In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria

Alam, Khorshed; Islam, Mahmudul; Gong, Kai; Abbasi, Muhammad Nazeer; Li, Ruijuan; Zhang, Youming; Li, Aiying

doi:10.1016/j.compbiomed.2021.105046

Cited by 9 publications

(7 citation statements)

References 60 publications

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“…T1PKS, Terpene, NAPAA and other NRPs were also most common in Gordonia hongkongensis EUFUS-Z298 [ 80 ], Burkholderia spp. [ 18 ], in activated sludge microbiome [ 81 ], and in Ktedonobacteria [ 82 ]. NAPAA, particularly e-poly-lysine, demonstrate notable antimicrobial efficacy, showcasing widespread utility in the food and pharmaceutical sectors.…”

Section: Discussionmentioning

confidence: 99%

“…Genes for the production, control, and resistance of secondary metabolites are often grouped to create biosynthetic gene clusters (BGCs) in microbial genomes [ 17 ]. Utilization of bioinformatics tools for the analysis of microbial genome sequences reported that a single genome may include 20–80 distinct BGCs [ 18 ]. On the other hand, a microorganism may possess certain BGCs but it may not express them in laboratory conditions [ 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Rahman,

Shimul,

Parvez

2024

PLoS ONE

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Corynebacterium glutamicum is a non-pathogenic species of the Corynebacteriaceae family. It has been broadly used in industrial biotechnology for the production of valuable products. Though it is widely accepted at the industrial level, knowledge about the genomic diversity of the strains is limited. Here, we investigated the comparative genomic features of the strains and pan-genomic characteristics. We also observed phylogenetic relationships among the strains based on average nucleotide identity (ANI). We found diversity between strains at the genomic and pan-genomic levels. Less than one-third of the C. glutamicum pan-genome consists of core genes and soft-core genes. Whereas, a large number of strain-specific genes covered about half of the total pan-genome. Besides, C. glutamicum pan-genome is open and expanding, which indicates the possible addition of new gene families to the pan-genome. We also investigated the distribution of biosynthetic gene clusters (BGCs) among the strains. We discovered slight variations of BGCs at the strain level. Several BGCs with the potential to express novel bioactive secondary metabolites have been identified. Therefore, by utilizing the characteristic advantages of C. glutamicum, different strains can be potential applicants for natural drug discovery.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Rahman,

Shimul,

Parvez

2024

PLoS ONE

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“…In terms of phylogeny, with the exception of three strains, all the selected potential strains, both at the intra-species and inter-species classification, were found to encode different numbers and types of bacteriocins GCs. Likewise, previous genome mining studies revealed a diverse distribution of secondary metabolites gene clusters, including bacteriocins, within intra-species strains of Burkholderia [ 36 ] and of Lactiplantibacillus plantarum [ 37 ], and within inter-species of Geobacillus [ 3 ]. In the same context, our study highlights the distinctive trait of every individual strain in terms of harboring bacteriocin gene clusters.…”

Section: Discussionmentioning

confidence: 99%

“…Another way of acquiring the bacteriocin-encoding genes can be via the horizontal gene transfer (HGT) [ 41 ]. The HGT and gene loss might also drive the variation in GCs between related strains [ 36 ] and the similarity of GCs between unrelated strains within the same population [ 43 ]. Furthermore, the distribution of secondary metabolite GCs, including bacteriocins, can be phylogenetically conserved, as was previously observed in Bacillus [ 32 , 44 , 45 ].…”

Section: Discussionmentioning

confidence: 99%

In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes

Teber,

Asakawa

2024

IJMS

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Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.

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“…More recently, the increasing data of Burkholderia genome sequences have shown a vast reservoir of NPs, such as non-ribosomal peptides (NRPs) and polyketides (PKs), with various pharmacological functions [12]. Many silent BGCs in Burkholderia genomes remain unexplored as potential drug development targets.…”

Section: Introductionmentioning

confidence: 99%

Isolation, complete genome sequencing and in silico genome mining of Burkholderia for secondary metabolites

Alam

Zhao

et al. 2022

BMC Microbiol

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Recent years, Burkholderia species have emerged as a new source of natural products (NPs) with increasing attractions. Genome mining suggests the Burkholderia genomes include many natural product biosynthetic gene clusters (BGCs) which are new targets for drug discovery. In order to collect more Burkholderia, here, a strain S-53 was isolated from the soil samples on a mountain area in Changde, P.R. China and verified by comparative genetic analysis to belong to Burkholderia. The complete genome of Burkholderia strain S-53 is 8.2 Mbps in size with an average G + C content of 66.35%. Its taxonomy was both characterized by 16S rRNA- and whole genome-based phylogenetic trees. Bioinformatic prediction in silico revealed it has a total of 15 NP BGCs, some of which may encode unknown products. It is expectable that availability of these BGCs will speed up the identification of new secondary metabolites from Burkholderia and help us understand how sophisticated BGC regulation works.

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In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria

Cited by 9 publications

References 60 publications

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes

Isolation, complete genome sequencing and in silico genome mining of Burkholderia for secondary metabolites

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