Genomic insights into Dactylosporangium sp. AC04546, a rubber degrader with three latex clearing proteins

Ann Anni Basik; Namiko Gibu; Yukimura Kawagiwa; Siuk-Mun Ng; Tiong Chia Yeo; Kumar Sudesh; Daisuke Kasai

doi:10.3389/fmicb.2024.1378082

Genomic insights into Dactylosporangium sp. AC04546, a rubber degrader with three latex clearing proteins

Front Microbiol. 2024 May 30:15:1378082. doi: 10.3389/fmicb.2024.1378082. eCollection 2024.

Authors

Ann Anni Basik¹, Namiko Gibu², Yukimura Kawagiwa², Siuk-Mun Ng³, Tiong Chia Yeo¹, Kumar Sudesh⁴, Daisuke Kasai²

Affiliations

¹ Sarawak Biodiversity Centre, Kuching, Sarawak, Malaysia.
² Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Japan.
³ Codon Genomics S/B, Seri Kembangan, Selangor, Malaysia.
⁴ Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia.

Abstract

With more than 100 rubber-degrading strains being reported, only 9 Lcp proteins isolated from Nocardia, Gordonia, Streptomyces, Rhodococcus, Actinoplanes, and Solimonas have been purified and biochemically characterized. A new strain, Dactylosporangium sp. AC04546 (strain JCM34239), isolated from soil samples collected in Sarawak Forest, was able to grow and utilize natural or synthetic rubber as the sole carbon source. Complete genome of Strain AC04546 was obtained from the hybrid assembly of PacBio Sequel II and Illumina MiSeq. Strain AC04546 has a large circular genome of 13.08 Mb with a G+C content of 72.1%. The genome contains 11,865 protein-coding sequences with 3 latex clearing protein (lcp) genes located on its chromosome. The genetic organization of the lcp gene cluster is similar to two other reported rubber-degrading strains-Actinoplanes sp. OR16 and Streptomyces sp. CFMR 7. All 3 Lcp from strain AC04546 were expressed in Escherichia coli and exhibited degrading activity against natural rubber. The distinctiveness of strain AC04546, along with other characterized rubber-degrading strains, is reported here.

Keywords: Dactylosporangium; actinobacteria; degradation; genome; rubber.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This project was funded by the Sarawak State Government and part of this work was also supported by JST-Mirai Program Grant Number JPMJMI19E6, Japan.