Emergence and evolution of the ERM proteins and merlin in metazoans

AbstractEzrin, radixin, moesin, and merlin are the cytoskeletal proteins which functions are specific to metazoans. They participate in cell cortex rearrangements, including cell-cell contact formation, and play important role in cancer progression. Here we perform a comprehensive phylogenetic analysis of the proteins spanning 87 species. The results describe a possible mechanism of the protein family origin in the root of Metazoa, paralogs diversification in vertebrates and acquisition of novel functions, including tumor suppression. In addition, a merlin paralog, present in most of vertebrates, but lost in mammals, has been described. We also highlight the set of amino acid variations within the conserved motifs as the candidates for determining physiological differences between the ERM paralogs.

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Emergence and Evolution of ERM Proteins and Merlin in Metazoans

Genome Biology and Evolution ◽

10.1093/gbe/evz265 ◽

2019 ◽

Vol 12 (1) ◽

pp. 3710-3724

Author(s):

Victoria Shabardina ◽

Yukie Kashima ◽

Yutaka Suzuki ◽

Wojciech Makalowski

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Cancer Progression ◽

Tumor Suppression ◽

Cytoskeletal Proteins ◽

Cell Cortex ◽

Cell Contact ◽

Conserved Motifs ◽

Erm Proteins ◽

First Time

Abstract Ezrin, radixin, moesin, and merlin are cytoskeletal proteins, whose functions are specific to metazoans. They participate in cell cortex rearrangement, including cell–cell contact formation, and play an important role in cancer progression. Here, we have performed a comprehensive phylogenetic analysis of the proteins spanning 87 species. The results describe a possible mechanism for the protein family origin in the root of Metazoa, paralogs diversification in vertebrates, and acquisition of novel functions, including tumor suppression. In addition, a merlin paralog, present in most vertebrates but lost in mammals, has been described here for the first time. We have also highlighted a set of amino acid variations within the conserved motifs as the candidates for determining physiological differences between ERM paralogs.

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Molecular Docking Analysis of Flavonoid Compounds with Matrix Metalloproteinase-8 for the Identification of Potential Effective Inhibitors

Letters in Drug Design & Discovery ◽

10.2174/1570180817999200831094703 ◽

2020 ◽

Vol 17 ◽

Author(s):

Amir Taherkhani ◽

Athena Orangi ◽

Shirin Moradkhani ◽

Zahra Khamverdi

Keyword(s):

Amino Acids ◽

Molecular Docking ◽

Amino Acid ◽

Matrix Metalloproteinase ◽

Ligand Binding ◽

Chronic Inflammation ◽

Cancer Progression ◽

Dimensional Structure ◽

Control Test ◽

Therapeutic Procedures

Background: Matrix metalloproteinase-8 (MMP-8) participates in degradation of different types of collagens in the extracellular matrix and basement membrane. Up-regulation of the MMP-8 has been demonstrated in many of disorders including cancer development, tooth caries, periodontal/peri-implant soft and hard tissue degeneration, and acute/chronic inflammation. Therefore, MMP-8 has become an encouraging target for therapeutic procedures for scientists. We carried out molecular docking approach to study the binding affinity of 29 flavonoids, as drug candidates, with the MMP-8. Pharmacokinetic and toxicological properties of the compounds were also studied. Moreover, it was attempted to identify the most important amino acids participating in ligand binding based on degree of each of the amino acids in the ligand-amino acid interaction network for MMP-8. Methods: Three-dimensional structure of the protein was gained from the RCSB database (PDB ID: 4QKZ). AutoDock version 4.0 and Cytoscape 3.7.2 were used for molecular docking and network analysis, respectively. Notably, the inhibitor of the protein in the crystalline structure of the 4QKZ was considered as a control test. Pharmacokinetic and toxicological features of compounds were predicted using bioinformatic web tools. Post-docking analyses were performed using BIOVIA Discovery Studio Visualizer version 19.1.0.18287. Results and Discussions: According to results, 24 of the studied compounds considered to be top potential inhibitors for MMP-8 based on their salient estimated free energy of binding and inhibition constant as compared with the control test: Apigenin-7-glucoside, nicotiflorin, luteolin, glabridin, taxifolin, apigenin, licochalcone A, quercetin, isorhamnetin, myricetin, herbacetin, kaemferol, epicatechin, chrysin, amentoflavone, rutin, orientin, epiafzelechin, quercetin-3-rhamnoside, formononetin, isoliquiritigenin, vitexin, catechine, isoquercitrin. Moreover, His-197 was found to be the most important amino acid involved in the ligand binding for the enzyme. Conclusion: The results of the current study could be used in the prevention and therapeutic procedures of a number of disorders such as cancer progression and invasion, oral diseases, and acute/chronic inflammation. Although, in vitro and in vivo tests are inevitable in the future.

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Identification of the gene encoding 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase in Burkholderia sp. HME13

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbaa066 ◽

2020 ◽

Vol 85 (3) ◽

pp. 626-629

Author(s):

Hisashi Muramatsu ◽

Hiroki Maguchi ◽

Taisuke Harada ◽

Takehiro Kashiwagi ◽

Chul-Sa Kim ◽

...

Keyword(s):

Amino Acid ◽

Sequence Analysis ◽

Amino Acid Sequence ◽

Propionic Acid ◽

Unknown Function ◽

Protein Family ◽

Amino Acid Sequence Analysis ◽

Gene Encoding

ABSTRACT Here, we report the identification of the gene encoding a novel enzyme, 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase, in Burkholderia sp. HME13. The enzyme converts 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid and H2O to 3-(2,5-dioxoimidazolidin-4-yl) propionic acid and H2S. Amino acid sequence analysis of the enzyme indicates that it belongs to the DUF917 protein family, which consists of proteins of unknown function.

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LAT1 and ASCT2 Related microRNAs as Potential New Therapeutic Agents against Colorectal Cancer Progression

Biomedicines ◽

10.3390/biomedicines9020195 ◽

2021 ◽

Vol 9 (2) ◽

pp. 195

Author(s):

Francisca Dias ◽

Cristina Almeida ◽

Ana Luísa Teixeira ◽

Mariana Morais ◽

Rui Medeiros

Keyword(s):

Colorectal Cancer ◽

Amino Acid ◽

Cancer Progression ◽

Cell Metabolism ◽

Tumor Development ◽

Amino Acid Transporters ◽

Epigenetic Alterations ◽

Therapeutic Approaches ◽

Colorectal Cancer Progression ◽

Made In

The development and progression of colorectal cancer (CRC) have been associated with genetic and epigenetic alterations and more recently with changes in cell metabolism. Amino acid transporters are key players in tumor development, and it is described that tumor cells upregulate some AA transporters in order to support the increased amino acid (AA) intake to sustain the tumor additional needs for tumor growth and proliferation through the activation of several signaling pathways. LAT1 and ASCT2 are two AA transporters involved in the regulation of the mTOR pathway that has been reported as upregulated in CRC. Some attempts have been made in order to develop therapeutic approaches to target these AA transporters, however none have reached the clinical setting so far. MiRNA-based therapies have been gaining increasing attention from pharmaceutical companies and now several miRNA-based drugs are currently in clinical trials with promising results. In this review we combine a bioinformatic approach with a literature review in order to identify a miRNA profile with the potential to target both LAT1 and ASCT2 with potential to be used as a therapeutic approach against CRC.

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Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

Acta Scientiae Veterinariae ◽

10.22456/1679-9216.81158 ◽

2018 ◽

Vol 44 (1) ◽

pp. 20

Author(s):

Eloiza Teles Caldart ◽

Helena Mata ◽

Cláudio Wageck Canal ◽

Ana Paula Ravazzolo

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Molecular Epidemiology ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Evolutionary Process ◽

Amino Acid Sequences ◽

Evolutionary Models ◽

Reconstruction Methods ◽

Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

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Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.8.2207-2210.2000 ◽

2000 ◽

Vol 44 (8) ◽

pp. 2207-2210 ◽

Cited By ~ 26

Author(s):

Nadia Maggi Solcà ◽

Marco Valerio Bernasconi ◽

Jean-Claude Piffaretti

Keyword(s):

Phylogenetic Analysis ◽

Helicobacter Pylori ◽

Amino Acid ◽

Resistant Strain ◽

Point Mutations ◽

Housekeeping Genes ◽

Amino Acid Substitutions ◽

Metronidazole Resistance ◽

Nucleotide Mutation ◽

Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

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Cell surface anchorage and ligand-binding domains of the Saccharomyces cerevisiae cell adhesion protein alpha-agglutinin, a member of the immunoglobulin superfamily.

Molecular and Cellular Biology ◽

10.1128/mcb.13.4.2554 ◽

1993 ◽

Vol 13 (4) ◽

pp. 2554-2563 ◽

Cited By ~ 82

Author(s):

D Wojciechowicz ◽

C F Lu ◽

J Kurjan ◽

P N Lipke

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Adhesion ◽

Amino Acid ◽

Cell Surface ◽

Consensus Sequence ◽

Binding Domain ◽

Immunoglobulin Superfamily ◽

Cell Contact ◽

Amino Acid Residues ◽

Adhesion Proteins

alpha-Agglutinin is a cell adhesion glycoprotein expressed on the cell wall of Saccharomyces cerevisiae alpha cells. Binding of alpha-agglutinin to its ligand a-agglutinin, expressed by a cells, mediates cell-cell contact during mating. Analysis of truncations of the 650-amino-acid alpha-agglutinin structural gene AG alpha 1 delineated functional domains of alpha-agglutinin. Removal of the C-terminal hydrophobic sequence allowed efficient secretion of the protein and loss of cell surface attachment. This cell surface anchorage domain was necessary for linkage to a glycosyl phosphatidylinositol anchor. A construct expressing the N-terminal 350 amino acid residues retained full a-agglutinin-binding activity, localizing the binding domain to the N-terminal portion of alpha-agglutinin. A 278-residue N-terminal peptide was inactive; therefore, the binding domain includes residues between 278 and 350. The segment of alpha-agglutinin between amino acid residues 217 and 308 showed significant structural and sequence similarity to a consensus sequence for immunoglobulin superfamily variable-type domains. The similarity of the alpha-agglutinin-binding domain to mammalian cell adhesion proteins suggests that this structure is a highly conserved feature of adhesion proteins in diverse eukaryotes.

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Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia

Medical Journal of Indonesia ◽

10.13181/mji.v24i4.1197 ◽

2015 ◽

Vol 24 (4) ◽

pp. 197-205

Author(s):

Dwi Wulandari ◽

Lisnawati Rachmadi ◽

Tjahjani M. Sudiro

Keyword(s):

Amino Acids ◽

Phylogenetic Analysis ◽

Amino Acid ◽

Asian American ◽

Protein Function ◽

Single Amino Acid ◽

Hpv16 E6 ◽

E6 And E7 ◽

Neutral Mutations

Background: E6 and E7 are oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its carcinogenic potential. The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function. This analysis could be used to reduce time, effort, and research cost as initial screening in selection of protein or isolates to be tested in vitro or in vivo.Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of Indonesian isolates, which were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.Results: Java variants and isolate ui66* belonged to European branch, while the others belonged to Asian and African branches. Twelve changes of amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G mutation was found only in Af2*.Conclusion: E6 proteins of HPV16 variants were more variable than E7. SNAP analysis showed that only E6 protein of African-2 branch had functional differences compared to HPV16R.

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Efficient alternatives to PSI-BLAST

Bulletin of the Polish Academy of Sciences Technical Sciences ◽

10.2478/v10175-012-0063-0 ◽

2012 ◽

Vol 60 (3) ◽

pp. 495-505

Author(s):

M. Startek ◽

S. Lasota ◽

M. Sykulski ◽

A. Bułak ◽

L. Noé ◽

...

Keyword(s):

Amino Acid ◽

Finite Automata ◽

Protein Family ◽

Homology Search ◽

Amino Acid Residues ◽

Protein Alignment ◽

Substitution Model ◽

Hierarchical Tree ◽

Context Specific ◽

Ncbi Blast

Abstract In this paper we present two algorithms that may serve as efficient alternatives to the well-known PSI BLAST tool: SeedBLAST and CTX-PSI Blast. Both may benefit from the knowledge about amino acid composition specific to a given protein family: SeedBLAST uses the advisedly designed seed, while CTX-PSI BLAST extends PSI BLAST with the context-specific substitution model. The seeding technique became central in the theory of sequence alignment. There are several efficient tools applying seeds to DNA homology search, but not to protein homology search. In this paper we fill this gap. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The seeds are represented by deterministic finite automata (DFAs) and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original BLAST and PSI-BLAST on several protein families. Our results demonstrate a superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. The contextual substitution model has been proven to increase sensitivity of protein alignment. In this paper we perform a next step in the contextual alignment program. We announce a contextual version of the PSI-BLAST algorithm, an iterative version of the NCBI-BLAST tool. The experimental evaluation has been performed demonstrating a significantly higher sensitivity compared to the ordinary PSI-BLAST algorithm.

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