Prediction of neurotoxins based on their function and source

We have developed a method NTXpred for predicting neurotoxins and classifying them based on their function and origin. The dataset used in this study consists of 582 non-redundant, experimentally annotated neurotoxins obtained from Swiss-Prot. A number of modules have been developed for predicting neurotoxins using residue composition based on feed-forwarded neural network (FNN), recurrent neural network (RNN), support vector machine (SVM) and achieved maximum accuracy of 84.19%, 92.75%, 97.72% respectively. In addition, SVM modules have been developed for classifying neurotoxins based on their source (e.g., eubacteria, cnidarians, molluscs, arthropods have been and chordate) using amino acid composition and dipeptide composition and achieved maximum overall accuracy of 78.94% and 88.07% respectively. The overall accuracy increased to 92.10%, when the evolutionary information obtained from PSI-BLAST was combined with SVM module of source classification. We have also developed SVM modules for classifying neurotoxins based on functions using amino acid, dipeptide composition and achieved overall accuracy of 83.11%, 91.10% respectively. The overall accuracy of function classification improved to 95.11%, when PSI-BLAST output was combined with SVM module. All the modules developed in this study were evaluated using five-fold cross-validation technique. The NTXpred is available at www.imtech.res.in/raghava/ntxpred/ and mirror site at http://bioinformatics.uams.edu/mirror/ntxpred.     

ω‐Turn: A novel β‐turn mimic in globular proteins stabilized by main‐chain to side‐chain CH···O interaction

Mimicry of structural motifs is a common feature in proteins. The 10‐membered hydrogen‐bonded ring involving the main‐chain C?O in a β‐turn can be formed using a side‐chain carbonyl group leading to Asx‐turn. We show that the N? H component of hydrogen bond can be replaced by a C^γ‐H group in the side chain, culminating in a nonconventional C? H···O interaction. Because of its shape this β‐turn mimic is designated as ω‐turn, which is found to occur ～three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C? H···O interaction occurring between the terminal residues, constraining the torsion angles ?_{i + 1}, ψ_{i + 1}, ?_{i + 2} and χ′_{1(i + 2)} (using the interacting C^γ atom). Based on these angles there are two types of ω‐turns, each of which can be further divided into two groups. C^β‐branched side‐chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal‐binding sites. N‐linked glycosylation occurs at the consensus pattern Asn‐Xaa‐Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω‐turn, which may be the recognition site for protein modification. Location between two β‐strands is the most common occurrence in protein tertiary structure, and being generally exposed ω‐turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. Proteins 2015; 83:203–214. © 2014 Wiley Periodicals, Inc.     

Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T

We report the 4.98-Mb genome sequence of Marinilabilia salmonicolor JCM 21150(T), which was isolated from marine mud in the year 1961. The draft genome of strain Marinilabilia salmonicolor JCM 21150(T) contains 4,982,627 bp with a G+C content of 41.92% and 4,227 protein coding genes, 52 tRNAs, and 3 rRNAs.     

Evidence for involvement of Th17 type responses in post kala azar dermal leishmaniasis (PKDL)

Background

Post kala-azar dermal leishmaniasis (PKDL), a dermal sequel of visceral leishmaniasis, caused by Leishmania donovani, constitutes an important reservoir for the parasite. Parallel functioning of counter acting immune responses (Th1/Th2) reflects a complex immunological scenario, suggesting the involvement of additional regulatory molecules in the disease pathogenesis.

Methodology/Principal Findings

In the present study, human cytokine/chemokine/receptor specific cDNA array technique was employed to identify modulations in gene expression of host immuno-determinants during PKDL, followed by evaluation of Th17 type responses by analyzing mRNA and protein expression of Th17 markers (IL-23, IL-17, RORγt) and performing functional assays using Leishmania antigen (TSLA) or recombinant (rec)IL-17. Array analysis identified key immuno-regulatory molecules including cytokines (TNF-α, IFN-γ, IL-10, IL-17), chemokines (MCP-1, MIP-1α), apoptotic molecules (FasL, TRAIL, IRF-1) and receptors (CD40, Fas). Up regulation in lesional expression of Th17 markers was observed during PKDL compared to control (IL-17 and IL-23, P = 0.0008; RORγt, P = 0.02). In follow-up samples, chemotherapy significantly down regulated expression of all markers. In addition, lesional expression of IL-17 was confirmed at protein level by Immuno-histochemistry. Further, systemic presence of Th17 responses (IL-17 and IL-23) was observed in plasma samples from PKDL patients. In functional assays, TSLA stimulated the secretion of IL-17 and IL-23 from PBMCs of PKDL patients, while recIL-17 enhanced the production of TNF-α as well as nitric oxide (NO) in PKDL compared to control (TNF-α, P = 0.0002; NO, P = 0.0013). Further, a positive correlation was evident between lesional mRNA expression of IL-17 and TNF-α during PKDL.

Conclusion/Significance

The results highlight key immune modulators in PKDL and provide evidence for the involvement of Th17 type responses in the disease pathogenesis.     

Anti-cancer drug KP1019 modulates epigenetics and induces DNA damage response in Saccharomyces cerevisiae

KP1019 comprises a class of ruthenium compounds having promising anticancer activity. Here, we investigated the molecular targets of KP1019 using Saccharomyces cerevisiae as a model organism. Our results revealed that in the absence of the N-terminal tail of histone H3, the growth inhibitory effect of KP1019 was markedly enhanced. Furthermore, H3K56A or rtt109Δ mutants exhibit hypersensitivity for KP1019. Moreover, KP1019 evicts histones from the mononucleosome and interacts specifically with histone H3. We have also shown that KP1019 treatment causes induction of Ribonucleotide Reductase (RNR) genes and degradation of Sml1p. Our results also suggest that DNA damage induced by KP1019 is primarily repaired through double-strand break repair (DSBR). In summary, KP1019 targets histone proteins, with important consequences for DNA damage responses and epigenetics.     

Biodegradation of Carbazole and Dibenzothiophene by Bacteria Isolated from Petroleum-Contaminated Sites

This study reports the isolation of bacterial cultures, capable of selective removal of nitrogen and sulfur from carbazole and dibenzothiophene, respectively. The isolates utilizing carbazole were found to be suitable for biorefining. These were designated as P10 and P11, and were identified as Pseudomonas sp. Growing cells of P10 and P11 could utilize 77% carbazole in 250 and 120 h, respectively. Isolates showing utilization of dibenzothiophene were not suitable for biorefining industry. Results suggest these Pseudomonas isolates may be useful in petroleum biorefining for the selective removal of organically bound nitrogen from petroleum.