scholarly journals Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12231
Author(s):  
Sergey Matveevsky ◽  
Tatiana Grishaeva
Keyword(s):  
Ubiquitin Ligase ◽  
Specific Binding ◽  
Amino Acid Sequences ◽  
Molecular Organization ◽  
X Chromosomes ◽  
Rates Of Evolution ◽  
Multifunctional Enzymes ◽  
Protein Conservation ◽  
Taxonomic Groups ◽  
Evolution Of Proteins

The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.

scholarly journals The TFIID Components Human TAFII140 andDrosophila BIP2 (TAFII155) Are Novel Metazoan Homologues of Yeast TAFII47 Containing a Histone Fold and a PHD Finger

2001 ◽  
Vol 21 (15) ◽  
pp. 5109-5121 ◽  
Author(s):  
Yann-Gaël Gangloff ◽  
Jean-Christophe Pointud ◽  
Sylvie Thuault ◽  
Lucie Carré ◽  
Christophe Romier ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Sequence Similarity ◽  
Protein A ◽  
Amino Acid Sequences ◽  
Molecular Organization ◽  
Phd Finger ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
High Degree

ABSTRACT The RNA polymerase II transcription factor TFIID comprises the TATA binding protein (TBP) and a set of TBP-associated factors (TAFIIs). TFIID has been extensively characterized for yeast, Drosophila, and humans, demonstrating a high degree of conservation of both the amino acid sequences of the constituent TAFIIs and overall molecular organization. In recent years, it has been assumed that all the metazoan TAFIIs have been identified, yet no metazoan homologues of yeast TAFII47 (yTAFII47) and yTAFII65 are known. Both of these yTAFIIs contain a histone fold domain (HFD) which selectively heterodimerizes with that of yTAFII25. We have cloned a novel mouse protein, TAFII140, containing an HFD and a plant homeodomain (PHD) finger, which we demonstrated by immunoprecipitation to be a mammalian TFIID component. TAFII140 shows extensive sequence similarity toDrosophila BIP2 (dBIP2) (dTAFII155), which we also show to be a component of DrosophilaTFIID. These proteins are metazoan homologues of yTAFII47 as their HFDs selectively heterodimerize with dTAFII24 and human TAFII30, metazoan homologues of yTAFII25. We further show that yTAFII65 shares two domains with theDrosophila Prodos protein, a recently described potential dTAFII. These conserved domains are critical for yTAFII65 function in vivo. Our results therefore identify metazoan homologues of yTAFII47 and yTAFII65.

scholarly journals Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME

2019 ◽  
Vol 47 (13) ◽  
pp. 6984-7002 ◽  
Author(s):  
Ingrid Rössler ◽  
Julia Embacher ◽  
Benjamin Pillet ◽  
Guillaume Murat ◽  
Laura Liesinger ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Specific Binding ◽  
Affinity Purification ◽  
Critical Role ◽  
Small Subunit ◽  
Protein Mutants ◽  
Protein Chaperones ◽  
Direct Binding ◽  
Evolution Of Proteins

Abstract Dedicated chaperones protect newly synthesized ribosomal proteins (r-proteins) from aggregation and accompany them on their way to assembly into nascent ribosomes. Currently, only nine of the ∼80 eukaryotic r-proteins are known to be guarded by such chaperones. In search of new dedicated r-protein chaperones, we performed a tandem-affinity purification based screen and looked for factors co-enriched with individual small subunit r-proteins. We report the identification of Nap1 and Tsr4 as direct binding partners of Rps6 and Rps2, respectively. Both factors promote the solubility of their r-protein clients in vitro. While Tsr4 is specific for Rps2, Nap1 has several interaction partners including Rps6 and two other r-proteins. Tsr4 binds co-translationally to the essential, eukaryote-specific N-terminal extension of Rps2, whereas Nap1 interacts with a large, mostly eukaryote-specific binding surface of Rps6. Mutation of the essential Tsr4 and deletion of the non-essential Nap1 both enhance the 40S synthesis defects of the corresponding r-protein mutants. Our findings highlight that the acquisition of eukaryote-specific domains in r-proteins was accompanied by the co-evolution of proteins specialized to protect these domains and emphasize the critical role of r-protein chaperones for the synthesis of eukaryotic ribosomes.

scholarly journals Antibodies against 70-kD heat shock cognate protein inhibit mediated nuclear import of karyophilic proteins.

1992 ◽  
Vol 119 (5) ◽  
pp. 1047-1061 ◽  
Author(s):  
N Imamoto ◽  
Y Matsuoka ◽  
T Kurihara ◽  
K Kohno ◽  
M Miyagi ◽  
...  
Keyword(s):  
Heat Shock ◽  
Nuclear Import ◽  
Cellular Localization ◽  
Nuclear Transport ◽  
Specific Binding ◽  
T Antigen ◽  
Amino Acid Sequences ◽  
Nuclear Accumulation ◽  
Heat Shock Cognate Protein ◽  
Cognate Protein

Previously, we found that anti-DDDED antibodies strongly inhibited in vivo nuclear transport of nuclear proteins and that these antibodies recognized a protein of 69 kD (p69) from rat liver nuclear envelopes that showed specific binding activities to the nuclear location sequences (NLSs) of nucleoplasmin and SV-40 large T-antigen. Here we identified this protein as the 70-kD heat shock cognate protein (hsc70) based on its mass, isoelectric point, cellular localization, and partial amino acid sequences. Competition studies indicated that the recombinant hsc70 expressed in Escherichia coli binds to transport competent SV-40 T-antigen NLS more strongly than to the point mutated transport incompetent mutant NLS. To investigate the possible involvement of hsc70 in nuclear transport, we examined the effect of anti-hsc70 rabbit antibodies on the nuclear accumulation of karyophilic proteins. When injected into the cytoplasm of tissue culture cells, anti-hsc70 strongly inhibited the nuclear import of nucleoplasmin, SV-40 T-antigen NLS bearing BSA and histone H1. In contrast, anti-hsc70 IgG did not prevent the diffusion of lysozyme or 17.4-kD FITC-dextran into the nuclei. After injection of these antibodies, cells continued RNA synthesis and were viable. These results indicate that hsc70 interacts with NLS-containing proteins in the cytoplasm before their nuclear import.

scholarly journals The problem of the ‘prebiotic and never born proteins’

2012 ◽  
Vol 12 (1) ◽  
pp. 94-98 ◽  
Author(s):  
Gerald E. Marsh
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Probabilistic Argument ◽  
Darwinian Selection ◽  
Evolution Of Proteins

AbstractIt has been argued that the limited set of proteins used by life as we know could not have arisen by the process of Darwinian selection from all possible proteins. This probabilistic argument has a number of implicit assumptions that may not be warranted. A variety of considerations are presented to show that the number of amino acid sequences that need to have been sampled during the evolution of proteins is far smaller than assumed by the argument.

The Study of Plant Phylogeny Using Amino Acid Sequences of Ribulose-1,5-Bisphosphate Carboxylase. IV. Proteaceae and Fagaceae and the Rate of Evolution of the Small Subunit

1984 ◽  
Vol 32 (3) ◽  
pp. 291 ◽  
Author(s):  
PG Martin ◽  
JM Dowd
Keyword(s):  
Amino Acid ◽  
Plate Tectonics ◽  
Phylogenetic Trees ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Plant Phylogeny ◽  
Rates Of Evolution ◽  
Molecular Evolutionary Clock

N-terminal, 40 amino acid sequences of ribulose bisphosphate carboxylase small subunit (SSU) are given for four species of Proteaceae, six of Fagaceae including four from Nothofagus, and seven from Solanaceae including six new sequences from Nicotiana. Phylogenetic trees, regarded as tentative since only one protein is involved, are given for each of the three groups and approximate positions of the families in the angiosperm tree are indicated. An example of the destabilizing of a hitherto invariant site is given. Working from the 'molecular evolutionary clock' hypothesis, and deriving time from plate tectonics, the data from both Proteaceae and Nothofagus lead to rates of evolution of SSU of one non-silent nucleotide substitution per 9 My. This agrees with an early Cretaceous origin of the angiosperms. A test is proposed to distinguish distributions that are the result of 'vicariance biogeography' from those due to 'dispersal biogeography'. It is concluded that distribution of Nicotiana is most likely due to dispersal.

Diversity of the trifunctional histidine biosynthesis gene (his) in cerealPhaeosphaeriaspecies

Genome ◽  
2007 ◽  
Vol 50 (6) ◽  
pp. 595-609 ◽  
Author(s):  
Chih-Li Wang ◽  
Arkadiusz Malkus ◽  
Sabina M. Zuzga ◽  
Pi-Fang Linda Chang ◽  
Barry M. Cunfer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Meiotic Recombination ◽  
Pcr Amplification ◽  
Amino Acid Sequences ◽  
Histidine Biosynthesis ◽  
Leaf Blotch ◽  
Rates Of Evolution ◽  
Biosynthesis Gene ◽  
Histidinol Dehydrogenase

Phaeosphaeria species are important causal agents of Stagonospora leaf blotch diseases in cereals. In this study, the nucleotide sequence and deduced polypeptide of the trifunctional histidine biosynthesis gene (his) are used to investigate the phylogenetic relationships and provide molecular identification among cereal Phaeosphaeria species. The full-length sequences of the his gene were obtained by PCR amplification and compared among cereal Phaeosphaeria species. The coding sequence of the his gene in wheat-biotype P. nodorum (PN-w) was 2697 bp. The his genes in barley-biotype P. nodorum (PN-b), two P. avenaria f. sp. triticea isolates (homothallic Pat1 and Pat3), and Phaeosphaeria species from Polish rye and dallis grass were 2694 bp. The his gene in heterothallic isolate Pat2, however, was 2693 bp because the intron had one fewer base. In P. avenaria f. sp. avenaria (Paa), the his gene was only 2670 bp long. The differences in the size of the his gene contributed to the variation in amino acid sequences in the gap region located between the phosphoribosyl-ATP pyrophosphohydrolase and histidinol dehydrogenase sub-domains. Based on nucleotide and deduced amino acid sequences of the his gene, Pat1 was not closely related to either PN-w or the Paa clade. It appears that rates of evolution of the his gene were fast in cereal Phaeosphaeria species. The possible involvement of meiotic recombination in genetic diversity of the his gene in P. nodorum is discussed.

Y-box proteins combine versatile cold shock domains and arginine-rich motifs (ARMs) for pleiotropic functions in RNA biology

2018 ◽  
Vol 475 (17) ◽  
pp. 2769-2784 ◽  
Author(s):  
Kenneth C. Kleene
Keyword(s):  
Amino Acid ◽  
Cold Shock ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Binding ◽  
Amino Acid Sequences ◽  
Site Specific ◽  
Terminal Domain ◽  
Rna Backbone ◽  
Specific Regulation

Y-box proteins are single-strand DNA- and RNA-binding proteins distinguished by a conserved cold shock domain (CSD) and a variable C-terminal domain organized into alternating short modules rich in basic or acidic amino acids. A huge literature depicts Y-box proteins as highly abundant, staggeringly versatile proteins that interact with all mRNAs and function in most forms of mRNA-specific regulation. The mechanisms by which Y-box proteins recognize mRNAs are unclear, because their CSDs bind a jumble of diverse elements, and the basic modules in the C-terminal domain are considered to bind nonspecifically to phosphates in the RNA backbone. A survey of vertebrate Y-box proteins clarifies the confusing names for Y-box proteins, their domains, and RNA-binding motifs, and identifies several novel conserved sequences: first, the CSD is flanked by linkers that extend its binding surface or regulate co-operative binding of the CSD and N-terminal and C-terminal domains to proteins and RNA. Second, the basic modules in the C-terminal domain are bona fide arginine-rich motifs (ARMs), because arginine is the predominant amino acid and comprises 99% of basic residues. Third, conserved differences in AA (amino acid) sequences between isoforms probably affect RNA-binding specificity. C-terminal ARMs connect with many studies, demonstrating that ARMs avidly bind sites containing specific RNA structures. ARMs crystallize insights into the under-appreciated contributions of the C-terminal domain to site-specific binding by Y-box proteins and difficulties in identifying site-specific binding by the C-terminal domain. Validated structural biology techniques are available to elucidate the mechanisms by which YBXprot (Y-box element-binding protein) CSDs and ARMs identify targets.

scholarly journals An in silico approach to analyze HCV genotype-specific binding-site variation and its effect on drug–protein interaction

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ramsha Khalid ◽  
Muhammad Faraz Anwar ◽  
Muhammad Aanish Raees ◽  
Sadaf Naeem ◽  
Syed Hani Abidi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Interaction ◽  
Protein Interactions ◽  
In Silico ◽  
Specific Binding ◽  
Antiviral Treatment ◽  
Amino Acid Sequences ◽  
Genotype 1A ◽  
Genotype Variation ◽  
Site Variation

AbstractGenotype variation in viruses can affect the response of antiviral treatment. Several studies have established approaches to determine genotype-specific variations; however, analyses to determine the effect of these variations on drug–protein interactions remain unraveled. We present an in-silico approach to explore genotype-specific variations and their effect on drug–protein interaction. We have used HCV NS3 helicase and fluoroquinolones as a model for drug–protein interaction and have investigated the effect of amino acid variations in HCV NS3 of genotype 1a, 1b, 2b and 3a on NS3-fluoroquinolone interaction. We retrieved 687, 667, 101 and 248 nucleotide sequences of HCV NS3 genotypes 1a, 1b, 2b, and 3a, respectively, and translated these into amino acid sequences and used for genotype variation analysis, and also to construct 3D protein models for 2b and 3a genotypes. For 1a and 1b, crystal structures were used. Drug–protein interactions were determined using molecular docking analyses. Our results revealed that individual genotype-specific HCV NS3 showed substantial sequence heterogeneity that resulted in variations in docking interactions. We believe that our approach can be extrapolated to include other viruses to study the clinical significance of genotype-specific variations in drug–protein interactions.

scholarly journals The random character of protein evolution and its effects on the reliability of phylogenetic information deduced from amino acid sequences and compositions

1980 ◽  
Vol 191 (2) ◽  
pp. 349-354 ◽  
Author(s):  
A Cornish-Bowden
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Random Effect ◽  
Cross Reactivity ◽  
Amino Acid Sequences ◽  
Random Errors ◽  
Phylogenetic Information ◽  
Rates Of Evolution ◽  
Related Pair

Because evolution occurs by random events, the actual number of substitutions that occur in any period is not exactly equal to the number expected from the mean rate of substitution, but is statistically distributed about it. In consequence, even if rates of evolution are constant in different lineages, ‘trees’ deduced from descendant protein sequences contain random errors. When there are fewer than about eight differences between the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based on amino acid sequence. In some cases, such as classification of mammals on the basis of cytochrome c structure, it appears to make little difference to the reliability of the results whether the sequences of the protein concerned are known or not. It may also be possible to obtain more reliable phylogenetic information from composition measurements on several kinds of protein than one could obtain from sequence measurements on a single kind of protein.

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