Structures of the rat proteasomal ATPases: determination of highly conserved structural motifs and rules for their spacing

Genetic studies of heat stress regulation in goat during hot climatic condition

Various direct and indirect environmental constraints have an impact on livestock performance. The physiological parameters, such as rectal temperature, heart rate, and respiratory rate, are the primary indicators of thermal stress. Under a stressed environment temperature humidity index (THI) had established as a vital measurement to identify the thermal stress in livestock. THI in association with climatic variations can define the environmental effect as stressful or comfortable for livestock. Goats are small ruminants that adapt to a wide range of ecological variations due to their anatomical and physiological characteristics. However, the productivity of animals declines at the individual level during thermal stress. Stress tolerance can be determined through genetic studies associated with at the cellular level using physiological as well as molecular approaches. Information on genetic association with thermal stress in goats is scanty, this severely affects their survival and hence productivity of livestock. The ever-increasing demand for food across the globe needs deciphering novel molecular markers as well as stress indicators that play a vital role in livestock improvement. This review represents an analysis of current knowledge of phenotypic differences during thermal stress and signifies the importance of physiological responses and their association at the cellular level in goats. The regulation of vital genes associated with thermal stress such as Aquaporins (AQP 0, 1, 2, 4, 5, 6, 8), aquaglyceroporins (AQP3, 7, 9, and 10) and super-aquaporins (AQP 11, 12); BAX inhibitors such as PERK (PKR like ER kinase), IRE 1(inositol-requiring-1); Redox regulating genes such as NOX; Transport of Na+ and K+ such as ATPase (ATP1A1) and several heat shock proteins have been implicated in heat-stress related adaptations have been elucidated. As these changes have a significant impact on production performance as well as on livestock productivity. Such efforts may help in the development of molecular markers and will assist the breeders to develop heat-tolerant goats with improved productivity.

Differential expression and characterization of ATP1A1 exon17 gene by high resolution melting analysis and RT-PCR in Indian goats

The investigation was carried out to analyse the genetic polymorphism and gene expression of ATP1A1 gene in four different Indian goat breeds by using high resolution melting (HRM) and real time-PCR. ATPase is electro-genic ion pump which is maintains the balance of sodium and potassium ions in animal cells. The transport of Na⁺& K⁺ is variable at cellular level during extreme hot period. Therefore, susceptible and tolerant animals were selected based on the physiological responses during hot period. Blood samples were collected from individuals, DNA was isolated. The 300 bp fragment of ATP1A1 gene was amplified by PCR and HRM genotyping was performed. The melting curves were analysed, differential temperature-shift plot showed three different genotypes in all the analysed samples. Out of the 135 samples, the distribution percentages were 55.56% (AA/blue), 33.33% (AC/red) and 11.11% (CC/green). The sequence variation revealed a SNP at 143rd position (A>C). The nucleotide diversity was 0.695 ± 0.403, 0.732 ± 0.424, 0.662 ± 0.433 and 0.687 ± 0.398 in Barbari, Jamunapari, Jakharna and Sirohi, respectively. The respiration rate (RR) was significantly different (P < 0.05) between AA and AC (t = 1.875, df = 38) genotype and heart rate (HR) was significantly different (P < 0.05) between AA and CC genotype. The relative expression pattern of ATP1A1 in SNP variants and non-variants animal tissues showed 19.09 and 6.93 fold higher than control (non-variant), respectively. Jamunapari showed higher fold value of ATP1A1 gene in comparison to Barbari, Jakharna and Sirohi. However, the heat stress-susceptible phenotype had significantly higher gene expression than stress-tolerant in all the breeds. The variation may be used as a marker for selection on the basis of physiological parameters and expression of ATP1A1 gene in goats indicating the specificity of expression in each tissue.

Proteome analysis after co-administration of clozapine or haloperidol to MK-801-treated rats

MK-801, a glutamergic, N-methyl-D-aspartate (NMDA)-receptor antagonist that mediates neurotransmission and has psychotomimetic properties, giving schizophrenia-like symptom. The objective of this study was to investigate the effects on the thalamic and cortical proteome of one typical (haloperidol) and one atypical (clozapine) antipsychotic drug in interaction with MK-801 in rats. Rats received subcutaneous injections of MK-801 or vehicle (controls) or MK-801 together with concurrent administration of haloperdol or clozapine for eight days. Protein samples from thalamus and cortex were analyzed with two-dimensional gel electrophoresis in combination with mass spectrometry. MK-801 induced alterations in the levels of three proteins in both cortex and thalamus. Clozapine reversed all the protein changes. Haloperidol reversed two. Both antipsychotics induced new protein changes in both cortex and thalamus not seen after MK-801-treatment by alone. In conclusion, the MK-801 animal model shows potential for investigation of different antipsychotic drugs and biochemical treatment effects in schizophrenia.

E3 ubiquitin ligase RNF2 interacts with the S6' proteasomal ATPase subunit and increases the ATP hydrolysis activity of S6'

We reported previously that the human RNF2 (RING finger protein 2) protein is an E3 ubiquitin ligase that interacts with the human ubiquitin-conjugating enzyme Hip-2/hE2-25K. In the present study, we show that RNF2 interacts with S6' ATPase, a subunit of the proteasomal 19 S regulatory complex. S6' interacts with RNF2 through its N-terminal RING domain, and RNF2 interacts with S6' through its C-terminal region. Interestingly, the RNF2-S6' interaction increases the ATP hydrolysis activity of the S6' protein. Moreover, S6' ATPase activity is highly increased in the presence of ubiquitinated proteins. The present study suggests that the E3 ubiquitin ligase RNF2 might have a dual function: facilitating the ubiquitination of its target substrates and recruiting the substrates to the proteasome. Furthermore, ATP hydrolysis in the E3/proteasome complex might act as an important signal for the protein degradation pathway.

Human immunodeficiency virus type 1 Tat binding protein-1 is a transcriptional coactivator specific for TR

The DNA-binding domain of nuclear hormone receptors functions as an interaction interface for other transcription factors. Using the DNA-binding domain of TRbeta1 as bait in the yeast two-hybrid system, we cloned the Tat binding protein-1 that was originally isolated as a protein binding to the human immunodeficiency virus type 1 Tat transactivator. Tat binding protein-1 has subsequently been identified as a member of the ATPase family and a component of the 26S proteasome. Tat binding protein-1 interacted with the DNA-binding domain but not with the ligand binding domain of TR in vivo and in vitro. TR bound to the amino-terminal portion of Tat binding protein-1 that contains a leucine zipper-like structure. In mammalian cells, Tat binding protein-1 potentiated the ligand-dependent transactivation by TRbeta1 and TRalpha1 via thyroid hormone response elements. Both the intact DNA-binding domain and activation function-2 of the TR were required for the transcriptional enhancement in the presence of Tat binding protein-1. Tat binding protein-1 did not augment the transactivation function of the RAR, RXR, PPARgamma, or ER. The intrinsic activation domain in Tat binding protein-1 resided within the carboxyl-terminal conserved ATPase domain, and a mutation of a putative ATP binding motif but not a helicase motif in the carboxyl-terminal conserved ATPase domain abolished the activation function. Tat binding protein-1 synergistically activated the TR-mediated transcription with the steroid receptor coactivator 1, p120, and cAMP response element-binding protein, although Tat binding protein-1 did not directly interact with these coactivators in vitro. In contrast, the N-terminal portion of Tat binding protein-1 directly interacted in vitro and in vivo with the TR-interacting protein 1 possessing an ATPase activity that interacts with the activation function-2 of liganded TR. Collectively, Tat binding protein-1 might function as a novel DNA-binding domain-binding transcriptional coactivator specific for the TR probably in cooperation with other activation function-2-interacting cofactors such as TR-interacting protein 1.

TBP-interacting protein TIP120A is a new global transcription activator with bipartite functional domains

BACKGROUND

We previously identified a TBP (TATA-binding protein)-interacting protein 120A (TIP120A) from rat liver nuclear extracts. TIP120A is thought to be a unique global transcription factor that can interact with TBP and can stimulate all classes of eukaryotic transcription.

RESULTS

We produced various truncation proteins of TIP120A to delineate its functional domains. TIP120A binds to TBP in the acidic amino acid-rich N-terminal region and in the leucine-rich C-terminal region. These regions exhibited an ability to stimulate basal transcription in vitro. In addition, these two regions overlap with domains that facilitate nonspecific DNA-binding of RNA polymerase II. The sequences of these two regions are significantly conserved among TIP120A homologues of eukaryotes.

CONCLUSIONS

TIP120A is a bipartite transcription factor, and both N-terminal and C-terminal regions exhibit TBP-binding activity and stimulate the basal transcription ability.

Tissue and cell distribution of a mammalian proteasomal ATPase, MSS1, and its complex formation with the basal transcription factors

The proteasome is an eukaryotic multi-subunit protease complex composed of one 20S core component and two 19S regulatory complexes. The regulatory complex contains 6 putative ATPases. We investigated tissue and cell distribution of one of these ATPases, MSS1 (mammalian suppressor of sgv1). MSS1 was ubiquitously present in rat tissues as was the 20S core component of proteasome. However, the ratio of MSS1 to 20S varied greatly among tissues and MSS1 was concentrated in the thymus. Glycerol gradient sedimentation analysis revealed that MSS1 is included in protein complexes whose density is lighter than that of the proteasome. MSS1 was distributed in mammalian cells ubiquitously, while proteasome was rather concentrated in the nuclei. Hence, a novel molecular status of MSS1 distinct from proteasome is implicated. Interestingly, multiple basal transcription factors for RNA polymerase II, including TBP, TFIIB, TFIIH, and TFIIF, were found to be associated with MSS1. These results suggest that MSS1, in addition to proteolysis, plays a role in DNA metabolism including transcriptional regulation.

The 26S proteasome: a molecular machine designed for controlled proteolysis

In eukaryotic cells, most proteins in the cytosol and nucleus are degraded via the ubiquitin-proteasome pathway. The 26S proteasome is a 2.5-MDa molecular machine built from approximately 31 different subunits, which catalyzes protein degradation. It contains a barrel-shaped proteolytic core complex (the 20S proteasome), capped at one or both ends by 19S regulatory complexes, which recognize ubiquitinated proteins. The regulatory complexes are also implicated in unfolding and translocation of ubiquitinated targets into the interior of the 20S complex, where they are degraded to oligopeptides. Structure, assembly and enzymatic mechanism of the 20S complex have been elucidated, but the functional organization of the 19S complex is less well understood. Most subunits of the 19S complex have been identified, however, specific functions have been assigned to only a few. A low-resolution structure of the 26S proteasome has been obtained by electron microscopy, but the precise arrangement of subunits in the 19S complex is unclear.

Mouse proteasomal ATPases Psmc3 and Psmc4: genomic organization and gene targeting

PSMC3 and PSMC4, components of the 19S complex of the 26S proteasome, show a significant degree of amino acid similarity, especially in the conserved ATPase domain (CAD). In this study, we characterized the mouse Psmc3 and Psmc4 genes. The genomic structures of both genes showed a significant degree of similarity. The Psmc3 gene was composed of 12 coding exons, whereas the Psmc4 gene had 11 exons. Exons encoding the leucine zipper domain and CAD were identical in number between the Psmc3 and Psmc4 genes. The Psmc3 gene mapped to mouse chromosome 2, whereas Psmc4 mapped to chromosome 7. We further addressed the biological roles of Psmc3 and Psmc4 through the generation of gene targeted mice. Both Psmc3- and Psmc4-deficient mice died before implantation, displaying defective blastocyst development. These findings indicate that Psmc3 and Psmc4 have similar and essential roles in early embryogenesis and further that both ATPases have noncompensatory functions in vivo.

Growth suppression of Escherichia coli by induction of expression of mammalian genes with transmembrane or ATPase domains

Growth inhibition of Escherichia coli host cells is frequently observed when some mammalian genes are induced to express exogenously. To find common features of these mammalian genes, an assay was designed for the isolation of these genes which show growth-inhibitory effect on E. coli by induction of expression. Of 38,000 clones derived from a mouse brain cDNA library, 64 cDNA clones were systematically selected out by this method, of which 45 clones had putative open reading frames encoding proteins with putative membrane-associated regions or ATP-binding/ATPase activities. These results show that a fraction of membrane-associated proteins or ATP-binding/ATPase genes can be isolated from cDNA libraries by our simple method.

Differential gene expression in male and female rat lenses undergoing cataract induction by transforming growth factor-beta (TGF-beta)

Epidemiologic studies in humans as well as immunohistologic studies in animals have demonstrated significant sex differences in the propensity to develop cataract. Several studies suggest that estrogen may play a protective role against cataractogenesis. Indeed, male and ovariectomized female rat lenses have a greater susceptibility to cataract induced by transforming growth factor-beta (TGF-beta) than do normal female lenses. However, in spite of the current evidence that estrogen may play a pivotal role in cataractogenesis, the molecular mechanisms behind this phenomenon are largely undetermined. Our study utilized the differential display procedure to examine gene up- and down-regulation in male, normal female and ovariectomized female rat lenses exposed to TGF-beta. Male and normal female rat lenses were cultured with or without 0.15 ng ml(-1)TGF-beta. Lenses were then harvested, and total RNA was isolated for analysis by reverse-transcriptase differential display. Differentially expressed mRNAs were subcloned, sequenced and identified through GenBank database searches. The original experiment was repeated with the addition of ovariectomized female TGF-beta(+/-) conditions, and all differential patterns of gene expression were verified using Northern blot and RT-PCR analysis. Screening of approximately 12% of the mRNA population led to the identification of 27 differentially expressed cDNAs. Notably, strong gender differences were found in expression levels of gammaB-crystallin. In addition, proteasome Z subunit was up-regulated in TGF-beta-treated male and ovariectomized female lenses, but was down-regulated in TGF-beta-treated normal female lenses. This pattern of expression is consistent with the increased susceptibility of male and ovariectomized lenses to TGF-beta-induced cataract. We conclude that differential display is a useful and expedient method for analysing changes in gene expression in the lens. Structural and functional studies of the genes identified in this study may further elucidate mechanisms underlying the TGF-beta-induced cataract formation and differential rates of cataractogenesis in males vs females. In particular, our data suggest that the role of proteasome Z subunit in TGF-beta-induced anterior subcapsular cataract warrants further investigation.

A 220-kDa activator complex of the 26 S proteasome in insects and humans. A role in type II programmed insect muscle cell death and cross-activation of proteasomes from different species

The S10b (SUG2) ATPase cDNA has been cloned by reverse transcription-polymerase chain reaction/rapid amplification of cDNA ends from mRNA of intersegmental muscles of the tobacco horn moth (Manduca sexta). The S10b ATPase is a component of the 26 S proteasome, and its concentration and that of its mRNA increase dramatically during development in a manner similar to other ATPases of the 19 S regulator of the 26 S proteasome. The S10b and S6' (TBP1) ATPases are also present in a complex of approximately 220 kDa in intersegmental muscles. The 220-kDa complex markedly activates (2-10-fold) the 26 S proteasome, even when bound to anti-S10b antibodies immobilized on Sepharose, and increases in concentration approximately 5-fold like the 26 S proteasome in the intersegmental muscles in preparation for the programmed death of the muscle cells. A similar activator complex is present in human brain and placenta. Free activator complexes cross-activate: the Manduca complex activates rat skeletal muscle 26 S proteasomes, and the placental complex activates Manduca 26 S proteasomes. The placental activator complex contains S10b and S6', but not p27. This 220-kDa activator complex has been evolutionarily conserved between species from insect to man and may have a fundamental role in proteasome regulation.

Multiple mammalian proteasomal ATPases, but not proteasome itself, are associated with TATA-binding protein and a novel transcriptional activator, TIP120

BACKGROUND

SUG1 belongs to proteasomal ATPase. Previous studies have demonstrated that SUG1 is associated with TBP. It is assumed to be involved in transcriptional regulation in addition to proteolysis. In this study, we investigated the association of mammalian SUG1 with TBP in more detail.

RESULTS

Pull-down experiments with TBP revealed multiple TBP-interacting proteins (TIPs) that were recovered dependent upon the presence of C-terminal conserved domain of TBP. By 2-D electrophoresis, we identified SUG1 in TIPs. By using far-Western analysis, we identified two proteins that could directly bind to TBP: SUG1 and another proteasomal ATPase (S4). Protein microsequencing and Western blotting identified all the remaining proteasomal ATPases (MSS1, TBP1, TBP7, and SUG2) in the TIP preparations. We present evidence that TBP and at least SUG1, MSS1, and S4 form a complex in the cell. However, no evidence of association of TBP with the 26S proteasome or its 19S regulatory unit was obtained. The molecular mass of the TBP/ATPases-complex, which also included a novel transcription regulatory factor, TIP120, was estimated to be approximately 800 kDa.

CONCLUSION

These results suggest that there is a novel multisubunit complex containing TBP and proteasomal ATPases. Based on our findings, we hypothesize that proteasomal ATPases are involved in transcriptional regulation in addition to proteolysis.

Identification of cDNAs induced by the tumor suppressor Tsc2 gene using a conditional expression system in Tsc2 mutant (Eker) rat renal carcinoma cells

Alteration of the rat homologue of the tuberous sclerosis 2 (TSC2) gene is associated with dominantly inherited cancer in the Eker rat model, indicating a tumor suppressor nature. The ability of Tsc2 to activate signal transduction and transcription suggests that genes induced by Tsc2 may mediate its biological roles. Using a subtractive hybridization approach in combination with tetracycline operator systems, we identified a set of downstream genes affected by Tsc2. Regulated expression of wild-type Tsc2 gene in Eker renal carcinomas (RCs) resulted in marked expression of cell arrest or programmed cell-death-related genes and stress-induced genes. Thus, the data suggest that Tsc2 might contribute to regulation of the cell cycle and cell survival.

Phosducin-like protein (PhLP), a regulator of G beta gamma function, interacts with the proteasomal protein SUG1

Phosducin-like protein (PhLP) and phosducin are highly homologous proteins that interact with the beta gamma subunits of guanine nucleotide binding proteins. While phosducin has a well-characterized role in retinal signal transduction, PhLP function remains unclear. To further understand the function of PhLP, we have examined other potential protein:protein interactions with PhLP using the yeast two-hybrid system. PhLP was found to interact with a mouse homologue of the yeast SUG1, a subunit of the 26S proteasome which may also indirectly modulate transcription. This interaction was further confirmed by an in vitro binding assay and co-immunoprecipitation of the two proteins in overexpression studies. Inhibition of proteasome function by lactacystin led to accumulation of high molecular weight, ubiquitin-immunoreactive protein precipitated by PhLP antiserum. We suggest that PhLP/SUG1 interaction may target PhLP for proteasomal degradation.

Sequence analysis of the AAA protein family

The AAA protein family, a recently recognized group of Walker-type ATPases, has been subjected to an extensive sequence analysis. Multiple sequence alignments revealed the existence of a region of sequence similarity, the so-called AAA cassette. The borders of this cassette were localized and within it, three boxes of a high degree of conservation were identified. Two of these boxes could be assigned to substantial parts of the ATP binding site (namely, to Walker motifs A and B); the third may be a portion of the catalytic center. Phylogenetic trees were calculated to obtain insights into the evolutionary history of the family. Subfamilies with varying degrees of intra-relatedness could be discriminated; these relationships are also supported by analysis of sequences outside the canonical AAA boxes: within the cassette are regions that are strongly conserved within each subfamily, whereas little or even no similarity between different subfamilies can be observed. These regions are well suited to define fingerprints for subfamilies. A secondary structure prediction utilizing all available sequence information was performed and the result was fitted to the general 3D structure of a Walker A/GTPase. The agreement was unexpectedly high and strongly supports the conclusion that the AAA family belongs to the Walker superfamily of A/GTPases.

SUG1, a component of the 26 S proteasome, is an ATPase stimulated by specific RNAs

SUG1 is an integral component of the 26 S proteasome. Belonging to a novel putative ATPase family, it shares four conserved motifs characteristic of ATP-dependent DNA/RNA helicases. Recombinant rat SUG1 (rSUG1) produced in Escherichia coli was highly purified and characterized in terms of its biochemical properties. The rSUG1 exhibited a Mg2+-dependent ATPase activity. The Km for ATP and Vmax of rSUG1 were 35 microM and 7 pmol of ATP/min/microg of protein, respectively. Both ATPase activity to release [32P]monophosphate and [32P]ATP-labeling activity were coordinately affected by cold ATP severely, GTP and UTP moderately, and CTP little. Interestingly, the rSUG1 ATPase activity was stimulated by poly(U) and poly(C), but not by poly(A), poly(G), or by any forms of DNAs tested. A UV cross-linking assay also indicated poly(U)- and poly(C)-stimulated labeling of rSUG1 with [alpha-32P]ATP. Moreover, the ATPase activity was facilitated by cellular poly(A)+ RNA, but not by poly(A)- RNA. RNA transcribed in vitro from cDNA encoding a b-Zip protein could stimulate the ATPase activity. This is the first report to demonstrate a specific RNA requirement for ATPase with respect to the proteasomal ATPases. Our present work suggests that SUG1 can specifically interact with protein-coding RNA (mRNA) and play some roles in mRNA metabolism.