Difference between revisions of "Part:BBa K1321306"

Revision as of 21:57, 21 October 2015

Komagataeibacter rhaeticus iGEM

Komagataeibacter rhaeticus is a obligate aerobe Gram negative cellulose-producing bacterial species. Imperial iGEM 2014 team isolated a strain of K. rhaeticus (named G. xylinus iGEM in the honour of the competition) from the Kombucha tea seed culture (Kombucha tea seed culture is a mixture of yeast, K. rhaeticus and other organisms, and is used to make the increasingly popular Kombucha tea). K. rhaeticus iGEM produces cellulose readily on different carbon feedstocks. Although K. rhaeticus iGEM does not produce as high amounts of cellulose as G. xylinus ATCC 53582 (see cellulose productivity on different feedstocks), it is more amenable to genetic engineering and testing of genetic constructs. BBa_K1321306 is a member of the K. rhaeticus genetic engineering toolkit (parts BBa_K1321295 - BBa_K1321332).

K. rhaeticus iGEM genome sequence

K. rhaeticus iGEM genome was sequenced as a part of Imperial iGEM 2014 project. The genome is approximately 3.4Mbp in size, with a GC content of 63.52% (see Figure 1). Autoannotation using Prokka (Seemann 2014) identified in total 3052 putative coding sequences, 59 tRNA sequences and 24 rRNA and other RNA sequences.

K. rhaeticus iGEM was sequenced using an Illumina MiSeq platform, with paired-end 250bp reads. After quality control and removal of low-quality reads, a total of approximately 0.51*10^9bp of sequenced data remained, representing approximately 150x coverage of the genome. Usually, a 50x coverage is considered sufficient for successful assembly. The full genome sequence as annotated contigs are available here File:IC14 G.xylinus igem genome.zip. This file contains the genome sequence as a fasta file and an annotated gff file (Prokka output, which requires Artemis genome browser for viewing). Note, that these files contain contigs, which are not yet ordered into a scaffold. This is a precaution to avoid mis-representation of the large-scale organization of the genome, as the genomes of the closest relatives have proven to be inappropriate for scaffolding. This does not however, affect the quality of the sequences themselves. Note that although the iGEM strain was initially thought to be a strain of Gluconacetobacter xylinus, a later analysis using 16s rRNA places it nearest to Komagataeibacter rhaeticus, meaning that iGEM likely belongs to this species.

Figure 1. Overview of the genome of K. rhaeticus iGEM. The genome is approximately 3.4Mbp in size, with a GC content of around 63% (internal circle) and approximately 3000 coding sequences (external circle; blue bands denote single CDSs. Note that this overview should be taken as a guide, as further analysis may reveal a more accurate organization of the contigs.

Culturing K. rhaeticus iGEM

K. rhaeticus iGEM growth rate varies depending on the culturing conditions. Growth rate is highest when K. rhaeticus is cultured at 30degC, 180rpm shaking in a well-aerated setting. However, in shaking conditions, the prevalence of cellulose non-producing mutants (cel- mutants) increases, which causes a decrease in the total yield of produced cellulose. For this reason, when high cellulose production is required, K. rhaeticus is often grown in static conditions, at 30degC, in a well-aerated setting. In shaking cultures, iGEM strain reaches stationary phase in 48-72 hours, whereas in static cultures, depending on the volume of the medium, it can take up to 15 days. When grown on HS-agar plates at 30degC, cellulose-producing colonies become visible within 48-72 hours, cel- mutant colonies between 24 and 48 hours. Cellulose producing colonies can be distinguished from cel- mutants by colony morphology: cel+ have a rough colony morphology, whereas cel- mutants have a smooth colony morphology (see Figure 2). The most commonly used medium for G.xylinum culturing is Hestrin-Schramm (HS) medium. HS medium contains the following components (for a detailed overview for K. rhaeticus culturing, see K. rhaeticus culturing on [http://2014.igem.org/Team:Imperial/Protocols Imperial 2014 wiki]: 2% (w/v) glucose 0.5% (w/v) yeast extract 0.5% (w/v) peptone 0.27% (w/v) Na2HPO4 0.15% (w/v) citric acid.

Figure 2. Different colony morphologies of cel+ and cel- K. rhaeticus colonies. Cel+ colonies have a rough colony morphology (left), whereas cel- have a smooth colony morphology(right). Plates were inoculated using 50µl of seed cultures grown to stationary phase, and incubated inverted at 30C for 8 days.

Cellulose productivity of K. rhaeticus iGEM

K. rhaeticus iGEM cellulose productivity depends strongly on the carbon feedstocks used. In HS-glucose media grown for 7 days at 30degC standing using 50ml HS medium in 250ml conical flasks (sealed with foam buns), cellulose productivity is approximately one fifth of that of ATCC 53582 strain (see Figure 3 for comparison of ATCC53582 and iGEM strains and experimental details). However, iGEM growth is not optimal in HS-glucose, because in HS-glycerol media and HS-sucrose media the cellulose productivity is increased. Furthermore, in HS-sucrose medium, cellulose productivity is higher than that of ATCC 53582, which is of industrial significance due to the high availability of sucrose (see Feedstocks for K. rhaeticus iGEM).

Feedstocks for K. rhaeticus iGEM

K. rhaeticus is commonly grown on HS-glucose. However, it can readily use other carbon feedstocks, including sucrose and glycerol. iGEM strain's cellulose productivity is highest when grown on glycerol, and higher than ATCC 53582 when grown on sucrose (see Figure 3). Although glycerol seems to result in highest cellulose production, the effects of routine culturing of ATCC 53582 on HS-glycerol media are unknown.

Natural antibiotics resistance of K. rhaeticus iGEM

Using optimal antibiotics concentrations with K. rhaeticus iGEM is critical for selection of transformed cells while not overly inhibiting cell growth. K. rhaeticus iGEM is naturally resistant to kanamycin, ampicillin and chloramphenicol concentrations normally used for E.coli (50µg/ml, 100µg/ml and 35µg/ml respectively; see Figure 4 for an experiment of iGEM natural antibiotic concentrations, experimental details, and comparison of ATCC and iGEM strains). The frequency of appearance of antibiotic-resistant colonies is dependent on the number of cells used for plating - with higher number of plated cells, colonies appear even at higher antibiotics concentrations. Imperial iGEM 2014 team found that iGEM strain forms antibiotic-resistant colonies up to 6x antibiotic concentrations (6x of those commonly used for E.coli), thus the recommended amounts of antibiotics for HS-plates after transformations are 350µg/ml kanamycin, 700µg/ml ampicillin and 245µg/ml chloramphenicol.

NOTE: Because the registry's standard plasmid backbone pSB1C3 is not capable of replication in Gluconacetobacter species, the K. rhaeticus genetic engineering toolkit is housed mainly in pSEVA331-Bb. pSEVA331-Bb is a non-standard backbone, which therefore can't be quality controlled by and maintained in the Registry. However, in order to make the K. rhaeticus toolkit available for the synthetic biology community, Imperial iGEM 2014 team has made it freely available upon request, with quality control provided (see Experience). To request, please contact Imperial iGEM 2014 team.

References:

Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxford, England). [Online] 30 (14), 2068–2069. Available from: doi:10.1093/bioinformatics/btu153 [Accessed: 10 July 2014].