scholarly journals Molecular evolution of NASP and conserved histone H3/H4 transport pathway

2021 ◽  
Author(s):  
Syed Nabeel-Shah ◽  
Kanwal Ashraf ◽  
Ronald E Pearlman ◽  
Jeffrey Fillingham
Keyword(s):  
Molecular Evolution ◽  
Functional Diversity ◽  
Protein Level ◽  
Family Members ◽  
Gc Content ◽  
Purifying Selection ◽  
Crown Group ◽  
Transport Pathway ◽  
Critical Function ◽  
Transport Pathways

Background: NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where some functional diversity has been reported. In humans, growing evidence implicates NASP miss-regulation in the development of a variety of cancers. Although a comprehensive phylogenetic analysis is lacking, NASP-family proteins that possess four TPR motifs are thought to be widely distributed across eukaryotes. Results: We characterize the molecular evolution of NASP by systematically identifying putative NASP orthologs across diverse eukaryotic lineages ranging from excavata to those of the crown group. We detect extensive silent divergence at the nucleotide level suggesting the presence of strong purifying selection acting at the protein level. We also observe a selection bias for high frequencies of acidic residues which we hypothesize is a consequence of their critical function(s), further indicating the role of functional constraints operating on NASP evolution. Our data indicate that TPR1 and TPR4 constitute the most rapidly evolving functional units of NASP and may account for the functional diversity observed among well characterized family members. We also show that NASP paralogs in ray-finned fish have different genomic environments with clear differences in their GC content and have undergone significant changes at the protein level suggesting functional diversification. Conclusion: We draw four main conclusions from this study. First, wide distribution of NASP throughout eukaryotes suggests that it was likely present in the last eukaryotic common ancestor (LECA) possibly as an important innovation in the transport of H3/H4. Second, strong purifying selection operating at the protein level has influenced the nucleotide composition of NASP genes. Further, we show that selection has acted to maintain a high frequency of functionally relevant acidic amino acids in the region that interrupts TPR2. Third, functional diversity reported among several well characterized NASP family members can be explained in terms of quickly evolving TPR1 and TPR4 motifs. Fourth, NASP fish specific paralogs have significantly diverged at the protein level with NASP2 acquiring a NNR domain.

scholarly journals Molecular evolution of NASP and conserved histone H3/H4 transport pathway

2021 ◽  
Author(s):  
Syed Nabeel-Shah ◽  
Kanwal Ashraf ◽  
Ronald E Pearlman ◽  
Jeffrey Fillingham
Keyword(s):  
Molecular Evolution ◽  
Functional Diversity ◽  
Protein Level ◽  
Family Members ◽  
Gc Content ◽  
Purifying Selection ◽  
Crown Group ◽  
Transport Pathway ◽  
Critical Function ◽  
Transport Pathways

Background: NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where some functional diversity has been reported. In humans, growing evidence implicates NASP miss-regulation in the development of a variety of cancers. Although a comprehensive phylogenetic analysis is lacking, NASP-family proteins that possess four TPR motifs are thought to be widely distributed across eukaryotes. Results: We characterize the molecular evolution of NASP by systematically identifying putative NASP orthologs across diverse eukaryotic lineages ranging from excavata to those of the crown group. We detect extensive silent divergence at the nucleotide level suggesting the presence of strong purifying selection acting at the protein level. We also observe a selection bias for high frequencies of acidic residues which we hypothesize is a consequence of their critical function(s), further indicating the role of functional constraints operating on NASP evolution. Our data indicate that TPR1 and TPR4 constitute the most rapidly evolving functional units of NASP and may account for the functional diversity observed among well characterized family members. We also show that NASP paralogs in ray-finned fish have different genomic environments with clear differences in their GC content and have undergone significant changes at the protein level suggesting functional diversification. Conclusion: We draw four main conclusions from this study. First, wide distribution of NASP throughout eukaryotes suggests that it was likely present in the last eukaryotic common ancestor (LECA) possibly as an important innovation in the transport of H3/H4. Second, strong purifying selection operating at the protein level has influenced the nucleotide composition of NASP genes. Further, we show that selection has acted to maintain a high frequency of functionally relevant acidic amino acids in the region that interrupts TPR2. Third, functional diversity reported among several well characterized NASP family members can be explained in terms of quickly evolving TPR1 and TPR4 motifs. Fourth, NASP fish specific paralogs have significantly diverged at the protein level with NASP2 acquiring a NNR domain.

scholarly journals Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Wenqi Ran ◽  
David M. Kristensen ◽  
Eugene V. Koonin
Keyword(s):  
Codon Usage ◽  
Protein Level ◽  
Codon Usage Bias ◽  
Protein Sequence ◽  
Gc Content ◽  
Protein Sequences ◽  
Microbial Evolution ◽  
Fine Tuning ◽  
Selection For ◽  
Genomic Gc Content

ABSTRACT The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (F opt ) being below 0.55. This apparent weak selection on codon usage contrasts with the strong purifying selection on amino acid sequences, with 65.8% of the gene-specific dN/dS ratios being below 0.1. For most of the genomes compared, a limited but statistically significant negative correlation between F opt and dN/dS was observed, which is indicative of a link between selection on protein sequence and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. Combined with previous observations on the selection for GC-rich codons in bacteria and archaea with GC-rich genomes, these findings suggest that selection for translational fine-tuning could be an important factor in microbial evolution that drives the evolution of genome GC content away from mutational equilibrium. This type of selection is particularly pronounced in slowly evolving, “high-status” genes. A significantly stronger link between the two aspects of selection is observed in free-living bacteria than in parasitic bacteria and in genes encoding metabolic enzymes and transporters than in informational genes. These differences might reflect the special importance of translational fine-tuning for the adaptability of gene expression to environmental changes. The results of this work establish the coupling between protein level selection and selection for translational optimization as a distinct and potentially important factor in microbial evolution. IMPORTANCE Selection affects the evolution of microbial genomes at many levels, including both the structure of proteins and the regulation of their production. Here we demonstrate the coupling between the selection on protein sequences and the optimization of codon usage in a broad range of bacteria and archaea. The strength of this coupling varies over a wide range and strongly and positively correlates with the genomic GC content. The cause(s) of the evolution of high GC content is a long-standing open question, given the universal mutational bias toward AT. We propose that optimization of codon usage could be one of the key factors that determine the evolution of GC-rich genomes. This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution.

scholarly journals Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

Calreticulin molecular evolution: a strong purifying and episodic diversifying selection result

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Rigers Bakiu
Keyword(s):  
Molecular Evolution ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Amino Acid Sequences ◽  
Over Expression ◽  
Diversifying Selection ◽  
Pathological Conditions ◽  
Weight Protein ◽  
Low Molecular Weight Protein

AbstractCalreticulin (CRT) is a low molecular weight protein present in vertebrates, invertebrates and higher plants. Its multiple functions have been demonstrated. It plays an important role as a chaperone and Ca2+ buffer inside sarcoplasmic/endoplasmic reticulum (SR/ER), and outside the ER in many physiological/pathological processes. Recently it has been observed that CRT over-expression or its absence is linked to various pathological conditions, such as malignant evolution and progression, and these facts really increased its study interests. Using an evolution approach CRT was further characterized. Several Bayesian phylogenetic analyses were performed using coding and amino acid sequences. CRT molecular evolution was investigated for the presence of negative or/and positive selection using HyPhy package. The results indicated that the purifying selection might have operated over the whole CRT primary structure. Although, an episodic diversifying selection was also found on the analyzed CRT sequences.

scholarly journals Multiomics analyses of vesicular transport pathway-specific transcripts and proteins in ovine amnion: responses to altered intramembranous transport

2019 ◽  
Vol 51 (7) ◽  
pp. 267-278 ◽  
Author(s):  
Cecilia Y. Cheung ◽  
Debra F. Anderson ◽  
Robert A. Brace
Keyword(s):  
Energy Metabolism ◽  
Amniotic Fluid ◽  
Intracellular Trafficking ◽  
Cytoplasmic Dynein ◽  
Transport Rate ◽  
Fluid Replacement ◽  
Transport Pathway ◽  
Fetal Sheep ◽  
Transport Pathways ◽  
Fetal Urine

Amniotic fluid volume (AFV) is determined by the rate of intramembranous (IM) transport of amniotic fluid (AF) across the amnion. This transport is regulated by fetal urine-derived stimulators and AF inhibitors. Our objective was to utilize a multiomics approach to determine the IM transport pathways and identify the regulators. Four groups of fetal sheep with experimentally induced alterations in IM transport rate were studied: control, urine drainage (UD), urine drainage with fluid replacement (UDR), and intra-amniotic fluid infusion (IA). Amnion, AF, and fetal urine were subjected to transcriptomics (RNA-Seq) and proteomics studies followed by Ingenuity Pathway Analysis. The analysis uncovered nine transport-associated pathways and four groups of differentially expressed transcripts and proteins. These can be categorized into mediators of vesicular uptake and endocytosis, intracellular trafficking, pathway activation and signaling, and energy metabolism. UD decreased IM transport rate and AFV in conjunction with enhanced expression of vesicular endocytosis regulators but reduced expression of intracellular trafficking mediators. With UDR, IM transport rate decreased and AFV increased. Energy metabolism activators increased while trafficking mediators decreased in expression. IA increased IM transport rate and AFV together with enhanced expressions of vesicular endocytosis and trafficking mediators. We conclude that IM transport across the amnion is regulated by multiple vesicular transcytotic and signaling pathways and that the mediators of intracellular trafficking most likely play an important role in determining the rate of IM transport. Furthermore, the motor protein cytoplasmic dynein light chain-1, which coexpressed in AF and fetal urine, may function as a urine-derived IM transport stimulator.

Na+ and Cl- transport across rabbit nonciliated bronchiolar epithelial (Clara) cells

1989 ◽  
Vol 256 (4) ◽  
pp. C893-C901 ◽  
Author(s):  
M. R. Van Scott ◽  
C. W. Davis ◽  
R. C. Boucher
Keyword(s):  
Ion Transport ◽  
Short Circuit ◽  
Flux Ratio ◽  
Open Circuit ◽  
Clara Cell ◽  
Clara Cells ◽  
Transport Pathway ◽  
Transport Pathways ◽  
Serum Free ◽  
Significant Difference

Radioisotopic flux measurements were performed on rabbit Clara cell epithelium cultured in serum-free hormone-supplemented medium to identify the major ion transport pathways in the cell type. Clara cells cultured in serum-free hormone-supplemented medium exhibit a large short-circuit current compared with cells maintained in serum-containing medium (45 microA/cm2 vs. 15 microA/cm2). The responses to amiloride and isoproterenol, however, are similar for cells grown in the two media. A net amiloride-sensitive movement of Na+ in the mucosal (M)-to-serosal (S) direction undershort- and open-circuit conditions is detected (1.48 and 0.67 mueq.h-1.cm-2, respectively). No statistically significant difference in the unidirectional fluxes of Cl- is apparent in the basal state, but a net flux of Cl- in the S-to-M direction is observed after exposure of the apical membrane to amiloride (0.93 mueq.h-1.cm-2). The partial ionic conductances for Na+ and Cl- estimated from the fluxes measured in the passive directions (JNaS----M, JClM----S) exceed the total tissue conductance by 20%. Ussing flux ratio analyses of Cl- movements at clamped potentials between -60 and +20 mV show that Cl- movements are not strictly through passive conductive pathways at negative potentials. The movement of Cl- can be modeled by passive diffusion combined with Cl- -Cl- exchange equal to 20% of total passive fluxes of Na+ and Cl-. These observations indicate that 1) Na+ absorption is the major active ion transport pathway across cultured Clara cells, 2) active Cl- secretion is minimal in the basal state, and 3) approximately 20% of the unidirectional Cl- fluxes occur via nonconductive pathways.

scholarly journals Molecular Evolution and Structural Features of IRAK Family Members

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e49771 ◽  
Author(s):  
Vijayakumar Gosu ◽  
Shaherin Basith ◽  
Prasannavenkatesh Durai ◽  
Sangdun Choi
Keyword(s):  
Molecular Evolution ◽  
Family Members ◽  
Structural Features

scholarly journals Inter- and Intraspecific Variation in Drosophila Genes with Sex-Biased Expression

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Lena Müller ◽  
Sonja Grath ◽  
Korbinian von Heckel ◽  
John Parsch
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Protein Sequence ◽  
Sequence Variation ◽  
Purifying Selection ◽  
Sexually Dimorphic ◽  
Expression Divergence ◽  
Sexually Dimorphic Expression ◽  
Dimorphic Expression

Genes with sexually dimorphic expression (sex-biased genes) often evolve rapidly and are thought to make an important contribution to reproductive isolation between species. We examined the molecular evolution of sex-biased genes in Drosophila melanogaster and D. ananassae, which represent two independent lineages within the melanogaster group. We find that strong purifying selection limits protein sequence variation within species, but that a considerable fraction of divergence between species can be attributed to positive selection. In D. melanogaster, the proportion of adaptive substitutions between species is greatest for male-biased genes and is especially high for those on the X chromosome. In contrast, male-biased genes do not show unusually high variation within or between populations. A similar pattern is seen at the level of gene expression, where sex-biased genes show high expression divergence between species, but low divergence between populations. In D. ananassae, there is no increased rate of adaptation of male-biased genes, suggesting that the type or strength of selection acting on sex-biased genes differs between lineages.

scholarly journals Volume-responsive sodium and proton movements in dog red blood cells.

1984 ◽  
Vol 84 (3) ◽  
pp. 379-401 ◽  
Author(s):  
J C Parker ◽  
V Castranova
Keyword(s):  
Membrane Potential ◽  
Red Blood Cells ◽  
Fluorescent Probe ◽  
Blood Cells ◽  
Indirect Method ◽  
Cell Types ◽  
The Other ◽  
Na Transport ◽  
Transport Pathway ◽  
Transport Pathways

Shrinkage of dog red blood cells (RBC) activates a Na transport pathway that is Cl dependent, amiloride sensitive, and capable of conducting Na-proton counterflow. It is possible to establish transmembrane gradients for either Na or protons and to demonstrate that each cation species can drive reciprocal movements of the other. The nature of the coupling between Na and proton movements was investigated using the fluorescent probe diS-C3(5) and also by an indirect method in which K movements through valinomycin channels were used to draw inferences about the membrane potential. No evidence was found to suggest that the Na-proton pathway activated by shrinkage of dog RBC is a conductive one. By exclusion, it is presumed that the coupling between the counterflow of Na and protons is electroneutral. The volume-activated Na-proton fluxes in dog RBC have certain properties that distinguish them from similar transport pathways in other cell types.

scholarly journals Plastic microbeads from cosmetic products: an experimental study of their hydrodynamic behaviour, vertical transport and resuspension in phytoplankton and sediment aggregates

Elem Sci Anth ◽  
2018 ◽  
Vol 6 ◽  
Author(s):  
Paula Möhlenkamp ◽  
Autun Purser ◽  
Laurenz Thomsen
Keyword(s):  
Plastic Material ◽  
Suspended Sediments ◽  
Physical Characteristics ◽  
Benthic Boundary Layer ◽  
Cosmetic Products ◽  
Transport Pathway ◽  
Transport Pathways ◽  
Waste Products ◽  
Hydrodynamic Behaviour ◽  
Algal Material

Hydrodynamic behaviour and the transport pathways of microplastics within the ocean environment are not well known, rendering accurate predictive models for dispersal management of such pollutants difficult to establish. In the natural environment, aggregation between plastic microbeads and phytodetritus or suspended sediments in rivers and oceans further complicate the patterns of dispersal. In this laboratory study, the physical characteristics and hydrodynamic behaviour of a selection of common plastic microbeads, as used in exfoliation skincare cosmetic products, were investigated. Additionally, the potential for aggregation of these microbeads with phytodetritus and suspended sediments, as well as the subsequent sinking and resuspension behaviour of produced aggregates, were investigated with roller tanks, settling columns and erosion chamber. Physical characteristics of the plastic microbeads showed great heterogeneity, with various densities, sizes and shapes of plastic material being utilised in products designed for the same purpose. The majority of the plastics investigated were positively buoyant in both freshwater and seawater. Aggregation between plastic microbeads and phytoplankton was observed to be swift, with even extremely high concentrations of plastics being rapidly scavenged by suspended algal material. Following aggregation to sizes of 300 to 4400 μm diameter, some formerly buoyant plastics were observed to settle through the water column and enter the benthic boundary layer with settling velocities ranging between 32 and 831 m day–1. These aggregates could be resuspended in the laboratory under critical shear velocities of 0.67–1.33 cm s–1 (free stream velocities of > 10 cm s–1). This rapid aggregation and subsequent settling indicates a potentially important transport pathway for these waste products, a pathway that should be considered when modelling discharge and transport of plastic microbeads and determining the ecosystems that may be at risk from exposure.

Sign in / Sign up

Export Citation Format

Share Document