STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/

Limitations of a Metabolic Network-Based Reverse Ecology Method for Inferring Host–Pathogen Interactions

Background Host–pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected. Results We re-evaluated the importance of the reverse ecology method for evaluating host–pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data. Our data analyses showed that host–pathogen interactions were more strongly influenced by genome size, primary network parameters (e.g., number of edges), oxygen requirement, and phylogeny than the reserve ecology-based measures. Conclusion These results indicate the limitations of the reverse ecology method; however, they do not discount the importance of adopting reverse ecology approaches altogether. Rather, we highlight the need for developing more suitable methods for inferring host–pathogen interactions and conducting more careful examinations of the relationships between metabolic networks and host–pathogen interactions

Features and Algorithms for Embedded Protein Sequence Classification with Class Imbalance

13301甲第5587号博士（学術）金沢大学博士論文本文Full 以下に掲載：Frontiers in Genetics 13(1) pp.Article No.885929-11p. 2022. Frontiers. 共著者：Fatma Indriani, Kunti Robiatul Mahmudah, Bedy Purnama, Kenji Sato

Comparative Genomics of Aeromonas hydrophila Secretion Systems and Mutational Analysis of hcp1 and vgrG1 Genes From T6SS

Virulent Aeromonas hydrophila causes severe motile Aeromonas septicemia in warmwater fishes. In recent years, channel catfish farming in the U.S.A. and carp farming in China have been affected by virulent A. hydrophila, and genome comparisons revealed that these virulent A. hydrophila strains belong to the same clonal group. Bacterial secretion systems are often important virulence factors; in the current study, we investigated whether secretion systems contribute to the virulent phenotype of these strains. Thus, we conducted comparative secretion system analysis using 55 A. hydrophila genomes, including virulent A. hydrophila strains from U.S.A. and China. Interestingly, tight adherence (TaD) system is consistently encoded in all the vAh strains. The majority of U.S.A. isolates do not possess a complete type VI secretion system, but three core elements [tssD (hcp), tssH, and tssI (vgrG)] are encoded. On the other hand, Chinese isolates have a complete type VI secretion system operon. None of the virulent A. hydrophila isolates have a type III secretion system. Deletion of two genes encoding type VI secretion system proteins (hcp1 and vgrG1) from virulent A. hydrophila isolate ML09-119 reduced virulence 2.24-fold in catfish fingerlings compared to the parent strain ML09-119. By determining the distribution of genes encoding secretion systems in A. hydrophila strains, our study clarifies which systems may contribute to core A. hydrophila functions and which may contribute to more specialized adaptations such as virulence. Our study also clarifies the role of type VI secretion system in A. hydrophila virulence

Proteome level analysis of drug-resistant Prevotella melaninogenica for the identification of novel therapeutic candidates

The management of infectious diseases has become more critical due to the development of novel pathogenic strains with enhanced resistance. Prevotella melaninogenica, a gram-negative bacterium, was found to be involved in various infections of the respiratory tract, aerodigestive tract, and gastrointestinal tract. The need to explore novel drug and vaccine targets against this pathogen was triggered by the emergence of antimicrobial resistance against reported antibiotics to combat P. melaninogenica infections. The study involves core genes acquired from 14 complete P. melaninogenica strain genome sequences, where promiscuous drug and vaccine candidates were explored by state-of-the-art subtractive proteomics and reverse vaccinology approaches. A stringent bioinformatics analysis enlisted 18 targets as novel, essential, and non-homologous to humans and having druggability potential. Moreover, the extracellular and outer membrane proteins were subjected to antigenicity, allergenicity, and physicochemical analysis for the identification of the candidate proteins to design multi-epitope vaccines. Two candidate proteins (ADK95685.1 and ADK97014.1) were selected as the best target for the designing of a vaccine construct. Lead B- and T-cell overlapped epitopes were joined to generate potential chimeric vaccine constructs in combination with adjuvants and linkers. Finally, a prioritized vaccine construct was found to have stable interactions with the human immune cell receptors as confirmed by molecular docking and MD simulation studies. The vaccine construct was found to have cloning and expression ability in the bacterial cloning system. Immune simulation ensured the elicitation of significant immune responses against the designed vaccine. In conclusion, our study reported novel drug and vaccine targets and designed a multi-epitope vaccine against the P. melaninogenica infection. Further experimental validation will help open new avenues in the treatment of this multi-drug-resistant pathogen

Using machine learning to predict protein-protein interactions between a zombie ant fungus and its carpenter ant host

Parasitic fungi produce proteins that modulate virulence, alter host physiology, and trigger host responses. These proteins, classified as a type of "effector," often act via protein-protein interactions (PPIs). The fungal parasite Ophiocordyceps camponoti-floridani (zombie ant fungus) manipulates Camponotus floridanus (carpenter ant) behavior to promote transmission. The most striking aspect of this behavioral change is a summit disease phenotype where infected hosts ascend and attach to an elevated position. Plausibly, interspecific PPIs drive aspects of Ophiocordyceps infection and host manipulation. Machine learning PPI predictions offer high-throughput methods to produce mechanistic hypotheses on how this behavioral manipulation occurs. Using D-SCRIPT to predict host-parasite PPIs, we found ca. 6000 interactions involving 2083 host proteins and 129 parasite proteins, which are encoded by genes upregulated during manipulated behavior. We identified multiple overrepresentations of functional annotations among these proteins. The strongest signals in the host highlighted neuromodulatory G-protein coupled receptors and oxidation-reduction processes. We also detected Camponotus structural and gene-regulatory proteins. In the parasite, we found enrichment of Ophiocordyceps proteases and frequent involvement of novel small secreted proteins with unknown functions. From these results, we provide new hypotheses on potential parasite effectors and host targets underlying zombie ant behavioral manipulation

Exploring The Interactions Between SARS-CoV-2 and Host Proteins.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current pandemic, Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is considered to be of zoonotic origin; it originated in non-human animals and was transmitted to humans. Since the early stage of the pandemic, however, the evidence of transmissions from humans to animals (reverse zoonoses) has been found in multiple animal species including mink, white-tailed deer, and pet and zoo animals. Furthermore, secondary zoonotic events of SARS-CoV-2, transmissions from animals to humans, have been also reported. It is suggested that non-human hosts can act as SARS-CoV-2 reservoirs where accumulated mutations in viral proteins could change the transmissibility and/or pathogenicity of the virus when it is spilled over again to human populations. Our goal, therefore, is to examine the SARS-CoV-2 genomic changes in non-human hosts and to identify the changes responsible for the adaptation of the virus in non-human hosts. Changes in the physicochemical properties of viral proteins potentially affect and influence their functions. Therefore, in this study, we compared SARS-CoV-2 proteins among human and non-human hosts and analyzed the differences in their physicochemical properties using the principal component analysis. In addition to the viral proteins from bat and pangolin, those from white-tailed deer and mink showed larger differences in the properties. Van der Waals volume, isoelectric point, charge, and thermostability index were found to be the main contributing factors. We next performed the comparisons of protein-protein interaction (PPI) prediction methods that use different features including physicochemical properties and those based on natural language processing. It showed that the Cross-attention PHV had slightly better performance scores than InterSPPI-HVPPI and LGCA-VHPPI. Finally, to examine the effect of changes in physicochemical properties in viral proteins against host proteins, PPI prediction was performed using the Cross-attention PHV between viral proteins from different SARS-CoV-2 variants and host proteins. The prediction scores between the different variants and host proteins from human and white-tailed deer were highly similar. The results showed that the analysis of physicochemical properties of viral proteins helps to understand how physicochemical properties of viral proteins affect viral-host PPIs and how viral proteins evolve to adapt different host cell environments

Abordagem à regulação da mobilidade do espermatozoide através da caracterização e modulação da vis de sinalização GSK/PPP1R2/PPP1

Doutoramento em BiologiaSperm motility acquisition and maintenance is a fundamental process for oocyte fertilization and consequently conception. The signaling events underling sperm motility acquisition have been studied for decades. However, many questions are still unanswered. Also, the limited options currently available for male contraception (condom, vasectomy and withdrawal) reflect the necessity of a new group of male contraceptives based on sperm motility modulation. GSK3/PPP1R2/PPP1 signaling pathway is involved in sperm motility acquisition during epididymis transit. The main goal for this work was to deepen the knowledge on the signaling events involved in human sperm motility by focusing on the characterization and modulation of the signaling pathway GSK3/PPP1R2/PPP1. We first designed, synthetized and characterized a disruptive bioportide based on cell penetrating peptide technology. In vitro studies revealed that the disruptive bioportide interferes with PPP1R2/PPP1CC2 interaction and restores PPP1CC2 activity. We also demonstrated that when exposed to the disruptive bioportide, sperm motility is significantly reduced. Aiming to identify sperm protein-protein interactions suitable for pharmacological intervention, we turn our attention to GSK3, a modulator of PPP1R2/PPP1CC2 interactions in sperm. We provide for the first time GSK3 human testis and sperm interactomes. We reported an isoforms specific role for GSK3 in human sperm motility and an in silico analysis revealed GSK3 and GSK3 interactions involved in sperm motility and potential targets for pharmacological intervention. In conclusion, we demonstrated that it is possible to target protein-protein interactions and modulate sperm complexes involved in motility using bioportides. Moreover, we identified new potential protein interactions involved in sperm motility and showed that the development of new type of male contraceptive based on inhibiting sperm motility is now achievable.A aquisição e manutenção da mobilidade do espermatozoide é fundamental para a fertilização do oócito e consequentemente conceção. Durante décadas, as vias de sinalização necessárias à aquisição de mobilidade por parte do espermatozoide foram alvo de intensos estudos. Contudo, este processo ainda não é inteiramente conhecido. Ademais, as limitadas opções disponíveis para contraceção masculina (preservativo, vasectomia e coito interrompido) refletem a necessidade de desenvolver um contracetivo masculino baseado na modulação da mobilidade do espermatozoide. A via de sinalização GSK3/PPP1R2/PPP1 está envolvida na aquisição de mobilidade do espermatozoide ao longo do transito do epidídimo. O objetivo principal deste trabalho é enriquecer o conhecimento dos eventos celulares necessários na mobilidade do espermatozoide através da caracterização e modulação da via de sinalização GSK3/PPP1R2/PPP1 em espermatozoides humanos. Desenhámos, sintetizámos e caracterizámos um bioportide que quebra interações proteicas baseado em tecnologia de cell penetrating peptides. Estudos in vitro revelaram que o bioportide de ruptura interfere com a interação PPP1R2/PPP1CC2 e é capaz de restabelecer a atividade da PPP1CC2. Também demonstramos que o bioportide reduz significativamente a mobilidade do espermatozoide. Com o objetivo de identificar interacções proteína-proteína adequadas à intervenção farmacológica, focámos a nossa atenção na proteína GSK3, um modulador da interação PPP1R2/PPP1CC2 em espermatozoides. Descrevemos pela primeira vez o interactoma da GSK3 no testículo e espermatozoide humanos e reportamos um papel específico da isoforma GSK3 na mobilidade do espermatozoide. Uma análise in silico revelou interatores da GSK3 e GSK3 que estão envolvidos na mobilidade do espermatozoide e potencialmente poderão ser alvos de intervenção farmacológica para um novo contraceptivo masculino. Em conclusão, demonstramos que é possível provocar a quebra de interações proteína-proteína e modular a mobilidade do espermatozoide usando de bioportides. Também identificamos potenciais novas interações proteicas envolvidas na mobilidade do espermatozoide. Finalmente, mostramos que é possível idealizar um novo tipo de contracepção masculina baseado na inibição da mobilidade do espermatozoide

Analysis and regulation of alternative splicing in the pig infarted myocardium

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 14-03-2017Esta tesis tiene embargado el acceso al texto completo hasta el 14-09-201