Molecular cloning of mouse p47, a second group mammalian RuvB DNA helicase-like protein: homology with those from human and Saccharomyces cerevisiae

C-FLIPL Modulated Wnt/β-Catenin Activation via Association with TIP49 Protein

Cellular FLICE-like inhibitory protein (c-FLIP_L) is a key inhibitory protein in the extrinsic apoptotic pathway. Recent studies showed that c-FLIP_L could translocate into the nucleus and might be involved in the Wnt signaling pathway. The nuclear function of c-FLIP_L was still unclear. Here we found a novel c-FLIP_L-associated protein TIP49, which is a nuclear protein identified as a cofactor in the transcriptional regulation of β-catenin. They had co-localization in the nucleus and the DED domain of c-FLIP_L was required for the association with TIP49. By performing ChIP experiments, C-FLIP_L was detected in the ITF-2 locus and facilitated TIP49 accumulation in the formation of complexes at the T-cell-specific transcription factor site of human ITF-2 promoter. When TIP49 knockdown, c-FLIP_L-driven Wnt activation, and cell proliferation were inhibited, suggesting that a role of nuclear c-FLIP_L involved in modulation of the Wnt pathway was in a TIP49-dependent manner. Elevated expression of c-FLIP_L and TIP49 that coincided in human lung cancers were analyzed in silico using the Oncomine database. Their high expressions were reconfirmed in six lung cancer cell lines and correlated with cell growth. The association of c-FLIP_L and TIP49 provided an additional mechanism involved in c-FLIP_L-mediated functions, including Wnt activation.

Rvb1–Rvb2: essential ATP-dependent helicases for critical complexesThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process

Rvb1 and Rvb2 are highly conserved, essential AAA+ helicases found in a wide range of eukaryotes. The versatility of these helicases and their central role in the biology of the cell is evident from their involvement in a wide array of critical cellular complexes. Rvb1 and Rvb2 are components of the chromatin-remodeling complexes INO80, Swr-C, and BAF. They are also members of the histone acetyltransferase Tip60 complex, and the recently identified R2TP complex present in Saccharomyces cerevisiae and Homo sapiens; a complex that is involved in small nucleolar ribonucleoprotein (snoRNP) assembly. Furthermore, in humans, Rvb1 and Rvb2 have been identified in the URI prefoldin-like complex. In Drosophila, the Polycomb Repressive complex 1 contains Rvb2, but not Rvb1, and the Brahma complex contains Rvb1 and not Rvb2. Both of these complexes are involved in the regulation of growth and development genes in Drosophila. Rvbs are therefore crucial factors in various cellular processes. Their importance in chromatin remodeling, transcription regulation, DNA damage repair, telomerase assembly, mitotic spindle formation, and snoRNP biogenesis is discussed in this review.

Overexpression and role of the ATPase and putative DNA helicase RuvB-like 2 in human hepatocellular carcinoma

Using a proteomic analysis of human hepatocellular carcinoma (HCC), we identified the overexpression in 4 tumors of RuvB-like 2 (RUVBL2), an ATPase and putative DNA helicase known to interact with beta-catenin and cellular v-myc myelocytomatosis viral oncogene homolog (c-myc). RUVBL2 expression was further analyzed in tumors with quantitative reverse-transcription polymerase chain reaction analysis and immunohistochemistry; in addition, RUVBL2 expression in a HuH7 cell line was silenced by small interfering RNA or increased with a lentiviral vector. RUVBL2 messenger RNA overexpression was confirmed in 72 of 96 HCC cases, and it was associated with poorly differentiated tumors (P = 0.02) and a poor prognosis (P = 0.02) but not with beta-catenin mutations or c-myc levels. Although RUVBL2 was strictly nuclear in normal hepatocytes, tumoral hepatocytes exhibited additional cytoplasmic staining. There was no mutation in the coding sequence of RUVBL2 in 10 sequenced cases. Silencing RUVBL2 in HuH7 HCC cells reduced cell growth (P < 0.001) and increased apoptosis, as shown by DNA fragmentation (P < 0.001) and caspase 3 activity (P < 0.005). This was associated with an increased expression of several proapoptotic genes and with an increased conformational activation of Bak-1 and Bax. On the other hand, HuH7 cells with an overexpression of RUVBL2 grew better in soft agar (P < 0.03), had increased resistance to C2 ceramide-induced apoptosis (P < 0.001), and gave rise to significantly larger tumors when injected into immunodeficient Rag2/gammac mice (P = 0.016).

CONCLUSION

RUVBL2 is overexpressed in a large majority of HCCs. RUVBL2 overexpression enhances tumorigenicity, and RUVBL2 is required for tumor cell viability. These results argue for a major role of RUVBL2 in liver carcinogenesis.

Genetic suppressors of Caenorhabditis elegans pha-4/FoxA identify the predicted AAA helicase ruvb-1/RuvB

FoxA transcription factors are critical regulators of gut development and function. FoxA proteins specify gut fate during early embryogenesis, drive gut differentiation and morphogenesis at later stages, and affect gut function to mediate nutritional responses. The level of FoxA is critical for these roles, yet we know relatively little about regulators for this family of proteins. To address this issue, we conducted a genetic screen for mutants that suppress a partial loss of pha-4, the sole FoxA factor of Caenorhabditis elegans. We identified 55 mutants using either chemical or insertional mutagenesis. Forty-two of these were informational suppressors that affected nonsense-mediated decay, while the remaining 13 were pha-4 suppressors. These 13 alleles defined at least six different loci. On the basis of mutational frequencies for C. elegans and the genetic dominance of four of the suppressors, we predict that many of the suppressors are either unusual loss-of-function mutations in negative regulators or rare gain-of-function mutations in positive regulators. We characterized one dominant suppressor molecularly and discovered the mutation alters a likely cis-regulatory region within pha-4 itself. A second suppressor defined a new locus, the predicted AAA+ helicase ruvb-1. These results indicate that our screen successfully found cis- or trans-acting regulators of pha-4.

Comparison of the nuclear proteomes of mammary epithelial cells at different stages of functional differentiation

The progression of stem cells to proliferating progenitor cells and finally to a quiescent differentiated state is a hallmark of organ development. This process proceeds through distinct steps and is regulated through cell-cell interactions and by systemically and locally acting factors. We have established a cell culture system which recapitulates features of mammary gland development in vitro and allows the comparison of three characteristic differentiation stages. Cell fate decisions relating to proliferation and differentiation are dependent on the function of proteins in the nucleus. Therefore, we have applied proteomic approaches, including 1- and 2-DE coupled with MS and a gel-free system, called protein sequence tag technology (PST), to assess the changes in the nuclear protein composition during differentiation of mammary epithelial cells. We identified about 250 individual proteins which are present in the nucleus of proliferating and functionally differentiated mammary epithelial cells. We functionally categorised the differentially expressed proteins and identified a multitude of proteins that regulate gene expression at the transcriptional or post-transcriptional level. This analysis greatly enriches our global view of the dynamic changes of nuclear proteins during the development of mammary epithelial cells and suggests models for the control of differentiation-specific protein expression.

Novel subunits of the mammalian Hsp90 signal transduction chaperone

As one of the major cellular chaperones, Hsp90 plays diverse roles in supporting and regulating wild-type and oncogenic signal transduction proteins. Hsp90 function itself is regulated by its various nonsubstrate subunits. To define Hsp90's predominant in vivo functions and the mechanisms for regulating this function, the human Hsp90 interactome was characterized using gel-based proteomics techniques. Results show that Hsp90's most prominent association is its previously described interaction with Hsp70, a primary chaperone capable of recognizing and binding hydrophobic peptide segments. Additionally, novel human proteins discovered in this study reveal that several newly described Hsp90 associations in yeast are conserved in the human cytoplasm. Additionally, other new Hsp90 subunits imply that a great deal of Hsp90 function may be directed to the assembly, regulation, or exploitation of the tubulin-based cytoskeleton network, particularly the mitotic spindle.

Dodecameric structure and ATPase activity of the human TIP48/TIP49 complex

TIP48 and TIP49 are two related and highly conserved eukaryotic AAA(+) proteins with an essential biological function and a critical role in major pathways that are closely linked to cancer. They are found together as components of several highly conserved chromatin-modifying complexes. Both proteins show sequence homology to bacterial RuvB but the nature and mechanism of their biochemical role remain unknown. Recombinant human TIP48 and TIP49 were assembled into a stable high molecular mass equimolar complex and tested for activity in vitro. TIP48/TIP49 complex formation resulted in synergistic increase in ATPase activity but ATP hydrolysis was not stimulated in the presence of single-stranded, double-stranded or four-way junction DNA and no DNA helicase or branch migration activity could be detected. Complexes with catalytic defects in either TIP48 or TIP49 had no ATPase activity showing that both proteins within the TIP48/TIP49 complex are required for ATP hydrolysis. The structure of the TIP48/TIP49 complex was examined by negative stain electron microscopy. Three-dimensional reconstruction at 20 A resolution revealed that the TIP48/TIP49 complex consisted of two stacked hexameric rings with C6 symmetry. The top and bottom rings showed substantial structural differences. Interestingly, TIP48 formed oligomers in the presence of adenine nucleotides, whilst TIP49 did not. The results point to biochemical differences between TIP48 and TIP49, which may explain the structural differences between the two hexameric rings and could be significant for specialised functions that the proteins perform individually.

Genes associated with the formation of germ cells from embryonic stem cells in cultures containing different glucose concentrations

In a previous study, we established a system for visualizing the development of germ cells from mouse embryonic stem (ES) cells in culture using knock-in ES clones in which visual reporter genes were expressed from the mouse vasa homolog, Mvh. While assessing various culture conditions, we found that germ-cell formation was markedly depressed in low glucose medium. Using a repeated polymerase chain reaction (PCR) subtraction method, we identified genes that were differentially expressed in low versus high glucose media. Three genes that were predominantly expressed in high glucose medium, thioredoxin-interacting protein (Txnip), pituitary tumor-transforming gene 1 (Pttg), and RuvB-like protein 2 (RuvBl2), were further investigated. These genes were also found to be highly expressed in adult and embryonic gonads, and RuvBl2 in particular, which encodes an ATP-dependent DNA helicase, was specifically detected in the spermatocytes and spermatids of the adult testis as well as in primordial germ cells. Furthermore, using a green fluorescent protein (GFP) fusion construct, we found that RuvBl2 was expressed in both the nucleus and cytoplasm of testicular germ cells. These findings suggest a possible relationship between glucose metabolism and germ-cell development.

Relocalization of human chromatin remodeling cofactor TIP48 in mitosis

TIP48 is a highly conserved eukaryotic AAA+ protein which is an essential cofactor for several complexes involved in chromatin acetylation and remodeling, transcriptional and developmental regulation and nucleolar organization and trafficking. We show that TIP48 abundance in HeLa cells did not change during the cell cycle, nor did its distribution in various biochemical fractions. However, we observed distinct changes in the subcellular localization of TIP48 during M phase using immunofluorescence microscopy. Our studies demonstrate that in interphase cells TIP48 was found mainly in the nucleus and exhibited a distinct localization in the nuclear periphery. As the cells entered mitosis, TIP48 was excluded from the condensing chromosomes but showed association with the mitotic apparatus. During anaphase, some TIP48 was detected in the centrosome colocalizing with tubulin but the strongest staining appeared in the mitotic equator associated with the midzone central spindle. Accumulation of TIP48 in the midzone and the midbody was observed in late telophase and cytokinesis. This redeployment of TIP48 during anaphase and cytokinesis was independent of microtubule assembly. The relocation of endogenous TIP48 to the midzone/midbody under physiological conditions suggests a novel and distinct function for TIP48 in mitosis and possible involvement in the exit of mitosis.

TIP49b, a regulator of activating transcription factor 2 response to stress and DNA damage

Activating transcription factor 2 (ATF2/CRE-BP1) is implicated in transcriptional control of stress-responsive genes. A yeast two-hybrid screen identified TBP-interacting protein 49b (TIP49b), a component of the INO80 chromatin-remodeling complex, as a novel ATF2-interacting protein. TIP49b's association with ATF2 is phosphorylation dependent and requires amino acids 150 to 248 of ATF2 (ATF2(150-248)), which are implicated in intramolecular inhibition of ATF2 transcriptional activities. Forced expression of TIP49b efficiently attenuated ATF2 transcriptional activities under normal growth conditions as well as after UV treatment, ionizing irradiation, or activation of p38 kinase, all of which induced ATF2 phosphorylation and increased TIP49b-ATF2 association. Constitutive expression of ATF2(150-248) peptide outcompeted TIP49b interaction with ATF2 and alleviated the suppression of ATF2 transcriptional activities. Expression of ATF2(150-248) in fibroblasts or melanoma but not in ATF2-null cells caused a profound G(2)M arrest and increased degree of apoptosis following irradiation. The interaction between ATF2 and TIP49b constitutes a novel mechanism that serves to limit ATF2 transcriptional activities and highlights the central role of ATF2 in the control of the cell cycle and apoptosis in response to stress and DNA damage.

A well-connected and conserved nucleoplasmic helicase is required for production of box C/D and H/ACA snoRNAs and localization of snoRNP proteins

Biogenesis of small nucleolar RNA-protein complexes (snoRNPs) consists of synthesis of the snoRNA and protein components, snoRNP assembly, and localization to the nucleolus. Recently, two nucleoplasmic proteins from mice were observed to bind to a model box C/D snoRNA in vitro, suggesting that they function at an early stage in snoRNP biogenesis. Both proteins have been described in other contexts. The proteins, called p50 and p55 in the snoRNA binding study, are highly conserved and related to each other. Both have Walker A and B motifs characteristic of ATP- and GTP-binding and nucleoside triphosphate-hydrolyzing domains, and the mammalian orthologs have DNA helicase activity in vitro. Here, we report that the Saccharomyces cerevisiae ortholog of p50 (Rvb2, Tih2p, and other names) is required for production of C/D snoRNAs in vivo and, surprisingly, H/ACA snoRNAs as well. Point mutations in the Walker A and B motifs cause temperature-sensitive or lethal growth phenotypes and severe defects in snoRNA accumulation. Notably, depletion of p50 (called Rvb2 in this study) also impairs localization of C/D and H/ACA core snoRNP proteins Nop1p and Gar1p, suggesting a defect(s) in snoRNP assembly or trafficking to the nucleolus. Findings from other studies link Rvb2 orthologs with chromatin remodeling and transcription. Taken together, the present results indicate that Rvb2 is involved in an early stage of snoRNP biogenesis and may play a role in coupling snoRNA synthesis with snoRNP assembly and localization.

The Saccharomyces cerevisiae RuvB-like protein, Tih2p, is required for cell cycle progression and RNA polymerase II-directed transcription

Two highly conserved RuvB-like putative DNA helicases, p47/TIP49b and p50/TIP49a, have been identified in the eukaryotes. Here, we study the function of Saccharomyces cerevisiae TIH2, which corresponds to mammalian p47/TIP49b. Tih2p is required for vegetative cell growth and localizes in the nucleus. Immunoprecipitation analysis revealed that Tih2p tightly interacts with Tih1p, the counterpart of mammalian p50/TIP49a, which has been shown to interact with the TATA-binding protein and the RNA polymerase II holoenzyme complex. Furthermore, the mutational study of the Walker A motif, which is required for nucleotide binding and hydrolysis, showed that this motif plays indispensable roles in the function of Tih2p. When a temperature-sensitive tih2 mutant, tih2-160, was incubated at the nonpermissive temperature, cells were rapidly arrested in the G(1) phase. Northern blot analysis revealed that Tih2p is required for transcription of G(1) cyclin and of several ribosomal protein genes. The similarities between the mutant phenotypes of tih2-160 and those of taf145 mutants suggest a role for TIH2 in the regulation of RNA polymerase II-directed transcription.

Expression of Xenopus homologs of the beta-catenin binding protein pontin52

Identification of pontin52 as an interaction partner of the Wnt/Wg signal transducer beta-catenin implicated a role for this protein in Wnt signaling. Here we describe the isolation of two Xenopus homologs of pontin52, Xpontin and Xreptin, and report the first expression pattern of vertebrate pontin52 homologs. Whole-mount in situ hybridization studies reveal a strong expression of Xpontin in neural crest cells and in later stages in different gastrointestinal organs. Xreptin is also expressed in neural crest cells, in particular in a subpopulation that give raise to the adrenal medulla.

Human TIP49b/RUVBL2 gene: genomic structure, expression pattern, physical link to the human CGB/LHB gene cluster on chromosome 19q13.3

Bacterial DNA helicase RuvB protein is an essential component in homologous recombination and DNA double-strand break repair. Here, we report the gene structure of TIP49b/RUVBL2, a second putative human homologue of the bacterial RuvB gene. This gene contains 15 exons and 14 introns. The TIP49b/RUVBL2 open reading frame encodes a protein of 463 amino acids, showing 43% identity with the RUVBL1 protein. The TIP49b/RUVBL2 gene is physically linked to the human CGB/LHB gene cluster on chromosome 19q13.3. Genomic sequence analysis revealed that the TIP49b/RUVBL2 gene is very close (55 nucleotides in length) to the LHB gene, in the opposite orientation. The very close co-location of the mouse homologues of the human TIP49b/RUVBL2 and LHB genes was also conserved on mouse chromosome 7. Co-ordinated transcriptional regulation between the TIP49b/RUVBL2 and LHB genes was not observed. TIP49b/RUVBL2, like RUVBL1, was expressed ubiquitously in all human tissues examined and more strongly in testis. As TIP49b/RUVBL2 is expected to be involved in recombination repair and is located in a chromosome region frequently amplified in breast cancer, we quantified TIP49b/RUVBL2 gene expression by using real-time quantitative RT-PCR in a series of breast tumour samples. None of the tumour samples showed an altered TIP49b/RUVBL2 transcription level relative to normal breast tissue.

Isolation, molecular characterization, and tissue-specific expression of ECP-51 and ECP-54 (TIP49), two homologous, interacting erythroid cytosolic proteins

We isolated two proteins, ECP-51 and ECP-54, from human erythrocyte cytosol by affinity chromatography using a peptide of the integral membrane protein stomatin as bait. Partial amino acid sequence information obtained by microsequencing allowed us to clone the respective cDNAs. Analysis of the nucleotide sequences revealed that ECP-51 and ECP-54 are homologous (44.2% amino acid identity) and contain ATP-binding sites. ECP-54 was identified as TIP49/RUVBL1/NMP238, which is a component of a large nuclear protein complex, possibly the RNA polymerase II holoenzyme; ECP-51 is a novel protein. Using the two-hybrid system, we showed that these proteins interact with each other. The interaction of ECP-51 and ECP-54 with the stomatin peptide and the localization to the nucleus and cytoplasm suggest an additional function for these proteins as chaperone components.