Yeast Origin Research Articles

Humanizing the yeast origin recognition complex

The Origin Recognition Complex (ORC) is an evolutionarily conserved six-subunit protein complex that binds specific sites at many locations to coordinately replicate the entire eukaryote genome. Though highly conserved in structure, ORC’s selectivity for replication origins has diverged tremendously between yeasts and humans to adapt to vastly different life cycles. In this work, we demonstrate that the selectivity determinant of ORC for DNA binding lies in a 19-amino acid insertion helix in the Orc4 subunit, which is present in yeast but absent in human. Removal of this motif from Orc4 transforms the yeast ORC, which selects origins based on base-specific binding at defined locations, into one whose selectivity is dictated by chromatin landscape and afforded with plasticity, as reported for human. Notably, the altered yeast ORC has acquired an affinity for regions near transcriptional start sites (TSSs), which the human ORC also favors.

Artificial blood: where are we now?

Background. The creation of artificial blood (AB) and/or its components can change medicine, but currently available artificial oxygen carriers (AOC) do not perform other blood functions: vascular volume maintenance, coagulation, immunity, transport of neurotransmitters, nutrients and waste.
 Objective. To describe the current situation regarding AB.
 Materials and methods. Analysis of literature data on this issue.
 Results and discussion. The need to create an AB is justified by the high cost of collecting, processing and storing donor blood, low infectious safety of drugs received against HIV, viral hepatitis B and C, cytomegalovirus, etc., reduction of the number of donors, problems with blood incompatibility. Immunological effects of blood transfusions are associated with a higher frequency of infectious processes during surgery, slowing of wound healing and progression of malignant diseases. Requirements for an ideal AB preparation include adequate oxygen uptake and delivery under physiological conditions, no toxic or physiological effects, ability to be eliminated and excreted by the human body, sufficient intravascular half-life, ease of use and storage, stability at room temperature, universal compatibility, availability and low cost, ability to maintain blood pressure and pH, viscosity similar to real blood. Available AOC include oxygen-transport solutions based on hemoglobin and perfluorocarbon compounds (PFC) in the form of emulsions. Natural (human, bovine) or genetically modified hemoglobin is used for the production of the former, and hemoglobin of yeast or bacterial origin can also be used. The advantages of hemoglobin solutions include the increased erythropoietin production, adequate oxygen delivery at a hemoglobin level of 20 g/L without side effects, complete absence of virus transmission and 25 % better reperfusion recovery than with real blood. Potential fields of AOC use include shock, organ ischemia, erythrocyte incompatibility, acute lung injury, organ storage for transplantation, cardioplegia, sickle cell anemia, tumor treatment, and air embolism. The main problem is the release of pro-inflammatory cytokines in response to hemoglobin solution administration. Side effects of these solutions include neuro- and nephrotoxicity, immunosuppression, vasoconstriction, coagulopathy, release of free radicals, and errors in blood tests. In turn, PFC does not bind oxygen, but dissolves it in proportion to the partial pressure. PFC are eliminated by phagocytes and eventually excreted by the lungs during respiration. PFC particles are much smaller than natural erythrocytes (0.2 vs. 7 μm) and are easier to deform, which facilitates their delivery to ischemic areas. Side effects of PFC include transient face flushing, headache and back pain, nausea, fever, anaphylactoid reactions, bleeding tendency, pulmonary edema, and acute right ventricular failure. Because high partial pressures are required to achieve the desired PFC effects, artificial lung ventilation may be required. In addition to hemoglobin-based AOC and PFC, hemoglobin in liposomal erythrocyte form, hemoglobin in nanocapsules, nanoarchitectonic complexes of hemoglobin are under development.
 Conclusions. 1. The creation of AB may revolutionize medicine. 2. The need to create an AB is justified by the high cost of collection, processing and storage of donor blood, its low infectious safety, reduction of the number of donors, problems due to blood incompatibility. 3. AOC include hemoglobin-based oxygen-transporting solutions and PFC emulsions. 4. Further studies are needed to improve existing AB preparations and create new ones.

Antimicrobial mechanisms and applications of yeasts.

Yeasts and humans have had a close relationship for millenia. Yeast have been used for food production since the first human societies. Since then, alternative uses have been discovered. Nowadays, antibiotic resistance constitutes a pressing need worldwide. In order to overcome this threat, one of the most important strategies is the search for new antimicrobials in natural sources. Moreover, biopreservation based on natural sources has emerged as an alternative to more common chemical preservatives. Yeasts constitute an underexploited source of antagonistic activity against other microorganisms. Here, we compile a summary of the antagonistic activity of yeast origin against other yeast and other microorganisms, such as bacteria or parasites. We present the mechanisms of action used by yeasts to display these activities. We also provide applications of these antagonistic activities in food industry and agriculture, medicine and veterinary, where yeast promise to play a pivotal role in the near future.

The dynamic nature of the human origin recognition complex revealed through five cryoEM structures.

Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to origin DNA, recruiting CDC6, and assembling the MCM replicative helicase on DNA. Here we report five cryoEM structures of the human ORC (HsORC) that illustrate the native flexibility of the complex. The absence of ORC1 revealed a compact, stable complex of ORC2-5. Introduction of ORC1 opens the complex into several dynamic conformations. Two structures revealed dynamic movements of the ORC1 AAA+ and ORC2 winged-helix domains that likely impact DNA incorporation into the ORC core. Additional twist and pinch motions were observed in an open ORC conformation revealing a hinge at the ORC5·ORC3 interface that may facilitate ORC binding to DNA. Finally, a structure of ORC was determined with endogenous DNA bound in the core revealing important differences between human and yeast origin recognition.

Bioinformatical dissection of fission yeast DNA replication origins.

Replication origins in eukaryotes form a base for assembly of the pre-replication complex (pre-RC), thereby serving as an initiation site of DNA replication. Characteristics of replication origin vary among species. In fission yeast Schizosaccharomyces pombe, DNA of high AT content is a distinct feature of replication origins; however, it remains to be understood what the general molecular architecture of fission yeast origin is. Here, we performed ChIP-seq mapping of Orc4 and Mcm2, two representative components of the pre-RC, and described the characteristics of their binding sites. The analysis revealed that fission yeast efficient origins are associated with two similar but independent features: a ≥15 bp-long motif with stretches of As and an AT-rich region of a few hundred bp. The A-rich motif was correlated with chromosomal binding of Orc, a DNA-binding component in the pre-RC, whereas the AT-rich region was associated with efficient binding of the DNA replicative helicase Mcm. These two features, in combination with the third feature, a transcription-poor region of approximately 1 kb, enabled to distinguish efficient replication origins from the rest of chromosome arms with high accuracy. This study, hence, provides a model that describes how multiple functional elements specify DNA replication origins in fission yeast genome.

Evolution of the Multielemental Content along the Red Wine Production Process from Tempranillo and Grenache Grape Varieties

In the present work, 38 elements were quantified in the different fractions generated by applying amateur winemaking methods. Inductively Coupled Plasma Mass Spectrometry was used as detection technique. Grapes were analyzed and separate metal profiles were also obtained for the skin and seeds. Additional vinification fractions included musts before and after the fermentation process. Meanwhile, solid fractions corresponded to the so-called hat, pressed pomace and the lees obtained after gravitational settling at the tank bottom. Wine was further analyzed. The obtained results revealed a different repartition depending on the particular element and winemaking solid and liquid fraction evaluated. The studies included vinification in presence and in absence of added yeast and grape geographical origin. Principal component analysis helped to discriminate among fractions and to determine the critical elements behaving differently. Finally, a mass balance allowed to unequivocally detect the migration of a given element to the winemaking fractions.

Effect of Several Nutrients and Environmental Conditions on Intracellular Melatonin Synthesis in Saccharomyces cerevisiae.

Melatonin is a bioactive compound that is present in fermented beverages and has been described to be synthesized by yeast during alcoholic fermentation. The aim of this study was to assess the capacity of intracellular and extracellular melatonin production by different Saccharomyces strains from diverse food origin and to study the effects of different fermentation parameters, such as sugar and nitrogen concentration, temperature or initial population, on melatonin production using a synthetic grape must medium. Melatonin from fermentation samples was analyzed by liquid chromatography mass spectrometry. Intracellular melatonin synthesis profile did not present differences between yeast strains. However, extracellular melatonin production depended on the yeast origin. Thus, we suggest that melatonin production and secretion during the different yeast growth phases follows a species-specific pattern. Other parameters that affected the fermentation process such as sugar content and low temperature had an impact on intracellular melatonin production profile, as well as the melatonin content within the cell. This study reports the effect of several conditions on the melatonin synthesis profile, highlighting its possible role as a signal molecule.

Evolution of the Eukaryotic Origin Recognition Complex

The Origin Recognition Complex (ORC) is a six-subunit complex that is highly conserved from yeasts to humans. However, the mechanism for finding its binding sites diverged from a base-specific mechanism in yeasts to a site-specific but base-agnostic mechanism in humans. Based on the atomic model of the yeast ORC bound to replication origin DNA, the 19-aa base-specificity determinant that interacts with the invariant Ts in the consensus sequence of the yeast origin DNA is missing in metazoans. We studied the physiological effect of removing this crucial element of ORC in yeast and found that the altered ORC∗ behaved more like a human ORC.

SPECIFIC FEATURES OF FERMENTATION OF THE MUST FROM WHITE GRAPE VARIETIES IN THE CONDITIONS OF THE ODESSA REGION

One of the most important problems of the modern wine technology is the production of high quality and competitive products. It is commonly known that the quality of a wine largely depends on the yeast race. The main requirement for yeast is completeness of fermentation, which depends on the amount of yeast involved, aeration, initial content of various substances in the must, temperature, pH of the environment. Using imported materials in the specific conditions of national winemaking requires laboratory and industrial research to rationalize the use of local and foreign pure yeast cultures and to accelerate the process of grape must fermentation. So, this study considers how the yeast origin and additional nutrition effect on grape must fermentation and influence the physicochemical and organoleptic characteristics of wine materials obtained from the white grape varieties Aromatny and Zagrei of the generative breeding by the National Scientific Centre Tairov Viticulture and Winemaking Institute. Besides, it has been concluded whether using additional nutrition is practical. It has been established that the fermentation process was complete in both the control and the experimental samples. There were no facts of underfermentation. When supplementary nitrogenous nutrition was used, the fermentation activity of yeast increased and the fermentation process ended faster. The dynamics of the total number of cells of the Aromatic and Zagrei varieties was the same during the years 2015–2017 and did not depend on the fermentation scheme. It has been found that the fermentation process does not depend on supplementary nutrition, but the yeast race effects on the physicochemical parameters, namely on the volatile acids content. The results obtained have shown the effect of a yeast race and supplementary nutrition on the organoleptic characteristics of these varieties. In Southern Ukraine, to control the quality characteristics of wine materials, using active dry yeast Saccharomyces cerevisiae with a two-stage nutrition complex has a positive effect on the physicochemical parameters of the corresponding grape variety and allows revealing its varietal characteristics.

Comprehensive Analysis of Replication Origins in Saccharomyces cerevisiae Genomes.

DNA replication initiates from multiple replication origins (ORIs) in eukaryotes. Discovery and characterization of replication origins are essential for a better understanding of the molecular mechanism of DNA replication. In this study, the features of autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae have been comprehensively analyzed as follows. Firstly, we carried out the analysis of the ARSs available in S. cerevisiae S288C. By evaluating the sequence similarity of experimentally established ARSs, we found that 94.32% of ARSs are unique across the whole genome of S. cerevisiae S288C and those with high sequence similarity are prone to locate in subtelomeres. Subsequently, we built a non-redundant dataset with a total of 520 ARSs, which are based on ARSs annotation of S. cerevisiae S288C from SGD and then supplemented with those from OriDB and DeOri databases. We conducted a large-scale comparison of ORIs among the diverse budding yeast strains from a population genomics perspective. We found that 82.7% of ARSs are not only conserved in genomic sequence but also relatively conserved in chromosomal position. The non-conserved ARSs tend to distribute in the subtelomeric regions. We also conducted a pan-genome analysis of ARSs among the S. cerevisiae strains, and a total of 183 core ARSs existing in all yeast strains were determined. We extracted the genes adjacent to replication origins among the 104 yeast strains to examine whether there are differences in their gene functions. The result showed that the genes involved in the initiation of DNA replication, such as orc3, mcm2, mcm4, mcm6, and cdc45, are conservatively located adjacent to the replication origins. Furthermore, we found the genes adjacent to conserved ARSs are significantly enriched in DNA binding, enzyme activity, transportation, and energy, whereas for the genes adjacent to non-conserved ARSs are significantly enriched in response to environmental stress, metabolites biosynthetic process and biosynthesis of antibiotics. In general, we characterized the replication origins from the genome-wide and population genomics perspectives, which would provide new insights into the replication mechanism of S. cerevisiae and facilitate the design of algorithms to identify genome-wide replication origins in yeast.

Rif1 promotes association of G-quadruplex (G4) by its specific G4 binding and oligomerization activities

Rif1 is a conserved protein regulating replication timing and binds preferentially to the vicinity of late-firing/dormant origins in fission yeast. The Rif1 binding sites on the fission yeast genome have an intrinsic potential to generate G-quadruplex (G4) structures to which purified Rif1 preferentially binds. We previously proposed that Rif1 generates chromatin architecture that may determine replication timing by facilitating the chromatin loop formation. Here, we conducted detailed biochemical analyses on Rif1 and its G4 binding. Rif1 prefers sequences containing long stretches of guanines and binds preferentially to the multimeric G4 of parallel or hybrid/mix topology. Rif1 forms oligomers and binds simultaneously to multiple G4. We present a model on how Rif1 may facilitate the formation of chromatin architecture through its G4 binding and oligomerization properties.

Valorization of Deproteinated Potato Juice Water into \u03b2-Glucan Preparation of C. utilis Origin: Comparative Study of Preparations Obtained by Two Isolation Methods

Purposeβ(1,3)/(1,6)-Glucan of yeast origin is a bioactive polysaccharide used in nutrition, healthcare, agriculture and wastewater treatment. Yeast cultivation focused on the biosynthesis of β-glucan with simultaneous utilization of industrial wastes as a culture medium is a new way of obtaining these functional polysaccharides. The aim of current study was to isolate and characterize the purified β(1,3)/(1,6)-glucan preparation from Candida utilis ATTC 9950 biomass propagated in waste deproteinated potato juice water with the addition of glycerol.MethodsThe production of biomass of tested C. utilis strain was carried on biofermentor scale. The isolation of cell wall β-glucan was tested with two different methods: the alkaline-acid procedure coupled with hot-water extraction (method 1) and isolation based on cell wall autoclaving, lipids extraction and proteolysis (method 2). The isolated fractions were further analyzed with infrared spectroscopy.ResultsObtained preparations contained approx. 82% of β(1,3)/(1,6)-glucan after shortened extraction comparing with procedures described in literature. Infrared spectra of examined preparations demonstrated highly similar pattern to β-glucan standard of Saccharomyces cerevisiae origin. The preparation produced by method 2 showed higher ratio of β(1,3)- to β(1,6)-glucan. The production efficiency for method 2 was 70%, while for the method 1 it was significantly lower, i.e. 49%, indicating substantial material losses during alkaline-acid purification.ConclusionsThe C. utilis ATCC 9950 yeast cultivated on waste deproteinated potato juice water supplemented with glycerol is a highly efficient system to obtain purified β-glucan preparation.Graphical

A polyploid admixed origin of beer yeasts derived from European and Asian wine populations.

Strains of Saccharomyces cerevisiae used to make beer, bread, and wine are genetically and phenotypically distinct from wild populations associated with trees. The origins of these domesticated populations are not always clear; human-associated migration and admixture with wild populations have had a strong impact on S. cerevisiae population structure. We examined the population genetic history of beer strains and found that ale strains and the S. cerevisiae portion of allotetraploid lager strains were derived from admixture between populations closely related to European grape wine strains and Asian rice wine strains. Similar to both lager and baking strains, ale strains are polyploid, providing them with a passive means of remaining isolated from other populations and providing us with a living relic of their ancestral hybridization. To reconstruct their polyploid origin, we phased the genomes of two ale strains and found ale haplotypes to both be recombinants between European and Asian alleles and to also contain novel alleles derived from extinct or as yet uncharacterized populations. We conclude that modern beer strains are the product of a historical melting pot of fermentation technology.

The scale-up cultivation of Candida utilis in waste potato juice water with glycerol affects biomass and \u03b2(1,3)/(1,6)-glucan characteristic and yield

New ideas on production of yeast origin β-glucan preparations for industrial application are attracting interest considering market development of that high-value functional polysaccharide. Sellecting an efficient yeast producer and designing culture conditions are a prerequisite for obtaining high yield of β-glucan. The aim of this study was to describe at the first time the influence of the mode of cultivation (shake-flasks and batch fermentation) and time of culture on characteristic and yield of biomass and β(1,3)/(1,6)-glucan preparations of Candida utilis ATCC 9950 after cultivation in medium based on waste potato juice water supplemented with 10% of glycerol. After shake-flask culture, the biomass was characterized by higher protein content (app. 26.5%) compared to 19% after batch fermentation while the cultivation on a biofermentor scale promoted polysaccharides biosynthesis. The highest output of purified β(1,3)/(1,6)-glucan preparation (5.3 gd.w./L), containing app. 85% of that polysaccharide, was found after 48 h cultivation in biofermentor. Batch fermentation promoted biosynthesis of alkali-insoluble β(1,3)/(1,6)-glucan fraction, decreasing the content of β(1,6)-glucan. The yield of β(1,3)/(1,6)-glucan synthesis was 0.063 (g/g glycerol), while the productivity of that polysaccharide reached 0.094 (g/L/h). Longer batch fermentation (72 h) resulted in reduction of production efficiency of β-glucan preparation under studied conditions. The results of the study provide a new efficient biotechnological solution to produce high-value β-glucan preparations of C. utilis origin based on valorization of agro-waste potato juice water with glycerol.

Nuclear Pore Complex Components in the Malaria Parasite Plasmodium berghei

The nuclear pore complex (NPC) is a large macromolecular assembly of around 30 different proteins, so-called nucleoporins (Nups). Embedded in the nuclear envelope the NPC mediates bi-directional exchange between the cytoplasm and the nucleus and plays a role in transcriptional regulation that is poorly understood. NPCs display modular arrangements with an overall structure that is generally conserved among many eukaryotic phyla. However, Nups of yeast or human origin show little primary sequence conservation with those from early-branching protozoans leaving those of the malaria parasite unrecognized. Here we have combined bioinformatic and genetic methods to identify and spatially characterize Nup components in the rodent infecting parasite Plasmodium berghei and identified orthologs from the human malaria parasite P. falciparum, as well as the related apicomplexan parasite Toxoplasma gondii. For the first time we show the localization of selected Nups throughout the P. berghei life cycle. Largely restricted to apicomplexans we identify an extended C-terminal poly-proline extension in SEC13 that is essential for parasite survival and provide high-resolution images of Plasmodium NPCs obtained by cryo electron tomography. Our data provide the basis for full characterization of NPCs in malaria parasites, early branching unicellular eukaryotes with significant impact on human health.

The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: Implications to protein function and drug design.

The de novo crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSir2rp1) has been solved at 1.99Å in complex with an acetyl-lysine peptide substrate. The structure is broadly commensurate with Hst2/SIRT2 proteins of yeast and human origin, reproducing many of the structural features common to these sirtuin deacetylases, including the characteristic small zinc-binding domain, and the larger Rossmann-fold domain involved in NAD+-binding interactions. The two domains are linked via a cofactor binding loop ordered in open conformation. The peptide substrate binds to the LiSir2rp1 protein via a cleft formed between the small and large domains, with the acetyl-lysine side chain inserting further into the resultant hydrophobic tunnel. Crystals were obtained only with recombinant LiSir2rp1 possessing an extensive internal deletion of a proteolytically-sensitive region unique to the sirtuins of kinetoplastid origin. Deletion of 51 internal amino acids (P253-E303) from LiSir2rp1 did not appear to alter peptide substrate interactions in deacetylation assays, but was indispensable to obtain crystals. Removal of this potentially flexible region, that otherwise extends from the classical structural elements of the Rossmann-fold, specifically the β8-β9 connector, appears to result in lower accumulation of the protein when expressed from episomal vectors in L. infantum SIR2rp1 single knockout promastigotes. The biological function of the large serine-rich insertion in kinetoplastid/trypanosomatid sirtuins, highlighted as a disordered region with strong potential for post-translational modification, remains unknown but may confer additional cellular functions that are distinct from their human counterparts. These unique molecular features, along with the resolution of the first kinetoplastid sirtuin deacetylase structure, present novel opportunities for drug design against a protein target previously established as essential to parasite survival and proliferation.

Influence of Yeast β-Glucan on Cookies Sensory Characteristics and Bioactivities

β-Glucan is biologically active polysaccharide, ubiquitously found in many grains, bacteria, and fungi and much yeast. The aim of this study was to determine the effect of substituting wheat flour by 1, 2, and 4% yeast isolated β-glucan in cookies on the sensory acceptance, antioxidants, oxidative stability, and quality evaluation which were investigated. According to the results, cookies supplemented at 2% yeast β-glucan were proved satisfactory on sensory quality perspective. During the storage study it was found that cookies made with 2 and 4% β-glucan have effectively (p>0.05) kept the peroxide value (PV) within acceptable range, demonstrating the promising role of β-glucan in deterring oxidative. It is further noted that 2 or 4% β-glucan incorporated cookies assimilated highest absorption spectra, suggesting the retardation in freshness losses, with having minimum microbial loads, showing microbiological safety. β-Glucan fortification in foods is technologically and economically feasible, suggesting that a significant prospect of β-glucan as low-cost food ingredient in formulating cookies at 2% offers exciting new use of β-glucan of yeast origin.

A novel library of -arylketones as potential inhibitors of \u03b1-glucosidase: Their design, synthesis, in vitro and in vivo studies

α-glucosidase is an essential enzyme located at the brush border of intestines. It is an important therapeutic target for type II diabetes. Herein we have designed a library of novel α-arylketones as inhibitors of α-glucosidase (yeast origin) via scaffold hopping and bioisosteric modification of known inhibitors of α-glucosidase. The design was validated through molecular docking that revealed strong binding interactions of the newly designed compounds against α-glucosidase. A library comprising of 15 compounds was synthesized in a combinatorial fashion, where the advanced amide intermediates were accessed through “shot gun” synthesis. The final compounds were characterized by 1H, 13C-NMR and with high resolution mass spectroscopy. In vitro screening of the compounds against yeast α-glucosidase revealed substantial inhibition with IC50s in the range of 4–10 μM (the standard drug acarbose inhibits α-glucosidase with an IC50 of 9.95 μM). Reaction kinetics suggested mixed type inhibition. Finally, in vivo studies of the most active compound 3c against Streptozotocin induced male albino Wistar rats revealed that its administration in the rats for about 4 weeks lead to a highly significant (P < 0.001) decrease in the fasting blood glucose (FBG) compared to the untreated diabetic rats. Moreover, lower dose of 3c had better control over FBG in contrast to high-dose.

Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe

A central step in the initiation of chromosomal DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) at late M and early G1 phase of the cell cycles. Since 1973, four proteins or protein complexes, including cell division control protein 6 (Cdc6)/Cdc18, minichromosome maintenance protein complex, origin recognition complex (ORC), and Cdt1, are known components of the pre-RC. Previously, we reported that a non-ORC protein binds to the essential element Δ9 of the Schizosaccharomyces pombe DNA-replication origin ARS3001. In this study, we identified that the non-ORC protein is Sap1. Like ORC, Sap1 binds to DNA origins during cell growth cycles. But unlike ORC, which binds to asymmetric AT-rich sequences through its nine AT-hook motifs, Sap1 preferentially binds to a DNA sequence of 5'-(A/T) n (C/G)(A/T)9-10(G/C)(A/T) n -3' (n ≥ 1). We also found that Sap1 and ORC physically interact. We further demonstrated that Sap1 is required for the assembly of the pre-RC because of its essential role in recruiting Cdc18 to DNA origins. Thus, we conclude that Sap1 is a replication-initiation factor that directly participates in the assembly of the pre-RC. DNA-replication origins in fission yeast are defined by possessing two essential elements with one bound by ORC and the other by Sap1.

Molecular Mechanism for Chromatin Regulation During MCM Loading in Mammalian Cells.

DNA replication is a fundamental process required for the accurate and timely duplication of chromosomes. During late mitosis to G1 phase, the MCM2-7 complex is loaded onto chromatin in a manner dependent on ORC, CDC6, and Cdt1, and chromatin becomes licensed for replication. Although every eukaryotic organism shares common features in replication control, there are also some differences among species. For example, in higher eukaryotic cells including human cells, no strict sequence specificity has been observed for replication origins, unlike budding yeast or bacterial replication origins. Therefore, elements other than beyond DNA sequences are important for regulating replication. For example, the stability and precise positioning of nucleosomes affects replication control. However, little is known about how nucleosome structure is regulated when replication licensing occurs. During the last decade, histone acetylation enzyme HBO1, chromatin remodeler SNF2H, and histone chaperone GRWD1 have been identified as chromatin-handling factors involved in the promotion of replication licensing. In this review, we discuss how the rearrangement of nucleosome formation by these factors affects replication licensing.