included genes
encoding proteins engaged in key metabolic pathways such as the tricarboxylic acid
cycle. The panel of loci possibly directly activated by BsrA included genes involved
in pilus/fimbria assembly, as well as secretion and transport systems. In addition,
DNA pull-down and regulatory analyses showed the involvement of PA2551,
PA3398, and PA5189 in regulation of bsrA expression, indicating that this gene is
part of an intricate regulatory network. Taken together, these findings reveal the existence
of a BsrA regulon, which performs important functions in P. aeruginosa
Insight into the Binding and Hydrolytic Preferences of hNudt16 Based on Nucleotide Diphosphate Substrates
Get PDFNudt16 is a member of the NUDIX family of hydrolases that show specificity towards substrates consisting of a
ucleoside diphosphate linked to another moiety X. Several substrates for hNudt16 and various possible biological functions have been reported. However, some of these
reports contradict each other and studies comparing the substrate specificity of the hNudt16 protein are limited. Therefore, we quantitatively compared the affinity of hNudt16 towards a set of previously published substrates, as well as identified novel potential substrates. Here, we show that
hNudt16 has the highest affinity towards IDP and GppG, with Kd below 100 nM. Other tested ligands exhibited a weaker affinity of several orders of magnitude. Among the investigated compounds, only IDP, GppG, m7GppG, AppA, dpCoA, and NADH were hydrolyzed by hNudt16 with
a strong substrate preference for inosine or guanosine containing compounds. A new identified substrate for hNudt16, GppG, which binds the enzyme with an affinity comparable to that of IDP, suggests another potential regulatory role of this protein. Molecular docking of hNudt16-ligand binding inside the hNudt16 pocket revealed two binding modes for representative substrates. Nucleobase stabilization by Π stacking interactions with His24 has been associated with strong binding of hNudt16 substrates
Halogen Atoms in the Protein–Ligand System. Structural and Thermodynamic Studies of the Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2
Get PDFAdditional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants
Get PDFThe change in the formal charge of 34 SARS-CoV-2 lineages from September 2020 to June 2021 was analyzed according to the monthly evidence of the European agency. The reported point mutations and small insertions are electrically neutral (17), positive (12), or negative (3). They had been found in the spike glycoprotein S, in the RBD and S1/S2 regions, crucial for initiation of viral infection. The most often observed were positive mutations, especially D614G and E484K, located in the region of S1/S2 junction, and in the receptor-binding domain (RBD), respectively. They are related to G and A switching. Positive mutations are stretching equally in both areas, but in the RBD region, they are more dispersed. In the set of analyzed virus variants, the increasing tendency in the number of positively charged residues in spike protein was observed. Furthermore, the well-documented WHO classes show an increase in the COVID-19 percentage case fatality with the positive increase in the spike crucial region’s total charge. The data mining, applying classifier algorithm based on the artificial neuronal network, confirms that the value and the distribution of additional positive charge in S may be important factors enabling virus impact to immunity. This may be promoted by the stronger long-range electrostatic attraction of the virus particle to the host cell, preceding the infection. The estimation of the potential energy for the RBD approaching the angiotensin-converting enzyme (ACE2) was presented
Diketopiperazine-Based, Flexible Tadalafil Analogues: Synthesis, Crystal Structures and Biological Activity Profile
Get PDFPhosphodiesterase 5 (PDE5) is one of the most extensively studied phosphodiesterases
that is highly specific for cyclic-GMP hydrolysis. PDE5 became a target for drug development based
on its efficacy for treatment of erectile dysfunction. In the present study, we synthesized four novel
analogues of the phosphodiesterase type 5 (PDE5) inhibitor—tadalafil, which differs in (i) ligand
flexibility (rigid structure of tadalafil vs. conformational flexibility of newly synthesized
compounds), (ii) stereochemistry associated with applied amino acid building blocks, and (iii)
substitution with bromine atom in the piperonyl moiety. For both the intermediate and final
compounds as well as for the parent molecule, we have established the crystal structures and
performed a detailed analysis of their structural features. The initial screening of the cytotoxic effect
on 16 different human cancer and non-cancer derived cell lines revealed that in most cases, the
parent compound exhibited a stronger cytotoxic effect than new derivatives, except for two cell
lines: HEK 293T (derived from a normal embryonic kidney, that expresses a mutant version of SV40
large T antigen) and MCF7 (breast adenocarcinoma). Two independent studies on the inhibition of
PDE5 activity, based on both pure enzyme assay and modulation of the release of nitric oxide from
platelets under the influence of tadalafil and its analogues revealed that, unlike a reference
compound that showed strong PDE5 inhibitory activity, the newly obtained compounds did not
have a noticeable effect on PDE5 activity in the range of concentrations tested. Finally, we
performed an investigation of the toxicological effect of synthesized compounds on Caenorhabditis
elegans in the highest applied concentration of 6a,b and 7a,b (160 μM) and did not find any effect
that would suggest disturbance to the life cycle of Caenorhabditis elegans. The lack of toxicity
observed in Caenorhabditis elegans and enhanced, strengthened selectivity and activity toward the
MCF7 cell line made 7a,b good leading structures for further structure activity optimization and
makes 7a,b a reasonable starting point for the search of new, selective cytotoxic agents
Mutations in GDAP1 Influence Structure and Function of the Trans-Golgi Network
Get PDFCharcot-Marie-Tooth disease (CMT) is a heritable neurodegenerative disease that displays great genetic heterogeneity. The genes and mutations that underlie this heterogeneity have been extensively characterized by molecular genetics. However, the molecular pathogenesis of the vast majority of CMT subtypes remains terra incognita. Any attempts to perform experimental therapy for CMT disease are limited by a lack of understanding of the pathogenesis at a molecular level. In this study, we aim to identify the molecular pathways that are disturbed by mutations in the
gene encoding GDAP1 using both yeast and human cell, based models of CMT-GDAP1 disease. We found that some mutations in GDAP1 led to a reduced expression of the GDAP1 protein and resulted in a selective disruption of the Golgi apparatus. These structural alterations are accompanied by functional disturbances within the Golgi. We screened over 1500 drugs that are available on the market using our yeast-based CMT-GDAP1 model. Drugs were identified that had both positive and negative effects on cell phenotypes. To the best of our knowledge, this study is the first report of the Golgi apparatus playing a role in the pathology of CMT disorders. The drugs we identified, using our yeast-based CMT-GDAP1 model, may be further used in translational research
Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina
Get PDFMucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component