• Our aim is to advance our understanding of biological systems,

    ranging from single species to multi-species systems and ecosystems,

    based on data from large-scale bioanalytical methods.

  • We develop, improve and apply

    computational methods

    for the interpretation of molecular information in biology.

  • We establish and analyse

    quantitative mathematical models.

CUBE News

Latest publications

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P
2018 - Nucleic Acids Res., in press

A promiscuous beta-glucosidase is involved in benzoxazinoid deglycosylation in Lamium galeobdolon.

In the plant kingdom beta-glucosidases (BGLUs) of the glycosidase hydrolase family 1 have essential function in primary metabolism and are particularly employed in secondary metabolism. They are essential for activation in two-component defence systems based on stabilisation of reactive compounds by glycosylation. Based on de novo assembly we isolated and functionally characterised BGLUs expressed in leaves of Lamium galeobdolon (LgGLUs). LgGLU1 could be assigned to hydrolysis of the benzoxazinoid GDIBOA (2,4-dihydroxy-1,4-benzoxazin-3-one glucoside). Within the Lamiaceae L. galeobdolon is distinguished by the presence GDIBOA in addition to the more common iridoid harpagide. Although LgGLU1 proved to be promiscuous with respect to accepted substrates, harpagide hydrolysis was not detected. Benzoxazinoids are characteristic defence compounds of the Poales but are also found in some unrelated dicots. The benzoxazinoid specific BGLUs have recently been identified for the grasses maize, wheat, rye and the Ranunculaceae Consolida orientalis. All enzymes share a general substrate ambiguity but differ in detailed substrate pattern. The isolation of the second dicot GDIBOA glucosidase LgGLU1 allowed it to analyse the phylogenetic relation of the distinct BGLUs also within dicots. The data revealed long periods of independent sequence evolution before speciation.

Hannemann L, Lucaciu CR, Sharma S, Rattei T, Mayer KFX, Gierl A, Frey M
2018 - Phytochemistry, 224-233

The Genetic Transformation of Chlamydia pneumoniae.

We demonstrate the genetic transformation of using a plasmid shuttle vector system which generates stable transformants. The equine N16 isolate harbors the 7.5-kb plasmid pCpnE1. We constructed the plasmid vector pRSGFPCAT-Cpn containing a pCpnE1 backbone, plus the red-shifted green fluorescent protein (RSGFP), as well as the chloramphenicol acetyltransferase (CAT) gene used for the selection of plasmid shuttle vector-bearing transformants. Using the pRSGFPCAT-Cpn plasmid construct, expression of RSGFP in koala isolate LPCoLN was demonstrated. Furthermore, we discovered that the human cardiovascular isolate CV-6 and the human community-acquired pneumonia-associated IOL-207 could also be transformed with pRSGFPCAT-Cpn. In previous studies, it was shown that spp. cannot be transformed when the plasmid shuttle vector is constructed from a different plasmid backbone to the homologous species. Accordingly, we confirmed that pRSGFPCAT-Cpn could not cross the species barrier in plasmid-bearing and plasmid-free , , , , and However, contrary to our expectation, pRSGFPCAT-Cpn did transform Furthermore, pRSGFPCAT-Cpn did not recombine with the wild-type plasmid of Taken together, we provide for the first time an easy-to-handle transformation protocol for that results in stable transformants. In addition, the vector can cross the species barrier to , indicating the potential of horizontal pathogenic gene transfer via a plasmid. The absence of tools for the genetic manipulation of has hampered research into all aspects of its biology. In this study, we established a novel reproducible method for transformation based on a plasmid shuttle vector system. We constructed a plasmid backbone shuttle vector, pRSGFPCAT-Cpn. The construct expresses the red-shifted green fluorescent protein (RSGFP) fused to chloramphenicol acetyltransferase in transformants stably retained pRSGFPCAT-Cpn and expressed RSGFP in epithelial cells, even in the absence of chloramphenicol. The successful transformation in using pRSGFPCAT-Cpn will advance the field of chlamydial genetics and is a promising new approach to investigate gene functions in biology. In addition, we demonstrated that pRSGFPCAT-Cpn overcame the plasmid species barrier without the need for recombination with an endogenous plasmid, indicating the potential probability of horizontal chlamydial pathogenic gene transfer by plasmids between chlamydial species.

Shima K, Wanker M, Skilton RJ, Cutcliffe LT, Schnee C, Kohl TA, Niemann S, Geijo J, Klinger M, Timms P, Rattei T, Sachse K, Clarke IN, Rupp J
2018 - mSphere, 5: in press