Objective Streptomyces thermotolerans is a
producer of Carbomycin, which is commonly utilized in the industry for
biotransforming Tylosin into acetylisovaleryltylosin. However, the whole genome
sequence information of this strain has not been reported. Herein, the whole
genome of S. thermotolerans ATCC
11416 was sequenced and analyzed by bioinformatics software to predict the
putative biosynthetic gene cluster (BGC) of secondary metabolites,
as well as comparative genomics research.
Methods The mycelium of S. thermotolerans ATCC 11416 was cropped, the qualified genomic DNA
was extracted, and the whole genome of S.
thermotolerans ATCC 11416 was sequenced using sequencing platform Illumina
combined with PacBio. The resultant genomic sequence was analyzed by anti-SMASH
software to find the BGC of secondary metabolites and the deduced compounds
produced by these BGC, and the transcription level of these BGC was identified
by qPCR. The whole genome of ATCC 11416 comparisons with other streptomyces
were analyzed by TBtools software.
Results The
genome of S. thermotolerans ATCC
11416 consisted of a linear chromosome with a genome size of 8 279 432 bp and
was presumed to contain 7356 genes with a GC content of 71.65%. It contained 66
tRNA and 18 rRNA sequences, and multiple repeats sequences had been identified.
The BGCs of 26 secondary metabolites were identified from the genome, of which
Cluster 8 was responsible for carbomycin biosynthesis. Using qPCR detection and
comparison with key genes in Cluster 8, it was found that the functional genes
in Clusters 1, 7, 13, 14, 15, 19 and 21 exhibited higher expression activity,
while those in Clusters 5, 6, 9, 11, 12, 16, 18 and 24 showed lower expression
activity. The functional genes in Clusters 2, 3, 4, 10, 17, 20, 22, 23 and 25
were almost not expressed, indicating putative silencing gene clusters. Among
the silent gene clusters, Clusters 4, 10, 17, 20, 23, and 26 were low
homologous with the known gene clusters and might be responsible for
synthesizing new compounds. Genomic comparative analysis showed that S. thermotolerans ATCC 11416 and S. ambofaciens ATCC 23877 exhibited
higher homology, and both produced 16-membered macrolide antibiotics. Genomic
rearrangement phenomena such as multiple flips and translocations were found in
genomic comparison.
Conclusion The thermotolerant actinomycete Streptomyces thermotolerans ATCC
11416 harbors a medium-sized genome containing 26 BGCs, including a number of
silent gene clusters with low homology. This lays the foundation for the subsequent
activation of these silent gene clusters through molecular biological
approaches to obtain new compounds.