Kollmar, Martin

[["dc.bibliographiccitation.firstpage","1302-4"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","Bioinformatics (Oxford, England)"],["dc.bibliographiccitation.lastpage","1304"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Hellkamp, Marcel"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:35:18Z"],["dc.date.available","2018-11-28T09:35:18Z"],["dc.date.issued","2015-04-15"],["dc.description.abstract","Conserved intron positions in eukaryotic genes can be used to reconstruct phylogenetic trees, to resolve ambiguous subfamily relationships in protein families and to infer the history of gene families. This version of GenePainter facilitates working with large datasets through options to select specific subsets for analysis and visualization, and through providing exhaustive statistics. GenePainter's application in phylogenetic analyses is considerably extended by the newly implemented integration of the exon-intron pattern conservation with phylogenetic trees."],["dc.identifier.doi","10.1093/bioinformatics/btu798"],["dc.identifier.pmid","25434742"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56975"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1367-4811"],["dc.title","GenePainter v. 2.0 resolves the taxonomic distribution of intron positions"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","202"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC evolutionary biology"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:38:51Z"],["dc.date.available","2018-11-28T09:38:51Z"],["dc.date.issued","2013-09-22"],["dc.description.abstract","The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions."],["dc.identifier.doi","10.1186/1471-2148-13-202"],["dc.identifier.pmid","24053117"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56979"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1471-2148"],["dc.title","Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","211"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC evolutionary biology"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.date.accessioned","2018-11-28T09:11:10Z"],["dc.date.available","2018-11-28T09:11:10Z"],["dc.date.issued","2017"],["dc.description.abstract","The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged."],["dc.identifier.doi","10.1186/s12862-017-1056-2"],["dc.identifier.pmid","28870165"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56969"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1471-2148"],["dc.title","Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","293-299"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","RNA biology"],["dc.bibliographiccitation.lastpage","299"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.date.accessioned","2018-11-28T09:12:33Z"],["dc.date.available","2018-11-28T09:12:33Z"],["dc.date.issued","2017"],["dc.description.abstract","mRNA decoding by tRNAs and tRNA charging by aminoacyl-tRNA synthetases are biochemically separated processes that nevertheless in general involve the same nucleotides. The combination of charging and decoding determines the genetic code. Codon reassignment happens when a differently charged tRNA replaces a former cognate tRNA. The recent discovery of the polyphyly of the yeast CUG sense codon reassignment challenged previous mechanistic considerations and led to the proposal of the so-called tRNA loss driven codon reassignment hypothesis. Accordingly, codon capture is caused by loss of a tRNA or by mutations in the translation termination factor, subsequent reduction of the codon frequency through reduced translation fidelity and final appearance of a new cognate tRNA. Critical for codon capture are sequence and structure of the new tRNA, which must be compatible with recognition regions of aminoacyl-tRNA synthetases. The proposed hypothesis applies to all reported nuclear and organellar codon reassignments."],["dc.identifier.doi","10.1080/15476286.2017.1279785"],["dc.identifier.pmid","28095181"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56971"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1555-8584"],["dc.title","How tRNAs dictate nuclear codon reassignments: Only a few can capture non-cognate codons"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3222-37"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Genome biology and evolution"],["dc.bibliographiccitation.lastpage","3237"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:34:03Z"],["dc.date.available","2018-11-28T09:34:03Z"],["dc.date.issued","2014"],["dc.description.abstract","The universal genetic code defines the translation of nucleotide triplets, called codons, into amino acids. In many Saccharomycetes a unique alteration of this code affects the translation of the CUG codon, which is normally translated as leucine. Most of the species encoding CUG alternatively as serine belong to the Candida genus and were grouped into a so-called CTG clade. However, the \"Candida genus\" is not a monophyletic group and several Candida species are known to use the standard CUG translation. The codon identity could have been changed in a single branch, the ancestor of the Candida, or to several branches independently leading to a polyphyletic alternative yeast codon usage (AYCU). In order to resolve the monophyly or polyphyly of the AYCU, we performed a phylogenomics analysis of 26 motor and cytoskeletal proteins from 60 sequenced yeast species. By investigating the CUG codon positions with respect to sequence conservation at the respective alignment positions, we were able to unambiguously assign the standard code or AYCU. Quantitative analysis of the highly conserved leucine and serine alignment positions showed that 61.1% and 17% of the CUG codons coding for leucine and serine, respectively, are at highly conserved positions, whereas only 0.6% and 2.3% of the CUG codons, respectively, are at positions conserved in the respective other amino acid. Plotting the codon usage onto the phylogenetic tree revealed the polyphyly of the AYCU with Pachysolen tannophilus and the CTG clade branching independently within a time span of 30–100 Ma."],["dc.identifier.doi","10.1093/gbe/evu152"],["dc.identifier.pmid","25646540"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56974"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1759-6653"],["dc.title","Molecular phylogeny of sequenced Saccharomycetes reveals polyphyly of the alternative yeast codon usage"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2274-88"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Genome biology and evolution"],["dc.bibliographiccitation.lastpage","2288"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Findeisen, Peggy"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Dempewolf, Silke"],["dc.contributor.author","Hertzog, Jonny"],["dc.contributor.author","Zietlow, Alexander"],["dc.contributor.author","Carlomagno, Teresa"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:37:30Z"],["dc.date.available","2018-11-28T09:37:30Z"],["dc.date.issued","2014-08-27"],["dc.description.abstract","Tubulins belong to the most abundant proteins in eukaryotes providing the backbone for many cellular substructures like the mitotic and meiotic spindles, the intracellular cytoskeletal network, and the axonemes of cilia and flagella. Homologs have even been reported for archaea and bacteria. However, a taxonomically broad and whole-genome-based analysis of the tubulin protein family has never been performed, and thus, the number of subfamilies, their taxonomic distribution, and the exact grouping of the supposed archaeal and bacterial homologs are unknown. Here, we present the analysis of 3,524 tubulins from 504 species. The tubulins formed six major subfamilies, α to ζ. Species of all major kingdoms of the eukaryotes encode members of these subfamilies implying that they must have already been present in the last common eukaryotic ancestor. The proposed archaeal homologs grouped together with the bacterial TubZ proteins as sister clade to the FtsZ proteins indicating that tubulins are unique to eukaryotes. Most species contained α- and/or β-tubulin gene duplicates resulting from recent branch- and species-specific duplication events. This shows that tubulins cannot be used for constructing species phylogenies without resolving their ortholog-paralog relationships. The many gene duplicates and also the independent loss of the δ-, ε-, or ζ-tubulins, which have been shown to be part of the triplet microtubules in basal bodies, suggest that tubulins can functionally substitute each other."],["dc.identifier.doi","10.1093/gbe/evu187"],["dc.identifier.pmid","25169981"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56976"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1759-6653"],["dc.title","Six subgroups and extensive recent duplications characterize the evolution of the eukaryotic tubulin protein family"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","258"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Biology"],["dc.bibliographiccitation.volume","19"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Plessmann, Uwe"],["dc.contributor.author","Mienkus, Peter"],["dc.contributor.author","Sternisek, Pia"],["dc.contributor.author","Perl, Thorsten"],["dc.contributor.author","Weig, Michael"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Bader, Oliver"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Schmitt, Hans Dieter"],["dc.date.accessioned","2022-01-11T14:06:08Z"],["dc.date.accessioned","2022-08-18T12:34:34Z"],["dc.date.available","2022-01-11T14:06:08Z"],["dc.date.available","2022-08-18T12:34:34Z"],["dc.date.issued","2021-12-04"],["dc.date.updated","2022-07-29T12:07:10Z"],["dc.description.abstract","Abstract\r\n \r\n Background\r\n Yeasts of the CTG-clade lineage, which includes the human-infecting Candida albicans, Candida parapsilosis and Candida tropicalis species, are characterized by an altered genetic code. Instead of translating CUG codons as leucine, as happens in most eukaryotes, these yeasts, whose ancestors are thought to have lost the relevant leucine-tRNA gene, translate CUG codons as serine using a serine-tRNA with a mutated anticodon, \r\n \r\n \r\n \r\n \r\n \r\n tRNA\r\n CAG\r\n Ser\r\n \r\n \r\n $ {\\mathrm{tRNA}}_{\\mathrm{CAG}}^{\\mathrm{Ser}} $\r\n . Previously reported experiments have suggested that 3–5% of the CTG-clade CUG codons are mistranslated as leucine due to mischarging of the \r\n \r\n \r\n \r\n \r\n \r\n tRNA\r\n CAG\r\n Ser\r\n \r\n \r\n $ {\\mathrm{tRNA}}_{\\mathrm{CAG}}^{\\mathrm{Ser}} $\r\n . The mistranslation was suggested to result in variable surface proteins explaining fast host adaptation and pathogenicity.\r\n \r\n \r\n Results\r\n In this study, we reassess this potential mistranslation by high-resolution mass spectrometry-based proteogenomics of multiple CTG-clade yeasts, including various C. albicans strains, isolated from colonized and from infected human body sites, and C. albicans grown in yeast and hyphal forms. Our data do not support a bias towards CUG codon mistranslation as leucine. Instead, our data suggest that (i) CUG codons are mistranslated at a frequency corresponding to the normal extent of ribosomal mistranslation with no preference for specific amino acids, (ii) CUG codons are as unambiguous (or ambiguous) as the related CUU leucine and UCC serine codons, (iii) tRNA anticodon loop variation across the CTG-clade yeasts does not result in any difference of the mistranslation level, and (iv) CUG codon unambiguity is independent of C. albicans’ strain pathogenicity or growth form.\r\n \r\n \r\n Conclusions\r\n Our findings imply that C. albicans does not decode CUG ambiguously. This suggests that the proposed misleucylation of the \r\n \r\n \r\n \r\n \r\n \r\n tRNA\r\n CAG\r\n Ser\r\n \r\n \r\n $ {\\mathrm{tRNA}}_{\\mathrm{CAG}}^{\\mathrm{Ser}} $\r\n might be as prevalent as every other misacylation or mistranslation event and, if at all, be just one of many reasons causing phenotypic diversity."],["dc.identifier.citation","BMC Biology. 2021 Dec 04;19(1):258"],["dc.identifier.doi","10.1186/s12915-021-01197-9"],["dc.identifier.pii","1197"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/97834"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/112931"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-507"],["dc.publisher","BioMed Central"],["dc.relation.eissn","1741-7007"],["dc.rights.holder","The Author(s)"],["dc.subject","Proteogenomics"],["dc.subject","Pathogen"],["dc.subject","Candida albicans"],["dc.subject","Genetic code"],["dc.title","Proteogenomics analysis of CUG codon translation in the human pathogen Candida albicans"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","77"],["dc.bibliographiccitation.journal","BMC Bioinformatics"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Hammesfahr, Björn"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Waack, Stephan"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-07T09:27:09Z"],["dc.date.available","2018-11-07T09:27:09Z"],["dc.date.issued","2013"],["dc.description.abstract","Background: All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa. Results: GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol. Conclusions: GenePainter is a tool to analyse gene structure conservation providing various visualization options. A stable version of GenePainter for all operating systems as well as documentation and example data are available at http://www.motorprotein.de/genepainter.html."],["dc.identifier.doi","10.1186/1471-2105-14-77"],["dc.identifier.isi","000316396200001"],["dc.identifier.pmid","23496949"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/8736"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/30467"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","Najko"],["dc.relation.issn","1471-2105"],["dc.relation.orgunit","Fakultät für Mathematik und Informatik"],["dc.rights","CC BY 2.0"],["dc.rights.uri","http://creativecommons.org/licenses/by/2.0"],["dc.title","GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2046-2057.e5"],["dc.bibliographiccitation.issue","13"],["dc.bibliographiccitation.journal","Current biology : CB"],["dc.bibliographiccitation.lastpage","2057.e5"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Schmitt, Hans Dieter"],["dc.contributor.author","Pan, Kuan-Ting"],["dc.contributor.author","Plessmann, Uwe"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Hurst, Laurence D"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:07:20Z"],["dc.date.available","2018-11-28T09:07:20Z"],["dc.date.issued","2018-07-09"],["dc.description.abstract","Although the \"universal\" genetic code is now known not to be universal, and stop codons can have multiple meanings, one regularity remains, namely that for a given sense codon there is a unique translation. Examining CUG usage in yeasts that have transferred CUG away from leucine, we here report the first example of dual coding: Ascoidea asiatica stochastically encodes CUG as both serine and leucine in approximately equal proportions. This is deleterious, as evidenced by CUG codons being rare, never at conserved serine or leucine residues, and predominantly in lowly expressed genes. Related yeasts solve the problem by loss of function of one of the two tRNAs. This dual coding is consistent with the tRNA-loss-driven codon reassignment hypothesis, and provides a unique example of a proteome that cannot be deterministically predicted. VIDEO ABSTRACT."],["dc.identifier.doi","10.1016/j.cub.2018.04.085"],["dc.identifier.pmid","29910077"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56968"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1879-0445"],["dc.title","Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","411"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC genomics"],["dc.bibliographiccitation.volume","15"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:38:13Z"],["dc.date.available","2018-11-28T09:38:13Z"],["dc.date.issued","2014-05-29"],["dc.description.abstract","Many eukaryotes have been shown to use alternative schemes to the universal genetic code. While most Saccharomycetes, including Saccharomyces cerevisiae, use the standard genetic code translating the CUG codon as leucine, some yeasts, including many but not all of the \"Candida\", translate the same codon as serine. It has been proposed that the change in codon identity was accomplished by an almost complete loss of the original CUG codons, making the CUG positions within the extant species highly discriminative for the one or other translation scheme."],["dc.identifier.doi","10.1186/1471-2164-15-411"],["dc.identifier.pmid","24885275"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56978"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1471-2164"],["dc.title","Predicting the fungal CUG codon translation with Bagheera"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]