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Title Journal of Molecular Evolution Issue data New York : Springer , 2017 ISSN 0022-28441432-1432 Form. Descr. časopisy - journals Year, No. Vol. 85 no. 1-2 (2017) Language English Country United States of America URL Link na zdrojový dokument Public work category GII Catal.org. BB301 - Univerzitná knižnica Univerzity Mateja Bela v Banskej Bystrici Database xpca - PUBLIKAČNÁ ČINNOSŤ References - PERIODIKÁ - Súborný záznam periodika (1) - PUBLIKAČNÁ ČINNOSŤ References PERIODIKÁ-Súborný záznam periodika ARTICLES 2017: On the possibility of an early evolutionary origin for the spliced leader trans-splicing 
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Title On the possibility of an early evolutionary origin for the spliced leader trans-splicing Author info Zuzana Krchňáková, Juraj Krajčovič, Matej Vesteg Author Krchňáková Zuzana (40%)
Co-authors Krajčovič Juraj (30%)
Vesteg Matej 1982- (30%) UMBFP09 - Katedra biológie a ekológie
Source document Journal of Molecular Evolution. Vol. 85, no. 1-2 (2017), pp. 37-45. - New York : Springer, 2017 Keywords biológia - biology evolučná biológia - evolutionary biology Language English Country United States of America systematics 57 Annotation © 2017 Springer Science+Business Media, LLC Trans-splicing is a process by which 5′- and 3′-ends of two pre-RNA molecules transcribed from different sites of the genome can be joined together to form a single RNA molecule. The spliced leader (SL) trans-splicing is mediated by the spliceosome and it allows the replacement of 5′-end of pre-mRNA by 5′(SL)-end of SL-RNA. This form of splicing has been observed in many phylogenetically unrelated eukaryotes. Either the SL trans-splicing (SLTS) originated in the last eukaryotic common ancestor (LECA) (or even earlier) and it was lost in most eukaryotic lineages, or this mechanism of RNA processing evolved several times independently in various unrelated eukaryotic taxa. The bioinformatic comparisons of SL-RNAs from various eukaryotic taxonomic groups have revealed the similarities of secondary structures of most SL-RNAs and a relative conservation of their splice sites (SSs) and Sm-binding sites (SmBSs). We propose that such structural and functional similarities of SL-RNAs are unlikely to have evolved repeatedly many times. Hence, we favor the scenario of an early evolutionary origin for the SLTS and multiple losses of SL-RNAs in various eukaryotic lineages. Public work category ADC No. of Archival Copy 40077 Repercussion category YAGUE-SANZ, Carlo - HERMAND, Damien. SL-quant : a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data. In GigaScience, 2018, vol. 7, no. 7.
LAROCHE-JOHNSTON, Félix - MONAT, Caroline - COULOMBE, Samy - COUSINEAU, Benoit. Bacterial group II introns generate genetic diversity by circularization and trans-splicing from a population of intron-invaded mRNAs. In PLoS genetics. ISSN 1553-7390, 2018, vol. 14, no. 11.
CLAYTON, Christine. Regulation of gene expression in trypanosomatids : living with polycistronic transcription. In Open biology. ISSN 2046-2441, 2019, vol. 9, no. 6, pp. [1-36].
DANKS, Gemma B. - GALBIATI, Heloisa - RAASHOLM, Martina - TORRES CLEUREN, Yamila N. - VALEN, Eivind - NAVRATILOVA, Pavla - THOMPSON, Eric M. Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. In BMC genomics. ISSN 1471-2164, 2019, vol. 20, no. 1, pp. 1-14.
GUMIŃSKA, Natalia - ZAKRYŚ, Bożena - MILANOWSKI, Rafał. A new type of circular RNA derived from nonconventional introns in nuclear genes of euglenids. In Journal of molecular biology. ISSN 0022-2836, 2021, vol. 433, no. 3.
XU, Bingbing - MENG, Yijun - JIN, Yongfeng. RNA structures in alternative splicing and back-splicing. In Wiley interdisciplinary reviews : RNA. ISSN 1757-7004, 2021, vol. 12, no. 1.
OLSON, Peter D. - TRACEY, Alan - BAILLIE, Andrew - JAMES, Katherine - DOYLE, Stephen R. - BUDDENBORG, Sarah K. - RODGERS, Faye H. - HOLROYD, Nancy - BERRIMAN, Matt. Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection. In BMC Biology. ISSN 1741-7007, 2020, vol. 18, no. 1.
CHENG, Lin - ZHANG, Yu - ZHANG, Yi - CHEN, Tao - XU, Yong Zhen - RONG, Yikang S. Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development. In PLoS genetics. ISSN 1553-7390, 2020, vol. 16, no. 10.
WENZEL, Marius A. - MULLER, Berndt - PETTITT, Jonathan. SLIDR and SLOPPR : flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data. In BMC Bioinformatics. ISSN 1471-2105, 2021, vol. 22, no. 1, pp. 1-30.
YANG, Hsiao-Pei - WENZEL, Marius - HAUSER, Duncan A. - NELSON, Jessica M. - XU, Xia - ELIAS, Marek - LI, Fay-Wei. Monodopsis and vischeria genomes shed new light on the biology of eustigmatophyte algae. In Genome biology and evolution. ISSN 1759-6653, 2021, vol. 13, no. 11, pp. 1-12.
CALVELO, Javier - BREHM, Klaus - IRIARTE, Andrés - KOZIOL, Uriel. Trans-splicing in the cestode Hymenolepis microstoma is constitutive across the life cycle and depends on gene structure and composition. In International journal for parasitology. ISSN 0020-7519, 2023, vol. 53, no. 2, pp. 103-117.
WAITHAKA, Albina - MAIAKOVSKA, Olena - GRIMM, Dirk - DO NASCIMENTO, Larissa Melo - CLAYTON, Christine. Sequences and proteins that influence mRNA processing in Trypanosoma brucei: evolutionary conservation of SR-domain and PTB protein functions. In PLoS neglected tropical diseases. ISSN 1935-2735, 2022, vol. 16, no. 10, pp. 1-31.
ALACID, Elisabet - IRWIN, Nicholas A. T. - SMILANSKY, Vanessa - MILNER, David S. - KILIAS, Estelle S. - LEONARD, Guy - RICHARDS, Thomas A. A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa. In Open biology. ISSN 2046-2441, 2022, vol. 12, no. 8, pp. 1-17.
GARRIDO, Oswgladys - FERRER, Elizabeth. Characterization of three cDNAs obtained by spliced leader-PCR screening of a Taenia solium cDNA library. In Uniciencia. ISSN 1011-0275, 2022, vol. 36, no. 1, pp. 1-10.
SCHIERWATER, Bernd - DESALLE, Rob. Invertebrate zoology: a tree of life approach. Boca Raton : CRC press, 2021. 627 p. ISBN 978-0-429-15905-3.
Catal.org. BB301 - Univerzitná knižnica Univerzity Mateja Bela v Banskej Bystrici Database xpca - PUBLIKAČNÁ ČINNOSŤ References PERIODIKÁ-Súborný záznam periodika 
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Title Journal of Molecular Evolution Issue data New York : Springer , 2012 ISSN 0022-28441432-1432 Form. Descr. časopisy - journals Year, No. Vol. 75 no. 3-4 (2012) Language English Country United States of America URL Link na zdrojový dokument Public work category GII Catal.org. BB301 - Univerzitná knižnica Univerzity Mateja Bela v Banskej Bystrici Database xpca - PUBLIKAČNÁ ČINNOSŤ References - PERIODIKÁ - Súborný záznam periodika (1) - PUBLIKAČNÁ ČINNOSŤ References PERIODIKÁ-Súborný záznam periodika ARTICLES 2012: Euglena gracilis and trypanosomatids possess common patterns in predicted mitochondrial targeting presequences journal
Title Journal of Molecular Evolution Issue data New York : Springer , 2012 ISSN 0022-28441432-1432 Form. Descr. časopisy - journals Year, No. Vol. 74 no. 3-4 (2012) Language English Country United States of America URL Link na zdrojový dokument Public work category GII Catal.org. BB301 - Univerzitná knižnica Univerzity Mateja Bela v Banskej Bystrici Database xpca - PUBLIKAČNÁ ČINNOSŤ References - PERIODIKÁ - Súborný záznam periodika (1) - PUBLIKAČNÁ ČINNOSŤ References PERIODIKÁ-Súborný záznam periodika ARTICLES 2012: Selective forces for the origin of spliceosomes journal
Title Euglena gracilis and trypanosomatids possess common patterns in predicted mitochondrial targeting presequences Author info Katarína Krnáčová ... [et al.] Author Krnáčová Katarína (40%)
Co-authors Vesteg Matej 1982- (30%)
Hampl Vladimír (5%)
Vlček Čestmír (5%)
Horváth Anton (20%)
Source document Journal of Molecular Evolution. Vol. 75, no. 3-4 (2012), pp. 119-129. - New York : Springer, 2012 Keywords červenoočká - Euglenoids - Euglenida genómy - genomes kinetoplastidy - kinetoplastids molekulárna fylogenetika - molecular phylogenetics Language English systematics 577 Annotation Euglena gracilis possessing chloroplasts of secondary green algal origin and parasitic trypanosomatids Trypanosoma brucei, Trypanosoma cruzi and Leishmania major belong to the protist phylum Euglenozoa. Euglenozoa might be among the earliest eukaryotic branches bearing ancestral traits reminiscent of the last eukaryotic common ancestor (LECA) or missing features present in other eukaryotes. LECA most likely possessed mitochondria of endosymbiotic alpha-proteobacterial origin. In this study, we searched for the presence of homologs of mitochondria-targeted proteins from other organisms in the currently available EST dataset of E. gracilis. The common motifs in predicted N-terminal presequences and corresponding homologs from T. brucei, T. cruzi and L. major (if found) were analyzed. Other trypanosomatid mitochondrial protein precursor (e. g., those involved in RNA editing) were also included in the analysis. Mitochondrial presequences of E. gracilis and these trypanosomatids seem to be highly variable in sequence length (5-118 aa), but apparently share statistically significant similarities. In most cases, the common (M/L)RR motif is present at the N-terminus and it is probably responsible for recognition via import apparatus of mitochondrial outer membrane. Interestingly, this motif is present inside the predicted presequence region in some cases. In most presequences, this motif is followed by a hydrophobic region rich in alanine, leucine, and valine. In conclusion, either RR motif or arginine-rich region within hydrophobic aa-s present at the N-terminus of a preprotein can be sufficient signals for mitochondrial import irrespective of presequence length in Euglenozoa. URL Link do databázy WoS Public work category ADC No. of Archival Copy 37274 Repercussion category FURUHASHI, Takeshi - OGAWA, Takumi - NAKAI, Rai - NAKAZAWA, Masami - OKAZAWA, Atsushi - PADERMSCHOKE, Adchara - NISHIO, Kazuki - HIRAI, Masami Yokota - ARITA, Masanori - OHTA, Daisaku. Wax ester and lipophilic compound profiling of Euglena gracilis by gas chromatography-mass spectrometry: toward understanding of wax ester fermentation under hypoxia. In Metabolomics. ISSN 1573-3882, 2015, vol. 11, no. 1, pp. 175-183.
MANTILLA, Brian S. - PAES, Lisvane S. - PRAL, Elizabeth M. F. - MARTIL, Daiana E. - THIEMANN, Otavio H. - FERNANDEZ-SILVA, Patricio - BASTOS, Erick L. - SILBER, Ariel M. Role of Delta(1)-Pyrroline-5-Carboxylate Dehydrogenase supports mitochondrial metabolism and host-cell invasion of trypanosoma cruzi. In Journal of biological chemistry. ISSN 0021-9258, 2015, vol. 290, no. 12, pp. 7767-7790.
TAMAKI, Shun - MARUTA, Takanori - SAWA, Yoshihiro - SHIGEOKA, Shigeru - ISHIKAWA, Takahiro. Biochemical and physiological analyses of NADPH-dependent thioredoxin reductase isozymes in Euglena gracilis. In Plant science. ISSN 0168-9452, 2015, vol. 236, pp. 29-36.
MARTINEZ-GARCIA, Marta - CAMPOS-SALINAS, Jenny - CABELLO-DONAYRE, Maria - PINEDA-MOLINA, Estela - GALVEZ, Francisco J. - ORREGO, Lina M. - SANCHEZ-CANETE, Maria P. - MALAGARIE-CAZENAVE, Sophie - KOELLER, David M. - PEREZ-VICTORIA, Jose M. LmABCB3, an atypical mitochondrial ABC transporter essential for Leishmania major virulence, acts in heme and cytosolic iron/sulfur clusters biogenesis. In Parasites & vectors. ISSN 1756-3305, 2016, vol. 9, art. no. 7.
ZIMORSKI, Verena - RAUCH, Cessa - VAN HELLEMOND, Jaap J. - TIELENS, Aloysius G.M. - MARTIN, William F. The mitochondrion of Euglena gracilis. In Advances in experimental medicine and biology. ISSN 0065-2598, 2017, no. 979, pp. 19-37.
IVANOVA, Irina M. - NEPOGODIEV, Sergey A. - SAALBACH, Gerhard - O'NEILL, Ellis C. - URBANIAK, Michael D. - FERGUSON, Michael A. J. - GURCHA, Sudagar S. - BESRA, Gurdyal S. - FIELD, Robert A. Fluorescent mannosides serve as acceptor substrates for glycosyltransferase and sugar-1-phosphate transferase activities in Euglena gracilis membranes. In Carbohydrate research. ISSN 0008-6215, 2017, vol. 438, pp. 26-38.
KUHAUDOMLARP, Sakonwan - PATRON, Nicola J. - HENRISSAT, Bernard - REJZEK, Martin - SAALBACH, Gerhard - FIELD, Robert A. Identification of Euglena gracilis β-1,3-glucan phosphorylase and establishment of a new glycoside hydrolase (GH) family GH149. In Journal of biological chemistry. ISSN 0021-9258, 2018, vol. 293, no. 8, pp. 2865-2876.
JARDIM, Armando - HARDIE, Darryl B. - BOITZ, Jan - BORCHERS, Christoph H. Proteomic profiling of leishmania donovani promastigote subcellular organelles. In Journal of proteome research. ISSN 1535-3893, 2018, vol. 17, no. 3, pp. 1194-1215.
BANDINI, Giulia - DAMEROW, Sebastian - GUTHER, Maria Lucia Sempaio - GUO, Hongjie - MEHLERT, Angela - FRANCO, Jose Carlos Paredes - BEVERLEY, Stephen - FERGUSON, Michael A. J. An essential, kinetoplastid-specific GDP-Fuc: beta-D-Gal alpha-1,2-fucosyltransferase is located in the mitochondrion of Trypanosoma brucei. In eLife. ISSN 2050-084X, 2021, vol. 10, art. no. e70272, pp. 1-27.
Database xpca - PUBLIKAČNÁ ČINNOSŤ References PERIODIKÁ-Súborný záznam periodika unrecognised
Title Selective forces for the origin of spliceosomes Author info Matej Vesteg, Zuzana Šándorová, Juraj Krajčovič Author Vesteg Matej 1982- (60%)
Co-authors Šándorová Zuzana (20%)
Krajčovič Juraj (20%)
Source document Journal of Molecular Evolution. Vol. 74, no. 3-4 (2012), pp. 226-231. - New York : Springer, 2012 Keywords biochémia - biochemistry molekulárna biológia - molekulová biológia - molecular biology evolučná biológia - evolutionary biology Language English Country United States of America systematics 577 Annotation It has been proposed that eukaryotic spliceosomes evolved from bacterial group II introns via constructive neutral changes. However, a more likely interpretation is that spliceosomes and group II introns share a common undefined RNA ancestor—a proto-spliceosome. Although, the constructive neutral evolution may have probably played some roles in the development of complexity including the evolution of modern spliceosomes, in fact, the origin, losses and the retention of spliceosomes can be explained straight-forwardly mainly by positive and negative selection: (1) proto-spliceosomes evolved in the RNA world as a mechanism to excise functional RNAs from an RNA genome and to join noncoding information (ancestral to exons) possibly designed to be degraded. (2) The complexity of proto-spliceosomes increased with the invention of protein synthesis in the RNP world and theywere adopted for (a) the addition of translation signal to RNAs via trans-splicing, and for (b) the exon-shuffling such as to join together exons coding separate protein domains, to translate themas a single unit and thus to facilitate the molecular interaction of protein domains needed to be assembled to functional catalytic complexes. (3) Finally, the spliceosomes were adopted for cis-splicing of (mainly) non-coding information (contemporary introns) to yield translatable mRNAs. (4) Spliceosome-negative organisms (i.e., prokaryotes) have been selected in the DNA–protein world to save a lot of energy. (5) Spliceosome-positive organisms (i.e., eukaryotes) have been selected, because they have been completely spliceosome-dependent Public work category ADC No. of Archival Copy 42335 Repercussion category VOSSEBERG, Julian - SNEL, Berend. Domestication of self-splicing introns during eukaryogenesis : the rise of the complex spliceosomal machinery. In Biology direct. ISSN 1745-6150, 2017, vol. 12, no. 30.
MCNAIR, Jytte Brender - DENNIS, Lynnclaire - KAUFFMAN, Louis H. Mereon matrix, the: Everything connected through (k)nothing. In Mereon Matrix, the : everything connected through (K)nothing. [Singapore] : World scientific publishing, 2018. ISBN 978-981323356-0, pp. 1-846.
MILANOWSKI, Rafal - KARNKOWSKA, Anna - ISHIKAWA, Takao - ZAKRYS, Bozena. Distribution of conventional and nonconventional introns in tubulin (alpha and beta) genes of euglenids. In Molecular biology and evolution. ISSN 0737-4038, 2014, vol. 31, no. 3, pp. 584-593.
DENNIS, L. - MCNAIR, J. Brender - REID, J. S. Dedication to Dr. Robert W. "Bob" Gray. In Mereon matrix : everything connected through (k)nothing. ISSN 0219-9769, 2018, vol. 62, pp. V-+.
PENNY, David - COLLINS, Lesley J. - DALY, Toni K. - COX, Simon J. The relative ages of Eukaryotes and Akaryotes. In Journal of molecular evolution. ISSN 0022-2844, 2014, vol. 79, no. 5-6, special issue, pp. 228-239.
IRIMIA, Manuel - ROY, Scott William. Origin of spliceosomal introns and alternative splicing. In Cold spring harbor perspectives in biology. ISSN 1943-0264, 2014, vol. 6, no. 6, pp. 1-24.
ISOMOTO, Nana - MAEDA, Yuri - TANAKA, Takahiro - FURUTA, Hiroyuki - IKAWA, Yoshiya. Fixation and accumulation of thermotolerant catalytic competence of a pair of ligase ribozymes through complex formation and cross ligation. In Journal of molecular evolution. ISSN 0022-2844, 2013, vol. 76, no. 1-2, pp. 48-58.
DENNIS, L. Preface observational evidence, mathematical verification and inimitable grace. In Mereon matrix : unity, perspective and paradox. Amsterdam : Elsevier, 2013. ISBN 978-0-12-404688-7, pp. XIX-+.
STOLTZFUS, Arlin. Constructive neutral evolution : exploring evolutionary theory's curious disconnect. In Biology direct. ISSN 1745-6150, 2012, vol. 7, art. no. 35, pp. 1-13.
MUSTAFIN, R. N. Basic mechanisms of the origin and evolution of protein-coding genes. In Uspekhi fiziologicheskikh nauk. ISSN 0301-1798, 2020, vol. 51, no. 4, pp. 64-81.
Catal.org. BB301 - Univerzitná knižnica Univerzity Mateja Bela v Banskej Bystrici Database xpca - PUBLIKAČNÁ ČINNOSŤ References PERIODIKÁ-Súborný záznam periodika unrecognised