Streptomyces sp. AC04842: Genomic Insights and Functional Expression of Its Latex Clearing Protein Genes (lcp1 and lcp2) When Cultivated With Natural and Vulcanized Rubber as the Sole Carbon Source

Abstract

Rubber-degrading Actinobacteria have been discovered and investigated since 1985. Only recently, through the advancement of genomic sequencing and molecular techniques, genes and pathways involved in rubber degradation are being revealed; however, the complete degradation pathway remains unknown. <i>Streptomyces</i> sp. AC04842 (JCM 34241) was discovered by screening at a Culture Collection Centre in Sarawak for <i>Actinomycetes</i> forming a clear zone on natural rubber latex agar. <i>Streptomyces</i> is a dominant and well-studied soil bacterium playing an important role in soil ecology including carbon recycling and biodegradation. <i>Streptomyces</i> sp. AC04842 draft genome revealed the presence of 2 putative latex clearing protein (<i>lcp</i>) genes on its chromosome and is closely related to <i>Streptomyces cellulosae</i>. Under the <i>Streptomyces</i> genus, there are a total of 64 putative <i>lcp</i> genes deposited in the GenBank and UniProt database. Only 1 <i>lcp</i> gene from <i>Streptomyces</i> sp. K30 has been characterized. Unlike <i>Streptomyces</i> sp. K30 which contained 1 <i>lcp</i> gene on its chromosome, <i>Streptomyces</i> sp. AC04842 contained 2 <i>lcp</i> genes on its chromosome. <i>Streptomyces</i> sp. AC04842 lcp1 and lcp2 amino acid sequences showed 46.13 and 69.11%, respectively, similarity to lcp sequences of <i>Streptomyces</i> sp. K30. Most rubber degrading strains were known to harbor only 1 <i>lcp</i> gene, and only recently, 2-3 <i>lcp</i> homologs have been reported. Several studies have shown that <i>lcp</i>-homolog expression increased in the presence of rubber. To study the expression of <i>lcp1</i> and <i>lcp2</i> genes for <i>Streptomyces</i> sp. AC04842, the strain was incubated in different types of rubber as the sole carbon source. In general, the <i>lcp1</i> gene was highly expressed, while the <i>lcp2</i> gene expression was upregulated in the presence of vulcanized rubber. Mixtures of natural and vulcanized rubber did not further increase the expression of both <i>lcp</i> genes compared with the presence of a specific rubber type. In this study, we paved the way to the exploration of lcp homologs and their function in degrading different types of rubber.