Analysis of structures, functions, and epitopes of cysteine protease from Spirometra erinaceieuropaei Spargana

MLapRVFL: Protein sequence prediction based on Multi-Laplacian Regularized Random Vector Functional Link

Protein sequence classification is a crucial research field in bioinformatics, playing a vital role in facilitating functional annotation, structure prediction, and gaining a deeper understanding of protein function and interactions. With the rapid development of high-throughput sequencing technologies, a vast amount of unknown protein sequence data is being generated and accumulated, leading to an increasing demand for protein classification and annotation. Existing machine learning methods still have limitations in protein sequence classification, such as low accuracy and precision of classification models, rendering them less valuable in practical applications. Additionally, these models often lack strong generalization capabilities and cannot be widely applied to various types of proteins. Therefore, accurately classifying and predicting proteins remains a challenging task. In this study, we propose a protein sequence classifier called Multi-Laplacian Regularized Random Vector Functional Link (MLapRVFL). By incorporating Multi-Laplacian and L2,1-norm regularization terms into the basic Random Vector Functional Link (RVFL) method, we effectively improve the model's generalization performance, enhance the robustness and accuracy of the classification model. The experimental results on two commonly used datasets demonstrate that MLapRVFL outperforms popular machine learning methods and achieves superior predictive performance compared to previous studies. In conclusion, the proposed MLapRVFL method makes significant contributions to protein sequence prediction.

Cloning and Expression of a New Trichinella spiralis Serine Protease and Its Role in Invading Host Intestinal Epithelium

BACKGROUND

In previous studies, a new Trichinella spiralis serine protease 1.1 (TsSP1.1) was identified in surface proteins of T. spiralis muscle larvae (ML) by proteomics analysis, but its functions in T. spiralis infection are unknown. The aim of this study was to investigate the roles of TsSP1.1 during larval intrusion of gut epithelium.

METHODS

From January 2019 to March 2021, complete TsSP1.1 cDNA sequence was cloned and expressed in Escherichia coli BL21 at the Department of Parasitology, Medical College of Zhengzhou University, Zhengzhou, China. Expression and location of TsSP1.1 in the parasite were investigated using indirect immunofluorescence assay (IIFA) and Western blotting. The in vitro intestinal epithelium cells (IECs) intrusion assay was used to ascertain the roles of TsSP1.1 during larval intrusion of IECs and gut epithelium.

RESULTS

TsSP1.1 was a surface and secretory protein, which was expressed at various T. spiralis stages, and principally localized at cuticle, stichosome and embryos of the nematode. rTsSP1.1 accelerated larval intrusion of IECs, whereas anti-rTsSP1.1 antibodies impeded larval intrusion. The acceleration and inhibtion was dose-dependently related to rTsSP1.1 and anti-TsSP1.1 antibodies. Block of the IIL with anti-rTsSP1.1 serum also impeded larval intrusion of gut mucosa.

CONCLUSION

TsSP1.1 participates in T. spiralis intrusion of gut epithelium.

Epidemiology, Diagnosis, and Prevention of Sparganosis in Asia

Sparganosis is a zoonotic parasitic disease caused by the larvae (spargana) of the genus Spirometra, which is widely distributed globally and threatens human health. More than 60 species of Spirometra have already been identified, and over 2000 cases have been reported. This review summarizes the prevalence of humans, frogs, snakes, and other animals with spargana. Furthermore, the infection mode, distribution, and site are summarized and analyzed. We also describe the epidemiology, molecular diagnosis, and other aspects which are of considerable significance to preventing sparganum.

Bioinformatics analysis of structures and ligand-bindings of predicted zymogen granule protein observed on Bali cattle (Bos javanicus) saliva

Objective

Previously, we have shown that predicted zymogen granule protein 16 homolog B (P-G3MZ19) existed in Bali cattle (Bos javanicus) saliva. It was suggested that P-G3MZ19 is a member of the mannose-binding lectin family that plays an essential role in innate immunity. In the present study, we aimed to analyze the structure and ligand-binding of P-3MZ19 in Bali cattle saliva.

Materials and Methods

Saliva of four adult healthy Bali cattle was collected, lyophilized, and subjected to two-dimensional (2-D) gel electrophoresis. The target spot of around 17 kDa related to P-G3MZ19 was excised for matrix-assisted laser desorption ionization time-of-flight mass spectrometer/time-of-flight mass spectrometer mass spectrometry analysis and sequencing. The structure and the ligand-binding of P-3MZ19 were analyzed using bioinformatics software programs published elsewhere.

Results

Based on Iterative Threading ASSEmbly Refinement the 3D model of P-G3MZ19 was suggested to have similarities to exo-alpha-sialidase (EC 3.2.1.18); while its ligand-binding sites consisted of seven residues, i.e., 25aa-26aa (Gly-Gly), 95aa (Phe), 138aa (Tyr), 140aa (Leu), 141aa (Gly), and 143aa (Thr).

Conclusion

The structure of P-G3MZ19 of Bali cattle saliva and its ligand-binding sites have been successfully determined by using bioinformatics techniques. The biological and immunological roles of the peptide are currently under investigation based on P-G3MZ19 synthetic peptides.

Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis

BACKGROUND

Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood.

RESULTS

In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development.

CONCLUSIONS

Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence.

Characterization of Two Trichinella spiralis Adult-Specific DNase II and Their Capacity to Induce Protective Immunity

Deoxyribonuclease II (DNase II) is a widespread endonuclease, which can degrade the DNA. Trichinella spiralis adult-specific DNase II-1 (TsDNase II-1) and DNase II-7 (TsDNase II-7) were identified in excretory-secretory (ES) or surface proteins of adult worm (AW) and intestinal infective larvae (IIL) using immunoproteomics with early infection sera. The aim of this study was to characterize the two T. spiralis DNase II enzymes and to investigate their role as potential vaccine candidate target molecules. The cDNA sequences of the two DNase II enzymes from 3 days old AWs of T. spiralis were cloned and expressed. The sequencing results showed that the complete cDNA sequences of the two DNase II enzymes were 1221 and 1161 bp long, and the predicted open reading frames encoded 347 and 348 amino acids, respectively. On Western blot analysis, natural TsDNase II-1 and TsDNase II-7 in the crude extracts of IIL, AWs, and newborn larvae (NBL) and AW ES proteins were recognized by both anti-rTsDNase II-1 and anti-rTsDNase II-7 sera. Indirect immunofluorescence test and qPCR showed that the two DNase II enzymes were highly expressed at AW and NBL stages and were mainly located at the cuticle and stichosome of the nematode. Vaccination with the two recombinant DNase II enzymes triggered prominent humoral responses that exhibited significant immune protection against T. spiralis larval infection, as demonstrated by the notable reduction in intestinal AW and muscle larva burdens. Specific antibodies to the two molecules evidently inhibited the in vitro parasite invasion of enterocytes and participated in the killing of NBL by an antibody-dependent cell-mediated cytotoxicity (ADCC) mode. The enzymes DNase II-1 and DNase II-7 are the potential target molecules for anti-Trichinella vaccine for blocking both larval invasion and development.

A cysteine protease from Spirometra erinaceieuropaei plerocercoid is a critical factor for host tissue invasion and migration

Sparganosis in humans caused by the plerocercoid larvae of Spirometra erinaceieuropaei is found worldwide, especially in Eastern Asia and the Far East. Previous studies have suggested that dissolution of plerocercoid body, plerocercoid invasion of host tissue, and migration are important processes for sparganosis progression. However, the mechanisms underlying these processes have yet to be determined. Here, we demonstrated the enzymatic property and involvement of a native 23kDa cysteine protease (Se23kCP), purified from plerocercoids, in sparganosis pathogenesis. Se23kCP is mature protease consisting of 216 amino acids and has a high sequence similarity with cathepsin L in various organisms. Se23kCP conjugated with N-glycans, which have a core fucose residue. Both cysteine and serine protease-specific activities were determined in Se23kCP and their optimal pHs were found to be different, indicating that Se23kCP has a wide range of substrate specificity. Se23kCP was secreted from tegumental vacuoles of the plerocercoid to host subcutaneous tissues and degraded human structural proteins, such as collagen and fibronectin. In addition, the plerocercoid body was lysed by Se23kCP, which facilitated larval invasion of host tissue. Our findings suggest that Se23kCP induces host tissue invasion and migration, and might be an essential molecule for sparganosis onset and progression.

The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion

BACKGROUND

Sparganosis is an infection with a larval Diphyllobothriidea tapeworm. From a rare cerebral case presented at a clinic in the UK, DNA was recovered from a biopsy sample and used to determine the causative species as Spirometra erinaceieuropaei through sequencing of the cox1 gene. From the same DNA, we have produced a draft genome, the first of its kind for this species, and used it to perform a comparative genomics analysis and to investigate known and potential tapeworm drug targets in this tapeworm.

RESULTS

The 1.26 Gb draft genome of S. erinaceieuropaei is currently the largest reported for any flatworm. Through investigation of β-tubulin genes, we predict that S. erinaceieuropaei larvae are insensitive to the tapeworm drug albendazole. We find that many putative tapeworm drug targets are also present in S. erinaceieuropaei, allowing possible cross application of new drugs. In comparison to other sequenced tapeworm species we observe expansion of protease classes, and of Kuntiz-type protease inhibitors. Expanded gene families in this tapeworm also include those that are involved in processes that add post-translational diversity to the protein landscape, intracellular transport, transcriptional regulation and detoxification.

CONCLUSIONS

The S. erinaceieuropaei genome begins to give us insight into an order of tapeworms previously uncharacterized at the genome-wide level. From a single clinical case we have begun to sketch a picture of the characteristics of these organisms. Finally, our work represents a significant technological achievement as we present a draft genome sequence of a rare tapeworm, and from a small amount of starting material.

Characterization of Spirometra erinaceieuropaei Plerocercoid Cysteine Protease and Potential Application for Serodiagnosis of Sparganosis

Background

Sparganosis is a neglected but important food-borne parasitic zoonosis. Clinical diagnosis of sparganosis is difficult because there are no specific manifestations. ELISA using plerocercoid crude or excretory–secretory (ES) antigens has high sensitivity but has cross-reactions with other helminthiases. The aim of this study was to characterize Spirometra erinaceieuropaei cysteine protease (SeCP) and to evaluate its potential application for serodiagnosis of sparganosis.

Methodology/Principal Findings

The full length SeCP gene was cloned, and recombinant SeCP (rSeCP) was expressed and purified. Western blotting showed that rSeCP was recognized by the serum of sparganum-infected mice, and anti-rSeCP serum recognized the native SeCP protein of plerocercoid crude or ES antigens. Expression of SeCP was observed at plerocercoid stages but not at the adult and egg stages. Immunolocalization identified SeCP in plerocercoid tegument and parenchymal tissue. The rSeCP had CP activity, and the optimum pH and temperature were 5.5 and 37°C, respectively. Enzymatic activity was significantly inhibited by E-64. rSeCP functions to degrade different proteins and the function was inhibited by anti-rSeCP serum and E-64. Immunization of mice with rSeCP induced Th2-predominant immune responses and anti-rSeCP antibodies had the potential capabilities to kill plerocercoids in an ADCC assay. The sensitivity of rSeCP-ELISA and ES antigen ELISA was 100% when performed on sera of patients with sparganosis. The specificity of rSeCP-ELISA and ES antigen ELISA was 98.22% (166/169) and 87.57% (148/169), respectively (P<0.05).

Conclusions

The rSeCP had the CP enzymatic activity and SeCP seems to be important for the survival of plerocercoids in host. The rSeCP is a potential diagnostic antigen for sparganosis.

Sparganosis is a neglected tropical disease; its diagnosis is difficult and it is often misdiagnosed. ELISA using the crude or ES antigens of plerocercoids cross reacts with other helminthiases. Cysteine protease is a type of hydrolase and plays important roles in the development and survival of parasites; it has been used for diagnostic markers and vaccine targets for some parasitic diseases. In this study, a 36 kDa Spirometra erinaceieuropaei cysteine protease (SeCP) was expressed and purified. The results showed that SeCP was a plerocercoid stage-specific protein located in the teguments and parenchymal tissue. The rSeCP had cysteine protease activity and functioned to degrade host proteins. Vaccination of mice with rSeCP induced high levels of IgG1 and anti-rSeCP antibodies with the ability to kill plerocercoids in an ADCC assay. The rSeCP had a high sensitivity and specificity for detecting anti-plerocercoid antibodies, and could be used as a potential antigen for serodiagnosis of sparganosis.

Protein sequence classification with improved extreme learning machine algorithms

Precisely classifying a protein sequence from a large biological protein sequences database plays an important role for developing competitive pharmacological products. Comparing the unseen sequence with all the identified protein sequences and returning the category index with the highest similarity scored protein, conventional methods are usually time-consuming. Therefore, it is urgent and necessary to build an efficient protein sequence classification system. In this paper, we study the performance of protein sequence classification using SLFNs. The recent efficient extreme learning machine (ELM) and its invariants are utilized as the training algorithms. The optimal pruned ELM is first employed for protein sequence classification in this paper. To further enhance the performance, the ensemble based SLFNs structure is constructed where multiple SLFNs with the same number of hidden nodes and the same activation function are used as ensembles. For each ensemble, the same training algorithm is adopted. The final category index is derived using the majority voting method. Two approaches, namely, the basic ELM and the OP-ELM, are adopted for the ensemble based SLFNs. The performance is analyzed and compared with several existing methods using datasets obtained from the Protein Information Resource center. The experimental results show the priority of the proposed algorithms.

The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion

BACKGROUND

Sparganosis is an infection with a larval Diphyllobothriidea tapeworm. From a rare cerebral case presented at a clinic in the UK, DNA was recovered from a biopsy sample and used to determine the causative species as Spirometra erinaceieuropaei through sequencing of the cox1 gene. From the same DNA, we have produced a draft genome, the first of its kind for this species, and used it to perform a comparative genomics analysis and to investigate known and potential tapeworm drug targets in this tapeworm.

RESULTS

The 1.26 Gb draft genome of S. erinaceieuropaei is currently the largest reported for any flatworm. Through investigation of β-tubulin genes, we predict that S. erinaceieuropaei larvae are insensitive to the tapeworm drug albendazole. We find that many putative tapeworm drug targets are also present in S. erinaceieuropaei, allowing possible cross application of new drugs. In comparison to other sequenced tapeworm species we observe expansion of protease classes, and of Kuntiz-type protease inhibitors. Expanded gene families in this tapeworm also include those that are involved in processes that add post-translational diversity to the protein landscape, intracellular transport, transcriptional regulation and detoxification.

CONCLUSIONS

The S. erinaceieuropaei genome begins to give us insight into an order of tapeworms previously uncharacterized at the genome-wide level. From a single clinical case we have begun to sketch a picture of the characteristics of these organisms. Finally, our work represents a significant technological achievement as we present a draft genome sequence of a rare tapeworm, and from a small amount of starting material.