For students
Research
Publications
Coworkers
Service
FTIR spectra libraries
Strain collection







Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL)

Abteilung Mikrobiologie
Technische Universität München
Weihenstephaner Berg 3
D-85350 Freising


Overlapping Genes: Bioinformatics and Evolution

Group leader: Dr. Zachary Ardern

Alina Glaub, MSc, PhD student
Dr. Chris Huptas, Postdoc
Stefan Wichmann, MSc, PhD Student

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

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

Böhm M-E, Huptas C, Krey V, Scherer S (2015) Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe. BMC Evolutionary Biology 15:246


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
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)

Paper
Thermally induced milk fouling: Survival of thermophilic spore Formers and potential of contamination (Dez 2019)

Paper
Optimality in the standard gentic code is robust with respect to comparison code sets (2019)

Paper
Accurate quantification of thermophilic spores in dairy powders (2019)

Paper
Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk (2017)

Paper
Resistance of thermophilic spore formers isolated from milk and whey products towards cleaning-in-place conditions: Influence of pH, temperature and milk residues (2019)

Paper
Proposal of Lysobacter pythonis sp. nov. isolated from royal pythons (Python regius) (2019)

Paper
The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth Phase (Dec 2018)

Paper
Reprogramming Human Siderocalin to Neutralize Petrobactin, the Essential Iron Scavenger of Anthrax Bacillus (2018)

Paper
Dysfunction, Disease, and the Limits of Selection (2018)

Paper
The Novel Anaerobiosis-Responsive Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai (Mai 2018)

Paper
A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting (2018)