Bioinformatic analysis of the chemotactic potential of Campylobacter concisus
Creators: name: BENTLEY, Michael
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 310204
subject: Genomics and transcriptomics
classificationCode: 310704
subject: Microbial genetics

description: Campylobacter concisus is a bacterium which colonizes the human oral cavity and the gastrointestinal tract. It has been isolated from patients suffering from gingivitis, gastroenteritis, Chron's disease and ulcerative colitis, yet it is also found in healthy people.  Chemotaxis has been regarded as a virulence factor for some bacteria, importantly directing motile bacteria towards sites of colonization and invasion. The chemotaxis of C. concisus has not been thoroughly studied as in other bacteria like E. coli and C. jejuni. Both have established models of the proteins involved, supported by wet laboratory assays that have revealed the compounds which attract or repel them. This study utilised bioinformatics methods to examine C. concisus chemotaxis genes and has compared them to the E. coli and C. jejuni models, to produce a model for C. concisus in an attempt to identify other potential chemoeffectors.
  
In chapter 2, complete genome sequences for E. coli and a selection of Campylobacter spp. were obtained and annotated. From these annotations, genes corresponding to the chemotaxis models for E. coli and C. jejuni were extracted and compared using multiple sequence alignment. In this study the Campylobacter spp. chemotaxis system composed of proteins CheA, CheB', CheR, CheV, CheW, CheY, CheX and MCP, was found to be similar to the E. coli model with an additional scaffold protein (CheV) and a different phosphatase (CheX rather than CheZ). Furthermore, comparing the lengths of the proteins revealed that most are of similar length except CheB' which for the Campylobacter spp. is missing a domain present in the E. coli model, altering its function. Examination of the annotations also showed that several Campylobacter spp. chemotaxis genes are located close enough together in the sequences to be in single transcripts and so, possibly in operons. This has potential implications for the expression of these genes.
 
In chapter 3, to investigate the conservation of chemotaxis genes across all C. concisus strains, all available sequences for this species were downloaded and annotated. From these annotations, chemotaxis genes were extracted and compared using multiple sequence analysis. This revealed that most of these genes are highly conserved across all strains but three genes have variations depending on the genomospecies. C. concisus is known to have two distinct genomic groups, or genomospecies, (GS A and GS B) based on unique sequences from the 23S rRNA gene.

A large number of genes labelled hypothetical in the annotations were examined by scanning these genes for protein domains from the PDB (Protein Data Bank) database to determine if any other chemotaxis genes were present. This revealed multiple MCP chemotaxis genes one of which responds to nitrate and nitrite plus other taxis genes. The model for C. jejuni contains multiple MCPs and other taxis genes.

In chapter 4, the variation of C. concisus genes in relation to the genomospecies was examined. A phylogenetic tree constructed for the CheB' protein revealed a distinct branching based on genomospecies and a possible clade formation within GS B. A comparison of two genomes from GS A and GS B, using an online average nucleotide identity calculator, returned a value of 87.94%. Extending this comparison to 224 available strains returned a result confirming the potential separation and typing of C. concisus strains into two different species based on the current genomospecies structure. Other GS based differences were evident in a statistical analysis of isolation site from the isolation references and in the order of genes around one of the chemotaxis genes.  Evidence points to one of these genomospecies being more prevalent in the oral cavity than the other. Further experimental work is needed to show if these genomospecies possess the phenotypical differences that would confirm this separation.

In conclusion, chemotaxis is important to all bacteria examined in this study as each species has a complete set of well conserved chemotaxis genes. C. concisus has been shown in this study to have multiple sensing genes to be further studied. Moreover, a whole new nitrate/nitrite sensing gene not previously reported in E. coli or C. jejuni has been found in the sequences of all C. concisus strains. Further experimental work with chemotaxis assays and RNA-seq is needed to confirm the expression of these genes.