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  • 1.
    Alkemar, Gunnar
    et al.
    Södertörn University, Avdelning Naturvetenskap. Stockholm Universtiy.
    Nygård, Odd
    Södertörn University, Avdelning Naturvetenskap.
    A possible tertiary rRNA interaction between expansion segments ES3 and ES6 in eukaryotic 40S ribosomal subunits2003In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 9, no 1, p. 20-24Article in journal (Refereed)
    Abstract [en]

    Eukaryotic 16S-like ribosomal RNAs contain 12 so-called expansion segments, i.e., sequences not included in the RNA secondary structure core common to eubacteria, archaea, and eukarya. Two of these expansion segments, ES3 and ES6, are juxtaposed in the recent three-dimensional model of the eukaryotic 40S ribosomal subunit. We have analyzed ES3 and ES6 sequences from more than 2900 discrete eukaryotic species, for possible sequence complementarity between the two expansion segments. The data show that ES3 and ES6 could interact by forming a helix consisting of seven to nine contiguous base pairs in almost all analyzed species. We, therefore, suggest that ES3 and ES6 form a direct RNA-RNA contact in the ribosome.

  • 2.
    Alkemar, Gunnar
    et al.
    Stockholms universitet, Wenner-Grens institut.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Comparative analysis of rRNA sequences from the large ribosomal subunit of more than 900 eukaryotic species reveals structural similarities in expansion segment ES39.Manuscript (preprint) (Other academic)
  • 3.
    Alkemar, Gunnar
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Probing the secondary structure of expansion segment ES6 in 18S ribosomal RNA2006In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 45, no 26, p. 8067-8078Article in journal (Refereed)
    Abstract [en]

    Expansion segment ES6 in 18S ribosomal RNA is, unlike many other expansion segments, present in all eukaryotes. The available data suggest that ES6 is located on the surface of the small ribosomal subunit. Here we have analyzed the secondary structure of the complete ES6 sequence in intact ribosomes from three eukaryotes, wheat, yeast, and mouse, representing different eukaryotic kingdoms. The availability of the ES6 sequence for modification and cleavage by structure sensitive chemicals and enzymatic reagents was analyzed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The experimental results were used to restrict the number of possible secondary structure models of ES6 generated by the folding software MFOLD. The modification data obtained from the three experimental organisms were very similar despite the sequence variation. Consequently, similar secondary structure models were obtained for the ES6 sequence in wheat, yeast, and mouse ribosomes. A comparison of sequence data from more than 6000 eukaryotes showed that similar structural elements could also be formed in other organisms. The comparative analysis also showed that the extent of compensatory base changes in the suggested helices was low. The in situ structure analysis was complemented by a secondary structure analysis of wheat ES6 transcribed and folded in vitro. The obtained modification data indicate that the secondary structure of the in vitro transcribed sequence differs from that observed in the intact ribosome. These results suggest that chaperones, ribosomal proteins, and/or tertiary rRNA interactions could be involved in the in vivo folding of ES6.

  • 4.
    Alkemar, Gunnar
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Secondary structure of two regions in expansion segments ES3 and ES6 with the potential of forming a tertiary interaction in eukaryotic 40S ribosomal subunits2004In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 10, no 3, p. 403-411Article in journal (Refereed)
    Abstract [en]

    The 18S rRNA of the small eukaryotic ribosomal subunit contains several expansion segments. Electron microscopy data indicate that two of the largest expansion segments are juxtaposed in intact 40S subunits, and data from phylogenetic sequence comparisons indicate that these two expansion segments contain complementary sequences that could form a direct tertiary interaction on the ribosome. We have investigated the secondary structure of the two expansion segments in the region around the putative tertiary interaction. Ribosomes from yeast, wheat, and mouse-three organisms representing separate eukaryotic kingdoms-were isolated, and the structure of ES3 and part of the ES6 region were analyzed using the single-strand-specific chemical reagents CMCT and DMS and the double-strand-specific ribonuclease V1. The modification patterns were analyzed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The investigated sequences were relatively exposed to chemical and enzymatic modification. This is in line with their indicated location on the surface at the solvent side of the subunit. The complementary ES3 and ES6 sequences were clearly inaccessible to single-strand modification, but available for cleavage by double-strand-specific RNase V1. The results are compatible with a direct helical interaction between bases in ES3 and ES6. Almost identical results were obtained with ribosomes from the three organisms investigated.

  • 5.
    Bartish, Galyna
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Moradi, Hossein
    Södertörn University, School of Life Sciences. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Amino acids Thr56 and Thr58 are not essential for elongation factor 2 function in yeast2007In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 274, no 20, p. 5285-5297Article in journal (Refereed)
    Abstract [en]

    Yeast elongation factor 2 is an essential protein that contains two highly conserved threonine residues, T56 and T58, that could potentially be phosphorylated by the Rck2 kinase in response to environmental stress. The importance of residues T56 and T58 for elongation factor 2 function in yeast was studied using site directed mutagenesis and functional complementation. Mutations T56D, T56G, T56K, T56N and T56V resulted in nonfunctional elongation factor 2 whereas mutated factor carrying point mutations T56M, T56C, T56S, T58S and T58V was functional. Expression of mutants T56C, T56S and T58S was associated with reduced growth rate. The double mutants T56M/T58W and T56M/T58V were also functional but the latter mutant caused increased cell death and considerably reduced growth rate. The results suggest that the physiological role of T56 and T58 as phosphorylation targets is of little importance in yeast under standard growth conditions. Yeast cells expressing mutants T56C and T56S were less able to cope with environmental stress induced by increased growth temperatures. Similarly, cells expressing mutants T56M and T56M/T58W were less capable of adapting to increased osmolarity whereas cells expressing mutant T58V behaved normally. All mutants tested were retained their ability to bind to ribosomes in vivo. However, mutants T56D, T56G and T56K were under-represented on the ribosome, suggesting that these nonfunctional forms of elongation factor 2 were less capable of competing with wild-type elongation factor 2 in ribosome binding. The presence of nonfunctional but ribosome binding forms of elongation factor 2 did not affect the growth rate of yeast cells also expressing wild-type elongation factor 2.

  • 6.
    Bartish, Galyna
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Importance of individual amino acids in the Switch I region in eEF2 studied by functional complementation in S. cerevisiae2008In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 90, no 5, p. 736-748Article in journal (Refereed)
    Abstract [en]

    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.

  • 7.
    Bartish, Galyna
    et al.
    Stockholms universitet.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    The functional importance of the N- and C-terminal regions in elongation factor 2 from S. cerevisiaeManuscript (preprint) (Other academic)
  • 8.
    Holmberg, Lovisa
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Nygård, Odd
    Södertörn University, Avdelning Naturvetenskap.
    Release of ribosome-bound 5S rRNA upon cleavage of the phosphodiester bond between nucleotides A54 and A55 in 5S rRNA2000In: Biological chemistry (Print), ISSN 1431-6730, E-ISSN 1437-4315, Vol. 381, no 11, p. 1041-1046Article in journal (Refereed)
    Abstract [en]

    Reticulocyte lysates contain ribosome-bound and free populations of 5S RNA. The free population is sensitive to nuclease cleavage in the internal loop B, at the phosphodiester bond connecting nucleotides A54 and A55. Similar cleavage sites were detected in 5S rRNA in 60S subunits and 80S ribosomes. However, 5S rRNA in reticulocyte polysomes is insensitive to cleavage unless ribosomes are salt-washed. This suggests that a translational factor protects the backbone surrounding A54 from cleavage in polysomes. Upon nuclease treatment of mouse 60S subunits or reticulocyte lysates a small population of ribosomes released its 5S rRNA together with ribosomal protein L5. Furthermore, rRNA sequences from 5.8S, 28S and 18S rRNA were released. In 18S rRNA the sequences mainly originate from the 630 loop and stem (helix 18) in the 5' domain, whereas in 28S rRNA a majority of fragments is derived from helices 47 and 81 in domains III and V, respectively. We speculate that this type of rRNA-fragmentation may mimic a ribosome degradation pathway.

  • 9.
    Larsson, Sofia L
    et al.
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Nygård, Odd
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Proposed secondary structure of eukaryote specific expansion segment 15 in 28S rRNA from mice, rats, and rabbits2001In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 40, no 10, p. 3222-3231Article in journal (Refereed)
    Abstract [en]

    The expansion segments in eukaryotic ribosomal RNAs are additional RNA sequences not found in the RNA core common to both prokaryotes and eukaryotes. These regions show large species-dependent variations in sequence and size. This makes it difficult to create secondary structure models for the expansion segments exclusively based on phylogenetic sequence comparison. Here we have used a combination of experimental data and computational methods to generate secondary structure models for expansion segment 15 in 28S rRNA in mice, rats, and rabbits. The experimental data were collected using the structure sensitive reagents DMS, CMCT, kethoxal, micrococcal nuclease, RNase TI, RNase CL3. RNase VI, and lead(II) acetate, ES15 was folded with the computer program RNAStructure 3.5 using modification data and phylogenetic similarities between different ES15 sequences. This program uses energy minimization to find the most stable secondary structure of an RNA sequence. The presented secondary structure models include several common structural motifs, but they also have characteristics unique to each organism. Overall, the secondary structure models showed indications of an energetically stable but dynamic structure, easily accessible from the solution by the modification reagents, suggesting that the expansion segment is located on the ribosomal surface.

  • 10.
    Larsson, Sofia L
    et al.
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Sloma, Marika S
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Nygård, Odd
    Södertörn University, Avdelning Naturvetenskap.
    Conformational changes in the structure of domains II and V of 28S rRNA in ribosomes treated with the translational inhibitors ricin or alpha-sarcin2002In: Biochimica et Biophysica Acta, Gene Structure and Expression, ISSN 0167-4781, E-ISSN 1879-2634, Vol. 1577, no 1, p. 53-62Article in journal (Refereed)
    Abstract [en]

    Ricin and alpha-sarcin modify neighbouring sites in the so-called sarcin/ricin (S/R) loop of 28S rRNA, thereby destroying the necessary dynamic flexibility of the ribosome, and inhibiting the elongation factor assisted steps of the elongation cycle. The effects of the two translational inhibitors on the conformation of domains 11 and V of 28 S rRNA were investigated by chemical modification of programmed mouse ribosomes pretreated with ricin or alpha-sarcin. The results showed that the two ribosome-inactivating proteins (RIP) influenced the structure of the ribosomal RNA. Inhibitor-affected sites were located at or near sites previously proposed to be involved in functional domains. The modification patterns obtained after ricin or alpha-sarcin treatment of ribosomes were partially overlapping. However, there were several inhibitor-specific structural changes in 28S rRNA. Such changes were found at positions located at the GTPase activating centre of the ribosome and in the S/R domain, indicating that the structure in these regions of the ribosomes differed after treatment with the two inhibitors. These changes are consistent with ricin and alpha-sarcin having specific effects on eEF-2 and eEF-1 interaction with the ribosome, respectively.

  • 11.
    Moradi, Hossein
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Simoff, Ivailo
    Södertörn University, School of Life Sciences. Stockholm University.
    Bartish, Galyna
    Södertörn University, School of Life Sciences. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Functional features of the C-terminal region of yeast ribosomal protein L52008In: Molecular Genetics and Genomics, ISSN 1617-4615, E-ISSN 1617-4623, Vol. 280, no 4, p. 337-350Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to analyze the functional importance of the C-terminus of the essential yeast ribosomal protein L5 (YrpL5). Previous studies have indicated that the C-terminal region of YrpL5 forms an alpha-helix with a positively charged surface that is involved in protein-5S rRNA interaction. Formation of an YrpL5 center dot 5S rRNA complex is a prerequisite for nuclear import of YrpL5. Here we have tested the importance of the alpha-helix and the positively charged surface for YrpL5 function in Saccharomyces cerevisiae using site directed mutagenesis in combination with functional complementation. Alterations in the sequence forming the putative alpha-helix affected the functional capacity of YrpL5. However, the effect did not correlate with a decreased ability of the protein to bind to 5S rRNA as all rpL5 mutants tested were imported to the nucleus whether or not the alpha-helix or the positively charged surface were intact. The alterations introduced in the C-terminal sequence affected the growth rate of cells expressing mutant but functional forms of YrpL5. The reduced growth rate was correlated with a reduced ribosomal content per cell indicating that the alterations introduced in the C-terminus interfered with ribosome assembly.

  • 12.
    Nygård, Odd
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Att söka skyddad geografisk- eller ursprungsbeteckning2012Book (Other (popular science, discussion, etc.))
  • 13. Nygård, Odd
    Etableringen av EU:s ekologiska nätverk Natura 2000 i Sverige: ett möte mellan två naturvårdskulturer2013Book (Other academic)
    Abstract [sv]

    Sveriges anslutning till EU i januari 1995 innebar att gemenskapens regler för bevarande av biologisk mångfald skulle genomföras i Sverige. Enligt dessa regler skulle ett ekologiskt nätverk av skyddade områden kallat Natura 2000 skapas för att garantera gynnsam bevarandestatus för ett urval av Europas arter och naturtyper. Hur nätverk skulle upprättas och vilka typer av objekt som skulle ingå i detta fanns angivet i art- och habitatdirektivet samt i fågeldirektivet.

    De båda direktiven hade arbetats fram inom EG vilket betydde att de baserades på en Centraleuropeisk naturvårdstradition samt att de i allt väsentligt var anpassade till de dåvarande medlemsstaternas behov och prioriteringar.

    I och med Sveriges inträde i unionen ställdes gemenskapens syn på naturvård mot en tradition som successivt vuxit fram under närmare ett sekels arbete med att bevara värdefull svensk natur. Denna tradition var bland annat anpassad till annorlunda naturförhållanden och baserades på andra förvaltningstraditioner, bevarandestrategier och naturvårdsprioriteringar.

    I boken beskrivs arbetet med att genomföra de båda naturvårdsdirektiven i Sverige: från medlemskapsförhandlingarna fram till dess att direktiven slutligen hade inkorporerats i svensk lagstiftning och huvudparten av de objekt som i dag ingår i Natura-nätverket hade identifierats och rapporterats till EU.I bokens avslutande kapitel diskuteras utfallet av det svenska arbetet med Natura 2000.

  • 14.
    Nygård, Odd
    et al.
    Södertörn University, School of Life Sciences.
    Alkemar, Gunnar
    Södertörn University, School of Life Sciences. Stockholm University.
    Larsson, Sofia L
    Södertörn University, School of Life Sciences. Stockhom University.
    Analysis of the secondary structure of expansion segment 39 in ribosomes from fungi, plants and mammals2006In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 357, no 3, p. 904-916Article in journal (Refereed)
    Abstract [en]

    The structure of expansion segment 39, E539, in eukaryotic 23 S-like ribosomal RNA was analysed using a combination of chemical and enzymic reagents. Ribosomes were isolated from yeast, wheat, mouse, rat and rabbit, five organisms representing three different eukaryotic kingdoms. The isolated ribosomes were treated with structure-sensitive chemical and enzymic reagents and the modification patterns analysed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The expansion segment was relatively accessible to modification by both enzymic and chemical probes, suggesting that ES39 was exposed on the surface of the ribosomes. The collected modification data were used in secondary structure modelling of the expansion segment. Despite considerable variation in both sequence and length between organisms from different kingdoms, the structure analysis of the expansion segment gave rise to structural fingerprints that allowed identification of homologous structures in ES39 from fungi, plants and mammals. The homologous structures formed an initial helix and an invariant hairpin connected to the initial helix via a long single-stranded loop. The remaining part of the ES39 sequences accounted for most of the length variation seen between the analysed species. This part could form additional, albeit less similar, hairpins. A comparison of ES39 sequences from other fungi, plants and mammals showed that identical structures could be formed in these organisms.

  • 15.
    Nygård, Odd
    et al.
    Södertörn University, School of Life Sciences, Coastal Management Research Center (COMREC). Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Wramner, Per
    Södertörn University, School of Life Sciences, Environmental science.
    Godset Almnäs i Norra Fågelås socken: odlingshistoria och markanvändning2012Report (Other academic)
  • 16. Nygård, Odd
    et al.
    Wramner, Per
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Terroir - ett nyckelbegrepp för att ge lokalproducerade livsmedel geografisk identitet2013In: Från matproduktion till gastronomi / [ed] Paulina Rytkönen, Madeleine Bonow, Per Wramner, Huddinge: Södertörns högskola , 2013, p. 201-235Chapter in book (Other academic)
  • 17.
    Simoff, Ivailo
    et al.
    Södertörn University, School of Life Sciences.
    Moradi, Hossein
    Södertörn University, School of Life Sciences.
    Nygård, Odd
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Environmental science.
    Functional characterization of ribosomal protein L15 from Saccharomyces cerevisiae2009In: Current Genetics, ISSN 0172-8083, E-ISSN 1432-0983, Vol. 55, no 2, p. 111-125Article in journal (Refereed)
    Abstract [en]

    In this study we provide general information on the little studied eukaryotic ribosomal protein rpL15. Saccharomyces cerevisiae has two genes, YRPL15A and YRPL15B that could potentially code for yeast rpL15 (YrpL15). YRPL15A is essential while YRPL15B is dispensable. However, a plasmid-borne copy of the YRPL15B gene, controlled by the GAL1 promoter or by the promoter controlling expression of the YRPL15A gene, can functionally complement YrpL15A in yeast cells, while the same gene controlled by the authentic promoter is inactive. Analysis of the levels of YrpL15B-mRNA in yeast cells shows that the YRPL15B gene is inactive in transcription. The function of YrpL15A is highly resilient to single and multiple amino acid substitutions. In addition, minor deletions from both the N- and C-terminal ends of YrpL15A has no effect on protein function, while addition of a C-terminal tag that could be used for detection of plasmid-encoded YrpL15A is detrimental to protein function. YrpL15A could also be replaced by the homologous protein from Arabidopsis thaliana despite almost 30% differences in the amino acid sequence, while the more closely related protein from Schizosaccharomyces pombe was inactive. The lack of function was not caused by a failure of the protein to enter the yeast nucleus.

  • 18.
    Simoff, Ivailo
    et al.
    Södertörn University, School of Life Sciences. Stockholms universitet.
    Moradi, Hossein
    Södertörn University, School of Life Sciences. Stockholms universitet.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Implications of N-terminal sequence elements in S. cerevisiae ribosomal protein L5Manuscript (preprint) (Other academic)
    Abstract [en]

    Yeast ribosomal protein L5 (YrpL5) is an essential 5S rRNA-binding protein that forms the central protuberance of the large ribosomal subunit. Formation of the binary rpL5.5S rRNA complex is a prerequisite for nuclear import of rpL5 and for ribosome assembly. The involvment of the N-terminal sequences of YrpL5 in 5S rRNA interaction and nuclear import was studied by mutagenesis and functional complementation in S. cerevisiae. Furthermore, the ability of YrpL5 orthologous proteins from M. musculus (MrpL5), D. melanogaster (DrpL5) and A. thaliana (ArpL5) were non-functional in yeast cells. Nuclear import of YrpL5 requires conserved sequence elements in the N-terminus. Despite the presence of these elements in ArpL5, this protein was not recognized by the nuclear import machinery in yeast. This failure was probably due to lack of stable complex formation with yeast 5S rRNA.

  • 19.
    Simoff, Ivailo
    et al.
    Södertörn University, School of Life Sciences.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Locating the nuclear localization signal in S. cerevisiae ribosomal protein L15AManuscript (preprint) (Other academic)
    Abstract [en]

    Newly synthesized ribosomal proteins (r-proteins) are efficiently transported from the cytoplasm to the site of ribosome assembly in the nucleolus. Nuclear import is facilitated by the presence of a nuclear localization signal (NLS) whereas the nucleolar accumulation requires a nucleolar localization signal (NoLS). In this study we located the NLS of the essential r-protein YrpL15A by studying the ability of various YrpL15A-gfp constructs to enter the nucleus and nucleolus. We found that the NLS signal is located in the C-terminal part of the protein. The identified sequence was sufficient to direct the reporter construct to the nucleus in yeast cells. This protein fragment contains a sequence that resembles a classical monopartite NLS. The fragment also contains a NoLS as seen by the partial co-localization of reporter construct with the nucleolar marker protein nop1. Orthologs of YrpL15A such as rpL15B from Arabidopsis thaliana and rpL15A from Schizosaccharomyces pombe were also able to enter the nucleus and nucleolus of yeast cells, suggesting that their NLS and NoLS are similar to that found in YrpL15. These results are discussed in relation to sequence similarities/dissimilarities. YrpL15A containing a C-terminal tag was unable to assemble into large ribosomal subunits that were transported to the cytoplasm.

  • 20. Sloma, Marika Salonen
    et al.
    Nygård, Odd
    Södertörn University, Avdelning Naturvetenskap.
    Chemical accessibility of 18S rRNA in native ribosomal complexes: Interaction sites of mRNA, tRNA and translation factors2001In: Biological chemistry (Print), ISSN 1431-6730, E-ISSN 1437-4315, Vol. 382, no 4, p. 661-668Article in journal (Refereed)
    Abstract [en]

    During protein synthesis the ribosome interacts with ligands such as mRNA, tRNA and translation factors. We have studied the effect of ribosome-ligand interaction on the accessibility of 18S rRNA for single strand-specific modification in ribosomal complexes that have been assembled in vivo, i. e. native polysomes. A comparison of the modification patterns derived from programmed and non-programmed ribosomes showed that bases in the 630- and 1060-loops (530- and 790-loops in E. coli) together with two nucleotides in helices 33 and 34 were protected from chemical modification. The majority of the protected sites were homologous to sites previously suggested to be involved in mRNA and/or tRNA binding in prokaryotes and eukaryotes, implying that the interaction sites for these ligands are similar, if not identical, in naturally occurring programmed ribosomes and in in vitro assembled ribosomal complexes. Additional differences between programmed and non-programmed ribosomes were found in hairpin 8. The bases in helix 8 showed increased exposure to chemical modification in the programmed ribosomes. In addition, structural differences in helices 36 and 37 were observed between native 80S run-off ribosomes and 80S ribosomes assembled from isolated 40S and 60S subunits.

  • 21.
    Sloma, Marika Salonen
    et al.
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Nygård, Odd
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Possible interaction sites of mRNA, tRNA, translation factors and the nascent peptide in 5S, 5.8S and 28S rRNA in in vivo assembled eukaryotic ribosomal complexes2001In: Biochimica et Biophysica Acta, Gene Structure and Expression, ISSN 0167-4781, E-ISSN 1879-2634, Vol. 1521, no 1-3, p. 30-38Article in journal (Refereed)
    Abstract [en]

    We have investigated possible interaction sites for mRNA, tRNA. translation factors and the nascent peptide on 5S, 5.8S and 28S rRNA in in vivo assembled translational active mouse ribosomes by comparing the chemical footprinting patterns derived from native polysomes, salt-washed polysomes (mainly lacking translational factors) and salt-washed runoff ribosomes (lacking mRNA, tRNA and translational factors). Several ligand-induced footprints were observed in 28S rRNA while no reactivity changes were seen in 5S and 5.8S rRNA. Footprints derived from mRNA, tRNA and/or the nascent peptide chain were observed in domain I of 28S rRNA (hairpin 23), in domain II (helix 37/38 and helices 42 and 43 and in the eukaryotic expansion segment 15), in domain IV (helices 67 and 74) and in domain V (helices 94 and 96 and in the peptidyl transferase ring). Some of the protected sites were homologous to sites previously suggested to be involved in mRNA. tRNA and/or peptide binding in in vitro assembled prokaryotic complexes. Additional footprints were located in regions that have not previously been found involved in ligand binding. Part of these sites could derive from the nascent peptide in the exit channel of the ribosome.

  • 22.
    Wramner, Per
    et al.
    Södertörn University, School of Life Sciences, Coastal Management Research Center (COMREC). Södertörn University, School of Life Sciences, Environmental science.
    Nygård, Odd
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Från naturskydd till bevarande av biologisk mångfald: Utvecklingen av naturvårdsarbetet i Sverige med särskild inriktning på områdesskyddet2010Report (Other academic)
    Abstract [sv]

    Boken beskriver och analyserar utvecklingen av naturvårdsarbetet i Sverige under dess första sekel. Tonvikten ligger på områdesskyddet och de naturvetenskapliga, naturvårdsideologiska och naturvårdspolitiska grunderna för detta. Tyngdpunkten ligger på den senare delen av naturskyddets utveckling i Sverige, en period som hittills endast tilldragit sig begränsat forskningsintresse.

    I en kommande bok kommer skeendena i samband med införandet av EU:s naturvårdsdirektiv i Sverige att behandlas mer ingående.

  • 23.
    Wramner, Per
    et al.
    Södertörn University, School of Life Sciences, Coastal Management Research Center (COMREC). Södertörn University, School of Life Sciences, Environmental science.
    Nygård, Odd
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Godset Almnäs i Norra Fågelås socken: natur- och naturvårdsförhållanden2012Report (Other academic)
  • 24.
    Wramner, Per
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Nygård, Odd
    Småskalig livsmedelsproduktion som ett instrument för att främja naturvården i odlingslandskapet2013In: Från matproduktion till gastronomi / [ed] Paulina Rytkönen, Madeleine Bonow, Per Wramner, Huddinge: Södertörns högskola , 2013, p. 181-200Chapter in book (Other academic)
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