AbstractsBiology & Animal Science

Genome, transcriptome and phenotype analyses of Corynebacteria with biotechnological relevance

by Arwa Al-Dilaimi

Institution: Universität Bielefeld
Year: 2016
Posted: 02/05/2017
Record ID: 2121059
Full text PDF: https://pub.uni-bielefeld.de/publication/2905065


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…