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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(4): 517-519

https://doi.org/10.48022/mbl.2411.11007

Received: November 18, 2024; Revised: December 2, 2024; Accepted: December 4, 2024

Complete Genome Sequence of Corallococcus coralloides KYC2213, a Myxobacterium Isolated from the Suncheon Bay Wetland in Korea

Yujin Ka, Chaehyeon Park, Gangmin Kim, and Kyungyun Cho*

Department of Biotechnology, Hoseo University, Asan 31499, Republic of Korea

Correspondence to :
Kyungyun Cho,         kycho@hoseo.edu

Abstract

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The whole genome sequence of the myxobacterium Corallococcus coralloides KYC2213, isolated from the Suncheon Bay Wetland in Korea, has been analyzed. The genome was assembled into a 9,655,077 bp circular chromosome with a G+C content of 70.73%. It contains 7,624 protein-coding genes, 9 rRNA genes, and 57 tRNA genes. Secondary metabolite biosynthetic gene clusters (smBGCs) were identified in 38 regions, 21 of which contained 85 non-ribosomal peptide synthetase and polyketide synthase genes. However, the majority of the smBGCs could not be linked to predictable products, with the exception of those for carotenoids, cystobactamids, geosmins, and the lipids VEPE/AEPE/TG-1.

Keywords: Corallococcus coralloides, genome sequence, myxobacteria

Body

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Myxobacteria are a group of gram-negative bacteria classified into the class Deltaproterobacteria and the order Myxococcales [1]. Corallococcus coralloides is a myxobacterium belonging to the family Myxococcaceae [2]. Myxobacteria produce a wide variety of bioactive secondary metabolites [3−5]. Secondary metabolites isolated from C. coralloides include corallopyronins, corallorazines, coralmycins, and corramycin [3−6]. Among these metabolites, corallopyronins, coralmycins, and corramycin exhibit antibacterial activity.

C. coralloides KYC2213 was isolated from a reed field in the Suncheon Bay Wetland in Korea. We sequenced the genome of C. coralloides KYC2213 because it produces compounds with a different antibiotic spectrum compared to those previously isolated from other C. coralloides strains. C. coralloides KYC2213 was cultured in casitone-yeast extract-starch (CYS) medium [7], and genomic DNA was extracted using the cetyltrimeth-ylammonium bromide (CTAB) method. The genome of C. coralloides KYC2213 was sequenced using the PacBio Revio system at Macrogen, Inc. In total, 152,585 HiFi reads (1,167,149,088 bp) were sequenced. De novo assembly was performed using the Flye assembler (v2.9.4). The resulting genome of C. coralloides KYC2213 is a circular chromosome of 9,655,077 bp with a DNA G+C content of 70.73%. Average Nucleotide Identity (ANI) analysis, using the OrthoANIu algorithm [8], revealed that the genome of strain KYC2213 shares 94.03% ANI with the genome of strain DSM 2259 (GenBank accession number: NC_017030), the type strain of C. coralloides. The 16S rRNA sequence showed 99.73% similarity between the two strains. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) revision 6.8. The annotated genome contains 7,624 protein-coding genes, 9 rRNA genes, 57 tRNA genes, 4 ncRNA genes, and 36 pseudogenes (Table 1).

Table 1 . Comparative genomic features of Corallococcus coralloides KYC2213 and DSM 2259T.

Genomic FeatureDSM 2259TKYC2213
Genome size (bp)10,080,6199,655,077
Number of contigs11
Genome coverage (%)100100
G+C content (%)69.970.73
Protein coding genes8,0427,624
rRNAs genes (5S, 16S, 23S)9 (3, 3, 3)9 (3, 3, 3)
tRNAs genes6057
ncRNAs genes44
Pseudogenes4036
CRISPR arrays12
GenBank accession numberNC_017030CP172866


Myxobacteria possess numerous secondary metabolite biosynthetic gene clusters (smBGCs) in their genomes [5]. To investigate the smBGCs in the genome of C. coralloides KYC2213, we used the antiSMASH program [9]. In the C. coralloides KYC2213 genome, smB-GCs were identified in 38 regions, with 85 non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) genes spread across 21 regions. The total length of the NRPS and PKS genes was 557,407 bp, accounting for 5.77% of the total genome. Most of the smBGCs have no known products, except for those associated with carotenoids, geosmins, the lipids VEPE/AEPE/TG-1, and cystobactamids (Table 2). Carotenoid and geosmin biosynthetic gene clusters are found in all myxobacterial species, except those in the genera Anaeromyxobacter, Labilithrix, and Vulgatibacter [5]. The gene clusters for VEPE/AEPE/TG-1 are present in all myxobacterial strains belonging to the suborder Cystobacterineae. Cystobactamids are topoisomerase inhibitors isolated from the myxobacteria Cystobacter velatus and Myxococcus fulvus [10]. A genome-wide comparative analysis using the antiSMASH program revealed that, among these smBGCs, the genes responsible for cystobactamid biosynthesize are present only in the genome of C. coralloides KYC2213 and are absent in the genome of the type strain, C. coralloides DSM 2259T.

Table 2 . Predicted secondary metabolite biosynthetic gene clusters in the genomes of C. coralloides DSM 2259T and KYC2213.

Secondary MetabolitesBiosynthetic Gene Loci*
DSM 2259T GenomeKYC2213 Genome
Carotenoids13910-1396035360-35410
CystobactamidsAbsent23200-23280
Geosmins36835-3684503905-03915
Myxochelins21835-21880Absent
VEPE/AEPE/TG-107680-0770031770-31790

*The locus tag prefixes “COCOR_RS” for the DSM 2259T genome and “ACIHQR” for the KYC2213 genome are omitted.

VEPE, 1-O-(13-methyl-1-Z-tetradecenyl)-2-O-(13-methyltetradecanoyl)-glycero-3-phosphatidylethanolamine

AEPE, 1-O-(13-methyltetradecyl)-2-O-(13-methyltetradecanoyl)-glycero-3-phosphatidylethanolamine

TG-1, 1,2-di-(13-methyltetradecanoyl)-3-(13-methyltetradecyl)-glycerol

Since most of the smBGCs have no known products, except for carotenoids, geosmins, the lipids VEPE/AEPE/TG-1, and cystobactamids, the whole genome sequence of C. coralloides KYC2213 is expected to be valuable for discovering the new secondary bioactive compounds.

Nucleotide Sequence Accession Number

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The complete genome sequence of Corallococcus coralloides KYC2213 has been deposited in GenBank under the accession number CP172866. The BioProject and BioSample accession numbers are PRJNA1180740 and SAMN44527573, respectively.

Acknowledgments

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This research was supported by the University Innovation Support Project Research Fund of Hoseo University in 2024 (2022-0342-03).

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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