Comparative genomics of Prauserella sp. Am3, an actinobacterium isolated from root nodules of Alnus nepalensis in India

Abstract

A novel actinomycete strain, assigned as Am3, was isolated from the root nodules of Alnus nepalensis at Mirik hills, India. Analysis of the 16s rRNA gene sequence placed this new strain within the genus Prauserella. The genome was sequenced by Illumina sequencing and resulting 5.33-Mbp high quality draft genome sequenced with a G + C content of 70.0 % and 4828 candidate protein-encoding genes. Phylogenetically, Prauserella clusters very close to Amycolatopsis and was previously placed under the genus Amycolatopsis. Our main focus was to reveal the genomic similarities and dissimilarities of the newly sequenced Prauserella sp. Am3 with the type strain, Prauserella rugosa DSM 43194 T, and to determine its relationship with Amycolatopsis, which is happened to be the closest genus of Prauserella. Taking an in silico approach, bioinformatic analysis revealed that the core genome of Amycolatopsis and Prauserella contained 1589 genes. The two Prauserella genomes shared approximately 4224 genes, and 237 and 245 unique genes were found in the P. rugosa and Prauserella sp. Am3 genomes, respectively. Analysis of various phylogenetic trees including a 16s rRNA gene tree, MLSA protein-based tree and concatenated core-genomebased tree, placed both Prauserella genomes together with Amycolatopsis halophila YIM 93233 as its closest neighbor. Blast Matrix analysis of the predicted proteomes revealed about 86 % homology between the two Prauserella genomes. Analysis of the strand variation property revealed the absence of replication-transcriptional selection. Overall, a high degree of similarity was found between the two Prauserella genomes and a high percentage of similarity occurred among the Prauserella genomes and Amycolatopsis halophila.

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

“…Although average nucleotide identities based on MUMmer (ANIm) supported the classification of these strains within the genus, the percentage of conserved proteins indicated that A. halophila might belong to a different genus ( Adamek et al, 2018 ). A five gene MLSA (with atpI , gyrA , ftsZ , secA and dnaK ) also indicated that A. halophila is more similar to members of the genus Prauserella than to Amycolatopsis species ( Bose et al, 2016 ). Therefore, we have applied a more comprehensive phylogenetic and taxogenomic approach to the genus ( Sangal et al, 2016 ) and analyzed 57 Amycolatopsis genome sequences belonging to 34 species, including five sequenced by us in this study.…”

Insight into the quality deterioration induced by microorganisms in Litopenaeus vannamei during superchilling storage

“…Those phyla are dominant in the intestinal microorganisms of crustaceans [1]. In day 10 sample, Oceanicaulis, Aliihoeflea, Prauserella, Chelativorans, Shewanella and Pseudoalteromonas were significantly increased, these genuses may involve in carbohydrate metabolism, amino acid metabolism, protein metabolism and amino acids metabolism [16][17][18][19][20][21]. Their changes showed that the balance between microorganisms of shrimp was destroyed as the host died and the environment changed, which may adversely affect muscle quality [1,22].…”

“…The result showed that gluconic acid increased significantly during storage, and had significantly relationship with Oceanicaulis, Aliihoeflea, Prauserella, Chelativorans and Pseudoalteromonas. Aliihoeflea and Chelativorans has been report to utilize the carbohydrates as their carbon source for growth [19,21], and Oceanicaulis and Prauserella were found be involved in carbohydrate transport and metabolism [16]. In the pre-storage, these microorganisms significantly increased, and the content of gluconic acid also increased; besides, most of organic acids and derivatives (e.g.…”

“…The above induces of protein quality showed highly significant correlation with Oceanicaulis, Prauserella, Chelativorans and Pseudoalteromonas (P < 0.01), and showed significant correlation with Aliihoeflea (P < 0.05). It is reported that catalase and oxidase exist in Chelativorans and Aliihoeflea [19,21]; the major functional of proteins of Prauserella include amino acid transport and metabolism [16]; therefore, the strong relation between the post-storage biomarker and induces of protein quality showed they may involve in quality deterioration from 0 to 10 day. Pseudoalteromonas was found to be the important microorganism for the spoilage of brown shrimp by degrading amino acids and proteins [17], which was in accordance with our findings.…”

An update on research on Frankia and actinorhizal plants on the occasion of the 18th meeting of the Frankia-actinorhizal plants symbiosis

“…Besides Frankia, other bacteria have been isolated from actinorhizal nodules and sequencing them has become a convenient approach to gain knowledge on their function and physiology (Bose et al 2016;Ghodhbane-Gtari et al 2014).…”