scholarly journals Insight into the Functional Diversification of Lipases in the Endoparasitoid Pteromalus puparum (Hymenoptera: Pteromalidae) by Genome-scale Annotation and Expression Analysis

Insects ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 227 ◽  
Author(s):  
Jiale Wang ◽  
Jiqiang Song ◽  
Qi Fang ◽  
Hongwei Yao ◽  
Fang Wang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Dietary Lipids ◽  
Parasitoid Wasps ◽  
Functional Diversification ◽  
Nutrition Environment ◽  
Multiple Alignments ◽  
Pteromalus Puparum ◽  
Hydrolytic Activities ◽  
Genome Scale ◽  
Insight Into

Lipases play essential roles in digestion, transport, and processing of dietary lipids in insects. For parasitoid wasps with a unique life cycle, lipase functions could be multitudinous in particular. Pteromalus puparum is a pupal endoparasitoid of butterflies. The female adult deposits eggs into its host, along with multifunctional venom, and the developing larvae consume host as its main nutrition source. Parasitoid lipases are known to participate in the food digestion process, but the mechanism remains unclear. P. puparum genome and transcriptome data were interrogated. Multiple alignments and phylogenetic trees were constructed. We annotated a total of 64 predicted lipase genes belonging to five lipase families and suggested that eight venom and four salivary lipases could determine host nutrition environment post-parasitization. Many putative venom lipases were found with incomplete catalytic triads, relatively long β9 loops, and short lids. Data analysis reveals the loss of catalytic activities and weak triacylglycerol (TAG) hydrolytic activities of lipases in venom. Phylogenetic trees indicate various predicted functions of lipases in P. puparum. Our information enriches the database of parasitoid lipases and the knowledge of their functional diversification, providing novel insight into how parasitoid wasps manipulate host lipid storage by using venom lipases.

scholarly journals Genome-scale reconstructions to assess metabolic phylogeny and organism clustering

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0240953
Author(s):  
Christian Schulz ◽  
Eivind Almaas
Keyword(s):  
Phylogenetic Trees ◽  
Metabolic Networks ◽  
Sulfur Metabolism ◽  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Significant Heterogeneity ◽  
Metabolic Reaction ◽  
High Quality ◽  
Conserved Genes ◽  
Genome Scale

Approaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct 975 genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees. We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers.

scholarly journals Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana

2020 ◽  
Author(s):  
shaoshan zhang ◽  
Qiong Liu ◽  
Chengcheng Lyu ◽  
Jinsong chen ◽  
Renfeng xiao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Phylogenetic Trees ◽  
Leaf Tissue ◽  
Stevia Rebaudiana ◽  
Full Length ◽  
Steviol Glycosides ◽  
Smrt Sequencing ◽  
Leaf Tissues ◽  
Sequencing Platforms ◽  
Insight Into

Abstract Background: Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of S. rebaudiana and play important roles in the synthesis of steviol glycosides. Results: Six stevia genotypes with significantly different concentrations of SGs were obtained by induction through various mutagenic methods, and the contents of seven glycosides (stevioboside, Reb B, ST, Reb A, Reb F, Reb D and Reb M) in their leaves were considerably different. Then, NGS and single-molecule real-time (SMRT) sequencing were combined to analyse leaf tissue from these six different genotypes to generate a more complete and correct full-length transcriptome of S. rebaudiana. Two phylogenetic trees of glycosyltransferases (SrUGTs) were constructed by the neighbour-joining method and successfully predicted the functions of SrUGTs involved in SG biosynthesis. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCNA) method was used to characterize the relationships between SrUGTs and SGs, and forty-four potential SrUGTs were finally obtained, including SrUGT85C2, SrUGT74G1, SrUGT76G1 and one SrUGT91D2, which have already been reported to be involved in the glucosylation of steviol glycosides, illustrating the reliability of our results.Conclusion: Combined with the results obtained by previous studies and those of this work, we systematically characterized glycosyltransferases in S. rebaudiana and forty-four candidate SrUGTs involved in the glycosylation of steviol glucosides were obtained. Moreover, the complete and correct full-length transcriptome obtained in this study will provide valuable support for further research investigating S. rebaudiana.

scholarly journals ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Marten Moore ◽  
Corinna Wesemann ◽  
Nikolaj Gossmann ◽  
Arne Sahm ◽  
Jan Krüger ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Translation Elongation ◽  
Web Based ◽  
Post Translational Modifications ◽  
Plant Kingdom ◽  
Multiple Alignments ◽  
Biochemical Assays ◽  
Evolutionarily Conserved ◽  
Redox Sensitivity ◽  
Conserved Amino Acids

Abstract Background Post-translational modifications (PTM) of amino acid (AA) side chains in peptides control protein structure and functionality. PTMs depend on the specific AA characteristics. The reactivity of cysteine thiol-based PTMs are unique among all proteinaceous AA. This pipeline aims to ease the identification of conserved AA of polypeptides or protein families based on the phylogenetic occurrence in the plant kingdom. The tool is customizable to include any species. The degree of AA conservation is taken as indicator for structural and functional significance, especially for PTM-based regulation. Further, this pipeline tool gives insight into the evolution of these potentially regulatory important peptides. Results The web-based or stand-alone pipeline tool Conserved Cysteine Finder (ConCysFind) was developed to identify conserved AA such as cysteine, tryptophan, serine, threonine, tyrosin and methionine. ConCysFind evaluates multiple alignments considering the proteome of 21 plant species. This exemplar study focused on Cys as evolutionarily conserved target for multiple redox PTM. Phylogenetic trees and tables with the compressed results of the scoring algorithm are generated for each Cys in the query polypeptide. Analysis of 33 translation elongation and release factors alongside of known redox proteins from Arabidopsis thaliana for conserved Cys residues confirmed the suitability of the tool for identifying conserved and functional PTM sites. Exemplarily, the redox sensitivity of cysteines in the eukaryotic release factor 1-1 (eRF1-1) was experimentally validated. Conclusion ConCysFind is a valuable tool for prediction of new potential protein PTM targets in a broad spectrum of species, based on conserved AA throughout the plant kingdom. The identified targets were successfully verified through protein biochemical assays. The pipeline is universally applicable to other phylogenetic branches by customization of the database.

scholarly journals Accumulation of Cerebrospinal Fluid Glycerophospholipids and Sphingolipids in Cognitively Healthy Participants With Alzheimer’s Biomarkers Precedes Lipolysis in the Dementia Stage

2020 ◽  
Vol 14 ◽  
Author(s):  
Alfred N. Fonteh ◽  
Abby J. Chiang ◽  
Xianghong Arakaki ◽  
Sarah P. Edminster ◽  
Michael G Harrington
Keyword(s):  
Cerebrospinal Fluid ◽  
Membrane Lipids ◽  
Significant Risk ◽  
Significant Risk Factor ◽  
Dietary Lipids ◽  
Supernatant Fraction ◽  
Brain Membrane ◽  
Prodromal Ad ◽  
Healthy Participants ◽  
Insight Into

Insight into lipids’ roles in Alzheimer’s disease (AD) pathophysiology is limited because brain membrane lipids have not been characterized in cognitively healthy (CH) individuals. Since age is a significant risk factor of AD, we hypothesize that aging renders the amyloid precursor protein (APP) more susceptible to abnormal processing because of deteriorating membrane lipids. To reflect brain membranes, we studied their lipid components in cerebrospinal fluid (CSF) and brain-derived CSF nanoparticle membranes. Based on CSF Aβ42/Tau levels established biomarkers of AD, we define a subset of CH participants with normal Aβ42/Tau (CH-NAT) and another group with abnormal or pathological Aβ42/Tau (CH-PAT). We report that glycerophospholipids are differentially metabolized in the CSF supernatant fluid and nanoparticle membrane fractions from CH-NAT, CH-PAT, and AD participants. Phosphatidylcholine molecular species from the supernatant fraction of CH-PAT were higher than in the CH-NAT and AD participants. Sphingomyelin levels in the supernatant fraction were lower in the CH-PAT and AD than in the CH-NAT group. The decrease in sphingomyelin corresponded with an increase in ceramide and dihydroceramide and an increase in the ceramide to sphingomyelin ratio in AD. In contrast to the supernatant fraction, sphingomyelin is higher in the nanoparticle fraction from the CH-PAT group, accompanied by lower ceramide and dihydroceramide and a decrease in the ratio of ceramide to sphingomyelin in CH-PAT compared with CH-NAT. On investigating the mechanism for the lipid changes in AD, we observed that phospholipase A2 (PLA2) activity was higher in the AD group than the CH groups. Paradoxically, acid and neutral sphingomyelinase (SMase) activities were lower in AD compared to the CH groups. Considering external influences on lipids, the clinical groups did not differ in their fasting blood lipids or dietary lipids, consistent with the CSF lipid changes originating from brain pathophysiology. The lipid accumulation in a prodromal AD biomarker positive stage identifies perturbation of lipid metabolism and disturbances in APP/Amyloid beta (Aβ) as early events in AD pathophysiology. Our results identify increased lipid turnover in CH participants with AD biomarkers, switching to a predominantly lipolytic state in dementia. This knowledge may be useful for targeting and testing new AD treatments.

scholarly journals Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana

2020 ◽  
Author(s):  
shaoshan zhang ◽  
Qiong Liu ◽  
Chengcheng Lyu ◽  
Jinsong chen ◽  
Renfeng xiao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Phylogenetic Trees ◽  
Leaf Tissue ◽  
Stevia Rebaudiana ◽  
Full Length ◽  
Steviol Glycosides ◽  
Smrt Sequencing ◽  
Leaf Tissues ◽  
Sequencing Platforms ◽  
Insight Into

Abstract Background: Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of S. rebaudiana and play important roles in the synthesis of steviol glycosides. Results: Six stevia genotypes with significantly different concentrations of SGs were obtained by induction through various mutagenic methods, and the contents of seven glycosides (stevioboside, Reb B, ST, Reb A, Reb F, Reb D and Reb M) in their leaves were considerably different. Then, NGS and single-molecule real-time (SMRT) sequencing were combined to analyse leaf tissue from these six different genotypes to generate a full-length transcriptome of S. rebaudiana. Two phylogenetic trees of glycosyltransferases (SrUGTs) were constructed by the neighbour-joining method and successfully predicted the functions of SrUGTs involved in SG biosynthesis. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCNA) method was used to characterize the relationships between SrUGTs and SGs, and forty-four potential SrUGTs were finally obtained, including SrUGT85C2, SrUGT74G1, SrUGT76G1 and one SrUGT91D2, which have already been reported to be involved in the glucosylation of steviol glycosides, illustrating the reliability of our results.Conclusion: Combined with the results obtained by previous studies and those of this work, we systematically characterized glycosyltransferases in S. rebaudiana and forty-four candidate SrUGTs involved in the glycosylation of steviol glucosides were obtained. Moreover, the full-length transcriptome obtained in this study will provide valuable support for further research investigating S. rebaudiana.

scholarly journals Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana

2020 ◽  
Author(s):  
Shaoshan Zhang ◽  
Qiong Liu ◽  
Chengcheng Lyu ◽  
Jinsong Chen ◽  
Renfeng Xiao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Phylogenetic Trees ◽  
Leaf Tissue ◽  
Stevia Rebaudiana ◽  
Full Length ◽  
Steviol Glycosides ◽  
Stevia Rebaudiana Bertoni ◽  
Leaf Tissues ◽  
Sequencing Platforms ◽  
Insight Into

Abstract Background: Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of S. rebaudiana and play important roles in the synthesis of steviol glycosides.Results: Six stevia genotypes with significantly different concentrations of SGs were obtained by induction through various mutagenic methods, and the contents of seven glycosides (stevioboside, Reb B, ST, Reb A, Reb F, Reb D and Reb M) in their leaves were considerably different. Then, NGS and single-molecule real-time (SMRT) sequencing were combined to analyse leaf tissue from these six different genotypes to generate a more complete and correct full-length transcriptome of S. rebaudiana . Two phylogenetic trees of glycosyltransferases (SrUGTs) were constructed by the neighbour-joining method and successfully predicted the functions of SrUGTs involved in SG biosynthesis. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCNA) method was used to characterize the relationships between SrUGTs and SGs, and forty-four potential SrUGTs were finally obtained, including SrUGT85C2 , SrUGT74G1 , SrUGT76G1 and one SrUGT91D2, which have already been reported to be involved in the glucosylation of steviol glycosides, illustrating the reliability of our results.Conclusion: Combined with the results obtained by previous studies and those of this work, we systematically characterized glycosyltransferases in S. rebaudiana and forty-four candidate SrUGTs involved in the glycosylation of steviol glucosides were obtained. Moreover, the complete and correct full-length transcriptome obtained in this study will provide valuable support for further research investigating S. rebaudiana .

scholarly journals Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

2018 ◽  
Vol 115 (43) ◽  
pp. 11096-11101 ◽  
Author(s):  
Elizabeth Brunk ◽  
Roger L. Chang ◽  
Jing Xia ◽  
Hooman Hefzi ◽  
James T. Yurkovich ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Global Analysis ◽  
Biomedical Sciences ◽  
Complex Interactions ◽  
Scientific Disciplines ◽  
Mechanistic Analysis ◽  
Protein Posttranslational Modifications ◽  
Cell Phenotypes ◽  
Genome Scale ◽  
Insight Into

Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coli. Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.

Maxillolabial complex in scelionids (Hymenoptera: Platygastroidea): morphology and phylogenetic implications

2017 ◽  
Vol 48 (4) ◽  
pp. 315-439 ◽  
Author(s):  
Ovidiu Alin Popovici ◽  
Lars Vilhelmsen ◽  
Lubomir Masner ◽  
István Mikó ◽  
Norman Johnson
Keyword(s):  
Phylogenetic Trees ◽  
Relevant Information ◽  
Parasitoid Wasps ◽  
Diverse Group ◽  
Phylogenetic Hypothesis ◽  
Line Drawings ◽  
Ground Plan ◽  
Phylogenetic Implications ◽  
Current Classification

The Platygastroidea is a highly diverse group of small to minute parasitoid wasps. Despite the reduced size, the morphology of the maxillolabial complex of scelionids is very diverse and phylogenetically informative. 81 characters are scored for 129 genera (representing 75% of the total number of known extant genera of scelionids), as well as for seven outgroup taxa. All taxa examined are illustrated with images, SEM micrographs and/or line drawings. Phylogenetic trees resulting from analyses conducted in TNT under various settings were not fully resolved, but some relationships were repeatedly retrieved. The Platygastroidea are usually corroborated. Nixoniini, Sparasionini, Plaumannion and Huddlestonium are frequently retrieved as the most basal platygastroid lineages. Psix and Paratelenomus often form a monophyletic group close to Gryonini. The Scelioninae, Teleasinae and Telenominae are not supported as monophyletic. However, some major scelionid clades are frequently retrieved, but these are not recognized in the current classification of Platygastroidea. The evolution of the palpal formula, highly variably in scelionids, and previously used in platygastroid systematics, is explored. The number of maxillary palpomeres in the ground plan of platygatroids is probably five, that of labial palpomeres two or three, given the variation among basal scelionids. Our study provides relevant information for resolving the phylogeny of the Platygastroidea, but additional character sources have to be explored to obtain a robust phylogenetic hypothesis.

scholarly journals Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Shaoshan Zhang ◽  
Qiong Liu ◽  
Chengcheng Lyu ◽  
Jinsong Chen ◽  
Renfeng Xiao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Phylogenetic Trees ◽  
Leaf Tissue ◽  
Stevia Rebaudiana ◽  
Full Length ◽  
Steviol Glycosides ◽  
Smrt Sequencing ◽  
Leaf Tissues ◽  
Sequencing Platforms ◽  
Insight Into

Abstract Background Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of S. rebaudiana and play important roles in the synthesis of steviol glycosides. Results Six stevia genotypes with significantly different concentrations of SGs were obtained by induction through various mutagenic methods, and the contents of seven glycosides (stevioboside, Reb B, ST, Reb A, Reb F, Reb D and Reb M) in their leaves were considerably different. Then, NGS and single-molecule real-time (SMRT) sequencing were combined to analyse leaf tissue from these six different genotypes to generate a full-length transcriptome of S. rebaudiana. Two phylogenetic trees of glycosyltransferases (SrUGTs) were constructed by the neighbour-joining method and successfully predicted the functions of SrUGTs involved in SG biosynthesis. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCNA) method was used to characterize the relationships between SrUGTs and SGs, and forty-four potential SrUGTs were finally obtained, including SrUGT85C2, SrUGT74G1, SrUGT76G1 and SrUGT91D2, which have already been reported to be involved in the glucosylation of steviol glycosides, illustrating the reliability of our results. Conclusion Combined with the results obtained by previous studies and those of this work, we systematically characterized glycosyltransferases in S. rebaudiana and forty-four candidate SrUGTs involved in the glycosylation of steviol glucosides were obtained. Moreover, the full-length transcriptome obtained in this study will provide valuable support for further research investigating S. rebaudiana.

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