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Overlapping Genes: Bioinformatics and Evolution

Group leader until 2021: Dr. Zachary Ardern

The redundancy of the genetic code, whereby an amino acid can be encoded by more than one possible nucleotide triplet (codon), enables overlapping protein sequences to be encoded in alternate reading frames of a nucleotide sequence.

The ‘overlapping genes: bioinformatics and evolution group’ is engaged in inferring the presence of unannotated overlapping genes (OLGs) in bacteria using the wealth of existing relevant bioinformatic data. This includes data on transcription and translation from various kinds of RNA sequencing as well as proteomics. Within RNA sequencing we have a particular focus on ribosome profiling.


We are also interested in the evolutionary history of OLGs, and what is required for a successful ‘overprinting’ event leading to an overlapping gene pair. The evolutionary aspect of our research includes investigating the structure of the genetic code and its contribution to overlapping protein-coding sequences.

TUM Masters students interested in conducting practical research or thesis work with us please contact Dr Zachary Ardern.


Publications

Nelson CW, Ardern Z, Goldberg TL, Meng C, Kuo C-H, Ludwig C, Kolokotronis S-O, Wei X (2020) Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic. eLife2020, 9:e59633, Doi:10.7554/eLife.59633

Ardern Z, Neuhaus K, Scherer S (2020) Are antisense proteins in Prokaryotes functional? Frontiers in Molecular Biosciences Vol 7:187. Doi:10.3389/fmolb.2020.00187

Glaub A, Huptas C, Neuhaus K, Ardern Z (2020) Recommendations for bacterial ribosome profiling experiments based on bioinformatics evaluation of published data. Journal of Biological Chemistry 3, 295(27):8999-9011. Doi:10.1074/jbc.RA119.012161

Nelson CW, Ardern Z, Wie X (2020) OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes. Molecular Biology and Evolution1-9.
 Doi:10.1093/molbev/msaa087

Wichmann S, Ardern Z (2019) Optimality in the standard genetic code is robust with respect to comparison code sets. BioSystems 185:104023. Doi:10.1016/j.biosystems.2019.104023

Scherer S, Neuhaus K, Bossert M, Mir K, Keim D, Simon S (2018) Finding new overlapping genes and their theory (FOG Theory). In: Information - and Communication Theory in Molecular Biology, edited by Bossert M (Springer International), pp 137-159.
 
Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, Neuhaus K (2017) Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome. PLoS One. 2017 Sep 13;12(9): e0184119

Mir K, Neuhaus K, Scherer S, Bossert M, Schober S (2012) Predicting statistical properties of open reading frames in bacterial genomes. PLOS one 7, 9,e45103:1-12

Neuhaus K, Oelke D, Fürst D, Scherer S, Keim DA (2010) Towards automatic detecting of overlapping genes - Clusters BLAST analysis of viral genomes. Pizzuti C, Ritchie MD, Giacobini M (Eds.). EvoBio 2010, LNCS 6023, 228-239.

 

 





News

Paper
High Counts of thermophilic spore Formers in dairy powders originate from persisting strains in processing lines (2020)

Paper
Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic (Okt. 2020)

Paper
Are antisense proteins in prokaryotes functional (2020)

Paper
Complementary use of cultivation and high-throughput amplicon sequencing reveals high biodiversity within raw milk microbiota (2020)

Paper
Recommendations for bacterial ribosome profiling experiments based on bioinformatics evaluation of published data (2020)

Paper
OLGenie: Estimating natural selection to predict functional overlapping genes (2020)

Paper
Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk (2020)

Paper
Brevilactibacter flavus gen.nov., sp. nov., a novel bacterium of the family Propionibactericeae isolated form raw milk and dairy products and reclassification of Probioniciclava sinopodophylli as Brevilactibacter sinopodophylli comb. nov. (2020)

Paper
A novel pH-regulated, unusual 603 bp overlapping protein coding gene pop is encoded antisense to ompA in Escherichia coli O157:H7 (EHEC). (2020)

Paper
Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate (2020)

Paper
Pseudomonas saxonica sp.nov. isolated from raw milk and skimmed milk concentrate. (2020)