Programmed cell death in bacteria: translational repression by mRNA end-pairing

The hok / sok and pnd systems of plasmids R1 and R483 mediate plasmid maintenance by killing plasmid-free cells. Translation of the exceptionally stable hok and pnd mRNAs is repressed by unstable antisense RNAs. The different stabilities of the killer mRNAs and their cognate repressors explain the onset of translation in plasmid-free cells. The full-length hok and pnd mRNAs are inert with respect to translation and antisense RNA binding. We have previously shown that the mRNAs contain two negative translational control elements. Thus, the mRNAs contain upstream anti-Shine–Dalgarno elements that repress translation by shielding the Shine–Dalgarno ele-ments. The mRNAs also contain fold-back-inhibition elements ( fbi  ) at their 3' ends that are required to maintain the inert mRNA configuration. Using genetic complementation, we show that the 3' fbi elements pair with the very 5' ends of the mRNAs. This pairing sets the low rate of 3' exonucleolytical processing, which is required for the accumulation of an activatable pool of mRNA. Unexpectedly, the hok and pnd mRNAs were found to contain translational activators at their 5' ends (termed tac  ). Thus, the fbi elements inhibit translation of the full-length mRNAs by sequestration of the tac elements. The fbi elements are removed by 3' exonucleolytical processing. Mutational ana-lyses indicate that the 3' processing triggers refolding of the mRNA 5' ends into translatable configurations in which the 5' tac elements base pair with the anti-Shine–Dalgarno sequences.     

Phosphatidic acid phosphatase 1 impairs SARS-CoV-2 replication by affecting the glycerophospholipid metabolism pathway

Viruses exploit the host lipid metabolism machinery to achieve efficient replication. We herein characterize the lipids profile reprogramming in vitro and in vivo using liquid chromatography-mass spectrometry-based untargeted lipidomics. The lipidome of SARS-CoV-2-infected Caco-2 cells was markedly different from that of mock-infected samples, with most of the changes involving downregulation of ceramides. In COVID-19 patients'' plasma samples, a total of 54 lipids belonging to 12 lipid classes that were significantly perturbed compared to non-infected control subjects'' plasma samples were identified. Among these 12 lipid classes, ether-linked phosphatidylcholines, ether-linked phosphatidylethanolamines, phosphatidylcholines, and ceramides were the four most perturbed. Pathway analysis revealed that the glycerophospholipid, sphingolipid, and ether lipid metabolisms pathway were the most significantly perturbed host pathways. Phosphatidic acid phosphatases (PAP) were involved in all three pathways and PAP-1 deficiency significantly suppressed SARS-CoV-2 replication. siRNA knockdown of LPIN2 and LPIN3 resulted in significant reduction of SARS-CoV-2 load. In summary, these findings characterized the host lipidomic changes upon SARS-CoV-2 infection and identified PAP-1 as a potential target for intervention for COVID-19.     

NTDB: Thermodynamic Database for Nucleic Acids,Version 2.0

The second release of Thermodynamic Database for Nucleic Acids, NTDB 2.0, includes more than 4600 entries (250% increase over release 1.0). It contains sequence types and details of several thermodynamic parameters (enthalpy, DeltaH; entropy, DeltaS; Gibbs free energy, DeltaG; melting temperature, T(m)), experimental models and methods for extracting thermodynamic parameters, buffer conditions as well as all relevant literature information. In addition, the database statistics and references related to NTDB are included. Information on normal and modified nucleobases and nucleosides are collected in a new section 'Nucleoside' whereby data collected thus far will be release in NTDB 2.0. The NTDB is freely available at http://ntdb.chem.cuhk.edu.hk.     

Holothuria triterpene glycosides: a comprehensive guide for their structure elucidation and critical appraisal of reported compounds

Phytochemistry Reviews - Sea cucumbers or holothurians are marine invertebrates, belonging to the phylum Echinodermata (kingdom Animalia). In Asia, they are commonly used as food, while they are...     

MCT-1 oncogene downregulates p53 and destabilizes genome structure in the response to DNA double-strand damage

Tumor suppressor p53 protein mediates checkpoint controls and the apoptotic program that are critical for maintaining genomic integrity and preventing tumorigenesis. Forced-induction of MCT-1 decreased p53 expression before and after genomic insults. While inhibiting protein synthesis, the levels of ubiquinated-p53 and the phospho-MDMA2 were significantly increased in ectopic MCT-1 cells. Abrogation of the proteosome degradation process attenuated p53 destabilization and p21 down-regulation by MCT-1. Concomitantly, MCT-1 overexpression enhanced the phosphorylation status of MAPK (ERK1/ERK2). While MCT-1 gene knockdown or MEK/ERK pathway inhibition dramatically reduced MAPK phosphorylation, the genotoxin-induced p53 and p21 production were noticeably elevated. Upon Etoposide treatment, ectopic MCT-1 cells relaxed S-phase and G2/M checkpoints followed by G1 phase progressing. Moreover, cells inducing with MCT-1 abridged accumulations of G2/M populations in the response to gamma-irradiation. The polyploidy (DNA content>4N) populations were increased in association with p53 loss in MCT-1 oncogenic cells. Alkaline comet assay validated that ectopic MCT-1 cells were less susceptibility to the genotoxicity. Furthermore, the allocation of nuclear MCT-1 induced by the genotoxic stress was moderately coincided with gamma-H2AX appearances. Throughout damage-repairing process, ectopic MCT-1 cells displayed many larger chromosomes and multiple chromosomal fusions compared to the controls that showed increase in chromosomal breaks/gaps and minute chromosomal fragments. Spectral karyotyping analysis precisely identified the acquisition of a single extra copy of chromosome 14 together with a complex genome organizations in ectopic MCT-1 cells, including extra copies of chromosome segments that had been translocated to derivative chromosomes 6 [der(6)] and 9 [der(9)]. In conclusion, MCT-1 deregulates p53-p21 network and impairs the damage checkpoints those are robustly connected to oncogenic chromosomal abnormalities.     

Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection

Hepatitis C virus (HCV) and human pegivirus (HPgV), formerly GBV-C, are the only known human viruses in the Hepacivirus and Pegivirus genera, respectively, of the family Flaviviridae. We present the discovery of a second pegivirus, provisionally designated human pegivirus 2 (HPgV-2), by next-generation sequencing of plasma from an HCV-infected patient with multiple bloodborne exposures who died from sepsis of unknown etiology. HPgV-2 is highly divergent, situated on a deep phylogenetic branch in a clade that includes rodent and bat pegiviruses, with which it shares <32% amino acid identity. Molecular and serological tools were developed and validated for high-throughput screening of plasma samples, and a panel of 3 independent serological markers strongly correlated antibody responses with viral RNA positivity (99.9% negative predictive value). Discovery of 11 additional RNA-positive samples from a total of 2440 screened (0.45%) revealed 93–94% nucleotide identity between HPgV-2 strains. All 12 HPgV-2 RNA-positive cases were identified in individuals also testing positive for HCV RNA (12 of 983; 1.22%), including 2 samples co-infected with HIV, but HPgV-2 RNA was not detected in non-HCV-infected individuals (p<0.0001), including those singly infected by HIV (p = 0.0075) or HBV (p = 0.0077), nor in volunteer blood donors (p = 0.0082). Nine of the 12 (75%) HPgV-2 RNA positive samples were reactive for antibodies to viral serologic markers, whereas only 28 of 2,429 (1.15%) HPgV-2 RNA negative samples were seropositive. Longitudinal sampling in two individuals revealed that active HPgV-2 infection can persist in blood for at least 7 weeks, despite the presence of virus-specific antibodies. One individual harboring both HPgV-2 and HCV RNA was found to be seronegative for both viruses, suggesting a high likelihood of simultaneous acquisition of HCV and HPgV-2 infection from an acute co-transmission event. Taken together, our results indicate that HPgV-2 is a novel bloodborne infectious virus of humans and likely transmitted via the parenteral route.     

FtsZ-ZapA-ZapB interactome of Escherichia coli

Bacterial cell division relies on the formation and contraction of the Z ring, coordinated and regulated by a dynamic protein complex called the divisome. The cell division factor ZapA interacts directly with FtsZ and thereby increases FtsZ protofilament association and Z-ring stability. Here, we investigated ZapB interaction with ZapA and its effect on Z-ring formation and FtsZ protofilament bundling. The combination of the ftsZ84 allele that encodes an FtsZ variant that polymerizes inefficiently with a zapB null mutant resulted in a synthetic defective phenotype. Overproduction of ZapA led to the formation of aberrant FtsZ helical structures and delocalization of ZapB. The N-terminal end of ZapB was essential for ZapB-ZapA interaction, and amino acid changes close to the N terminus of ZapB exhibited reduced interaction with ZapA. Sedimentation assays showed that ZapB interacts strongly with ZapA and reduces ZapA's interaction with FtsZ in vitro. The morphology of the structures formed by ZapA and ZapB together was similar to the cables formed by ZapB in the presence of CaCl(2), a known ZapB bundling agent. The in vivo and in vitro data support a model in which ZapA interacts strongly with ZapB and the ZapA-ZapB interaction is favored over ZapA-FtsZ.     

Visual perception of ambiguous figures: synchronization based neural models

We develop and study two neural network models of perceptual alternations. Both models have a star-like architecture of connections with a central element connected to a set of peripheral elements. A particular perception is simulated in terms of partial synchronization between the central element and some sub-group of peripheral elements. The first model is constructed from phase oscillators and the mechanism of perceptual alternations is based on chaotic intermittency under fixed parameter values. Similar to experimental evidence, the distribution of times between perceptual alternations is represented by the gamma distribution. The second model is built of spiking neurons of the Hodgkin–Huxley type. The mechanism of perceptual alternations is based on plasticity of inhibitory synapses which increases the inhibition from the central unit to the neural assembly representing the current percept. As a result another perception is formed. Simulations show that the second model is in good agreement with behavioural data on switching times between percepts of ambiguous figures and with experimental results on binocular rivalry of two and four percepts. This article is part of a special issue on Neuronal Dynamics of Sensory Coding. This special issue is in honour of Professor Pepe Segundo who is one of the pioneers in the study of neural coding. Pepe has been an active participant in many Neural Coding Workshops sharing his great knowledge and experience of research in this field. I (R. Borisyuk) was very happy to meet Pepe for the first time in Prague when attending the first Neural Coding Workshop in 1995. From that time we regularly met at Neural Coding Workshops and these meetings have always been very stimulating and fruitful for my research. Remarkably, the first paper I studied at the beginning of my scientific career was a seminal paper by Moore et al. (1970). For me, this paper provided a great opportunity to learn the basic statistical techniques for the analysis of multiple spike trains and neural coding. According to the Institute of Scientific Information, this paper has been cited 380 times! This exciting paper has inspired my research into the synaptic and functional connectivity of neural circuits derived from spike-train recordings (Borisyuk et al. 1985; Stuart et al. 2005) and guided my search for new ideas on neural coding.