A comparative study of odorant binding protein genes: differential expression of the PBP1-GOBP2 gene cluster inManduca sexta(Lepidoptera) and the organization of OBP genes inDrosophila melanogaster(Diptera)

2002 ◽  
Vol 205 (6) ◽  
pp. 719-744 ◽  
Author(s):  
Richard G. Vogt ◽  
Matthew E. Rogers ◽  
Marie-dominique Franco ◽  
Ming Sun
Keyword(s):  
Gene Family ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Cell Communication ◽  
Gene Families ◽  
Cell Types ◽  
Amino Acid Sequence Similarity ◽  
Olfactory Sensilla ◽  
Wide Range ◽  
Odorant Binding

SUMMARYInsects discriminate odors using sensory organs called olfactory sensilla, which display a wide range of phenotypes. Sensilla express ensembles of proteins, including odorant binding proteins (OBPs), olfactory receptors (ORs) and odor degrading enzymes (ODEs); odors are thought to be transported to ORs by OBPs and subsequently degraded by ODEs. These proteins belong to multigene families. The unique combinatorial expression of specific members of each of these gene families determines, in part, the phenotype of a sensillum and what odors it can detect. Furthermore, OBPs, ORs and ODEs are expressed in different cell types, suggesting the need for cell–cell communication to coordinate their expression. This report examines the OBP gene family. In Manduca sexta, the genes encoding PBP1Msex and GOBP2Msex are sequenced, shown to be adjacent to one another, and characterized together with OBP gene structures of other lepidoptera and Drosophila melanogaster. Expression of PBP1Msex, GOBP1Msex and GOBP2Msex is characterized in adult male and female antenna and in larval antenna and maxilla. The genomic organization of 25 D. melanogaster OBPs are characterized with respect to gene locus, gene cluster, amino acid sequence similarity, exon conservation and proximity to OR loci, and their sequences are compared with 14 M. sexta OBPs. Sensilla serve as portals of important behavioral information, and genes supporting sensilla function are presumably under significant evolutionary selective pressures. This study provides a basis for studying the evolution of the OBP gene family, the regulatory mechanisms governing the coordinated expression of OBPs, ORs and ODEs, and the processes that determine specific sensillum phenotypes.

scholarly journals Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study

2020 ◽  
Vol 37 (9) ◽  
pp. 2584-2600 ◽  
Author(s):  
Bryan D Clifton ◽  
Jamie Jimenez ◽  
Ashlyn Kimura ◽  
Zeinab Chahine ◽  
Pablo Librado ◽  
...  
Keyword(s):  
Gene Family ◽  
Sequence Similarity ◽  
Gene Families ◽  
Read Depth ◽  
Specific Gene ◽  
Protein Variant ◽  
Protein Coding ◽  
Expression Levels ◽  
Number Variation ◽  
Reference Quality

Abstract Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3–7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3′ ends, with 3–5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.

scholarly journals NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica

2019 ◽  
Vol 116 (33) ◽  
pp. 16448-16453 ◽  
Author(s):  
Julia M. Diaz ◽  
Sydney Plummer ◽  
Colleen M. Hansel ◽  
Peter F. Andeer ◽  
Mak A. Saito ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Cell Types ◽  
Redox Balance ◽  
Superoxide Production ◽  
Marine Phytoplankton ◽  
Marine Diatom ◽  
High Sequence Similarity ◽  
Whole Cells ◽  
Wide Range ◽  
Diphenylene Iodonium

Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.

scholarly journals Programmed Translational Frameshift in the Bacteriophage P2 FETUD Tail Gene Operon

2002 ◽  
Vol 184 (23) ◽  
pp. 6522-6531 ◽  
Author(s):  
Gail E. Christie ◽  
Louise M. Temple ◽  
Becky A. Bartlett ◽  
Tina S. Goodwin
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Initiation Site ◽  
Translation Initiation Site ◽  
Amino Acid Sequence Similarity ◽  
Reading Frame ◽  
Coding Regions ◽  
Translational Frameshift ◽  
Bacteriophage P2 ◽  
Contractile Tail

ABSTRACT The major structural components of the P2 contractile tail are encoded in the FETUD tail gene operon. The sequences of genes F I and F II, encoding the major tail sheath and tail tube proteins, have been reported previously (L. M. Temple, S. L. Forsburg, R. Calendar, and G. E. Christie, Virology 181:353-358, 1991). Sequence analysis of the remainder of this operon and the locations of amber mutations Eam30, Tam5, Tam64, Tam215, Uam25, Uam77, Uam92, and Dam6 and missense mutation Ets55 identified the coding regions for genes E, T, U, and D, completing the sequence determination of the P2 genome. Inspection of the DNA sequence revealed a new open reading frame overlapping the end of the essential tail gene E. Lack of an apparent translation initiation site and identification of a putative sequence for a programmed translational frameshift within the E gene suggested that this new reading frame (E′) might be translated as an extension of gene E, following a −1 translational frameshift. Complementation analysis demonstrated that E′ was essential for P2 lytic growth. Analysis of fusion polypeptides verified that this reading frame was translated as a −1 frameshift extension of gpE, with a frequency of approximately 10%. The arrangement of these two genes within the tail gene cluster of phage P2 and their coupling via a translational frameshift appears to be conserved among P2-related phages. This arrangement shows a striking parallel to the organization in the tail gene cluster of phage lambda, despite a lack of amino acid sequence similarity between the tail gene products of these phage families.

scholarly journals Lamprey Lecticans Link New Vertebrate Genes to the Origin and Elaboration of Vertebrate Tissues

2020 ◽  
Author(s):  
Zachary D. Root ◽  
David Jandzik ◽  
Cara Allen ◽  
Margaux Brewer ◽  
Marek Romášek ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Gene Families ◽  
Cell Types ◽  
Specific Cell ◽  
Skeletal Tissue ◽  
Genomic Arrangement ◽  
New Gene ◽  
Morphological Novelties ◽  
Head Skeleton

ABSTRACTThe evolution of vertebrates from an invertebrate chordate ancestor involved the evolution of new organs, tissues, and cell types. It was also marked by the origin and duplication of new gene families. If, and how, these morphological and genetic innovations are related is an unresolved question in vertebrate evolution. Hyaluronan is an extracellular matrix (ECM) polysaccharide important for water homeostasis and tissue structure. Vertebrates possess a novel family of hyaluronan binding proteins called Lecticans, and studies in jawed vertebrates (gnathostomes) have shown they function in many of the cells and tissues that are unique to vertebrates. This raises the possibility that the origin and/or expansion of this gene family helped drive the evolution of these vertebrate novelties. In order to better understand the evolution of the lectican gene family, and its role in the evolution of vertebrate morphological novelties, we investigated the phylogeny, genomic arrangement, and expression patterns of all lecticans in the sea lamprey (Petromyzon marinus), a jawless vertebrate. Though both P. marinus and gnathostomes have four lecticans, our phylogenetic and syntenic analyses suggest lamprey lecticans are the result of one or more cyclostome-specific duplications. Despite the independent expansion of the lamprey and gnathostome lectican families, we find highly conserved expression of lecticans in vertebrate-specific and mesenchyme-derived tissues. We also find that, unlike gnathostomes, lamprey expresses its lectican paralogs in distinct subpopulations of head skeleton precursors, potentially reflecting an ancestral diversity of skeletal tissue types. Together, these observations suggest that the ancestral pre-duplication lectican had a complex expression pattern, functioned to support mesenchymal histology, and likely played a role in the evolution of vertebrate-specific cell and tissue types.

scholarly journals Phylogenetic diversification of sirtuin genes with a description of a new family member

2020 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala ◽  
Michael W. Vandewege ◽  
Federico G. Hoffmann
Keyword(s):  
Gene Family ◽  
Family Member ◽  
Gene Families ◽  
Last Common Ancestor ◽  
Gene Repertoire ◽  
Origin And Evolution ◽  
New Family ◽  
Wide Range ◽  
Evolutionary Context ◽  
History Of

AbstractStudying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural work, as the correct interpretation of their results needs to be done in a robust evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our goal is to take advantage of the genomic data available in public databases to advance our understanding of how sirtuin genes are related to each other, and to characterize the gene repertoire in species representative of all the main groups of vertebrates. Our results show a well-resolved phylogeny that represents a significant improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin family member (SIRT3-like) that was apparently lost in amniotes, but retained in all other groups of jawed vertebrates. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

scholarly journals CAARS: comparative assembly and annotation of RNA-Seq data

2018 ◽  
Vol 35 (13) ◽  
pp. 2199-2207 ◽  
Author(s):  
Carine Rey ◽  
Philippe Veber ◽  
Bastien Boussau ◽  
Marie Sémon
Keyword(s):  
Gene Family ◽  
De Novo ◽  
Sequence Similarity ◽  
Gene Families ◽  
Supplementary Information ◽  
Model Organisms ◽  
Difficult Case ◽  
Rna Seq ◽  
Comparative Analyses ◽  
Family Reconstruction

Abstract Motivation RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction. Results We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses. Availability and implementation CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A novel negevirus isolated from Aedes vexans mosquitoes in Finland

2020 ◽  
Vol 165 (12) ◽  
pp. 2989-2992
Author(s):  
Maija T. Suvanto ◽  
Phuoc Truong Nguyen ◽  
Ruut Uusitalo ◽  
Essi M. Korhonen ◽  
Giulia Faolotto ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Boreal Forests ◽  
Sequence Similarity ◽  
Protein A ◽  
Gc Content ◽  
Amino Acid Sequence Similarity ◽  
Aedes Vexans ◽  
Sequence Identity ◽  
Wide Range

Abstract Negeviruses are insect-specific enveloped RNA viruses that have been detected in mosquitoes and sandflies from various geographical locations. Here, we describe a new negevirus from Northern Europe, isolated from pool of Aedes vexans mosquitoes collected in Finland, designated as Mekrijärvi negevirus (MEJNV). MEJNV had a typical negevirus genome organization, is 9,740 nucleotides in length, and has a GC content of 47.53%. The MEJNV genome contains three ORFs, each containing the following identified conserved domains: ORF1 (7,068 nt) encodes a viral methyltransferase, an FtsJ-like methyltransferase, a viral RNA helicase, and an RNA-dependent RNA polymerase, ORF2 (1,242 nt) encodes a putative virion glycoprotein, and ORF3 (660 nt) encodes a putative virion membrane protein. A distinctive feature relative to other currently known negeviruses is a 7-nucleotide-long overlap between ORF1 and ORF2. MEJNV shares the highest sequence identity with Ying Kou virus from China, with 67.71% nucleotide and 75.19% and 59.00% amino acid sequence identity in ORF 1 and ORF 2, respectively. ORF3 had the highest amino acid sequence similarity to Daeseongdong virus 1 and negevirus Nona 1, both with 77.61% identity, and to Ying Kou virus, with 71.22% identity. MEJNV is currently the northernmost negevirus described. Our report supports the view that negeviruses are a globally distributed, diverse group of viruses that can be found from mosquitoes in a wide range of terrestrial biomes from tropical to boreal forests.

scholarly journals Predicting and Clustering Plant CLE Genes with a New Method Developed Specifically for Short Amino Acid Sequences

2020 ◽  
Author(s):  
Zhe Zhang ◽  
Lei Liu ◽  
Melis Kucukoglu ◽  
Dongdong Tian ◽  
Robert M. Larkin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
Sequence Similarity ◽  
Gene Prediction ◽  
Cell Communication ◽  
Amino Acid Sequences ◽  
Evolutionary Analysis ◽  
Dependent Manner ◽  
Amino Acid Residues ◽  
A Site

Abstract Background: The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results: We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions: Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.

scholarly journals PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

GigaScience ◽  
2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Sion C Bayliss ◽  
Harry A Thorpe ◽  
Nicola M Coyle ◽  
Samuel K Sheppard ◽  
Edward J Feil
Keyword(s):  
Allelic Variation ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Orthologous Gene ◽  
Gene Families ◽  
Iterative Refinement ◽  
Bacterial Populations ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Similarity Thresholds

Abstract Background Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets. Results Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family. Conclusions We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.

scholarly journals Novel Aeromonas hydrophila PPD134/91 Genes Involved in O-Antigen and Capsule Biosynthesis

2002 ◽  
Vol 70 (5) ◽  
pp. 2326-2335 ◽  
Author(s):  
Y. L. Zhang ◽  
E. Arakawa ◽  
K. Y. Leung
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Aeromonas Hydrophila ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Inhibitory Effect ◽  
Amino Acid Sequence Similarity ◽  
O Antigen ◽  
Serotype O ◽  
Surface Polysaccharides

ABSTRACT The sequences of the O-antigen and capsule gene clusters of the virulent Aeromonas hydrophila strain PPD134/91 were determined. The O-antigen gene cluster is 17,296 bp long and comprises 17 genes. Seven pathway genes for the synthesis of rhamnose and mannose, six transferase genes, one O unit flippase gene, and one O-antigen chain length determinant gene were identified by amino acid sequence similarity. PCR and Southern blot analysis were performed to survey the distribution of these 17 genes among 11 A. hydrophila strains of different serotypes. A. hydrophila PPD134/91 might belong to serotype O:18, as represented by JCM3980; it contained all the same O-antigen genes as JCM3980 (97 to 100% similarity at the DNA and amino acid levels). The capsule gene cluster of A. hydrophila PPD134/91 is 17,562 bp long and includes 13 genes, which were assembled into three distinct regions similar to those of the group II capsule gene cluster of Escherichia coli and other bacteria. Regions I and III contained four and two capsule transport genes, respectively. Region II had five genes which were highly similar to capsule synthesis pathway genes found in other bacteria. Both the purified O-antigen and capsular polysaccharides increased the ability of the avirulent A. hydrophila strain PPD35/85 to survive in naïve tilapia serum. However, the purified surface polysaccharides had no inhibitory effect on the adhesion of A. hydrophila PPD134/91 to carp epithelial cells.

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