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Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL)

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


Functional characterization of overlapping genes in bacteria 

Group leaders:

PD Dr. Klaus Neuhaus (ZIEL Core Facility Microbiome / NGS)
Prof. Dr. Siegfried Scherer

Michaela Kreitmeier, MSc, PhD Student
Sonja Vanderhaeghen, MSc, PhD Student
Anika Wahl, MSc, PhD Student
Romy Wecko, Technician
Barbara Zehentner, MSc, PhD Student


The coding density of protein coding genes in prokaryotic genomes is probably much higher than previously assumed. Apart from unknown intergenic genes, in some surprising cases the same DNA sequence encodes two proteins in different reading frames (overlapping genes). 



Research on overlapping genes in bacteria is in its infancy and their evolution is an enigma open to scientific investigation. We use experimental approaches to elucidate presence, expression and function of overlapping genes. Such knowledge is important for understanding the de novo origin and evolution of such fascinating gene pairs




The project started within the Priority Program „Information- and communication theory in molecular biology” (
InKoMBio SPP 1395) using an interdisciplinary approach which involved the TUM (Chair of Microbial Ecology, Prof. Siegfried Scherer), Konstanz University (Chair of Data Analysis and Visualization, Prof. Daniel Keim) and Ulm University (Chair “Telecommunications and Applied Information Theory“, Prof. Martin Bossert).



Publications

Vanderhaeghen S, Barbara Zehentner B, Scherer S, Neuhaus K, Ardern Z (2018) The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. Scientific Reports, www.nature.com/srep/ in press

Hücker SM, Vanderhaeghen S, Abellan-Schneyder I, Wecko R, Simon S, Scherer S , Neuhaus K
(2018) 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. BMC Evolutionary Biology, BMC Evolutionary Biology 18:21. doi: 10.1186/s12862-018-1134-0

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.

Neuhaus K, Landstorfer R, Simon S, Schober S, Wright PR, Smith C, Backofen R, Wecko R, Keim DA, Scherer S (2017) 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. BMC Genomics 18:216 DOI 10.1186/s12864-017-3586-9.

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 12: e0184119.

Neuhaus K, Landstorfer R, Fellner L, Simon S, Schafferhans A, Goldberg T, Marx H, Ozoline ON, Rost B, Kuster B, Keim DA and Scherer S (2016) Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics 17:133.

Fellner L, Simon S, Scherling C, Witting M, Schober S, Polte C, Schmitt-Kopplin P, Keim DA, Scherer S, Neuhaus K (2015) Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting. BMC Evolutionary Biology 15:283.

Simon S, Mittelstädt S, Kwon BC, Stoffel A, Landstorfer R, Neuhaus K, Mühlig A, Scherer S, Keim DA (2015) VisExpress: Visual exploration of differential gene expression data. Info Vis 16:48-73.

Fellner L, Bechtel N, Witting MA, Simon S, Schmitt-Kopplin P, Keim D, Scherer S, Neuhaus K (2013) Phenotype of htgA (mbiA), a recently evolved orphan gene of Escherichia and Shigella, completely overlapping in antisense of yaaW. FEMS Microbiol Lett 350:57-64.

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

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.

Loessner M, Gäng S, Scherer S (1999) Evidence for a Holin-Like Protein Gene Fully Embedded Out of Frame in the Endolysin Gene of Staphylococcus aureus Bacteriophage 187. J Bacteriol 181:4452-4460.






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)

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

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

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

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

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

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

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

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

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

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

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

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

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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)

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

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

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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)

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

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

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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)

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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)

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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)