Elsevier

Journal of Biotechnology

Volume 159, Issue 3, 15 June 2012, Pages 235-248
Journal of Biotechnology

The transcriptional regulatory network of Corynebacterium jeikeium K411 and its interaction with metabolic routes contributing to human body odor formation

https://doi.org/10.1016/j.jbiotec.2012.01.021Get rights and content

Abstract

Lipophilic corynebacteria are involved in the generation of volatile odorous products in the process of human body odor formation by degrading skin lipids and specific odor precursors. Therefore, these bacteria represent appropriate model systems for the cosmetic industry to examine axillary malodor formation on the molecular level. To understand the transcriptional control of metabolic pathways involved in this process, the transcriptional regulatory network of the lipophilic axilla isolate Corynebacterium jeikeium K411 was reconstructed from the complete genome sequence. This bioinformatic approach detected a gene-regulatory repertoire of 83 candidate proteins, including 56 DNA-binding transcriptional regulators, nine two-component systems, nine sigma factors, and nine regulators with diverse physiological functions. Furthermore, a cross-genome comparison among selected corynebacterial species of the taxonomic cluster 3 revealed a common gene-regulatory repertoire of 44 transcriptional regulators, including the MarR-like regulator Jk0257, which is exclusively encoded in the genomes of this taxonomical subline. The current network reconstruction comprises 48 transcriptional regulators and 674 gene-regulatory interactions that were assigned to five interconnected functional modules. Most genes involved in lipid degradation are under the combined control of the global cAMP-sensing transcriptional regulator GlxR and the LuxR-family regulator RamA, probably reflecting the essential role of lipid degradation in C. jeikeium. This study provides the first genome-scale in silico analysis of the transcriptional regulation of metabolism in a lipophilic bacterium involved in the formation of human body odor.

Highlights

► The gene-regulatory repertoire of the lipophilic species C. jeikeium K411 was deduced from its complete genome sequence and the transcriptional regulatory network was reconstructed. ► Genes associated with human body odor formation are under the transcriptional control of GlxR and McbR. ► This study provides the first systems view on metabolic pathways contributing to the formation of human body odor.

Introduction

In the recent past, a growing effort was made by the cosmetic industry to understand human body odor formation on a molecular level (Barzantny et al., 2012). This emerging field of biotechnological research is apparently of high relevance, as a global market volume of 12.6 billion US$ has been predicted for 2015 (Global Industry Analysts, 2011). The deodorant industry is more and more interested in creating technologically advanced or even gender-specific products. Especially the development of long-lasting deodorants specifically targeting axillary bacteria and enzymes rather than having an overall antimicrobial effect is constantly in the focus of research (Lyon et al., 1996). In this context, axillae dominated by lipophilic corynebacteria have been correlated with the development of strong body odor (Taylor et al., 2003) and the impact of active deodorant components on these bacteria has been investigated in first attempts (Brune et al., 2006a). One prominent representative of this group of bacteria is Corynebacterium jeikeium, a natural resident of the human skin predominantly colonizing moist areas of the body (Grice et al., 2009, Wichmann et al., 1985). It can be regarded as a model organism, because transcriptomic and proteomic methods have been established and the whole genome sequence of the axilla isolate K411 is available (Brune et al., 2007, Hansmeier et al., 2007, Tauch et al., 2005). Its natural habitat is characterized by the presence of odorless secretions from eccrine, apocrine and sebaceous glands containing a variety of proteins, lipids and other nutrients (Bojar et al., 2004, Greene et al., 1970, Labows et al., 1979, Wilke et al., 2007). The genome sequence of C. jeikeium K411 revealed the lack of a fatty acid synthase gene, constituting the lipid-dependent (“lipophilic”) lifestyle of this organism (Tauch et al., 2005). Fatty acids are important building blocks for cellular metabolites and essential for membrane and mycolic acid biosynthesis in C. jeikeium, particularly since this bacterium is unable to utilize glucose or acetate as sole carbon source, demonstrating its strong adaption to the human host tissue (Tauch et al., 2005).

The involvement of lipophilic corynebacteria in human body odor formation has been proposed several years ago (James et al., 2004) and four major routes and mechanisms contributing to human axillary odor are reported in the current literature (Barzantny et al., 2012). The biotransformation of steroid derivatives is believed to have only a marginal influence on odor intensity (Preti and Leyden, 2010), whereas short-chain fatty acids like 3-methyl-2-hexenoic acid and sulfanylalkanols like 3-methyl-3-sulfanyl-hexan-1-ol were shown to be major components of human axillary odor (Natsch et al., 2006). These substances are secreted as glutamine- and glycine–cysteine-conjugated precursors, respectively, which are released upon cleavage by corynebacterial enzymes (Natsch et al., 2003, Natsch et al., 2004). Additionally, it is proposed that the partial degradation of unusual long-chain fatty acids by lipophilic corynebacteria in the human axilla generates volatile odorous fatty acids (James et al., 2004). The complete genome sequence of C. jeikeium K411 revealed the presence of a comprehensive set of fatty acid degrading enzymes to ensure the survival of the bacterium in its natural lipid-rich habitat. At least 30 genes potentially involved in β-oxidation were found in the genome, whereof most enzymatic functions relevant for the degradation of fatty acids are encoded by several paralogs (Barzantny et al., 2012, Tauch et al., 2005). Since fatty acid degradation is an essential pathway for C. jeikeium, it is very likely that it underlies a tight and highly interconnected regulation to quickly adapt to environmental changes in lipid composition and to minimize energy consumption by coexpression of redundant genes. However, there is a lack of knowledge regarding the transcriptional control of genes contributing to human body odor formation. The only exception is the transcriptional regulator McbR that represses the aecD gene involved in the cleavage of cysteine-linked sulfanylalkanols (Brune et al., 2011).

To ensure the flow of information from the external environment to the gene level, bacteria use the transcriptional regulatory network (TRN), which represents the total sum of transcriptional regulatory interactions in an organism (Ma et al., 2004, Seshasayee et al., 2006). Therein, DNA-binding transcriptional regulators are the main components, as they are able to sense diverse stimuli and bind specific operator sequences to control and modulate the transcription of their target genes (Madan Babu and Teichmann, 2003). Regulatory networks can be described as directed graphs, in which nodes represent regulators and their target genes and directed edges indicate regulatory interactions between them (Babu et al., 2004). The TRN contains highly significant reoccurring network motifs like single input motifs, feed forward loops, autoregulation, and regulatory cascades (Dobrin et al., 2004, Mangan and Alon, 2003, Milo et al., 2002, Shen-Orr et al., 2002, Yu et al., 2003). The interconnection of such motifs represents the architectural backbone of the TRN, optimizes cellular metabolism and the overall fitness of the bacterial cell, and reflects the adaption of the bacterium to its predominant habitat. TRNs have been investigated in detail for several species like the model organism Escherichia coli or the amino acid producer Corynebacterium glutamicum (Gama-Castro et al., 2011, Schröder and Tauch, 2010). By transferring these findings onto the deduced transcriptional regulatory repertoire of C. jeikeium, we intend to characterize the TRN for this species. Based on a systematic genome-scale in silico analysis, we describe the transcriptional regulatory repertoire of C. jeikeium, the modularity of regulatory functions and its interaction with metabolic routes contributing to human body odor formation.

Section snippets

Detection of the transcriptional regulatory repertoire of C. jeikeium K411

The assignment of candidate genes to the transcriptional regulatory repertoire of C. jeikeium K411 was performed by means of a combined bioinformatic approach using several tools and programs for the prediction of protein domains and the detection of orthologous proteins (Brune et al., 2005). All web-based tools and programs were used with default parameter settings if not otherwise stated. First, all proteins of C. jeikeium K411 containing putative DNA-binding domains were detected using the

The repertoire of regulatory genes of C. jeikeium K411

Transcriptional regulators are the central components in bacterial gene regulatory networks that sense internal and external stimuli and adequately modulate the transcription of target genes. Their DNA-binding ability is usually mediated by a structurally conserved HTH motif recognizing a specific operator sequence (Aravind et al., 2005). In the past, research focused mainly on the elucidation of TRNs of model organisms, like Bacillus subtilis or E. coli (Fadda et al., 2009, Gama-Castro et al.,

Conclusions

This study presents the bioinformatic workflow from the complete genome sequence towards the transcriptional regulatory network of C. jeikeium and contributes to a better understanding of the regulation of metabolic pathways associated with human body odor formation. The deduced transcriptional regulatory repertoire of C. jeikeium contains a limited number of regulatory proteins involved in the control of central carbohydrate metabolism. This lack of regulatory genes coincides with the loss of

Acknowledgments

HB and EF acknowledge the scholarships granted by the CLIB-Graduate Cluster Industrial Biotechnology co-financed by the Ministry of Innovation, Science, and Research of North Rhine Westphalia.

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