Nucleolar assembly of the rRNA processing machinery in living cells

To understand how nuclear machineries are targeted to accurate locations during nuclear assembly, we investigated the pathway of the ribosomal RNA (rRNA) processing machinery towards ribosomal genes (nucleolar organizer regions [NORs]) at exit of mitosis. To follow in living cells two permanently transfected green fluorescence protein-tagged nucleolar proteins, fibrillarin and Nop52, from metaphase to G1, 4-D time-lapse microscopy was used. In early telophase, fibrillarin is concentrated simultaneously in prenucleolar bodies (PNBs) and NORs, whereas PNB-containing Nop52 forms later. These distinct PNBs assemble at the chromosome surface. Analysis of PNB movement does not reveal the migration of PNBs towards the nucleolus, but rather a directional flow between PNBs and between PNBs and the nucleolus, ensuring progressive delivery of proteins into nucleoli. This delivery appeared organized in morphologically distinct structures visible by electron microscopy, suggesting transfer of large complexes. We propose that the temporal order of PNB assembly and disassembly controls nucleolar delivery of these proteins, and that accumulation of processing complexes in the nucleolus is driven by pre-rRNA concentration. Initial nucleolar formation around competent NORs appears to be followed by regroupment of the NORs into a single nucleolus 1 h later to complete the nucleolar assembly. This demonstrates the formation of one functional domain by cooperative interactions between different chromosome territories.     

An InCytes from MBC Selection: Nucleolar Separation from Chromosomes during Aspergillus nidulans Mitosis Can Occur Without Spindle Forces

How the nucleolus is segregated during mitosis is poorly understood and occurs by very different mechanisms during closed and open mitosis. Here we report a new mechanism of nucleolar segregation involving removal of the nucleolar-organizing regions (NORs) from nucleoli during Aspergillus nidulans mitosis. This involves a double nuclear envelope (NE) restriction which generates three NE-associated structures, two daughter nuclei (containing the NORs), and the nucleolus. Therefore, a remnant nucleolar structure can exist in the cytoplasm without NORs. In G1, this parental cytoplasmic nucleolus undergoes sequential disassembly releasing nucleolar proteins to the cytoplasm as nucleoli concomitantly reform in daughter nuclei. By depolymerizing microtubules and mutating spindle assembly checkpoint function, we demonstrate that a cycle of nucleolar “segregation” can occur without a spindle in a process termed spindle-independent mitosis (SIM). During SIM physical separation of the NOR from the nucleolus occurs, and NE modifications promote expulsion of the nucleolus to the cytoplasm. Subsequently, the cytoplasmic nucleolus is disassembled and rebuilt at a new site around the nuclear NOR. The data demonstrate the existence of a mitotic machinery for nucleolar segregation that is normally integrated with mitotic spindle formation but that can function without it.     

Regulation of mTOR Complex 1 (mTORC1) by Raptor Ser863 and Multisite Phosphorylation

The rapamycin-sensitive mTOR complex 1 (mTORC1) promotes protein synthesis, cell growth, and cell proliferation in response to growth factors and nutritional cues. To elucidate the poorly defined mechanisms underlying mTORC1 regulation, we have studied the phosphorylation of raptor, an mTOR-interacting partner. We have identified six raptor phosphorylation sites that lie in two centrally localized clusters (cluster 1, Ser⁶⁹⁶/Thr⁷⁰⁶ and cluster 2, Ser⁸⁵⁵/Ser⁸⁵⁹/Ser⁸⁶³/Ser⁸⁷⁷) using tandem mass spectrometry and generated phosphospecific antibodies for each of these sites. Here we focus primarily although not exclusively on raptor Ser⁸⁶³ phosphorylation. We report that insulin promotes mTORC1-associated phosphorylation of raptor Ser⁸⁶³ via the canonical PI3K/TSC/Rheb pathway in a rapamycin-sensitive manner. mTORC1 activation by other stimuli (e.g. amino acids, epidermal growth factor/MAPK signaling, and cellular energy) also promote raptor Ser⁸⁶³ phosphorylation. Rheb overexpression increases phosphorylation on raptor Ser⁸⁶³ as well as on the five other identified sites (e.g. Ser⁸⁵⁹, Ser⁸⁵⁵, Ser⁸⁷⁷, Ser⁶⁹⁶, and Thr⁷⁰⁶). Strikingly, raptor Ser⁸⁶³ phosphorylation is absolutely required for raptor Ser⁸⁵⁹ and Ser⁸⁵⁵ phosphorylation. These data suggest that mTORC1 activation leads to raptor multisite phosphorylation and that raptor Ser⁸⁶³ phosphorylation functions as a master biochemical switch that modulates hierarchical raptor phosphorylation (e.g. on Ser⁸⁵⁹ and Ser⁸⁵⁵). Importantly, mTORC1 containing phosphorylation site-defective raptor exhibits reduced in vitro kinase activity toward the substrate 4EBP1, with a multisite raptor 6A mutant more strongly defective that single-site raptor S863A. Taken together, these data suggest that complex raptor phosphorylation functions as a biochemical rheostat that modulates mTORC1 signaling in accordance with environmental cues.     

Nucleolar cycle and localization of NORs in early embryos of Parascaris univalens

During early embryogenesis of the nematode Parascaris univalens (2n=2) the processes of chromatin diminution and segregation of the germ and somatic cell lineages take place simultaneously. In this study we analyzed the nucleolar cycle in early embryos, both in germinal and somatic blastomeres, by means of silver staining and antibodies against the nucleolar protein fibrillarin. We observed an identical nucleolar cycle in both types of blastomeres, hence, the chromatin diminution process has no effect on the nucleolar cycle of somatic blastomeres. We report the existence of outstanding differences between this cycle and those previously reported during early embryogenesis of other species. There is a true nucleolar cycle in early embryos that shows a peculiar nucleolar disorganization at prophase, and a preferential localization of prenucleolar bodies only on the euchromatic regions during nucleologenesis. Moreover, fibrillarin does not form a perichromosomal sheath in metaphase or anaphase holocentric chromosomes, probably owing to their special centromeric organization. The number and location of nucleolus organizer regions (NORs) in the chromosomal complement have been determined using silver impregnation, chromomycin A₃/distamycin A staining, and fluorescent in situ hybridization using an rDNA probe. There are only two NORs, one per chromosome, and these are lost in blastomeres after chromatin diminution. Moreover, the constant presence of two nucleoli in somatic blastomeres suggests that NORs are not affected during the fragmentation of euchromatic regions when this process occurs.     

Position-dependent NOR activity in barley

Two types of intraspecific nucleolar dominance/suppression are described for barley,Hordeum vulgare L. When the nucleolus organizing regions (NORs) originally belonging to chromosomes 6 and 7 are combined by translocation in one chromosome, NOR 6 is dominant over NOR 7. Neither significant loss of rDNA nor its hypermethylation is the reason for the reduced nucleolus forming activity of NOR 7. Intrachromosomal NOR suppression probably does not occur in isochromosome 6s, which has two NORs 6 in one chromosome. Meiotic and somatic pairing of the homologous arms might be the reason for early fusion of their nucleoli and thus for the lower than expected maximum number of interphase nucleoli. Variable suppression of a partial NOR (6³) is described for descendants of crosses between translocation lines with split NORs 6 and 7. In these cases also, the reduced activity of the partial NOR 6³ is not due to deletion of rDNA as shown by in situ hybridization. Unstable methylation of NOR 6³ in heterozygous F₁ individuals is probably the cause of this phenomenon.     

Distribution and association of mTOR with its cofactors,raptor and rictor,in cumulus cells and oocytes during meiotic maturation in mice

Mammalian target of rapamycin (mTOR), a Ser/Thr protein kinase, is the catalytic component of two distinct signaling complexes, mTOR‐raptor complex (mTORC1) and mTOR‐rictor complex (mTORC2). Recently, studies have demonstrated mitosis‐specific roles for mTORC1, but the functions and expression dynamics of mTOR complexes during meiotic maturation remain unclear. In the present study, to evaluate the roles of respective mTOR complexes in maternal meiosis and compare them with those in mitosis, we sought to elucidate the spatiotemporal immunolocalization of mTOR, the kinase‐active Ser2448‐ and Ser2481‐phosphorylated mTOR, and raptor and rictor during cumulus‐cell mitosis and oocyte meiotic maturation in mice. mTOR principally accumulated around the chromosomes and on the spindle. Phosphorylated mTOR (Ser2448 and Ser2481) exhibited elevated fluorescence intensities in the cytoplasm and punctate localization adjacent to the chromosomes, on the spindle poles, and on the midbody during mitotic and meiotic maturation, suggesting functional homology of mTOR between the two cell division systems, despite their mechanistically distinctive spindles. Raptor colocalized with mTOR during both types of cell division, indicating that mTORC1 is predominantly associated with these events. Mitotic rictor uniformly distributed through the cytoplasm, and meiotic rictor localized around the spindle poles of metaphase‐I oocytes, suggesting functional divergence of mTORC2 between mitosis and female meiosis. Based on the general function of mTORC2 in the organization of the actin cytoskeleton, we propose that mTORC1 controls spindle function during mitosis and meiosis, while mTORC2 contributes to actin‐dependent asymmetric division during meiotic maturation in mice. Mol. Reprod. Dev. 80: 334–348, 2013. © 2013 Wiley Periodicals, Inc.     

Fibrillarin: a new protein of the nucleolus identified by autoimmune sera

Autoimmune serum from a patient with scleroderma was shown by indirect immunofluorescence to label nucleoli in a variety of cells tested including: rat kangaroo PtK2, Xenopus A6, 3T3, HeLa, and human peripheral blood lymphocytes. Immunoblot analysis of nucleolar proteins with the scleroderma antibody resulted in the labeling of a single protein band of 34 kD molecular weight with a pI of 8.5. Electron microscopic immunocytochemistry demonstrated that the protein recognized by the scleroderma antiserum was localized exclusively in the fibrillar region of the nucleolus which included both dense fibrillar and fibrillar center regions. Therefore, we have named this protein "fibrillarin". Fibrillarin was found on putative chromosomal nucleolar organizer regions (NORs) in metaphase and anaphase, and during telophase fibrillarin was found to be an early marker for the site of formation of the newly forming nucleolus. Double label indirect immunofluorescence and immunoelectron microscopy on normal, actinomycin D-segregated, and DRB-treated nucleoli showed that fibrillarin and nucleolar protein B23 were predominantly localized to the fibrillar and granular regions of the nucleolus, respectively. RNase A and DNase I digestion of cells in situ demonstrated that fibrillarin was partially removed by RNase and completely removed by DNase. These results suggest that fibrillarin is a widely occurring basic nonhistone nucleolar protein whose location and nuclease sensitivity may indicate some structural and/or functional role in the rDNA-containing dense fibrillar and fibrillar center regions of the nucleolus.     

In nucleoli, the steady state of nucleolar proteins is leptomycin B-sensitive

Background information. The nucleolus is a dynamic structure. It has been demonstrated that nucleolar proteins rapidly associate with and dissociate from nucleolar components in continuous exchanges with the nucleoplasm using GFP (green fluorescent protein)‐tagged proteins. However, how the exchanges within one nucleolus and between nucleoli within the nuclear volume occurred is still poorly understood. Results. The movement of PAGFP (photoactivatable GFP)‐tagged proteins that become visible after photoactivation can be followed. In the present study, we establish the protocol allowing quantification of the traffic of PAGFP‐tagged nucleolar proteins in nuclei containing two nucleoli. The traffic in the activated area, at the periphery of the activated area and to the neighbouring nucleolus is measured. Protein B23 is rapidly replaced in the activated area, and at the periphery of the activated area the steady state suggests intranucleolar recycling of B23; this recycling is LMB (leptomycin B)‐sensitive. The pool of activated B23 is equally distributed in the volume of the two nucleoli within 2 min. The three‐dimensional distribution of the proteins Nop52 and fibrillarin is less rapid than that of B23 but is also LMB‐sensitive. In contrast, traffic of fibrillarin from the nucleoli to the CB (Cajal body) was not modified by LMB. Conclusions. We propose that the steady state of nucleolar proteins in nucleoli depends on the affinity of the proteins for their partners and on intranucleolar recycling. This steady state can be impaired by LMB but not the uptake in the neighbouring nucleolus or the CB.     

Detection of fibrillarin in nucleolar remnants and the nucleolar matrix

In order to gain further insights into the fundamental structure of the nucleolus, nucleolar remnants of Xenopus and chickens were examined for the presence of fibrillarin and nucleolus organizer region (NOR) silver staining. Nucleolar remnants of Xenopus nucleated red blood cells were found to contain easily detectable amounts of fibrillarin and NOR silver staining. Upon examination of various tissues, fibrillarin and NOR silver staining were detected in nucleoli of Xenopus liver hepatocytes and within nucleoli of oocytes and follicle cells from ovaries of mature female toads. By comparison, nucleolar remnants of adult chicken nucleated red blood cells contained only trace amounts of fibrillarin and NOR silver staining, whereas red blood cell nucleolar remnants of immature chicks had easily detectable amounts of fibrillarin and NOR silver staining. Nucleoli from hepatocytes of both adult and immature chickens demonstrated comparable levels of fibrillarin and NOR silver staining. Since fibrillarin was found in nucleolar remnant structures, we tested for (and detected) its presence in residual nucleoli of in situ nuclear matrix derived from HeLa cells. These findings are discussed in terms of the basic structural and functional organization of the nucleolus.     

Number and Nuclear Localisation of Nucleoli in Mammalian Spermatocytes

In seven mammalian species, including man, the position and number of nucleoli in pachytene spermatocyte nuclei were studied from electron microscope (EM) nuclear sections or bivalent microspreads. The number and position of the nucleolar organiser regions (NORs) in mitotic and meiotic chromosomes were also analysed, using silver staining techniques and in situ hybridisation protocols. The general organisation of pachytene spermatocyte nucleoli was almost the same, with only minor morphological differences between species. The terminal NORs of Thylamys elegans (Didelphoidea, Marsupialia), Dromiciops gliroides (Microbiotheridae, Marsupialia), Phyllotys osgoodi (Rodentia, Muridae) and man, always gave rise to peripheral nucleoli in the spermatocyte nucleus. In turn, the intercalated NORs from Octodon degus, Ctenomys opimus (Rodentia, Octodontidae) and Chinchilla lanigera (Rodentia, Cavidae), gave rise to central nucleoli. In species with a single nucleolar bivalent, just one nucleolus is formed, while in those with multiple nucleolar bivalents a variable number of nucleoli are formed by association of different nucleolar bivalents or NORs that occupy the same nuclear peripheral space (Phyllotis and man). It can be concluded that the position of each nucleolus within the spermatocyte nucleus is mainly dependent upon: (1) the position of the NOR in the nucleolar bivalent synaptonemal complex (SC), (2) the nuclear pathway of the nucleolar bivalent SC, being both telomeric ends attached to the nuclear envelope, and (3) the association between nucleolar bivalents by means of their NOR-nucleolar domains that occupy the same nuclear space. Thus, the distribution of nucleoli within the nuclear space of spermatocytes is non-random and it is consistent with the existence of a species-specific meiotic nuclear architecture.     

Structural insights of mTOR complex 1

The mammalian target of rapamycin (mTOR), also known as the mechanistic target of rapamycin, is a central cell growth regulating kinase that forms large molecular complexes in all eukaryotic cells. A paper recently published in Science reports the architecture of mTOR complex 1 (mTORC1) and provides molecular insights into the regulation and substrate selectivity of mTORC1.The mammalian target of rapamycin (mTOR) exists in two different complexes, mTORC1 and mTORC2, which are distinguished by unique accessory protein Raptor and Rictor, respectively¹. Rapamycin is an mTORC1-specific inhibitor, which complexes with the FK506-binding 12 kDa protein (FKBP12) and inhibits Raptor-bound, but not Rictor-bound, mTOR. Rapamycin analogs have been used clinically to treat a number of human diseases, including cancer². A wide range of both extra- and intracellular signals, including growth factors, nutrient status and stress conditions, have been shown to regulate mTORC1 to control cell growth. Most notably, mTORC1 is hyperactivated by oncogenic PI3K-Akt signaling and promotes tumor growth¹.mTORC1 promotes cell growth through phosphorylation of a large number of cellular proteins, including the ribosomal S6 kinase 1 (S6K1) and eIF-4E-binding protein 1 (4E-BP1)³. Although mTORC2 shares the same catalytic kinase subunit with mTORC1, it phosphorylates substrates very different from those of mTORC1 and thus exerts different cellular functions. Despite the extensive studies, the mechanistic understanding of mTORC1 activation and substrate selectivity are rather limited, chiefly due to the lack of three dimensional structure of mTORC1. Understanding of mTORC1 molecular architecture is also of high importance for developing pharmacological drugs to target this pathway.Cryo-electron microscopy (cryo-EM) studies have shown that mTOR forms an obligate dimer with an overall rhomboid shape and a central cavity⁴. However, the reliability of the handedness of the reconstruction and the position of individual subunits was significantly compromised due to the low-resolution (26 Å) reconstruction. A subsequent study presented the 3.2 Å crystal structure of a complex of N-terminally truncated human mTOR and mLST8, which is a subunit commonly present in both mTORC1 and mTORC2. This crystal structure revealed more details of the structure of mTOR kinase domain as well as its inhibition by FKBP12-rapamycin complex⁵. However, information on the subunit arrangement within mTORC1 was missing because only a truncated mTOR fragment was analyzed and the Raptor subunit, which plays a key role in mTORC1 regulation and substrate selectivity, was lacking.In a recent paper published in Science, the architecture of human mTORC1 was revealed by high-resolution cryo-EM⁶. The authors purified mTORC1 complex (human mTOR together with Raptor, and mLST8) bound to FKBP12-rapamycin from insect cells. Single particle analysis of cryo-EM yielded a reconstruction with an overall resolution of 5.9 Å. To complement the reconstruction of mTORC1, the authors also resolved the structure of the fungus Chaetomium thermophilum Raptor (CtRaptor), which exhibits 44% sequence identity to human Raptor. The overall shape of the reconstruction agrees with that observed by low-resolution cyro-EM⁴; however, it appears that the handedness of the previous reconstruction was not assigned correctly. Generally, mTORC1 adopts a cage-like, dimeric architecture and appears in a hollow lozenge shape, in which Raptor and mLST8 contribute peripheral parts of the complex and make up the pinnacles of the longer and shorter axes of the lozenge, respectively. Interestingly, the N-terminus of mTOR, which was not resolved in previous study⁵, contains two α-helical solenoids. The larger section is a highly curved super-helix, which is named the “horn”, while the smaller region adopts a relatively linear arrangement and is referred to as the “bridge”⁶. Both sections are predominantly exposed to the environment, indicating a potential role in binding mTOR regulators. In addition, the horn and bridge HEAT domains pack against one another, and the first HEAT repeat of the horn region interlocks with the adjacent mTOR FAT domain, through which the two mTOR subunits forms a dimer independent of Raptor⁶. Another interesting observation is that the conformation of the kinase domain appears unaffected by dimerization, suggesting that the regulation of mTORC1 may be mainly through controlling substrate access to the active site.The authors further investigated how Raptor contributes to the formation of mTORC1 complex. Raptor interacts with mTOR through an α-solenoid stack formed between the horn and bridge domains of mTOR via the Raptor armadillo domain⁶. It is proposed that Raptor stabilizes the N-terminal region of mTOR by providing roughly two-thirds of the interaction surface with HEAT domains. As mentioned above, the formation of mTORC1 dimer is dependent on interaction of mTOR domains, but not Raptor, thus a model is suggested that Raptor binding may stabilize mTOR N-terminal conformation without directly engaging in dimer formation.The structure of mTORC1 also provides implications of mTORC1 substrate selectivity and delivery. Previous report has revealed that mTOR FRB domain and mLST8 prevent activity toward non-cognate substrates by limiting access to the ATP-binding cleft⁵. According to the current architecture, Raptor binding further restricts the access to the active site, resulting in the enclosure of the active site cleft from all directions and reduction of its width to ∼20 Å⁶. Moreover, binding of FKBP12-rapamycin complex to the FRB domain of mTORC1 further reduces the active site cleft to ∼10 Å⁶. Taken together, this model shows how architectural subunits of mTORC1 and FKBP12-rapamycin limit access to the recessed mTOR active site (Figure 1). It is notable that in contrary to previous findings⁴, this study indicates that FKBP12-rapamycin binding has no effect on mTORC1 stability.Open in a separate windowFigure 1Schematic model of mTORC1 substrate selectivity and delivery. (A) Substrate recruitment is dependent on their TOR signaling (TOS) motif binding to Raptor TOS-binding site. mTOR FRB domain and mLST8 prevent phosphorylation towards non-cognate substrates by limiting the access to the ATP-binding cleft. Raptor binding further restricts the access to the active site, resulting in the enclosure of the active site cleft from all directions. Only when the TOS motif present in the substrate is recognized by Raptor, substrates can be delivered to the mTOR kinase active site and phosphorylated. (B) The FKBP12-rapamycin complex binding to the FRB domain further blocks the active site cleft and prevents the access of substrate to kinase active site.In summary, the new structure reveals insights into the mTORC1 architecture and important clues for mTORC1 functional regulation. The kinase domain of mTOR maintains a constitutively active conformation at all times. Association with Raptor limits substrate accessibility to the mTOR kinase active site as the Raptor RNC domain is positioned directly at the mTOR active site cleft, thereby explaining how Raptor modulates substrate selectivity of mTORC1. Furthermore, the new structure explains mTORC1 inhibition by FKBP12-rapamycin through blocking substrate accessibility to the mTOR kinase active site. It should be noted that the architecture of mTORC1 still needs further improvement as the current resolution (5.9 Å) is not sufficient to reveal amino acid side chains of subunits and critical sites for dimer formation and activity control.     

ULTRASTRUCTURE OF THE NUCLEOLUS DURING THE CHINESE HAMSTER CELL CYCLE

Changes in the structure of the nucleolus during the cell cycle of the Chinese hamster cell in vitro were studied. Quantitative electron microscopic techniques were used to establish the size and volume changes in nucleolar structures. In mitosis, nucleolar remnants, "persistent nucleoli," consisting predominantly of ribosome-like granular material, and a granular coating on the chromosomes were observed. Persistent nucleoli were also observed in some daughter nuclei as they were leaving telophase and entering G₁. During very early G₁, a dense, fibrous material characteristic of interphase nucleoli was noted in the nucleoplasm of the cells. As the cells progressed through G₁, a granular component appeared which was intimately associated with the fibrous material. By the middle of G₁, complete, mature nucleoli were present. The nucleolar volume enlarged by a factor of two from the beginning of G₁ to the middle of S primarily due to the accumulation of the granular component. During the G₂ period, there was a dissolution or breakdown of the nucleolus prior to the entry of the cells into mitosis. Correlations between the quantitative aspects of this study and biochemical and cytochemical data available in the literature suggest the following: nucleolar reformation following division results from the activation of the nucleolar organizer regions which transcribe for RNA first appearing in association with protein as a fibrous component (45S RNA) and then later as a granular component (28S and 32S RNA).     

Silver staining of the nucleoli of pig embryonic kidney cells during the hyperactivation and inhibition of the synthesis of nucleolar RNA by UV microirradiation

Silver staining of the nucleoli in pig embryo kidney cells (PK) was studied during the cell cycle and also upon mature nucleoli modifications induced by UV microirradiation. During anaphase only four silver-stained granules were revealed in each daughter set of chromosomes in the four nucleolus-organizing regions (NORs). In the following 1-2 hours, the number of granules in the NORs rapidly increased up to 25-30 per nucleus. During the next 20-25 hours of the cell cycle, the number of silver-stained granules was slowly doubling as the nucleoli grew in size. UV microirradiation of one nucleolus in the nucleus with two nucleoli induced a profound degradation of the injured nucleolus and a compensatory hypertrophy of the intact one. Such nucleolar modifications were accompanied by redistribution of the silver-stained granules between the injured and non-injured nucleoli and by alterations in the levels of nucleolar RNA synthesis in the NORs. These data support a hypothesis that silver-stained proteins may be involved in the regulation of the nucleolar activity.