scholarly journals Multiomics study of a heterotardigrade, Echinisicus testudo, suggests convergent evolution of anhydrobiosis-related proteins in Tardigrada

2020 ◽  
Author(s):  
Yumi Murai ◽  
Maho Yagi-Utsumi ◽  
Masayuki Fujiwara ◽  
Masaru Tomita ◽  
Koichi Kato ◽  
...  
Keyword(s):  
Water Content ◽  
Molecular Mechanism ◽  
Convergent Evolution ◽  
Structural Changes ◽  
Extreme Environments ◽  
Random Coil ◽  
Related Protein ◽  
Α Helix ◽  
Related Proteins

AbstractMany limno-terrestrial tardigrades can enter an ametabolic state upon desiccation, in which the animals can withstand extreme environments. To date, studies of the molecular mechanism have predominantly investigated the class Eutardigrada, and that in the Heterotardigrada, remains elusive. To this end, we report a multiomics study of the heterotardigrade Echiniscus testudo, which is one of the most desiccation-tolerant species. None of the previously identified tardigrade-specific anhydrobiosis-related genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families of novel abundant heat-soluble proteins and the proteins exhibited structural changes from random coil to α-helix as the water content decreased in vitro. These characteristics are analogous to those of anhydrobiosis-related protein in eutardigrades, while there is no conservation at the sequence level. Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada.

scholarly journals Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yumi Murai ◽  
Maho Yagi-Utsumi ◽  
Masayuki Fujiwara ◽  
Sae Tanaka ◽  
Masaru Tomita ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Extreme Environments ◽  
Soluble Proteins ◽  
Random Coil ◽  
Rna Seq ◽  
Stress Response Genes ◽  
Molecular Components

Abstract Background Many limno-terrestrial tardigrades can enter an ametabolic state, known as anhydrobiosis, upon desiccation, in which the animals can withstand extreme environments. Through genomics studies, molecular components of anhydrobiosis are beginning to be elucidated, such as the expansion of oxidative stress response genes, loss of stress signaling pathways, and gain of tardigrade-specific heat-soluble protein families designated CAHS and SAHS. However, to date, studies have predominantly investigated the class Eutardigrada, and molecular mechanisms in the remaining class, Heterotardigrada, still remains elusive. To address this gap in the research, we report a multiomics study of the heterotardigrade Echiniscus testudo, one of the most desiccation-tolerant species which is not yet culturable in laboratory conditions. Results In order to elucidate the molecular basis of anhydrobiosis in E. testudo, we employed a multi-omics strategy encompassing genome sequencing, differential transcriptomics, and proteomics. Using ultra-low input library sequencing protocol from a single specimen, we sequenced and assembled the 153.7 Mbp genome annotated using RNA-Seq data. None of the previously identified tardigrade-specific abundant heat-soluble genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families novel abundant heat-soluble proteins, which we named E. testudo Abundant Heat Soluble (EtAHS), that are predicted to contain large stretches of disordered regions. Likewise the AHS families in eutardigrada, EtAHS shows structural changes from random coil to alphahelix as the water content was decreased in vitro. These characteristics of EtAHS proteins are analogous to those of CAHS in eutardigrades, while there is no conservation at the sequence level. Conclusions Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada. (276/350).

scholarly journals Astrocytes Are More Vulnerable than Neurons to Silicon Dioxide Nanoparticle Toxicity in Vitro

Toxics ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 51
Author(s):  
Jorge Humberto Limón-Pacheco ◽  
Natalie Jiménez-Barrios ◽  
Alejandro Déciga-Alcaraz ◽  
Adriana Martínez-Cuazitl ◽  
Mónica Maribel Mata-Miranda ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Silicon Dioxide ◽  
Culture Media ◽  
Brain Cell ◽  
Attenuated Total Reflection ◽  
Random Coil ◽  
Silicon Dioxide Nanoparticles ◽  
Neurotoxic Effects ◽  
Α Helix

Some studies have shown that silicon dioxide nanoparticles (SiO2-NPs) can reach different regions of the brain and cause toxicity; however, the consequences of SiO2-NPs exposure on the diverse brain cell lineages is limited. We aimed to investigate the neurotoxic effects of SiO2-NP (0–100 µg/mL) on rat astrocyte-rich cultures or neuron-rich cultures using scanning electron microscopy, Attenuated Total Reflection-Fourier Transform Infrared spectroscopy (ATR-FTIR), FTIR microspectroscopy mapping (IQ mapping), and cell viability tests. SiO2-NPs were amorphous particles and aggregated in saline and culture media. Both astrocytes and neurons treated with SiO2-NPs showed alterations in cell morphology and changes in the IR spectral regions corresponding to nucleic acids, proteins, and lipids. The analysis by the second derivative revealed a significant decrease in the signal of the amide I (α-helix, parallel β-strand, and random coil) at the concentration of 10 µg/mL in astrocytes but not in neurons. IQ mapping confirmed changes in nucleic acids, proteins, and lipids in astrocytes; cell death was higher in astrocytes than in neurons (10–100 µg/mL). We conclude that astrocytes were more vulnerable than neurons to SiO2-NPs toxicity. Therefore, the evaluation of human exposure to SiO2-NPs and possible neurotoxic effects must be followed up.

Effects of in-Office and at-Home Bleaching on Human Enamel and Dentin: An in vitro Application of Fourier Transform Infrared Study

2008 ◽  
Vol 62 (11) ◽  
pp. 1274-1279 ◽  
Author(s):  
Feride Severcan ◽  
Kurtulus Gokduman ◽  
Ayca Dogan ◽  
Sukran Bolay ◽  
Saadet Gokalp
Keyword(s):  
Fourier Transform ◽  
Structural Changes ◽  
Protein Denaturation ◽  
Random Coil ◽  
Protein Ratio ◽  
Band Frequency ◽  
Human Enamel ◽  
Ft Ir ◽  
At Home

In-office and at-home bleaching techniques are widely used methods for the whitening of teeth. However, the safety of these techniques has not been clarified yet. The aim of the current study is to investigate the in-office- and at-home-bleaching-induced structural and quantitative changes in human enamel and dentin at the molecular level, under in vitro conditions. The Fourier transform mid-infrared (mid-FT-IR) spectroscopic technique was used to monitor bleaching-induced structural changes. Band frequency and intensity values of major absorptions such as amide A, amide I, phosphate (PO4), and carbonate (CO3−2) bands, for treatment groups and control, were measured and compared. The results revealed that both procedures have negligible effects on dentin constituents. In office-bleached enamel, in addition to demineralization, a decrease in protein and polysaccharide concentrations, mineral-to-protein ratio, and the strength of hydrogen bonds around NH groups, as well as a change in protein secondary structure were observed. The protein structure changed from β-sheet to random coil, which is an indication of protein denaturation. However, no significant variations were observed for at-home bleached enamel. The control, at-home, and in-office bleached enamel samples were differentiated with a high accuracy using cluster analysis based on FT-IR data. This study revealed that office bleaching caused deleterious alterations in the composition and structure of enamel that significantly affected the crystallinity and mineralization of the tissue. Therefore, at-home bleaching seems to be much safer than in-office bleaching in terms of molecular variations.

scholarly journals Evolution of polymer formation within the actin superfamily

2017 ◽  
Vol 28 (19) ◽  
pp. 2461-2469 ◽  
Author(s):  
Patrick R. Stoddard ◽  
Tom A. Williams ◽  
Ethan Garner ◽  
Buzz Baum
Keyword(s):  
Convergent Evolution ◽  
Atp Hydrolysis ◽  
Linear Polymers ◽  
Related Protein ◽  
Protein Families ◽  
Structure And Dynamics ◽  
Polymer Formation ◽  
Filament Structure ◽  
Related Proteins ◽  
Actin Superfamily

While many are familiar with actin as a well-conserved component of the eukaryotic cytoskeleton, it is less often appreciated that actin is a member of a large superfamily of structurally related protein families found throughout the tree of life. Actin-related proteins include chaperones, carbohydrate kinases, and other enzymes, as well as a staggeringly diverse set of proteins that use the energy from ATP hydrolysis to form dynamic, linear polymers. Despite differing widely from one another in filament structure and dynamics, these polymers play important roles in ordering cell space in bacteria, archaea, and eukaryotes. It is not known whether these polymers descended from a single ancestral polymer or arose multiple times by convergent evolution from monomeric actin-like proteins. In this work, we provide an overview of the structures, dynamics, and functions of this diverse set. Then, using a phylogenetic analysis to examine actin evolution, we show that the actin-related protein families that form polymers are more closely related to one another than they are to other nonpolymerizing members of the actin superfamily. Thus all the known actin-like polymers are likely to be the descendants of a single, ancestral, polymer-forming actin-like protein.

Phospholipids modulate the biophysical properties and vasoactivity of PACAP-(1—38)

2002 ◽  
Vol 93 (4) ◽  
pp. 1377-1383 ◽  
Author(s):  
Takaya Tsueshita ◽  
Salil Gandhi ◽  
Hayat Önyüksel ◽  
Israel Rubinstein
Keyword(s):  
Conformational Transition ◽  
Critical Micellar Concentration ◽  
Random Coil ◽  
Cheek Pouch ◽  
Hamster Cheek Pouch ◽  
Pituitary Adenylate Cyclase ◽  
Peripheral Microcirculation ◽  
Α Helix

The purpose of this study was to elucidate the interactions between pituitary adenylate cyclase-activating peptide (PACAP)-(1—38) and phospholipids in vitro and to determine whether these phenomena modulate, in part, the vasorelaxant effects of the peptide in the intact peripheral microcirculation. We found that the critical micellar concentration of PACAP-(1—38) was 0.4–0.9 μM. PACAP-(1—38) significantly increased the surface tension of a dipalmitoylphosphatidylcholine monolayer and underwent conformational transition from predominantly random coil in saline to α-helix in the presence of distearoyl-phosphatidylethanolamine-polyethylene glycol (molecular mass of 2,000 Da) sterically stabilized phospholipid micelles (SSM) ( P < 0.05). Using intravital microscopy, we found that aqueous PACAP-(1—38) evoked significant concentration-dependent vasodilation in the intact hamster cheek pouch that was significantly potentiated when PACAP-(1—38) was associated with SSM ( P < 0.05). The vasorelaxant effects of aqueous PACAP-(1—38) were mediated predominantly by PACAP type 1 (PAC1) receptors, whereas those of PACAP-(1—38) in SSM predominantly by PACAP/vasoactive intestinal peptide type 1 and 2 (VPAC1/VPAC2) receptors. Collectively, these data indicate that PACAP-(1—38) self-associates and interacts avidly with phospholipids in vitro and that these phenomena amplify peptide vasoactivity in the intact peripheral microcirculation.

scholarly journals NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B

2020 ◽  
Vol 117 (48) ◽  
pp. 30391-30399
Author(s):  
Qiang Luo ◽  
Baihui Wang ◽  
Zhen Wu ◽  
Wen Jiang ◽  
Yueyue Wang ◽  
...  
Keyword(s):  
Interaction Mechanism ◽  
Histone Chaperones ◽  
Related Protein ◽  
Nucleosome Assembly ◽  
Nucleosome Assembly Protein ◽  
Vitro Binding ◽  
Multiple Interaction ◽  
Α Helix

Nucleosome Assembly Protein 1 (NAP1) family proteins are evolutionarily conserved histone chaperones that play important roles in diverse biological processes. In this study, we determined the crystal structure ofArabidopsisNAP1-Related Protein 1 (NRP1) complexed with H2A-H2B and uncovered a previously unknown interaction mechanism in histone chaperoning. Both in vitro binding and in vivo plant rescue assays proved that interaction mediated by the N-terminal α-helix (αN) domain is essential for NRP1 function. In addition, the C-terminal acidic domain (CTAD) of NRP1 binds to H2A-H2B through a conserved mode similar to other histone chaperones. We further extended previous knowledge of the NAP1-conserved earmuff domain by mapping the amino acids of NRP1 involved in association with H2A-H2B. Finally, we showed that H2A-H2B interactions mediated by αN, earmuff, and CTAD domains are all required for the effective chaperone activity of NRP1. Collectively, our results reveal multiple interaction modes of a NAP1 family histone chaperone and shed light on how histone chaperones shield H2A-H2B from nonspecific interaction with DNA.

Correlation of Structural Changes at Different Levels of the Jejunal Villus with Positive and Negative Net Water Transport in Vivo and in Vitro

1975 ◽  
Vol 53 (3) ◽  
pp. 439-450 ◽  
Author(s):  
T. F. McElligott ◽  
I. T. Beck ◽  
P. K. Dinda ◽  
S. Thompson
Keyword(s):  
Epithelial Cells ◽  
Water Content ◽  
Water Transport ◽  
Structural Changes ◽  
Morphological Changes ◽  
Sugar Transport ◽  
Apical Part ◽  
Different Levels

Experiments were done for identification and localization of certain structural changes at different levels of jejunal villus of the hamster during positive and negative water transport across the intestine in vivo and in vitro. Positive transport occurred when the mucosal surface of the intestine was bathed (in vitro experiments) or perfused (in vivo experiments) with isotonic Krebs–Ringer bicarbonate solution containing 10 mM glucose, and negative water transport was achieved by rendering this solution hypertonic with 150 mM mannitol. Results indicate that during positive net water transport, the intestine in vivo transported more fluid and exhibited a more conspicuous dilatation of the lateral intercellular spaces (L.I.S.) than did the in vitro preparation. Dilatation of the L.I.S. in both preparations was present only in the apical part of the villus, suggesting that this is the principal site of water absorption. When the mucosal solution was made hypertonic with mannitol, the L.I.S. in the in vivo intestine totally collapsed, whereas in the in vitro intestine these spaces remained open very slightly. These morphological changes correspond well with our finding that in the presence of the hypertonic mucosal solution there was a greater net negative water transport in vivo than in vitro. Incubation of the intestine in the isotonic mucosal solution produced subnuclear swelling of the mid-villus epithelial cells, and this morphological change was associated with an increase in the water content of the tissue. Perfusion of the in vivo intestine with the isotonic solution produced neither the swellings nor the increase in water content of the tissue. In the presence of hypertonic mucosal solution there was a water loss from the tissue both in vivo and in vitro, and these swellings were not observed. These results are discussed in relation to intestinal sugar transport and to the maturity of the epithelial cells, and it is concluded that transport studies on in vitro preparations may provide valid information on a qualitative basis, if not on a strictly quantitative basis.

scholarly journals Purification and Characterization of a New CRISP-Related Protein from Scapharca broughtonii and Its Immunomodulatory Activity

Marine Drugs ◽  
2020 ◽  
Vol 18 (6) ◽  
pp. 299
Author(s):  
Wanying Liu ◽  
Sixue Bi ◽  
Chunlei Li ◽  
Hang Zheng ◽  
Zhongyi Guo ◽  
...  
Keyword(s):  
Secretory Protein ◽  
Marine Organisms ◽  
Random Coil ◽  
Raw 264.7 Cells ◽  
Immunomodulatory Activity ◽  
Related Protein ◽  
Stat3 Signaling ◽  
Functional Product ◽  
Scapharca Broughtonii ◽  
Α Helix

More and more attention has been paid to bioactive compounds isolated from marine organisms or microorganisms in recent years. At the present study, a new protein coded as HPCG2, was purified from Scapharca broughtonii by stepwise chromatography methods. The molecular weight of HPCG2 was determined to be 30.71 kDa by MALDI-TOF-MS. The complete amino acid sequence of HPCG2 was obtained by tandem mass spectrometry combined with transcriptome database analysis, and its secondary structure was analyzed using circular dichroism. HPCG2 comprised 251 amino acids and contained 28.4% α-helix, 26% β-sheet, 18.6% β-turn, and 29.9% random coil. HPCG2 was predicted to be a cysteine-rich secretory protein-related (CRISP-related) protein by domain prediction. Moreover, HPCG2 was proved to possess the immunomodulatory effect on the murine immune cells. MTT assay showed that HPCG2 promoted the proliferation of splenic lymphocytes and the cytotoxicity of NK cells against YAC-1 cells. Flow cytometry test revealed that HPCG2 enhanced the phagocytic function of macrophages and polarized them into M1 type in RAW264.7 cells. In particular, Western blot analysis indicated that the immunomodulatory mechanism of HPCG2 was associated with the regulation on TLR4/JNK/ERK and STAT3 signaling pathways in RAW 264.7 cells. These results suggested that HPCG2 might be developed as a potential immunomodulatory agent or new functional product from marine organisms.

scholarly journals The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation

2020 ◽  
Author(s):  
Anita Pras ◽  
Bert Houben ◽  
Francesco A. Aprile ◽  
Renée Seinstra ◽  
Rodrigo Gallardo ◽  
...  
Keyword(s):  
Protein Aggregation ◽  
Structural Changes ◽  
Colloidal Stability ◽  
Positive Charge ◽  
Amyloid Formation ◽  
Related Protein ◽  
Age Related ◽  
Related Proteins ◽  
Protein Toxicity ◽  
Charge Interactions

AbstractWhile aggregation-prone proteins are known to accelerate ageing and cause age-related diseases, the cellular mechanisms that drive their cytotoxicity remain unresolved. The orthologous proteins MOAG-4, SERF1A and SERF2 have recently been identified as cellular modifiers of such cytotoxicity. Using a peptide array screening approach on human amyloidogenic proteins, we found that SERF2 interacted with specific patterns of negatively charged and hydrophobic, aromatic amino acids. The absence of such patterns, or the neutralization of the positive charge in SERF2, prevented these interactions and abolished the amyloid-promoting activity of SERF2. In a protein aggregation model in the nematode C. elegans, protein aggregation was suppressed by mutating the endogenous locus of MOAG-4 to neutralize charge. Our data indicate that charge interactions are required for MOAG-4 and SERF2 to promote aggregation. Such charged interactions might accelerate the primary nucleation of amyloid by initiating structural changes and by decreasing colloidal stability. Our finding that negatively charged segments are overrepresented in amyloid-forming proteins suggests that inhibition of charge interactions deserves exploration as a strategy to target age-related protein toxicity.Significance StatementHow aging causes relatively common diseases such as Alzheimer’s and Parkinson’s is still a mystery. Since toxic structural changes in proteins are likely to be responsible, we investigated biological mechanisms that could drive such changes. We made use of a modifying factor called SERF2, which accelerates structural changes and aggregation of several disease-related proteins. Through a peptide-binding screen, we found that SERF2 acts on negatively charged protein regions. The abundance of such regions in the disease-related proteins explains why SERF has its effect. Removing positive charge in SERF was sufficient to suppress protein aggregation in models for disease. We propose that blocking charge-interactions with SERF or other modifiers could serve as a general approach to treat age-related protein toxicity.

Elastin modulation and modification by homocysteine: a key factor in the pathogenesis of Pseudoexfoliation syndrome?

2018 ◽  
Vol 103 (7) ◽  
pp. 985-992 ◽  
Author(s):  
Manohar Rebecca ◽  
Ramakrishnan Gayathri ◽  
Renganathan Bhuvanasundar ◽  
Krishnamoorthy Sripriya ◽  
Balekudaru Shantha ◽  
...  
Keyword(s):  
Structural Changes ◽  
Systemic Disease ◽  
Mrna Level ◽  
Pseudoexfoliation Syndrome ◽  
Human Lens ◽  
Amyloid Formation ◽  
Homocysteine Thiolactone ◽  
Key Factor ◽  
Α Helix

BackgroundPseudoexfoliation syndrome (PXF) is an idiopathic, elastogenesis-associated systemic disease characterised by amyloid-like material aggregates in the eye. Elevated plasma and aqueous humour (aqH) homocysteine (Hcy) is reportedly associated with PXF. This study is aimed to probe Hcy-mediated alterations in elastin expression.MethodologyLens level of Hcy (total Hcy (tHcy)), mRNA expression of Eln, CBS and MTR in lens capsule, protein expression of elastin in aqH were estimated by enzyme immunoassay, quantitative PCR and western blot, respectively in PXF, PXF with glaucoma (PXF-G) cases, in comparison with cataract-alone disease controls. Human lens epithelial cells (hLECs) were exposed to Hcy and homocysteine thiolactone (HCTL) to evaluate elastin expression in vitro. Furthermore, elastin recombinant protein was incubated with Hcy and HCTL to assess secondary and tertiary structural modifications based on circular dichroism spectroscopy, spectrophotometric and SEM studies.ResultsThe lens tHcy was significantly high in PXF (p=0.02) and PXF-G (p=0.009). Eln expression was elevated in PXF and PXF-G (p=0.0007). Elastin level in aqH was elevated in PXF (p=0.01) and PXF-G (p=0.002). Hcy (200 µM) and HCTL (1 µM) promoted elastin expression at mRNA level by 36-fold (p=0.02) and 10-fold (p=0.05), respectively, and at protein level by nearly two-fold in cultured hLECs. Secondary structure changes in elastin protein caused by Hcy were evident from 34.11% drop in α-helix and 6.17% gain in β-sheet. Fluorescence, spectral assays and SEM analyses showed aggregation and amyloid formation of elastin with homocysteinylation.ConclusionThe study reveals that lens accumulation of Hcy associated with hyperhomocysteinaemia is characteristic of PXF that augments elastin expression. Hcy causes structural changes promoting elastin aggregation, thereby contributing to defective elastin in PXF and PXF-G.

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