Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan

Alkhateeb, Rabeaa S.; Vorhölter, Frank-Jörg; Rückert, Christian; Mentz, Almut; Wibberg, Daniel; Hublik, Gerd; Niehaus, Karsten; Pühler, Alfred

doi:10.1016/j.jbiotec.2016.03.020

Cited by 38 publications

(21 citation statements)

References 67 publications

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“…TSS positions were retrieved from Biocyc and the literature and were placed on the alignments of the regulatory regions. A TSS turnover was detected if the TSS of two homologous regulatory regions were distant of more than five nucleotides on the alignments.…”

Section: Methodsmentioning

confidence: 99%

Transcriptional start site turnover in the evolution of bacterial paralogous genes – the pelE‐pelD virulence genes in Dickeya

et al. 2016

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After a gene duplication event, the resulting paralogous genes frequently acquire distinct expression profiles, roles, and/or functions but the underlying mechanisms are poorly understood. While transcription start site (TSS) turnover, i.e., the repositioning of the TSS during evolution, is widespread in eukaryotes, it is less documented in bacteria. Using pelD and pelE, two closely related paralogous genes encoding key virulence factors in Dickeya, a gamma proteobacterial genus of phytopathogens, we show that pelE has been selected as an initiator of bacterial aggression, while pelD acts at a later stage, thanks to modifications in the transcriptional regulation of these two genes. This expression change is linked to a few mutations that caused a shift in the position of the pelETSS and the rapid divergence in the regulation of these genes after their duplication. Genomic surveys detected additional examples of putative turnovers in other bacteria. This first report of TSS shifting in bacteria suggests that this mechanism could play a major role in paralogous genes fixation in prokaryotes.

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Section: Methodsmentioning

confidence: 99%

Transcriptional start site turnover in the evolution of bacterial paralogous genes – the pelE‐pelD virulence genes in Dickeya

et al. 2016

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“…In addition, little is known about non‐genic‐type promoters, including intragenic, antisense and orphan promoters. Although some of these promoters have been experimentally identified, they have not yet been characterized (Yamamoto et al ., ; Mejia‐Guerra et al ., ; Alkhateeb et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Identification of Arabidopsis genic and non‐genic promoters by paired‐end sequencing of TSS tags

et al. 2017

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Information about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein-coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA-type promoters, but not for Coreless-type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene.

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“…However, the functions of many Xanthomonas RNAs remain widely unclear [117]. In X. campestris, subsequent to the identification of small RNAs [135,150,151], antisense transcripts were found that cover the promoter region of xanthan biosynthetic key genes [116]. Such data clearly confirm that RNA-Seq has a potential to enhance genome annotation, thereby delivering a new foundation for consecutive functional experiments.…”

Section: Validation and Augmentation Of Genome Annotations Based On Tmentioning

confidence: 76%

“…The wider application of RNA-Seq is starting to increase the availability of experimentally determined transcriptional start sites. This is likely to result in higher quality start codon predictions, as recently indicated for Xcc B100 [116]. In contrast to protein-coding genes, the identification of RNA genes is still poorly conceived.…”

Section: Genomic Basicsmentioning

confidence: 97%

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Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan

Cited by 38 publications

References 67 publications

Transcriptional start site turnover in the evolution of bacterial paralogous genes – the pelE‐pelD virulence genes in Dickeya

Transcriptional start site turnover in the evolution of bacterial paralogous genes – the pelE‐pelD virulence genes in Dickeya

Identification of Arabidopsis genic and non‐genic promoters by paired‐end sequencing of TSS tags

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

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