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Sökning: L773:0300 9084 OR L773:1638 6183

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1.
  • Abdulkarim, Farhad, et al. (författare)
  • Missense substitutions lethal to essential functions of EF-Tu
  • 1991
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 73:12, s. 1457-1464
  • Tidskriftsartikel (refereegranskat)abstract
    • We have used a simple selection and screening method to isolate function defective mutants of EF-Tu. From 28 mutants tested, 12 different missense substitutions, individually lethal to some essential function of EF-Tu, were identified by sequencing. In addition we found a new non-lethal missense mutation. The frequency of isolation of unique mutations suggests that this method can be used to easily isolate many more. The lethal mutations occur in all three structural domains of EF-Tu, but most are in domain II. We aim to use these mutants to define functional domains on EF-Tu.
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2.
  • Andersson, Rolf E, et al. (författare)
  • Antibacterial activity of plantaricin SIK-83, a bacteriocin produced by Lactobacillus plantarum
  • 1988
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 70:3, s. 381-390
  • Tidskriftsartikel (refereegranskat)abstract
    • Lactobacillus plantarum SIK-83 produces a bacteriocin, designated plantaricin SIK-83, which inhibits 66 of 68 lactic acid bacteria from the genera Lactobacillus, Leuconostoc, Pediococcus and Streptococcus. A 500-fold dilution of L. plantarum SIK-83 MRS culture supernatant with phosphate buffer was sufficient to kill 105 cells/ml of Pediococcus pentosaceus within 120s. The killing of a sensitive population followed exponential kinetics. It shown that the bacteriocin binds specifically to sensitive cells but not to nonsensitive lactic acid bacteria, the producer strain or Gram-negative bacteria. Sensitive cells, after exposure to the bacteriocin, could be rescued by treatment with proteolytic enzymes. In buffer, plantaricin SIK-83 was adsorbed to the cell surface almost immediately, and morphological lesions were observed within 2 h after the cells were exposed to the bacteriocin. The lethal mode of action appeared to be due to damage to the cell membrane, resulting in cell lysis, which was detected by electron microscopy and by determination of released intracellular components. © 1988.
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3.
  • Bilgin, Neş'e, et al. (författare)
  • Mutations in ribosomal proteins L7/L12 perturb EF-G and EF-Tu functons
  • 1988
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 70:5, s. 611-618
  • Tidskriftsartikel (refereegranskat)abstract
    • In vitro cycling rates of E. coli ribosomes and of elongation factors EF-Tu and EF-G have been obtained and these are compatible with translation rates in vivo. We show that the rate of translocation is faster than 50 s-1 and therefore that the EF-G function is not a rate limiting step in protein synthesis. The in vivo phenotype of some L7/L12 mutants could be accounted for by perturbed EF-Tu as well as EF-G functions. The S12 mutants that we studied were, in contrast, only perturbed in their EF-Tu function, while their EF-G interaction was not impaired in relation to wild type ribosomes.
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4.
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5.
  • Karlsson, E., et al. (författare)
  • Snake toxins with high selectivity for subtypes of muscarinic acetylcholine receptors
  • 2000
  • Ingår i: Biochimie. - 0300-9084 .- 1638-6183. ; 82:9-10, s. 793-806
  • Tidskriftsartikel (refereegranskat)abstract
    • There are five subtypes of muscarinic acetylcholine receptors (M-1 to M-5) which control a large number of physiological processes, such as the function of heart and smooth muscles, glandular secretion, release of neurotransmitters, gene expression and cognitive functions as learning and memory. A selective ligand is very useful for studying the function of a subtype in presence of other subtypes, which is the most common situation, since a cell or an organ usually has several subtypes. There are many non-selective muscarinic ligands, but only few selective ones. Mambas, African snakes of genus Dendroaspis have toxins, muscarinic toxins, that are selective for M-1, M-2 and M-4 receptors. They consist of 63-66 amino acids and four disulfides which form four loops. They are members of a large group of snake toxins, three-finger toxins; three loops are extended like the middle fingers of a hand and the disulfides and the shortest loop are in the palm of the hand. Some of the toxins target the allosteric site which is located in a cleft of the receptor molecule close to its extracellular part. A possible explanation to the good selectivity is that the toxins bind to the allosteric site, but because of their size they probably also bind to extracellular parts of the receptors which are rather different in the various subtypes. Some other allosteric ligands also have good selectivity, the alkaloid brucine and derivatives are selective for M-1, M-3 and M-4 receptors. Muscarinic toxins have been used in several types of experiments. For instance radioactively labeled M-1 and M-4 selective toxins were used in autoradiography of hippocampus from Alzheimer patients. One significant change in the receptor content was detected in one region of the hippocampus, dentate gyrus, where M-4 receptors were reduced by 50% in patients as compared to age-matched controls. Hippocampus is essential for memory consolidation. M-4 receptors in dentate gyrus may play a role, since they decreased in Alzheimers disease which destroys the memory. Another indication of the role of M-4 receptors for memory is that injection of the M-4 selective antagonist muscarinic toxin 3 (M-4-toxin 1) into rat hippocampus produced amnesia.
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6.
  • Spillmann, Dorothe (författare)
  • Heparan sulfate : anchor for viral intruders?
  • 2001
  • Ingår i: Biochimie. - 0300-9084 .- 1638-6183. ; 83:8, s. 811-817
  • Tidskriftsartikel (refereegranskat)abstract
    • Heparan sulfates (HS) are ubiquitous, polyanionic carbohydrate chains linked to core proteins in cell membranes and extracellular matrices of all eukaryotes. Due to the complex nature of the HS-biosynthesis, a wealth of different structures are produced. These seem to have a well defined distribution in different tissues and cells throughout development. Binding of endogenous proteins with different functional properties such as growth factors, adhesion molecules or enzymes, is one of the functions of HS. Besides interaction with endogenous factors, glycosaminoglycans (GAG) and especially HS have also been demonstrated to function as receptors for a number of different pathogens. What roles may HS play in the pathogenesis and tropism of different intruders like parasites or viruses? What implications does binding of viruses to HS have for the development of drugs or the application of viral vectors for gene targeting? In this review an attempt is made to collect our present knowledge on viral usage of HS and the implications that follow.
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7.
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8.
  • Baldassarre, Maurizio, et al. (författare)
  • Amyloid fibril formation by bovine alpha(1)-acid glycoprotein in a reducing environment : The role of disulfide bridges on the observed aggregation kinetics
  • 2015
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 118, s. 244-252
  • Tidskriftsartikel (refereegranskat)abstract
    • Bovine alpha(1)-acid glycoprotein (bAGP), a thermostable counterpart of its human homologue, is a positive acute phase protein involved in binding and transportation of a large number of bin-active molecules and drugs across the body. We have investigated the effect of low pH and reducing conditions on the structure of the protein and found that it aggregates at high temperatures. The aggregates show a fibrillar structure when observed with electron microscopy. Aggregation assays using the amyloid-specific dye Thioflavin T show the presence of a lag phase which was neither abolished nor shortened when seeds were added. A priori reduction of the two disulfide bridges of bAGP, on the other hand, abolished the lag phase and reveals a connection between the kinetics of reduction and aggregation. We provide a kinetic interpretation and the corresponding rate laws allowing to model the process of fibril formation by bAGP under reducing conditions. Our interpretation allows to assess the role of disulfide bridges on the fibrillation kinetics of bAGP and can provide a more accurate interpretation of the fibrillation kinetics of other amyloidogenic proteins containing disulfide bridges.
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9.
  • Banerjee, Debapriya, et al. (författare)
  • Spectroscopic and DFT studies on 6-Aminophenanthridine and its derivatives provide insights in their activity towards ribosomal RNA
  • 2014
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 97, s. 194-199
  • Tidskriftsartikel (refereegranskat)abstract
    • 6-Aminophenanthridine (6AP), a plant alkaloid possessing antiprion activity, inhibits ribosomal RNA dependent protein folding activity of the ribosome (referred as PFAR). We have compared 6AP and its three derivatives 6AP8Cl, 6AP8CF3 and 6APi for their activity in inhibition of PFAR. Since PFAR inhibition requires 6AP and its derivatives to bind to the ribosomal RNA (rRNA), we have measured the binding affinity of these molecules to domain V of 23S rRNA using fluorescence spectroscopy. Our results show that similar to the antiprion activity, both the inhibition of PFAR and the affinity towards rRNA follow the order 6AP8CF3 > 6AP8Cl > 6AP, while 6APi is totally inactive. To have a molecular insight for the difference in activity despite similarities in structure, we have calculated the nucleus independent chemical shift using first principles density functional theory. The result suggests that the deviation of planarity in 6APi and steric hindrance from its bulky side chain are the probable reasons which prevent it from interacting with rRNA. Finally, we suggest a probable mode of action of 6AP, 6AP8CF3 and 6AP8Cl towards rRNA.
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10.
  • Bartish, Galyna, et al. (författare)
  • Importance of individual amino acids in the Switch I region in eEF2 studied by functional complementation in S. cerevisiae
  • 2008
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 90:5, s. 736-748
  • Tidskriftsartikel (refereegranskat)abstract
    • Elongation factor 2 (eEF2) is a member of the G-protein super family. G-proteins undergo conformational changes associated with binding of the guanosine nucleotide and hydrolysis of the bound GTP. These structural rearrangements affects the Switch I region (also known as the Effector loop). We have studied the role of individual amino acids in the Switch I region (amino acids 25-73) of S. cerevisiae eEF2 using functional complementation in yeast. 21 point mutations in the Switch I region were created by site-directed mutagenesis. Mutants K49R, E52Q, A53G, F55Y, K60R, Q63A, T68S, 169M and A73G were functional while mutants R54H, F55N, D57A, D57E, D57S, R59K, R59M, Q63E, R65A, R65N, T68A and T68M were inactive. Expression of mutants K49R, A53G, Q63A, 169M and A73G was associated with markedly decreased growth rates and yeast cells expressing mutants A53G and 169M became temperature sensitive. The functional capacity of eEF2 in which the major part Switch I (amino acids T56 to 169) was converted into the homologous sequence found in EF-G from E. coli was also studied. This protein chimera could functionally replace yeast eEF2 in vivo. Yeast cells expressing this mutant grew extremely slowly, showed increased cell death and became temperature sensitive. The ability of the mutant to replace authentic eEF2 in vivo indicates that the structural rearrangement of Switch I necessary for eEF2 function is similar in eukaryotes and bacteria. The effect of two point mutations in the P-loop was also studied. Mutant A25G but not A25V could functionally replace yeast eEF2 even if cells expressing the mutant grew slowly. The A25G mutation converted the consensus sequences AXXXXGK[T/S] in eEF2 to the corresponding motif GXXXXGK[T/S] found in all other G-proteins, suggesting that the alanine found in the P-loop of peptidyltranslocases are not essential for function.
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11.
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12.
  • Bjorkhem, I (författare)
  • Five decades with oxysterols
  • 2013
  • Ingår i: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 95:3, s. 448-454
  • Tidskriftsartikel (refereegranskat)
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13.
  • Burchacka, Ewa, et al. (författare)
  • Substrate profiling of Finegoldia magna SufA protease, inhibitor screening and application to prevent human fibrinogen degradation and bacteria growth in vitro.
  • 2014
  • Ingår i: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 103C:May 22, s. 137-143
  • Tidskriftsartikel (refereegranskat)abstract
    • SufA, which belongs to the subtilisin-like serine protease family, contains a non-canonical Asp-His-Ser catalytic triad. Under in vitro conditions, SufA is capable of human fibrinogen hydrolysis leading to inhibition of fibrin network formation, thus suggesting its important role in the development and progression of Finegoldia magna infections. In addition, it has been demonstrated that SufA can hydrolyze antibacterial peptides such as LL-37 and the chemokine MIG/CXCL 9, hence evading host defence mechanisms. Although the SufA protease from F. magna was discovered several years ago, its optimal substrate preference has not yet been identified. Considering the role of SufA, we have focused on the profiling of its substrate sequence preference spanning S1-S3 binding pockets using the FRET (fluorescence resonance energy transfer) approach. Next, based on the structure of the P1 residue of the developed substrate, we narrowed the inhibitor screening to the phosphonic analogues of amino acids containing an arginine-like side chain. Among all the compounds tested, only Cbz-6-AmNphth(P)(OPh)2 showed any inhibitory activity against SufA displaying k2/Ki value of 10 800 M(-1) s(-1). In addition, it prevented SufA-mediated human fibrinogen hydrolysis in vitro and exhibited potent antibacterial activity against F. magna, Staphylococcus aureus and Escherichia coli. Herein, we report on the substrate specificity, synthesis and kinetic evaluation of phosphonic inhibitors of SufA protease from F. magna which could help to establish its function in pathogenesis development and may lead to the elaboration of new antibacterial drugs.
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14.
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15.
  • Croitoru, Victor, et al. (författare)
  • RNA chaperone activity of translation initiation factor IF1
  • 2006
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 88:12, s. 1875-1882
  • Tidskriftsartikel (refereegranskat)abstract
    • Translation initiation factor IF1 is an indispensable protein for translation in prokaryotes. No clear function has been assigned to this factor so far. In this study we demonstrate an RNA chaperone activity of this protein both in vivo and in vitro. The chaperone assays are based on in vivo or in vitro splicing of the group I intron in the thymidylate synthase gene (td) from phage T4 and an in vitro RNA annealing assay. IF1 wild-type and mutant variants with single amino acid substitutions have been analyzed for RNA chaperone activity. Some of the IF1 mutant variants are more active as RNA chaperones than the wild-type. Furthermore, both wild-type IF1 and mutant variants bind with high affinity to RNA in a band-shift assay. It is suggested that the RNA chaperone activity of IF1 contributes to RNA rearrangements during the early phase of translation initiation.
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16.
  • Daniel, Chammiran, et al. (författare)
  • RNA editing of non-coding RNA and its role in gene regulation
  • 2015
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 117, s. 22-27
  • Forskningsöversikt (refereegranskat)abstract
    • It has for a long time been known that repetitive elements, particularly Alu sequences in human, are edited by the adenosine deaminases acting on RNA, ADAR, family. The functional interpretation of these events has been even more difficult than that of editing events in coding sequences, but today there is an emerging understanding of their downstream effects. A surprisingly large fraction of the human transcriptome contains inverted Alu repeats, often forming long double stranded structures in RNA transcripts, typically occurring in introns and UTRs of protein coding genes. Alu repeats are also common in other primates, and similar inverted repeats can frequently be found in non-primates, although the latter are less prone to duplex formation. In human, as many as 700,000 Alu elements have been identified as substrates for RNA editing, of which many are edited at several sites. In fact, recent advancements in transcriptome sequencing techniques and bioinformatics have revealed that the human editome comprises at least a hundred million adenosine to inosine (A-to-I) editing sites in Alu sequences. Although substantial additional efforts are required in order to map the editome, already present knowledge provides an excellent starting point for studying cis-regulation of editing. In this review, we will focus on editing of long stem loop structures in the human transcriptome and how it can effect gene expression.
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17.
  • Davies, Victoria S., et al. (författare)
  • Repeated short excursions from thermoneutrality suffice to restructure brown adipose tissue
  • 2023
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 210, s. 40-49
  • Tidskriftsartikel (refereegranskat)abstract
    • Given the presence of brown adipose tissue in adult humans, an important issue is whether human brown adipose tissue is recruitable. Cold exposure is the canonical recruitment treatment; however, in experimental animals (mice), recruitment of brown adipose tissue is normally induced by placing the mice in constant cold, a procedure not feasible in humans. For possible translational applications, we have therefore investigated whether shorter daily excursions from thermoneutrality would suffice to qualitatively and quantitatively induce recruitment in mice. Mice, housed at thermoneutrality (30 °C) to mimic human conditions, were transferred every day for 4 weeks to cool conditions (18 °C), for 0, 15, 30, 120 and 420 min (or placed constantly in 18 °C). On the examination day, the mice were not exposed to cold. Very short daily exposures (≤30 minutes) were sufficient to induce structural changes in the form of higher protein density in brown adipose tissue, changes that may affect the identification of the tissue in e.g. computer tomography and other scan studies. To estimate thermogenic capacity, UCP1 protein levels were followed. No UCP1 protein was detectable in inguinal white adipose tissue. In the interscapular brown adipose tissue, a remarkable two-phase reaction was seen. Very short daily exposures (≤30 minutes) were sufficient to induce a significant increase in total UCP1 levels. For attainment of full cold acclimation, the mice had, however, to remain exposed to the cold. The studies indicate that marked alterations in brown adipose tissue composition can be induced in mammals through relatively modest stimulation events.
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18.
  • Dhumal, Tushar Tukaram, et al. (författare)
  • Molecular explorations of the Leishmania donovani 6-phosphogluconolactonase enzyme, a key player in the pentose phosphate pathway
  • 2022
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 202, s. 212-225
  • Tidskriftsartikel (refereegranskat)abstract
    • The enzymes of the pentose phosphate pathway are vital to survival in kinetoplastids. The second step of the pentose phosphate pathway involves hydrolytic cleavage of 6-phosphogluconolactone to 6- phosphogluconic acid by 6-phosphogluconolactonase (6PGL). In the present study, Leishmania dono-vani 6PGL (Ld6PGL) was cloned and overexpressed in bacterial expression system. Comparative sequence analysis revealed the conserved sequence motifs, functionally and structurally important residues in 6PGL family. In silico amino acid substitution study and interacting partners of 6PGL were predicted. The Ld6PGL enzyme was found to be active in the assay and in the parasites. Specificity was confirmed by Western blot analysis. The similar to 30 kDa protein was found to be a dimer in MALDI, glutaraldehyde cross-linking and size exclusion chromatography studies. Kinetic analysis and structural stability studies of Ld6PGL were performed with denaturants and at varied temperature. Computational 3D Structural modelling of Ld6PGL elucidates that it has a similar a/b hydrolase fold structural topology as in other members of 6PGL family. The three loops are found in extended form when the structure is compared with the human 6PGL (Hs6PGL). Further, enzyme substrate binding mode and its mechanism were investigated using the molecular docking and molecular simulation studies. Interesting dynamics action of substrate 6-phosphogluconolactone was observed into active site during MD simulation. Interesting differences were observed between host and parasite enzyme which pointed towards its potential to be explored as an antileishmanial drug target. This study forms the basis for further analysis of the role of Ld6PGL in combating oxidative stress in Leishmania.
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19.
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20.
  • Dos Reis, Suzana, et al. (författare)
  • Mode of action of the antiprion drugs 6AP and GA on ribosome assisted protein folding
  • 2011
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 93:6, s. 1047-1054
  • Tidskriftsartikel (refereegranskat)abstract
    • The ribosome, the protein synthesis machinery of the cell, has also been implicated in protein folding. This activity resides within the domain V of the main RNA component of the large subunit of the ribosome. It has been shown that two antiprion drugs 6-aminophenanthridine (GAP) and Guanabenz (GA) bind to the ribosomal RNA and inhibit specifically the protein folding activity of the ribosome. Here, we have characterized with biochemical experiments, the mode of inhibition of these two drugs using ribosomes or ribosomal components active in protein folding (referred to as 'ribosomal folding modulators' or RFMs) from both bacteria Escherichia con and yeast Saccharomyces cerevisiae, and human carbonic anhydrase (HCA) as a sample protein. Our results indicate that 6AP and GA inhibit the protein folding activity of the ribosome by competition with the unfolded protein for binding to the ribosome. As a result, the yield of the refolded protein decreases, but the rate of its refolding remains unaffected. Further, 6AP- and GA mediated inhibition of RFM mediated refolding can be reversed by the addition of RFMs in excess. We also demonstrate with delayed addition of the ribosome and the antiprion drugs that there is a short time-span in the range of seconds within which the ribosome interacts with the unfolded protein. Thus we conclude that the protein folding activity of the ribosome is conserved from bacteria to eukaryotes and most likely the substrate for RFMs is an early refolding state of the target protein.
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21.
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22.
  • Ehrenberg, Måns, et al. (författare)
  • Maximum rrn promoter activity in Escherichia coli at saturating concentrations of free RNA polymerase
  • 2010
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 92:1, s. 12-20
  • Tidskriftsartikel (refereegranskat)abstract
    • During fast growth, the rrn P1 promoters of Escherichia coli operate at their maximum strength, but below their maximum activity (V-max), since they are not saturated with RNA polymerase. Since higher concentrations of free RNA polymerase are expected to be found in strains carrying rrn deletions, we have analyzed reported electron micrographs of rrn operons from rrn deletion strains growing at maximal rates (at 37 degrees C) in LB medium [1]. We conclude that, in a strain with four of the seven rrn operons inactivated by partial deletions, transcripts are initiated at rrn P1 promoters 1.6-fold more rapidly than in the wild-type strain and the entirety of the rrn operon is transcribed at a 1.5-fold higher average elongation rate due to shortened pauses in the 16S and 23S regions. Under this condition, traffic congestion occurs in front of a pause site in the 5' leader region of the rrn operon near the beginning of the 16S gene; the congestion extends all the way back to the promoter, impedes promoter clearance and limits the promoter activity to one initiation per 0.56 s. This corresponds to a promoter activity of 107 transcripts/min and is assumed to be close to the V-max of rrn P1 promoters.
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23.
  • Ehrenberg, Måns, et al. (författare)
  • Medium-dependent control of the bacterial growth rate
  • 2013
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 95:4, s. 643-658
  • Forskningsöversikt (refereegranskat)abstract
    • By combining results from previous studies of nutritional up-shifts we here re-investigate how bacteria adapt to different nutritional environments by adjusting their macromolecular composition for optimal growth. We demonstrate that, in contrast to a commonly held view the macromolecular composition of bacteria does not depend on the growth rate as an independent variable, but on three factors: (i) the genetic background (i.e. the strain used), (ii) the physiological history of the bacteria used for inoculation of a given growth medium, and (iii) the kind of nutrients in the growth medium. These factors determine the ribosome concentration and the average rate of protein synthesis per ribosome, and thus the growth rate. Immediately after a nutritional up-shift, the average number of ribosomes in the bacterial population increases exponentially with time at a rate which eventually is attained as the final post-shift growth rate of all cell components. After a nutritional up-shift from one minimal medium to another minimal medium of higher nutritional quality, ribosome and RNA polymerase syntheses are co-regulated and immediately increase by the same factor equal to the increase in the final growth rate. However, after an up-shift from a minimal medium to a medium containing all 20 amino acids, RNA polymerase and ribosome syntheses are no longer coregulated; a smaller rate of synthesis of RNA polymerase is compensated by a gradual increase in the fraction of free RNA polymerase, possibly due to a gradual saturation of mRNA promoters. We have also analyzed data from a recent publication, in which it was concluded that the macromolecular composition in terms of RNA/protein and RNA/DNA ratios is solely determined by the effector molecule ppGpp. Our analysis indicates that this is true only in special cases and that, in general, medium adaptation also depends on factors other than ppGpp.
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24.
  • Eneyskaya, Elena V., et al. (författare)
  • Transglycosylating and hydrolytic activities of the beta-mannosidase from Trichoderma reesei
  • 2009
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 91:5, s. 632-638
  • Tidskriftsartikel (refereegranskat)abstract
    • A purified beta-mannosidase (EC 3.2.1.25) from the fungus Trichoderma reesei has been identified as a member of glycoside hydrolase family 2 through mass spectrometry analysis of tryptic peptides. In addition to hydrolysis, the enzyme catalyzes substrate transglycosylation with p-nitrophenyl beta-mannopyranoside. Structures of the major and minor products of this reaction were identified by NMR analysis as p-nitrophenyl mannobiosides and p-nitrophenyl mannotriosides containing beta-(1 -> 4) and beta-(1 -> 3) linkages. The rate of donor substrate hydrolysis increased in presence of acetonitrile and dimethylformamide, while transglycosylation was weakly suppressed by these organic solvents. Differential ultraviolet spectra of the protein indicate that a rearrangement of the hydrophobic environment of the active site following the addition of the organic solvents may be responsible for this hydrolytic activation.
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25.
  • Fange, David, et al. (författare)
  • Identification of enzyme inhibitory mechanisms from steady-state kinetics
  • 2011
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 93:9, s. 1623-1629
  • Tidskriftsartikel (refereegranskat)abstract
    • Enzyme inhibitors are used in many areas of the life sciences, ranging from basic research to the combat of disease in the clinic. Inhibitors are traditionally characterized by how they affect the steady-state kinetics of enzymes, commonly analyzed on the assumption that enzyme-bound and free substrate molecules are in equilibrium. This assumption, implying that an enzyme-bound substrate molecule has near zero probability to form a product rather than dissociate, is valid only for very inefficient enzymes. When it is relaxed, more complex but also more information-rich steady-state kinetics emerges. Although solutions to the general steady-state kinetics problem exist, they are opaque and have been of limited help to experimentalists. Here we reformulate the steady-state kinetics of enzyme inhibition in terms of new parameters. These allow for assessment of ambiguities of interpretation due to kinetic scheme degeneracy and provide an intuitively simple way to analyze experimental data. We illustrate the method by concrete examples of how to assess scheme degeneracy and obtain experimental estimates of all available rate and equilibrium constants. We suggest simple, complementary experiments that can remove ambiguities and greatly enhance the accuracy of parameter estimation.
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26.
  • Freyhult, Eva, et al. (författare)
  • New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria
  • 2007
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 89:10, s. 1276-1288
  • Tidskriftsartikel (refereegranskat)abstract
    • There are at least 21 subfunctional classes of tRNAs in most cells that, despite a very highly conserved and compact common structure, must interact specifically with different cliques of proteins or cause grave organismal consequences. Protein recognition of specific tRNA substrates is achieved in part through class-restricted tRNA features called tRNA identity determinants. In earlier work we used TFAM, a statistical classifier of tRNA function, to show evidence of unexpectedly large diversity among bacteria in tRNA identity determinants. We also created a data reduction technique called function logos to visualize identity determinants for a given taxon. Here we show evidence that determinants for lysylated isoleucine tRNAs are not the same in Proteobacteria as in other bacterial groups including the Cyanobacteria. Consistent with this, the lysylating biosynthetic enzyme TilS lacks a C-terminal domain in Cyanobacteria that is present in Proteobacteria. We present here, using function logos, a map estimating all potential identity determinants generally operational in Cyanobacteria and Proteobacteria. To further isolate the differences in potential tRNA identity determinants between Proteobacteria and Cyanobacteria, we created two new data reduction visualizations to contrast sequence and function logos between two taxa. One, called Information Difference logos (ID logos), shows the evolutionary gain or retention of functional information associated to features in one lineage. The other, Kullback–Leibler divergence Difference logos (KLD logos), shows recruitments or shifts in the functional associations of features, especially those informative in both lineages. We used these new logos to specifically isolate and visualize the differences in potential tRNA identity determinants between Proteobacteria and Cyanobacteria. Our graphical results point to numerous differences in potential tRNA identity determinants between these groups. Although more differences in general are explained by shifts in functional association rather than gains or losses, the apparent identity differences in lysylated isoleucine tRNAs appear to have evolved through both mechanisms.
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27.
  • Hammann, Philippe, et al. (författare)
  • A method to map changes in bacterial surface composition induced by regulatory RNAs in Escherichia coli and Staphylococcus aureus
  • 2014
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 106C, s. 175-179
  • Tidskriftsartikel (refereegranskat)abstract
    • We have adapted a method to map cell surface proteins and to monitor the effect of specific regulatory RNAs on the surface composition of the bacteria. This method involves direct labeling of surface proteins of living bacteria using fluorescent dyes and a subsequent separation of the crude extract by 2D gel electrophoresis. The strategy yields a substantial enrichment in surface proteins over cytoplasmic proteins. We validated this method by monitoring the effect of the regulatory RNA MicA in Escherichia colt, which regulates the synthesis of several outer membrane proteins, and highlighted the role of Staphylococcus aureus RNAIII for the maintenance of cell wall integrity.
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28.
  • Haraldson, Klas, et al. (författare)
  • LRRC3B gene is frequently epigenetically inactivated in several epithelial malignancies and inhibits cell growth and replication
  • 2012
  • Ingår i: Biochimie. - : Elsevier. - 0300-9084 .- 1638-6183. ; 94:5, s. 1151-1157
  • Tidskriftsartikel (refereegranskat)abstract
    • Chromosome 3 specific NotI microarrays containing 180 NotI linking clones associated with 188 genes were hybridized to NotI representation probes prepared using matched tumor/normal samples from major epithelial cancers: breast (47 pairs), lung (40 pairs) cervical (43 pairs), kidney (34 pairs of clear cell renal cell carcinoma), colon (24 pairs), ovarian (25 pairs) and prostate (18 pairs). In all tested primary tumors (compared to normal controls) methylation and/or deletions was found. For the first time we showed that the gene LRRC3B was frequently methylated and/or deleted in breast carcinoma - 32% of samples, cervical - 35%, lung - 40%, renal - 35%, ovarian - 28%, colon - 33% and prostate cancer - 44%. To check these results bisulfite sequencing using cloned PCR products with representative two breast, one cervical, two renal, two ovarian and two colon cancer samples was performed. In all cases methylation was confirmed. Expression analysis using RT-qPCR showed that LRRC3B is strongly down-regulated at the latest stages of RCC and ovarian cancers. In addition we showed that LRRC3B exhibit strong cell growth inhibiting activity (more than 95%) in colony formation experiments in vitro in KRC/Y renal cell carcinoma line. All these data suggest that LRRC3B gene could be involved in the process of carcinogenesis as a tumor suppressor gene.
  •  
29.
  • Harish, Ajith, et al. (författare)
  • Akaryotes and Eukaryotes are independent descendants of a universal common ancestor
  • 2017
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 138, s. 168-183
  • Tidskriftsartikel (refereegranskat)abstract
    • We reconstructed a global tree of life (ToL) with non-reversible and non-stationary models of genome evolution that root trees intrinsically. We implemented Bayesian model selection tests and compared the statistical support for four conflicting ToL hypotheses. We show that reconstructions obtained with a Bayesian implementation (Klopfstein et al., 2015) are consistent with reconstructions obtained with an empirical Sankoff parsimony (ESP) implementation (Harish et al., 2013). Both are based on the genome contents of coding sequences for protein domains (superfamilies) from hundreds of genomes. Thus, we conclude that the independent descent of Eukaryotes and Akaryotes (archaea and bacteria) from the universal common ancestor (UCA) is the most probable as well as the most parsimonious hypothesis for the evolutionary origins of extant genomes. Reconstructions of ancestral proteomes by both Bayesian and ESP methods suggest that at least 70% of unique domain-superfamilies known in extant species were present in the UCA. In addition, identification of a vast majority (96%) of the mitochondrial superfamilies in the UCA proteome precludes a symbiotic hypothesis for the origin of eukaryotes. Accordingly, neither the archaeal origin of eukaryotes nor the bacterial origin of mitochondria is supported by the data. The proteomic complexity of the UCA suggests that the evolution of cellular phenotypes in the two primordial lineages, Akaryotes and Eukaryotes, was driven largely by duplication of common superfamilies as well as by loss of unique superfamilies. Finally, innovation of novel superfamilies has played a surprisingly small role in the evolution of Akaryotes and only a marginal role in the evolution of Eukaryotes.
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30.
  • Harish, Ajith, et al. (författare)
  • Empirical genome evolution models root the tree of life
  • 2017
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 138, s. 137-155
  • Tidskriftsartikel (refereegranskat)abstract
    • A reliable phylogenetic reconstruction of the evolutionary history of contemporary species depends on a robust identification of the universal common ancestor (UCA) at the root of the Tree of Life (ToL). That root polarizes the tree so that the evolutionary succession of ancestors to descendants is discernable. In effect, the root determines the branching order and the direction of character evolution. Typically, conventional phylogenetic analyses implement time-reversible models of evolution for which character evolution is un-polarized. Such practices leave the root and the direction of character evolution undefined by the data used to construct such trees. In such cases, rooting relies on theoretic assumptions and/or the use of external data to interpret unrooted trees. The most common rooting method, the outgroup method is clearly inapplicable to the ToL, which has no outgroup. Both here and in the accompanying paper (Harish and Kurland, 2017) we have explored the theoretical and technical issues related to several rooting methods. We demonstrate (1) that Genome-level characters and evolution models are necessary for species phylogeny reconstructions. By the same token, standard practices exploiting sequence-based methods that implement gene-scale substitution models do not root species trees; (2) Modeling evolution of complex genomic characters and processes that are non-reversible and non-stationary is required to reconstruct the polarized evolution of the ToL; (3) Rooting experiments and Bayesian model selection tests overwhelmingly support the earlier finding that akaryotes and eukaryotes are sister clades that descend independently from UCA (Harish and Kurland, 2013); (4) Consistent ancestral state reconstructions from independent genome samplings confirm the previous finding that UCA features three fourths of the unique protein domain-superfamilies encoded by extant genomes.
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31.
  • Harish, Ajith, et al. (författare)
  • Reply to Caetano-Anolles et al. comment on "Empirical genome evolution models root the tree of life"
  • 2018
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 149, s. 137-138
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • We recently analyzed the robustness of competing evolution models developed to identify the root of the Tree of Life: 1) An empirical Sankoff parsimony (ESP) model (Harish and Kurland, 2017), which is a nonstationary and directional evolution model; and 2) An a priori ancestor (APA) model (Kim and Caetano-Anolles, 2011) that is a stationary and reversible evolution model. Both Bayesian model selection tests as well as maximum parsimony analyses demonstrate that the ESP model is, overwhelmingly, the better model. Moreover, we showed that the APA model is not only sensitive to artifacts, but also that the underlying assumptions are neither empirically grounded nor biologically realistic.
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32.
  • Harish, Ajith, et al. (författare)
  • Rooted phylogeny of the three superkingdoms.
  • 2013
  • Ingår i: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 95:8, s. 1593-1604
  • Tidskriftsartikel (refereegranskat)abstract
    • The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant genomes of the three superkingdoms, each encoding a proteome that partially overlaps all others. This alone implies that the common ancestor to the superkingdoms was very complex. Such ancestral complexity is confirmed by phylogenetic reconstructions. In addition, the divergence of proteomes from the complex ancestor in each superkingdom is both reductive in numbers of unique SFs as well as cumulative in the abundance of surviving SFs. These data suggest that the common ancestor was not the first cell lineage and that modern global phylogeny is the crown of a "recently" re-rooted tree. We suggest that a bottlenecked survivor of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree.
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33.
  • Hauryliuk, Vasili, et al. (författare)
  • Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3
  • 2006
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 88:7, s. 747-757
  • Tidskriftsartikel (refereegranskat)abstract
    • In eukaryotes, termination of mRNA translation is triggered by the essential polypeptide chain release factors eRF1, recognizing all three stop codons, and eRF3, a member of the GTPase superfamily with a role that has remained opaque. We have studied the kinetic and thermodynamic parameters of the interactions between eRF3 and GTP, GDP and the non-hydrolysable GTP analogue GDPNP in the presence (K-D(GDP) = 1.3 +/- 0.2 mu M, K-D(GTP) approximate to 200 mu M and K-D(GDPNP) > 160 mu M) as well as absence (K-D(GDP) = 1.9 +/- 0.3 mu M, K-D(GTP) 0.7 +/- 0.2 mu M and K-D(GDPNP) approximate to 200 mu M) of eRF1. From the present data we propose that (i) free eRF3 has a strong preference to bind GDP compared to GTP (ii) eRF3 in complex with eRF1 has much stronger affinity to GTP than free eRF3 (iii) eRF3 in complex with PABP has weak affinity to GTP (iv) eRF3 in complex with eRF1 does not have strong affinity to GDPNP, implying that GDPNP is a poor analogue of GTP for eRF3 binding.
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34.
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35.
  • Jamroskovic, Jan, et al. (författare)
  • Probing the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution
  • 2022
  • Ingår i: Biochimie. - : Elsevier. - 0300-9084 .- 1638-6183. ; 199, s. 81-91
  • Tidskriftsartikel (refereegranskat)abstract
    • Cytosine-rich DNA can fold into four-stranded intercalated structures called i-motifs (iMs) under acidic conditions through the formation of hemi-protonated C:C+ base pairs. However, the folding and stability of iMs rely on many other factors that are not yet fully understood. Here, we combined biochemical and biophysical approaches to determine the factors influencing iM stability under a wide range of experimental conditions. By using high-resolution primer extension assays, circular dichroism, and absorption spectroscopies, we demonstrate that the stabilities of three different biologically relevant iMs are not dependent on molecular crowding agents. Instead, some of the crowding agents affected overall DNA synthesis. We also tested a range of small molecules to determine their effect on iM stabilization at physiological temperature and demonstrated that the G-quadruplex-specific molecule CX-5461 is also a promising candidate for selective iM stabilization. This work provides important insights into the requirements needed for different assays to accurately study iM stabilization, which will serve as important tools for understanding the contribution of iMs in cell regulation and their potential as therapeutic targets.
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36.
  • Jansson, Lena, 1979, et al. (författare)
  • Carbohydrate binding specificities and crystal structure of the cholera toxin-like B-subunit from Citrobacter freundii.
  • 2010
  • Ingår i: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 92:5, s. 482-90
  • Tidskriftsartikel (refereegranskat)abstract
    • Enterotoxigenic Escherichia coli and Vibrio cholerae are well known causative agents of severe diarrheal diseases. Both pathogens produce AB(5) toxins, with one enzymatically active A-subunit and a pentamer of receptor-binding B-subunits. The primary receptor for both B-subunits is the GM1 ganglioside (Galbeta3GalNAcbeta4(NeuAcalpha3)Galbeta4GlcbetaCer), but the B-subunits from porcine isolates of E. coli also bind neolacto-(Galbeta4GlcNAcbeta-)terminated glycoconjugates and the B-subunits from human isolates of E. coli (hLTB) have affinity for blood group A type 2-(GalNAcalpha3(Fucalpha2)Galbeta4GlcNAcbeta-)terminated glycoconjugates. A B-subunit with 73% sequence identity to the B-subunits of cholera toxin and the heat-labile toxin of E. coli is produced by certain strains of enteropathogenic E. coli and by Citrobacter freundii. This C. freundii B-subunit (CFXB) has now been expressed in V. cholerae, and isolated in high yields. Glycosphingolipid binding studies show that CFXB binds to the GM1 ganglioside with high affinity. In addition, CFXB has high affinity for both neolacto-terminated and blood group A type 2-terminated glycoconjugates. The crystal structure of the pentameric arrangement of C. freundii B-subunits display high structural similarity with related proteins from E. coli and V. cholerae and oligosaccharide binding sites can be identified on the protein surface. Small changes in the 88-95 loop connecting the GM1 and blood group A binding sites explains the minor changes in affinity seen for these two ligands. However, the enhanced affinity of CFXB for neolacto-terminated structures can be sought in the Lys34Tyr substitution affording additional hydrogen bond interactions between the tyrosyl side chain and the GlcNAcbeta3Galb4Glcbeta1 segment of neolactotetraosylceramide via bridging water molecules.
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37.
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38.
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39.
  • Kalinovich, Anastasia V., et al. (författare)
  • UCP1 in adipose tissues: two steps to full browning
  • 2017
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 134, s. 127-137
  • Tidskriftsartikel (refereegranskat)abstract
    • The possibility that brown adipose tissue thermogenesis can be recruited in order to combat the development of obesity has led to a high interest in the identification of "browning agents", i.e. agents that increase the amount and activity of UCP1 in brown and brite/beige adipose tissues. However, functional analysis of the browning process yields confusingly different results when the analysis is performed in one of two alternative steps. Thus, in one of the steps, using cold acclimation as a potent model browning agent, we find that if the browning process is followed in mice initially housed at 21 °C (the most common procedure), there is only weak molecular evidence for increases in UCP1 gene expression or UCP1 protein abundance in classical brown adipose tissue; however, in brite/beige adipose depots, there are large increases, apparently associating functional browning with events only in the brite/beige tissues. Contrastingly, in another step, if the process is followed starting with mice initially housed at 30 °C (thermoneutrality for mice, thus similar to normal human conditions), large increases in UCP1 gene expression and UCP1 protein abundance are observed in the classical brown adipose tissue depots; there is then practically no observable UCP1 gene expression in brite/beige tissues. This apparent conundrum can be resolved when it is realized that the classical brown adipose tissue at 21 °C is already essentially fully differentiated and thus expands extensively through proliferation upon further browning induction, rather than by further enhancing cellular differentiation. When the limiting factor for thermogenesis, i.e. the total amount of UCP1 protein per depot, is analyzed, classical brown adipose tissue is by far the predominant site for the browning process, irrespective of which of the two steps is analyzed. There are to date no published data demonstrating that alternative browning agents would selectively promote brite/beige tissues versus classical brown tissue to a higher degree than does cold acclimation. Thus, to restrict investigations to examine adipose tissue depots where only a limited part of the adaptation process occurs (i.e. the brite/beige tissues) and to use initial conditions different from the thermoneutrality normally experienced by adult humans may seriously hamper the identification of therapeutically valid browning agents. The data presented here have therefore important implications for the analysis of the potential of browning agents and the nature of human brown adipose tissue.
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40.
  • Khaustova, Nadezhda A, et al. (författare)
  • Selectin-independent adhesion during ovarian cancer metastasis.
  • 2017
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 142, s. 197-206
  • Tidskriftsartikel (refereegranskat)abstract
    • PURPOSE: Ovarian cancer (OvCa) progression mainly takes place by intraperitoneal spread. Adhesion of tumor cells to the mesothelial cells which form the inner surface of the peritoneum is a crucial step in this process. Cancer cells use in principle different molecules of the leukocyte adhesion cascade to facilitate adhesion. This cascade is initiated by selectin-ligand interactions followed by integrin - extracellular matrix protein interactions. Here we address the question whether all tumor cells predominantly employ selectin-dependent leukocyte-like adhesion cascade (SDAC) or whether they use integrin mediated adhesion for OvCa progression as well.METHODS: A comparative transcriptomic analysis of the human OvCa cell lines OVCAR8 and SKOV3 was performed. Intraperitoneal xenograft model of OVCAR8 cells was used to determine whether there is a correlation between SDAC gene expression and the metastatic potential of the control cells and the cells overexpressing c-Fos. Transcriptomic analysis of OVCAR8 and SKOV3 samples was performed using microarrays.RESULTS: One-third of the protein-coding genes involved in SDAC exhibited lower expression levels in OVCAR8 than in SKOV3 cells. In contrast to SKOV3 cells, c-Fos overexpression in OVCAR8 cells did not significantly influence the expression of SDAC genes. Intraperitoneal xenograft model of OVCAR8 cells unexpectedly demonstrated that the aggressiveness of OVCAR8 tumors was not depended on the c-Fos expression level and was comparable to that of SKOV3 control tumors. Gene expression analysis of tumors suggests that SKOV3-derived tumor progression was mainly depended on SDAC. Progression of OVCAR8 tumors relied on other cell adhesion molecules that do not interact with selectins.CONCLUSIONS: High expression of c-Fos in ovarian cancer cells is not always associated with reduced metastatic potential. Low expression level of SDAC genes may not ensure low OvCa metastatic potential hence alternative adhesion mechanisms involving laminin-integrin interactions exist as well.
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41.
  • Kirsebom, Leif A. (författare)
  • RNase P RNA mediated cleavage : substrate recognition and catalysis
  • 2007
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 89:10, s. 1183-1194
  • Forskningsöversikt (refereegranskat)abstract
    • The universally conserved endoribonuclease P consists of one RNA subunit and, depending on its origin, a variable number of protein subunits. RNase P is involved in the processing of a large variety of substrates in the cell, the preferred substrate being tRNA precursors. Cleavage activity does not require the presence of the protein subunit(s) in vitro. This is true for both prokaryotic and eukaryotic RNase P RNA suggesting that the RNA based catalytic activity has been preserved during evolution. Progress has been made in our understanding of the contribution of residues and chemical groups both in the substrate as well as in RNase P RNA to substrate binding and catalysis. Moreover, we have access to two crystal structures of bacterial RNase P RNA but we still lack the structure of RNase P RNA in complex with its substrate and/or the protein subunit. Nevertheless, these recent advancements put us in a new position to study the way and nature of interactions between in particular RNase P RNA and its substrate. In this review I will discuss various aspects of the RNA component of RNase P with an emphasis on our current understanding of the interaction between RNase P RNA and its substrate.
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42.
  • Kmiec, Beata, et al. (författare)
  • Phenotypical consequences of expressing the dually targeted Presequence Protease, AtPreP, exclusively in mitochondria
  • 2014
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 100C, s. 167-170
  • Tidskriftsartikel (refereegranskat)abstract
    • Endosymbiotic organelles, mitochondria and chloroplasts, are sites of an intensive protein synthesis and degradation. A consequence of these processes is production of both free targeting peptides, i.e. mitochondrial presequences and chloroplastic transit peptides, and other short unstructured peptides. Mitochondrial, as well as chloroplastic peptides are degraded by Presequence Protease (Prep), which is dually targeted to mitochondrial matrix and chloroplastic stroma. Elimination of PreP in Arabidopsis thaliana leads to growth retardation, chlorosis and impairment of mitochondrial functions potentially due to the accumulation of targeting peptides. In this work we analyzed the influence of the restoration of mitochondrial peptide degradation by AtPreP on plant phenotype. We showed that exclusive mitochondrial expression of AtPreP results in total restoration of the proteolytic activity, but it does not restore the wild-type phenotype. The plants grow shorter roots and smaller rosettes compared to the plants expressing AtPreP1 in both mitochondria and chloroplasts. With this analysis we are aiming at understanding the physiological impact of the role of the dually targeted AtPreP in single type of destination organelle.
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43.
  • Kodama, Yutaka, et al. (författare)
  • A novel protein phosphorylation pathway involved in osmotic-stress response in tobacco plants
  • 2009
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 91:4, s. 533-539
  • Tidskriftsartikel (refereegranskat)abstract
    • Osmotic stress is one of the severest environmental pressures for plants, commonly occurring under natural growing condition due to drought, salinity, cold and wounding. Plants sensitively respond to these stresses by activating a set of genes, which encode proteins necessary to overcome the crises. We screened such genes from tobacco plants, and identified a particular clone, which encoded a 45 kDa protein kinase belonging to the plant receptor-like cytoplasmic protein kinase class-VII, NAK (novel Arabidopsis protein kinase) group. The clone was consequently designated as NtNAK (Nicotiana tabacum AK, accession number: DQ447159). GFP-NtNAK fusion protein was localized in both cytoplasm and nucleus, and bacterially expressed NtNAK exhibited in vitro kinase activity. Its transcripts were clearly induced upon treatments of leaves with salt, mannitol, low temperature and also with abscisic and jasmonic acids and ethylene. These properties indicated NtNAK to be a typical osmo-stress-responsive protein kinase. Its target protein(s) were then screened by the yeast two-hybrid system, and one clone encoding a 32 kDa protein was identified. The protein resembled a potato stress-responsive protein CK251806, and designated as NtCK25 (accession number: DQ448851). Bacterially expressed NtCK25 was phosphorylated by NtNAK, and NtCK25-GFP fusion protein was exclusively localized in nucleus. The structure of NtCK25 was found to be similar to a human nuclear body protein, SP110, which is involved in DNA/protein binding regulation. This suggested that, perceiving osmo-stress signal, NtNAK phosphorylates and activates NtCK25, which might function in regulation of nucleus function. The present study thus suggests that NtNAK/NtCK25 constitutes a novel phosphorylation pathway for osmotic-stress response in plants.
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44.
  • Kurland, Charles (författare)
  • Carl R. Woese in memoriam Obituary
  • 2013
  • Ingår i: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 95:9, s. 1661-1662
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
  •  
45.
  •  
46.
  • Kurland, Charles, et al. (författare)
  • The origins of modem proteomes
  • 2007
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 89:12, s. 1454-1463
  • Tidskriftsartikel (refereegranskat)abstract
    • Distributions of phylogenetically related protein domains (fold superfamilies), or FSFs, among the three Superkingdoms (trichotomy) are assessed. Very nearly 900 of the 1200 FSFs of the trichotomy are shared by two or three Superkingdoms. Parsimony analysis of FSF distributions suggests that the FSF complement of the last common ancestor to the trichotomy was more like that of modem eukaryotes than that of archaea and bacteria. Studies of length distributions among members of orthologous families of proteins present in all three Superkingdoms reveal that such lengths are significantly longer among eukaryotes than among bacteria and archaea. The data also reveal that proteins lengths of eukaryotes are more broadly distributed than they are within archaeal and bacterial members of the same orthologous families. Accordingly, selective pressure for a minimal size is significantly greater for orthologous protein lengths in archaea and bacteria than in eukaryotes. Alignments of orthologous proteins of archaea, bacteria and eukaryotes are characterized by greater sequence variation at their N-terminal and C-terminal domains, than in their central cores. Length variations tend to be localized in the terminal sequences; the conserved sequences of orthologous families are localized in a central core. These data are consistent with the interpretation that the genomes of the last common ancestor (LUCA) encoded a cohort of FSFs not very different from that of modem eukaryotes. Divergence of bacterial and archaeal genomes from that common ancestor may have been accompanied by more intensive reductive evolution of proteomes than that expressed in eukaryotes. Dollo's Law suggests that the evolution of novel FSFs is a very slow process, while laboratory experiments suggests that novel protein genesis from preexisting FSFs can be relatively rapid. Reassortment of FSFs to create novel proteins may have been mediated by genetic recombination before the advent of more efficient splicing mechanisms.
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47.
  • Kurland, Charles, et al. (författare)
  • The phylogenomics of protein structures : The backstory
  • 2015
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 119, s. 284-302
  • Forskningsöversikt (refereegranskat)abstract
    • In this introductory retrospective, evolution as viewed through gene trees is inspected through a lens compounded from its founding operational assumptions. The four assumptions of the gene tree culture that are singularly important to evolutionary interpretations are: a. that protein-coding sequences are molecular fossils; b. that gene trees are equivalent to species trees; c. that the tree of life is assumed to be rooted in a simple akaryote cell implying that akaryotes are primitive, and d. that the notion that all or most incongruities between alignment-based gene trees are due to horizontal gene transfer (HGT), which includes the endosymbiotic models postulated for the origins of eukaryotes. What has been unusual about these particular assumptions is that though each was taken on board explicitly, they are defended in the face of factual challenge by a stolid disregard for the conflicting observations. The factual challenges to the mainstream gene tree-inspired evolutionary view are numerous and most convincingly summarized as: Genome trees tell a very different story. Phylogeny inferred from genomic assortments of homologous protein structural-domains does not support any one of the four principle evolutionary interpretations of gene trees: a. 3D protein domain structures are the molecular fossils of evolution, while coding sequences are transients; b. Species trees are very different from gene trees; c. The ToL is rooted in a surprisingly complex universal common ancestor (UCA) that is distinct from any specific modern descendant and d. HGT including endosymbiosis is a negligible player in genome evolution from UCA to the present.
  •  
48.
  • Kuzmenko, Anton, et al. (författare)
  • Mitochondrial translation initiation machinery : conservation and diversification
  • 2014
  • Ingår i: Biochimie. - : Elsevier. - 0300-9084 .- 1638-6183. ; 100C, s. 132-140
  • Tidskriftsartikel (refereegranskat)abstract
    • The highly streamlined mitochondrial genome encodes almost exclusively a handful of transmembrane components of the respiratory chain complex. In order to ensure the correct assembly of the respiratory chain, the products of these genes must be produced in the correct stoichiometry and inserted into the membrane, posing a unique challenge to the mitochondrial translational system. In this review we describe the proteins orchestrating mitochondrial translation initiation: bacterial-like general initiation factors mIF2 and mIF3, as well as mitochondria-specific components - mRNA-specific translational activators and mRNA-nonspecific accessory initiation factors. We consider how the fast rate of evolution in these organelles has not only created a system that is divergent from that of its bacterial ancestors, but has led to a huge diversity in lineage specific mechanistic features of mitochondrial translation initiation among eukaryotes.
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49.
  • Lagunas-Rangel, Francisco Alejandro, et al. (författare)
  • Epigenetics in the early divergent eukaryotic Giardia duodenalis : An update
  • 2019
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 156, s. 123-128
  • Forskningsöversikt (refereegranskat)abstract
    • Giardia duodenalis is a flagellated unicellular eukaryotic microorganism that usually parasitizes the small intestine of humans and many other vertebrates causing diarrheal disease throughout the world. Notably, Giardia despite minimization of most cellular systems shows different strategies to adapt to environmental conditions, evade the immune system and resist exposure to antimicrobial agents. Over the past years, epigenetic regulation of gene expression has been shown to have a relevant role in the parasite's biology. Interestingly, analysis of the Giardia genome revealed the presence of enzymes responsible for post-translational modification in histones, therefore suggesting that epigenetic mechanisms may regulate gene expression in this parasite. Thus, the purpose of this review is to summarize how epigenetic mechanisms play relevant roles in the pathogenicity of Giardia, with a particular emphasis on the molecular mechanisms associated with parasite differentiation, antigenic variation and antimicrobial resistance.
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50.
  • Lagunas-Rangel, Francisco Alejandro (författare)
  • KDM6B (JMJD3) and its dual role in cancer
  • 2021
  • Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 184, s. 63-71
  • Tidskriftsartikel (refereegranskat)abstract
    • Epigenetic modifications play a fundamental role in the regulation of gene expression and cell fate. During the development of cancer, epigenetic modifications appear that favor cell proliferation and migration, but at the same time prevent differentiation and apoptosis, among other processes. KDM6B is a histone demethylase that specifically removes methyl groups from H3K27me3, thus allowing re-expression of its target genes. It is currently known that KDM6B can act as both a tumor suppressor and an oncogene depending on the cellular context. Therefore, in this work we summarize the current knowledge of the role that KDM6B plays in different oncological contexts, and we try to orient it towards its clinical application.
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