scholarly journals Evolution of hes gene family in vertebrates: the hes5 cluster genes have specifically increased in frogs

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Aya Kuretani ◽  
Takayoshi Yamamoto ◽  
Masanori Taira ◽  
Tatsuo Michiue
Keyword(s):  
Genome Duplication ◽  
Single Gene ◽  
Early Embryogenesis ◽  
Amino Acid Sequences ◽  
Elephant Shark ◽  
Spotted Gar ◽  
Helix Loop Helix ◽  
Frog Species ◽  
Species Specific ◽  
Enhancer Of Split

Abstract Background hes genes are chordate homologs of Drosophila genes, hairy and enhancer of split, which encode a basic helix-loop-helix (bHLH) transcriptional repressor with a WRPW motif. Various developmental functions of hes genes, including early embryogenesis and neurogenesis, have been elucidated in vertebrates. However, their orthologous relationships remain unclear partly because of less conservation of relatively short amino acid sequences, the fact that the genome was not analyzed as it is today, and species-specific genome duplication. This results in complicated gene names in vertebrates, which are not consistent in orthologs. We previously revealed that Xenopus frogs have two clusters of hes5, named “the hes5.1 cluster” and “the hes5.3 cluster”, but the origin and the conservation have not yet been revealed. Results Here, we elucidated the orthologous and paralogous relationships of all hes genes of human, mouse, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark and three species of frogs, Xenopus tropicalis (X. tropicalis), X. laevis, Nanorana parkeri, by phylogenetic and synteny analyses. Any duplicated hes5 were not found in mammals, whereas hes5 clusters in teleost were conserved although not as many genes as the three frog species. In addition, hes5 cluster-like structure was found in the elephant shark genome, but not found in cyclostomata. Conclusion These data suggest that the hes5 cluster existed in the gnathostome ancestor but became a single gene in mammals. The number of hes5 cluster genes were specifically large in frogs.

scholarly journals Evolution of hes Gene Family in Vertebrates: hes5 Cluster Genes Were Specifically Increased in Xenopus

2021 ◽  
Author(s):  
Aya Kuretani ◽  
Takayoshi Yamamoto ◽  
Masanori Taira ◽  
Tatsuo Michiue
Keyword(s):  
Early Embryogenesis ◽  
Amino Acid Sequences ◽  
Specific Gene ◽  
Synteny Analysis ◽  
Conserved Synteny ◽  
Elephant Shark ◽  
Spotted Gar ◽  
Helix Loop Helix ◽  
Species Specific ◽  
Enhancer Of Split

Abstract Background hes genes are chordate homologs of Drosophila genes, hairy and enhancer of split, which encode a basic helix-loop-helix (bHLH) transcriptional repressor with a WRPW motif. Various developmental functions of hes genes, including early embryogenesis and neurogenesis, have been elucidated in vertebrates. However, their orthologous relationships remain unclear partly because of less conservation of relatively short amino acid sequences, less conserved synteny, and species-specific gene duplication. This results in complicated gene names in vertebrates, which are not consistent in orthologs. In a previous study, we revealed that Xenopus frogs have two clusters of hes5, named “the hes5.1 cluster” and “the hes5.3 cluster.” The origin has not yet been revealed. Results Here, we elucidated the orthologous and paralogous relationships of all hes genes of human, mouse, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark, and Xenopus frogs (X. tropicalis and X. laevis) by phylogenic and synteny analysis. Any clusters of hes5 were not found in amniotes, whereas duplicated hes5 clusters in teleost were found although not as many genes as Xenopus. In addition, hes5 cluster-like structure was found in the elephant shark genome, but not found in cyclostomata. Conclusion These data suggest that the hes5 cluster existed in the gnathostome ancestor, but was lost in amniotes.

scholarly journals Molecular Evolution of Tubulins in Diatoms

2022 ◽  
Vol 23 (2) ◽  
pp. 618
Author(s):  
Kirill V. Khabudaev ◽  
Darya P. Petrova ◽  
Yekaterina D. Bedoshvili ◽  
Yelena V. Likhoshway ◽  
Mikhail A. Grachev
Keyword(s):  
Amino Acids ◽  
Posttranslational Modification ◽  
Molecular Mechanisms ◽  
Morphological Diversity ◽  
Amino Acid Sequences ◽  
Transcriptome Data ◽  
Eukaryotic Proteins ◽  
Large Diatom ◽  
Species Specific ◽  
Β Tubulin

Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the problem of elucidating the molecular mechanisms of genetically programmed morphogenesis, the structure and evolution of diatom tubulins have not been studied previously. Based on available genomic and transcriptome data, we analyzed the phylogeny of the predicted amino acid sequences of diatom α-, β- and γ-tubulins and identified five groups for α-tubulins, six for β-tubulins and four for γ-tubulins. We identified characteristic amino acids of each of these groups and also analyzed possible posttranslational modification sites of diatom tubulins. According to our results, we assumed what changes occurred in the diatom tubulin structures during their evolution. We also identified which tubulin groups are inherent in large diatom taxa. The similarity between the evolution of diatom tubulins and the evolution of diatoms suggests that molecular changes in α-, β- and γ-tubulins could be one of the factors in the formation of a high morphological diversity of diatoms.

The vacuolar proton pump of Dictyostelium discoideum: molecular cloning and analysis of the 100 kDa subunit

1996 ◽  
Vol 109 (5) ◽  
pp. 1041-1051 ◽  
Author(s):  
T. Liu ◽  
M. Clarke
Keyword(s):  
Dictyostelium Discoideum ◽  
Proton Pump ◽  
Single Gene ◽  
Consensus Sequence ◽  
Amino Acid Sequences ◽  
Contractile Vacuole ◽  
Proton Pumps ◽  
Variable Regions ◽  
Endosomal Membranes ◽  
Vacuolar Proton Pump

The vacuolar proton pump is a highly-conserved multimeric enzyme that catalyzes the translocation of protons across the membranes of eukaryotic cells. Its largest subunit (95-116 kDa) occurs in tissue and organelle-specific isoforms and thus may be involved in targeting the enzyme or modulating its function. In amoebae of Dictyostelium discoideum, proton pumps with a 100 kDa subunit are found in membranes of the contractile vacuole complex, an osmoregulatory organelle. We cloned the cDNA that encodes this 100 kDa protein and found that its sequence predicts a protein 45% identical (68% similar) to the corresponding mammalian proton pump subunit. Like the mammalian protein, the predicted Dictyostelium sequence contains six possible transmembrane domains and a single consensus sequence for N-linked glycosylation. Southern blot analysis detected only a single gene, which was designated vatM. Using genomic DNA and degenerate oligonucleotides based on conserved regions of the protein as primers, we generated products by polymerase chain reaction that included highly variable regions of this protein family. The cloned products were identical in nucleotide sequence to vatM, arguing that Dictyostelium cells contain only a single isoform of this proton pump subunit. Consistent with this interpretation, the amino acid sequences of peptides derived from a protein associated with endosomal membranes (Adessu et al. (1995) J. Cell Sci. 108, 3331–3337) match the predicted sequence of the protein encoded by vatM. Thus, a single isoform of the 100 kDa proton pump subunit appears to serve in both the contractile vacuole system and the endosomal/lysosomal system of Dictyostelium, arguing that this subunit is not responsible for regulating the differing abundance and function of proton pumps in these two compartments. Gene targeting experiments suggest that this subunit plays important (possibly essential) roles in Dictyostelium cells.

Sexual Selection, Timing and an X–Y Homologous Gene: Did Homo Sapiens Speciate on the Y Chromosome?

2004 ◽  
Author(s):  
Tim J. Crow
Keyword(s):  
Sexual Selection ◽  
Sex Chromosome ◽  
Homo Sapiens ◽  
Single Gene ◽  
Critical Role ◽  
Hominid Evolution ◽  
Homologous Gene ◽  
Chromosomal Change ◽  
Species Specific ◽  
Sex Chromosome Aneuploidies

This chapter provides a theory of the speciation of modern Homo sapiens, that a single gene played a critical role in the transition from a precursor species. The theory is founded upon the following: firstly, the premise that hemispheric asymmetry is the defining feature of the human brain and the only plausible correlate of language; secondly, an argument for a specific candidate region (the Xq21.3/Yp11.2 region of homology) based upon the reciprocal deficits associated with the sex chromosome aneuploidies, and the course of chromosomal change in hominid evolution; and thirdly, a particular evolutionary mechanism (sexual selection acting on an X-Y-linked gene) to account for species-specific modification of what initially was a saltational change. These postulates relate to the case of modern Homo sapiens. On the basis of the recent literature, the discussion argues that the third premise has general significance as a mechanism of speciation.

Modelling transcriptional feedback loops: the role of Gro/TLE1 in Hes1 oscillations

2006 ◽  
Vol 364 (1842) ◽  
pp. 1155-1170 ◽  
Author(s):  
Samuel Bernard ◽  
Branka Čajavec ◽  
Laurent Pujo-Menjouet ◽  
Michael C Mackey ◽  
Hanspeter Herzel
Keyword(s):  
Transcription Initiation ◽  
Periodic Pattern ◽  
Transcriptional Repressors ◽  
Helix Loop Helix ◽  
Family Protein ◽  
Theoretical Predictions ◽  
Numerical Bifurcation ◽  
Enhancer Of Split ◽  
Transcriptional Feedback

The transcriptional repressor Hes1, a basic helix-loop-helix family protein, periodically changes its expression in the presomitic mesoderm. Its periodic pattern of expression is retained in a number of cultured murine cell lines. In this paper, we introduce an extended mathematical model for Hes1 oscillatory expression that includes regulation of Hes1 transcription by Drosophila Groucho (Gro) or its vertebrate counterpart, the transducine-like enhancer of split/Groucho-related gene product 1 (TLE1). Gro/TLE1 is a necessary corepressor required by a number of DNA-binding transcriptional repressors, including Hes1. Models of direct repression via Hes1 typically display an expression overshoot after transcription initiation which is not seen in the experimental data. However, numerical simulation and theoretical predictions of our model show that the cofactor Gro/TLE1 reduces the overshoot and is thus necessary for a rapid and finely tuned response of Hes1 to activation signals. Further, from detailed linear stability and numerical bifurcation analysis and simulations, we conclude that the cooperativity coefficient ( h ) for Hes1 self-repression should be large (i.e. h ≥4). Finally, we introduce the characteristic turnaround duration, and show that for our model the duration of the repression loop is between 40 and 60 min.

scholarly journals The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 622 ◽  
Author(s):  
Yi Sun ◽  
Chao Liu ◽  
Moli Huang ◽  
Jian Huang ◽  
Changhong Liu ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Teleost Fish ◽  
Clock Gene ◽  
Genome Duplication ◽  
Clock Genes ◽  
Gene Families ◽  
Regulatory Mechanisms ◽  
Spotted Gar ◽  
Circadian Clock Genes ◽  
Lepisosteus Oculatus

Circadian rhythms are biological rhythms with a period of approximately 24 h. While canonical circadian clock genes and their regulatory mechanisms appear highly conserved, the evolution of clock gene families is still unclear due to several rounds of whole genome duplication in vertebrates. The spotted gar (Lepisosteus oculatus), as a non-teleost ray-finned fish, represents a fish lineage that diverged before the teleost genome duplication (TGD), providing an outgroup for exploring the evolutionary mechanisms of circadian clocks after whole-genome duplication. In this study, we interrogated the spotted gar draft genome sequences and found that spotted gar contains 26 circadian clock genes from 11 families. Phylogenetic analysis showed that 9 of these 11 spotted gar circadian clock gene families have the same number of genes as humans, while the members of the nfil3 and cry families are different between spotted gar and humans. Using phylogenetic and syntenic analyses, we found that nfil3-1 is conserved in vertebrates, while nfil3-2 and nfil3-3 are maintained in spotted gar, teleost fish, amphibians, and reptiles, but not in mammals. Following the two-round vertebrate genome duplication (VGD), spotted gar retained cry1a, cry1b, and cry2, and cry3 is retained in spotted gar, teleost fish, turtles, and birds, but not in mammals. We hypothesize that duplication of core clock genes, such as (nfil3 and cry), likely facilitated diversification of circadian regulatory mechanisms in teleost fish. We also found that the transcription factor binding element (Ahr::Arnt) is retained only in one of the per1 or per2 duplicated paralogs derived from the TGD in the teleost fish, implicating possible subfuctionalization cases. Together, these findings help decipher the repertoires of the spotted gar’s circadian system and shed light on how the vertebrate circadian clock systems have evolved.

scholarly journals High-Affinity Copper Transport and Snq2 Export Permease of Saccharomyces cerevisiae Modulate Cytotoxicity of PR-10 from Theobroma cacao

2009 ◽  
Vol 22 (1) ◽  
pp. 39-51 ◽  
Author(s):  
Cristina Pungartnik ◽  
Aline Clara da Silva ◽  
Sarah Alves de Melo ◽  
Karina Peres Gramacho ◽  
Júlio Cézar de Mattos Cascardo ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Theobroma Cacao ◽  
Single Gene ◽  
Copper Transport ◽  
Amino Acid Sequences ◽  
Yeast Cells ◽  
Antioxidant Defenses ◽  
Copper Transporter ◽  
High Affinity ◽  
Yeast Mutants

A pathogenesis-related (PR) protein from Theobroma cacao (TcPR-10) was identified from a cacao–Moniliophthora perniciosa interaction cDNA library. Nucleotide and amino acid sequences showed homology with other PR-10 proteins having P loop motif and Betv1 domain. Recombinant TcPR-10 showed in vitro and in vivo ribonuclease activity, and antifungal activity against the basidiomycete cacao pathogen M. perniciosa and the yeast Saccharomyces cerevisiae. Fluorescein isothiocyanate-labeled TcPR-10 was internalized by M. perniciosa hyphae and S. cerevisiae cells and inhibited growth of both fungi. Energy and temperature-dependent internalization of the TcPR-10 suggested an active importation into the fungal cells. Chronical exposure to TcPR-10 of 29 yeast mutants with single gene defects in DNA repair, general membrane transport, metal transport, and antioxidant defenses was tested. Two yeast mutants were hyperresistant compared with their respective isogenic wild type: ctr3Δ mutant, lacking the high-affinity plasma membrane copper transporter and mac1Δ, the copper-sensing transcription factor involved in regulation of high-affinity copper transport. Acute exposure of exponentially growing yeast cells revealed that TcPR-10 resistance is also enhanced in the Snq2 export permease-lacking mutant which has reduced intracellular presence of TcPR-10.

scholarly journals Two genetically and molecularly distinct functions involved in early neurogenesis reside within the Enhancer of split locus of Drosophila melanogaster.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 803-823 ◽  
Author(s):  
C Delidakis ◽  
A Preiss ◽  
D A Hartley ◽  
S Artavanis-Tsakonas
Keyword(s):  
Function Analysis ◽  
Single Copy ◽  
Postembryonic Development ◽  
P Element ◽  
Phenotypic Analysis ◽  
Helix Loop Helix ◽  
Gene Enhancer ◽  
Concomitant Reduction ◽  
Nuclear Component ◽  
Enhancer Of Split

Abstract Molecular correlation of the genetic aspects of the function of the neurogenic gene Enhancer of split [E(spl)] has previously been hampered by the densely transcribed nature of the chromosomal region within which it resides. We present data indicating that two distinct molecular species contribute to E(spl) function. Analysis of new E(spl) alleles has allowed us to define two complementing functions within the locus. Subsequent phenotypic analysis of different E(spl) deficiencies combined with P element-transformed constructs has demonstrated that these two functions correspond to: (1) a family of helix-loop-helix (HLH) protein-encoding genes and (2) the single copy gene E(spl) m9/10, whose product shares homology with G-protein beta subunits. The zygotically active E(spl) HLH genes can, at least partially, substitute for one another's functions and their total copy number determines the activity of the locus. E(spl) m9/10 acts synergistically with the E(spl) HLH genes and other neurogenic genes in the process of neurogenesis. The maternal component of E(spl) m9/10 has the most pronounced effect in neurogenesis, while its zygotic component is predominantly required during postembryonic development. The lethality of trans-heterozygotes of null E(spl) deficiency alleles with a strong Delta point mutation is a result of the concomitant reduction in activity of both E(spl) HLH and m9/10 functions. Immunocytochemical localization of the E(spl) m9/10 protein has revealed that it is a ubiquitously distributed nuclear component in embryonic, larval and imaginal tissues.

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