Identification of a novel receptor for an invertebrate oxytocin/vasopressin superfamily peptide: molecular and functional evolution of the oxytocin/vasopressin superfamily

Annetocin is structurally related to an OT (oxytocin)/VP (vasopressin) family peptide, which has been isolated from the earthworm Eisenia foetida and has been shown to induce OT-like egg-laying behaviour. We now report the identification of an endogenous AnR (annetocin receptor). The deduced AnR precursor displays high sequence similarity with OT/VP receptors. Genomic analysis of the AnR gene revealed that the intron-inserted position is conserved between the AnR gene and the mammalian OT/VP receptor genes. These results indicate that AnR and mammalian OT/VP receptors share a common ancestor gene. Administration of annetocin to the AnR expressed in Xenopus oocytes induced a calcium-dependent signal transduction. Reverse transcriptase–PCR analysis and in situ hybridization showed that the AnR gene is expressed specifically in the nephridia located in the clitellum region, although the nephridia are distributed throughout the worm body. This result suggests that annetocin induces egg-laying behaviour through its action on the nephridia. This is the first description concerning the functional correlation between an invertebrate OT/VP-related peptide and egg-laying behaviour.

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Coevolution ofaah: Adps-Like Gene with the Host Bacterium Revealed by Comparative Genomic Analysis

The Scientific World JOURNAL ◽

10.1100/2012/504905 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Liyan Ping ◽

Matthias Platzer ◽

Gaiping Wen ◽

Nicolas Delaroque

Keyword(s):

Stop Codon ◽

Sequence Similarity ◽

General Pattern ◽

Genomic Analysis ◽

Dna Binding Proteins ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Host Bacterium ◽

High Sequence Similarity ◽

Lepidopteran Larvae

A protein named AAH was isolated from the bacteriumMicrobacterium arborescensSE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell) but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of theaahgene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes. The phylogeny ofdps-like proteins showed strong correlation with the phylogeny of host bacteria. A conserved genomic synteny was identified in some taxonomically related Actinobacteria, suggesting that the ancestor genes had incorporated into the genome before the divergence of Micrococcineae from other families. Theaahgene had evolved new function but still retained the typical dodecameric structure.

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Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus

Viruses ◽

10.3390/v12121373 ◽

2020 ◽

Vol 12 (12) ◽

pp. 1373

Author(s):

Sang Guen Kim ◽

Sung Bin Lee ◽

Sib Sankar Giri ◽

Hyoun Joong Kim ◽

Sang Wha Kim ◽

...

Keyword(s):

Genome Size ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Gc Content ◽

Genomic Analysis ◽

Open Reading Frames ◽

Comparative Genomic ◽

Limited Information ◽

High Sequence Similarity ◽

A Genome

Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.

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Expression of paralogs of cytochrome P45021a1 pseudogene (Cyp21a1-ps) and endogenous retrovirus SC1 (SC1) in the rat ovary during the ovulatory process

Journal of Endocrinology ◽

10.1677/joe-08-0108 ◽

2008 ◽

Vol 198 (1) ◽

pp. 231-241

Author(s):

Lawrence L Espey ◽

Rebecca A Garcia ◽

Haruhiro Kondo ◽

Bunpei Ishizuka ◽

Shinya Yoshioka ◽

...

Keyword(s):

Sequence Similarity ◽

Ovarian Tissue ◽

Endogenous Retrovirus ◽

High Sequence Similarity ◽

Reductase Gene ◽

Rat Ovary ◽

Equine Chorionic Gonadotropin ◽

Ovulatory Follicles ◽

Ovulatory Process

This study assesses the relatively high incidence of the expression of paralogs of several pseudogenes within the cascade of expression of functional genes in the rat ovary in response to an ovulation-stimulating dose of gonadotropin. Immature Wistar rats were primed with 10 IU equine chorionic gonadotropin subcutaneously, and 48 h later the 12-h ovulatory process was initiated by 10 IU hCG subcutaneously. Ovarian RNA was extracted at 0, 2, 4, 8, 12, and 24 h after injecting the animals with hCG. The RNA extracts were used for RT-PCR differential display to detect gene expression in the ovarian tissue. Sequence analyses of differentially expressed cDNAs revealed that ∼27% (i.e. 22/82 clones) of the transcripts were fragments of paralogs of known pseudogenes. Out of the 22 clones reported here, 12 have high sequence similarity to the cytochrome P450 pseudogene Cyp21a1-ps, and 5 have high sequence similarity to both the Cyp21a1-ps and the aldo-keto reductase gene Akr1c6. The remaining five clones were paralogs of the endogenous retrovirus SC1 that has heavily infested the rat genome. Northern analyses reveal that peak expression of all the 22 paralogs occurs at 4–8 h into the ovulatory process. In situ hybridization shows that expression of these pseudogenes is primarily in the granulosa layer of ovulatory follicles. In summary, the results reveal that ovarian expression of Cyp21a1-ps- and SC1-like pseudogenes occurs concurrently with the ovulatory process.

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Phylogenetic analyses and genomic variation of the 2019-nCoV

Journal of Pharmaceutical and Biopharmaceutical Research ◽

10.25082/jpbr.2020.01.004 ◽

2020 ◽

Vol 2 (1) ◽

pp. 126-130

Author(s):

Faiz Ul Haq ◽

◽

Sidrah Saleem ◽

Muhammad Imran ◽

Ayesha Ghazal ◽

...

Keyword(s):

Phylogenetic Tree ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Genomic Variation ◽

Molecular Characteristics ◽

Phylogenetic Tree Analysis ◽

High Sequence Similarity ◽

Human Environment ◽

Bat Coronavirus

There is a rising global concern about the SARS CoV-2 as a public health threat. Complete genome sequence have been released by the worldwide scientific community for understanding the molecular characteristics and evolutionary origin of this virus. Aim of the current context is to present phylogenetic relationship and genomic variation of 2019-nCoV. Based on availability of genomic information, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Middle East respiratory syndrome, severe acute respiratory syndrome and Bat coronavirus. The phylogenetic tree analysis suggested that SARS CoV-2 significantly clustered with bat SARS like coronavirus genome, however structural analysis revealed mutation in Spike Glycoprotein and nucleocapsid protein. However our phylogenetic and genomic analysis suggests that bats can be the reservoir for this virus. Lack of forest might be the fact in association of bats with human environment. It is also difficult to study on bats due to absence of proper reagent and availability of few species for research. We confirm high sequence similarity (>99%) among sequenced SARS CoV-2 genomes, and 96% genome identity with the bat coronavirus, confirming the notion of a zoonotic origin of SARS CoV-2.

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Probing Dictyostelium severin structure and function by cross linking to actin

Biochemistry and Cell Biology ◽

10.1139/o04-002 ◽

2004 ◽

Vol 82 (2) ◽

pp. 343-350

Author(s):

Joanna Summerscales ◽

John F Dawson

Keyword(s):

Structural Model ◽

Sequence Similarity ◽

Comparative Modeling ◽

Actin Binding ◽

Cross Linking ◽

High Sequence Similarity ◽

Calcium Dependent ◽

A Minor ◽

And Function ◽

Chemical Cross Linking

DS151 is the first 151 amino acids of the Dictyostelium discoidium protein severin, which shares high sequence similarity with segment 1 of the actin-severing protein gelsolin. DS151 is able to mediate the depolymerization of F-actin in a calcium-dependent fashion, much like segment 1 of gelsolin. A structural model of DS151 was obtained by comparative modeling studies with segment 1 of gelsolin. This model was tested by studies of chemical cross linking between DS151 and bound actin, suggesting that Cys residues on DS151 are cross linked with Lys residues of actin. The model suggests that Cys125 of DS151 cross links with either Lys326 or Lys328 of actin. Mutagenesis of DS151 demonstrates that Cys125 of DS151 dominates the cross linking, whereas Cys25 of DS151 makes a minor con tribution through a longer-range cross link with Cys374 of actin, which likely involves flexibility of both proteins in that region.Key words: actin-binding proteins, homology modeling, chemical cross linking, actin-severing proteins.

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Characterization of a new duplicate δ-opioid receptor from zebrafish

Journal of Molecular Endocrinology ◽

10.1677/jme.1.02136 ◽

2006 ◽

Vol 37 (3) ◽

pp. 391-403 ◽

Cited By ~ 38

Author(s):

Noelia Pinal-Seoane ◽

Ivan Rodríguez Martin ◽

Veronica Gonzalez-Nuñez ◽

Ezequiel Marron Fernandez de Velasco ◽

Francisco Alvar Alvarez ◽

...

Keyword(s):

Opioid Receptor ◽

Sequence Similarity ◽

Duplicate Genes ◽

Receptor Density ◽

Brain Areas ◽

High Sequence Similarity ◽

Competition Binding ◽

Δ Opioid Receptor

A new full-length cDNA (ZFOR4) that encodes an opioid receptor has been isolated from the teleost zebrafish. The encoded polypeptide is 375 amino acids long and shows high sequence similarity to other δ-opioid receptors, including ZFOR1, the other δ-opioid receptor from zebrafish previously characterized by us. In situ hybridization studies have revealed that ZFOR4 mRNA is highly expressed in particular brain areas that coincide with the expression of the δ-opioid receptor in other species. Pharmacological analysis of ZFOR4 shows specific and saturable binding with [3H] diprenorphine, displaying one binding site with KD = 3.42 ± 0.38 nM and a receptor density of 6231 ± 335 fmol/mg protein. Competition-binding experiments were performed using [3H]diprenorphine and several unlabelled ligands (peptidic and non-peptidic). The order of affinity obtained is Met-enkephalin>Naloxone>Leu-enkephalin>Dynorphin A≫BW373U86>Morphine≫≫ [D-Pen2,D-Pen5]-Enkephalin, U69,593. [35S]GTPγS stimulation studies show that the endogenous ligands Met- and Leu-enkephalin and the non-peptidic δ agonist BW373U86 were able to fully activate ZFOR4. Our results prove the existence of two functional duplicate genes of the δ-opioid receptor in the teleost zebrafish.

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Expression and Association of Group IV Nitrogenase NifD and NifH Homologs in the Non-Nitrogen-Fixing Archaeon Methanocaldococcus jannaschii

Journal of Bacteriology ◽

10.1128/jb.00876-07 ◽

2007 ◽

Vol 189 (20) ◽

pp. 7392-7398 ◽

Cited By ~ 37

Author(s):

Christopher R. Staples ◽

Surobhi Lahiri ◽

Jason Raymond ◽

Lindsay Von Herbulis ◽

Biswarup Mukhophadhyay ◽

...

Keyword(s):

Sequence Similarity ◽

Constitutive Expression ◽

Genomic Analysis ◽

Group Iv ◽

Structural Proteins ◽

Nitrogen Fixing ◽

Fundamental Function ◽

High Sequence Similarity ◽

Methanocaldococcus Jannaschii ◽

Two Hybrid

ABSTRACT Using genomic analysis, researchers previously identified genes coding for proteins homologous to the structural proteins of nitrogenase (J. Raymond, J. L. Siefert, C. R. Staples, and R. E. Blankenship, Mol. Biol. Evol. 21:541-554, 2004). The expression and association of NifD and NifH nitrogenase homologs (named NflD and NflH for “Nif-like” D and H, respectively) have been detected in a non-nitrogen-fixing hyperthermophilic methanogen, Methanocaldococcus jannaschii. These homologs are expressed constitutively and do not appear to be directly involved with nitrogen metabolism or detoxification of compounds such as cyanide or azide. The NflH and NflD proteins were found to interact with each other, as determined by bacterial two-hybrid studies. Upon immunoisolation, NflD and NflH copurified, along with three other proteins whose functions are as yet uncharacterized. The apparent presence of genes coding for NflH and NflD in all known methanogens, their constitutive expression, and their high sequence similarity to the NifH and NifD proteins or the BchL and BchN/BchB proteins suggest that NflH and NflD participate in an indispensable and fundamental function(s) in methanogens.

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Genomic analysis of C-type lectins

Biochemical Society Symposium ◽

10.1042/bss0690059 ◽

2002 ◽

Vol 69 ◽

pp. 59-72 ◽

Cited By ~ 85

Author(s):

Kurt Drickamer ◽

Andrew J. Fadden

Keyword(s):

Biological Effects ◽

Cell Signalling ◽

Genomic Analysis ◽

Binding Activity ◽

Immunoglobulin Superfamily ◽

Carbohydrate Binding ◽

Carbohydrate Recognition ◽

Calcium Dependent ◽

Binding Domains ◽

Carbohydrate Recognition Domains

Many biological effects of complex carbohydrates are mediated by lectins that contain discrete carbohydrate-recognition domains. At least seven structurally distinct families of carbohydrate-recognition domains are found in lectins that are involved in intracellular trafficking, cell adhesion, cell–cell signalling, glycoprotein turnover and innate immunity. Genome-wide analysis of potential carbohydrate-binding domains is now possible. Two classes of intracellular lectins involved in glycoprotein trafficking are present in yeast, model invertebrates and vertebrates, and two other classes are present in vertebrates only. At the cell surface, calcium-dependent (C-type) lectins and galectins are found in model invertebrates and vertebrates, but not in yeast; immunoglobulin superfamily (I-type) lectins are only found in vertebrates. The evolutionary appearance of different classes of sugar-binding protein modules parallels a development towards more complex oligosaccharides that provide increased opportunities for specific recognition phenomena. An overall picture of the lectins present in humans can now be proposed. Based on our knowledge of the structures of several of the C-type carbohydrate-recognition domains, it is possible to suggest ligand-binding activity that may be associated with novel C-type lectin-like domains identified in a systematic screen of the human genome. Further analysis of the sequences of proteins containing these domains can be used as a basis for proposing potential biological functions.

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Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton

Plant Methods ◽

10.1186/s13007-021-00712-x ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Mohamed Ramadan ◽

Muna Alariqi ◽

Yizan Ma ◽

Yanlong Li ◽

Zhenping Liu ◽

...

Keyword(s):

Genetic Transformation ◽

Sequence Similarity ◽

High Specificity ◽

Transformation Method ◽

High Sequence Similarity ◽

Single Experiment ◽

Next Generation Sequencing Technology ◽

Cotton Transformation ◽

Assembly Method ◽

Multiple Genes

Abstract Background Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

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Evolution of Chi motifs in Proteobacteria

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa054 ◽

2021 ◽

Author(s):

Angélique Buton ◽

Louis-Marie Bobay

Keyword(s):

Sequence Similarity ◽

Bacterial Species ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Large Dataset ◽

High Sequence Similarity ◽

Strand Breaks ◽

E Coli ◽

Dna Motif ◽

And Staphylococcus Aureus

Abstract Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

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