Complete genome sequence of <i>Archangium gephyra</i> KYC5002, a myxobacterium producing argyrins and tubulysins

Sunjin Lee; Hyesook Hyun; Juo Choi; Seohui Park; Chaehyeon Park; Yujin Ka; Kyungyun Cho

doi:10.7845/kjm.2023.3099

https://doi.org/10.7845/kjm.2023.3099

Complete genome sequence of Archangium gephyra KYC5002, a myxobacterium producing argyrins and tubulysins

Korean J. Microbiol. 2023;59(4):362-365

Published online December 31, 2023

Sunjin Lee, Hyesook Hyun, Juo Choi, Seohui Park, Chaehyeon Park, Yujin Ka, and Kyungyun Cho^*

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

Correspondence to: *E-mail: kycho@hoseo.edu; Tel.: +82-41-540-5627; Fax: +82-41-540-9538

Received November 21, 2023; Revised December 12, 2023; Accepted December 12, 2023.

Abstract: The whole genome sequence of the argyrin- and tubulysin-producing myxobacterium Archangium gephyra KYC5002 was analyzed. The genome of A. gephyra KYC5002 was assembled into a 13,249,988 bp circular genome with a G + C content of 68.8%, containing 10,298 protein-coding genes, 12 rRNA genes, and 95 tRNA genes. In the A. gephyra KYC5002 genome, 53 secondary metabolite biosynthetic gene clusters (BGCs) were detected in 46 regions; the total length of these genes was 6.81% of the total genome. The genome was predicted to contain BGCs for argyrins, carotenoids, DKxanthenes, gephyronic acid, geosmins, microviridins, myxochellins, and tubulysins.; Keywords : Archangium gephyra, argyrin, genome sequence, myxobacteria, tubulysin

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Myxobacteria are a group of gram-negative bacteria classified into the phylum Myxococcota and order Myxococcales. Archangium gephyra is a myxobacterium belonging to the family Cystobacteraceae and order Myxococcales (Reichenbach, 2005). Myxobacteria produce diverse bioactive secondary metabolites (Weissman and Müller, 2010; Herrmann et al., 2017; Hyun and Cho, 2018). Secondary metabolites isolated from A. gephyra strains include gephyronic acid (Sasse et al., 1995), melithiazols (Sasse et al., 1999), tubulysins (Sasse et al., 2000), argyrins (Sasse et al., 2002), archazolids (Sasse et al., 2003), and aurafurons (Kunze et al., 2005).

Archangium gephyra KYC5002 is a natural dispersed variant of A. gephyra KYC2615, isolated from Gyeongju, Gyeongsangbuk-do, Republic of Korea (Hyun et al., 2021; Yu et al., 2023). Most myxobacteria isolated from nature grow in liquid media producing aggregated cells. In contrast, A. gephyra KYC5002 strain grows dispersed in liquid media, allowing quantitation. Archangium gephyra KYC5002 is also known as MEHO_002 strain (Choi et al., 2021). Archangium gephyra KYC5002 produces argyrins and tubulysins (Yu et al., 2023). Argyrins are octapeptides with immunosuppressive and antitumorigenic activities (Sasse et al., 2002; Nickeleit et al., 2008). Tubulysins are cytotoxic to eukaryotes because they induce the depolymerization of β-tubulin, causing microtubules to disassemble (Sasse et al., 2000; Khalil et al., 2006). We sequenced the genome of A. gephyra KYC5002 because it produces argyrins and tubulysins, unlike DSM 2261^T, which is the A. gephyra type strain.

Archangium gephyra KYC5002 was cultured in CYS medium (Shin et al., 2013), and the genomic DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method (Wilson, 2001). The whole A. gephyra KYC5002 genome was sequenced using the PacBio Sequel IIe system and Illumina HiSeq Xten sequencing platform at Macrogen, Inc. In total, 29,174 HiFi reads (221,452,323 bp) were sequenced using the PacBio Sequel IIe system, and 13,758,734 short reads (2,077,568,834 bp) were sequenced using the Illumina platform. De novo assembly was conducted using the Flye assembler (v2.4.2) (Kolmogorov et al., 2019) with PacBio HiFi reads only, followed by error correction of the contig bases with Illumina reads using Pilon (v1.21) (Walker et al., 2014). The resultant A. gephyra KYC5002 whole genome is a circular chromosome of 13,249,988 bp with a G + C content of 68.8%. When calculated using the OrthoANIu algorithm (Yoon et al., 2017), the genome of strain KYC5002 had an average nucleotide identity (ANI) of 92.18% with the genome of strain DSM 2261^T (GenBank accession number: CP011509.1), the type strain of A. gephyra, and the 16S rRNA sequence was 99.11% similar. Annotation using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) revision 6.6 (Tatusova et al., 2016) revealed that the genome comprises 10,298 protein-coding genes, 12 rRNA genes, 95 tRNA genes, 4 ncRNA genes, and 38 pseudogenes (Table 1).

Table 1 General genomic features of Archangium gephyra KYC5002 compared to type strain A. gephyra DSM 2261^T

Genomic feature	Value
Genomic feature	DSM 2261^T	KYC5002
Genome size (bp)	12,489,432	13,249,988
Number of contig	1	1
Genome coverage (%)	100	100
G + C content (%)	69.4	68.8
Protein coding genes	9,798	10,298
rRNA genes (5S, 16S, 23S)	9 (3, 3, 3)	12 (4, 4, 4)
tRNA genes	90	95
ncRNA genes	4	4
Pseudogenes	99	38
CRISPR arrays	-	2
GenBank accession number	CP011509	CP137851

Myxobacteria have many secondary metabolite biosynthetic gene clusters (BGCs) in their genomes (Hyun and Cho, 2018). Therefore, we analyzed the secondary metabolite biosynthetic genes present in the A. gephyra KYC5002 genome using the antiSMASH program (Blin et al., 2023). Fifty-two BGSs were detected in 46 regions, and the combined sequence length of these BGCs was 901,678 bp or 6.81% of the genome. The genome was predicted to contain BGCs for argyrins, carotenoids, DKxanthenes, gephyronic acid, geosmins, microviridins, myxochellins, and tubulysins (Table 2). Genome-wide comparative analysis using the antiSMASH program showed that, of these BGCs, those that biosynthesize argyrins, DKxanthenes, gephyronic acid, and tubulysins were present only in the genome of A. gephyra KYC5002 and absent in the genome of the type strain A. gephyra DSM 2261^T (Table 2). The whole genome sequence of A. gephyra KYC5002 is expected to be useful for studying the production of secondary bioactive compounds.

Table 2 Secondary metabolite biosynthetic gene clusters whose products can be predicted in the A. gephyra DSM 2261^T and KYC5002 genomes

Secondary metabolites	Biosynthetic gene loci^{^*}
Secondary metabolites	DSM 2261^T	KYC5002
Argyrin	-	26410-26430
DKxanthene	-	21410-21485
Gephyronic acid	-	30395-30450
Tubulysin	-	43510-43545
Alkylpyrone	09316-09320	04825-04845
Carotenoid	01865-01876	43750-43800
Geosmin 1	02305-02307	41780-41790
Geosmin 2	08732	12540
2-Hydroxysorangiadenosine	03302-03326	36340-36410
1-Nonadecene/(14Z)-1,14-nonadecadiene	01680	43600
Microviridin	02991-02992	38055-38060
Myxochellin	04409-04418	30555-30580
VEPE/AEPE/TG-1	03053-03058	37750-37790

*The locus tag prefixes “AA314” for the DSM 2261^T genome and “KYC5002” for the KYC5002 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.

Nucleotide sequence accession number

The complete genome sequence of Archangium gephyra KYC5002 has been deposited in GenBank under the accession number CP137851. The strain was deposited in the Korean Collection for Type Cultures (KCTC) under the accession number KCTC14104BP.

적 요: Argyrin과 tubulysin을 생산하는 점액세균 Archangium gephyra KYC5002의 전장 유전체 서열을 분석하였다. KYC 5002 균주의 유전체는 13,249,988 bp 크기로 68.8%의 G + C 함량을 갖는 원형의 유전체로 조립되었다. 단백질을 암호화하는 유전자는 10,298개이었고, rRNA 유전자는 12개, tRNA 유전자는 95개이었다. KYC5002 균주의 유전체에는 46개 지역에서 53개 이차대사산물 생합성 유전자군이 탐색되었는데, 이들 유전자들의 총 길이는 전체 유전체의 6.81%에 해당하였다. KYC5002 균주의 유전체에는 argyrins, carotenoids, DKxanthenes, gephyronic acid, geosmins, microviridins, myxochellins, tubulysins 등을 생산하는 이차대사 생합성 유전자군들이 존재하는 것으로 분석되었다.

Acknowledgments: This research was supported by MECOX CureMed Co. and the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2021R1I1A3044432).

Conflict of Interest: The authors have no conflict of interest to report.

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