scholarly journals Archaeosine Modification of Archaeal tRNA: Role in Structural Stabilization

2020 ◽  
Vol 202 (8) ◽  
Author(s):  
Ben Turner ◽  
Brett W. Burkhart ◽  
Katrin Weidenbach ◽  
Robert Ross ◽  
Patrick A. Limbach ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Tertiary Structure ◽  
Temperature Sensitive ◽  
Content Type ◽  
Structural Stabilization ◽  
Thermococcus Kodakarensis ◽  
Methanosarcina Mazei ◽  
The Stability ◽  
A Site

ABSTRACT Archaeosine (G+) is a structurally complex modified nucleoside found quasi-universally in the tRNA of Archaea and located at position 15 in the dihydrouridine loop, a site not modified in any tRNA outside the Archaea. G+ is characterized by an unusual 7-deazaguanosine core structure with a formamidine group at the 7-position. The location of G+ at position 15, coupled with its novel molecular structure, led to a hypothesis that G+ stabilizes tRNA tertiary structure through several distinct mechanisms. To test whether G+ contributes to tRNA stability and define the biological role of G+, we investigated the consequences of introducing targeted mutations that disrupt the biosynthesis of G+ into the genome of the hyperthermophilic archaeon Thermococcus kodakarensis and the mesophilic archaeon Methanosarcina mazei, resulting in modification of the tRNA with the G+ precursor 7-cyano-7-deazaguansine (preQ0) (deletion of arcS) or no modification at position 15 (deletion of tgtA). Assays of tRNA stability from in vitro-prepared and enzymatically modified tRNA transcripts, as well as tRNA isolated from the T. kodakarensis mutant strains, demonstrate that G+ at position 15 imparts stability to tRNAs that varies depending on the overall modification state of the tRNA and the concentration of magnesium chloride and that when absent results in profound deficiencies in the thermophily of T. kodakarensis. IMPORTANCE Archaeosine is ubiquitous in archaeal tRNA, where it is located at position 15. Based on its molecular structure, it was proposed to stabilize tRNA, and we show that loss of archaeosine in Thermococcus kodakarensis results in a strong temperature-sensitive phenotype, while there is no detectable phenotype when it is lost in Methanosarcina mazei. Measurements of tRNA stability show that archaeosine stabilizes the tRNA structure but that this effect is much greater when it is present in otherwise unmodified tRNA transcripts than in the context of fully modified tRNA, suggesting that it may be especially important during the early stages of tRNA processing and maturation in thermophiles. Our results demonstrate how small changes in the stability of structural RNAs can be manifested in significant biological-fitness changes.

scholarly journals Mechanism for Stabilizing mRNAs Involved in Methanol-Dependent Methanogenesis of Cold-Adaptive Methanosarcina mazei zm-15

2013 ◽  
Vol 80 (4) ◽  
pp. 1291-1298 ◽  
Author(s):  
Yi Cao ◽  
Jie Li ◽  
Na Jiang ◽  
Xiuzhu Dong
Keyword(s):  
Half Life ◽  
Content Type ◽  
Methanosarcina Mazei ◽  
Reverse Transcription Quantitative Pcr ◽  
Aceticlastic Methanogenesis ◽  
The Stability ◽  
Zoige Wetland ◽  
Mrna Half Life

ABSTRACTMethylotrophic methanogenesis predominates at low temperatures in the cold Zoige wetland in Tibet. To elucidate the basis of cold-adapted methanogenesis in these habitats,Methanosarcina mazeizm-15 was isolated, and the molecular basis of its cold activity was studied. For this strain, aceticlastic methanogenesis was reduced 7.7-fold during growth at 15°C versus 30°C. Methanol-derived methanogenesis decreased only 3-fold under the same conditions, suggesting that it is more cold adaptive. Reverse transcription-quantitative PCR (RT-qPCR) detected <2-fold difference in the transcript abundances ofmtaA1,mtaB1, andmtaC1, the methanol methyltransferase (Mta) genes, in 30°C versus 15°C culture, whileackAandptamRNAs, encoding acetate kinase (Ack) and phosphotransacetylase (Pta) in aceticlastic methanogenesis, were 4.5- and 6.8-fold higher in 30°C culture than in 15°C culture. Thein vivohalf-lives ofmtaA1andmtaC1B1mRNAs were similar in 30°C and 15°C cultures. However, thepta-ackAmRNA half-life was significantly reduced in 15°C culture compared to 30°C culture. Using circularized RNA RT-PCR, large 5′ untranslated regions (UTRs) (270 nucleotides [nt] and 238 nt) were identified formtaA1andmtaC1B1mRNAs, while only a 27-nt 5′ UTR was present in thepta-ackAtranscript. Removal of the 5′ UTRs significantly reduced thein vitrohalf-lives ofmtaA1andmtaC1B1mRNAs. Remarkably, fusion of themtaA1ormtaC1B15′ UTRs topta-ackAmRNA increased itsin vitrohalf-life at both 30°C and 15°C. These results demonstrate that the large 5′ UTRs significantly enhance the stability of the mRNAs involved in methanol-derived methanogenesis in the cold-adaptiveM. mazeizm-15.

Site-specific mutagenesis of cdc2+, a cell cycle control gene of the fission yeast Schizosaccharomyces pombe

1986 ◽  
Vol 6 (10) ◽  
pp. 3523-3530
Author(s):  
R Booher ◽  
D Beach
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Cell Cycle Control ◽  
Temperature Sensitive ◽  
Protein Kinase Activity ◽  
Atp Binding Site ◽  
Leu2 Gene ◽  
Cdc2 Gene ◽  
A Site

The cdc2+ gene of Schizosaccharomyces pombe is homologous to the CDC28 gene of Saccharomyces cerevisiae. Both genes share limited homology with vertebrate protein kinases and have protein kinase activity. cdc2+ has been subjected to mutagenesis in vitro. A null allele of the gene, constructed by insertion of the S. cerevisiae LEU2 gene into a site within the gene, has a phenotype similar to that of many temperature-sensitive alleles of cdc2. Mutations within the predicted ATP-binding site and in a region which may be a site of phosphorylation result in loss of cdc2+ activity. A single substitution of Gly-146 to Asp-146 has been identified in cdc2-1w, a dominant activated allele of the gene. The four introns within the cdc2+ gene have been deleted. The resulting gene not only functions in fission yeast but also rescues cdc28(Ts) strains of S. cerevisiae, a property which is not shared by the genomic cdc2+ gene.

scholarly journals Bacillus cereus NVH 0500/00 Can Adhere to Mucin but Cannot Produce Enterotoxins during Gastrointestinal Simulation

2015 ◽  
Vol 82 (1) ◽  
pp. 289-296 ◽  
Author(s):  
Varvara Tsilia ◽  
Frederiek-Maarten Kerckhof ◽  
Andreja Rajkovic ◽  
Marc Heyndrickx ◽  
Tom Van de Wiele
Keyword(s):  
Bacillus Cereus ◽  
Food Poisoning ◽  
Intestinal Bacteria ◽  
Low Ph ◽  
Final Concentration ◽  
Adhesion Assay ◽  
Content Type ◽  
The Stability ◽  
Bacterial Concentrations

ABSTRACTAdhesion to the intestinal epithelium could constitute an essential mechanism ofBacillus cereuspathogenesis. However, the enterocytes are protected by mucus, a secretion composed mainly of mucin glycoproteins. These may serve as nutrients and sites of adhesion for intestinal bacteria. In this study, the food poisoning bacteriumB. cereusNVH 0500/00 was exposedin vitroto gastrointestinal hurdles prior to evaluation of its attachment to mucin microcosms and its ability to produce nonhemolytic enterotoxin (Nhe). The persistence of mucin-adherentB. cereusafter simulated gut emptying was determined using a mucin adhesion assay. The stability of Nhe toward bile and pancreatin (intestinal components) in the presence of mucin agar was also investigated.B. cereuscould grow and simultaneously adhere to mucin duringin vitroileal incubation, despite the adverse effect of prior exposure to a low pH or intestinal components. The final concentration ofB. cereusin the simulated lumen at 8 h of incubation was 6.62 ± 0.87 log CFU ml−1. At that point, the percentage of adhesion was approximately 6%. No enterotoxin was detected in the ileum, due to either insufficient bacterial concentrations or Nhe degradation. Nevertheless, mucin appears to retainB. cereusand to supply it to the small intestine after simulated gut emptying. Additionally, mucin may play a role in the protection of enterotoxins from degradation by intestinal components.

scholarly journals Structural Stabilization of Human Transthyretin by Centella asiatica (L.) Urban Extract: Implications for TTR Amyloidosis

Biomolecules ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 128 ◽  
Author(s):  
Fredrick Nwude Eze ◽  
Ladda Leelawatwattana ◽  
Porntip Prapunpoj
Keyword(s):  
Protein Misfolding ◽  
Quaternary Structure ◽  
Centella Asiatica ◽  
Structural Stabilization ◽  
Flight Mass Spectrometry ◽  
Transmission Electron ◽  
Small Molecule Ligands ◽  
Therapeutic Development ◽  
The Stability

Transthyretin is responsible for a series of highly progressive, degenerative, debilitating, and incurable protein misfolding disorders known as transthyretin (TTR) amyloidosis. Since dissociation of the homotetrameric protein to its monomers is crucial in its amyloidogenesis, stabilizing the native tetramer from dissociating using small-molecule ligands has proven a viable therapeutic strategy. The objective of this study was to determine the potential role of the medicinal herb Centella asiatica on human transthyretin (huTTR) amyloidogenesis. Thus, we investigated the stability of huTTR with or without a hydrophilic fraction of C. asiatica (CAB) against acid/urea-mediated denaturation. We also determined the influence of CAB on huTTR fibrillation using transmission electron microscopy. The potential binding interactions between CAB and huTTR was ascertained by nitroblue tetrazolium redox-cycling and 8-anilino-1-naphthalene sulfonic acid displacement assays. Additionally, the chemical profile of CAB was determined by liquid chromatography quadruple time-of-flight mass spectrometry (HPLC-QTOF-MS). Our results strongly suggest that CAB bound to and preserved the quaternary structure of huTTR in vitro. CAB also prevented transthyretin fibrillation, although aggregate formation was unmitigated. These effects could be attributable to the presence of phenolics and terpenoids in CAB. Our findings suggest that C. asiatica contains pharmaceutically relevant bioactive compounds which could be exploited for therapeutic development against TTR amyloidosis.

scholarly journals The 5′ NAD Cap of RNAIII Modulates Toxin Production in Staphylococcus aureus Isolates

2019 ◽  
Vol 202 (6) ◽  
Author(s):  
Hector Gabriel Morales-Filloy ◽  
Yaqing Zhang ◽  
Gabriele Nübel ◽  
Shilpa Elizabeth George ◽  
Natalya Korn ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Secondary Structure ◽  
Quorum Sensing ◽  
Opportunistic Pathogen ◽  
Toxin Production ◽  
Dual Function ◽  
Content Type ◽  
The Stability

ABSTRACT Nicotinamide adenosine dinucleotide (NAD) has been found to be covalently attached to the 5′ ends of specific RNAs in many different organisms, but the physiological consequences of this modification are largely unknown. Here, we report the occurrence of several NAD-RNAs in the opportunistic pathogen Staphylococcus aureus. Most prominently, RNAIII, a central quorum-sensing regulator of this bacterium’s physiology, was found to be 5′ NAD capped in a range from 10 to 35%. NAD incorporation efficiency into RNAIII was found to depend in vivo on the −1 position of the P3 promoter. An increase in RNAIII’s NAD content led to a decreased expression of alpha- and delta-toxins, resulting in reduced cytotoxicity of the modified strains. These effects seem to be caused neither by changes in RNAIII’s secondary structure nor by a different translatability upon NAD attachment, as indicated by unaltered patterns in in vitro chemical probing and toeprinting experiments. Even though we did not observe any effect of this modification on RNAIII’s secondary structure or translatability in vitro, additional unidentified factors might account for the modulation of exotoxins in vivo. Ultimately, the study constitutes a step forward in the discovery of new roles of the NAD molecule in bacteria. IMPORTANCE Numerous organisms, including bacteria, are endowed with a 5′ NAD cap in specific RNAs. While the presence of the 5′ NAD cap modulates the stability of the modified RNA species, a significant biological function and phenotype have not been assigned so far. Here, we show the presence of a 5′ NAD cap in RNAIII from S. aureus, a dual-function regulatory RNA involved in quorum-sensing processes and regulation of virulence factor expression. We also demonstrate that altering the natural NAD modification ratio of RNAIII leads to a decrease in exotoxin production, thereby modulating the bacterium’s virulence. Our work unveils a new layer of regulation of RNAIII and the agr system that might be linked to the redox state of the NAD molecule in the cell.

Phytochemical screening and potential of natural dye colourant from pomegranate (Punica granatum L.)

2016 ◽  
Vol 45 (1) ◽  
pp. 38-44 ◽  
Author(s):  
S. Mohajer ◽  
R.M. Taha ◽  
S.Z. Azmi
Keyword(s):  
Polyvinyl Alcohol ◽  
Antioxidant Activities ◽  
Punica Granatum ◽  
Natural Dye ◽  
Coating System ◽  
Content Type ◽  
Ic50 Values ◽  
The Stability

Purpose – The purpose of this paper is to identify the most dominant pigment of pomegranate explants for natural color coatings and detect the presence of phytochemical constituents and comparison of the antioxidant activities. Design/methodology/approach – Extracts of leaf, stem, peel and seed of in vitro and in vivo growth cultures were prepared for phytochemical constituent and antioxidant activity. The supernatant from 95 per cent methanol was mixed with 15 per cent polyvinyl alcohol (PVA) with the ratio of 1:1 to form a coating system. Findings – Although glycosides was not found in this species, tests for tannins and flavonoids were positive in all samples. The IC50 values were also comparable to commercial antioxidant ascorbic acid with 34.92 per cent inhibition. Chlorophyll a and b were detected in stem and leaf using UV-photospectrometer in 420 and 645 nm wavelengths ranges. The effects of heat and salt on the stability of natural dye colorants mixed with polyvinyl alcohol to form a basic coating system were indicated negatively in in vivo and in vitro growth cultures. Originality/value – The paper shows that further improvement with co-pigmentations may give a notable mixture from pomegranate extraction for the paint materials or nail varnish. It was also indicated that pomegranate contains some compounds such as polyphenolics that can donate electron/hydrogen easily.

In vitro biomechanical analysis of three anterior thoracolumbar implants

2000 ◽  
Vol 93 (2) ◽  
pp. 252-258 ◽  
Author(s):  
Patrick W. Hitchon ◽  
Vijay K. Goel ◽  
Thomas N. Rogge ◽  
James C. Torner ◽  
Andrew P. Dooris ◽  
...  
Keyword(s):  
Axial Rotation ◽  
Biomechanical Analysis ◽  
Rigid Fixation ◽  
Angular Rotation ◽  
Content Type ◽  
Light Emitting ◽  
Vertebral Bodies ◽  
The Stability ◽  
Fine Print

Object. The goal of this study was to evaluate the comparative efficacy of three commonly used anterior thoracolumbar implants: the anterior thoracolumbar locking plate (ATLP), the smooth-rod Kaneda (SRK), and the Z-plate. Methods. In vitro testing was performed using the T9—L3 segments of human cadaver spines. An L-1 corpectomy was performed, and stabilization was achieved using one of three anterior devices: the ATLP in nine spines, the SRK in 10, and the Z-plate in 10. Specimens were load tested with 1.5-, 3-, 4.5-, and 6-Nm in flexion and extension, right and left lateral bending, and right and left axial rotation. Angular motion was monitored using two video cameras that tracked light-emitting diodes attached to the vertebral bodies. Testing was performed in the intact state in spines stabilized with one of the three aforementioned devices after the devices had been fatigued to 5000 cycles at ± 3 Nm and after bilateral facetectomy. There was no difference in the stability of the intact spines with use of the three devices. There were no differences between the SRK- and Z-plate—instrumented spines in any state. In extension testing, the mean angular rotation (± standard deviation) of spines instrumented with the SRK (4.7 ± 3.2°) and Z-plate devices (3.3 ± 2.3°) was more rigid than that observed in the ATLP-stabilized spines (9 ± 4.8°). In flexion testing after induction of fatigue, however, only the SRK (4.2 ± 3.2°) was stiffer than the ATLP (8.9 ± 4.9°). Also, in extension postfatigue, only the SRK (2.4 ± 3.4°) provided more rigid fixation than the ATLP (6.4 ± 2.9°). All three devices were equally unstable after bilateral facetectomy. The SRK and Z-plate anterior thoracolumbar implants were both more rigid than the ATLP, and of the former two the SRK was stiffer. Conclusions. The authors' results suggest that in cases in which profile and ease of application are not of paramount importance, the SRK has an advantage over the other two tested implants in achieving rigid fixation immediately postoperatively.

Transcriptional regulation of the uptake [NiFe]hydrogenase genes in Rhodobacter capsulatus

2005 ◽  
Vol 33 (1) ◽  
pp. 28-32 ◽  
Author(s):  
P.M. Vignais ◽  
S. Elsen ◽  
A. Colbeau
Keyword(s):  
Gene Expression ◽  
Rhodobacter Capsulatus ◽  
Response Regulator ◽  
Regulatory System ◽  
Integration Host Factor ◽  
Host Factor ◽  
Promoter Recognition ◽  
The Stability ◽  
A Site

Transcription of the hupSL genes, which encode the uptake [NiFe]hydrogenase of Rhodobacter capsulatus, is specifically activated by H2. Three proteins are involved, namely the H2-sensor HupUV, the histidine kinase HupT and the transcriptional activator HupR. hupT and hupUV mutants have the same phenotype, i.e. an increased level of hupSL expression (assayed by phupS::lacZ fusion) in the absence of H2; they negatively control hupSL gene expression. HupT can autophosphorylate its conserved His217, and in vitro phosphotransfer to Asp54 of its cognate response regulator, HupR, was demonstrated. The non-phosphorylated form of HupR binds to an enhancer site (5′-TTG-N5-CAA) of phupS localized at −162/−152 nt and requires integration host factor to activate fully hupSL transcription. HupUV is an O2-insensitive [NiFe]hydrogenase, which interacts with HupT to regulate the phosphorylation state of HupT in response to H2 availability. The N-terminal domain of HupT, encompassing the PAS domain, is required for interaction with HupUV. This interaction with HupT, leading to the formation of a (HupT)2–(HupUV)2 complex, is weakened in the presence of H2, but incubation of HupUV with H2 has no effect on the stability of the heterodimer/tetramer, HupUV–(HupUV)2, equilibrium. HupSL biosynthesis is also under the control of the global two-component regulatory system RegB/RegA, which controls gene expression in response to redox. RegA binds to a site close to the −35 promoter recognition site and to a site overlapping the integration host factor DNA-binding site (5′-TCACACACCATTG, centred at −87 nt) and acts as a repressor.

scholarly journals Candida albicans PEP12 Is Required for Biofilm Integrity and In Vivo Virulence

2009 ◽  
Vol 9 (2) ◽  
pp. 266-277 ◽  
Author(s):  
Suresh K. A. Palanisamy ◽  
Melissa A. Ramirez ◽  
Michael Lorenz ◽  
Samuel A. Lee
Keyword(s):  
Candida Albicans ◽  
Lipolytic Activity ◽  
Infection Model ◽  
Temperature Sensitive ◽  
Null Mutant ◽  
Macrophage Infection ◽  
Content Type ◽  
Vacuolar Acidification

ABSTRACT To investigate the role of the prevacuolar secretion pathway in biofilm formation and virulence in Candida albicans, we cloned and analyzed the C. albicans homolog of the Saccharomyces cerevisiae prevacuolar trafficking gene PEP12. C. albicans PEP12 encodes a deduced t-SNARE that is 28% identical to S. cerevisiae Pep12p, and plasmids bearing C. albicans PEP12 complemented the abnormal vacuolar morphology and temperature-sensitive growth of an S. cerevisiae pep12 null mutant. The C. albicans pep12 Δ null mutant was defective in endocytosis and vacuolar acidification and accumulated 40- to 60-nm cytoplasmic vesicles near the plasma membrane. Secretory defects included increased extracellular proteolytic activity and absent lipolytic activity. The pep12Δ null mutant was more sensitive to cell wall stresses and antifungal agents than the isogenic complemented strain or the control strain DAY185. Notably, the biofilm formed by the pep12Δ mutant was reduced in overall mass and fragmented completely upon the slightest disturbance. The pep12Δ mutant was markedly reduced in virulence in an in vitro macrophage infection model and an in vivo mouse model of disseminated candidiasis. These results suggest that C. albicans PEP12 plays a key role in biofilm integrity and in vivo virulence.

scholarly journals Identification of a region on hypoxia-inducible-factor prolyl 4-hydroxylases that determines their specificity for the oxygen degradation domains

2007 ◽  
Vol 408 (2) ◽  
pp. 231-240 ◽  
Author(s):  
Diego Villar ◽  
Alicia Vara-Vega ◽  
Manuel O. Landázuri ◽  
Luis Del Peso
Keyword(s):  
Transcription Factors ◽  
Tertiary Structure ◽  
Hypoxia Inducible Factor ◽  
Domain Swapping ◽  
Dependent Manner ◽  
Low Oxygen ◽  
Protein Levels ◽  
The Stability

HIFs [hypoxia-inducible (transcription) factors] are essential for the induction of an adaptive gene expression programme under low oxygen partial pressure. The activity of these transcription factors is mainly determined by the stability of the HIFα subunit, which is regulated, in an oxygen-dependent manner, by a family of three prolyl 4-hydroxylases [EGLN1–EGLN3 (EGL nine homologues 1–3)]. HIFα contains two, N- and C-terminal, independent ODDs (oxygen-dependent degradation domains), namely NODD and CODD, that, upon hydroxylation by the EGLNs, target HIFα for proteasomal degradation. In vitro studies indicate that each EGLN shows a differential preference for ODDs, However, the sequence determinants for such specificity are unknown. In the present study we showed that whereas EGLN1 and EGLN2 acted upon any of these ODDs to regulate HIF1α protein levels and activity in vivo, EGLN3 only acted on the CODD. With the aim of identifying the region within EGLNs responsible for their differential substrate preference, we investigated the activity and binding pattern of different EGLN deletions and chimaeric constructs generated by domain swapping between EGLN1 and EGLN3. These studies revealed a region of 97 residues that was sufficient to confer the characteristic substrate binding observed for each EGLN. Within this region, we identified the minimal sequence (EGLN1 residues 236–252) involved in substrate discrimination. Importantly, mapping of these sequences on the EGLN1 tertiary structure indicates that substrate specificity is determined by a region relatively remote from the catalytic site.

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