TY - JOUR A1 - Mitzscherling, Julia A1 - MacLean, Joana A1 - Lipus, Daniel A1 - Bartholomäus, Alexander A1 - Mangelsdorf, Kai A1 - Lipski, André A1 - Roddatis, Vladimir A1 - Liebner, Susanne A1 - Wagner, Dirk T1 - Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste JF - International journal of systematic and evolutionary microbiology N2 - Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6%) and Nocardioides dubius KSL-104(T) (98.3%). The genomic DNA G+C content of strain NGK65(T) was 68.2%. Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)). KW - Nocardioides alcanivorans KW - hexadecane KW - plastic degradation KW - terrestrial KW - plastisphere KW - bacteria Y1 - 2022 U6 - https://doi.org/10.1099/ijsem.0.005319 SN - 1466-5026 SN - 1466-5034 VL - 72 IS - 4 PB - Microbiology Society CY - London ER - TY - THES A1 - Bartholomäus, Alexander T1 - Analyzing Transcriptional and Translational Control in E. coli using Deep-Seq Data Y1 - 2016 ER - TY - JOUR A1 - Avcilar-Kucukgoze, Irem A1 - Bartholomäus, Alexander A1 - Varela, Juan A. Cordero A1 - Kaml, Robert Franz-Xaver A1 - Neubauer, Peter A1 - Budisa, Nediljko A1 - Ignatova, Zoya T1 - Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli JF - Nucleic acids research N2 - Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth. Y1 - 2016 U6 - https://doi.org/10.1093/nar/gkw697 SN - 0305-1048 SN - 1362-4962 VL - 44 SP - 8324 EP - 8334 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Feist, Peter A1 - Sin, Celine A1 - Zhang, Gong A1 - Valleriani, Angelo A1 - Ignatova, Zoya T1 - Bacteria differently regulate mRNA abundance to specifically respond to various stresses JF - Geology N2 - Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up-and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs. KW - transcription KW - translation KW - deep sequencing KW - Escherichia coli KW - copy numbers Y1 - 2016 U6 - https://doi.org/10.1098/rsta.2015.0069 SN - 1364-503X SN - 1471-2962 VL - 374 PB - Royal Society CY - London ER - TY - JOUR A1 - Del Campo, Cristian A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Ignatova, Zoya T1 - Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005613 SN - 1553-7404 VL - 11 IS - 10 PB - PLoS CY - San Fransisco ER -