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Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL)

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

Funktionale Charakterisierung von überlappenden Genen in Bakterien

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

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

Die Codierungsdichte für proteincodierende Gene in prokaryotischen Genomen ist vermutlich deutlich höher als bisher gedacht. Neben unbekannten intergenischen Genen codiert in einigen sehr überraschenden Fällen dieselbe DNA Sequenz für zwei verschiedene Proteine, weil zwei verschiedene Leseraster translatiert werden (Überlappende Gene = OLGs). 



Überlappende Gene bei Bakterien wurden bisher allerdings kaum bearbeitet und ihre Entstehung ist ein Rätsel, dessen Lösung intensive Forschungsarbeit erfordert. Wir bearbeiten diese Fragestellung im Rahmen dieser Arbeitsgruppe mit experimentellen Methoden, um die Funktion und Expression solcher faszinierender Genpaare zu analysieren.
Dieses Wissen ist wichtig, um die de novo Entstehung sowie die Evolution überlappender Gene zu verstehen (Overlapping Genes: Bioinformatics and Evolution)






Publikationen

Hücker SM, Vanderhaegen 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 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(9): 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 Evol Biol. 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, 1-26, Doi: 10.1177/1473871615612883


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, 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.

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


Aktuelles

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

Paper
Denkvoraussetzungen und weltanschauliche Überzeugungen in der Biologie (2017)

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)