Elongation Phase Research Articles

The Many Roles of Binding Cooperativity in the Control of DNA Replication

The Many Roles of Binding Cooperativity in the Control of DNA Replication

Multisite rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation.

Control of complex intracellular pathways such as protein synthesis is critical to organism survival, but is poorly understood. Translation of a reading frame in eukaryotic mRNA is preceded by a scanning process in which a subset of translation factors helps guide ribosomes to the start codon. Here, we perform comparative analysis of the control status of this scanning step that sits between recruitment of the small ribosomal subunit to the m7GpppG‐capped 5′end of mRNA and of the control exerted by downstream phases of polypeptide initiation, elongation and termination. We have utilized a detailed predictive model as guidance for designing quantitative experimental interrogation of control in the yeast translation initiation pathway. We have built a synthetic orthogonal copper‐responsive regulatory promoter (PCuR3) that is used here together with the tet07 regulatory system in a novel dual‐site in vivo rate control analysis strategy. Combining this two‐site strategy with calibrated mass spectrometry to determine translation factor abundance values, we have tested model‐based predictions of rate control properties of the in vivo system. We conclude from the results that the components of the translation machinery that promote scanning collectively function as a low‐flux‐control system with a capacity to transfer ribosomes into the core process of polypeptide production that exceeds the respective capacities of the steps of polypeptide initiation, elongation and termination. In contrast, the step immediately prior to scanning, that is, ribosome recruitment via the mRNA 5′ cap‐binding complex, is a high‐flux‐control step.

To Splice or to Transcribe: SKIP-Mediated Environmental Fitness and Development in Plants

Gene expression in eukaryotes is controlled at multiple levels, including transcriptional and post-transcriptional levels. The transcriptional regulation of gene expression is complex and includes the regulation of the initiation and elongation phases of transcription. Meanwhile, the post-transcriptional regulation of gene expression includes precursor messenger RNA (pre-mRNA) splicing, 5′ capping, and 3′ polyadenylation. Among these events, pre-mRNA splicing, conducted by the spliceosome, plays a key role in the regulation of gene expression, and the efficiency and precision of pre-mRNA splicing are critical for gene function. Ski-interacting protein (SKIP) is an evolutionarily conserved protein from yeast to humans. In plants, SKIP is a bifunctional regulator that works as a splicing factor as part of the spliceosome and as a transcriptional regulator via interactions with the transcriptional regulatory complex. Here, we review how the functions of SKIP as a splicing factor and a transcriptional regulator affect environmental fitness and development in plants.

Intensity of spring wheat transpiration due to weather factors and methods of basic tillage

The paper presents the study of daily course transpiration of the three upper leaves of cultivars of spring hard wheat of different origin, grown against the background of two methods of primary tillage in different conditions of the vegetation period according to weather factors. The studies were carried out according to the method of rapid weighing using the torsion scales VT-500 three times during the day (9:00, 12:00 and 15:00 hours) in the phases of stem elongation and wheat earing. The paper identifies cultivar specificity of the course of daytime transpiration, the influence of soil tillage methods on the amount of transpiration, as well as a significant dependence on weather factors over the years of study. The results can be used in practical breeding with the perspective assessment of varieties according to the transpiration activity of the leaves in the most important phases of the spring wheat growing season. In connection with changes in the climatic factor in the direction of increasing aridity, it is important to know the patterns of the response of the plant organism to the extreme conditions and the possibility of its use in breeding practice. The results obtained can substantiate the needs to use various methods of basic processing to reduce negative weather factors.

Reduced Growth and Nitrogen Uptake During Waterlogging at Tillering Permanently Affect Yield Components in Late Sown Oats.

In Mediterranean Europe, winter cereals can experience soil waterlogging starting from crop establishment up to stem elongation and, in late sowings, this stress is combined with temperatures favorable to plant metabolism. Oats response to waterlogging has been rarely investigated, but these species seems to recover better than other cereals. In a 2-year experiment, Avena sativa and Avena byzantina were sown at the end of winter in pots placed outdoors. At the two-tiller stage, plants were exposed to waterlogging for periods ranging from 0 to 35 days. The dry weight and the N-concentration of shoots and roots were determined on waterlogged plants and drained controls at the start and the end of each waterlogging period, and at maturity. At maturity, the grain yield and its components were determined. To relate oat response to its specific morphological and developmental traits, results were compared to the published results in wheat and barley. Both oat species suffered severe damage during waterlogging: the uptake of nitrogen and the N-concentration of shoots were reduced after 7 days, tiller initiation and root growth after 14 days, and shoot growth after 21 days. All plants survived waterlogging, and the relative growth rates of roots and shoots and the net uptake rate of nitrogen were resumed during recovery. Nevertheless, at maturity, the straw and root biomass were markedly lower with all waterlogging durations, and grain yield decreased by 42% up to approximately 81% following an asymptotic equation. The most affected yield components were the number of panicles per plant and the number of kernels per panicle, but their relative sensitivity changed according to waterlogging duration. The slight increase in tiller fertility in response to short waterlogging and the small and irregular decrease in the number of kernels per spikelet suggest that the two oats could recover the initiation and size of inflorescences better than other winter cereals. Despite this, waterlogging in spring was highly detrimental to these oats because of severe damage under waterlogging and because of the inability to initiate new tillers and adequately resume root growth during recovery, once plants had achieved the phase of stem elongation.

A Novel Gene Contributing to the Initiation of Fatty Acid Biosynthesis in Escherichia coli.

Type II fatty acid biosynthesis in bacteria can be broadly classified into the initiation and elongation phases. The biochemical functions defining each step in the two phases have been studied in vitro Among the β-ketoacyl-acyl carrier protein (ACP) synthases, FabH catalyzes the initiation reaction, while FabB and FabF, which primarily catalyze the elongation reaction, can also drive initiation as side reactions. A role for FabB and FabF in the initiation of fatty acid biosynthesis would be supported by the viability of the ΔfabH mutant. In this study, we show that the ΔfabH and ΔyiiD mutations were synthetically lethal and that ΔfabH ΔrelA ΔspoT and ΔfabH ΔdksA synthetic lethality was rescued by the heterologous expression of yiiD In the ΔfabH mutant, the expression of yiiD was positively regulated by (p)ppGpp. The growth defect, reduced cell size, and altered fatty acid profile of the ΔfabH mutant and the growth defect of the ΔfabH ΔfabF fabB15(Ts) mutant in oleate- and palmitate-supplemented medium at 42°C were rescued by the expression of yiiD from a multicopy plasmid. Together, these results indicate that the yiiD-encoded function supported initiation of fatty acid biosynthesis in the absence of FabH. We have renamed yiiD as fabYIMPORTANCE Fatty acid biosynthesis is an essential process conserved across life forms. β-Ketoacyl-ACP synthases are essential for fatty acid biosynthesis. FabH is a β-ketoacyl-ACP synthase that contributes to the initiation of fatty acid biosynthesis in Escherichia coli In this study, we present genetic and biochemical evidence that the yiiD (renamed fabY)-encoded function contributes to the biosynthesis of fatty acid in the absence of FabH activity and that under these conditions, the expression of FabY was regulated by the stringent response factors (p)ppGpp and DksA. Combined inactivation of FabH and FabY resulted in growth arrest, possibly due to the loss of fatty acid biosynthesis. A molecule(s) that inhibits the two activities can be an effective microbicide.

Microstructure evolution during the extrusion of a 6351 aluminum alloy tube

Abstract The aluminum alloy AA 6351 is a precipitation hardened alloy of the Al-Mg-Si system, additionally containing Mn and Fe. In this study, the microstructural characterization during processing of a thick wall extruded AA 6351 tube was carried out. Several complementary techniques for microstructural characterization were used, such as polarized light optical microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, backscattered electron diffraction, X-ray diffraction, hardness and electrical conductivity measurements. The main characteristics of the grains and precipitates were analyzed. After solidification, the presence of a relatively homogeneous grain distribution with an average diameter of about 100 µm and an intermetallic phase with elongated morphology rich in Al, Fe, Mn and Si was observed. During extrusion, the initial grain size was reduced to about one-fifth of the initial diameter and the elongated phase, probably a-Al(Fe,Mn)Si, was fractured and redistributed and the resulting fragments were aligned in the extrusion direction. A peripheral coarse grain zone was detected and analyzed near the outer and inner surfaces of the tube.

De novo MEPCE nonsense variant associated with a neurodevelopmental disorder causes disintegration of 7SK snRNP and enhanced RNA polymerase II activation

In eukaryotes, the elongation phase of transcription by RNA polymerase II (RNAP II) is regulated by the transcription elongation factor b (P-TEFb), composed of Cyclin-T1 and cyclin-dependent kinase 9. The release of RNAP II is mediated by phosphorylation through P-TEFb that in turn is under control by the inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex. The 7SK snRNP consists of the 7SK non-coding RNA and the proteins MEPCE, LARP7, and HEXIM1/2. Biallelic LARP7 loss-of-function variants underlie Alazami syndrome characterized by growth retardation and intellectual disability. We report a boy with global developmental delay and seizures carrying the de novo MEPCE nonsense variant c.1552 C > T/p.(Arg518*). mRNA and protein analyses identified nonsense-mediated mRNA decay to underlie the decreased amount of MEPCE in patient fibroblasts followed by LARP7 and 7SK snRNA downregulation and HEXIM1 upregulation. Reduced binding of HEXIM1 to Cyclin-T1, hyperphosphorylation of the RNAP II C-terminal domain, and upregulated expression of ID2, ID3, MRPL11 and snRNAs U1, U2 and U4 in patient cells are suggestive of enhanced activation of P-TEFb. Flavopiridol treatment and ectopic MEPCE protein expression in patient fibroblasts rescued increased expression of six RNAP II-sensitive genes and suggested a possible repressive effect of MEPCE on P-TEFb-dependent transcription of specific genes.

Organization and regulation of gene transcription.

The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymeraseII may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being definedthat rationalize transcriptional organization and regulation, and that will guide future investigations.

Differential transcriptome dynamics during the onset of conceptus elongation and between female and male porcine embryos

BackgroundPorcine embryos undergo rapid differentiation and expansion between Days 8 and 12 before attaching to the maternal uterine epithelial surface after Day 13. It is known that maternal recognition of pregnancy and successful implantation are driven by mutual interactions between the elongated conceptus and the maternal endometrium. While most of the genes involved in regulation of embryo development are located on autosomal chromosomes, gene expression on sex chromosomes is modulating development through sex-specific transcription. To gain more insights into the dynamic transcriptome of preimplantation embryos at the onset of elongation and into X-linked gene expression, RNA-seq analyses were performed for single female and male porcine embryos collected on Days 8, 10, and 12 of pregnancy.ResultsA high number of genes were differentially expressed across the developmental stages (2174 and 3275 for Days 8 vs 10, and 10 vs 12, respectively). The majority of differentially expressed genes (DEGs) were involved in embryo elongation, development, and embryo-maternal interaction. Interestingly, a number of DEGs was found with respect to embryo sex (137, 37, and 56 on Days 8, 10 and 12, respectively). At Day 8, most of these DEGs were X-linked (96). Strikingly, the number of DEGs encoded on the X chromosome dramatically decreased from Day 10 to Day 12.ConclusionsThe obtained results deepen the understanding about temporary transcriptomic changes in porcine embryos during the phase of conceptus elongation, meanwhile reveal dynamic compensation of X chromosome in the female and distinct transcriptional differences between female and male embryos.

Single-Molecular Heteroamyloidosis of Human Islet Amyloid Polypeptide.

Human amyloids and plaques uncovered post mortem are highly heterogeneous in structure and composition, yet literature concerning the heteroaggregation of amyloid proteins is extremely scarce. This knowledge deficiency is further exacerbated by the fact that peptide delivery is a major therapeutic strategy for targeting their full-length counterparts associated with the pathologies of a range of human diseases, including dementia and type 2 diabetes (T2D). Accordingly, here we examined the coaggregation of full-length human islet amyloid polypeptide (IAPP), a peptide associated with type 2 diabetes, with its primary and secondary amyloidogenic fragments 19-29 S20G and 8-20. Single-molecular aggregation dynamics was obtained by high-speed atomic force microscopy, augmented by transmission electron microscopy, X-ray diffraction, and super-resolution stimulated emission depletion microscopy. The coaggregation significantly prolonged the pause phase of fibril elongation, increasing its dwell time by 3-fold. Surprisingly, unidirectional elongation of mature fibrils, instead of protofilaments, was observed for the coaggregation, indicating a new form of tertiary protein aggregation unknown to existing theoretical models. Further in vivo zebrafish embryonic assay indicated improved survival and hatching, as well as decreased frequency and severity of developmental abnormalities for embryos treated with the heteroaggregates of IAPP with 19-29 S20G, but not with 8-20, compared to the control, indicating the therapeutic potential of 19-29 S20G against T2D.

Counterintuitive consequences of competitive pathways in supramolecular polymerizations

Competition between supramolecular polymers for the same monomers can lead to strong responses in these systems. Using numerical simulations, we show that the sharpness and asymmetry of the transition from one thermodynamically stable polymer to another upon changing temperature is determined by the most unstable rather than the most stable supramolecular polymer. The width and asymmetry of the transitions are shown to depend on the relative and absolute nucleation penalties of the competing supramolecular polymerizations.

Characterization of the unique In Vitro effects of unsaturated fatty acids on the formation of amyloid β fibrils.

Accumulation of amyloid ß (Aß) peptides, the major component of amyloid fibrils in senile plaques, is one of the main causes of Alzheimer’s disease. Docosahexaenoic acid (DHA) is a fatty acid abundant in the brain, and is reported to have protective effects against Alzheimer’s disease, although the mechanistic effects of DHA against Alzheimer’s pathophysiology remain unclear. Because dietary supplementation of DHA in Aß precursor protein transgenic mice ameliorates Aß pathology and behavioral deficits, we hypothesize that DHA may affect the fibrillization and deposition of Aß. Here we studied the effect of different types of fatty acids on Aß fibril formation by in vitro Aß fibrillization assay. Formation of amyloid fibrils consists of two steps, i.e., the initial nucleation phase and the following elongation phase. We found that unsaturated fatty acids, especially DHA, accelerated the formation of Aß fibrils with a unique short and curved morphology in its nucleation phase, which did not elongate further into the long and straight, mature Aß fibrils. Addition of DHA afterwards did not modify the morphology of the mature Aß(1–40) fibrils. The short and curved Aß fibrils formed in the presence of DHA did not facilitate the elongation phase of Aß fibril formation, suggesting that DHA promotes the formation of “off-pathway” conformers of Aß. Our study unravels a possible mechanism of how DHA acts protectively against the pathophysiology of Alzheimer’s disease.

Virion-associated, host-derived DHX9/RNA helicase A enhances the processivity of HIV-1 reverse transcriptase on genomic RNA

DHX9/RNA helicase A (RHA) is a host RNA helicase that participates in many critical steps of the HIV-1 life cycle. It co-assembles with the viral RNA genome into the capsid core. Virions deficient in RHA are less infectious as a result of reduced reverse transcription efficiency, demonstrating that the virion-associated RHA promotes reverse transcription before the virion gains access to the new host's RHA. Here, we quantified reverse-transcription intermediates in HIV-1-infected T cells to clarify the mechanism by which RHA enhances HIV-1 reverse transcription efficiency. Consistently, purified recombinant human RHA promoted reverse transcription efficiency under in vitro conditions that mimic the early reverse transcription steps prior to capsid core uncoating. We did not observe RHA-mediated structural remodeling of the tRNALys3-viral RNA-annealed complex. RHA did not enhance the DNA synthesis rate until incorporation of the first few nucleotides, suggesting that RHA participates primarily in the elongation phase of reverse transcription. Pre-steady-state and steady-state kinetic studies revealed that RHA has little impact on the kinetics of single-nucleotide incorporation. Primer extension assays performed in the presence of trap dsDNA disclosed that RHA enhances the processivity of HIV-1 reverse transcriptase (RT). The biochemical assays used here effectively reflected and explained the low RT activity in HIV-1 virions produced from RHA-depleted cells. Moreover, RT activity in our assays indicated that RHA in HIV-1 virions is required for the efficient catalysis of (-)cDNA synthesis during viral infection before capsid uncoating. Our study identifies RHA as a processivity factor of HIV-1 RT.

New Strategy on Antimicrobial-resistance: Inhibitors of DNA Replication Enzymes.

Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance. This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials. DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors. Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far. This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.

The development of agrotechnical basics for intensive growing of spring barley varieties for forage purposes under conditions of the Forest-Steppe

The technology of spring barley growing, which involves crop treatment in the phase of stem elongation with plant growth regulator Terpal and application of complete mineral fertilizer in a dose of N90P45K45, has been improved. It has been established that complex application of mineral fertilizers in a dose of N90P45K45 and plant growth regulator Terpal had a positive effect on the spring barley yield (6.39 t/ha) and feed quality (13.9 %). Regression dependences between the index of spring barley grain yield and technological methods have been established.

Research on TiH2 Preparation Mechanism and Structure Properties of Al-Ti-C Mother Alloy

Structure properties of Al-Ti-C mother alloy which was prepared by TiH2 and graphite method were studied by various characterization methods.Results demonstrated that the synthesis process of Al-Ti-C alloy contained three stages.Firstly,TiH2 and graphite was respectively used as titanium and carbon sources.Secondly,titanium reacted with aluminum and graphite,producing Ti-Al,C-Al,Ti-C compounds.Finally,these compounds formed Al-Ti-C alloy.It was equiaxed or dendrite structure with grain size of 20～40μm.There were needle-like and elongated phases in alloy matrix.There are petal primary crystals containing Ti,C,Fe and Si on grain boundaries.Ti and C distribute evenly along grain boundaries and grains.Ti and C enrichment and segregation occurred close to the primary phase.Cryolites were conducive to wetting of carbon and aluminum, the second phase generated more fully in the grain.

State of the art and future perspectives on the use of non-invasive neuromodulation in peripartum psychiatric disorders

State of the art and future perspectives on the use of non-invasive neuromodulation in peripartum psychiatric disorders

Retinoic acid worsens ATG10-dependent autophagy impairment in TBK1-mutant hiPSC-derived motoneurons through SQSTM1/p62 accumulation

ABSTRACT Mutations in the TBK1 (TANK binding kinase 1) gene are causally linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TBK1 phosphorylates the cargo receptors OPTN and SQSTM1 regulating a critical step in macroautophagy/autophagy. Disruption of the autophagic flux leads to accumulation of cytosolic protein aggregates, which are a hallmark of ALS. hiPSC-derived TBK1-mutant motoneurons (MNs) showed reduced TBK1 levels and accumulation of cytosolic SQSTM1-positive aggresomes. By screening a library of nuclear-receptor-agonists for modifiers of the SQSTM1 aggregates, we identified 4-hydroxy(phenyl)retinamide (4HPR) as a potent modifier exerting detrimental effects on mutant-TBK1 motoneurons fitness exacerbating the autophagy overload. We have shown by TEM that TBK1-mutant motoneurons accumulate immature phagophores due a failure in the elongation phase, and 4HPR further worsens the burden of dysfunctional phagophores. 4HPR-increased toxicity was associated with the upregulation of SQSTM1 in a context of strongly reduced ATG10, while rescue of ATG10 levels abolished 4HPR toxicity. Finally, we showed that 4HPR leads to a downregulation of ATG10 and to an accumulation of SQSTM1+ aggresomes also in hiPSC-derived C9orf72-mutant motoneurons. Our data show that cultured human motoneurons harboring mutations in TBK1 gene display typical ALS features, like decreased viability and accumulation of cytosolic SQSTM1-positive aggresomes. The retinoid 4HPR appears a strong negative modifier of the fitness of TBK1 and C9orf72-mutant MNs, through a pathway converging on the mismatch of initiated autophagy and ATG10 levels. Thus, autophagy induction appears not to be a therapeutic strategy for ALS unless the specific underlying pathway alterations are properly addressed. Abbreviations 4HPR: 4-hydroxy(phenyl)retinamide; AKT: AKT1 serine/threonine kinase 1; ALS: amyotrophic lateral sclerosis; ATG: autophagy related; AVs: autophagic vesicle; C9orf72: chromosome 9 open reading frame 72; CASP3: caspase 3; CHAT: choline O-acetyltransferase; CYCS: cytochrome c, somatic; DIV: day in vitro; FTD: frontotemporal dementia; FUS: FUS RNA binding protein; GFP: green fluorescent protein; hiPSCs: human induced pluripotent stem cells; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MNs: motoneurons; mRFP: monomeric red fluorescent protein; MTOR: mechanistic target of rapamycin kinase; NFE2L2/NRF2: nuclear factor, erythroid 2 like 2; RARA: retinoic acid receptor alpha; SLC18A3/VACHT: solute carrier family 18 (vesicular acetylcholine transporter), member 3; SQSTM1/p62: sequestosome 1; TBK1: TANK binding kinase 1; TEM: transmission electron microscopy

The perforatorium and postacrosomal sheath of rat spermatozoa share common developmental origins and protein constituents†.

The perinuclear theca (PT) is a cytosolic protein capsule that surrounds the nucleus of eutherian spermatozoa. Compositionally, it is divided into two regions: the subacrosomal layer (SAL) and the postacrosomal sheath (PAS). In falciform spermatozoa, a third region of the PT emerges that extends beyond the nuclear apex called the perforatorium. The formation of the SAL and PAS differs, with the former assembling early in spermiogenesis concomitant with acrosome formation, and the latter dependent on manchette descent during spermatid elongation. The perforatorium also forms during the elongation phase of spermiogenesis, suggesting that like the PAS, its assembly is facilitated by the manchette. The temporal similarity in biogenesis between the PAS and perforatorium led us to compare their molecular composition using cell fractionation and immunodetection techniques. Although the perforatorium is predominantly composed of its endemic protein FABP9/PERF15, immunolocalization indicates that it also shares proteins with the PAS. These include WBP2NL/PAWP, WBP2, GSTO2, and core histones, which have been implicated in early fertilization and zygotic events. The compositional homogeny between the PAS and perforatorium supports our observation that their development is linked. Immunocytochemistry indicates that both PAS and perforatorial biogenesis depend on the transport and deposition of cytosolic proteins by the microtubular manchette. Proteins translocated from the manchette pass ventrally along the spermatid head into the apical perforatorial space prior to PAS deposition in the wake of manchette descent. Our findings demonstrate that the perforatorium and PAS share a mechanism of developmental assembly and thereby contain common proteins that facilitate fertilization.