scholarly journals Comparative venom gland transcriptomics ofNaja kaouthia(monocled cobra) from Malaysia and Thailand: elucidating geographical venom variation and insights into sequence novelty

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3142 ◽  
Author(s):  
Kae Yi Tan ◽  
Choo Hock Tan ◽  
Lawan Chanhome ◽  
Nget Hong Tan
Keyword(s):  
Expression Patterns ◽  
Gene Families ◽  
Venom Gland ◽  
Acid Oxidase ◽  
Amino Acid Oxidase ◽  
Sequence Alignments ◽  
Illumina Hiseq ◽  
Multiple Sequence ◽  
Toxin Genes ◽  
Transcriptional Pattern

BackgroundThe monocled cobra (Naja kaouthia) is a medically important venomous snake in Southeast Asia. Its venom has been shown to vary geographically in relation to venom composition and neurotoxic activity, indicating vast diversity of the toxin genes within the species. To investigate the polygenic trait of the venom and its locale-specific variation, we profiled and compared the venom gland transcriptomes ofN. kaouthiafrom Malaysia (NK-M) and Thailand (NK-T) applying next-generation sequencing (NGS) technology.MethodsThe transcriptomes were sequenced on the Illumina HiSeq platform, assembled and followed by transcript clustering and annotations for gene expression and function. Pairwise or multiple sequence alignments were conducted on the toxin genes expressed. Substitution rates were studied for the major toxins co-expressed in NK-M and NK-T.Results and discussionThe toxin transcripts showed high redundancy (41–82% of the total mRNA expression) and comprised 23 gene families expressed in NK-M and NK-T, respectively (22 gene families were co-expressed). Among the venom genes, three-finger toxins (3FTxs) predominated in the expression, with multiple sequences noted. Comparative analysis and selection study revealed that 3FTxs are genetically conserved between the geographical specimens whilst demonstrating distinct differential expression patterns, implying gene up-regulation for selected principal toxins, or alternatively, enhanced transcript degradation or lack of transcription of certain traits. One of the striking features that elucidates the inter-geographical venom variation is the up-regulation of α-neurotoxins (constitutes ∼80.0% of toxin’s fragments per kilobase of exon model per million mapped reads (FPKM)), particularly the long-chain α-elapitoxin-Nk2a (48.3%) in NK-T but only 1.7% was noted in NK-M. Instead, short neurotoxin isoforms were up-regulated in NK-M (46.4%). Another distinct transcriptional pattern observed is the exclusively and abundantly expressed cytotoxin CTX-3 in NK-T. The findings suggested correlation with the geographical variation in proteome and toxicity of the venom, and support the call for optimising antivenom production and use in the region. Besides, the current study uncovered full and partial sequences of numerous toxin genes fromN. kaouthiawhich have not been reported hitherto; these includeN. kaouthia-specificl-amino acid oxidase (LAAO), snake venom serine protease (SVSP), cystatin, acetylcholinesterase (AChE), hyaluronidase (HYA), waprin, phospholipase B (PLB), aminopeptidase (AP), neprilysin, etc. Taken together, the findings further enrich the snake toxin database and provide deeper insights into the genetic diversity of cobra venom toxins.

scholarly journals Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3955 ◽  
Author(s):  
Yiling Niu ◽  
Tingting Zhao ◽  
Xiangyang Xu ◽  
Jingfu Li
Keyword(s):  
Gene Family ◽  
Solanum Lycopersicum ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Families ◽  
Shoot Meristem ◽  
Axillary Shoot ◽  
Multiple Sequence ◽  
Genome Wide ◽  
First Time

Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth.

scholarly journals Functional Characterization of a Venom Protein Calreticulin in the Ectoparasitoid Pachycrepoideus vindemiae

Insects ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 29 ◽  
Author(s):  
Lei Yang ◽  
Beibei Wang ◽  
Liming Qiu ◽  
Bin Wan ◽  
Yi Yang ◽  
...  
Keyword(s):  
Expression System ◽  
Functional Characterization ◽  
Venom Gland ◽  
Amino Acid Identity ◽  
Immunohistochemical Localization ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Venom Protein ◽  
Pupal Parasitoids ◽  
Venom Proteins

Venom proteins act in the immunological interactions between parasitoids and their host insects. The effect of venom proteins on host immunity is not fully understood in pupal parasitoids. We identified the functions of a venom protein, calreticulin (PvCRT), in the pupal ectoparasitoid Pachycrepoideus vindemiae. Here, we report that PvCRT features a signal peptide and two conserved “calreticulin” domains. Multiple sequence alignments show that PvCRT shares 83.54% amino acid identity with CRT from both Pteromalus puparum and Nasonia vitripennis, which infers a close relationship among these three species. Using qPCR analysis, we found a lower expression level of PvCRT (0.27-fold) in the venom apparatus compared to the corresponding carcass. Immunohistochemical localization revealed that PvCRT was ubiquitously expressed in venom gland. The expression of the PvCRT gene in Drosophila transgenic lines via the UAS/Gal4 binary expression system reduced the self-encapsulation phenotype of tu(1)Sz1 mutants. Additionally, studies on humoral immunity indicate that PvCRT does not affect the antimicrobial immune responses of the host. This work on an ectoparasitoid will increase our understanding of venom–mediated host-parasitoid interactions.

scholarly journals MipLAAO, a new L-amino acid oxidase from the redtail coral snake Micrurus mipartitus

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4924 ◽  
Author(s):  
Paola Rey-Suárez ◽  
Cristian Acosta ◽  
Uday Torres ◽  
Mónica Saldarriaga-Córdoba ◽  
Bruno Lomonte ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Venom Gland ◽  
Bactericidal Effect ◽  
Nucleotide Sequencing ◽  
Acid Oxidase ◽  
Amino Acid Oxidase ◽  
Homologous Proteins ◽  
Edema Formation ◽  
The Difference

L-amino acid oxidases (LAAOs) are ubiquitous enzymes in nature. Bioactivities described for these enzymes include apoptosis induction, edema formation, induction or inhibition of platelet aggregation, as well as antiviral, antiparasite, and antibacterial actions. With over 80 species, Micrurus snakes are the representatives of the Elapidae family in the New World. Although LAAOs in Micrurus venoms have been predicted by venom gland transcriptomic studies and detected in proteomic studies, no enzymes of this kind have been previously purified from their venoms. Earlier proteomic studies revealed that the venom of M. mipartitus from Colombia contains ∼4% of LAAO. This enzyme, here named MipLAAO, was isolated and biochemically and functionally characterized. The enzyme is found in monomeric form, with an isotope-averaged molecular mass of 59,100.6 Da, as determined by MALDI-TOF. Its oxidase activity shows substrate preference for hydrophobic amino acids, being optimal at pH 8.0. By nucleotide sequencing of venom gland cDNA of mRNA transcripts obtained from a single snake, six isoforms of MipLAAO with minor variations among them were retrieved. The deduced sequences present a mature chain of 483 amino acids, with a predicted pI of 8.9, and theoretical masses between 55,010.9 and 55,121.0 Da. The difference with experimentally observed mass is likely due to glycosylation, in agreement with the finding of three putative N-glycosylation sites in its amino acid sequence. A phylogenetic analysis of MmipLAAO placed this new enzyme within the clade of homologous proteins from elapid snakes, characterized by the conserved Serine at position 223, in contrast to LAAOs from viperids. MmipLAAO showed a potent bactericidal effect on S. aureus (MIC: 2 µg/mL), but not on E. coli. The former activity could be of interest to future studies assessing its potential as antimicrobial agent.

scholarly journals The N –methyl D–aspartate receptor glycine site and D–serine metabolism: an evolutionary perspective

2004 ◽  
Vol 359 (1446) ◽  
pp. 943-964 ◽  
Author(s):  
Michael J. Schell
Keyword(s):  
Nmda Receptor ◽  
Divergence Time ◽  
Postnatal Period ◽  
Serine Racemase ◽  
Acid Oxidase ◽  
Glycine Site ◽  
Amino Acid Oxidase ◽  
Sequence Alignments ◽  
Peroxisomal Enzyme ◽  
Serine Metabolism

The N –methyl D–aspartate (NMDA) type of glutamate receptor requires two distinct agonists to operate. Glycine is assumed to be the endogenous ligand for the NMDA receptor glycine site, but this notion has been challenged by the discovery of high levels of endogenous D–serine in the mammalian forebrain. I have outlined an evolutionary framework for the appearance of a glycine site in animals and the metabolic events leading to high levels of D–serine in brain. Sequence alignments of the glycine–binding regions, along with the scant experimental data available, suggest that the properties of invertebrate NMDA receptor glycine sites are probably different from those in vertebrates. The synthesis of D–serine in brain is due to a pyridoxal–5'–phosphate (B 6 )–requiring serine racemase in glia. Although it remains unknown when serine racemase first evolved, data concerning the evolution of B 6 enzymes, along with the known occurrences of serine racemases in animals, point to D–serine synthesis arising around the divergence time of arthropods. D–Serine catabolism occurs via the ancient peroxisomal enzyme D–amino acid oxidase (DAO), whose ontogenetic expression in the hindbrain of mammals is delayed until the postnatal period and absent from the forebrain. The phylogeny of D–serine metabolism has relevance to our understanding of brain ontogeny, schizophrenia and neurotransmitter dynamics.

The conservation of phosphate-binding residues among PHT1 transporters suggests that distinct transport affinities are unlikely to result from differences in the phosphate-binding site

2016 ◽  
Vol 44 (5) ◽  
pp. 1541-1548 ◽  
Author(s):  
S. Antony Ceasar ◽  
Alison Baker ◽  
Stephen P. Muench ◽  
S. Ignacimuthu ◽  
Stephen A. Baldwin
Keyword(s):  
Binding Site ◽  
Homology Modelling ◽  
Expression Patterns ◽  
Phosphate Transporter ◽  
Phosphate Binding ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Equivalent Position ◽  
Major Facilitator

The plant PHosphate Transporter 1 (PHT1) family of membrane proteins belongs to the major facilitator super family and plays a major role in the acquisition of inorganic phosphate (Pi) from the soil and its transport within the plant. These transporters have been well characterized for expression patterns, localization, and in some cases affinity. Furthermore, the crystal structure of a high-affinity eukaryotic phosphate transporter from the fungus Piriformospora indica (PiPT) has revealed important information on the residues involved in Pi transport. Using multiple-sequence alignments and homology modelling, the phosphate-binding site residues were shown to be well conserved between all the plant PHT1 proteins, Saccharomyces cerevisiae PHO84 and PiPT. For example, Asp 324 in PiPT is conserved in the equivalent position in all plant PHT1 and yeast transporters analyzed, and this residue in ScPHO84 was shown by mutagenesis to be important for both the binding and transport of Pi. Moreover, Asp 45 and Asp 149, which are predicted to be involved in proton import, and Lys 459, which is putatively involved in Pi-binding, are all fully conserved in PHT1 and ScPHO84 transporters. The conserved nature of the residues that play a key role in Pi-binding and transport across the PHT1 family suggests that the differing Pi affinities of these transporters do not reside in differences in the Pi-binding site. Recent studies suggest that phosphate transporters could possess dual affinity and that post-translational modifications may be important in regulating affinity for phosphate.

scholarly journals A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-based Multiple Sequence Alignment

2020 ◽  
Author(s):  
David Roe ◽  
Cynthia Vierra-Green ◽  
Chul-Woo Pyo ◽  
Daniel E. Geraghty ◽  
Stephen R. Spellman ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Single Gene ◽  
Killer Cell ◽  
Genotypic Diversity ◽  
Gene Families ◽  
Alignment Algorithm ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Kir Haplotypes

AbstractHuman chromosome 19q13.4 contains genes encoding killer-cell immunoglobulin-like receptors (KIR). Reported haplotype lengths range from 67 to 269 kilobases and contain 4 to 18 genes. The region has certain properties such as single nucleotide variation, structural variation, homology, and repetitive elements that make it hard to align accurately beyond single gene alleles. To the best of our knowledge, a multiple sequence alignment of KIR haplotypes has never been published or presented. Such an alignment would be useful to precisely define KIR haplotypes and loci, provide context for assigning alleles (especially fusion alleles) to genes, infer evolutionary history, impute alleles, interpret and predict co-expression, and generate markers. In order to extend the framework of KIR haplotype sequences in the human genome reference, 27 new sequences were generated including 24 haplotypes from 12 individuals of African American ancestry that were selected for genotypic diversity and novelty to the reference, to bring the total to 68 full length genomic KIR haplotype sequences. We leveraged these data and tools from our long-read KIR haplotype assembly algorithm to define and align KIR haplotypes at <5 kb resolution on average. We then used a standard alignment algorithm to refine that alignment down to single base resolution. This processing demonstrated that the high-level alignment recapitulates human-curated annotation of the human haplotypes as well as a chimpanzee haplotype. Further, assignments and alignments of gene alleles were consistent with their human curation in haplotype and allele databases. These results define KIR haplotypes as 14 loci containing 9 genes. The multiple sequence alignments have been applied in two software packages as probes to capture and annotate KIR haplotypes and as markers to genotype KIR from WGS.

scholarly journals Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sandra Regina Maruyama ◽  
Luana Aparecida Rogerio ◽  
Patricia Domingues Freitas ◽  
Marta Maria Geraldes Teixeira ◽  
José Marcos Chaves Ribeiro
Keyword(s):  
Amino Acid ◽  
Phylogenetic Relationships ◽  
Single Gene ◽  
Gene Families ◽  
Distance Measures ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Protein Coding ◽  
Phylogenomic Analyses ◽  
Amino Acid Distance

AbstractThe increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.

Purification and Characterization of Lupus Anticoagulant Like Protein from Agkistrodon Halys Brevicaudus Venom

1996 ◽  
Vol 76 (06) ◽  
pp. 0993-0997
Author(s):  
Zhao-Yan Li ◽  
Xiao-Wei Wu ◽  
Tie-Fu Yu ◽  
Eric C-Y Lian
Keyword(s):  
Amino Acid ◽  
Lupus Anticoagulant ◽  
Inhibitory Effect ◽  
Clotting Factor ◽  
Acid Oxidase ◽  
Crude Venom ◽  
Amino Acid Oxidase ◽  
Sds Page ◽  
The Individual ◽  
Reducing Condition

SummaryBy means of CM-Sephadex C-25, DEAE-Sephadex A-50, Sephadex G-200, and Sephadex G-75 chromatographies, a lupus anticoagulant like protein (LALP) from Agkistrodon halys brevicaudus was purified. On SDS-PAGE, the purified LALP had a molecular weight of 25,500 daltons under non-reducing condition and 15,000 daltons under reducing condition. The isoelectric point was pH 5.6. Its N terminal amino acid sequencing revealed a mixture of 2 sequences: DCP(P/S)(D/G)WSSYEGH(C/R)Q(Q/K). It was devoid of phospho-lipaseA, fibrino(geno)lytic, 5′-nucleotidase, L-amino acid oxidase, phosphomonoesterase, phosphodiesterase and thrombin-like activities, which were found in crude venom. In the presence of LALP, PT, aPTT, and dRVVT of human plasma were markedly prolonged and its effects were concentration-dependent but time-independent. The inhibitory effect of LALP on the plasma clotting time was enhanced by decreasing phospholipid concentration in TTI test. The individual clotting factor activity was not affected by LALP when higher dilutions of LALP-plasma mixture were used for assay. Russell’s viper venom time was shortened when high phospholipid confirmatory reagent was used. Therefore, the protein has lupus anticoagulant property.

Impairment of Platelet Aggregation by Echis colorata Venom Mediated by L-Amino Acid Oxidase or H2O2

1982 ◽  
Vol 48 (03) ◽  
pp. 277-282 ◽  
Author(s):  
I Nathan ◽  
A Dvilansky ◽  
T Yirmiyahu ◽  
M Aharon ◽  
A Livne
Keyword(s):  
Hydrogen Peroxide ◽  
Amino Acid ◽  
Platelet Aggregation ◽  
Snake Venom ◽  
Oxidase Activity ◽  
Enzyme Preparation ◽  
Acid Oxidase ◽  
Crude Venom ◽  
Amino Acid Oxidase ◽  
Hemostatic Disorders

SummaryEchis colorata bites cause impairment of platelet aggregation and hemostatic disorders. The mechanism by which the snake venom inhibits platelet aggregation was studied. Upon fractionation, aggregation impairment activity and L-amino acid oxidase activity were similarly separated from the crude venom, unlike other venom enzymes. Preparations of L-amino acid oxidase from E.colorata and from Crotalus adamanteus replaced effectively the crude E.colorata venom in impairment of platelet aggregation. Furthermore, different treatments known to inhibit L-amino acid oxidase reduced in parallel the oxidase activity and the impairment potency of both the venom and the enzyme preparation. H2O2 mimicked characteristically the impairment effects of L-amino acid oxidase and the venom. Catalase completely abolished the impairment effects of the enzyme and the venom. It is concluded that hydrogen peroxide formed by the venom L-amino acid oxidase plays a role in affecting platelet aggregation and thus could contribute to the extended bleeding typical to persons bitten by E.colorata.

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