Adaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42

Abstract

Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.

Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers

“…This finding is in contrast to that of Kitasatospora sp. SUK42, which occupies the stems of Antidesma neurocarpum Miq, adapted to an endophytic lifestyle via genome reduction ( Zin et al., 2021 ). On one hand, the genomic reduction did not occur in all endophytic actinobacterial genera.…”

Production of antibacterial and antioxidant agents by Actinobacteria using soybean meal as a nitrogen source

“…Strain SLM12ES, on the other hand, was separated from strain Kal2-11 and located in the clade with Streptomyces graminearus NBRC 15420, Streptomyces murinus NBRC 14802, and Streptomyces griseofuscus NBRC 12870 (Figure 2). Genus Streptomyces and Kitasatospora belong to the family Streptomycetaceae and both of them are prolific producers of many bioactive compounds [35,36]. Their morphology are so similar that it is difficult to determine only based on their appearences.…”

Endophytism: A Multidimensional Approach to Plant–Prokaryotic Microbe Interaction

“…Type-III and Type-VI protein secretion systems, necessary to deliver effector proteins into the plant by pathogens, are altogether absent or present scarcely in endophytic bacteria ( Liu W. et al, 2018 ). Endophytes have been found to undergo a reduction in genome size, which is associated with differences in niche specialization ( Lòpez-Fernàndez et al, 2015 ; Zin et al, 2021 ). Some bacterial endophytes also downregulate flagella biosynthesis and upregulate functions related to flagellar motor rotation to mask up their flagellin PAMPs and move fast within plants during colonization.…”