Enhanced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families

Gene ◽  
2008 ◽  
Vol 407 (1-2) ◽  
pp. 199-215 ◽  
Author(s):  
Parantu K. Shah ◽  
Lokesh P. Tripathi ◽  
Lars Juhl Jensen ◽  
Murad Gahnim ◽  
Christopher Mason ◽  
...  
Keyword(s):  
Serine Proteases ◽  
Gene Families ◽  
Member Gene

scholarly journals Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1744
Author(s):  
Stefania Pilati ◽  
Giulia Malacarne ◽  
David Navarro-Payá ◽  
Gabriele Tomè ◽  
Laura Riscica ◽  
...  
Keyword(s):  
Gene Networks ◽  
Functional Characterization ◽  
Gene Families ◽  
Stilbene Synthase ◽  
Breeding Programs ◽  
Transcriptomic Data ◽  
Network Analyses ◽  
Manual Curation ◽  
Inference Methods

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.

scholarly journals Sedolisins, a New Class of Secreted Proteases from Aspergillus fumigatus with Endoprotease or Tripeptidyl-Peptidase Activity at Acidic pHs

2006 ◽  
Vol 72 (3) ◽  
pp. 1739-1748 ◽  
Author(s):  
Utz Reichard ◽  
Barbara Léchenne ◽  
Abdul R. Asif ◽  
Frank Streit ◽  
Eric Grouzmann ◽  
...  
Keyword(s):  
Aspergillus Fumigatus ◽  
Signal Sequence ◽  
Gene Families ◽  
Peptidase Activity ◽  
New Class ◽  
Tripeptidyl Peptidase ◽  
Genes Encoding ◽  
Member Gene ◽  
Culture Supernatants ◽  
Hydrolysis Of

ABSTRACT The secreted proteolytic activity of Aspergillus fumigatus is of potential importance as a virulence factor and in the industrial hydrolysis of protein sources. The A. fumigatus genome contains sequences that could encode a five-member gene family that produces proteases in the sedolisin family (MEROPS S53). Four putative secreted sedolisins with a predicted 17- to 20-amino-acid signal sequence were identified and termed SedA to SedD. SedA produced heterologously in Pichia pastoris was an acidic endoprotease. Heterologously produced SedB, SedC, and SedD were tripeptidyl-peptidases (TPP) with a common specificity for tripeptide-p-nitroanilide substrates at acidic pHs. Purified SedB hydrolyzed the peptide Ala-Pro-Gly-Asp-Arg-Ile-Tyr-Val-His-Pro-Phe to Arg-Pro-Gly, Asp-Arg-Ile, and Tyr-Val-His-Pro-Phe, thereby confirming TPP activity of the enzyme. SedB, SedC, and SedD were detected by Western blotting in culture supernatants of A. fumigatus grown in a medium containing hemoglobin as the sole nitrogen source. A degradation product of SedA also was observed. A search for genes encoding sedolisin homologues in other fungal genomes indicates that sedolisin gene families are widespread among filamentous ascomycetes.

scholarly journals Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study

2020 ◽  
Vol 12 (3) ◽  
pp. 185-202
Author(s):  
Xia Han ◽  
Jindan Guo ◽  
Erli Pang ◽  
Hongtao Song ◽  
Kui Lin
Keyword(s):  
Gene Family ◽  
De Novo ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Genome Phylogeny ◽  
Partial Homology

Abstract How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.

Identification of stage-specifically expressed genes of Trichinella spiralis by suppression subtractive hybridization

Parasitology ◽  
2007 ◽  
Vol 134 (10) ◽  
pp. 1443-1455 ◽  
Author(s):  
M. Y. LIU ◽  
X. L. WANG ◽  
B. Q. FU ◽  
C. Y. LI ◽  
X. P. WU ◽  
...  
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Serine Proteases ◽  
Zinc Finger Protein ◽  
Trichinella Spiralis ◽  
Gene Families ◽  
Subtractive Hybridization ◽  
Cdna Clones ◽  
Dnase Ii ◽  
Finger Protein ◽  
Old Adult

SUMMARYNewborn larvae (NBL) and adult (Ad) stage-specifically expressed genes or members of gene families of Trichinella spiralis were identified by suppression subtractive hybridization (SSH)†. Six cDNA clones were identified as NBL stage-specific, including 1 member of the T. spiralis gene family encoding glutamic acid-rich proteins, 2 clones encoding novel serine proteases, 2 closely related clones encoding proteins that are members of a deoxyribonuclease II (DNase II)-like family and 1 clone with no similarity to known genes. Four stage-specific clones encoding homologues of retinoid X receptor, caveolin, C2H2 type zinc finger protein and a putative protein with no homology to known sequences were obtained from 3-day-old adult worms. One gene specifically up-regulated in the 5-day-old adult worms encoding a putative cuticle collagen was also identified.

scholarly journals Interactions between Syntaxins Identify at Least Five SNARE Complexes within the Golgi/Prevacuolar System of the Arabidopsis Cell

2001 ◽  
Vol 12 (12) ◽  
pp. 3733-3743 ◽  
Author(s):  
Anton A. Sanderfoot ◽  
Valya Kovaleva ◽  
Diane C. Bassham ◽  
Natasha V. Raikhel
Keyword(s):  
Single Gene ◽  
Adaptor Protein ◽  
Gene Families ◽  
Snare Complex ◽  
Transport Vesicles ◽  
Protein Receptors ◽  
Member Gene ◽  
Model Plant Arabidopsis Thaliana ◽  
Prevacuolar Compartment ◽  
Golgi Network

The syntaxin family of soluble N-ethyl maleimide sensitive factor adaptor protein receptors (SNAREs) is known to play an important role in the fusion of transport vesicles with specific organelles. Twenty-four syntaxins are encoded in the genome of the model plant Arabidopsis thaliana. These 24 genes are found in 10 gene families and have been reclassified as syntaxins of plants (SYPs). Some of these gene families have been previously characterized, with the SYP2-type syntaxins being found in the prevacuolar compartment (PVC) and the SYP4-type syntaxins on thetrans-Golgi network (TGN). Here we report on two previously uncharacterized syntaxin groups. The SYP5 group is encoded by a two-member gene family, whereas SYP61 is a single gene. Both types of syntaxins are localized to multiple compartments of the endomembrane system, including the TGN and the PVC. These two groups of syntaxins form SNARE complexes with each other, and with other Arabidopsis SNAREs. On the TGN, SYP61 forms complexes with the SNARE VTI12 and either SYP41 or SYP42. SYP51 and SYP61 interact with each other and with VTI12, most likely also on the TGN. On the PVC, a SYP5-type syntaxin interacts specifically with a SYP2-type syntaxin, as well as the SNARE VTI11, forming a SNARE complex likely involved in TGN-to-PVC trafficking.

scholarly journals Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations

2022 ◽  
Author(s):  
Qing Xiong ◽  
Angel Tsz-Yau Wan ◽  
Xiao-Yu Liu ◽  
Cathy Sin-Hang Fung ◽  
Xiaojun Xiao ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Serine Proteases ◽  
Drug Targets ◽  
Gene Families ◽  
House Dust Mites ◽  
Divergent Evolution ◽  
Allergy Prevention ◽  
Lytic Enzymes ◽  
Fungal Cell ◽  
Wide Range

Abstract Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing roughly 1–2% of the allergic diseases globally; however, their evolutionary origin, diverse lifestyles including reversible parasitism and quick adaptation to rather new human household environments have not been illustrated at genomic level, which hamper the allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this comparative genomics study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the divergent evolution of astigmatic mites. In the monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases (UGTs), which enriched their capacities of adapting to rapidly changing household environments. The gene diversification after tandem duplications provided plenty of genetic resources for their adaptations of sensing environmental signals, digestion, and detoxification. Whilst many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UGTs and several important fungal cell wall lytic enzymes, which enable the detoxification and associated digestive functions and provide perfect drug targets for pest control. Our comparative study sheds light on the rapid divergent evolution of astigmatic mites from the divergence of Acariformes to their diversification and provides novel insights into the genetic adaptations and even control of human household pests.

scholarly journals Plant P450s as versatile drivers for evolution of species-specific chemical diversity

2013 ◽  
Vol 368 (1612) ◽  
pp. 20120426 ◽  
Author(s):  
Björn Hamberger ◽  
Søren Bak
Keyword(s):  
Metabolic Pathways ◽  
Gene Families ◽  
Plant Evolution ◽  
Chemical Diversity ◽  
Raw Material ◽  
Divergent Evolution ◽  
Substantial Contribution ◽  
Functional Diversification ◽  
Specific Chemical ◽  
Member Gene

The irreversible nature of reactions catalysed by P450s makes these enzymes landmarks in the evolution of plant metabolic pathways. Founding members of P450 families are often associated with general (i.e. primary) metabolic pathways, restricted to single copy or very few representatives, indicative of purifying selection. Recruitment of those and subsequent blooms into multi-member gene families generates genetic raw material for functional diversification, which is an inherent characteristic of specialized (i.e. secondary) metabolism. However, a growing number of highly specialized P450s from not only the CYP71 clan indicate substantial contribution of convergent and divergent evolution to the observed general and specialized metabolite diversity. We will discuss examples of how the genetic and functional diversification of plant P450s drives chemical diversity in light of plant evolution. Even though it is difficult to predict the function or substrate of a P450 based on sequence similarity, grouping with a family or subfamily in phylogenetic trees can indicate association with metabolism of particular classes of compounds. Examples will be given that focus on multi-member gene families of P450s involved in the metabolic routes of four classes of specialized metabolites: cyanogenic glucosides, glucosinolates, mono- to triterpenoids and phenylpropanoids.

scholarly journals Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss

GigaScience ◽  
2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Brooke L Whitelaw ◽  
Ira R Cooke ◽  
Julian Finn ◽  
Rute R da Fonseca ◽  
Elena A Ritschard ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Serine Proteases ◽  
Bacterial Species ◽  
Resistance Mutation ◽  
Minor Component ◽  
Gene Families ◽  
Venom Gland ◽  
Evolutionary Patterns ◽  
Novel Gene ◽  
Voltage Gated Sodium Channels

Abstract Background Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland. Findings To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non–tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a diverse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source. Conclusions We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family.

PacBio sequencing of gene families — A case study with wheat gluten genes

Gene ◽  
2014 ◽  
Vol 533 (2) ◽  
pp. 541-546 ◽  
Author(s):  
Wei Zhang ◽  
Paul Ciclitira ◽  
Joachim Messing
Keyword(s):  
Wheat Gluten ◽  
Gene Families ◽  
Pacbio Sequencing
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