Mis3 with a conserved RNA binding motif is essential for ribosome biogenesis and implicated in the start of cell growth and S phase checkpoint

SRPK1‑siRNA suppresses K562 cell growth and induces apoptosis via the PARP‑caspase3 pathway

Serine-arginine protein kinase 1 (SRPK1) has been used as an important signal mediator, and is associated with cancer development. However, studies have yet to determine whether SRPK1 suppresses leukemia cell growth and induces apoptosis. Studies have also yet to reveal the underlying mechanisms. In the present study, the effects of downregulating SRPK1 gene expression on chronic myeloid leukemia cell lines (K562 cells) were investigated through RNA interference (RNAi) and the proliferation inhibition and apoptosis induction of SRPK1 in K562 cells were analyzed. K562 cells were transfected with two different concentrations of siRNA, and the transfection efficiency was detected via flow cytometry. The expression of SRPK1 was detected via reverse transcription‑quantitative polymerase chain reaction. K562 cell proliferation and apoptosis were analyzed using MTT and flow cytometry respectively. The roles of caspase‑3, poly (ADP‑ribose) polymerase (PARP), p53 and B-cell lymphoma (Bcl)‑2/Bcl‑2 associated X, apoptosis regulator (Bax) proteins in the apoptosis of human K562 cells were further examined through western blot analysis. The SRPK1 expression was lower in the K562 cells transfected with SRPK1‑siRNA compared with untransfected cells. The inhibition rate in the transfected groups was increased compared with the untransfected groups. Compared with control groups, the number of apoptotic cells in the SRPK1‑silenced groups increased. The number of early apoptotic cells also increased. The cleaved caspase‑3, cleaved PARP and p53 expression levels were significantly increased in the RNAi groups compared with control groups. Conversely, the Bcl‑2/Bax rate was significantly lower. In conclusion, the knockdown of the SRPK1 gene by RNAi inhibited the proliferation of K562 cells and induced their apoptosis. Apoptosis was induced by the activation of the PARP‑caspase3 pathway.

Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast

Ribosome formation in Saccharomyces cerevisiae requires a large number of transiently associated assembly factors that coordinate processing and folding of pre-rRNA and binding of ribosomal proteins. Krr1 and Faf1 are two interacting proteins present in early 90 S precursor particles of the small ribosomal subunit. Here, we determined a co-crystal structure of the core domain of Krr1 bound to a 19-residue fragment of Faf1 at 2.8 Å resolution. The structure reveals that Krr1 consists of two packed K homology (KH) domains, KH1 and KH2, and resembles archaeal Dim2-like proteins. We show that KH1 is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1. KH2 contains a canonical RNA-binding surface and additionally associates with an α-helix of Faf1. Specific disruption of the Krr1-Faf1 interaction impaired early 18 S rRNA processing at sites A0, A1, and A2 and caused cell lethality, but it did not prevent incorporation of the two proteins into pre-ribosomes. The Krr1-Faf1 interaction likely maintains a critical conformation of 90 S pre-ribosomes required for pre-rRNA processing. Our results illustrate the versatility of KH domains in protein interaction and provide insight into the role of Krr1-Faf1 interaction in ribosome biogenesis.

Two-step, extensive alterations in the transcriptome from G0 arrest to cell division in Schizosaccharomyces pombe

Body cells in multicellular organisms are in the G0 state, in which cells are arrested and terminally differentiated. To understand how the G0 state is maintained, the genes that are specifically expressed or repressed in G0 must be identified, as they control G0. In the fission yeast Schizosaccharomyces pombe, haploid cells are completely arrested under nitrogen source starvation with high viability. We examined the global transcriptome of G0 cells and cells on the course to resume vegetative growth. Approximately 20% of the transcripts of approximately 5000 genes increased or decreased more than fourfold in the two-step transitions that occur prior to replication. Of the top 30 abundant transcripts in G0, 23 were replaced by ribosome- and translation-related transcripts in the dividing vegetative state. Eight identified clusters with distinct alteration patterns of approximately 2700 transcripts were annotated by Gene Ontology. Disruption of 53 genes indicated that nine of them were necessary to support the proper G0 state. These nine genes included two C2H2 zinc finger transcription factors, a cyclin-like protein implicated in phosphorylation of RNA polymerase II, two putative autophagy regulators, a G-protein activating factor, and two CBS domain proteins, possibly involved in AMP-activated kinase.

Biophysical characterisation reveals structural disorder in the nucleolar protein, Dribble

Dribble (DBE) is an essential protein in Drosophila that belongs to the evolutionarily conserved Krr1p protein family. Proteins in this family are localised in the cell nucleolus and are important for the processing of ribosomal RNAs. However, little is known about their structural and biophysical properties. We have expressed and purified full-length DBE protein from Escherichia coli. Consistent with the native role of DBE in RNA processing, recombinant DBE was shown to bind RNA homo-polymers in vitro. By bioinformatics, size-exclusion chromatography, equilibrium sedimentation analysis, controlled proteolysis, and a variety of spectroscopic techniques, we have found that DBE is a monomeric protein in solution containing both alpha- and beta-structures. Moreover, the structure of DBE is expanded and significantly disordered (approximately 45% disordered). Natively disordered proteins are thought to provide a disproportionately large surface area and structural plasticity for nucleic acid binding. We therefore propose that the presence of structural disorder is an important feature of DBE that facilitates the protein to interact with RNAs in the nucleolus.

RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe

Fission yeast is a useful model for RNA interference because it has single-copy genes for components of the RNAi pathway such as argonaute, dicer and RNA-dependent RNA polymerase (RdRP). Functions for RNAi revealed in S. pombe, such as heterochromatic silencing and chromosome segregation, are likely to be ancient because they are shared with some other eukaryotes. The underlying mechanisms are being rapidly unraveled.

Suppression of a mitotic mutant by tRNA-Ala anticodon mutations that produce a dominant defect in late mitosis

Cold-sensitive dominant mutants scn1 and scn2 of Schizosaccharomyces pombe were isolated by their ability to suppress temperature-sensitive cut9-665 defective in an essential subunit (human Apc6/budding yeast Cdc16 ortholog) of anaphase promoting complex/cyclosome (APC/C). APC/C mutants were defective in metaphase/anaphase transition, whereas single scn mutants showed the delay in anaphase spindle elongation at 20 degrees C. The scn mutants lost viability because of chromosome missegregation, and were sensitive to a tubulin poison. To understand the scn phenotypes, mutant genes were identified. Surprisingly, scn1 and scn2 have the same substitution in the anticodon of two different tRNA-Ala (UGC) genes. UGC was altered to UGU so that the binding of the tRNA-Ala to the ACA Thr codon in mRNA became possible. As cut9-665 contained an Ala535Thr substitution, wild-type Cut9 protein was probably produced in scn mutants. Indeed, plasmid carrying tRNA-Ala (UGU) conferred cold-sensitivity to wild-type and suppressed cut9-665 in a dominant fashion. The previously identified scn1(+) (renamed as scn3(+)) turned out to be a high copy suppressor for scn1 and scn2. These are the first tRNA mutants that cause a mitotic defect.

The small subunit processome is required for cell cycle progression at G1

Without ribosome biogenesis, translation of mRNA into protein ceases and cellular growth stops. We asked whether ribosome biogenesis is cell cycle regulated in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and we determined that it is not regulated in the same manner as in metazoan cells. We therefore turned our attention to cellular sensors that relay cell size information via ribosome biogenesis. Our results indicate that the small subunit (SSU) processome, a complex consisting of 40 proteins and the U3 small nucleolar RNA necessary for ribosome biogenesis, is not mitotically regulated. Furthermore, Nan1/Utp17, an SSU processome protein, does not provide a link between ribosome biogenesis and cell growth. However, when individual SSU processome proteins are depleted, cells arrest in the G1 phase of the cell cycle. This arrest was further supported by the lack of staining for proteins expressed in post-G1. Similarly, synchronized cells depleted of SSU processome proteins did not enter G2. This suggests that when ribosomes are no longer made, the cells stall in the G1. Therefore, yeast cells must grow to a critical size, which is dependent upon having a sufficient number of ribosomes during the G1 phase of the cell cycle, before cell division can occur.

Functional and physical interactions of Faf1p, a Saccharomyces cerevisiae nucleolar protein

We report the discovery and characterisation of a novel nucleolar protein of Saccharomyces cerevisiae. We identified this protein encoded by ORF YIL019w, designated in SGD base as Faf1p, in a two hybrid interaction screen using the known nucleolar protein Krr1 as bait. The presented data indicate that depletion of the Faf1 protein has an impact on the 40S ribosomal subunit biogenesis resulting from a decrease in the production of 18S rRNA. The primary defect is apparently due to inefficient processing of 35S rRNA at the A(0), A(1), and A(2) cleavage sites.

Identification of premycorrhiza-related plant genes in the association between Quercus robur and Piloderma croceum

•  An in vitro system with micropropagated oaks (Quercus robur) and the ectomycorrhizal fungus Piloderma croceum, which is characterized by a delayed mycorrhiza formation, was used to identify plant transcripts upregulated in the premycorrhizal phase. •  Complementary DNA (cDNA) populations of uninoculated roots and fungal mycelium were subtracted from a cDNA population of inoculated roots. Differential expression was confirmed by reverse Northern and 50 clones for different polypeptides were found to be up-regulated. Twenty-nine clones were investigated in more detail. •  For approximately half of the cDNA fragments no homologies could be identified in databases. The residual fragments code for polypeptides with homologies to known proteins involved in signal perception and transmission, stress responses, metabolism and growth. •  Since many of the identified genes have not yet been described in the context of symbiotic events, their potential roles during early phases of the recognition process are discussed.

Cti1/C1D interacts with condensin SMC hinge and supports the DNA repair function of condensin

Condensin is a conserved five-subunit complex containing two SMC (structural maintenance of chromosomes) and three non-SMC subunits and plays a major role in mitotic chromosome condensation. Condensin also acts in interphase and is required for DNA repair and replication checkpoint control. We attempted to study the function of the condensin in greater detail by means of the isolation of interacting proteins with the two-hybrid system. Using the hinge domain of Cut3/SMC4 as bait, we found one Cut three-interacting (Cti) 14-kDa nuclear protein, Cti1. GST pull-down assay and immunoprecipitation supported physical interaction between Cti1 and condensin. Cti1 is similar to human C1D, which associates tightly with genomic DNA and functions to activate DNA protein kinase. SpC1D is essential for viability. The null mutant could germinate but arrest after replication, indicating that it is required for interphase growth. Importantly, an elevated dosage of spC1D suppressed the temperature, UV irradiation, and hydroxyurea sensitivity of the mutant of Cnd2, a non-SMC subunit of condensin. Upon exposure to hydroxyurea, spC1D accumulated on the nuclear chromatin, and the fraction of spC1D that was chromatin-bound increased. Cti1 is the first example of the protein that interacts with the hinge domain of SMC. Cti1 may have a supporting role for the DNA repair function of condensin.

Yph1p, an ORC-interacting protein: potential links between cell proliferation control, DNA replication, and ribosome biogenesis

Immunoprecipitation of the origin recognition complex (ORC) from yeast extracts identified Yph1p, an essential protein containing a BRCT domain. Two Yph1p complexes were characterized. Besides ORC, MCM proteins, cell-cycle regulatory proteins, checkpoint proteins, 60S ribosomal proteins, and preribosome particle proteins were found to be associated with Yph1p. Yph1p is predominantly nucleolar and is required for 60S ribosomal subunit biogenesis and possibly for translation on polysomes. Proliferating cells depleted of Yph1p arrest in G(1) or G(2), with no cells in S phase, or significantly delay S phase progression after release from a hydroxyurea arrest. Yph1p levels decline as cells commit to exit the cell cycle, and levels vary depending on energy source. Yph1p may link cell proliferation control to DNA replication, ribosome biogenesis, and translation on polysomes.

Fission yeast homolog of murine Int-6 protein, encoded by mouse mammary tumor virus integration site, is associated with the conserved core subunits of eukaryotic translation initiation factor 3

The murine int-6 locus, identified as a frequent integration site of mouse mammary tumor viruses, encodes the 48-kDa eIF3e subunit of translation initiation factor eIF3. Previous studies indicated that the catalytically active core of budding yeast eIF3 consists of five subunits, all conserved in eukaryotes, but does not contain a protein closely related to eIF3e/Int-6. Whereas the budding yeast genome does not encode a protein closely related to murine Int-6, fission yeast does encode an Int-6 ortholog, designated here Int6. We found that fission yeast Int6/eIF3e is a cytoplasmic protein associated with 40 S ribosomes. FLAG epitope-tagged Tif35, a putative core eIF3g subunit, copurified with Int6 and all five orthologs of core eIF3 subunits. An int6 deletion (int6Delta) mutant was viable but grew slowly in minimal medium. This slow growth phenotype was accompanied by a reduction in the amount of polyribosomes engaged in translation and was complemented by expression of human Int-6 protein. These findings support the idea that human and Schizosaccharomyces pombe Int-6 homologs are involved in translation. Interestingly, haploid int6Delta cells showed unequal nuclear partitioning, possibly because of a defect in tubulin function, and diploid int6Delta cells formed abnormal spores. We propose that Int6 is not an essential subunit of eIF3 but might be involved in regulating the activity of eIF3 for translation of specific mRNAs in S. pombe.