Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus

Creason, Allison; Davis, Edward W.; Putnam, M. L.; Vandeputte, Olivier M.; Chang, Jeff H.

doi:10.3389/fpls.2014.00406

Cited by 33 publications

(50 citation statements)

References 56 publications

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“…The strains in this cluster can be divided into two subgroups based on phylogenetic and taxogenomic data (Figs 1, 2, 3 and Supplementary Tables 1–3), a result in line with an earlier report29. The strains within this taxon, which include plant pathogens and some environmental isolates, have a genome size ranging between 5.17–6.24 Mb and a fairly narrow GC content (64.1–64.7 mol%; Fig.…”

Section: Resultssupporting

confidence: 86%

“…; this taxon encompasses two species (Supplementary Tables 1–3). The remaining sixteen R. fascians strains, including the type strain (LMG3623 T ), formed the second subgroup together with five unclassified strains (Supplementary Tables 1–3) that matches clade I in the above study29. These strains can be assigned to six predicted species based on dDDH, FBS score of >70 and ANIb-G values of >94%; five of these taxa correspond to taxa delineated by Creason et al 29…”

Section: Resultsmentioning

confidence: 63%

“…Furthermore, a number of gene clusters have been found to vary between major rhodococcal clades, emphasizing extensive variation at the genomic level27. Similarly, phylogenetic groups of rhodococcal species have been detected based on other genes, such as alkB 28 and from the analysis of a limited number of rhodococcal genomes29. Thus, there is a clear need to further unravel taxonomic relationships within the genus Rhodococcus , particularly given the importance of R. equi , a facultative intracellular pathogen of animals, especially foals30, Rhodococcus fascians , a phytopathogen of numerous dicotyledonous plants31 and R. erythropolis which is capable of numerous industrially significant bioconversions and biodegradations32.…”

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confidence: 99%

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Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Sangal

Goodfellow

Jones

et al. 2016

Sci Rep

108

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Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 63%

mentioning

confidence: 99%

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Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Sangal

Goodfellow

Jones

et al. 2016

Sci Rep

108

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“…Thus, RS30410, located immediately upstream of fcrA and encoding a putative membrane protein, was not cotranscribed with fcrA. Interestingly, RS30410 is conserved upstream of fcrA across the diverse phylogenetic clades of rhodococci (30), while the surrounding genomic context is not. In contrast, a homolog of RS30410 is not present upstream of fcr1 in mycobacterial species, suggesting that RS30410 is not essential for the activity of fcrA.…”

Section: Production Of Wes In Rha1mentioning

confidence: 96%

A Fatty Acyl Coenzyme A Reductase Promotes Wax Ester Accumulation in Rhodococcus jostii RHA1

Round

Roccor

et al. 2017

Appl Environ Microbiol

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Many rhodococci are oleaginous and, as such, have considerable potential for the sustainable production of lipid-based commodity chemicals. Herein, we demonstrated that Rhodococcus jostii RHA1, a soil bacterium that catabolizes a wide range of organic compounds, produced wax esters (WEs) up to 0.0002% of its cellular dry weight during exponential growth on glucose. These WEs were fully saturated and contained primarily 31 to 34 carbon atoms. Moreover, they were present at higher levels during exponential growth than under lipid-accumulating conditions. Bioinformatics analyses revealed that RHA1 contains a gene encoding a putative fatty acyl coenzyme A (acyl-CoA) reductase (FcrA). The purified enzyme catalyzed the NADPH-dependent transformation of stearoyl-CoA to stearyl alcohol with a specific activity of 45 Ϯ 3 nmol/mg · min and dodecanal to dodecanol with a specific activity of 5,300 Ϯ 300 nmol/mg · min. Deletion of fcrA did not affect WE accumulation when grown in either carbon-or nitrogen-limited medium. However, the ΔfcrA mutant accumulated less than 20% of the amount of WEs as the wild-type strain under conditions of nitric oxide stress. A strain of RHA1 overproducing FcrA accumulated WEs to ϳ13% cellular dry weight under lipid-accumulating conditions, and their acyl moieties had longer average chain lengths than those in wild-type cells (C 17 versus C 16 ). The results provide insight into the biosynthesis of WEs in rhodococci and facilitate the development of this genus for the production of highvalue neutral lipids. IMPORTANCE Among the best-studied oleaginous bacteria, rhodococci have considerable potential for the sustainable production of lipid-based commodity chemicals, such as wax esters. However, many aspects of lipid synthesis in these bacteria are poorly understood. The current study identifies a key enzyme in wax ester synthesis in rhodococci and exploits it to significantly improve the yield of wax esters in bacteria. In so doing, this work contributes to the development of novel bioprocesses for an important class of oleochemicals that may ultimately allow us to phase out their unsustainable production from sources such as petroleum and palm oil.KEYWORDS fatty acyl-CoA reductase, lipid accumulation, Rhodococcus, wax esters, metabolic engineering M any bacterial species, particularly the mycolic acid-producing Actinobacteria, synthesize neutral lipids for energy storage. For example, the soil bacterium Rhodococcus jostii RHA1 (referred to as RHA1 here) accumulates neutral lipids up to 70% of cellular dry weight (CDW) in response to environmental stresses, such as nitrogen limitation (1-3). These neutral lipids are primarily triacylglycerides (TAGs) and are stored in lipid bodies within the cytoplasm (4). Proteins associated with these carbon storage organelles (5) facilitate the dynamic shuffling of lipids between utilization and storage, allowing the bacterium to sequester intracellular energy reserves as needed. Due in

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“…Whole genome sequences have been successfully applied to reconstruct the phylogenetic relationships of several bacterial genera, e.g. Pseudomonas (Baltrus et al 2011) and Rhodococcus (Creason et al 2014). Due to the complex taxonomic status of Erwinia and Pantoea, whole genome sequence data has the potential to provide a detailed, well-supported, standard basis for these two genera.…”

Section: Introductionmentioning

confidence: 99%

Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data

Zhang

Qiu

2015

Antonie van Leeuwenhoek

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The genera Erwinia and Pantoea contain species that are devastating plant pathogens, non-pathogen epiphytes, and opportunistic human pathogens. However, some controversies persist in the taxonomic classification of these two closely related genera. The phylogenomic analysis of these two genera was investigated via a comprehensive analysis of 25 Erwinia genomes and 23 Pantoea genomes. Single-copy orthologs could be extracted from the Erwinia/Pantoea core-genome to reconstruct the Erwinia/Pantoea phylogeny. This tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome; strains from the same species showed ANI values ≥96% and isDDH values >70%. These data confirm that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of Erwinia/Pantoea, e.g. Pantoea agglomerans 299R was not clustered into a single group with other P. agglomerans strains, and the ANI values and isDDH values between them were <91% and around 43.8%, respectively. These data indicate P. agglomerans 299R should not be classified into the P. agglomerans species. In addition, another strain (Pantoea sp. At_9b) was identified that may represent a novel Pantoea species. We also evaluated the performance of six commonly used housekeeping genes (atpD, carA, gyrB, infB, recA, and rpoB) in phylogenetic inference. A single gene was not enough to obtain a reliable species tree, and it was necessary to use the multilocus sequence analysis of the six marker genes to recover the Erwinia/Pantoea phylogeny.

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Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus

Cited by 33 publications

References 56 publications

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

A Fatty Acyl Coenzyme A Reductase Promotes Wax Ester Accumulation in Rhodococcus jostii RHA1

Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data

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