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
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
The small RNA RssR regulates myo-inositol degradation by Salmonella enterica (Dec.2018)

Paper
Activity of a Holin-Endolysin System in the Insecticidal Pathogenicity Island of Yersinia enterocolitica (2018)

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

Paper
Insecticidal Toxicity of Yersinia frederiksenii Involves the Novel Enterotoxin YacT (2018)

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

Paper
Dynamic Proteome Alteration and Functional Modulation of Human Saliva Induced by Dietary Chemosensory Stimuli (2018)

Paper
Genome sequence of the novel virulent bacteriophage PMBT14 with lytic avtivity against Pseudomonas fluorescens DSM 50090 (2018)

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

Paper
Thermal treatment of skim milk concentrates in a novel shear-heating device: Reduction of thermophilic spores and physical properties (Febr. 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)

Paper
Thermal resistance of vegetative thermophilic spore forming bacilli in skim milk isolated from dairy Environments (2017)

Paper
Comparison between Listeria sensu stricto and Listeria sensu lato strains identifies novel determinants involved in infection (2017)

Paper

Paper
Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq-ryhB encodes the regulatory RNA RyhB and a Peptide, RyhP. (2017)

Paper
Complete circular genome sequence and temperature independent adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698 (2017)

Paper
Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai Genome (2017)

Paper
Spoilage of Microfiltered and Pasteurized Extended Shelf Life Milk Is Mainly Induced by Psychrotolerant Spore-Forming Bacteria that often Originate from Recontamination (2017)

Paper
Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation. (2016)

Paper
Comparative Bioinformatics and Experimental Analysis of the Intergenic Regulatory Regions of Bacillus cereus hbl and nhe Enterotoxin Operons and the Impact of CodY on Virulence Heterogeneity (Mai 2016)

Paper
Acidified nitrite inhibits proliferation of Listeria monocytogenes - Transcriptional analysis of a preservation method (März 2016)

Paper
Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

Paper
Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting (Dez. 2015)

Paper
Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe (Nov. 2015)