Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer

Daugavet, M. A.; Shabelnikov, Sergey; Podgornaya, O. I.

doi:10.1186/s12859-020-03599-y

Cited by 6 publications

(5 citation statements)

References 82 publications

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“…However, gene transfer from eukaryotic organisms is a unique way of acquiring genetic material in prokaryotes, which could also indicate plausible genetic evolution in phages. This method of gene transfer has been reported earlier in phages infecting Listeria and Wolbachia [28,38]. We found a similar phenomenon in B1 subcluster phages wherein gene products predominantly found in eukaryotes were predicted to be present.…”

Section: Discussionsupporting

confidence: 86%

Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages

Das,

Arora,

Nadar

et al. 2024

J Basic Microbiol

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Bacteriophages infecting Mycobacterium smegmatis mc2155 are numerous and, hence, are classified into clusters based on nucleotide sequence similarity. Analyzing phages belonging to clusters/subclusters can help gain deeper insights into their biological features and potential therapeutic applications. In this study, for genomic characterization of B1 subcluster mycobacteriophages, a framework of online tools was developed, which enabled functional annotation of about 55% of the previously deemed hypothetical proteins in B1 phages. We also studied the phenotype, lysogeny status, and antimycobacterial activity of 10 B1 phages against biofilm and an antibiotic‐resistant M. smegmatis strain (4XR1). All 10 phages belonged to the Siphoviridae family, appeared temperate based on their spontaneous release from the putative lysogens and showed antibiofilm activity. The highest inhibitory and disruptive effects on biofilm were 64% and 46%, respectively. This systematic characterization using a combination of genomic and experimental tools is a promising approach to furthering our understanding of viral dark matter.

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Section: Discussionsupporting

confidence: 86%

Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages

Das,

Arora,

Nadar

et al. 2024

J Basic Microbiol

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“…However, gene transfer from eukaryotic organisms is a unique way of acquisition of genetic material in prokaryotes which could also indicate plausible genetic evolution in phages. This method of gene transfer has been reported earlier in phages infecting Listeria and Wolbachia (52,53). Through HMMER analysis, we found two such gene products in B1 sub-cluster phages that potentially indicate horizontal gene acquisition from eukaryotes.…”

Section: Evidence Of Horizontal Gene Transfersupporting

confidence: 66%

Insights into the genomic features, lifestyle and therapeutic potential of B1 sub-cluster mycobacteriophages

Das,

Arora,

Nadar

et al. 2023

Preprint

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BackgroundA large number (about 1200) of mycobacteriophages (phages) have been isolated onMycobacterium smegmatismc2155. Their genome analysis shows high sequence diversity; therefore, based on nucleotide sequence similarity and genomic architecture, the related phages have been grouped in clusters and sub-clusters. However, a deeper study of mycobacteriophages has been conducted only for a few clusters. This study explores the traits of phages belonging to the B1 sub-cluster. We have attempted to functionally annotate and experimentally characterize B1 phages to get an insight into their biology and explore their therapeutic potential.MethodsAnalysis of B1 sub-cluster phage genomes to understand their key characteristics & lifestyle and to determine the putative function of hypothetical proteins (HPs), we developed a framework with a specific set of computational tools available online. For the experimental characterization, mycobacteriophages were isolated from environmental samples and were examined for their morphology, lysogeny status, effect on biofilm and activity against drug-resistantM. smegmatis. The B1 sub-cluster phages were identified by PCR using the specific primers.ResultsWe have predicted the function of about 55% of the 77 representative proteins in B1 phages, which were previously deemed hypothetical. We studied ten B1 phages (Phages 1-10)which included their morphological characteristics, lysogeny status and antibiofilm activity. TEM analysis, showing an average head & tail size of 65 nm and 202.12 nm, respectively. The turbid morphology of several plaques suggested these phages to be temperate. To verify, we tested their potential to lysogenizeM. smegmatisand later found the spontaneous release from the putative lysogens. Interestingly, a putative RepA-like protein was identified in B1 phage genomes, indicating a possibility of extrachromosomal replication of prophages. Further, the impact ofPhages 1-10onM. smegmatisbiofilm was found to be potent; the highest inhibitory and disruptive effect of phages (at a fixed titre of 108pfu/ml) was 64% and 46%, respectively. Also, all ten phages could kill 4XR1 (the isoniazid-resistantM. smegmatisstrain).ConclusionWe believe this combination of experimental analysis and exploration of genomic features of mycobacteriophages belonging to a sub-cluster can provide deeper insights into mycobacteriophage biology and also help in understanding their therapeutic potential.

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“…6E ) with 24, 22, and 17 different gene variants, respectively. Except for DnaG, all other proteins are associated with HGT including cysteine-rich proteins ( 41 ).…”

Section: Resultsmentioning

confidence: 99%

Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis

Schwarzerova,

Zeman,

Babak

et al. 2024

Microbiol Spectr

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The study presents an innovative pipeline for detecting horizontal gene transfer (HGT) among a collection of sequenced genomes from gut microbiota. Herein, chicken and porcine gut microbiota were analyzed. Based on statistical analysis, we propose that nearly identical genes co-shared between distinct genera can be evidence for a previous event of mobilization of that gene from genome to genome via HGT. Data mining, computational analysis, and network analysis were used to investigate genomes of 452 isolates of chicken or porcine origin to detect genes involved in HGT. The proposed pipeline is user-friendly and includes network visualization. The study highlights that different species and strains of the same genera typically carry different cargo of mobilized genes. The pipeline is capable of identifying not yet characterized genes, as well as genes that are usually co-transferred with genes involved in resistance, virulence, and/or mobilization. Among the analyzed genome collection, the main reservoirs of the HGT genes were found in Phocaeicola spp. ( Bacteroidaceae ) and UBA9475 spp. (early Pseudoflavonifractor , Oscillospiraceae ). Altogether, over 6,000 genes suspected of HGT were identified. Genes associated with intracellular trafficking and secretion and DNA repair were enriched, while genes of unknown and general functions were dominant but not enriched. Only 15 genes were co-shared between Gram-positive and Gram-negative bacteria, mostly genes directly associated with mobilome or antibiotic resistance. However, most HGTs were identified among different genera of the same phylum. Therefore, we suggest that a significant selection pressure exists on gene variants at the phylum level. IMPORTANCE Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.

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Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer

Cited by 6 publications

References 82 publications

Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages

Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages

Insights into the genomic features, lifestyle and therapeutic potential of B1 sub-cluster mycobacteriophages

Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis

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