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G Rudenko

Publications and source records attributed to G Rudenko.

36 records · Page 2Linked to original sources
PubMed1995

Three-dimensional structure of the human 'protective protein': structure of the precursor form suggests a complex activation mechanism.

BACKGROUND: The human 'protective protein' (HPP) forms a multi-enzyme complex with beta-galactosidase and neuraminidase in the lysosomes, protecting these two glycosidases from degradation. In humans, deficiency of HPP leads to the lysosomal storage disease galactosialidosis. Proteolytic cleavage of the precursor form of HPP involves removal of a 2 kDa excision peptide and results in a carboxypeptidase activity. The physiological relevance of this activity is, as yet, unknown. RESULTS: The crystal structure of the 108 kDa dimer of the precursor HPP has been elucidated by making extensive use of twofold density averaging. The monomer consists of a 'core' domain and a 'cap' domain. Comparison with the distantly related wheat serine carboxypeptidase dimer shows that the two subunits in the HPP dimer differ by 15 degrees in mutual orientation. Also, the helical subdomain forming part of the cap domains is very different. In addition, the HPP precursor cap domain contains a 'maturation' subdomain of 49 residues which fills the active-site cleft. Merely removing the 'excision' peptide located in the maturation subdomain does not render the catalytic triad solvent accessible. CONCLUSIONS: The activation mechanism of HPP is unique among proteases with known structure. It differs from the serine proteases in that the active site is performed in the zymogen, but is blocked by a maturation subdomain. In contrast to the zinc metalloproteases and aspartic proteases, the chain segment physically rendering the catalytic triad solvent inaccessible in HPP is not cleaved off to form the active enzyme. The activation must be a multi-step process involving removal of the excision peptide and major conformational changes of the maturation subdomain, whereas the conformation of the enzymatic machinery is probably almost, or completely, unaffected.

Amino Acid Sequence↗
PubMed1995

Genomic organization of an invariant surface glycoprotein gene family of Trypanosoma brucei.

The genomic organization of a gene family for the invariant surface glycoprotein, ISG75 (invariant surface glycoprotein with a molecular mass of 75 kDa), from Trypanosoma brucei is described. In T. brucei strain 427 ISG75 genes are present in tandem arrays at two loci, A and B, containing 5 and 2 copies, respectively. At the 3'-end of locus A, a single gene was identified that encodes a structural isoform of ISG75. This isoform contains a unique amino-terminal domain, whereas the rest of the protein is nearly identical to the polypeptides encoded by the other genes. This isoform is transcribed into a stable mRNA, but the expression of the derived polypeptide was below the detection limit. The ISG75 gene clusters are present on chromosomal bands 9' and 10, supporting the hypothesis of Gottesdiener et al. [25] that these bands contain allelic chromosomes. The total number of ISG75 genes is strain dependent, but at least one copy of the unique isoform is present in every variant tested.

Amino Acid Sequence↗
PubMed1994

VSG gene expression site control in insect form Trypanosoma brucei.

When the African trypanosome Trypanosoma brucei is taken up from mammals by a tse-tse fly, it replaces its variant surface glycoprotein (VSG) coat by a procyclin coat. Transcription of VSG genes stops in the fly, but transcription of sequences derived from the promoter area of the VSG expression site(s) remains high. Whether this is due to continuing high activity of one promoter or to low activity of many promoters was unclear. We have used the small differences between the sequences of different expression sites to show that multiple expression site promoters are active in insect form trypanosomes. This is confirmed by the low expression of single copy marker genes introduced into the transcribed area. However, if the expression site promoter is removed from the genomic location of the expression site and inserted in the non-transcribed spacer of the ribosomal DNA (rDNA), it is derepressed. Derepression of transcription can also be accomplished by replacing the promoter of an expression site by an rDNA promoter. We conclude that the down-regulation of VSG gene expression site promoters in insect form trypanosomes is affected by both the DNA sequence of the promoter and the genomic context in which it resides.

Animals↗
PubMed1993

N-glycosylation and deletion mutants of the human MDR1 P-glycoprotein.

P-glycoproteins are heavily glycosylated plasma membrane proteins, which confer multidrug resistance by pumping a range of different drugs from the cell. To investigate the significance of the conserved N-glycosylation sites present in the putative first extracellular loop of P-glycoproteins, we mutated one, two, or all three of these sites present in the human MDR1 P-glycoprotein. We also deleted a stretch of 20 amino acids, containing two of the three N-glycosylation sites. The effects of these mutations were studied by transfection into drug-sensitive cells. In vincristine-resistant transfected clones selected for similar steady state levels of membrane-bound P-glycoprotein, the absence of N-glycosylation did not alter the level or pattern of (cross-)resistance. However, the absence of N-glycosylation sites drastically reduced the efficiency with which drug-resistant clones could be generated. These findings suggest that N-glycosylation contributes to proper routing or stability of P-glycoprotein but not to drug transport per se. The deletion mutants demonstrated a clearly decreased and altered drug resistance pattern, even with a high level of P-glycoprotein in the plasma membrane. This, and possibly the observed lack of glycosylation of the remaining intact glycosylation sequence, suggests a constrained P-glycoprotein structure. Our findings support the current model for P-glycoprotein structure.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1992

The PARP and VSG genes of Trypanosoma brucei do not resemble RNA polymerase II transcription units in sensitivity to Sarkosyl in nuclear run-on assays.

Addition of the ionic detergent N-lauroylsarcosine (Sarkosyl) affects the efficiency of transcription of genes of the protozoan Trypanosoma brucei in nuclear run-on assays. Transcription of the PARP (procyclin or procyclic acidic repetitive protein), variant cell surface glycoprotein (VSG) and ribosomal RNA (rRNA) genes was resistant or increased after addition of Sarkosyl. In contrast, the transcription of seven protein coding house keeping genes and the mini-exon donor RNA (medRNA) genes was completely abolished by the addition of Sarkosyl, while the transcription of the 5S rRNA genes showed an intermediate sensitivity. We conclude that Sarkosyl can be used to discriminate between the different types of trypanosome transcription units. The PARP and VSG protein coding genes had previously been postulated to be transcribed by an RNA polymerase I-like enzyme on the basis of their resistance to the RNA polymerase II inhibitor alpha-amanitin. This model is now supported by their resistance to the addition of Sarkosyl.

Animals↗
PubMed1992

In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach.

A modular method for pursuing structure-based inhibitor design in the framework of a design cycle is presented. The approach entails four stages: (1) a design pathway is defined in the three-dimensional structure of a target protein; (2) this pathway is divided into subregions; (3) complementary building blocks, also called fragments, are designed in each subregion; complementarity is defined in terms of shape, hydrophobicity, hydrogen bond properties and electrostatics; and (4) fragments from different subregions are linked into potential lead compounds. Stages (3) and (4) are qualitatively guided by force-field calculations. In addition, the designed fragments serve as entries for retrieving existing compounds from chemical databases. This linked-fragment approach has been applied in the design of potentially selective inhibitors of triosephosphate isomerase from Trypanosoma brucei, the causative agent of sleeping sickness.

Animals↗
PubMed1991

RNA polymerase I can mediate expression of CAT and neo protein-coding genes in Trypanosoma brucei.

We show that the ribosomal RNA (rRNA) promoter can efficiently direct expression of protein-coding genes in the parasitic protozoan Trypanosoma brucei. The rRNA promoter was characterized by: (i) point mutations at the rRNA transcription initiation site which completely abolished its promoter function in transient CAT transformation assays; (ii) the alpha-amanitin resistance of transcription of rRNA promoter-neomycin phosphotransferase (neo) genes in stably transformed trypanosomes; and (iii) the nucleolar location of neo RNA, synthesized under the control of the rRNA promoter. The rRNA promoter-derived CAT mRNA required a 3' splice acceptor site and the neo mRNA was trans-spliced and polyadenylated. In situ hybridization revealed neo RNA at the nucleolus in stably transformed trypanosomes in which rRNA promoter-neo constructs were integrated either at a rRNA locus or at a locus for the procyclic acidic repetitive protein (PARP) coding genes. We postulate that trans-splicing, by uncoupling the requirement for transcription of protein-coding genes by RNA polymerase II, allows RNA polymerase I mediated protein-coding gene transcription, presumably because a 5' cap can be transferred to the pre-mRNA by trans-splicing.

Amanitins↗
PubMed1990

Procyclic acidic repetitive protein (PARP) genes located in an unusually small alpha-amanitin-resistant transcription unit: PARP promoter activity assayed by transient DNA transfection of Trypanosoma brucei.

At least one of the procyclic acidic repetitive protein (PARP or procyclin) loci of Trypanosoma brucei is a small (5- to 6-kilobase) polycistronic transcription unit which is transcribed in an alpha-amanitin-resistant manner. Its single promoter, as mapped by run-on transcription analysis and UV inactivation of transcription, is located immediately upstream of the first alpha-PARP gene. Transcription termination occurs in a region approximately 3 kilobases downstream of the beta-PARP gene. The location of the promoter was confirmed by its ability to direct transcription of the bacterial chloramphenicol acetyltransferase gene in insect-form (procyclic) T. brucei. The putative PARP promoter is located in the region between the 3' splice acceptor site (nucleotide position 0) and nucleotide position -196 upstream of the alpha-PARP genes. Regulatory regions influencing the levels of PARP expression may be located further upstream. We conclude that a single promoter, which is located very close to the 3' splice acceptor site of the alpha-PARP genes, directs the transcription of a small, polycistronic, and alpha-amanitin-resistant transcription unit.

Amanitins↗
PubMed1989

Alpha-amanitin resistant transcription of protein coding genes in insect and bloodstream form Trypanosoma brucei.

The variant cell surface glycoprotein (VSG) gene expression sites of the protozoan Trypanosoma brucei are transcribed by an unusual alpha-amanitin resistant RNA polymerase. All other protein coding genes of T.brucei examined to date are transcribed by an alpha-amanitin sensitive RNA polymerase, presumably RNA polymerase II. We now show that transcription of protein coding genes by alpha-amanitin resistant RNA polymerases is not unique to the bloodstream form expressed VSG gene expression sites, but also occurs in insect form trypanosomes, which do not express VSG genes. In insect form trypanosomes transcription of the procyclin or PARP genes is resistant to alpha-amanitin to a degree comparable with that of VSG and ribosomal RNA (rRNA) genes. Comparison of the alpha-amanitin resistantly transcribed PARP and VSG gene families shows that they both produce one of the most abundant mRNAs [1-3% of poly(A)+] and they both encode the major cell surface proteins of their respective life cycle stages. Transcription of a subset of functionally comparable protein coding genes is thus mediated by an RNA polymerase which differs from the regular RNA polymerase II.

Amanitins↗
PubMed1989

Transcription of telomere repeats in protozoa.

The telomerically located variant cell surface glycoprotein (VSG) gene expression sites of the protozoan parasite Trypanosoma brucei are transcribed by an unusual alpha-amanitin resistant RNA polymerase. We show that the telomere GGGTTA repeats located at the chromosome ends of T. brucei and the related protozoan T. equiperdum are also transcribed by alpha-amanitin resistant RNA polymerases. This transcription predominantly proceeds unidirectionally towards the end of the chromosome, in both bloodstream and insect form trypanosomes and results in the generation of heterogeneously sized steady state RNA. We postulate that telomere repeat transcription results from readthrough downstream of telomeric genes. Telomere repeat transcription was found in all seven protozoan species tested, but was alpha-amanitin resistant only in trypanosome species which exhibited antigenic variation. The data indicate that in some trypanosome species a subset of telomeres is transcribed by a different type of RNA polymerase.

Amanitins↗
PubMed1987

Crosses of two independently derived transgenic mice demonstrate functional complementation of the genes encoding heavy (HLA-B27) and light (beta 2-microglobulin) chains of HLA class I antigens.

In man a number of diseases are associated with certain alleles of MHC antigens. The most pronounced example is ankylosing spondylitis, which is strongly associated with HLA-B27. As a first step towards a model system to study the basis of this association, transgenic mice were generated that showed cell surface expression of the HLA-B27 antigen biochemically indistinguishable from HLA-B27 antigen expressed on human cells. This result was obtained by crossing two independently derived strains of mice, one of which is transgenic for the HLA-B27 heavy chain gene, and the other carrying and expressing the human beta 2m gene. Examination of HLA-B27 and human beta 2m mRNA in various tissues shows the two genes to be expressed in a coordinate fashion. The mRNA levels follow those of endogenous H-2 Class I genes.

Animals↗
PubMed1986

Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to domain VII of other eukaryotic 28S rRNAs.

We have localized the six ribosomal RNAs (rRNAs) which encode the 28S rRNA region of Trypanosoma brucei. These six rRNAs include two large rRNAs, 28S alpha (approx. 1840 nt) and 28S beta (approx. 1570 nt), and four small rRNAs of approximate sizes 220, 180, 140 and 70 nt. Three of these four small rRNAs (180, 70 and 140) are found at the 3' end of the 28S rRNAs region. Sequence analysis of this area shows that these three small rRNAs encode Domain VII, the last domain of secondary structure in the 28S rRNAs of eukaryotes. Hybridization of labeled nascent RNA to the cloned repeat unit and S1 nuclease protection analysis of putative precursors show that transcription initiates approximately 1.2 kb upstream of the 18S rRNA and terminates after the last small rRNA (140) at the 3' end of the 28S rRNA region. Analysis of three putative rRNA precursors suggests that the small rRNAs are not processed from the primary transcript until after the usual processing of the 5.8S rRNA region.

Base Sequence↗
PubMedDate not supplied

Targeting of exogenous DNA into Trypanosoma brucei requires a high degree of homology between donor and target DNA.

Integration of exogenous DNA into the trypanosome genome occurs by homologous recombination only. To test whether a high degree of homology between donor and target DNA is required, we have inserted marker genes for drug resistance into the promoter area of variant surface glycoprotein (VSG) gene expression sites of Trypanosoma brucei, using targeting fragments from two expression sites that are 92% identical. We observed integrations into expression sites that are known to be perfectly matched to the donor flanks, and into subsets of uncharacterized expression sites that are specific for each type of targeting fragment, and that could be similar or identical to the donor flanks. This requirement for very high homology was found in both procyclic and bloodstream-form trypanosomes. We speculate that trypanosomes have a mismatch repair system that suppresses recombination between divergent DNA sequences, and we discuss ways in which the trypanosome might circumvent the requirement for perfect DNA homology in the duplicative transposition of a VSG gene into a VSG gene expression site.

Animals↗
PubMedDate not supplied

Mechanisms mediating antigenic variation in Trypanosoma brucei.

Antigenic variation in Trypanosoma brucei is a highly sophisticated survival strategy involving switching between the transcription of one of an estimated thousand variant surface glycoprotein (VSG) genes. Switching involves either transcriptional control, resulting in switching between different VSG expression sites; or DNA rearrangement events slotting previously inactive VSG genes into an active VSG expression site. In recent years, considerable progress has been made in techniques allowing us to genetically modify infective bloodstream form trypanosomes. This is allowing us to reengineer VSG expression sites, and look at the effect on the mechanisms subsequently used for antigenic variation. We can now begin a dissection of a highly complicated survival strategy mediated by many different mechanisms operating simultaneously.

Animals↗