Signal-3L: A 3-layer approach for predicting signal peptides

Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures

Many proteins contain cleavable signal or transit peptides that direct them to their final subcellular locations. Such peptides are usually predicted from sequence alone using methods such as TargetP 2.0 and SignalP 6.0. While these methods are usually very accurate, we show here that an analysis of a protein's AlphaFold2-predicted structure can often be used to identify false positive predictions. We start by showing that when given a protein's full-length sequence, AlphaFold2 builds experimentally annotated signal and transit peptides in orientations that point away from the main body of the protein. This indicates that AlphaFold2 correctly identifies that a signal is not destined to be part of the mature protein's structure and suggests, as a corollary, that predicted signals that AlphaFold2 folds with high confidence into the main body of the protein are likely to be false positives. To explore this idea, we analyzed predicted signal peptides in 48 proteomes made available in DeepMind's AlphaFold2 database (https://alphafold.ebi.ac.uk). Applying TargetP 2.0 and SignalP 6.0 to the 561,562 proteins in the database results in 95,236 being predicted to contain a cleavable signal or transit peptide. In 95.1% of these cases, the AlphaFold2 structure of the full-length protein is fully consistent with the prediction of TargetP 2.0 or SignalP 6.0. In the remaining 4.9% of cases where the AlphaFold2 structure does not appear consistent with the prediction, the signal is often only predicted with low confidence. The potential false positives identified here may be useful for training even more accurate signal prediction methods.

Enhancement of violaxanthin accumulation in Nannochloropsis oceanica by overexpressing a carotenoid isomerase gene from Phaeodactylum tricornutum

Nannochloropsis has been considered as a promising feedstock for the industrial production of violaxanthin. However, a rational breeding strategy for the enhancement of violaxanthin content in this microalga is still vacant, thereby limiting its industrial application. All-trans-lycopene locates in the first branch point of carotenogenesis. The carotenoid isomerase (CRTISO), catalyzing the lycopene formation, is thus regarded as a key enzyme for carotenogenesis. Phaeodactylum tricornutum can accumulate high-level carotenoids under optimal conditions. Therefore, it is feasible to improve violaxanthin level in Nannochloropsis by overexpression of PtCRTISO. Protein targeting analysis of seven PtCRTISO candidates (PtCRTISO1–6 and PtCRTISO-like) demonstrated that PtCRTISO4 was most likely the carotenoid isomerase of P. tricornutum. Moreover, the transcriptional pattern of PtCRTISO4 at different cultivation periods was quite similar to other known carotenogenesis genes. Thus, PtCRTISO4 was transformed into N. oceanica. Compared to the wild type (WT), all three transgenic lines (T1–T3) of N. oceanica exhibited higher levels of total carotenoid and violaxanthin. Notably, T3 exhibited the peak violaxanthin content of 4.48 mg g^–1 dry cell weight (DCW), which was 1.68-folds higher than WT. Interestingly, qRT-polymerase chain reaction (PCR) results demonstrated that phytoene synthase (NoPSY) rather than ζ-carotene desaturase (NoZDS) and lycopene β-cyclase (NoLCYB) exhibited the highest upregulation, suggesting that PtCRTISO4 played an additional regulatory role in terms of carotenoid accumulation. Moreover, PtCRTISO4 overexpression increased C18:1n-9 but decreased C16:1n-7, implying that C18:1 may serve as a main feedstock for xanthophyll esterification in Nannochloropsis. Our results will provide valuable information for the violaxanthin production from Nannochloropsis.

Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4

Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N'-diacetyl-β-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with K_m = 0.24 mM and k_cat = 30.0 s^-1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains-2x Fn3/Big3 and a carbohydrate binding module-that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.

De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.)

Vietnamese ginseng (Panax vietnamensis Ha et Grushv.), also known as Ngoc Linh ginseng, is a high-value herb in Vietnam. Vietnamese ginseng has been proven to be effective in enhancing the immune system, human memory, anti-stress, anti-inflammatory, anti-cancer, and prevent aging. The present study reports the first draft whole-genome of Vietnamese ginseng and the identification of potential genes involved in the triterpenoid metabolic pathway. De novo whole-genome assembly was performed successfully from a data of approximately 139 Gbps of 394,802,120 high quality reads to generate 9815 scaffolds with an N50 value of 572,722 bp from the leaf of Vietnamese ginseng. The assembled genome of Vietnamese ginseng is 3,001,967,204 bp long containing 79,374 gene models. Among them, there are 55,012 genes (69.30%) were annotated by various public molecular biology databases. The potential genes involved in triterpenoid saponin biosynthesis in Vietnamese ginseng and their metabolic pathway were also predicted." Three genes encoding squalene monooxygenase isozymes in Vietnamese ginseng were cloned, sequenced and characterized. Moreover, expression levels of several key genes involved in terpenoid biosynthesis in different parts of Vietnamese ginseng were also analyzed. The SSR markers were detected by various programs from both of assembly full dataset of Vietnamese ginseng genome and predicted genes. The present work provided important data of the draft whole-genome of Vietnamese ginseng for further studies to understand the role of genes involved in ginsenoside biosynthesis and their metabolic pathway at the molecular level of this rare medicinal species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01076-1.

Changes in composition and levels of hemolymph proteins during metamorphosis of Manduca sexta

The tobacco hornworm, Manduca sexta, is a lepidopteran model species widely used to study insect biochemical processes. Some of its larval hemolymph proteins are well studied, and a detailed proteomic analysis of larval plasma proteins became available in 2016, revealing features such as correlation with transcriptome data, formation of immune complexes, and constitution of an immune signaling system in hemolymph. It is unclear how the composition of these proteins may change in other developmental stages. In this paper, we report the proteomes of cell-free hemolymph from prepupae, pupae on day 4 and day 13, and young adults. Of the 1824 proteins identified, 907 have a signal peptide and 410 are related to immunity. Drastic changes in abundance of the storage proteins, lipophorins and vitellogenin, for instance, reflect physiological differences among prepupae, pupae, and adults. Considerably more proteins lacking signal peptide are present in the late pupae, suggesting that plasma contains relatively low concentrations of intracellular components released from remodeling tissues during metamorphosis. The defense proteins detected include 43 serine proteases and 11 serine protease homologs. Some of these proteins are members of the extracellular immune signaling network found in feeding larvae, and others may play additional roles and hence confer new features in the later life stages. In summary, the proteins and their levels revealed in this study, together with their transcriptome data, are expected to stimulate focused explorations of humoral immunity and other physiological systems in wandering larvae, pupae, and adults of M. sexta and shed light upon functional and comparative genomic research in other holometabolous insects.

Using the Chou’s Pseudo Component to Predict the ncRNA Locations Based on the Improved K-Nearest Neighbor (iKNN) Classifier

Background:

The non-coding RNA identification at the organelle genome level is a challenging task. In our previous work, an ncRNA dataset with less than 80% sequence identity was built, and a method incorporating an increment of diversity combining with support vector machine method was proposed.

Objective:

Based on the ncRNA_361 dataset, a novel decision-making method-an improved KNN (iKNN) classifier was proposed.

Methods:

In this paper, based on the iKNN algorithm, the physicochemical features of nucleotides, the degeneracy of genetic codons, and topological secondary structure were selected to represent the effective ncRNA characters. Then, the incremental feature selection method was utilized to optimize the feature set.

Results:

The results of iKNN indicated that the decision-making method of mean value is distinctly superior to the traditional decision-making method of majority vote the Increment of Diversity Combining Support Vector Machine (ID-SVM). The iKNN algorithm achieved an overall accuracy of 97.368% in the jackknife test, when k=3.

Conclusion:

It should be noted that the triplets of the structure-sequence mode under reading frames not only contains the entire sequence information but also reflects whether the base was paired or not, and the secondary structural topological parameters further describe the ncRNA secondary structure on the spatial level. The ncRNA dataset and the iKNN classifier are freely available at http://202.207.14.87:8032/fuwu/iKNN/index.asp.

Insights into Machine Learning-based Approaches for Virtual Screening in Drug Discovery: Existing Strategies and Streamlining Through FP-CADD

BACKGROUND

Machine learning is an active area of research in computer science by the availability of big data collection of all sorts prompting interest in the development of novel tools for data mining. Machine learning methods have wide applications in computer-aided drug discovery methods. Most incredible approaches to machine learning are used in drug designing, which further aid the process of biological modelling in drug discovery. Mainly, two main categories are present which are Ligand-Based Virtual Screening (LBVS) and Structure-Based Virtual Screening (SBVS), however, the machine learning approaches fall mostly in the category of LBVS.

OBJECTIVES

This study exposits the major machine learning approaches being used in LBVS. Moreover, we have introduced a protocol named FP-CADD which depicts a 4-steps rule of thumb for drug discovery, the four protocols of computer-aided drug discovery (FP-CADD). Various important aspects along with SWOT analysis of FP-CADD are also discussed in this article.

CONCLUSION

By this thorough study, we have observed that in LBVS algorithms, Support Vector Machines (SVM) and Random Forest (RF) are those which are widely used due to high accuracy and efficiency. These virtual screening approaches have the potential to revolutionize the drug designing field. Also, we believe that the process flow presented in this study, named FP-CADD, can streamline the whole process of computer-aided drug discovery. By adopting this rule, the studies related to drug discovery can be made homogeneous and this protocol can also be considered as an evaluation criterion in the peer-review process of research articles.

Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring

Signal peptides play an important role in guiding and transferring transmembrane proteins and secreted proteins. In recent years, with the explosive growth of protein sequences, computationally predicting signal peptides and their cleavage sites from protein sequences is highly desired. In this work, we present an improved approach, Signal-3L 3.0, for signal peptide recognition and cleavage-site prediction using a 3-layer hybrid method of integrating deep learning algorithms and window-based scoring. There are three main components in the Signal-3L 3.0 prediction engine: (1) a deep bidirectional long short-term memory (Bi-LSTM) network with a soft self-attention learns abstract features from sequences to determine whether a query protein contains a signal peptide; (2) the statistics propensity window-based cleavage site screening method is applied to generate the set of candidate cleavage sites; (3) the prediction of a conditional random field with a hybrid convolutional neural network (CNN) and Bi-LSTM is fused with the window-based score for identifying the final unique cleavage site. Experimental results on the benchmark datasets show that the new deep learning-driven Signal-3L 3.0 yields promising performance. The online server of Signal-3L 3.0 is available at http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/.

Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, a number of studies have provided an understanding of the origin and evolution of this protein family. Here, we report a comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences that have been centralized in a dedicated database, we have been able to use phylogenetic reconstructions to increase our understanding of the evolutionary processes underlying the diversification of non-animal peroxidases. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlates with the presence or absence of certain organelles or with specific biological processes. Examination of almost 2000 organisms determined that ascorbate peroxidases (APxs) and cytochrome c peroxidases (CcPs) are present in those containing chloroplasts and mitochondria, respectively. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prxs) are only found in fungi with wood-decay and plant-degradation abilities. Class III peroxidases (CIII Prxs) are only found in streptophyte algae and land plants, and have been subjected to large family expansion. Biochemical activities of APx, CcP, and CIII Prx assessed using protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of the non-animal peroxidase encoding sequences.

An algal enzyme required for biosynthesis of the most abundant marine carotenoids

Fucoxanthin and its derivatives are the main light-harvesting pigments in the photosynthetic apparatus of many chromalveolate algae and represent the most abundant carotenoids in the world's oceans, thus being major facilitators of marine primary production. A central step in fucoxanthin biosynthesis that has been elusive so far is the conversion of violaxanthin to neoxanthin. Here, we show that in chromalveolates, this reaction is catalyzed by violaxanthin de-epoxidase-like (VDL) proteins and that VDL is also involved in the formation of other light-harvesting carotenoids such as peridinin or vaucheriaxanthin. VDL is closely related to the photoprotective enzyme violaxanthin de-epoxidase that operates in plants and most algae, revealing that in major phyla of marine algae, an ancient gene duplication triggered the evolution of carotenoid functions beyond photoprotection toward light harvesting.

Thermotogales origin scenario of eukaryogenesis

How eukaryotes were generated is an enigma of evolutionary biology. Widely accepted archaeal-origin eukaryogenesis scenarios, based on similarities of genes and related characteristics between archaea and eukaryotes, cannot explain several eukaryote-specific features of the last eukaryotic common ancestor, such as glycerol-3-phosphate-type membrane lipids, large cells and genomes, and endomembrane formation. Thermotogales spheroids, having multicopy-integrated large nucleoids and producing progeny in periplasm, may explain all of these features as well as endoplasmic reticulum-type signal cleavage sites, although they cannot divide. We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). We propose that Thermotogales ancestor spheroids came to divide owing to the archaeal cell division genes horizontally transferred via virus-related particles, forming the first eukaryotic common ancestor (FECA). Referring to the hypothesis, the archaeal information-processing system would have been established in FECA by random joining DNAs excised from the MILG, which contained horizontally transferred archaeal and bacterial DNAs, followed by reorganization by the MILG-enabled homologous recombination. Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. The random joining of DNAs likely provided the basic mechanisms for eukaryotic evolution: producing the diversity by the formations of supergroups, novel genes, and introns that are involved in exon shuffling.

iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou's 5-step rule

Among different post-translational modifications (PTMs), one of the most important one is the lysine crotonylation in proteins. Its importance cannot be undermined related to different diseases and essential biological practice. The key step for finding the hidden mechanisms of crotonylation along with their occurrence sites is to completely apprehend the mechanism behind this biological process. In previously reported studies, researchers have used different techniques, like position weighted matrix (PWM), support vector machine (SVM), k nearest neighbors (KNN), and many others. However, the maximum prediction accuracy achieved was not such high. To address this, herein, we propose an improved predictor for lysine crotonylation sites named iCrotoK-PseAAC, in which we have incorporated various position and composition relative features along with statistical moments into PseAAC. The results of self-consistency testing were 100% accurate, while the 10-fold cross validation gave 99.0% accuracy. Based on the validation and comparison of model, it is concluded that the iCrotoK-PseAAC is more accurate than the previously proposed models.

Bioinformatics analysis of Ras homologue enriched in the striatum, a potential target for Huntington's disease therapy

Huntington's disease (HD) is a lethal neurodegenerative disorder for which no cure is available yet. It is caused by abnormal expansion of a CAG triplet in the gene encoding the huntingtin protein (Htt), with consequent expansion of a polyglutamine repeat in mutated Htt (mHtt). This makes mHtt highly unstable and aggregation prone. Soluble mHtt is linked to cytotoxicity and neurotoxicity, whereas mHtt aggregates are thought to be neuroprotective. While Htt and mHtt are ubiquitously expressed throughout the brain and peripheral tissues, HD is characterized by selective degradation of the corpus striatum, without notable alterations in peripheral tissues. Screening for mRNAs preferentially expressed in rodent striatum led to the discovery of a GTP binding protein homologous to Ras family members. Due to these features, the newly discovered protein was termed Ras Homolog Enriched in Striatum (RHES). The aetiological role of RHES in HD has been ascribed to its small ubiquitin-like modifier (SUMO)-E3 ligase function. RHES sumoylates mHtt with higher efficiency than wild-type Htt, thereby protecting mHtt from degradation and increasing the amounts of the soluble form. Although RHES is an attractive target for HD treatment, essential information about protein structure and function are still missing. With the aim of investigating RHES 3D structure and function, bioinformatic analyses and molecular modelling have been performed in the present study, based on which, RHES regions predicted to be involved in the interaction with mHtt or the SUMO-E2 ligase Ubc9 have been identified. These regions have been used to design peptides aimed at inhibiting RHES interactions and, therefore, mHtt sumoylation; in turn, these peptides will be used to develop small molecule inhibitors by both rational design and virtual screening of large compound libraries. Once identified, RHES sumoylation inhibitors may open the road to the development of therapeutic agents against the severe, and currently untreatable, HD.

Characterization and expression in Pichia pastoris of a raw starch degrading glucoamylase (GA2) derived from Aspergillus flavus NSH9

The Aspergillus flavus NSH9 gene, encoding a pH and thermostable glucoamylase with a starch binding domain (SBD), was expressed in Pichia pastoris to produce recombinant glucoamylase (rGA2). The full-length glucoamylase gene (2039 bp), and cDNA (1839 bp) encode a 612 amino acid protein most similar to glucoamylase from Aspergillus oryzae RIB40; the first 19 amino acids are presumed to be a signal peptide for secretion, and the SBD is at the C-terminal. The cDNA was successfully secreted by Pichia at 8.23 U mL^-1, and the rGA2 was found to be: a 80 kDa monomer, stable from pH 3.0-9.0, with optimum catalytic activity at pH 5.0, active at temperatures up to 80°C (rGA2 retained 58% of its activity after 60 min of incubation at 70°C), and metal ions such as Na⁺, K⁺, Ca⁺⁺ and Mg⁺⁺ enhanced rGA2 enzyme activity. The starch degrading ability of rGA2 was also observed on raw sago starch and where prolonged incubation generated larger, deeper, holes on the starch granules, indicating rGA2 is an excellent candidate for industrial starch processing applications.

Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition

Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth.

A Brief History of Protein Sorting Prediction

Ever since the signal hypothesis was proposed in 1971, the exact nature of signal peptides has been a focus point of research. The prediction of signal peptides and protein subcellular location from amino acid sequences has been an important problem in bioinformatics since the dawn of this research field, involving many statistical and machine learning technologies. In this review, we provide a historical account of how position-weight matrices, artificial neural networks, hidden Markov models, support vector machines and, lately, deep learning techniques have been used in the attempts to predict where proteins go. Because the secretory pathway was the first one to be studied both experimentally and through bioinformatics, our main focus is on the historical development of prediction methods for signal peptides that target proteins for secretion; prediction methods to identify targeting signals for other cellular compartments are treated in less detail.

Three dimensional structure prediction of panomycocin, a novel Exo-β-1,3-glucanase isolated from Wickerhamomyces anomalus NCYC 434 and the computational site-directed mutagenesis studies to enhance its thermal stability for therapeutic applications

Panomycocin is a naturally produced potent antimycotic/antifungal protein secreted by the yeast Wickerhamomyces anomalus NCYC 434 with an exo-β-1,3-glucanase activity. In this study the three dimensional structure of panomycocin was predicted and the computational site-directed mutagenesis was performed to enhance its thermal stability in liquid formulations over the body temperature for topical therapeutic applications. Homology modeling was performed with MODELLER and I-TASSER. Among the generated models, the model with the lowest energy and DOPE score was selected for further loop modeling. The loop model was optimized and the reliability of the model was confirmed with ERRAT, Verify 3D and Ramachandran plot values. Enhancement of the thermal stability of the model was done using contemporary servers and programs such as SPDBViewer, CNA, I-Mutant2.0, Eris, AUTO-MUTE and MUpro. In the region outside the binding site of the model Leu52 Arg, Phe223Arg and Gly254Arg were found to be the best thermostabilizing mutations with 6.26 K, 6.26 K and 8.27 K increases, respectively. In the binding site Glu186Arg was found to be the best thermostabilizer mutation with a 9.58 K temperature increase. The results obtained in this study led us to design a mutant panomycocin that can be used as a novel antimycotic/antifungal drug in a liquid formulation for topical applications over the normal body temperature.

The classical NLRP3 inflammasome controls FADD unconventional secretion through microvesicle shedding

Fas-associated death domain (FADD) is a key adaptor molecule involved in numerous physiological processes including cell death, proliferation, innate immunity and inflammation. Therefore, changes in FADD expression have dramatic cellular consequences. In mice and humans, FADD regulation can occur through protein secretion. However, the molecular mechanisms accounting for human FADD secretion were still unknown. Here we report that canonical, non-canonical, but not alternative, NLRP3 inflammasome activation in human monocytes/macrophages induced FADD secretion. NLRP3 inflammasome activation by the bacterial toxin nigericin led to the proinflammatory interleukin-1β (IL-1β) release and to the induction of cell death by pyroptosis. However, we showed that FADD secretion could occur in absence of increased IL-1β release and pyroptosis and, reciprocally, that IL-1β release and pyroptosis could occur in absence of FADD secretion. Especially, FADD, but not IL-1β, secretion following NLRP3 inflammasome activation required extracellular glucose. Thus, FADD secretion was an active process distinct from unspecific release of proteins during pyroptosis. This FADD secretion process required K⁺ efflux, NLRP3 sensor, ASC adaptor and CASPASE-1 molecule. Moreover, we identified FADD as a leaderless protein unconventionally secreted through microvesicle shedding, but not exosome release. Finally, we established human soluble FADD as a new marker of joint inflammation in gout and rheumatoid arthritis, two rheumatic diseases involving the NLRP3 inflammasome. Whether soluble FADD could be an actor in these diseases remains to be determined. Nevertheless, our results advance our understanding of the mechanisms contributing to the regulation of the FADD protein expression in human cells.

Building a platform for predicting functions of serine protease-related proteins in Drosophila melanogaster and other insects

Serine proteases (SPs) and serine protease homologs (SPHs) play essential roles in insect physiological processes including digestion, defense and development. Studies of insect genomes, transcriptomes and proteomes have generated a vast amount of information on these proteins, dwarfing the biological data acquired from a few model species. The large number and high diversity of homologous sequences makes it a challenge to use the limited functional information for making predictions across a broad taxonomic group of insects. In this work, we have extensively updated the framework of knowledge on the SP-related proteins in Drosophila melanogaster by identifying 52 new SPs/SPHs, classifying the 257 proteins into four groups (CLIP, gut, single- and multi-domain SPs/SPHs), and detecting inherent connections among phylogenetic relationships, genomic locations and expression profiles for 99 of the genes. Information on the existence of specific proteins in eggs, larvae, pupae and adults is presented to facilitate future research. More importantly, we have developed an approach to reveal close homologous or orthologous relationships among SPs/SPHs from D. melanogaster, Anopheles gambiae, Apis mellifera, Manduca sexta, and Tribolium castaneum thus inspiring functional studies in these and other holometabolous insects. This approach is useful for tackling similar problems on large and diverse protein families in other groups of organisms.

Prediction of Signal Peptides in Proteins from Malaria Parasites

Signal peptides are N-terminal presequences responsible for targeting proteins to the endomembrane system, and subsequent subcellular or extracellular compartments, and consequently condition their proper function. The significance of signal peptides stimulates development of new computational methods for their detection. These methods employ learning systems trained on datasets comprising signal peptides from different types of proteins and taxonomic groups. As a result, the accuracy of predictions are high in the case of signal peptides that are well-represented in databases, but might be low in other, atypical cases. Such atypical signal peptides are present in proteins found in apicomplexan parasites, causative agents of malaria and toxoplasmosis. Apicomplexan proteins have a unique amino acid composition due to their AT-biased genomes. Therefore, we designed a new, more flexible and universal probabilistic model for recognition of atypical eukaryotic signal peptides. Our approach called signalHsmm includes knowledge about the structure of signal peptides and physicochemical properties of amino acids. It is able to recognize signal peptides from the malaria parasites and related species more accurately than popular programs. Moreover, it is still universal enough to provide prediction of other signal peptides on par with the best preforming predictors.

In silico prediction, phylogenetic and bioinformatic analysis of SoPCS gene, survey of its protein characterization and gene expression in response to cadmium in Saccharum officinarum

Phytochelatin synthase isolated from microorganisms, yeasts, algae and plant, serve a fundamental role in reducing heavy metals. In this research the in silico PCS gene structure (SoPCS) of sugarcane, its secondary and 3D protein structure, physicochemical properties, cell localization and phylogenetic tree were predicted utilizing bioinformatics tools. SoPCS expression in the leaves and roots of sugarcane in tissue culture treated with cadmium was also studied utilizing real time PCR. The predicted SoPCS gene contains 1524 nucleotides, a protein encoded with 508 amino acids of which the molecular weight is 55953.3 Da, 6 exons and 5 introns. The subcellular position of the enzyme is mitochondrion or cytoplasmic. Two domains belonging to the phytochelatin synthase family with similar features was found in Pfam having more than 97% similarity with the predicted SoPCS protein. Phylogeny analyses of plant species were well isolated from other organisms. Ten disulfide-bonded cysteines were excluded from the structure of SoPCS. The predicted 3D structure of SoPCS showed that it is able to bind to L-gamma-glutamylcysteine as substrate. The binding site sequence of PCS included amino acids 52(Q),55(P),56(A),57(F), 58(C),103(G),104(I),151(S),163(G),165(F),206(D), 213(R). The common amino acid with conserved sequence in the binding site of the plant was 103Gly. Gene expression indicated that SoPCS has an important role in the response of sugarcane to cadmium with potential use in genetic engineering to remove metal contaminants in the environment. This is the first characterization of a PCS from sugarcane.

Host Cell Proteome of Physcomitrella patens Harbors Proteases and Protease Inhibitors under Bioproduction Conditions

Host cell proteins are inevitable contaminants of biopharmaceuticals. Here, we performed detailed analyses of the host cell proteome of moss ( Physcomitrella patens) bioreactor supernatants using mass spectrometry and subsequent bioinformatics analysis. Distinguishing between the apparent secretome and intracellular contaminants, a complex extracellular proteolytic network including subtilisin-like proteases, metallo-proteases, and aspartic proteases was identified. Knockout of a subtilisin-like protease affected the overall extracellular proteolytic activity. Besides proteases, also secreted protease-inhibiting proteins such as serpins were identified. Further, we confirmed predicted cleavage sites of 40 endogenous signal peptides employing an N-terminomics approach. The present data provide novel aspects to optimize both product stability of recombinant biopharmaceuticals as well as their maturation along the secretory pathway. Data are available via ProteomeXchange with identifier PXD009517.

iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC

Protein hydroxylation is a posttranslational modification (PTM), in which a CH group in Pro (P) or Lys (K) residue has been converted into a COH group, or a hydroxyl group (−OH) is converted into an organic compound. Closely associated with cellular signaling activities, this type of PTM is also involved in some major diseases, such as stomach cancer and lung cancer. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of P or K, which ones can be hydroxylated, and which ones cannot? With the explosive growth of protein sequences in the post-genomic age, the problem has become even more urgent. To address such a problem, we have developed a predictor called iHyd-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition (PseAAC) and introducing the “Random Forest” algorithm to operate the calculation. Rigorous jackknife tests indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for iHyd-PseCp has been established at http://www.jci-bioinfo.cn/iHyd-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences

Catalyzed by adenosine deaminase (ADAR), the adenosine to inosine (A-to-I) editing in RNA is not only involved in various important biological processes, but also closely associated with a series of major diseases. Therefore, knowledge about the A-to-I editing sites in RNA is crucially important for both basic research and drug development. Given an uncharacterized RNA sequence that contains many adenosine (A) residues, can we identify which one of them can be of A-to-I editing, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such an important problem based on the RNA sequence information alone. To fill this empty area, we have proposed a predictor called iRNA-AI by incorporating the chemical properties of nucleotides and their sliding occurrence density distribution along a RNA sequence into the general form of pseudo nucleotide composition (PseKNC). It has been shown by the rigorous jackknife test and independent dataset test that the performance of the proposed predictor is quite promising. For the convenience of most experimental scientists, a user-friendly web-server for iRNA-AI has been established at http://lin.uestc.edu.cn/server/iRNA-AI/, by which users can easily get their desired results without the need to go through the mathematical details.

iPhos-PseEn: identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier

Protein phosphorylation is a posttranslational modification (PTM or PTLM), where a phosphoryl group is added to the residue(s) of a protein molecule. The most commonly phosphorylated amino acids occur at serine (S), threonine (T), and tyrosine (Y). Protein phosphorylation plays a significant role in a wide range of cellular processes; meanwhile its dysregulation is also involved with many diseases. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of S, T, or Y, which ones can be phosphorylated, and which ones cannot? To address this problem, we have developed a predictor called iPhos-PseEn by fusing four different pseudo component approaches (amino acids’ disorder scores, nearest neighbor scores, occurrence frequencies, and position weights) into an ensemble classifier via a voting system. Rigorous cross-validations indicated that the proposed predictor remarkably outperformed its existing counterparts. For the convenience of most experimental scientists, a user-friendly web-server for iPhos-PseEn has been established at http://www.jci-bioinfo.cn/iPhos-PseEn, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

A Novel Modeling in Mathematical Biology for Classification of Signal Peptides

The molecular structure of macromolecules in living cells is ambiguous unless we classify them in a scientific manner. Signal peptides are of vital importance in determining the behavior of newly formed proteins towards their destined path in cellular and extracellular location in both eukaryotes and prokaryotes. In the present research work, a novel method is offered to foreknow the behavior of signal peptides and determine their cleavage site. The proposed model employs neural networks using isolated sets of prokaryote and eukaryote primary sequences. Protein sequences are classified as secretory or non-secretory in order to investigate secretory proteins and their signal peptides. In comparison with the previous prediction tools, the proposed algorithm is more rigorous, well-organized, significantly appropriate and highly accurate for the examination of signal peptides even in extensive collection of protein sequences.

Serine protease-related proteins in the malaria mosquito, Anopheles gambiae

Insect serine proteases (SPs) and serine protease homologs (SPHs) participate in digestion, defense, development, and other physiological processes. In mosquitoes, some clip-domain SPs and SPHs (i.e. CLIPs) have been investigated for possible roles in antiparasitic responses. In a recent test aimed at improving quality of gene models in the Anopheles gambiae genome using RNA-seq data, we observed various discrepancies between gene models in AgamP4.5 and corresponding sequences selected from those modeled by Cufflinks, Trinity and Bridger. Here we report a comparative analysis of the 337 SP-related proteins in A. gambiae by examining their domain structures, sequence diversity, chromosomal locations, and expression patterns. One hundred and ten CLIPs contain 1 to 5 clip domains in addition to their protease domains (PDs) or non-catalytic, protease-like domains (PLDs). They are divided into five subgroups: CLIPAs (22) are clip_1-5-PLD; CLIPBs (29), CLIPCs (12) and CLIPDs (14) are mainly clip-PD; most CLIPEs (33) have a domain structure of PD/PLD-PLD-clip-PLD_0-1. While expression of the CLIP genes in group-1 is generally low and detected in various tissue- and stage-specific RNA-seq libraries, some putative GPs/GPHs (i.e. single domain gut SPs/SPHs) in group-2 are highly expressed in midgut, whole larva or whole adult libraries. In comparison, 46 SPs, 26 SPHs, and 37 multi-domain SPs/SPHs (i.e. PD/PLD-PLD_≥1) in group-3 do not seem to be specifically expressed in digestive tract. There are 16 SPs and 2 SPH containing other types of putative regulatory domains (e.g. LDLa, CUB, Gd). Of the 337 SP and SPH genes, 159 were sorted into 46 groups (2-8 members/group) based on similar phylogenetic tree position, chromosomal location, and expression profile. This information and analysis, including improved gene models and protein sequences, constitute a solid foundation for functional analysis of the SP-related proteins in A. gambiae.

Hemolymph proteins of Anopheles gambiae larvae infected by Escherichia coli

Anopheles gambiae is a major vector of human malaria and its immune system in part determines the fate of ingested parasites. Proteins, hemocytes and fat body in hemolymph are critical components of this system, mediating both humoral and cellular defenses. Here we assessed differences in the hemolymph proteomes of water- and E. coli-pricked mosquito larvae by a gel-LC-MS approach. Among the 1756 proteins identified, 603 contained a signal peptide but accounted for two-third of the total protein amount on the quantitative basis. The sequence homology search indicated that 233 of the 1756 may be related to defense. In general, we did not detect substantial differences between the control and induced plasma samples in terms of protein numbers or levels. Protein distributions in the gel slices suggested post-translational modifications (e.g. proteolysis) and formation of serpin-protease complexes and high Mr immune complexes. Based on the twenty-five most abundant proteins, we further suggest that major functions of the larval hemolymph are storage, transport, and immunity. In summary, this study provided first data on constitution, levels, and possible functions of hemolymph proteins in the mosquito larvae, reflecting complex changes occurring in the fight against E. coli infection.

Vibrio vulnificus VvhA induces Th1 and Tfh cells to proliferate against Vibrio vulnificus in a mouse model of infection

AIM

To characterize the roles of VvhA in host's acquired immune response to Vibrio vulnificus infection.

MATERIALS & METHODS

The recombinant VvhA fusion protein was used to immunize mice and the anti-VvhA polyclonal antibody was produced in vivo for prophylactic and therapeutic efficacy assay. The roles of VvhA in T helper (Th) cells differentiation were analyzed by vvhA-deleted mutant during the early phase of infection, while the ratio of Th2 and T follicular helper (Tfh) cells were examined in VvhA immunization.

RESULTS

Anti-VvhA antibody exhibited neutralization activity against V. vulnificus. Wild-type strain induced higher level of Th1 cells than the mutant, and the concentrations of IgG2a and IFN-γ were increased during the early phase of infection. The spontaneous development of Tfh was observed in immunized model, and the serum IL-21 was increased.

CONCLUSION

V. vulnificus VvhA elicited cellular and humoral immune responses by Th1 and Tfh cells to provide protection against VvhA.

Haemophilus parasuis cytolethal distending toxin induces cell cycle arrest and p53-dependent apoptosis

Haemophilus parasuis is the causative agent of Glasser’s disease in pigs. Cytolethal distending toxin (CDT) is an important virulence factor of H. parasuis. It is composed of three subunits: CdtA, CdtB and CdtC and all were successfully expressed in soluble form in Escherichia coli when the signal peptides were removed. Purified CdtB had DNase activity, i.e. caused DNA double strand damage, in vitro and in vivo prior to cell arrest and apoptosis. Flow cytometry analysis showed CdtB alone could induce cell cycle arrest and apoptosis in PK-15 porcine kidney and pulmonary alveolar macrophage (PAM) cells, which could be enhanced by CdtA or/and CdtC. CDT holotoxin could lead to significant cell distension, G₂ arrest and apoptotic death in PK-15 and PAM cells. The apoptosis induced by CDT holotoxin was significantly inhibited by pifithrin-α, which indicates that it is p53-dependent. The results suggest that H. parasuis CDT holotoxin is a major virulence factor.

Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle-Associated Genes

Mango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq. Approximately 400 million reads were generated and de novo assembled into 107,744 unigenes, with a mean length of 1,717 bp and with this information an online Mango RNA-Seq Database (http://bioinfo.bti.cornell.edu/cgi-bin/mango/index.cgi) which is a valuable genomic resource for molecular research into the biology of mango fruit was created. RNA-Seq analysis suggested that the pathway leading to biosynthesis of the cuticle component, cutin, is up-regulated during overripening. This data was supported by analysis of the expression of several putative cuticle-associated genes and by gravimetric and microscopic studies of cuticle deposition, revealing a complex continuous pattern of cuticle deposition during fruit development and involving substantial accumulation during ripening/overripening.

2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function

Involved with important cellular or gene functions and implicated with many kinds of cancers, piRNAs, or piwi-interacting RNAs, are of small non-coding RNA with around 19–33 nt in length. Given a small non-coding RNA molecule, can we predict whether it is of piRNA according to its sequence information alone? Furthermore, there are two types of piRNA: one has the function of instructing target mRNA deadenylation, and the other does not. Can we discriminate one from the other? With the avalanche of RNA sequences emerging in the postgenomic age, it is urgent to address the two problems for both basic research and drug development. Unfortunately, to the best of our knowledge, so far no computational methods whatsoever could be used to deal with the second problem, let alone deal with the two problems together. Here, by incorporating the physicochemical properties of nucleotides into the pseudo K-tuple nucleotide composition (PseKNC), we proposed a powerful predictor called 2L-piRNA. It is a two-layer ensemble classifier, in which the first layer is for identifying whether a query RNA molecule is piRNA or non-piRNA, and the second layer for identifying whether a piRNA is with or without the function of instructing target mRNA deadenylation. Rigorous cross-validations have indicated that the success rates achieved by the proposed predictor are quite high. For the convenience of most biologists and drug development scientists, the web server for 2L-piRNA has been established at http://bioinformatics.hitsz.edu.cn/2L-piRNA/, by which users can easily get their desired results without the need to go through the mathematical details.

Signal-3L 2.0: A Hierarchical Mixture Model for Enhancing Protein Signal Peptide Prediction by Incorporating Residue-Domain Cross-Level Features

Signal peptides play key roles in targeting and translocation of integral membrane proteins and secretory proteins. However, signal peptides present several challenges for automatic prediction methods. One challenge is that it is difficult to discriminate signal peptides from transmembrane helices, as both the H-region of the peptides and the transmembrane helices are hydrophobic. Another is that it is difficult to identify the cleavage site between signal peptides and mature proteins, as cleavage motifs or patterns are still unclear for most proteins. To solve these problems and further enhance automatic signal peptide recognition, we report a new Signal-3L 2.0 predictor. Our new model is constructed with a hierarchical protocol, where it first determines the existence of a signal peptide. For this, we propose a new residue-domain cross-level feature-driven approach, and we demonstrate that protein functional domain information is particularly useful for discriminating between the transmembrane helices and signal peptides as they perform different functions. Next, in order to accurately identify the unique signal peptide cleavage sites along the sequence, we designed a top-down approach where a subset of potential cleavage sites are screened using statistical learning rules, and then a final unique site is selected according to its evolution conservation score. Because this mixed approach utilizes both statistical learning and evolution analysis, it shows a strong capacity for recognizing cleavage sites. Signal-3L 2.0 has been benchmarked on multiple data sets, and the experimental results have demonstrated its accuracy. The online server is available at www.csbio.sjtu.edu.cn/bioinf/Signal-3L/ .

Constitutive expression and characterization of a surface SRS (NcSRS67) protein of Neospora caninum with no orthologue in Toxoplasma gondii

Neospora caninum is a parasite of the Apicomplexa phylum responsible for abortion and losses of fertility in cattle. As part of its intracellular cycle, the first interaction of the parasite with the target cell is performed with the surface proteins known as the SRS superfamily (Surface Antigen Glycoprotein - Related Sequences). SAG related or SRS proteins have been a target of intense research due to its immunodominant pattern, exhibiting potential as diagnostic and/or vaccine candidates. The aim of this study was the cloning, expression and characterization of the gene NcSRS67 of N. caninum using a novel designed plasmid. The coding sequence of NcSRS67 (without the signal peptide and the GPI anchor) was cloned and expressed constitutively instead of the ccdB system of pCR-Blunt II-TOPO. The protein was purified in a nickel sepharose column and identified by mass spectrometry (MS/MS). The constitutive expression did not affect the final bacterial growth, with a similar OD 600nm compared to the non-transformed strains. The recombinant NcSRS67 was over expressed and the native form was detected by the anti-rNcSRS67 serum on 1D western blot as a single band of approximately 38kDa as predicted. On an in vitro assay, the inhibitory effect of the polyclonal antiserum anti-rNcSRS67 was nearly 20% on adhesion/invasion of host cells. The NcSRS67 native protein was localised on part of the surface of N. caninum tachyzoite when compared to the nucleus by confocal immunofluorescence.

Metabolic engineering of Ustilago trichophora TZ1 for improved malic acid production

Ustilago trichophora RK089 has been found recently as a good natural malic acid producer from glycerol. This strain has previously undergone adaptive laboratory evolution for enhanced substrate uptake rate resulting in the strain U. trichophora TZ1. Medium optimization and investigation of process parameters enabled titers and rates that are able to compete with those of organisms overexpressing major parts of the underlying metabolic pathways. Metabolic engineering can likely further increase the efficiency of malate production by this organism, provided that basic genetic tools and methods can be established for this rarely used and relatively obscure species.

Here we investigate and adapt existing molecular tools from U. maydis for use in U. trichophora. Selection markers from U. maydis that confer carboxin, hygromycin, nourseothricin, and phleomycin resistance are applicable in U. trichophora. A plasmid was constructed containing the ip-locus of U. trichophora RK089, resulting in site-specific integration into the genome. Using this plasmid, overexpression of pyruvate carboxylase, two malate dehydrogenases (mdh1, mdh2), and two malate transporters (ssu1, ssu2) was possible in U. trichophora TZ1 under control of the strong P_etef promoter. Overexpression of mdh1, mdh2, ssu1, and ssu2 increased the product (malate) to substrate (glycerol) yield by up to 54% in shake flasks reaching a titer of up to 120 g L⁻¹. In bioreactor cultivations of U. trichophora TZ1 P_etefssu2 and U. trichophora TZ1 P_etefmdh2 a drastically lowered biomass formation and glycerol uptake rate resulted in 29% (Ssu1) and 38% (Mdh2) higher specific production rates and 38% (Ssu1) and 46% (Mdh2) increased yields compared to the reference strain U. trichophora TZ1. Investigation of the product spectrum resulted in an 87% closed carbon balance with 134 g L⁻¹ malate and biomass (73 g L⁻¹), succinate (20 g L⁻¹), CO₂ (¹7 g L⁻¹), and α-ketoglutarate (8 g L⁻¹) as main by-products.

These results open up a wide range of possibilities for further optimization, especially combinatorial metabolic engineering to increase the flux from pyruvate to malic acid and to reduce by-product formation.

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Metabolic engineering tools established for U. trichophora

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Potentially carbon neutral process through CO₂ co-metabolism

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Optimized malic acid production from glycerol by overexpression of rTCA cycle

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Specific production rate and yield increased up to 38% and 46%, respectively

Multiple gene and transcript variants encoding trout C-polysaccharide binding proteins are differentially but strongly induced after infection with Aeromonas salmonicida

Two 'trout C-polysaccharide-binding proteins,' TCBP1 and -2, with relevance to early inflammatory events have been discovered in the last century. The present study characterises the respective cDNA sequences from rainbow trout (Oncorhynchus mykiss), including multiple TCBP1 transcript variants. These variants are generated either by the use of alternative splice sites or the exclusion of exons. The longest mRNA isoform, TCBP1-1, encodes a 245-aa protein with a large signal peptide and a complement component C1q domain. The shortest mRNA isoform, TCBP1-5, contains a premature termination codon and hence fails to encode a functional factor. The 224-aa-long TCBP2 protein consists of a comparably shorter signal peptide and a pentraxin domain. Evolutionary analyses clearly separated TCBP1 and -2 because of distinctive protein motifs. Expression profiling in the liver, spleen, and head kidney tissues of healthy trout revealed that TCBP2 mRNA concentrations were higher than the concentrations of all five TCBP1 mRNA isoforms together. The hepatic levels of these TCBP1 variants increased significantly upon infection with Aeromonas salmonicida, whereas TCBP2 transcript levels rose moderately. As the biological function of TCBP1 is barely understood, we tagged this factor with the green fluorescent protein and visualised its expression in HEK-293 cells. Overexpression of TCBP1 increased the level of active NF-κB factors and induced cell death, indicating its involvement in proapoptotic NF-κB-dependent signalling routes.

SEC-Translocon Dependent Extracytoplasmic Proteins of Candidatus Liberibacter asiaticus

Citrus Huanglongbing (HLB) is the most destructive citrus disease worldwide. HLB is associated with three species of the phloem-limited, gram-negative, fastidious α-proteobacteria: Candidatus Liberibacter asiaticus (Las), Ca. L. americanus (Lam), and Ca. L. africanus (Laf) with Las being the most widespread species. Las has not been cultured in artificial media, which has greatly hampered our efforts to understand its virulence mechanisms. Las contains a complete Sec-translocon, which has been suggested to transport Las proteins including virulence factors into the extracytoplasmic milieu. In this study, we characterized the Sec-translocon dependent, signal peptide containing extracytoplasmic proteins of Las. A total of 166 proteins of Las-psy62 strain were predicted to contain signal peptides targeting them out of the cell cytoplasm via the Sec-translocon using LipoP, SigalP 3.0, SignalP 4.1, and Phobius. We also predicated SP containing extracytoplasmic proteins for Las-gxpsy and Las-Ishi-1, Lam, Laf, Ca. L. solanacearum (Lso), and L. crescens (Lcr). For experimental validation of the predicted extracytoplasmic proteins, Escherichia coli based alkaline phosphatase (PhoA) gene fusion assays were conducted. A total of 86 out of the 166 predicted Las proteins were experimentally validated to contain signal peptides. Additionally, Las-psy62 lepB (CLIBASIA_04190), the gene encodes signal peptidase I, was able to partially complement the amber mutant of lepB of E. coli. This work will contribute to the identification of Sec-translocon dependent effector proteins of Las, which might be involved in virulence of Las.

A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica

An endogenous retrovirus that is present in the sea slug Elysia chlorotica is expressed in all individuals at the end of the annual life cycle. But the precise role of the virus, if any, in slug senescence or death is unknown. We have determined the genomic sequence of the virus and performed a phylogenetic analysis of the data. The 6060-base pair genome of the virus possesses a reverse transcriptase-domain-containing protein that shows similarity to retrotransposon sequences found in Aplysia californica and Strongylocentrotus purpuratus. However, nucleotide BLAST analysis of the whole genome resulted in hits to only a few portions of the genome, indicating that the Elysia chlorotica retrovirus is novel, has not been previously sequenced, and does not have great genetic similarity to other known viral species. When more invertebrate retroviral genomes are examined, a more precise phylogenetic placement of the Elysia chlorotica retrovirus can be determined.

A viral histone H4 suppresses insect insulin signal and delays host development

Parasitization by an endoparasitoid wasp, Cotesia plutellae, alters host development of Plutella xylostella by extending larval period and preventing metamorphosis. Insulin signal plays a crucial role in mediating insect development and controlling blood sugar level in insects. In this study, three insulin-like peptide genes (PxILP1-3) were predicted from the genome of P. xylostella. However, only PxILP1 was confirmed to be expressed in P. xylostella. Starvation suppressed the expression level of PxILP1 and up-regulated plasma trehalose level. RNA interference against PxILP1 mimicked starvation effect and extended the larval period of P. xylostella. Parasitized larvae exhibited significantly lower levels of PxILP1 expression compared to nonparasitized larvae. Injection of wasp-symbiotic polydnavirus C. plutellae bracovirus (CpBV) also suppressed PxILP1 expression and extended the larval period. Injection of a viral segment (CpBV-S30) containing a viral histone H4 (CpBV-H4) also suppressed PxILP1 expression. Co-injection of CpBV-S30 and double-stranded RNA (dsCpBV-H4) specific to CpBV-H4 rescued the suppression of PxILP1 expression. Injection of CpBV-S30 significantly extended larval development. Co-injection of CpBV-S30 with dsCpBV-H4 rescued the delay of larval development. Injection of a bovine insulin to parasitized larvae prevented parasitoid development. These results indicate that parasitism of C. plutellae can down-regulate host insulin signaling with the help of parasitic factor CpBV-H4.