A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239 T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus

Abstract

The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239T was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17T, Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239T, including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS), the mesophilic Amycolatopsis taiwanensis subclade (ATS) and the thermophilic A. methanolica subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.

Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach

“…A. halophila YIM93223 T is clearly an outlier with a genome size of 5.6 Mb and a 67.8 mol% GC content. Amycolatopsis salitolerans consistently clusters with A. halophila in 16S rRNA gene trees ( Guan et al, 2012 ; Tang et al, 2016 ; Sanchez-Hidalgo et al, 2018 ; Wang et al, 2018 ) and thus likely belongs to the same genus. A. salitolerans is reported to have a GC content of 66.4% ( Guan et al, 2012 ); whilst this value needs confirmation from whole genome sequence data, it is similar to that for A. halophila YIM93223 T and is outwith the range for strains of Amycolatopsis sensu stricto ( Figure 3 ).…”

“…Of the other singletons, A. sacchari DSM 44468 T is consistently associated with A. dongchuanensis in 16S rRNA gene trees [e.g. ( Wang et al, 2018 ); group I in Sanchez-Hidalgo et al (2018) and Tang et al (2016) ], whilst the A. nigrescens is probably closely related to Amycolatopsis minnesotensis ( Tang et al, 2016 ; Sanchez-Hidalgo et al, 2018 ; Wang et al, 2018 ). Similarly, A. taiwanensis is consistently associated with Amycolatopsis helveola and Amycolatopsis pigmentata ( Tang et al, 2016 ; Sanchez-Hidalgo et al, 2018 ; Wang et al, 2018 ).…”

Actinobacteria Derived from Algerian Ecosystems as a Prominent Source of Antimicrobial Molecules

“…Later, from the fermentation broth of Saccharothrix algeriensis NRRL B-24137 (fully sequenced strain) isolated from a Saharan soil sample collected in 1992 at a palm grove in Adrar (southwest of Algeria), Merrouche et al [82,83] isolated the new dithiolopyrrolone derivatives valerylpyrrothine (6), isovalerylpyrrothine (7), and formylpyrrothine (8) by addition of valeric acid to the culture medium and the known aureothricin (9), exhibiting a moderate bioactivity against some filamentous fungi and yeasts such as Mucor ramanniamus, Penicillium expansum, and Aspergillus carbonarius. Moreover, the new crotonyl-pyrrothine (10), sorbyl-pyrrothine (11), 2-hexonyl-pyrrothine (12), and 2-methyl-3-pentenyl-pyrrothine (13) were obtained by addition of sorbic acid to the culture medium. Compound 11 resulted in the most active in the series against Gram-positive bacteria.…”

“…These substances find different applications including medicine, biotechnology, and agriculture [9] in addition to the industrially relevant enzymes (e.g., cellulases, chitinases, and xylanases) responsible for the production of biofuels and biochemicals [10,11]. The actinobacteria genome is rich in biosynthetic gene clusters (a group of two or more genes that together encode a biosynthetic pathway) coding for known and/or novel metabolites with potential to discover new therapeutic agents [12,13]. In particular, actinobacteria synthesize a large number of bioactive metabolites of which antibiotics cover the major proportion.…”

The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid

“…Amycolatopsis species are grouped into three major subclades: the mesophilic or moderately thermophilic A. orientalis subclade (AOS); the thermophilic A. methanolica subclade (AMS); and the mesophilic A. taiwanensis subclade (ATS) [41,42]. The AOS subclade is formed by nine groups designated A-E and G-J, while the ATS and AMS subclades are formed by groups F1 and F2, respectively [41,43]. The phylogenetic tree associated the strains isolated here (SO1.1, SO1.2, SNC, and SST) with group A of the AOS subclade, which is known to contain mesophilic and moderately thermophilic strains.…”