Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions

The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.

Characterization of a novel inulosucrase from Lactiplantibacillus plantarum

Fructansucrases produce fructans by polymerizing the fructose moiety released from sucrose. Here, we describe the recombinant expression and characterization of a unique fructansucrase from Lactiplantibacillus plantarum DKL3 that showed low sequence similarity with previously characterized fructansucrases. The optimum pH and temperature of fructansucrase were found to be 4.0 and 35 °C, respectively. Enzyme activity increased in presence of Ca2+ and distinctly in presence of Mn2+. The enzyme was characterized as an inulosucrase (LpInu), based on the production of an inulin-type fructan as assessed byNMR spectroscopy and methylation analysis. In addition to β-2,1-linkages, the inulin contained a few β-2,1,6-linked branchpoints. High-performance size exclusion chromatography with refractive index detection (HPSEC-RI) revealed the production of inulin with a lower molecular weight compared to other characterized bacterial inulin. LpInu and its inulin product represent novel candidates to be explored for possible food and biomedical applications.

Identification of Novel NSD1 variations in four Pediatric cases with sotos Syndrome

OBJECTIVE

Sotos syndrome (SOTOS) is an uncommon genetic condition that manifests itself with the following distinctive features: prenatal overgrowth, facial abnormalities, and intellectual disability. This disorder is often associated with haploinsufficiency of the nuclear receptor-binding SET domain protein 1 (NSD1)gene. We investigated four pediatric cases characterized by early-onset overgrowth and developmental delay. The primary objective of this study was to achieve accurate genetic diagnoses.

DESIGN&METHODS

A sequential analysis approach comprising chromosomal karyotyping, whole exome sequencing, and microarray analysis was conducted.

RESULTS

All four cases exhibited variations in the NSD1 gene, with the identification of four previously unreported de novo variants, each specific to one case.Specifically, Case 1 carried the NSD1 (NM_022455): c.2686 C > T(p.Q896X) variant, Case 2 had the NSD1 (NM_022455): c.2858_2859delCT(p.S953X) variant, Case 3 displayed a chromosomal aberration, chr5: 5q35.2q35.3(176,516,604-176,639,249)×1, which encompassed the 5'-untranslated region of NSD1, and Case 4 harbored the NSD1 (NM_022455): c.6397T > G(p.C2133G) variant.

CONCLUSION

This study not only provided precise diagnoses for these cases but also supplied significant evidence to facilitate informed consultations. Furthermore, our findings expanded the spectrum of mutations associated with SOTOS.

Structural heterogeneity assessment among the isoforms of fungal 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase: a comparative in silico perspective

Background

The primary amino acid sequence of a protein is a translated version from its gene sequence which carries important messages and information concealed therein. The present study unveils the structure-function and evolutionary aspects of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) proteins of fungal origin. ACCD, an important plant growth-promoting microbial enzyme, is less frequent in fungi compared to bacteria. Hence, an inclusive understanding of fungal ACC deaminases (fACCD) has brought forth here.

Results

In silico investigation of 40 fACCD proteins recovered from NCBI database reveals that fACCD are prevalent in Colletotrichum (25%), Fusarium (15%), and Trichoderma (10%). The fACCD were found 16.18–82.47 kDa proteins having 149–750 amino acid residues. The enzyme activity would be optimum in a wide range of pH having isoelectric points 4.76–10.06. Higher aliphatic indices (81.49–100.13) and instability indices > 40 indicated the thermostability nature. The secondary structural analysis further validates the stability owing to higher α-helices. Built tertiary protein models designated as ACCNK1–ACCNK40 have been deposited in the PMDB with accessions PM0083418–39 and PM0083476–93. All proteins were found as homo-dimer except ACCNK13, a homo-tetramer.

Conclusions

Hence, these anticipated features would facilitate to explore and identify novel variants of fungal ACCD in vitro aiming to industrial-scale applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00294-0.

• First comprehensive in silico annotation of fungal ACC deaminases (fACCD).

• Colletotrichum, Fusarium, and Trichoderma are predominant to possess fACCD.

• fACCD are 16.18–82.47 kDa proteins with optimal pH between 4.76 and 10.06.

• Majority are thermostable with higher aliphatic indices and instability indices < 40.

• fACCD are found as homo-dimer except ACCNK13, a homo-tetramer.

Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences

The structural consequences of ongoing mutations on the SARS-CoV-2 spike-protein remains to be fully elucidated. These mutations could change the binding affinity between the virus and its target cell. Moreover, obtaining new mutations would also change the therapeutic efficacy of the designed drug candidates. To evaluate these consequences, 3D structure of a mutant spike protein was predicted and checked for stability, cavity sites, and residue depth. The docking analyses were performed between the 3D model of the mutated spike protein and the ACE2 protein and an engineered therapeutic ACE2 against COVID-19. The obtained results revealed that the N501Y substitution has altered the interaction orientation, augmented the number of interface bonds, and increased the affinity against the ACE2. On the other hand, the P681H mutation contributed to the increased cavity size and relatively higher residue depth. The binding affinity between the engineered therapeutic ACE2 and the mutant spike was significantly higher with a distinguished binding orientation. It could be concluded that the mutant spike protein increased the affinity, preserved the location, changed the orientation, and altered the interface amino acids of its interaction with both the ACE2 and its therapeutic engineered version. The obtained results corroborate the more aggressive nature of mutated SARS-CoV-2 due to their higher binding affinity. Moreover, designed ACe2-baased therapeutics would be still highly effective against covid-19, which could be the result of conserved nature of cellular ACE2.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10989-021-10346-1.

Assessing the effects of PMM2 variants on protein stability

Phosphomannomutase 2 deficiency, PMM2-CDG, is the most frequent disorder of protein N-glycosylation. It is an autosomal recessive disease with a broad clinical and biochemical phenotype. Trying to predict the impact of novel variants is often a challenge due to the high number of variants and the difficulty to establish solid genotype-phenotype correlations. A potential useful strategy is to use computational chemistry calculations as a tool from which relevant information on the structural impact of novel variants may be deduced. Here we present our analyses based on four well-known PMM2 deleterious variants (p.(Leu32Arg), p.(Asp65Tyr), p.(Phe119Leu), p.(Arg141His)) and the polymorphic p.(Glu197Ala) for which we have predicted the effect on protein stability. Our work predicts the effect of different amino acid residues on the conformation and stability of PMM2. These computational simulations are, therefore, an extremely useful methodology which, in combination with routinely used in silico methods of pathogenicity prediction, may help to reveal the structural impact of novel variants at the protein level, potentially leading to a better understanding of target biological molecules.

The biochemical association between R157H mutation in human αB-crystallin and development of cardiomyopathy: Structural and functional analyses of the mutant protein

In human αB-crystallin or HspB5, the substitution of arginine residue at position 157 with histidine has been reported to cause cardiomyopathy. In this study, the impact of R157H mutation on the structure, stability and functional properties of human αB-crystallin was investigated using a variety of spectroscopic techniques and microscopic analyses. Our spectroscopic analyses revealed that this mutation has a negligible impact on the secondary and tertiary structures of HspB5 but its quaternary structure underwent fundamental changes. Although the chemical stability of the mutant protein remained largely unchanged, the differential scanning calorimetry (DSC) measurement suggested that its thermal stability was reduced. As examined with transmission electron microscopy, αB-crystallin and its mutant indicated a similar tendency for the amyloid fibril formation under thermochemical stress. Dynamic light scattering (DLS) analysis suggested important changes in the quaternary (oligomeric) structures of the mutant protein as compared with the native protein counterpart. Also, the mutant protein indicated an improved chaperone-like activity under in vitro assessment. In a pH-dependent manner, the side chains of arginine and histidine have different capabilities for establishing hydrogen bonds and electrostatic interaction (salt bridge) and this variation may be sufficient to produce the larger changes that ultimately alter the interaction of this protein with other target proteins. Overall, the pathogenic contribution of this mutation in cardiomyopathy can be explained by its role in quaternary structure/stability alteration of the mutated protein.

Current knowledge on enzymatic PET degradation and its possible application to waste stream management and other fields

Enzymatic hydrolysis of polyethylene terephthalate (PET) has been the subject of extensive previous research that can be grouped into two categories, viz. enzymatic surface modification of polyester fibers and management of PET waste by enzymatic hydrolysis. Different enzymes with rather specific properties are required for these two processes. Enzymatic surface modification is possible with several hydrolases, such as lipases, carboxylesterases, cutinases, and proteases. These enzymes should be designated as PET surface–modifying enzymes and should not degrade the building blocks of PET but should hydrolyze the surface polymer chain so that the intensity of PET is not weakened. Conversely, management of PET waste requires substantial degradation of the building blocks of PET; therefore, only a limited number of cutinases have been recognized as PET hydrolases since the first PET hydrolase was discovered by Müller et al. (Macromol Rapid Commun 26:1400–1405, 2005). Here, we introduce current knowledge on enzymatic degradation of PET with a focus on the key class of enzymes, PET hydrolases, pertaining to the definition of enzymatic requirements for PET hydrolysis, structural analyses of PET hydrolases, and the reaction mechanisms. This review gives a deep insight into the structural basis and dynamics of PET hydrolases based on the recent progress in X-ray crystallography. Based on the knowledge accumulated to date, we discuss the potential for PET hydrolysis applications, such as in designing waste stream management.

Evaluating the effect of BDNF Val66Met polymorphism on complex formation with HAP1 and Sortilin1 via structural modeling

Brain derived neurotrophic factor (BDNF) has a critical role in the neurogenesis, differentiation, survival of the neurons, regulation of the appetite, and energy homeostasis. Two key proteins, Huntingtin associated protein-1 (HAP1) and sortilin1, regulate the intracellular trafficking and stabilization of the precursor proBDNF through interaction with its prodomain region and mark it for secretion. Evidence suggests that the most frequent single nucleotide polymorphism (SNP) of BDNF gene (rs6265) has been associated with different psychiatric, neurodegenerative and eating disorders. In this study, structural bioinformatics and molecular dynamics (MD) simulations were applied, in order to get precise insights into the impact of Val66Met polymorphism on the proBDNF structure and its interaction with HAP1 and Sortilin1. Homology modeling, structure validation, refinement and also protein-protein docking were performed using appropriate servers. The stability, the fluctuations and the compactness of protein complexes were measured by MD simulation parameters including root mean square deviation (RMSD), root mean square fluctuation (RMSF) and Radius of gyration (Rg), respectively. The mutant proBDNF complexes with HAP1 and Sortilin1 revealed higher RMSD and RMSF values and also variable R_g over time compared with wild-type proBDNF. These computational results indicated that, wild-type proBDNF possessed more stable structure in binding with HAP1 and Sortilin1 compared with its mutant form. Therefore, Val66Met SNP could be deleterious due to making structural changes. It may cause a decrease in proBDNF secretion, which could possibly lead to different psychiatric, neurodegenerative and eating disorders. Further experimental lab studies are required for a more accurate conclusion.

Novel mutations and their genotype-phenotype correlations in patients with Noonan syndrome, using next-generation sequencing

PURPOSE

Noonan Syndrome (NS) is an autosomal dominant disorder with many variable and heterogeneous conditions. The genetic basis for 20-30% of cases is still unknown. This study evaluates Iranian Noonan patients both clinically and genetically for the first time.

MATERIALS/METHODS

Mutational analysis of PTPN11 gene was performed in 15 Iranian patients, using PCR and Sanger sequencing at phase one. Then, as phase two, Next Generation Sequencing (NGS) in the form of targeted resequencing was utilized for analysis of exons from other related genes. Homology modelling for the novel founded mutations was performed as well. The genotype, phenotype correlation was done according to the molecular findings and clinical features.

RESULTS

Previously reported mutation (p.N308D) in some patients and a novel mutation (p.D155N) in one of the patients were identified in phase one. After applying NGS methods, known and new variants were found in four patients in other genes, including: CBL (p. V904I), KRAS (p. L53W), SOS1 (p. I1302V), and SOS1 (p. R552G). Structural studies of two deduced novel mutations in related genes revealed deficiencies in the mutated proteins. Following genotype, phenotype correlation, a new pattern of the presence of intellectual disability in two patients was registered.

CONCLUSIONS

NS shows strong variable expressivity along the high genetic heterogeneity especially in distinct populations and ethnic groups. Also possibly unknown other causative genes may be exist. Obviously, more comprehensive and new technologies like NGS methods are the best choice for detection of molecular defects in patients for genotype, phenotype correlation and disease management.

The Factor Structure of the Adapted WHO Quality of Life BREF questionnaire in a sample of adolescents in Nigeria

INTRODUCTION

The World Health Organization's Quality of Life Instrument (WHOQOL-BREF) is widely validated and popularly used in assessing perceived quality of life (QOL) of adolescents and the general population. Though the WHOQOL-BREF has been used in some studies in Nigeria, its theoretical structure has not been comprehensively investigated. This study examined the factor structure of the Adopted WHOQOL-BREF questionnaire and it theoretical structure in a large sample of adolescents in Nigeria.

METHODS

Data on demographic characteristics and QOL were extracted from 1,963 adolescents who participated in a state-wide study on psychosocial functioning and quality of life of adolescents in Benue State, Nigeria. Descriptive statistics were used to present the distribution of the data while Cronbach's alpha and Polychoric ordinal alpha were used to describe the internal consistency (reliability) of the adapted WHOQOL-BREF and alpha value of 0.700 was considered reliable. Structural analysis was performed to extract the underlying factors while confirmatory factor analyses were used to assess some hypothesized structure of the adapted WHO-QOL BREF. Relative Chi-square test (χ²/df) value ≤3.0 was regarded a good fit while multiple fit indexes with values ≥0.90 (for acceptable fit) were used for assessing diverse aspects of the models. All analyses were performed at 5% significance level using IBM SPSS statistics version 20, R package and AMOS version 21.

RESULTS

Participants were mostly male (54.8%) and 14.7±1.4 years old with 51.0% residing in rural areas. The overall internal consistency of the 4-factor model was 0.862 (for Cronbach's Alpha) and 0.989 (for Polychoric Alpha) while the 2-factor model had 0.870 (for Cronbach's Alpha) and 0.990 (for Polychoric Alpha). The Cattelle's Scree plot, Horn's parallel analysis and the confirmatory factor analysis revealed a 2-factor model as the best model for the WHO-QOL BREF. The 23-item 2-factor structure had a relative Chi-square test value χ²/df < 3 = 2.98, p < 0.001 with all fit indices within the acceptable range.

CONCLUSION

The adapted WHO QOL BREF can be safely used to assess quality of life among Adolescents in Nigeria and related settings. Using the two factors extracted in the present study may yield better results in settings similar to the present study location.

Human Papilloma Virus Vaccine Awareness and Vaccination History in Patients Attending STI Clinics in Lagos and Ibadan, Nigeria

HPV is one of the most common causes of sexually transmitted disease in both men and women worldwide. It is transmitted through vaginal, anal, and oral sex. This study provided information on the Human Papilloma Virus (HPV) vaccine awareness and vaccination history in relation to the level of antibodies to (HPV) in the population at risk in Nigeria. Patients attending STI clinics at Lagos and Ibadan were recruited and informed consent was obtained from all the participants. Using semi structured questionnaire, vaccination history, demography and past experiences of the patients were obtained. Whole blood samples were obtained and the sera screened for specific antibodies to HPV using ELISA test kits for determination of IgG to HPV by DIA PRO Diagnostic Bioprobes Milano-Italy according to the manufacturer's instruction. Of the170 samples analysed 50 (29.4%) samples were positive for HPV. Thirty (17.6%) were from females and 20 (11.7%) of them were males. Thirty-five (35%) of the 100 women participants were aware of HPV vaccine. 15(15%) women did not take the vaccine because they did not know where to get it while 20 (20%) of them could not afford it. It was also noted that there is higher prevalence among the middle-aged women. A high prevalence of HPV antibodies was observed in the study yet none of the participants had received the HPV vaccine thus the antibodies may be from infection. Implication is that the 30 women who tested positive for the HPV antibodies may be at risk of cervical cancer.