Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11T (= DSM 44721T)

Rückert C, Albersmeier A, Al-Dilaimi A, et al. Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11T (= DSM 44721T). Standards in Genomic Sciences. 2013;9(3):505-513.Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium, which contains Gram-positive and non-spore forming bacteria with a high G+C content. C. terpenotabidum was isolated from soil based on its ability to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria. It displays tolerance to salts (up to 8%) and is related to Corynebacterium variabile involved in cheese ripening. As this is a type strain of Corynebacterium, this project describing the 2.75 Mbp long chromosome with its 2,369 protein-coding and 72 RNA genes will aid the Genomic Encyclopedia of Bacteria and Archaea project

Whole-Genome Sequence of Pseudoalteromonas sp. NC201, a Probiotic Strain for Litopenaeus stylirostris Hatcheries in New Caledonia

Sorieul L, Rückert C, Al-Dilaimi A, et al. Whole-Genome Sequence of Pseudoalteromonas sp. NC201, a Probiotic Strain for Litopenaeus stylirostris Hatcheries in New Caledonia. Microbiology resource announcements. 2019;8(34): e00477-19.The marine bacterium Pseudoalteromonas sp. strain NC201 has shown probiotic potential in Litopenaeus stylirostris rearing. In this study, the complete genome of NC201 was sequenced. This genome consists of a chromosome (4.13Mb) and a chromid (1.24Mb). The genome contains gene clusters coding for antibacterial peptides and secondary metabolites. Copyright © 2019 Sorieul et al

Biosynthetic reconstitution of deoxysugar phosphoramidate metalloprotease inhibitors using an N-P-bond-forming kinase

Baulig A, Helmle I, Bader M, et al. Biosynthetic reconstitution of deoxysugar phosphoramidate metalloprotease inhibitors using an N-P-bond-forming kinase. CHEMICAL SCIENCE. 2019;10(16):4486-4490.Phosphoramidon is a potent metalloprotease inhibitor and a widespread tool in cell biology research. It contains a dipeptide backbone that is uniquely linked to a 6-deoxysugar via a phosphoramidate bridge. Herein, we report the identification of a gene cluster for the formation of phosphoramidon and its detailed characterization. In vitro reconstitution of the biosynthesis established TalE as a phosphoramidate-forming kinase and TalC as the glycosyltransferase which installs the L-rhamnose moiety by phosphoester linkage

Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production

Bogen C, Al-Dilaimi A, Albersmeier A, et al. Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production. BMC Genomics. 2013;14(1): 926.BACKGROUND: Microalgae are gaining importance as sustainable production hosts in the fields of biotechnology and bioenergy. A robust biomass accumulating strainof the genus Monoraphidium (SAG 48.87) was investigated in this work as apotential feedstock for biofuel production. The genome was sequenced, annotated, and key enzymes for triacylglycerol formation were elucidated. RESULTS: Monoraphidium neglectum was identified as an oleaginous species with favourable growth characteristics as well as a high potential for crude oil production, based on neutral lipid contents of approximately 21% (dry weight) under nitrogen starvation, composed of predominantly C18:1 and C16:0 fatty acids. Further characterization revealed growth in a relatively wide pH range and salt concentrations of up to 1.0% NaCl, in which the cells exhibited larger structures. This first full genome sequencing of a member of the Selenastraceae revealed a diploid, approximately 68 Mbp genome with a G + C content of 64.7%. The circular chloroplast genome was assembled to a 135,362 bp single contig, containing 67 protein-coding genes. The assembly of the mitochondrial genome resulted in two contigs with an approximate total size of 94 kb, the largest known mitochondrial genome within algae. 16,761 protein-coding genes were assigned to the nuclear genome. Comparison of gene sets with respect to functional categories revealed a higher gene number assigned to the category "carbohydrate metabolic process" and in "fatty acid biosynthetic process" in M. neglectum when compared to Chlamydomonas reinhardtii and Nannochloropsis gaditana, indicating a higher metabolic diversity for applications in carbohydrate conversions of biotechnological relevance. CONCLUSIONS: The genome of M. neglectum, as well as the metabolic reconstruction of crucial lipid pathways, provides new insights into the diversity of the lipid metabolism in microalgae. The results of this work provide a platform to encourage the development of this strain for biotechnological applications and production concepts

Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors

Trost E, Al-Dilaimi A, Papavasiliou P, et al. Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors. BMC Genomics. 2011;12(1): 383.ABSTRACT: Corynebacterium ulcerans has been detected as a commensal in domestic and wild animals that may serve as reservoirs for zoonotic infections. During the last decade, the frequency and severity of human infections associated with C. ulcerans appear to be increasing in various countries. As the knowledge of genes contributing to the virulence of this bacterium was very limited, the complete genome sequences of two C. ulcerans strains detected in the metropolitan area of Rio de Janeiro were determined and characterized by comparative genomics: C. ulcerans 809 was initially isolated from an elderly woman with fatal pulmonary infection and C. ulcerans BR-AD22 was recovered from a nasal sample of an asymptomatic dog. The circular chromosome of C. ulcerans 809 has a total size of 2,502,095 bp and encodes 2,182 predicted proteins, whereas the genome of C. ulcerans BR-AD22 is 104,279 bp larger and comprises 2,338 protein-coding regions. The minor difference in size of the two genomes is mainly caused by additional prophage-like elements in the C. ulcerans BR-AD22 chromosome. Both genomes show a highly similar order of orthologous coding regions; and both strains share a common set of 2,076 genes, demonstrating their very close relationship. A screening for prominent virulence factors revealed the presence of phospholipase D (Pld), neuraminidase H (NanH), endoglycosidase E (EndoE), and subunits of adhesive pili of the SpaDEF type that are encoded in both C. ulcerans genomes. The rbp gene coding for a putative ribosome-binding protein with striking structural similarity to Shiga-like toxins was additionally detected in the genome of the human isolate C. ulcerans 809. The molecular data deduced from the complete genome sequences provides considerable knowledge of virulence factors in C. ulcerans that is increasingly recognized as an emerging pathogen. This bacterium is apparently equipped with a broad and varying set of virulence factors, including a novel type of a ribosome-binding protein. Whether the respective protein contributes to the severity of human infections (and a fatal outcome) remains to be elucidated by genetic experiments with defined bacterial mutants and host model systems

Genome, transcriptome and phenotype analyses of Corynebacteria with biotechnological relevance

Al-Dilaimi A. Genome, transcriptome and phenotype analyses of Corynebacteria with biotechnological relevance. Bielefeld: Universität Bielefeld; 2016.In the course of the pan-genome sequencing project for the genus Corynebacterium, two bacteria, Corynebacterium glyciniphilum and Corynebacterium vitaeruminis, attracted attention due to their strong historical background towards L-serine and vitamin B production, respectively. In this context, the aim of this thesis was to characterize these bacteria based on their genome, transcriptome and phenotype by applying state-of-the-art high-throughput technologies, metabolic reconstructions and identification of specific genetic features. The first accomplishment of this study was the valid description of C. glyciniphilum as a new species of the genus Corynebacterium based on chemotaxonomic and phylogenetic as well as enzymatic and morphological studies. Genome sequencing revealed that this species possesses the largest genome of its genus. In addition, an approach combining phenotypic, genomic and transcriptomic data allowed to the optimization of genome annotation and provided insights into the extended metabolic repertoire of this bacterium. Due to the common background in amino acid production, the transcriptome of C. glyciniphilum was compared to the previously published transcriptome of C. glutamicum. Thereby, parallels were identified in terms of the transcriptional architecture, such as promoter and ribosome-binding site motifs. However, the two bacteria reflected divergence in terms of the regulation on the transcriptome and translatome level. While the transcriptome of C. glutamicum reflects a wider range of cis-regulatory elements influencing the translation of transcripts, C. glyciniphilum possesses an enlarged protein-coding regulatory repertoire, such as sigma factors and response regulators. Nonetheless, the existence of two glycine riboswitches arranged in tandem and located in the leader sequence of the glycine cleavage system transcript provides an explanation for the previously described high glycine tolerance of C. glyciniphilum that supports an enhanced L-serine production. The second bacterium investigated in this thesis was the cow rumen isolate C. vitaeruminis. The characterization of this bacterium by correlating phenotype and genome features revealed a high adaptation to the ruminal habitat. The analysis of the genome sequence architecture revealed the presence of two prophage regions in addition to two CRISPR loci, of which one is the largest known within the phylum Actinobacteria. In addition, a gene cluster encoding a complete CRISPR-Cas9 system has been identified within the two CRISPR loci. Recently, this CRISPR-Cas system type became famous in the field of targeted gene editing due to its specificity, simplicity and versatility. Further, comparative gene content analysis of C. vitaeruminis and closely related bacteria as well as C. glutamicum reflected an adaptation to low oxygen levels and the competence for persistence and colonization of the rumen. Complementary analyses on the phenotype and genome level pointed out a mutualistic relationship between C. vitaeruminis, the microbial community in the rumen and its host. Screening of metabolized carbon sources revealed preferences for mono- and di-carboxylic acids, which are the by-products of a normal fiber digesting rumen microbiota. Moreover, the demonstrated production of significant amounts of riboflavin and niacin under anaerobic conditions indicates a potential supplementation of the rumen with this vitamin by C. vitaeruminis. The combination of complementary information derived from the genome, transcriptome and phenotype applied in this thesis resulted in an extensive in-depth characterization of two bacteria. Both possess biotechnologically interesting features that can be used to enhance the yield of amino acids, like L-serine and L-methionine, or B vitamins, like riboflavin and niacin, in other bacteria. Furthermore, the identified CRISRP-Cas9 system of C. vitaeruminis provides opportunity for a customized application in corynebacteria. Taking together, this thesis demonstrates that a complementary application of state-of-the-art technologies on different omics levels in combination with sophisticated bioinformatic application tools provides a valuable tool for a precise characterization and gain of new biological perspectives on the lifestyle of organisms

Bioinformatics in Germany: toward a national-level infrastructure

Tauch A, Al-Dilaimi A. Bioinformatics in Germany: toward a national-level infrastructure. Briefings in Bioinformatics. 2017;20(2):370-374.The German Network for Bioinformatics Infrastructure (de.NBI) is a national initiative funded by the German Federal Ministry of Education and Research (BMBF). The mission of de.NBI is (i) to provide high-quality bioinformatics services to users in basic and applied life sciences research from academia, industry and biomedicine; (ii) to offer bioinformatics training to users in Germany and Europe through a wide range of workshops and courses; and (iii) to foster the cooperation of the German bioinformatics community with international network structures such as the European life-sciences Infrastructure for biological Information (ELIXIR). The network was launched by the BMBF in March 2015 and now includes 40 service projects operated by 30 project partners that are organized in eight service centers. The de.NBI staff develops further and maintains almost 100 bioinformatics services for the human, plant and microbial research fields and provides comprehensive training courses to support users with different expertise levels in bioinformatics. In the future, de.NBI will expand its activities to the European level, as the de.NBI consortium was assigned by the BMBF to establish and run the German node of ELIXIR. The Author 2017. Published by Oxford University Press

Complete Genome Sequence of Corynebacterium vitaeruminis DSM 20294T, isolated from the cow rumen as a vitamin B producer

Al-Dilaimi A, Albersmeier A, Kalinowski J, Rückert C. Complete Genome Sequence of Corynebacterium vitaeruminis DSM 20294T, isolated from the cow rumen as a vitamin B producer. Journal of Biotechnology. 2014;189:70-71.We report the complete genome sequence of Corynebacterium vitaeruminis DSM 20294(T) which was identified as the producer of B vitamins in the rumen of cows. The genome of C. vitaeruminis DSM 20294(T) consists of a single replicon, the chromosome with a size of 2,931,780 bp and a G + C content of 65.53%. The genome encodes for 2,580 protein coding genes, among them those for a complete pathway to synthesize biotin. (C) 2014 Elsevier B.V. All rights reserved

Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T)

Rückert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R, Kalinowski J. Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T). Standards in Genomic Sciences. 2012;7(2):284-293.Corynebacterium halotolerans Chen et al. 2004 is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. C. halotolerans, isolated from a saline soil, belongs to the non-lipophilic, non-pathogenic corynebacteria. It displays a high tolerance to salts (up to 25%) and is related to the pathogenic corynebacteria C. freneyi and C. xerosis. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the Genomic Encyclopedia of Bacteria and Archaea project

Revisiting Corynebacterium glyciniphilum (ex Kubota et al. 1972) sp. nov., nom. rev., isolated from putrefied banana

Al-Dilaimi A, Bednarz H, Lömker A, Niehaus K, Kalinowski J, Rückert C. Revisiting Corynebacterium glyciniphilum (ex Kubota et al. 1972) sp. nov., nom. rev., isolated from putrefied banana. International journal of systematic and evolutionary microbiology. 2015;65(Pt 1):177-182.: A corynebacterium, designated AJ 3170(T), was isolated in the eighties from putrefied bananas. Since then, no further updates concerning the strain description or phylogenetic classification of this species were made. However, phylogenetic analysis of this strain using 16S rRNA and in silico DNA-DNA hybridization confirms the membership to the genus Corynebacterium and clusters AJ 3170(T) with Corynebacterium variabile DSM 44702(T), Corynebacterium terpenotabidum IFO 14764(T) and Corynebacterium nuruki S6-4(T) in one subgroup. Furthermore, a combination of enzymatic, chemical, and morphological characterization technics was applied to describe the strain AJ 3170(T). The strain grows well at pH 6-10 and at 30-41 °C. The predominant major fatty acids were C16:0 (42.15 %), C18:1 ω9c (41.6 %) and C18:0 10-methyl (TBSA) (8.56 %). Cell wall and whole-cell sugar composition could be determined. On the basis of phenotypic, chemotaxonomic and phylogenetic characterization, it is proposed that the strain AJ 3170(T) represents a novel species, for which the name Corynebacterium glyciniphilum sp. nov. is proposed. The type strain is AJ 3170(T) (=DSM 45795(T) =ATCC 21341(T))