Ktedonobacter racemifer
Scientific Classification:
Domain: Bacteria
Phylum: Chloroflexi
Class: Ktedonobacteria
Order: Ktedonobacterales
Family: Ktedonobacteraceae
Genus: Ktedonobacter
Species: Ktedonobacter racemifer
Ktedonobacter racemifer is a gram-positive, aerobic, non-motile, filamentous bacterium from the '''Chloroflexi''' phylum[1]. K. racemifer was first isolated in 2006 in forest soil from a black forest wood in Gerenzano, Lombardy, Northern Italy [1]. K. racemifer was the first identified member of the Ktedonobacter family and has since been identified as containing a type II polyketide synthase [2] [3].
Morphology and Characteristics
Electron microscopy images of K. racemifer show that K. racemifer colones have a grape-like appearance[2]. The individual bacterial cells are rod-shaped and frequently produce spherical spores[1]. When it was first characterized, K. racemifer was initially mistaken as an Actinobacteria due to its similar filamentous resemblance to Thermomonospora spp.[2]. Additionally, K. racemifer forms spores which detach from individual cells to cluster in groups of three or more[1][2]. These spores have a typical diameter of 1.6-1.8 µm[2]. The amino acids composing peptidoglycan in K. racemifer are ornithine, alanine, glutamic acid, serine, and glycine[2].
Growth Conditions
K. racemifer is suitable for growth on Streptomyces Medium 65, and grows in small, spherical, cream-colored colonies on Medium 65 [4]. These colonies are typically 3-4 mm in diameter[2]. While K. racemifer is an aerobic heterotroph, it has also been observed to grow under microaerophilic conditions[2]. The exact mechanism of K. racemifer ATP acquisition is unknown. It was not observed to grow under anaerobic conditions[2]. As a heterotroph, it uses sugars and peptides as a carbon source[1]. K. racemifer has been observed to grow optimally in temperature ranges from 28-33 °C[1].
Optimal salinity conditions of 10 grams per liter sodium chloride have been observed, but K. racemifer is inhibited at salinity concentrations from 30 grams per liter sodium chloride[1]. K. racemifer prefers slightly acidic pHs, and has been observed to grow between pH values 4.8 and 6.8 with an optimal pH of 6.0[1]. No growth was observed at pH values of 3.9 and 7.5[2]. K. racemifer appears to be at least somewhat resistant to lysozymes, with no growth inhibition seen at a lysozyme concentration of 100 µg/mL[2]. In addition, K. racemifer has showcased significant antibiotic resistance; it has been shown as resistant to 5 µg/mL rifampin and thiostrepton. However, it is sensitive to novobiocin, ramoplanin and nalidixic acid in concentrations of 5 µg/mL alongside apramycin and kanamycin in concentrations of 5 µg/mL.
Genome
While K. racemifer has morphological similarities to the Actinobacteria phylum, rRNA sequencing shows that K. racemifer has the highest similarity to bacteria from the Chloroflexi phylum[2]. While ''Sorangium cellulosum'' has since been characterized as larger, upon its discovery K. racemifer contained the largest described prokaryotic genome with over 13.6 million base pairs[1]. 11,453 protein-coding genes and 87 RNA genes with 8 RNA operons are present in the genome of K. racemifer[1][5]. No pseudogenes have been identified from the genome of K. racemifer, but the functions of many other genes have been identified[2]. 416 genes have been identified as serving in energy conservation, while 1,028 genes are involved with carbohydrate and amino acid metabolism[1]. Interestingly, K. racemifer contains 20 genes classified under the “cell motility” functional category despite no K. racemifer motility having been observed.
K. racemifer contains many Clusters of Orthologous Genes (COGs), resulting in a large amount of genetic redundancy in its genome[1]. Comparisons of the K. racemifer genome to that of Sphaerobacter thermophilus and Thermomicrobium roseum showed that K. racemifer contains 9,539 unique genes that have no homologs in the comparison genomes[1]. The enormous genome length of K. racemifer shows many genes that are related to transposons; 601 individual genes encode transposases. In addition, 151 individual genes encode for integrase proteins and 107 genes encode for resolvases[1].
Polyketide Synthase
In 2015, K. racemifer was identified as a non-actinobacterial strain containing a type II polyketide synthase, a gene cluster with the potential to encode for enzymes producing a type of secondary metabolite, type II polyketides[3]. 217 individual genes have been identified from the K. racemifer genome as involved in secondary metabolite biosynthesis[1]. Prior to this discovery, no type II polyketide synthases had been identified in bacteria outside of the Actinomyces phylum[3]. This finding has led to further bioprospecting into the polyketide production potential of K. racemfier and related strains.
In addition to natural product research on the potential native type II polyketide produced from K. racemifer, studies have been conducted on the potential for the individual type II polyketide synthase enzymes from K. racemifer for use in combinatorial biosynthesis[6].. In 2019, the critical ketosynthase chain length factor enzyme from K. racemifer was able to be heterologously expressed in ''Escherichia coli'' along with other non-actinobacterial polyketide synthase enzymes[6]. The authors hypothesized that the closer phylogenetic relationship between Chloroflexi and E. coli as compared to the relationship between Actinobacteria and E. coli allowed for the relative ease of K. racemifer ketosynthase chain length factor heterologous expression in E. coli compared to previously studied Actinobacteria ketosynthase chain length factors[6].
References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 Chang, Y., Land, M., Hauser, L., Chertkov, O., Del Rio, T.G., Nolan, M., Copeland, A., Tice, H., Cheng, J.-F., Lucas, S., et al. (2011). Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T). Stand. Genomic Sci. 5, 97–111.
- ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 Cavaletti, L., Monciardini, P., Bamonte, R., Schumann, P., Rohde, M., Sosio, M., and Donadio, S. (2006). New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil. Applied and Environmental Microbiology 72, 4360–4369.
- ↑ 3.0 3.1 3.2 Hillenmeyer, M.E., Vandova, G.A., Berlew, E.E., and Charkoudian, L.K. (2015). Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters. PNAS 112, 13952–13957.
- ↑ Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., and Dawyndt, P. (2014). StrainInfo introduces electronic passports for microorganisms. Systematic and Applied Microbiology 37, 42–50.
- ↑ Han, K., Li, Z., Peng, R., Zhu, L., Zhou, T., Wang, L., Li, S., Zhang, X., Hu, W., Wu, Z., et al. (2013). Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Scientific Reports 3, 1–7.
- ↑ 6.0 6.1 6.2 Cummings, M., Peters, A.D., Whitehead, G.F.S., Menon, B.R.K., Micklefield, J., Webb, S.J., and Takano, E. (2019). Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli. PLoS Biol 17, e3000347.