The border fresidues of the dihydrofolate reductase domain inEscherichia coli β-galactosidase correspond to the positions of introns 1 and 5 of dihydrofolate reductase of chicken

Summary In-galactosidase ofEscherichia coli residues 820–934 are similar to residues in dihydrofolate reductase ofE. coli. Dihydrofolate reductase ofE. coli and chicken are also similar and have identical tertiary structures. I used the similarity of the three-dimensional structure of prokaryotic and eukaryotic dihydrofolage reductases to align the chicken dihydrofolate reductase and the similar residues of-galactosidase. The positions of introns 1 and 5 of the chicken dihydrofolate reductase gene correspond exactly to the start and the end of the dihydrofolate reductase-like domain in the-galactosidase polypeptide chain. This equivalence of intron positions in a eukaryotic gene and domain structure in a prokaryotic protein was interpreted as evidence for a common origin of both genes.     

Yeast adenylate kinase is active simultaneously in mitochondria and cytoplasm and is required for non-fermentative growth

Displacement of the single copy structural gene for yeast adenylate kinase (long version) by a disrupted nonfunctional allele is tolerated in haploid cells. Since adenylate kinase activity is a pre-requisite for cell viability, the survival of haploid disruption mutants is indicative of the presence of an adenylate kinase isozyme in yeast, capable of forming ADP from AMP and, thus, of complementing the disrupted allele. The phenotype of these disruption mutants is pet, showing that complementation occurs only under fermentative conditions. Even on glucose, growth of the disruption mutants is slow. Adenylate kinase activity is found both in mitochondria and cytoplasm of wild type yeast. The disruption completely destroys the activity in mitochondria, whereas in the cytoplasmic fraction about 10% is retained. An antibody raised against yeast mitochondrial adenylate kinase recognizes cross-reacting material both in mitochondria and cytoplasm of the wild type, but fails to do so in each of the respective mutant fractions. The data indicate that yeast adenylate kinase (long version, AKY2) simultaneously occurs and is active in mitochondria and cytoplasm of the wild type. Nevertheless, it lacks a cleavable pre-sequence for import into mitochondria. A second, minor isozyme, encoded by a separate gene, is present exclusively in the cytoplasm.     

Disruption of the autism-related gene Pak1 causes stereocilia disorganization,hair cell loss,and deafness in mice

Several clinical studies have reported that hearing loss is correlated with autism in children. However, little is known about the underlying mechanism between hearing loss and autism. p21-activated kinases(PAKs)are a family of serine/threonine kinases that can be activated by multiple signaling molecules, particularly the Rho family of small GTPases. Previous studies have shown that Pak1 mutations are associated with autism. In the present study, we take advantage of Pak1 knockout(Pak1à/à) mice to investigate the role of PAK1 in hearing function. We find that PAK1 is highly expressed in the postnatal mouse cochlea and that PAK1 deficiency leads to hair cell(HC) apoptosis and severe hearing loss. Further investigation indicates that PAK1 deficiency downregulates the phosphorylation of cofilin and ezrin-radixin-moesin and the expression of b II-spectrin, which further decreases the HC synapse density in the basal turn of cochlea and disorganized the HC stereocilia in all three turns of cochlea in Pak1à/àmice. Overall, our work demonstrates that the autism-related gene Pak1 plays a crucial role in hearing function. As the first candidate gene linking autism and hearing loss, Pak1 may serve as a potential target for the clinical diagnosis of autism-related hearing loss.     

Analysis of a Candida albicans gene that encodes a novel mechanism for resistance to benomyl and methotrexate

Summary The pathogenic yeast, Candida albicans, is insensitive to the anti-mitotic drug, benomyl, and to the dihydrofolate reductase inhibitor, methotrexate. Genes responsible for the intrinsic drug resistance were sought by transforming Saccharomyces cerevisiae, a yeast sensitive to both drugs, with genomic C. albicans libraries and screening on benomyl or methotrexate. Restriction analysis of plasmids isolated from benomyl- and methotrexate-resistant colonies indicated that both phenotypes were encoded by the same DNA fragment. Sequence analysis showed that the fragments were nearly identical and contained a long open reading frame of 1694 bp (ORF1) and a small ORF of 446 bp (ORF2) within ORF1 on the opposite strand. By site-directed mutagenesis, it was shown that ORF1 encoded both phenotypes. The protein had no sequence similarity to any known proteins, including -tubulin, dihydrofolate reductase, and the P-glycoprotein of the multi-drug resistance family. The resistance gene was detected in several C. albicans strains and in C. stellatoidea by DNA hybridization and by the polymerase chain reaction.     

Yeast Pak1 kinase associates with and activates Snf1

Members of the Snf1/AMP-activated protein kinase family are activated under conditions of nutrient stress by a distinct upstream kinase. Here we present evidence that the yeast Pak1 kinase functions as a Snf1-activating kinase. Pak1 associates with the Snf1 kinase in vivo, and the association is greatly enhanced under glucose-limiting conditions when Snf1 is active. Snf1 kinase complexes isolated from pak1Delta mutant strains show reduced specific activity in vitro, and affinity-purified Pak1 kinase is able to activate the Snf1-dependent phosphorylation of Mig1 in vitro. Purified Pak1 kinase promotes the phosphorylation of the Snf1 polypeptide on threonine 210 within the activation loop in vitro, and an increased dosage of the PAK1 gene causes increased Snf1 threonine 210 phosphorylation in vivo. Deletion of the PAK1 gene does not produce a Snf phenotype, suggesting that one or more additional protein kinases is able to activate Snf1 in vivo. However, deletion of the PAK1 gene suppresses many of the phenotypes associated with the deletion of the REG1 gene, providing genetic evidence that Pak1 activates Snf1 in vivo. The closest mammalian homologue of yeast Pak1 kinase, calcium-calmodulin-dependent protein kinase kinase beta, may play a similar role in mammalian nutrient stress signaling.     

Phosphorylation of the 24p3 protein secreted from mouse uterus in vitro and in vivo

The 24p3 protein is a 25 KDa glycoprotein, having been purified from mouse uterine fluid. Thr⁵⁴, Ser⁸⁸, and Thr¹²⁸/Ser¹²⁹ on the protein molecule were predicted to be the phosphorylation site of casein kinase II, protein kinase C, and cAMP-dependent protein kinase, respectively. Incorporation of phosphate to this protein from [-³²P]-ATP was tested in the solution suitable for the three kinases. Neither casein kinase II nor cAMP-dependent protein kinase reacted to the 24p3 protein; however, protein kinase C demonstrated phosphorylation to this protein. This phosphorylation may be competing with a polypeptide segment: Arg⁷⁹-Tyr-Trp-Ilu-Arg-Thr-Phe-Val-Pro-Ser⁸⁸-Ser-Arg-Ala-Gly-Gln-Phe-Thr-Leu-Gly⁹⁷ in the 24p3 protein molecule. To support this theory, Ser⁸⁸ is a phosphorylation site of protein kinase C on 24p3 protein. The enzyme kinetic parameter, based on the Michaelis-Menten equation, determined Km to be 2.96 M in the phosphorylation of 24p3 protein by the kinase. Both of the phosphorylated and dephosphorylated form of 24p3 protein can enhance the cAMP-dependent protein kinase activity in vitro. In addition, this experiment will show for the first time that serine-phosphorylated 24p3 protein exists in mouse uterine tissue.     

A mutation in Aspergillus nidulans which affects the regulation of nitrite reductase and is tightly linked to its structural gene.

Summary The selection of nis-5, a mutation which is tightly linked to the structural genes for nitrate reductase (niaD) and nitrite reductase (niiA) but which only affects nitrite reductase activities, is described. nis-5 single mutants have only 40% of the wild type activity of nitrite reductase after induction by nitrate and, for this reason, grow poorly on nitrate and nitrite. Nitrate reductase activity is not affected, and nis-5 is shown to complement with a niaD^- mutation but not with a niiA^- mutation.When grown without inducer, nis-5 strains have higher than the non-induced wild type activity of nitrite reductase. This low, constitutive activity is insensitive to repression by ammonium. These facts explain why the nis-5 mutation weakly suppresses many nirA^- and areA^r mutations for utilization of nitrite.Three of the possible explanations of this unusual phenotype are considered. Studies of nitrite reductase in cell-free extracts provided no evidence for the already unlikely possibility that nis-5 is a structural gene mutation resulting in the observed phenotype because of alteration in the catalytic activity and/or stability of the nitrite reductase.A more plausible explanation is that it defines a receptor site for either the nirA gene product and/or the areA gene product. However, no evidence for this has yet been obtained from a study of double mutants carrying nis-5 and areA or nirA mutations.A third possibility is that nis-5 creates a new, but inefficient promoter or initiator, which is not subject to the normal control systems (and therefore causes constitutive, deprepressed synthesis) but whose physical presence reduces maximal enzyme synthesis. The presence of a translocation in nis-5 strains suggests a means by which niiA could come to be under the control of another promoter/initiator.     

The cleavable prepiece of an imported mitochondrial protein is sufficient to direct cytosolic dihydrofolate reductase into the mitochondrial matrix

The cleavable prepiece of the precursor to yeast cytochrome c oxidase subunit IV (an imported mitochondrial protein) was attached to the amino-terminus of mouse dihydrofolate reductase (a cytosolic protein) by gene fusion. The resulting fusion protein was imported into the matrix of isolated, energized yeast mitochondria and cleaved to a polypeptide whose size was similar to that of authentic dihydrofolate reductase.     

The adenylate kinase family in yeast: identification of URA6 as a multicopy suppressor of deficiency in major AMP kinase.

The gene URA6 encoding uridylate kinase (UK) from Saccharomyces cerevisiae was isolated as a multicopy suppressor of the respiratory-deficient phenotype of an S. cerevisiae mutant defective in the gene AKY2 encoding AMP kinase (AK). The URA6 gene also restored temperature resistance to two different temperature-sensitive mutations in the gene encoding Escherichia coli AK. By contrast, the gene encoding UK of Dictyostelium discoideum on a multicopy yeast shuttle plasmid, expressed under control of the constitutive yeast AKY2 promoter, failed to complement the deficiency in yeast, although such transformants expressed high UK activity. We show that yeast UK exerts significant AK activity which is responsible for the complementation and is absent in the analogous enzyme from D. discoideum. Since UK also significantly phosphorylates CMP (but not GMP), it must be considered an unspecific short-form nucleoside monophosphate kinase. Wild-type mitochondria lack UK activity, but import AKY2. Since multicopy transformation with URA6 heals the Pet- phenotype of AKY2 disruption mutants, the presence of AKY2 in the mitochondrial intermembrane space is not required to maintain respiratory competence. However, furnishing UK with the bipartite intermembrane space-targeting presequence of cytochrome c1 improves the growth rates of AKY2 mutants with nonfermentable substrates, suggesting that AK activity in mitochondria is helpful, though not essential for oxidative growth.     

The identification of a Caenorhabditis elegans homolog of p34cdc2 kinase

We have identified a Caenorhabditis elegans homolog of p34^cdc2 kinase. The C. elegans homolog, ncc-1, is -60% identical to p34^cdc2 of Homo sapiens. When expressed from a constitutive yeast promoter, ncc-1 is capable of complementing a conditional lethal mutation in the CDC28 gene of Saccharomyces cerevisiae, indicating that this C. elegans homolog can properly regulate the cell cycle.     

Structure and expression of the Lyt-3 agene of C.AKR mice

The mouse Lyt-3 ^agene, which encodes the Lyt-3.1 T-cell surface alloantigen of the C.AKR strain, has been cloned, and the nucleotide sequence of its exons and more than 2 kb of 5 flanking sequence have been determined. The gene extends over approximately 16 kb of DNA and consists of six exons encoding leader, leader plus V-like domain, membrane-proximal, transmembrane, and cytoplasmic domains. The only difference between the coding region of the Lyt-3 ^agene and the cDNA sequences reported for Lyt-3 ^b(Nakauchi et al. 1987, Panaccio et al. 1987) is at position 77 of the mature protein where Lyt-3 ^aencodes serine and Lyt-3 ^bencodes arginine. This substitution must therefore be the basis for the serological distinction between the Lyt-3.1 and Lyt-3.2 alloantigens. Potential TATA and CAAT sequences, two Sp1 protein binding sites, two extended repeats of the dinucleotide, CA, a number of short inverted repeats, and an inverted segment of the mouse B1 repetitive sequence are found 5 to the Lyt-3 ^agene. Two consensus poly-A addition signals and a complete copy of the mouse B1 sequence are found 3 to the gene. Both B1-related regions are flanked by short direct repeats suggesting that they arose by an insertional mechanism. Cotransfection of the Lyt-3 ^agene together with a cloned Lyt-2 ^agene resulted in expression of both Lyt-2 and Lyt-3.1 on the surface of Ltk^– and BW5147 cells. Transfection of the Lyt-3 ^agene without Lyt-2 ^aled to expression of Lyt-3-related cellular RNA but did not result in surface expression of Lyt-3.1, suggesting that the Lyt-3 glycoprotein is not expressed on the cell surface in the absence of Lyt-2.     

p21-activated kinase 1 determines stem-like phenotype and sunitinib resistance via NF-κB/IL-6 activation in renal cell carcinoma

The p21-activated kinase 1 (PAK1), a serine/threonine kinase that orchestrates cytoskeletal remodeling and cell motility, has been shown to function as downstream node for various oncogenic signaling pathways to promote cell proliferation, regulate apoptosis and accelerate mitotic abnormalities, resulting in tumor formation and invasiveness. Although alterations in PAK1 expression and activity have been detected in various human malignancies, its potential biological and clinical significance in renal cell carcinoma (RCC) remains obscure. In this study, we found increased PAK1 and phosphorylated PAK1 levels in tumor tissues according to TNM stage progression. Elevated phosphorylated PAK1 levels associated with progressive features and indicated unfavorable overall survival (OS) as an independent adverse prognosticator for patients with RCC. Moreover, PAK1 kinase activation with constitutive active PAK1 mutant T423E promoted growth, colony formation, migration, invasion and stem-like phenotype of RCC cells, and vice versa, in PAK1 inhibition by PAK1 kinase inactivation with specific PAK1 shRNA, dead kinase PAK1 mutant K299R or allosteric inhibitor IPA3. Stem-like phenotype due to sunitinib administration via increased PAK1 kinase activation could be ameliorated by PAK1 shRNA, PAK1 mutant K299R and IPA3. Furthermore, nuclear factor-κB (NF-κB)/interleukin-6 (IL-6) activation was found to be responsible for PAK1-mediated stem-like phenotype following sunitinib treatment. Both IL-6 neutralizing antibody and IPA3 administration enhanced tumor growth inhibition effect of sunitinib treatment on RCC cells in vitro and in vivo. Our results unraveled that oncogenic activation of PAK1 defines an important mechanism for maintaining stem-like phenotype and sunitinib resistance through NF-κB/IL-6 activation in RCC, lending PAK1-mediated NF-κB/IL-6 activation considerable appeal as novel pharmacological therapeutic targets against sunitinib resistance.Arising from the renal tubular epithelial cells, renal cell carcinoma (RCC) accounts for ∼4% of all malignant diseases and 90% of renal malignancies in adults.^{1, 2} Although most RCCs are detected incidentally by the widespread use of abdominal imaging examinations for unrelated symptoms, ∼25–30% of patients are still diagnosed with metastatic disease.³ In addition, 20% of patients with localized RCC undergoing radical surgery experience relapse and develop metastatic RCC (mRCC) during follow-up.^{4, 5} Unfortunately, mRCC is refractory chemotherapy and radiotherapy with a 5-year survival rate of ^<10%.⁶ Immunotherapy with interleukin 2 (IL-2) and/or interferon-α (IFN-α) is the standard treatment for mRCC and has limited efficacy by substantial number of adverse effects.⁷ Despite the significant improvement in mRCC treatment with antiangiogenesis drugs such as sunitinib and sorafinib, its duration of therapeutic effect is often short.⁸ Clearly, this dire situation mandates better understanding of the molecular mechanism of RCC carcinogenesis so that novel targets could be identified for effective therapies.The p21-activated kinases (PAKs) are a family of conversed nonreceptor serine/threonine kinases that function as key regulators of pleiotropic physiological processes including cytoskeleton dynamics and cell polarity, motility, invasion and survival.⁹ Currently, 6 PAKs have been classified into group I PAKs (PAK1–3) and group II PAKs (PAK4–6) on the basis of structural and functional similarities.¹⁰ As the best-characterized member of the PAK family, PAK1 was identified as a protein that interacts with cell division cycle 42 (CDC42) and RAC1.¹¹ In addition to CDC42 and RAC1, other signaling including PI3K/Akt can also lead to the activation of PAK1.¹² PAK1 phosphorylation at threonine-423 (T423) by upstream signaling has been linked to its activation, as substitution of the acidic residue glutamic acid (E) at this site yields a constitutively active PAK1 T423E enzyme.¹³ Activation and localization of PAK1 lead to mediated physiological effects of downstream signaling via activating additional kinases and other effectors by phosphorylating them at specific serine and threonine residues or through protein–protein interaction.⁹PAK1 expression and activity are upregulated in different human tumors, such as breast, lung, colorectal, liver and kidney cancers,^{14, 15, 16} and are associated with tumor invasiveness, metastasis and poor prognosis. Besides, PAK1 is also a component of various signaling pathways, including mitogen-activated protein kinase (MAPK), JUN N-terminal Kinase (JNK) and nuclear factor-κB (NF-κB) pathways, all of which are believed to be important in carcinogenesis.⁹ Moreover, PAK1 has been found to play critical roles in anoikis resistance that facilitates metastasis by allowing tumor cells to survive following detachment from the matrix in original tissue and travelling to distant sites. Resistance to anoikis program represents a molecular basis for cancer progression and drug resistance.^{15, 17} The regulation of phosphorylation and function of Snail by PAK1 signaling kinase may contribute to the process of epithelial–mesenchymal transition (EMT) that plays a pivotal role in the conversion of early-stage tumors into invasive malignancies.¹⁸ EMT induction in cancer cells results in the acquisition of stem-like phenotype and drug resistance trait.^{19, 20}Based on these previous findings, we hypothesized that PAK1-mediated stem-like phenotype might induce sunitinib resistance and involve in RCC tumor progression. Our present study revealed that upregulation of PAK1 kinase activity conferred stem-like phenotype via NF-κB/IL-6 activation in vitro and in vivo that defines a novel potential mechanism underlying tumor metastasis and sunitinib resistance in RCC patients.     

Stable yeast transformation with chimeric plasmids using a 2 micron-circular DNA-less strain as a recipient.

Summary By using two chimeric plasmids containing yeast URA3 gene as a selection marker and 2 m yeast DNA linked to the bacterial plasmid pCR1, a yeast strain devoid of any 2 m DNA sequence was transformed. Recovery in E. coli of plasmids from yeast transformants showed that the 2 m-less strain was able to maintain the chimeric plasmids as autonomous replicons, with very infrequent plasmid recombination. Hybridization experiments gave no evidence for integration of the URA3 DNA sequence in the chromosomal DNA. The transformed clones showed a high stability of the ura⁺ character during vegetative multiplication, even in the absence of selective pressure. The specific activity of orotidine 5 monophosphate decarboxylase (coded by the URA3 gene) was 5 to 10 fold higher than in the wild type.These features should offer new possibilities for cloning with yeast.     

Genetic Evidence for Pak1 Autoinhibition and Its Release by Cdc42

Pak1 protein kinase of Schizosaccharomyces pombe, a member of the p21-GTPase-activated protein kinase (PAK) family, participates in signaling pathways including sexual differentiation and morphogenesis. The regulatory domain of PAK proteins is thought to inhibit the kinase catalytic domain, as truncation of this region renders kinases more active. Here we report the detection in the two-hybrid system of the interaction between Pak1 regulatory domain and the kinase catalytic domain. Pak1 catalytic domain binds to the same highly conserved region on the regulatory domain that binds Cdc42, a GTPase protein capable of activating Pak1. Two-hybrid, mutant, and genetic analyses indicated that this intramolecular interaction rendered the kinase in a closed and inactive configuration. We show that Cdc42 can induce an open configuration of Pak1. We propose that Cdc42 interaction disrupts the intramolecular interactions of Pak1, thereby releasing the kinase from autoinhibition.     

Biochemical properties of rice adenylate kinase and subcellular location in plant cells

Previously, we characterized nucleotide sequences of two cDNAs encoding adenylate kinase from rice plants (Oryza sativa L.). Each cDNA (Adk-a or Adk-b) was cloned into the expression vector pET 11d-GST to produce GST-AK fusion proteins in Escherichia coli. Recombinant proteins were cleaved by thrombin, and GST-free adenylate kinase proteins were obtained. Enzyme activity profiles of different pH and inhibition effects to the enzyme by Ap5A (adenosine-5-pentaphospho-5-adenosine) indicates that both adenylate kinase proteins have similar biochemical characteristics. Among the nucleoside monophosphates (AMP, CMP, GMP and UMP) investigated, only AMP reacted with ATP. Furthermore, using the antiserum against the rice adenylate kinase proteins, the cellular location of adenylate kinase proteins was examined by immunomicroscopic analysis in combination with a subcellular fractionation method. The results indicated that adenylate kinase proteins were distributed largely in cytosol of rice cells.Abbreviations AK adenylate kinase - IPTG isopropylthio--D-galactoside - Ap5A adenosine-5-pentaphospho-5-adenosine - PEP phosphoenol pyruvate - GST glutathione S-transferase - BSA bovine serum albumin - FITC fluorescein isothiocyanate     

In vivo import of yeast adenylate kinase into mitochondria affected by site-directed mutagenesis.

Site-directed mutagenesis and deletions were used to study mitochondrial import of a major yeast adenylate kinase, Aky2p. This enzyme lacks a cleavable presequence and occurs in active and apparently unprocessed form both in mitochondria and cytoplasm. Mutations were applied to regions known to be surface-exposed and to diverge between short and long isoforms. In vertebrates, short adenylate kinase isozymes occur exclusively in the cytoplasm, whereas long versions of the enzyme have mitochondrial locations. Mutations in the extra loop of the yeast (long-form) enzyme did not affect mitochondrial import of the protein, whereas variants altered in the central, N- or C-terminal parts frequently displayed increased or, in the case of a deletion of the 8 N-terminal triplets, decreased import efficiencies. Although the N-terminus is important for targeting adenylate kinase to mitochondria, other parameters like internal sequence determinants and folding velocity of the nascent protein may also play a role.