1
|
Wang Q, Zhang L, Zhang Y, Chen H, Song J, Lyu M, Chen R, Zhang L. Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7. Front Microbiol 2022; 13:1008648. [PMID: 36419435 PMCID: PMC9677121 DOI: 10.3389/fmicb.2022.1008648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.
Collapse
Affiliation(s)
- Qian Wang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lei Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yiju Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianghua Song
- College of Horticulture, Anhui Agricultural University, Hefei, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lixin Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lixin Zhang,
| |
Collapse
|
2
|
Zhang B, Sun H, Zhao F, Wang Q, Pan Q, Tong Y, Ren H. Characterization and Genomic Analysis of a Novel Jumbo Bacteriophage vB_StaM_SA1 Infecting Staphylococcus aureus With Two Lysins. Front Microbiol 2022; 13:856473. [PMID: 35572667 PMCID: PMC9096886 DOI: 10.3389/fmicb.2022.856473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The development of new antimicrobial agents is critically needed due to the alarming increase in antibiotic resistance in bacterial pathogens. Phages have been widely considered as effective alternatives to antibiotics. A novel phage vB_StaM_SA1 (hereinafter as SA1) that can infect multiple Staphylococcus strains was isolated from untreated sewage of a pig farm, which belonged to Myoviridae family. At MOI of 0.1, the latent period of phage SA1 was 55 min, and the final titer reached about 109 PFU/mL. The genome of phage SA1 was 260,727 bp, indicating that it can be classified as a jumbo phage. The genome of SA1 had 258 ORFs and a serine tRNA, while only 53 ORFs were annotated with functions. Phage SA1 contained a group of core genes that was characterized by multiple RNA polymerase subunits and also found in phiKZ-related jumbo phages. The phylogenetic tree showed that phage SA1 was a phiKZ-related phage and was closer to jumbo phages compared with Staphylococcus phages with small genome. Three proteins (lys4, lys210, and lys211) were predicted to be associated with lysins, and two proteins with lytic function were verified by recombinant expression and bacterial survival test. Both lys210 and lys211 possessed efficient bactericidal ability, and lys210 could lyse all test strains. The results show that phage SA1 and lys210/lys211 could be potentially used as antibiotic agents to treat Staphylococcus infection.
Collapse
Affiliation(s)
- Bingyan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
3
|
Ahmad AA, Addy HS, Huang Q. Biological and Molecular Characterization of a Jumbo Bacteriophage Infecting Plant Pathogenic Ralstonia solanacearum Species Complex Strains. Front Microbiol 2021; 12:741600. [PMID: 34646257 PMCID: PMC8504454 DOI: 10.3389/fmicb.2021.741600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
A jumbo phage infecting Ralstonia solanacearum species complex strains, designated RsoM2USA, was isolated from soil of a tomato field in Florida, United States, and belongs to the family Myoviridae. The phage has a long latent period of 270 min and completed its infection cycle in 360 min with a burst size of approximately 32 particles per cell. With a genome size of 343,806 bp, phage RsoM2USA is the largest Ralstonia-infecting phage sequenced and reported to date. Out of the 486 ORFs annotated for RsoM2USA, only 80 could be assigned putative functions in replication, transcription, translation including 44 tRNAs, and structure with the main structural proteins experimentally confirmed. Phylogenetic analyses placed RsoM2USA in the same clade as Xanthomonas phage XacN1, prompting a proposal of a new genus for the two jumbo phages. Jumbo phage RsoM2USA is a lytic phage and has a wide host range, infecting each of the three newly established Ralstonia species: R. solanacearum, R. pseudosolanacearum, and R. syzygii, and significantly reduced the virulence of its susceptible R. solanacearum strain RUN302 in tomato plants, suggesting that this jumbo phage has the potential to be developed into an effective control against diseases caused by R. solanacearum species complex strains.
Collapse
Affiliation(s)
- Abdelmonim Ali Ahmad
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
- Department of Plant Pathology, Faculty of Agriculture, Minia University, El-Minia, Egypt
| | - Hardian Susilo Addy
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
- Department of Plant Protection, Faculty of Agriculture, University of Jember, Jember, Indonesia
| | - Qi Huang
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| |
Collapse
|
4
|
Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus. J Virol 2021; 95:e0239120. [PMID: 34287047 DOI: 10.1128/jvi.02391-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here we present three novel S. aureus "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content is similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and non-virion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. Importance of work: This study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss is an active process in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making them a potential vector for horizontal gene transfer in the environment.
Collapse
|
5
|
Sasaki R, Miyashita S, Ando S, Ito K, Fukuhara T, Takahashi H. Isolation and Characterization of a Novel Jumbo Phage from Leaf Litter Compost and Its Suppressive Effect on Rice Seedling Rot Diseases. Viruses 2021; 13:v13040591. [PMID: 33807245 PMCID: PMC8066314 DOI: 10.3390/v13040591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 11/16/2022] Open
Abstract
Jumbo phages have DNA genomes larger than 200 kbp in large virions composed of an icosahedral head, tail, and other adsorption structures, and they are known to be abundant biological substances in nature. In this study, phages in leaf litter compost were screened for their potential to suppress rice seedling rot disease caused by the bacterium Burkholderia glumae, and a novel phage was identified in a filtrate-enriched suspension of leaf litter compost. The phage particles consisted of a rigid tailed icosahedral head and contained a DNA genome of 227,105 bp. The phage could lyse five strains of B. glumae and six strains of Burkholderia plantarii. The phage was named jumbo Burkholderia phage FLC6. Proteomic tree analysis revealed that phage FLC6 belongs to the same clade as two jumbo Ralstonia phages, namely RSF1 and RSL2, which are members of the genus Chiangmaivirus (family: Myoviridae; order: Caudovirales). Interestingly, FLC6 could also lyse two strains of Ralstonia pseudosolanacearum, the causal agent of bacterial wilt, suggesting that FLC6 has a broad host range that may make it especially advantageous as a bio-control agent for several bacterial diseases in economically important crops. The novel jumbo phage FLC6 may enable leaf litter compost to suppress several bacterial diseases and may itself be useful for controlling plant diseases in crop cultivation.
Collapse
Affiliation(s)
- Ryota Sasaki
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Sugihiro Ando
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Kumiko Ito
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan;
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
- Correspondence: ; Tel.: +81-812-2757-4300
| |
Collapse
|
6
|
Fu Y, Liang L, Deng S, Wu Y, Yuan Y, Gao M. Novel spore lytic enzyme from a Bacillus phage leading to spore killing. Enzyme Microb Technol 2020; 142:109698. [PMID: 33220860 DOI: 10.1016/j.enzmictec.2020.109698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/03/2023]
Abstract
Bacterial spores maintain metabolic dormancy and have high resistance to external pressure. Germination requires degradation of the spore cortex and the participation of germination-specific cortex-lytic enzymes (GSLEs). Previously reported GSLEs have been identified in bacteria and facilitate germination. In this study, we have characterized a novel spore lytic enzyme, Ply67, from Bacillus pumilus phage vB_BpuM_BpSp. Ply67 had a similar cortex-lytic activity to GSLEs but disrupted the inner membranes (IMs) of spores, leading to spore killing rather than germination. The amino acid sequence of the complete protein, Ply67FL, exhibited 40% homology to the GSLE SleB. Domain prediction showed that Ply67FL was composed of three domains: a signal peptide, N-terminal domain protein and C-terminal domain protein. Ply67FL rapidly caused E. coli cells lysis when it was expressed in E. coli. The protein containing the C-terminal domain protein, Ply67C, could kill B. pumilus spores. The protein containing the N-terminal domain protein, Ply67N, could combine with the decoated B. pumilus spores, indicating that N-terminal was the binding domain and C-terminal was the hydrolase domain. The protein lacking the signal peptide but containing the N-terminal and C-terminal domain proteins, Ply67, had activity against spores of various Bacillus species. The surface of spores treated with Ply67 shrank and the permeability barrier was disrupted, and the inner contents leaked out. Immunoelectron microscopic observation showed that Ply67 was mainly acted on the spore cortex. Overall, Ply67 is a novel spore lytic enzyme that differs from other GSLEs not only in amino acid sequence but also in activity against spores, and Ply67 might have the potential to kill spores of pathogenic Bacillus species, e.g., B. cereus and B. anthracis.
Collapse
Affiliation(s)
- Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Leiqin Liang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Sangsang Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Yihui Yuan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China.
| |
Collapse
|
7
|
Wang J, Zhao F, Sun H, Wang Q, Zhang C, Liu W, Zou L, Pan Q, Ren H. Isolation and characterization of the Staphylococcus aureus bacteriophage vB_SauS_SA2. AIMS Microbiol 2019; 5:285-307. [PMID: 31663062 PMCID: PMC6787349 DOI: 10.3934/microbiol.2019.3.285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/25/2019] [Indexed: 12/28/2022] Open
Abstract
A novel bacteriophage vB_SauS_SA2 (hereafter designated SA2) that infects Staphylococcus aureus was isolated. At a multiplicity of infection (MOI) of 0.1, phage SA2 had a latent period of about 10 min with a burst size of 293 PFUs/infected cell (PFU, plaque forming unit). Phage SA2 had a double-stranded DNA genome with a length of 89,055 bp and a G + C content of 31.9%. The genome contained 130 open reading frames (ORFs), 28 of which had assigned functions, and 18 were unique. One tRNA gene (tRNAAsn ) was discovered, and no virulence genes were identified. Its genome showed very low similarity with phage genomes deposited in public databases (75% nucleotide identity and 7% query coverage). The unique characteristics of phage SA2 led to the proposal of a new Siphoviridae genus named 'SA2likevirus'.
Collapse
Affiliation(s)
- Jia Wang
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Feiyang Zhao
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Shandong 266109, China
| | - Qian Wang
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Can Zhang
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Wenhua Liu
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Ling Zou
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Shandong 266109, China
| | - Huiying Ren
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| |
Collapse
|
8
|
Abstract
Bacillus spp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect a Bacillus pumilus strain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.
Collapse
|
9
|
Abstract
Tailed bacteriophages with genomes larger than 200 kbp are classified as Jumbo phages, and are rarely isolated by conventional methods. These phages are designated “jumbo” owing to their most notable features of a large phage virion and large genome size. However, in addition to these, jumbo phages also exhibit several novel characteristics that have not been observed for phages with smaller genomes, which differentiate jumbo phages in terms of genome organization, virion structure, progeny propagation, and evolution. In this review, we summarize available reports on jumbo phages and discuss the differences between jumbo phages and small-genome phages. We also discuss data suggesting that jumbo phages might have evolved from phages with smaller genomes by acquiring additional functional genes, and that these additional genes reduce the dependence of the jumbo phages on the host bacteria.
Collapse
Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
| |
Collapse
|