SUMO Paralog Specific Functions Revealed through Systematic Analysis of Human Knockout Cell Lines and Gene Expression Data

The small ubiquitin-related modifiers (SUMOs) regulate nearly every aspect of cellular function, from gene expression in the nucleus to ion transport at the plasma membrane. In humans, the SUMO pathway has five SUMO paralogs with sequence homologies that range from 45% to 97%. SUMO1 and SUMO2 are the most distantly related paralogs, and also the best studied. To what extent SUMO1, SUMO2 and the other paralogs impart unique and non-redundant effects on cellular functions, however, has not been systematically examined and is therefore not fully understood. For instance, knockout studies in mice have revealed conflicting requirements for the paralogs during development and studies in cell culture have relied largely on transient paralog overexpression or knockdown. To address the existing gap in understanding, we first analyzed SUMO paralog gene expression levels in normal human tissues and found unique patterns of SUMO1-3 expression across 30 tissue types, suggesting paralog-specific functions in adult human tissues. To systematically identify and characterize unique and non-redundant functions of the SUMO paralogs in human cells, we next used CRISPR-Cas9 to knock out SUMO1 and SUMO2 expression in osteosarcoma (U2OS) cells. Analysis of these knockout cell lines revealed essential functions for SUMO1 and SUMO2 in regulating cellular morphology, PML nuclear body structure, responses to proteotoxic and genotoxic stress, and control of gene expression. Collectively, our findings reveal non-redundant regulatory roles for SUMO1 and SUMO2 in controlling essential cellular processes and provide a basis for more precise SUMO-targeting therapies.

Elucidating the Functions of Non-Coding RNAs from the Perspective of RNA Modifications

It is now commonly accepted that most of the mammalian genome is transcribed as RNA, yet less than 2% of such RNA encode for proteins. A majority of transcribed RNA exists as non-protein-coding RNAs (ncRNAs) with various functions. Because of the lack of sequence homologies among most ncRNAs species, it is difficult to infer the potential functions of ncRNAs by examining sequence patterns, such as catalytic domains, as in the case of proteins. Added to the existing complexity of predicting the functions of the ever-growing number of ncRNAs, increasing evidence suggests that various enzymes modify ncRNAs (e.g., ADARs, METTL3, and METTL14), which has opened up a new field of study called epitranscriptomics. Here, we examine the current status of ncRNA research from the perspective of epitranscriptomics.

Ssu72 Dual-Specific Protein Phosphatase: From Gene to Diseases

More than 70% of eukaryotic proteins are regulated by phosphorylation. However, the mechanism of dephosphorylation that counteracts phosphorylation is less studied. Phosphatases are classified into 104 distinct groups based on substrate-specific features and the sequence homologies in their catalytic domains. Among them, dual-specificity phosphatases (DUSPs) that dephosphorylate both phosphoserine/threonine and phosphotyrosine are important for cellular homeostasis. Ssu72 is a newly studied phosphatase with dual specificity that can dephosphorylate both phosphoserine/threonine and phosphotyrosine. It is important for cell-growth signaling, metabolism, and immune activation. Ssu72 was initially identified as a phosphatase for the Ser5 and Ser7 residues of the C-terminal domain of RNA polymerase II. It prefers the cis configuration of the serine–proline motif within its substrate and regulates Pin1, different from other phosphatases. It has recently been reported that Ssu72 can regulate sister chromatid cohesion and the separation of duplicated chromosomes during the cell cycle. Furthermore, Ssu72 appears to be involved in the regulation of T cell receptor signaling, telomere regulation, and even hepatocyte homeostasis in response to a variety of stress and damage signals. In this review, we aim to summarize various functions of the Ssu72 phosphatase, their implications in diseases, and potential therapeutic indications.

Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2?

A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile (Ophiophagus hannah) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin (Manis javanica) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic.

Impact of Dose and Route of administration on Antibody Responses of Chickens Inoculated with inactivated Avian Influenza H5 Vaccine.

Avian influenza viruses (AIV) poses significant threats to human and animal lives globally, and in spite of availability of vaccines, only few studies have established the role of passively acquired antibodies in the protection of chickens in sub Saharan Africa. The present study evaluated the influence of dose and route of administration of AI H5 inactivated vaccine on the humoral immune response of ISA brown chickens. Ninety “one-day-old” chickens were purchased from three major commercial hatcheries A, B and C (n = 30 chicks per hatchery), respectively. Results showed significant differences (P < 0.001) in the mean antibody titre levels at day 21 of age between chicks from hatcheries C (2,205.0 ± 409.1) and A (57.7 ± 49.9) at 21 days of age when either 0.2 ml or 0.5 ml of the vaccine was administered IM or SC. In addition, there were intra- and inter dose significant differences (P < 0.001) between the chicks at 21, 28, 35 and 42 days of age. Furthermore, intra- and inter route significant differences (P < 0.001) were detected between the chicks at 21 and 35 days of age. Overall, the AI H5 vaccine studied had variable outcomes and poorly immunogenic. Further studies should be conducted to characterize the T- and B-lymphocytes in chickens post AI H5 vaccines administration, and evaluate the sequence homologies between imported AI H5 vaccines and circulating AIV strains in Nigeria.

Simultaneous Suppression of Two Distinct Serotonin N-Acetyltransferase Isogenes by RNA Interference Leads to Severe Decreases in Melatonin and Accelerated Seed Deterioration in Rice

Serotonin N-acetyltransferase (SNAT) is the penultimate enzyme in the melatonin biosynthetic pathway, in which serotonin is converted into N-acetylserotonin (NAS) in plants. To date, two SNAT isogenes with low amino acid sequence homologies have been identified. Their single suppression in rice has been reported, but their double suppression in rice has not yet been attempted. Here, we generated double-suppression transgenic rice (snat1+2) using the RNA interference technique. The snat1+2 exhibited retarded seedling growths in conjunction with severe decreases in melatonin compared to wild-types and single-suppression rice plants (snat1 or snat2). The laminar angle was decreased in the snat1+2 rice compared to that of the wild-types and snat1, but was comparable to that of snat2. The reduced germination speed in the snat1+2 was comparable to that of snat2. Seed-aging testing revealed that snat1 was the most severely deteriorated, followed by snat1+2 and snat2, suggesting that melatonin is positively involved in seed longevity.

Plant Aquaporins

This mini-review briefly presents the main types of plant aquaporins, highlighting their importance for different plant species and for plant cellular functions. Aquaporins (AQPs), families of water channel proteins (WCPs) are transmembrane proteins that are present in prokaryotes, animals, plants, and humans. The plant aquaporins are part of the Major Intrinsic Proteins (MIPs) family which resides in the following plant organs: roots, stems, leaves, flowers, fruits, and seeds. According to the sub-cellular localization, to their sequence homologies and to their phylogenetic distribution, plant aquaporins have been divided in five subgroups: (a) plasma membrane intrinsic proteins (PIPs); (b) tonoplast intrinsic proteins (TIPs); (c) Nodulin26-like intrinsic membrane proteins (NIPs); (d) small basic intrinsic proteins (SIPs) and (e) uncharacterized intrinsic proteins (XIPs). Different subclasses of the plant aquaporins allow several types of transport using: water, glycerol, urea, hydrogen peroxide, organic acids, ethanol, methanol, arsenite, lactic acid, and gaseous compounds. Plant aquaporins have a significant role in cell response to cold stress, photosynthesis, plant growth, cell elongation, reproduction, and seed germination.

R3D Prediction Model: Remote Homology Prediction using Protein Contact Map with Dimensionality Reduction

Bioinformatics is one of a developing field that utilizations evaluation to extort information from Biological Data. Bioinformatics approaches are regularly utilized for significant activities that create expansive informational collections. Two basic tremendous scale practices that use bioinformatics are genomics and proteomics. Proteins are the far reaching, complex atoms that are essential for normal working of cells. 20% of the human body is involved proteins. Proteins are involved smaller units called amino acids, which are building squares of proteins. Protein remote homology identification and recognition are focal issues in bioinformatics. Sequence homologies are a vital source of data about proteins. In this research, the framework propose different strategy that diminishes the high dimensionality of the vector representation in remote homology detection by utilizing models that are characterized at the 3D level and consequently are very structurally and practically related. Subsequently, the 3D models are mapped from the protein primary sequence. The framework proposes to address the issue of remote homology identification by reducing 3D structure models. The new technique, called remote homology identification by the Reduction of 3D models (remote-R3D), is introduced and tested on various protein families.

RAD51 promotes non-homologous genetic rearrangements that are prevented by 53BP1

Homologous recombination (HR), which requires long sequence homologies, is considered a high fidelity mechanism, preserving genome stability. In contrast, we show here that the central HR players RAD51 or BRCA2, promote genetic instability, fostering translocations and capture of ectopic chromosomal sequences when joining distant DNA breaks. Surprisingly, these events do not involve sequence homologies. Moreover, our data reveal that 53BP1 protects against RAD51-mediated non-homologous genetic rearrangements. Finally, analysis of a large panel of breast tumors revealed that BRCA2 proficiency is associated with increased frequency of capture of non-homologous sequences at junctions of structural variants (translocations, duplications, inversions, deletions). These data reveal that HR proteins (RAD51, BRCA2) possess the intrinsic capacity to generate genetic instability through sequence homology-independent processes, and that 53BP1 protects against it. We propose that BRCA2/RAD51-mediated genome instability occurs in the course of sequence homology search for HR.