Fluorescent proteins that are fused to nuclear localization signals (NLSs) or nucleolar localization signals (NoLSs) are commonly used to investigate the accumulation of proteins within the nucleus and nucleolus. These reporters allow for the in vivo evaluation of signal sequence function, independent of the surrounding protein context. Here, we present a standardized protocol for measuring nuclear and nucleolar accumulation using NLS- and NoLS-fusion reporters. The workflow integrates plasmid construction, transfection, expression control, imaging and computational analysis to minimize artifacts and enhance reproducibility. This framework provides a robust basis for the reliable quantification of NLS- and NoLS-mediated localization and allows for the comparison of nuclear transport mechanisms across studies.

A coordinated and generalized plant response to adverse environmental factors largely depends on the proper and finely-tuned regulation of intercellular transport via plasmodesmata (PD). However, the knowledge of the whole network of PD-controlling mechanisms is far from complete. Earlier, a cellular factor, Kunitz peptidase inhibitor-like protein (KPILP), that affects PD gating and plays a proviral role, was identified in Nicotiana benthamiana plants. Here we characterized its homolog from N. tabacum, NtKPILP, which is hardly detectable in leaves of intact plants, in contrast to roots, flowers and seeds where NtKPILP is highly expressed. However, its mRNA accumulation in leaves increases in response to various stresses, including viral infection. NtKPILP was demonstrated to affect chloroplast functioning. Using the virus-induced gene silencing approach, we have shown that NtKPILP downregulation negatively affects intercellular transport of macromolecules, inducing callose deposition at PD and suppressing beta-1,3-glucanase mRNA accumulation. Together, the obtained results indicate that NtKPILP is a viral infection-responsive cellular factor that is involved in PD permeability regulation, sharing thus the features of KPILPs from other Nicotiana species.

Lung inflammation, pneumonia, is an acute respiratory disease of varying etiology that has recently drawn much attention during the COVID-19 pandemic as lungs are among the main targets for SARS-CoV-2. Multiple other etiological agents are associated with pneumonias. Here, we describe a newly-recognized pathology, namely abnormal lipid depositions in the lungs of patients who died from COVID-19 as well as from non-COVID-19 pneumonias. Our analysis of both semi-thin and Sudan III-stained lung specimens revealed extracellular and intracellular lipid depositions irrespective of the pneumonia etiology. Most notably, lipid depositions were located within vessels adjacent to inflamed regions, where they apparently interfere with the blood flow. Structurally, the lipid droplets in the inflamed lung tissue were homogeneous and lacked outer membranes as assessed by electron microscopy. Morphometric analysis of lipid droplet deposition area allowed us to distinguish the non-pneumonia control lung specimens from the macroscopically intact area of the pneumonia lung and from the inflamed area of the pneumonia lung. Our measurements revealed a gradient of lipid deposition towards the inflamed region. The pattern of lipid distribution proved universal for all pneumonias. Finally, lipid metabolism in the lung tissue was assessed by the fatty acid analysis and by expression of genes involved in lipid turnover. Chromato-mass spectrometry revealed that unsaturated fatty acid content was elevated at inflammation sites compared to that in control non-inflamed lung tissue from the same individual. The expression of genes involved in lipid metabolism was altered in pneumonia, as shown by qPCR and in silico RNA-seq analysis. Thus, pneumonias of various etiologies are associated with specific lipid abnormalities; therefore, lipid metabolism can be considered to be a target for new therapeutic strategies.

To date, seven human coronaviruses (HCoVs) have been identified. Four of these viruses typically manifest as a mild respiratory disease, whereas the remaining three can cause severe conditions that often result in death. The reasons for these differences remain poorly understood, but they may be related to the properties of individual viral proteins. The nucleocapsid (N) protein plays a crucial role in the packaging of viral genomic RNA and the modification of host cells during infection, in part due to its capacity to form dynamic biological condensates via liquid-liquid phase separation (LLPS). In this study, we investigated the capacity of N proteins derived from all HCoVs to form condensates when transiently expressed in cultured human cells. Some of the transfected cells were observed to contain cytoplasmic granules in which most of the N proteins were accumulated. Notably, the N proteins of SARS-CoV and SARS-CoV-2 showed a significantly reduced tendency to form cytoplasmic condensates. The condensate formation was not a consequence of overexpression of N proteins, as is typical for LLPS-inducing proteins. These condensates contained components of stress granules (SGs), indicating that the expression of N proteins caused the formation of SGs, which integrate N proteins. Thus, the N proteins of two closely related viruses, SARS-CoV and SARS-CoV-2, have the capacity to antagonize SG induction and/or assembly, in contrast to all other known HCoVs.

The troponin complex—consisting of three subunits: troponin C (TnC), cardiac troponin I (cTnI) and cardiac troponin T (cTnT)—plays a key role in the regulation of myocardial contraction. Troponins are preferentially localized in the cytoplasm and bind to myofibrils. However, numerous, albeit scattered, studies have shown the presence of troponins in the nuclei of muscle cells. There is increasing evidence that the nuclear localization of troponins may be functionally important, making troponins an important nuclear player in the pathogenesis of various diseases including cancer and myopathies. Further studies in this area could potentially lead to the development of treatments for certain pathologies. In this review, we collected and discussed recent data on the properties of non-canonically localized cardiac troponins, the molecular mechanisms leading to this non-canonical localization, and the possible functions or pathological effects of these non-canonically localized troponins.

Among flowering plants, genome size varies remarkably, by >2200-fold, and this variation depends on the loss and gain of noncoding DNA sequences that form distinct heterochromatin complexes during interphase. In plants with giant genomes, most chromatin remains condensed during interphase, forming a dense network of heterochromatin threads called interphase chromonemata. Using super-resolution light and electron microscopy, we studied the ultrastructure of chromonemata during and after replication in root meristem nuclei of Nigella damascena L. During S-phase, heterochromatin undergoes transient decondensation locally at DNA replication sites. Due to the abundance of heterochromatin, the replication leads to a robust disassembly of the chromonema meshwork and a general reorganization of the nuclear morphology visible even by conventional light microscopy. After replication, heterochromatin recondenses, restoring the chromonema structure. Thus, we show that heterochromatin replication in interphase nuclei of giant-genome plants induces a global nuclear reorganization.

AbstractAmong land plants, genome sizes vary remarkably by > 2,200-fold. This variation depends on the loss and gain of non-coding DNA sequences, forming different heterochromatin complexes during interphase. In plants with a giant genome, the major part of chromatin stays condensed in interphase, forming a dense meshwork of heterochromatin threads, called interphase chromonemata. Using super-resolution light and electron microscopy, we studied the ultrastructure of chromonemata during and after replication in root meristem nuclei ofNigella damascenaL. During S-phase, heterochromatin undergoes transient decompaction locally at the active sites of DNA synthesis, and due to the heterochromatin abundance, chromonema replication is accompanied by a robust chromonema meshwork disassembly, which led to the general reorganization of the nucleus morphology visible even by conventional light microscopy. After replication, the heterochromatin condenses again, restoring the chromonema structure. Thus, we showed that heterochromatin replication in interphase nuclei of giant-genome plants induces a global chromonema decondensation and reorganization.

Reversibly glycosylated polypeptides (RGPs) have been identified in many plant species and play an important role in cell wall formation, intercellular transport regulation, and plant–virus interactions. Most plants have several RGP genes with different expression patterns depending on the organ and developmental stage. Here, we report on four members of the RGP family in N. benthamiana. Based on a homology search, NbRGP1-3 and NbRGP5 were assigned to the class 1 and class 2 RGPs, respectively. We demonstrated that NbRGP1–3 and 5 mRNA accumulation increases significantly in response to tobacco mosaic virus (TMV) infection. Moreover, all identified class 1 NbRGPs (as distinct from NbRGP5) suppress TMV intercellular transport and replication in N. benthamiana. Elevated expression of NbRGP1–2 led to the stimulation of callose deposition at plasmodesmata, indicating that RGP-mediated TMV local spread could be affected via a callose-dependent mechanism. It was also demonstrated that NbRGP1 interacts with TMV movement protein (MP) in vitro and in vivo. Therefore, class 1 NbRGP1–2 play an antiviral role by impeding intercellular transport of the virus by affecting plasmodesmata callose and directly interacting with TMV MP, resulting in the reduced viral spread and replication.

An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells. Development of B-cell lymphomas may be potentially due to the action of the HIV-1 Tat protein, which is actively released from HIV-1-infected cells, on uninfected B cells. The exact mechanism of Tat-induced B-cell lymphomagenesis has not yet been precisely identified. Here, we ectopically expressed either Tat or its TatC22G mutant devoid of transactivation activity in the RPMI 8866 lymphoblastoid B cell line and performed a genome-wide analysis of host gene expression. Stable expression of both Tat and TatC22G led to substantial modifications of the host transcriptome, including pronounced changes in antiviral response and cell cycle pathways. We did not find any strong action of Tat on cell proliferation, but during prolonged culturing, Tat-expressing cells were displaced by non-expressing cells, indicating that Tat expression slightly inhibited cell growth. We also found an increased frequency of chromosome aberrations in cells expressing Tat. Thus, Tat can modify gene expression in cultured B cells, leading to subtle modifications in cellular growth and chromosome instability, which could promote lymphomagenesis over time.

Margarita A. Kurnaeva, Arthur O. Zalevsky, Eugene A. Arifulin , Olga M. Lisitsyna, Anna V. Tvorogova, Maria Y. Shubina, Gleb P. Bourenkov, Yana R. Musinova, Andrey V. Golovin, Yegor S. Vassetzky, Eugene V. Sheval* Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia European Molecular Biology Laboratory, Hamburg, Germany Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia

During evolution, viruses had to adapt to an increasingly complex environment of eukaryotic cells. Viral proteins that need to enter the cell nucleus or associate with nucleoli possess nuclear localization signals (NLSs) and nucleolar localization signals (NoLSs) for nuclear and nucleolar accumulation, respectively. As viral proteins are relatively small, acquisition of novel sequences seems to be a more complicated task for viruses than for eukaryotes. Here, we carried out a comprehensive analysis of the basic domain (BD) of HIV-1 Tat to show how viral proteins might evolve with NLSs and NoLSs without an increase in protein size. The HIV-1 Tat BD is involved in several functions, the most important being the transactivation of viral transcription. The BD also functions as an NLS, although it is substantially longer than a typical NLS. It seems that different regions in the BD could function as NLSs due to its enrichment with positively charged amino acids. Additionally, the high positive net charge inevitably causes the BD to function as an NoLS through a charge-specific mechanism. The integration of NLSs and NoLSs into functional domains enriched with positively charged amino acids might be a mechanism that allows the condensation of different functional sequences in small protein regions and, as a result, reduces protein size, influencing the origin and evolution of NLSs and NoLSs in viruses. IMPORTANCE Here, we investigated the molecular mechanism of nuclear localization signal (NLS) and nucleolar localization signal (NoLS) integration into the basic domain of HIV-1 Tat (49RKKRRQRRR57) and found that these two supplementary functions (i.e., function of NLS and function of NoLS) are embedded in the basic domain amino acid sequence. The integration of NLSs and NoLSs into functional domains of viral proteins enriched with positively charged amino acids is a mechanism that allows the concentration of different functions within small protein regions. Integration of NLS and NoLS into functional protein domains might have influenced the viral evolution, as this could prevent an increase in the protein size.

The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, is one of the most important events in the evolution of eukaryotic cells. How proteins were selected for import into the forming nucleus remains an open question. Here, we demonstrate that functional NLSs may be integrated in the nucleotide-binding domains of both eukaryotic and prokaryotic proteins and may coevolve with these domains. The presence of sequences similar to NLSs in the DNA-binding domains of prokaryotic proteins might have created an advantage for nuclear accumulation of these proteins during evolution of the nuclear-cytoplasmic barrier, influencing which proteins accumulated and became compartmentalized inside the forming nucleus (i.e., the content of the nuclear proteome). This article was reviewed by Sergey Melnikov and Igor Rogozin. Reviewed by Sergey Melnikov and Igor Rogozin. For the full reviews, please go to the Reviewers’ comments section.

Ocular inflammation contributes to the pathogenesis of blind-causing retinal degenerative diseases, such as age-related macular degeneration (AMD) or photic maculopathy. Here, we report on inflammatory mechanisms that are associated with retinal degeneration induced by bright visible light, which were revealed while using a rabbit model. Histologically and electrophysiologically noticeable degeneration of the retina is preceded and accompanied by oxidative stress and inflammation, as evidenced by granulocyte infiltration and edema in this tissue, as well as the upregulation of total protein, pro-inflammatory cytokines, and oxidative stress markers in aqueous humor (AH). Consistently, quantitative lipidomic studies of AH elucidated increase in the concentration of arachidonic (AA) and docosahexaenoic (DHA) acids and lyso-platelet activating factor (lyso-PAF), together with pronounced oxidative and inflammatory alterations in content of lipid mediators oxylipins. These alterations include long-term elevation of prostaglandins, which are synthesized from AA via cyclooxygenase-dependent pathways, as well as a short burst of linoleic acid derivatives that can be produced by both enzymatic and non-enzymatic free radical-dependent mechanisms. The upregulation of all oxylipins is inhibited by the premedication of the eyes while using mitochondria-targeted antioxidant SkQ1, whereas the accumulation of prostaglandins and lyso-PAF can be specifically suppressed by topical treatment with cyclooxygenase inhibitor Nepafenac. Interestingly, the most prominent antioxidant and anti-inflammatory benefits and overall retinal protective effects are achieved by simultaneous administrating of both drugs indicating their synergistic action. Taken together, these findings provide a rationale for using a combination of mitochondria-targeted antioxidant and cyclooxygenase inhibitor for the treatment of inflammatory components of retinal degenerative diseases.

The cell nucleus contains different domains and nuclear bodies, whose position relative to each other inside the nucleus can vary depending on the physiological state of the cell. Changes in the three-dimensional organization are associated with the mobility of individual components of the nucleus. In this chapter, we present a protocol for live-cell imaging and analysis of nuclear body mobility. Unlike other similar protocols, our image analysis pipeline includes non-rigid compensation for global motion of the nucleus before particle tracking and trajectory analysis, leading to precise detection of intranuclear movements. The protocol described can be easily adapted to work with most cell lines and nuclear bodies.

Fibrillarin (FBL) is an essential nucleolar protein that participates in pre-rRNA methylation and processing. The methyltransferase domain of FBL is an example of an extremely well-conserved protein domain in which the amino acid sequence was not substantially modified during the evolution from Archaea to Eukaryota . An additional N-terminal glycine–arginine-rich (GAR) domain is present in the FBL of eukaryotes. Here, we demonstrate that the GAR domain is involved in FBL functioning and integrates the functions of the nuclear localization signal and the nucleolar localization signal (NoLS). The methylation of the arginine residues in the GAR domain is necessary for nuclear import but decreases the efficiency of nucleolar retention via the NoLS. The presented data indicate that the GAR domain can be considered an evolutionary innovation that integrates several functional activities and thereby adapts FBL to the highly compartmentalized content of the eukaryotic cell.

The study objective is to analyze the content of spermatozoa with single and double-stranded DNA breaks in different age groups. Materials and methods . The level of DNA fragmentation was studied in 300 ejaculate samples obtained from 266 sub- or infertile men. The group 1 included 150 samples obtained from 131 patients under the age of 45 (21–44 years), the group 2 included 150 samples obtained from 135 patients above the age of 45 (45–68 years). Mean ages were 34.8 ± 3.9 and 48.6 ± 3.1 years, respectively. The number of sperm with fragmented DNA was evaluated using the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) method on ejaculate smears. The number of spermatozoa with >15 % of fragmented DNA was considered elevated. Standard semen analysis was performed in 117 and 97 men from the groups 1 and 2, respectively. Results . The number of sperm with fragmented DNA varied in ejaculated samples from 1.5 to 64.5 %. Mean number of sperm with DNA breaks in the group 1 (12.0 ± 6.0 %) was significantly lower than in the group 2 (16.1 ± 8.3 %, p <0.05). Mean sperm count in the ejaculate of the group 1 (267.0 ± 198.7 million) was significantly higher than in the group 2 (201.0 ± 162.9 million, p = 0.02). Conclusion . We revealed that in men over the age of 45 years, the percentage of spermatozoa with DNA fragmentation is higher than in men under 45 years of age, it may indirectly indicate an increased level of reactive oxygen species in the seminal plasma in older patients.

The study objective is to analyze the content of spermatozoa with single and double-stranded DNA breaks in different age groups.Materials and methods. The level of DNA fragmentation was studied in 300 ejaculate samples obtained from 266 sub- or infertile men. The group 1 included 150 samples obtained from 131 patients under the age of 45 (21–44 years), the group 2 included 150 samples obtained from 135 patients above the age of 45 (45–68 years). Mean ages were 34.8 ± 3.9 and 48.6 ± 3.1 years, respectively. The number of sperm with fragmented DNA was evaluated using the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) method on ejaculate smears. The number of spermatozoa with >15 % of fragmented DNA was considered elevated. Standard semen analysis was performed in 117 and 97 men from the groups 1 and 2, respectively.Results. The number of sperm with fragmented DNA varied in ejaculated samples from 1.5 to 64.5 %. Mean number of sperm with DNA breaks in the group 1 (12.0 ± 6.0 %) was significantly lower than in the group 2 (16.1 ± 8.3 %, p <0.05). Mean sperm count in the ejaculate of the group 1 (267.0 ± 198.7 million) was significantly higher than in the group 2 (201.0 ± 162.9 million, p = 0.02).Conclusion. We revealed that in men over the age of 45 years, the percentage of spermatozoa with DNA fragmentation is higher than in men under 45 years of age, it may indirectly indicate an increased level of reactive oxygen species in the seminal plasma in older patients.

The nuclear accumulation of proteins may depend on the presence of short targeting sequences, which are known as nuclear localization signals (NLSs). Here, we found that NLSs are predicted in some cytosolic proteins and examined the hypothesis that these NLSs may be functional under certain conditions. As a model, human cardiac troponin I (hcTnI) was used. After expression in cultured non-muscle or undifferentiated muscle cells, hcTnI accumulated inside nuclei. Several NLSs were predicted and confirmed by site-directed mutagenesis in hcTnI. Nuclear import occurred via the classical karyopherin-α/β nuclear import pathway. However, hcTnI expressed in cultured myoblasts redistributed from the nucleus to the cytoplasm, where it was integrated into forming myofibrils after the induction of muscle differentiation. It appears that the dynamic retention of proteins inside cytoplasmic structures can lead to switching between nuclear and cytoplasmic localization.

Biopolymers and Cell� 2019� Vol� 35� N 3 the nucleus, near chromocenters� No signals were detected in cytoplasm� Pre-treatment with RNAase resulted in the disappearance of sig-nals� Conclusion� Thus, the transcription of pericentromeric satellite DNA observed in NSLC in mice occured mainly in CAF but not associated macrophages or malignant cells� Treatment with cytotoxic drugs induced appearance of CAF markers in fibroblasts .Thus, treatment with cytostatics does not induce death of CAF but promote fibroblasts transition into CAF�

Cell nucleus is characterized by strong compartmentalization of structural components in its three-dimensional space. Certain genomic functions are accompanied by changes in the localization of chromatin loci and nuclear bodies. Here we review recent data on the mobility of nuclear components and the role of this mobility in genome functioning.