Characterization of the genes responsible for rubber degradation in Actinoplanes sp. strain OR16

Abstract

A Gram-positive rubber-degrading bacterium, Actinoplanes sp. strain OR16 (strain NBRC 114529), is able to grow on agar plates containing natural and synthetic rubber as the sole sources of carbon and energy. When this strain was grown on natural rubber latex overlay agar plates, translucent halos around the cells were observed. To identify the natural rubber degradation genes and other features of its metabolism, its complete genome sequence was determined. The genome of OR16 consists of 9,293,892 bp and comprises one circular chromosome (GenBank accession number AP019371.1) with a G + C content of 70.3%. The genome contains 8238 protein-coding and 18 rRNA genes. A homology search of the genome sequence revealed that three genes ( lcp1 , lcp2 , and lcp3 ) are homologous to an extracellular latex-clearing protein (Lcp) of Streptomyces sp. K30. RT-PCR analysis revealed that lcp1 and lcp2 seem to constitute an operon. Purified lcp gene products have oxygen consumption activity toward natural rubber latex, suggesting that all these genes encode rubber-degrading enzymes in OR16. Quantitative reverse transcription-PCR analysis indicated that the transcription of these genes is induced during the growth of OR16 on natural rubber. The genes located adjacent to lcp1 and lcp3 , which code for a TetR/AcrR-type transcriptional regulator, can bind to the promoter regions of these lcp genes. It is suggested that the putative regulators play a role in regulating the transcription of the lcp genes. These results strongly suggested that three lcp genes are required for the utilization of natural rubber in strain OR16. Key Points • The complete genome sequence of Actinoplanes sp. strain OR16 was determined. • Three lcp genes which are involved in the natural rubber degradation in OR16 were identified. • Transcription of these lcp genes is induced during utilization of rubber in OR16. • Two regulators, which bind to the promoter regions of lcp, were determined. Electronic supplementary material The online version of this article (10.1007/s00253-020-10700-1) contains supplementary material, which is available to authorized users.

Microbial Degradation of Rubber: Actinobacteria

“…strain 835A to degrade NR vulcanizates [ 45 ]. Since then, more than 100 rubber-degrading bacteria have been identified from different habitats, most belonging to the phylum, Actinobacteria ( Streptomyces , Gordonia , Nocardia , Rhodococcus , and Actinoplanes ), rarely found among Gram-negative bacteria, Myxobacteria and fungi [ 46 , 47 ] (details in Section 3.2 , Section 3.4 , and Section 6.4 ). Rubber degrading bacteria converts rubber into derivatives such as isoprenoids, aldehydes, keto groups and 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD) that can be used as value-added molecules, biofuels, polyurethanes, or other polymers [ 48 ].…”

“…Several quantitative lcp gene expression studies have been carried out using qPCR (real time polymerase chain reaction); Nocardia sp. strain NVL3 lcp gene showed 1596-fold higher in the presence of IR [ 61 ], Actinoplanes strain OR16 showed increase of 22.2-fold, 17.1-fold, 335-fold for lcp 1, lcp 2 and lcp 3 gene respectively when cultivated in NR [ 47 ], while Streptomyces sp. K30 and G. polyisoprenivorans VH2 showed expression of lcp gene when cultivated with poly-( cis -1,4-isoprene) compared to those grown with glucose or sodium acetate [ 57 , 62 ].…”

Rubber Degrading Strains of Microtetraspora and Dactylosporangium

“…5), their amino acid sequences were also separate (21.4% to 94.1% similarity) from other known lcp genes (Table 1). Almost all rubber-degrading Actinobacteria, including Streptomyces, Nocardia, and Rhodococcus species have a single lcp homolog 15 . We believe that Actinobacterial strains adapt by incorporating lcp genes into their chromosome through their plasmid (G. polyisoprenivorans VH2) which leads to the presence of more than 1 unique lcp homolog as seen in Microtetraspora sp.…”

“…strain CFMR7 and Actinoplanes sp. strain OR16 15,16 . TATR gene is located next to the lcp genes for both Microtetraspora sp.…”

Rubber Degrading Strains: Microtetraspora and Dactylosporangium

“…CFMR-7 [77] and Actinoplanes sp. strain OR16 [78], whereby 2-lcp homologs are located adjacent to each other, followed by oxiAB genes, with 1-lcp homolog located far apart (Figure 6). The lcp2 and lcp3 gene for Dactylosporangium sp.…”