Evidence for Two Putative Holin-Like Peptides Encoding Genes of Bacillus pumilus Strain WAPB4

Aunpad, Ratchaneewan; Panbangred, Watanalai

doi:10.1007/s00284-011-0074-3

Cited by 16 publications

(15 citation statements)

References 13 publications

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“…However, the functions of these specific ORFs have not yet been identified. The bacteriocin-related holin-like peptide BhlA from Bacillus showed antibacterial activity against several Gram-positive bacteria, including MRSA and Micrococcus luteus by destroying cell membranes [122]. BhlA consists of 70 amino acid residues with a single transmembrane domain at the N-terminus, a number of highly charged amino acid residues at the C-terminus.…”

Section: Resultsmentioning

confidence: 99%

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Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species

2016

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BackgroundGram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species.ResultsWe identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales.ConclusionsOur extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3224-y) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…BhlA consists of 70 amino acid residues with a single transmembrane domain at the N-terminus, a number of highly charged amino acid residues at the C-terminus. The presence of hydrophilic residues and the membrane topology of BhlA make it different from holins [122]. …”

Section: Resultsmentioning

confidence: 99%

Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species

2016

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“… 31 This gene also has strong BLAST matches to a “bhlA protein,” an unconfirmed holin-like protein. 32,33 While this could be the “missing” holin gene, we assigned bacteriocin function due to its much more statistically significant match (E-value < 1E-100 compared to 1E-13). Fern/Willow and Xenia contain a putative metallo-hydrolase, a type of β-lactamase (gp48/58).…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of 9 novelPaenibacillus larvaebacteriophages

et al. 2016

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American Foulbrood Disease, caused by the bacterium Paenibacillus larvae, is one of the most destructive diseases of the honeybee, Apis mellifera. Our group recently published the sequences of 9 new phages with the ability to infect and lyse P. larvae. Here, we characterize the genomes of these P. larvae phages, compare them to each other and to other sequenced P. larvae phages, and putatively identify protein function. The phage genomes are 38–45 kb in size and contain 68–86 genes, most of which appear to be unique to P. larvae phages. We classify P. larvae phages into 2 main clusters and one singleton based on nucleotide sequence identity. Three of the new phages show sequence similarity to other sequenced P. larvae phages, while the remaining 6 do not. We identified functions for roughly half of the P. larvae phage proteins, including structural, assembly, host lysis, DNA replication/metabolism, regulatory, and host-related functions. Structural and assembly proteins are highly conserved among our phages and are located at the start of the genome. DNA replication/metabolism, regulatory, and host-related proteins are located in the middle and end of the genome, and are not conserved, with many of these genes found in some of our phages but not others. All nine phages code for a conserved N-acetylmuramoyl-L-alanine amidase. Comparative analysis showed the phages use the “cohesive ends with 3′ overhang” DNA packaging strategy. This work is the first in-depth study of P. larvae phage genomics, and serves as a marker for future work in this area.

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“…The lysis module consisted of two holin genes and a putative peptidoglycan hydrolase; the first holin was predicted to be a type III with one predicted transmembrane domain, while the second was predicted to be a type I holin with three predicted transmembrane domain regions. The employment of two holin genes is not typical, having been reported previously in only a few phage genomes (27)(28)(29)(30)(31). The overall organization of the genome was found to be similar to that of many group A streptococcal prophages and differed significantly from the group C streptococcal lytic phage C1 (32).…”

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confidence: 63%

Genomic Sequencing of High-Efficiency Transducing Streptococcal Bacteriophage A25: Consequences of Escape from Lysogeny

et al. 2018

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Lytic bacteriophage A25, which infects and several related species, has been used to better understand phage-microbe interactions due to its ability to mediate high-efficiency transduction. Most of these studies, however, are decades old and were conducted prior to the advent of next-generation sequencing and bioinformatics. The aim of our study was to gain a better understanding of the mechanism of high-efficiency transduction through analysis of the A25 genome. We show here that phage A25 is related to a family of genome prophages and became a lytic phage following escape from lysogeny. A lambdoid-like residual lysogeny module consisting of an operator site with two promoters and a-like antirepressor gene was identified, but the genes for the cI-like repressor and integrase are missing. Additionally, the genetic organization of the A25 genome was found to be modular in nature and similar to that of many prophages of as well as from other streptococcal species. A study of A25 homology to all annotated prophages within revealed near identity within the remnant lysogeny module of the A25 phage genome to the corresponding regions in resident prophages of genome strains MGAS10270 (M2), MGAS315 (M3), MGAS10570 (M4), and STAB902 (M4). Host range studies of MGAS10270, MGAS315, and MGAS10750 demonstrated that these strains were resistant to A25 infection. The resistance mechanism of superinfection immunity was confirmed experimentally through complementation of the operator region and -like repressor from prophage MGAS10270.2 into susceptible strains SF370, CEM1Δ4 (SF370ΔSpyCIM1), and ATCC 12204, which rendered all three strains resistant to A25 infection. prediction of packaging through homology analysis of the terminase large subunit from bacteriophages within the known packaging mechanism of Gram-positive bacteria as well as the evidence of terminally redundant and/or circularly permuted sequences suggested that A25 grouped with phages employing the less stringent -type packaging mechanisms, which likely explains the characteristic A25 high-efficiency transduction capabilities. Only a few examples of lytic phages appearing following loss of part or all of the lysogeny module have been reported previously, and the genetic mosaicism of A25 suggests that this event may not have been a recent one. However, the discovery that this lytic bacteriophage shares some of the genetic pool of prophages emphasizes the importance of genetic and biological characterization of bacteriophages when selecting phages for therapeutics or disinfectants, as phage-phage and phage-microbe interactions can be complex, requiring more than just assessment of host range and carriage of toxoid or virulence genes. Bacteriophages (bacterial viruses) play an important role in the shaping of bacterial populations as well as the dissemination of bacterial genetic material to new strains, resulting in the spread of virulence factors and antibiotic resistance genes. This study identified the genetic origins of phage A25 and uncovered the molecular mechan...

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Evidence for Two Putative Holin-Like Peptides Encoding Genes of Bacillus pumilus Strain WAPB4

Cited by 16 publications

References 13 publications

Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species

Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species

Comparative genomics of 9 novelPaenibacillus larvaebacteriophages

Genomic Sequencing of High-Efficiency Transducing Streptococcal Bacteriophage A25: Consequences of Escape from Lysogeny

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