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3. Accurate annotation of protein-coding genes in mitochondrial genomes

Author

Al-Arab, Marwa, Höner zu Siederdissen, Christian, Tout, Kifah R., Sahyoun, Abdullah H., Stadler, Peter F., Bernt, Matthias, and Publica

Abstract

Mitochondrial genome sequences are available in large number and new sequences become published nowadays with increasing pace. Fast, automatic, consistent, and high quality annotations are a prerequisite for downstream analyses. Therefore, we present an automated pipeline for fast de novo annotation of mitochondrial protein-coding genes. The annotation is based on enhanced phylogeny-aware hidden Markov models (HMMs). The pipeline builds taxon-specific enhanced multiple sequence alignments (MSA) of already annotated sequences and corresponding HMMs using an approximation of the phylogeny. The MSAs are enhanced by fixing unannotated frameshifts, purging of wrong sequences, and removal of non-conserved columns from both ends. A comparison with reference annotations highlights the high quality of the results. The frameshift correction method predicts a large number of frameshifts, many of which are unknown. A detailed analysis of the frameshifts in nad3 of the Archosauria-Testudines group has been conducted.

Published
2017

4. Correction: Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Author

Hölzer, Martin, primary, Krähling, Verena, additional, Amman, Fabian, additional, Barth, Emanuel, additional, Bernhart, Stephan H., additional, Carmelo, Victor A. O., additional, Collatz, Maximilian, additional, Doose, Gero, additional, Eggenhofer, Florian, additional, Ewald, Jan, additional, Fallmann, Jörg, additional, Feldhahn, Lasse M., additional, Fricke, Markus, additional, Gebauer, Juliane, additional, Gruber, Andreas J., additional, Hufsky, Franziska, additional, Indrischek, Henrike, additional, Kanton, Sabina, additional, Linde, Jörg, additional, Mostajo, Nelly, additional, Ochsenreiter, Roman, additional, Riege, Konstantin, additional, Rivarola-Duarte, Lorena, additional, Sahyoun, Abdullah H., additional, Saunders, Sita J., additional, Seemann, Stefan E., additional, Tanzer, Andrea, additional, Vogel, Bertram, additional, Wehner, Stefanie, additional, Wolfinger, Michael T., additional, Backofen, Rolf, additional, Gorodkin, Jan, additional, Grosse, Ivo, additional, Hofacker, Ivo, additional, Hoffmann, Steve, additional, Kaleta, Christoph, additional, Stadler, Peter F., additional, Becker, Stephan, additional, and Marz, Manja, additional

Published
2017
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6. Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes

Author

Sahyoun, Abdullah H., Hölzer, Martin, Jühling, Frank, Höner zu Siederdissen, Christian, Al-Arab, Marwa, Tout, Kifah, Marz, Manja, Middendorf, Martin, Stadler, Peter F., Bernt, Matthias, and Publica

Subjects
Evolution, Molecular, RNA, Transfer, Leu, RNA, Transfer, Crustacea, Genome, Mitochondrial, Mutation, Anticodon, RNA, Animals, Codon, Sequence Alignment, Porifera
Abstract

Remolding of tRNAs is a well-documented process in mitochondrial genomes that changes the identity of a tRNA. It involves a duplication of a tRNA gene, a mutation that changes the anticodon and the loss of the ancestral tRNA gene. The net effect is a functional tRNA that is more closely related to tRNAs of a different alloacceptor family than to tRNAs with the same anticodon in related species. Beyond being of interest for understanding mitochondrial tRNA function and evolution, tRNA remolding events can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. Therefore, it is important to identify and catalog these events. Here we describe novel methods to detect tRNA remolding in large-scale data sets and apply them to survey tRNA remolding throughout animal evolution. We identify several novel remolding events in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived from ancestral events.

Published
2015

7. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells:[Plus] Corrigendum

Author

Hölzer, Martin, Krähling, Verena, Amman, Fabian, Barth, Emanuel, Bernhart, Stephan H., Carmelo, Victor Adriano Okstoft, Collatz, Maximilian, Doose, Gero, Eggenhofer, Florian, Ewald, Jan, Fallmann, Jörg, Feldhahn, Lasse M., Fricke, Markus, Gebauer, Juliane, Gruber, Andreas J., Hufsky, Franziska, Indrischek, Henrike, Kanton, Sabina, Linde, Jörg, Mostajo, Nelly, Ochsenreiter, Roman, Riege, Konstantin, Rivarola-Duarte, Lorena, Sahyoun, Abdullah H., Saunders, Sita J., Seemann, Ernst Stefan, Tanzer, Andrea, Vogel, Bertram, Wehner, Stefanie, Wolfinger, Michael T., Backofen, Rolf, Gorodkin, Jan, Grosse, Ivo, Hofacker, Ivo, Hoffmann, Steve, Kaleta, Christoph, Stadler, Peter F., Becker, Stephan, Marz, Manja, Hölzer, Martin, Krähling, Verena, Amman, Fabian, Barth, Emanuel, Bernhart, Stephan H., Carmelo, Victor Adriano Okstoft, Collatz, Maximilian, Doose, Gero, Eggenhofer, Florian, Ewald, Jan, Fallmann, Jörg, Feldhahn, Lasse M., Fricke, Markus, Gebauer, Juliane, Gruber, Andreas J., Hufsky, Franziska, Indrischek, Henrike, Kanton, Sabina, Linde, Jörg, Mostajo, Nelly, Ochsenreiter, Roman, Riege, Konstantin, Rivarola-Duarte, Lorena, Sahyoun, Abdullah H., Saunders, Sita J., Seemann, Ernst Stefan, Tanzer, Andrea, Vogel, Bertram, Wehner, Stefanie, Wolfinger, Michael T., Backofen, Rolf, Gorodkin, Jan, Grosse, Ivo, Hofacker, Ivo, Hoffmann, Steve, Kaleta, Christoph, Stadler, Peter F., Becker, Stephan, and Marz, Manja

Abstract

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.

Published
2016

8. GC skew and mitochondrial origins of replication

Author

Sahyoun, Abdullah H., Bernt, Matthias, Stadler, Peter F., Tout, Kifah R., and Publica

Subjects
GC-skew, chordata, replication origins, Mitochondria
Abstract

The comprehensive understanding of mitochondrial genome evolution requires a detailed mechanistic picture of mitogenomic replication. Despite many previous efforts it has remained a non-trivial problem to determine the origins of replication and trace their fate across rearrangements of the gene order even in the small genomes of animal mitochondria. We elaborate here on the observation that the GC skew is correlated with the distance from the replication origins. This effect has been explained as a consequence of the standard model of mitochondrial DNA replication, i.e. the strand displacement model. According to this model chemical damage accumulates proportional to the duration that DNA is exposed in single-stranded form during replication (Dssh) which depends on the relative position with respect to the replication origins. Based on this model we developed a computational method to infer the positions of both the heavy strand and the light strand origin from nucleotide skew data. In a comprehensive survey of deuterostome mitochondria we infer conserved replication origins for the vast majority of vertebrates and cephalochordates. Deviations from the consensus picture are presumably associated with genome rearrangements.

Published
2014

9. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Author

Hölzer, Martin, primary, Krähling, Verena, additional, Amman, Fabian, additional, Barth, Emanuel, additional, Bernhart, Stephan H., additional, Carmelo, Victor A. O., additional, Collatz, Maximilian, additional, Doose, Gero, additional, Eggenhofer, Florian, additional, Ewald, Jan, additional, Fallmann, Jörg, additional, Feldhahn, Lasse M., additional, Fricke, Markus, additional, Gebauer, Juliane, additional, Gruber, Andreas J., additional, Hufsky, Franziska, additional, Indrischek, Henrike, additional, Kanton, Sabina, additional, Linde, Jörg, additional, Mostajo, Nelly, additional, Ochsenreiter, Roman, additional, Riege, Konstantin, additional, Rivarola-Duarte, Lorena, additional, Sahyoun, Abdullah H., additional, Saunders, Sita J., additional, Seemann, Stefan E., additional, Tanzer, Andrea, additional, Vogel, Bertram, additional, Wehner, Stefanie, additional, Wolfinger, Michael T., additional, Backofen, Rolf, additional, Gorodkin, Jan, additional, Grosse, Ivo, additional, Hofacker, Ivo, additional, Hoffmann, Steve, additional, Kaleta, Christoph, additional, Stadler, Peter F., additional, Becker, Stephan, additional, and Marz, Manja, additional

Published
2016
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10. MOF Acetyl Transferase Regulates Transcription and Respiration in Mitochondria

Author

Chatterjee, Aindrila, primary, Seyfferth, Janine, additional, Lucci, Jacopo, additional, Gilsbach, Ralf, additional, Preissl, Sebastian, additional, Böttinger, Lena, additional, Mårtensson, Christoph U., additional, Panhale, Amol, additional, Stehle, Thomas, additional, Kretz, Oliver, additional, Sahyoun, Abdullah H., additional, Avilov, Sergiy, additional, Eimer, Stefan, additional, Hein, Lutz, additional, Pfanner, Nikolaus, additional, Becker, Thomas, additional, and Akhtar, Asifa, additional

Published
2016
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12. MOF maintains transcriptional programs regulating cellular stress response

Author

Sheikh, B N, primary, Bechtel-Walz, W, additional, Lucci, J, additional, Karpiuk, O, additional, Hild, I, additional, Hartleben, B, additional, Vornweg, J, additional, Helmstädter, M, additional, Sahyoun, A H, additional, Bhardwaj, V, additional, Stehle, T, additional, Diehl, S, additional, Kretz, O, additional, Voss, A K, additional, Thomas, T, additional, Manke, T, additional, Huber, T B, additional, and Akhtar, A, additional

Published
2015
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15. Mitochondrial Genome Evolution

Author

Bernt, Matthias, primary, Machné, Rainer, additional, Sahyoun, Abdullah H, additional, Middendorf, Martin, additional, and Stadler, Peter F, additional

Published
2013
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16. MOF maintains transcriptional programs regulating cellular stress response

Author

Sheikh, B N, Bechtel-Walz, W, Lucci, J, Karpiuk, O, Hild, I, Hartleben, B, Vornweg, J, Helmstädter, M, Sahyoun, A H, Bhardwaj, V, Stehle, T, Diehl, S, Kretz, O, Voss, A K, Thomas, T, Manke, T, Huber, T B, and Akhtar, A

Abstract

MOF (MYST1, KAT8) is the major H4K16 lysine acetyltransferase (KAT) in Drosophila and mammals and is essential for embryonic development. However, little is known regarding the role of MOF in specific cell lineages. Here we analyze the differential role of MOF in proliferating and terminally differentiated tissues at steady state and under stress conditions. In proliferating cells, MOF directly binds and maintains the expression of genes required for cell cycle progression. In contrast, MOF is dispensable for terminally differentiated, postmitotic glomerular podocytes under physiological conditions. However, in response to injury, MOF is absolutely critical for podocyte maintenance in vivo. Consistently, we detect defective nuclear, endoplasmic reticulum and Golgi structures, as well as presence of multivesicular bodies in vivo in podocytes lacking Mof following injury. Undertaking genome-wide expression analysis of podocytes, we uncover several MOF-regulated pathways required for stress response. We find that MOF, along with the members of the non-specific lethal but not the male-specific lethal complex, directly binds to genes encoding the lysosome, endocytosis and vacuole pathways, which are known regulators of podocyte maintenance. Thus, our work identifies MOF as a key regulator of cellular stress response in glomerular podocytes.

Published
2016
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17. The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis.

Author

Kolora, Sree Rohit, Faria, Rui, Weigert, Anne, Schaffer, Stefan, Grimm, Annegret, Henle, Klaus, Sahyoun, Abdullah H., Stadler, Peter F., Nowick, Katja, Bleidorn, Christoph, and Schlegel, Martin

Subjects
LACERTA, MITOCHONDRIAL DNA, REPTILES, REPTILE phylogeny, TRANSFER RNA, RIBOSOMAL RNA
Abstract

We sequenced the mitochondrial genome of the Western green lizard (Lacerta bilineata) using Illumina technology and additional Sanger sequencing. The assembled 17 086 bp mitogenome had a GC content of 40.32% and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region (CR), with a gene order identical to the chordate consensus. In addition, we re-sequenced the mitogenome of the closely related Eastern green lizardL. viridisusing the same techniques as forL. bilineata. The mitogenomes ofL. bilineataandL. viridisshowed a sequence identity of 94.4% and 99.9%, respectively, relative to the previously publishedL. viridismitogenome. The phylogenetic reconstruction based on 17 Lacertinae mitogenomes usingAnolis carolinensisas the outgroup supportedL. bilineataand its sister speciesL. viridisas distinct lineages. [ABSTRACT FROM PUBLISHER]

Published
2017
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18. Mutual Transformability of the Formulas of the Languages Of Markov L2ω AND Rω.

Author

Gorgy, F. W. and Sahyoun, A. H.

Subjects
*MATHEMATICAL transformations, *MATHEMATICAL logic, *MARKOV processes, *MATHEMATICAL formulas, *MARKOV operators
Abstract

The article presents solutions for transformability of formulas of language L2ω into formulas of language of яω. It presents formulas of language L2ω (FL2ω) to solve for formulas of language L2ω into formulas of language of яω. It defines an algorithm γω to solve for formulas of language L2ω into formulas of language of L2ω.

Published
1987
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19. Mutual Transformability of the Formulas of the Languages Of Markov L2ω AND Rω.

Author

Gorgy, F. W. and Sahyoun, A. H.

Subjects
MATHEMATICAL transformations, MATHEMATICAL logic, MARKOV processes, MATHEMATICAL formulas, MARKOV operators
Abstract

The article presents solutions for transformability of formulas of language L2ω into formulas of language of яω. It presents formulas of language L2ω (FL2ω) to solve for formulas of language L2ω into formulas of language of яω. It defines an algorithm γω to solve for formulas of language L2ω into formulas of language of L2ω.

Published
1987
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