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The KRR1 gene encodes a protein required for 18S rRNA synthesis and 40S ribosomal subunit assembly in Saccharomyces cerevisiae.

100%
Gromadka R., Rytka J.
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2000
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vol. 47
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issue 4
993-1005
EN
The newly discovered Saccharomyces cerevisiae gene KRR1 (YCL059c) encodes a protein essential for cell viability. Krr1p contains a motif of clustered basic amino acids highly conserved in the evolutionarly distant species from yeast to human. We demonstrate that Krr1p is localized in the nucleolus. The KRR1 gene is highly expressed in dividing cells and its expression ceases almost completely when cells enter the stationary phase. In vivo depletion of Krr1p leads to drastic reduction of 40S ribosomal subunits due to defective 18S rRNA synthesis. We propose that Krr1p is required for proper processing of pre-rRNA and the assembly of preribosomal 40S subunits.
2
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Kolejny wielki genom poznany przy udziale polskich laboratoriów genom ziemniaka zsekwencjonowany

81%
Gromadka R., Gawor J., Szczęsny P., Zagórski W.
Kosmos
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2011
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vol. 60
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issue 3-4
491-497
PL
W połowie lipca 2011, w Nature ukazał się artykuł "Sekwencja genomu ziemniaka i jej analiza" autorstwa Konsorcjum Sekwencjonowania Genomu Ziemniaka (PGSC). W skład tego Konsorcjum wchodziły 32 zespoły z 14 krajów - znaczących producentów ziemniaków. Współautorami ze strony polskiej, tej wielo autorskiej pracy (94 badaczy, 25 zespołów wiodących) byli członkowie zespołu z Instytutu Biochemii i Biofizyki PAN. Prace Konsorcjum, rozpoczęte w 2007 roku, wspierane były przez rządy państw uczestniczących w programie, w tym Polskiego Ministerstwa Nauki i Szkolnictwa Wyższego, (projekt 47/PGS/2006/01). To trzeci wielki genom (po S. cerevisiae i P. caudatum) w którego poznaniu uczestniczyli pracownicy IBB PAN. Konsorcjum zsekwencjonowało dwa szczepy ziemniaka DM1-3 516 R44 and RH 89-039-16. Szczep DM zsekwencjonowano metodą "shotgun" wykorzystując m. in. platformę sekwencjonowań genomowych IBB PAN (sekwenator Roche GS FLX Titanium 454). Metodami ab initio określono zasób genów kodowanych przez otrzymane sekwencje. Wyniki zweryfikowano analizami transkryptomu objawiającego się w różnych tkankach, czy stadiach rozwojowych oraz w wyniku kontrolowanego stresu. Sumarycznie zidentyfikowano w otrzymanej sekwencji 39031 genów kodujących białka. 25,3% tych genów koduje transkrypty mogące podlegać alternatywnemu składaniu, a więc kontrolujące średnio 2-3 odmienne białka. Wydaje się więc, że w genomie ziemniaka zakodowana jest informacja na temat syntezy ok. 100,000 różnych białek. Porównanie sekwencji DM and RH dowodzi, że ziemniak to roślina wysoce heterozygotyczna. Mutacje punktowe (SNP) występują średnio co 40 nukleotydów, a insercje lub delecje co 394 pary zasad. Wskazuje to wyraźnie, że genom ziemniaka jest niestabilny, co zapewne znajduje swoje odbicie w łatwej degeneracji odmian uprawnych.
EN
In mid-July 2011 Nature published the paper "Genome sequence and analysis of the tuber crop potato" by the Potato Genome Sequencing Consortium - PGSC. This international consortium consisted of 32 teams from 14 countries that are significant potato producers are active in potato breeding programs. The Polish team, representing the PAS Institute of Biochemistry and Biophysics, co-authored the paper, which was signed by 94 consortium members from 25 leading institutions. The work, begun in 2007, was funded by the participating countries' governments - including Poland's Ministry of Science and Higher Education - within the 47/PGS/2006/01. After the yeast and paramecium genomes this is the third large genome sequencing in which IBB teams have participated. Consortium sequenced two strains of potato DM1-3 516 R44 and RH 89-039-16. The DM strain was sequenced by the consortium using the "Shotgun method" on genome sequencing platforms, one of which was created in Warsaw (Roche GS FLX Titanium 454 sequencer).The second strain sequenced was a laboratory S. tuberosum heterodiploid RH 89-039-16. Ab initio predictions of genes and their functions were verified by RNA transcriptome analysis done for various tissues, development stages and under stress. This allowed for the identification of 39031 gene-coding proteins. 25,3% of these genes produce RNA that undergoes splicing, coding for an average of 2-3 different proteins. It therefore seems that the potato genome codes for approximately 100 000 different proteins. Comparisons of the DM and RH sequences show that the potato exhibits high heterozygosity. Single-nucleotiste polymorphisms (SNP) are encountered on average every 40 nucleotides, while insertions or deletions (so-called indel) of an average length of 12.8 nucleotides are encountered on average every 394 base pairs. This data clearly shows that gene damage in the potato genome is a frequent occurrence, which accounts for the easy degeneration of industrial strains.
3
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Functional and physical interactions of Krr1p, a Saccharomyces cerevisiae nucleolar protein.

81%
Gromadka R., Karkusiewicz I., Rempoła B., Rytka J.
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vol. 51
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issue 1
173-187
EN
The Krr1 protein of Saccharomyces cerevisiae is involved in processing of pre-rRNA and assembly of pre-ribosomal 40S subunits. To further investigate the function of Krr1p we constructed a conditional cold sensitive mutant krr1-21, and isolated seven genes from Schizosaccharomyces pombe whose products suppressed the cold sensitive phenotype of krr1-21 cells. Among the multicopy suppressors we found genes coding for translation elongation factor EF-1α, a putative ribose methyltransferase and five genes encoding ribosomal proteins. Using the tandem affinity purification (TAP) method we identified thirteen S. cerevisiae ribosomal proteins interacting with Krr1p. Taken together, these results indicate that Krr1p interacts functionally as well as physically with ribosomal proteins. Northern blot analysis revealed that changes in the level of krr1-21 mRNA were accompanied by similar changes in the level of mRNAs of genes encoding ribosomal proteins. Thus, Krr1p and the genes encoding ribosomal proteins it interacts with seem to be coordinately regulated at the level of transcription.
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