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J Kjems

Publications and source records attributed to J Kjems.

49 records · Page 3Linked to original sources

A unique tRNA intron in the variable loop of the extreme thermophile Thermofilum pendens and its possible evolutionary implications.

We describe, for the first time, an intron that is located in the variable loop of a tRNA. It is 18 nucleotides long and occurs within a precursor tRNAGly from the extreme thermophile Thermofilum pendens. The variable loop is less critical for tRNA function than the anticodon arm where other class III introns occur. This raises the possibility that tRNAs with a large variable loop (type II) arose from those with a small variable loop (type I) by retaining a splicing-deficient intron.

Base Sequence↗

Large intramolecular movement in human complement protein C3 induced by methylamine. A small-angle scattering study using monoclonal antibodies as markers.

The reaction of methylamine with complement protein C3, which involves cleavage of a labile thiol ester bond, yields a large intramolecular rearrangement. This is shown by small-angle neutron and X-ray scattering using a Fab antibody as a marker. For the C3(Fab) 1:1 complex, the methylamine reaction yields an increase in the radius of gyration, R, from 4.6 nm to 6.0 nm. In the absence of Fab the corresponding R values increase from 4.4 nm to 5.1 nm. It is estimated that the methylamine-induced increase in R may correspond to a movement of the epitope to a position 5 nm away from the centre of gravity of the C3 molecule. In agreement with this finding, the maximum distance within the C3(Fab) complex increases from 16 nm to 22 nm as a result of the methylamine reaction. In order to explain this conformational change, it is tentatively suggested that the methylamine-induced cleavage of the C3 thiol ester bond leads to a domain rotation within the C3 molecule. In agreement with this idea, the data is consistent with a model which enables a globular domain within the molecule to rotate without redistributing the molecular mass more than that corresponding to the radii of gyration observed.

Antibodies, Monoclonal↗

Comparison of transfer RNA and ribosomal RNA intron splicing in the extreme thermophile and archaebacterium Desulfurococcus mobilis.

The structure of the exon-intron boundary was compared for an intron within 23S ribosomal RNA of Desulfurococcus mobilis and a newly discovered intron in tRNA(Met) from the same organism. The occurrence of a putative common structural feature suggests that intron excision occurs by the same mechanism. The possible recognition of this structural feature by the cleavage enzyme was investigated for the ribosomal RNA intron using RNA substrates exhibiting various exon and intron deletions. The results support the involvement of the structural features in the cleavage process. The evolutionary implications of these results are considered.

Archaea↗

Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium Desulfurococcus mobilis.

The intron of the 23S rRNA gene of D. mobilis is excised from the pre-23S RNA at specific sites in vivo and subsequently ligated to form a stable circular RNA, with a normal 5'-3' phosphodiester bond, containing the entire intron sequence; 95% of this RNA codes for a protein of 194 amino acids that can be expressed in E. coli. Crude cell extracts from D. mobilis also induce a two-step slicing reaction in vitro, producing the same circular intron RNA but a low yield of ligated exons. Cleavage depends on the RNA structure adjacent to the cleavage site and yields a 3'-terminal phosphate. Splicing is enhanced by GTP, but does not require divalent metal ions. The cleavage and exon-splicing reactions resemble those found for tRNA introns in eukaryotes and a possible structural rationale for this similarity is considered together with its possible implications for the origin of eukaryotic rRNA and tRNA introns.

Amino Acid Sequence↗

Gene organization, transcription signals and processing of the single ribosomal RNA operon of the archaebacterium Thermoproteus tenax.

The single ribosomal RNA (rRNA) operon from the extreme thermophile and archaebacterium Thermoproteus tenax was sequenced. Sites of transcriptional initiation and termination were established and the processing sites on the primary transcript were mapped with nuclease S1. The operon contained genes coding for 16S and 23S RNAs but lacked those coding for tRNA and 5S RNA. Transcription initiates 175 bp upstream from the start of the 16S RNA gene (Wich et al., EMBO J. 6, 523-528, 1987) and terminates 49 bp downstream from the 23S RNA gene within a long pyrimidine sequence. An open reading frame downstream from the rRNA operon is transcribed. The sequences bordering both 16S and 23S RNA genes can form putative processing stems in the primary transcript that involve the whole of the 16S-23S RNA spacer. The stems contain irregular features that constitute processing signals and are conserved in other archaebacteria. The 16S RNA stem is cut prior to that of the 23S RNA and RNA maturation follows. An unusual 14 bp helix can form between the extremities of the transcript such that the whole transcript is highly structured and a fork-like structure is formed together with the processing stems. The 23S RNA sequence was aligned with other available 23S-like RNA sequences (Leffers et al., J. Mol. Biol. 195, in press): a putative secondary structure exhibiting archaebacterial-specific features was deduced using comparative sequence analyses. A rooted phylogenetic tree was also derived for the archaebacteria that confirms their division into three major subgroups.

Archaea↗

Evolutionary relationships amongst archaebacteria. A comparative study of 23 S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile and a thermophilic methanogen.

The 23 S RNA genes representative of each of the main archaebacterial subkingdoms, Desulfurococcus mobilis an extreme thermophile, Halococcus morrhuae an extreme halophile and Methanobacterium thermoautotrophicum a thermophilic methanogen, were cloned and sequenced. The inferred RNA sequences were aligned with all the available 23 S-like RNAs of other archaebacteria, eubacteria/chloroplasts and the cytoplasm of eukaryotes. Universal secondary structural models containing six major structural domains were refined, and extended, using the sequence comparison approach. Much of the present structure was confirmed but six new helices were added, including one that also exists in the eukaryotic 5.8 S RNA, and extensions were made to several existing helices. The data throw doubt on whether the 5' and 3' ends of the 23 S RNA interact, since no stable helix can form in either the extreme thermophile or the methanogen RNA. A few secondary structural features, specific to the archaebacterial RNAs were identified; two of these were supported by a comparison of the archaebacterial RNA sequences, and experimentally, using chemical and ribonuclease probes. Seven tertiary structural interactions, common to all 23 S-like RNAs, were predicted within unpaired regions of the secondary structural model on the basis of co-variation of nucleotide pairs; two lie in the region of the 23 S RNA corresponding to 5.8 S RNA but they are not conserved in the latter. The flanking sequences of each of the RNAs could base-pair to form long RNA processing stems. They were not conserved in sequence but each exhibited a secondary structural feature that is common to all the archaebacterial stems for both 16 S and 23 S RNAs and constitutes a processing site. Kingdom-specific nucleotides have been identified that are associated with antibiotic binding sites at functional centres in 23 S-like RNAs: in the peptidyl transferase centre (erythromycin-domain V) the archaebacterial RNAs classify with the eukaryotic RNAs; at the elongation factor-dependent GTPase centre (thiostrepton-domain II) they fall with the eubacteria, and at the putative amino acyl tRNA site (alpha-sarcin-domain VI) they resemble eukaryotes. Two of the proposed tertiary interactions offer a structural explanation for how functional coupling of domains II and V occurs at the peptidyl transferase centre. Phylogenetic trees were constructed for the archaebacterial kingdom, and for the other two kingdoms, on the basis of the aligned 23 S-like RNA sequences.(ABSTRACT TRUNCATED AT 400 WORDS)

Archaea↗

Dodecylsulfate-induced dissociation of human alpha 2-macroglobulin. An investigation using small-angle neutron scattering and the equilibrium dialysis technique.

The dodecylsulfate-induced dissociation of the tetrameric alpha 2-macroglobulin molecule from human plasma has been investigated by the small-angle neutron scattering (SANS) method. The great advantage with the SANS method is that, by using deuterated dodecylsulfate, and contrast variation by changing the D2O/H2O ratio of the solvent, we can selectively study just the protein part, or the dodecylsulfate part, of the protein-dodecylsulfate complex. More than a thousandfold excess of dodecylsulfate (on a molar basis) is needed in order to dissociate alpha 2-macroglobulin to particles with, on average, half the original molecular mass. By combining the SANS data with results obtained by the equilibrium dialysis technique it follows that, under these circumstances, approximately one thousand dodecylsulfate molecules are associated per alpha 2-macroglobulin molecule. From the significant increase in the radius of gyration, which accompanies the dissociation process, we can conclude that the dissociation is associated with a drastic change in conformation of the protein molecule. From measurements where the dodecylsulfate part of the complex dominates the SANS signal we also get an indication that the dodecylsulfate is randomly distributed along the polypeptide chain, rather than being arranged in large clusters at certain regions of the protein molecule. By fitting the parameters of a binding model to the experimental data we obtain the result that most of the more than one thousand bound dodecylsulfate molecules, necessary for dissociation, are involved in the change in conformation, and the dissociation process is, in fact, driven by the binding of a very few extra dodecylsulfate molecules to the dissociation products. These data indicate that the dodecylsulfate-induced dissociation of alpha 2-macroglobulin is probably more complicated than just breaking, for instance, a hydrophobic interaction.

Dialysis↗

Novel expression of the ribosomal RNA genes in the extreme thermophile and archaebacterium Desulfurococcus mobilis.

The single 16S/23S rRNA operon of the sulfur-dependent extreme thermophile Desulfurococcus mobilis is transcriptionally uncoupled from the single 5S RNA gene. Transcription of the former operon initiates at five sites, P5-P1. RNA polymerases intiating at sites P5-P2 terminate and then reinitiate at the next downstream site, thus providing a queue of polymerases at the primary initiation site P1. Putative promoter sequences that are AT-rich lie upstream from each site. Termination occurs at two main sites within long pyrimidine sequences downstream from the 23S RNA gene. A processing site for both large RNAs occurs at a secondary structural feature common to other archaebacterial rRNAs. Transcription of 5S RNA starts mainly at P1/5S at the 5' end of the gene with a low level of initiation from two upstream sites; a similar mechanism of initiation-termination-reinitiation appears to operate and the sites are all preceded by AT-rich promoter-like sequences. Termination occurs a few nucleotides beyound the 3' end of the 5S RNA. The mature RNA contains 133 nucleotides, has a 78% GC bp content and exhibits an unusually extended version of helix I with heterogeneous ends. The expression of the rRNA genes shows characteristics of eukaryotes, eubacteria and archaebacteria.

Journal Article↗

Solution structure of human plasma fibronectin using small-angle X-ray and neutron scattering at physiological pH and ionic strength.

Human plasma fibronectin has been investigated at physiological pH and ionic strength, by using small-angle X-ray and neutron scattering techniques. The results indicate that the molecule is disc shaped with an axial ratio of about 1:10. In fact, an ellipsoid of revolution with semiaxes a = 1.44 nm and b = c = 13.8 nm is in agreement with the experimental scattering data, and can also fully explain the rather extreme hydrodynamic parameters reported for fibronectin. The X-ray data gave a radius of gyration of 8.9 nm and a molecular weight of 510,000, whereas the neutron data gave slightly larger values, 9.5 nm and 530,000, respectively. From the volume of the best fitting ellipsoid we obtain a degree of hydration of 0.61 g H2O/g protein (dry weight). Neutron data, recorded at different D2O concentrations in the solvent, gave a match point of 43% D2O, which indicates that approximately 80% of the hydrogens bound to oxygen and nitrogen are exchangeable.

Fibronectins↗

A neutron scattering study of the ternary complex EF-Tu.GTP-valyl-tRNAVal1A.

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNAVal1A has been investigated in a hepes buffer of "pH" 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D2O where EF-Tu (42% D2O) and tRNA (71% D2O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNAVal1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same, 2.38 and 2.47 nm, respectively.

Binding Sites↗

Comparison of eubacterial and eukaryotic 5S RNA structures: a chemical modification study.

The 5S RNAs from Bacillus stearothermophilus and Saccharomyces cerevisiae were probed by nucleotide-specific reagents, with a view to compare and contrast their higher order structures. The progressive unfolding of the RNAs during heating, in the presence and absence of magnesium, was monitored. Evidence was provided for the double-helical segments which occur in the secondary structural models of both RNAs. The results also placed constraints on the possible structuring of the remainder of the RNA and yielded some insight into ways of folding up the molecule. Together with the data from our earlier studies, employing ribonucleases, these results provide a detailed picture of the structuring and topography of the 5S RNAs. The main structural differences between the eubacterial and eukaryotic RNAs occur throughout the loop D/helix IV/loop E/helix V arm; in particular strong evidence is provided for loop D of the eukaryotic RNA being involved in a tertiary interaction.

Geobacillus stearothermophilus↗