1
|
Hou Y, Wu Z, Ren L, Chen Y, Zhang YA, Zhou Y. Characterization and application of a lytic jumbo phage ZPAH34 against multidrug-resistant Aeromonas hydrophila. Front Microbiol 2023; 14:1178876. [PMID: 37415809 PMCID: PMC10321303 DOI: 10.3389/fmicb.2023.1178876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/18/2023] [Indexed: 07/08/2023] Open
Abstract
Aeromonas hydrophila is an emerging foodborne pathogen causing human gastroenteritis. Aeromonas species isolated from food such as seafood presented multidrug-resistance (MDR), raising serious concerns regarding food safety and public health. The use of phages to infect bacteria is a defense against drug-resistant pathogens. In this study, phage ZPAH34 isolated from the lake sample exerted lytic activity against MDR A. hydrophila strain ZYAH75 and inhibited the biofilm on different food-contacting surfaces. ZPAH34 has a large dsDNA genome of 234 kb which belongs to a novel jumbo phage. However, its particle size is the smallest of known jumbo phages so far. Based on phylogenetic analysis, ZPAH34 was used to establish a new genus Chaoshanvirus. Biological characterization revealed that ZPAH34 exhibited wide environmental tolerance, and a high rapid adsorb and reproductive capacity. Food biocontrol experiments demonstrated that ZPAH34 reduces the viable count of A. hydrophila on fish fillets (2.31 log) and lettuce (3.28 log) with potential bactericidal effects. This study isolated and characterized jumbo phage ZPAH34 not only enriched the understanding of phage biological entity diversity and evolution because of its minimal virion size with large genome but also was the first usage of jumbo phage in food safety to eliminate A. hydrophila.
Collapse
Affiliation(s)
- Yuting Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhihao Wu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Li Ren
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yuan Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yong-An Zhang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zhou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
2
|
Boshoff A. Chaperonin: Co-chaperonin Interactions. Subcell Biochem 2023; 101:213-246. [PMID: 36520309 DOI: 10.1007/978-3-031-14740-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Co-chaperonins function together with chaperonins to mediate ATP-dependent protein folding in a variety of cellular compartments. Chaperonins are evolutionarily conserved and form two distinct classes, namely, group I and group II chaperonins. GroEL and its co-chaperonin GroES form part of group I and are the archetypal members of this family of protein folding machines. The unique mechanism used by GroEL and GroES to drive protein folding is embedded in the complex architecture of double-ringed complexes, forming two central chambers that undergo conformational rearrangements that enable protein folding to occur. GroES forms a lid over the chamber and in doing so dislodges bound substrate into the chamber, thereby allowing non-native proteins to fold in isolation. GroES also modulates allosteric transitions of GroEL. Group II chaperonins are functionally similar to group I chaperonins but differ in structure and do not require a co-chaperonin. A significant number of bacteria and eukaryotes house multiple chaperonin and co-chaperonin proteins, many of which have acquired additional intracellular and extracellular biological functions. In some instances, co-chaperonins display contrasting functions to those of chaperonins. Human HSP60 (HSPD) continues to play a key role in the pathogenesis of many human diseases, in particular autoimmune diseases and cancer. A greater understanding of the fascinating roles of both intracellular and extracellular Hsp10 on cellular processes will accelerate the development of techniques to treat diseases associated with the chaperonin family.
Collapse
Affiliation(s)
- Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Makhanda/Grahamstown, South Africa.
| |
Collapse
|
3
|
Sokolova OS, Pichkur EB, Maslova ES, Kurochkina LP, Semenyuk PI, Konarev PV, Samygina VR, Stanishneva-Konovalova TB. Local Flexibility of a New Single-Ring Chaperonin Encoded by Bacteriophage AR9 Bacillus subtilis. Biomedicines 2022; 10:biomedicines10102347. [PMID: 36289609 PMCID: PMC9598537 DOI: 10.3390/biomedicines10102347] [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: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective new group were discovered in giant bacteriophages; however, structures have been determined for only two of them. Here, using cryo-EM, we resolved a structure of a new chaperonin encoded by gene 228 of phage AR9 B. subtilis. This structure has similarities and differences with members of both groups, as well as with other known phage chaperonins, which further proves their diversity.
Collapse
Affiliation(s)
- Olga S. Sokolova
- Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen 518172, China
| | - Evgeny B. Pichkur
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | | | - Lidia P. Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel I. Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Petr V. Konarev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
| | - Valeriya R. Samygina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
| | | |
Collapse
|
4
|
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
|
5
|
Host Cyanobacteria Killing by Novel Lytic Cyanophage YongM: A Protein Profiling Analysis. Microorganisms 2022; 10:microorganisms10020257. [PMID: 35208712 PMCID: PMC8875764 DOI: 10.3390/microorganisms10020257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 02/01/2023] Open
Abstract
Cyanobacteria are autotrophic prokaryotes that can proliferate robustly in eutrophic waters through photosynthesis. This can lead to outbreaks of lake “water blooms”, which result in water quality reduction and environmental pollution that seriously affect fisheries and aquaculture. The use of cyanophages to control the growth of cyanobacteria is an important strategy to tackle annual cyanobacterial blooms. YongM is a novel lytic cyanophage with a broad host spectrum and high efficiency in killing its host, cyanobacteria FACHB-596. However, changes in cyanophage protein profile during infestation and killing of the host remains unknown. To characterize the proteins and its regulation networks involved in the killing of host cyanobacteria by YongM and evaluate whether this strain YongM could be used as a chassis for further engineering to be a powerful tool in dealing with cyanobacterial blooms, we herein applied 4D label-free high-throughput quantitative proteomics to analyze differentially expressed proteins (DEPs) involved in cyanobacteria host response infected 1 and 8 h with YongM cyanophage. Metabolic pathways, such as photosynthesis, photosynthesis-antennal protein, oxidative phosphorylation, ribosome, carbon fixation, and glycolysis/glycol-isomerization were significantly altered in the infested host, whereas DEPs were associated with the metabolic processes of photosynthesis, precursor metabolites, energy production, and organic nitrogen compounds. Among these DEPs, key proteins involved in YongM-host interaction may be photosystem I P700 chlorophyll-a apolipoprotein, carbon dioxide concentration mechanism protein, cytochrome B, and some YongM infection lysis-related enzymes. Our results provide comprehensive information of protein profiles during the invasion and killing of host cyanobacteria by its cyanophage, which may shed light on future design and manipulation of artificial cyanophages against water blooms.
Collapse
|
6
|
Trifonova TS, Moiseenko AV, Bourkaltseva MV, Shaburova OV, Shaytan AK, Krylov VN, Sokolova OS. [DNA mapping in the capsid of giant bacteriophage phiEL (Caudovirales: Myoviridae: Elvirus) by analytical electron microscopy]. Vopr Virusol 2022; 66:434-441. [PMID: 35019250 DOI: 10.36233/0507-4088-80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Giant phiKZ-like bacteriophages have a unique protein formation inside the capsid, an inner body (IB) with supercoiled DNA molecule wrapped around it. Standard cryo-electron microscopy (cryo-EM) approaches do not allow to distinguish this structure from the surrounding nucleic acid of the phage. We previously developed an analytical approach to visualize protein-DNA complexes on Escherichia coli bacterial cell slices using the chemical element phosphorus as a marker. In the study presented, we adapted this technique for much smaller objects, namely the capsids of phiKZ-like bacteriophages. MATERIAL AND METHODS Following electron microscopy techniques were used in the study: analytical (AEM) (electron energy loss spectroscopy, EELS), and cryo-EM (images of samples subjected to low and high dose of electron irradiation were compared). RESULTS We studied DNA packaging inside the capsids of giant bacteriophages phiEL from the Myoviridae family that infect Pseudomonas aeruginosa. Phosphorus distribution maps were obtained, showing an asymmetrical arrangement of DNA inside the capsid. DISCUSSION We developed and applied an IB imaging technique using a high angle dark-field detector (HAADF) and the STEM-EELS analytical approach. Phosphorus mapping by EELS and cryo-electron microscopy revealed a protein formation as IB within the phage phiEL capsid. The size of IB was estimated using theoretical calculations. CONCLUSION The developed technique can be applied to study the distribution of phosphorus in other DNA- or RNA-containing viruses at relatively low concentrations of the element sought.
Collapse
Affiliation(s)
- T S Trifonova
- FSAEI HE «People's Friendship University of Russia», Physical, Mathematical, and Natural Sciences Department; FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - A V Moiseenko
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty; FSBIS «N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences»
| | | | - O V Shaburova
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - A K Shaytan
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - V N Krylov
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - O S Sokolova
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| |
Collapse
|
7
|
Kurochkina LP, Semenyuk PI, Sokolova OS. Structural and Functional Features of Viral Chaperonins. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1-9. [PMID: 35491019 DOI: 10.1134/s0006297922010011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Chaperonins provide proper folding of proteins in vivo and in vitro and, as was thought until recently, are characteristic of prokaryotes, eukaryotes, and archaea. However, it turned out that some bacteria viruses (bacteriophages) encode their own chaperonins. This review presents results of the investigations of the first representatives of this new chaperonin group: the double-ring EL chaperonin and the single-ring OBP and AR9 chaperonins. Biochemical properties and structure of the phage chaperonins were compared within the group and with other known group I and group II chaperonins.
Collapse
Affiliation(s)
- Lidia P Kurochkina
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Pavel I Semenyuk
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga S Sokolova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
8
|
Nazir A, Ali A, Qing H, Tong Y. Emerging Aspects of Jumbo Bacteriophages. Infect Drug Resist 2021; 14:5041-5055. [PMID: 34876823 PMCID: PMC8643167 DOI: 10.2147/idr.s330560] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/30/2021] [Indexed: 01/21/2023] Open
Abstract
The bacteriophages have been explored at a huge scale as a model system for their applications in many biological-related fields. Jumbo phages with a large genome size from 200 to 500 kbp were not previously assigned a great value, and characterized by complex structures coupled with large virions with a wide variety of hosts. The origin of most of the jumbo phages was not well understood; however, many other prominent features have been discovered recently. In the current review, we strive to unearth the most advanced characteristics of jumbo phages, particularly their significance and structural organization that holds immense value to the viral life cycle. The unique characteristics of jumbo phages are the basis of variations in different types of phages concerning their organization at the genomic level, virion structure, evolution, and progeny propagation. The presence of tRNA and additional translation-related genes along with chaperonin genes mark the ability of these phages for being independent of host molecular machinery enabling them to have wide host options. A large number of jumbo phages have been isolated from various sources through advanced standard screening methods. The current review has summarized the available data on jumbo phages and discussed the genome orientation of jumbo phages, translational machinery, diversity and evolution of jumbo phages. In the studies conducted, jumbo phages possessed special additional genes that helps to reduce the dependence of jumbo phages on their hosts. Furthermore, their genomes might have evolved from smaller genome phages.
Collapse
Affiliation(s)
- Amina Nazir
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Azam Ali
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| |
Collapse
|
9
|
Panina IS, Mamchur AA, Yaroshevich IA, Zlenko DV, Pichkur EB, Kudryavtseva SS, Muronetz VI, Sokolova OS, Stanishneva-Konovalova TB. Study of GroEL Conformational Mobility by Cryo-Electron Microscopy and Molecular Dynamics. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Bacterial chaperonin GroEL is a complex ring-shaped protein oligomer that promotes the folding of other proteins by encapsulating them in the cavity. There is very little structural information about the disordered C-terminal fragment of the GroEL subunits, which is involved in the folding of the substrate protein. A 3D reconstruction of the GroEL apo-form was obtained by cryo-electron microscopy (cryo-EM) with a resolution of 3.02 Å and supplemented by molecular dynamics (MD) calculations. The results of cryo-EM and MD are in good agreement and demonstrate a diverse mobility of the protein subunit domains. The MD results predict the dynamics and the network of intramolecular contacts of the C-terminal sections of the protein. These results are of great importance for the subsequent study of the mechanism of protein folding in the GroEL cavity.
Collapse
|
10
|
Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| |
Collapse
|
11
|
Krylov V, Bourkaltseva M, Pleteneva E, Shaburova O, Krylov S, Karaulov A, Zhavoronok S, Svitich O, Zverev V. Phage phiKZ-The First of Giants. Viruses 2021; 13:149. [PMID: 33498475 PMCID: PMC7909554 DOI: 10.3390/v13020149] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
The paper covers the history of the discovery and description of phiKZ, the first known giant bacteriophage active on Pseudomonas aeruginosa. It also describes its unique features, especially the characteristic manner of DNA packing in the head around a cylinder-shaped structure ("inner body"), which probably governs an ordered and tight packaging of the phage genome. Important properties of phiKZ-like phages include a wide range of lytic activity and the blue opalescence of their negative colonies, and provide a background for the search and discovery of new P. aeruginosa giant phages. The importance of the phiKZ species and of other giant phage species in practical phage therapy is noted given their broad use in commercial phage preparations.
Collapse
Affiliation(s)
- Victor Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Maria Bourkaltseva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Elena Pleteneva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Olga Shaburova
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Sergey Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia;
| | - Sergey Zhavoronok
- Department of Infectious Diseases, Belarusian State Medical University, 220116 Minsk, Belarus;
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| |
Collapse
|
12
|
Abstract
Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.
Collapse
|
13
|
Maturation of Pseudo-Nucleus Compartment in P. aeruginosa, Infected with Giant phiKZ Phage. Viruses 2020; 12:v12101197. [PMID: 33096802 PMCID: PMC7589130 DOI: 10.3390/v12101197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022] Open
Abstract
The giant phiKZ phage infection induces the appearance of a pseudo-nucleus inside the bacterial cytoplasm. Here, we used RT-PCR, fluorescent in situ hybridization (FISH), electron tomography, and analytical electron microscopy to study the morphology of this unique nucleus-like shell and to demonstrate the distribution of phiKZ and bacterial DNA in infected Pseudomonas aeruginosa cells. The maturation of the pseudo-nucleus was traced in short intervals for 40 min after infection and revealed the continuous spatial separation of the phage and host DNA. Immediately after ejection, phage DNA was located inside the newly-identified round compartments; at a later infection stage, it was replicated inside the pseudo-nucleus; in the mature pseudo-nucleus, a saturated internal network of filaments was observed. This network consisted of DNA bundles in complex with DNA-binding proteins. On the other hand, the bacterial nucleoid underwent significant rearrangements during phage infection, yet the host DNA did not completely degrade until at least 40 min after phage application. Energy dispersive x-ray spectroscopy (EDX) analysis revealed that, during the infection, the sulfur content in the bacterial cytoplasm increased, which suggests an increase of methionine-rich DNA-binding protein synthesis, whose role is to protect the bacterial DNA from stress caused by infection.
Collapse
|
14
|
Multisubunit RNA Polymerases of Jumbo Bacteriophages. Viruses 2020; 12:v12101064. [PMID: 32977622 PMCID: PMC7598289 DOI: 10.3390/v12101064] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as “jumbo phages”. Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)—a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.
Collapse
|
15
|
Lood C, Danis‐Wlodarczyk K, Blasdel BG, Jang HB, Vandenheuvel D, Briers Y, Noben J, van Noort V, Drulis‐Kawa Z, Lavigne R. Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages. Environ Microbiol 2020; 22:2165-2181. [PMID: 32154616 PMCID: PMC7318152 DOI: 10.1111/1462-2920.14979] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 03/06/2020] [Indexed: 11/28/2022]
Abstract
Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms.
Collapse
Affiliation(s)
- Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
| | - Katarzyna Danis‐Wlodarczyk
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Bob G. Blasdel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Ho Bin Jang
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Dieter Vandenheuvel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Yves Briers
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Jean‐Paul Noben
- Biomedical Research Institute and Transnational University LimburgHasselt UniversityDiepenbeekBelgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| |
Collapse
|
16
|
Bracher A, Paul SS, Wang H, Wischnewski N, Hartl FU, Hayer-Hartl M. Structure and conformational cycle of a bacteriophage-encoded chaperonin. PLoS One 2020; 15:e0230090. [PMID: 32339190 PMCID: PMC7185714 DOI: 10.1371/journal.pone.0230090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionarily distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionarily more ancient chaperonin prior to acquisition of the encapsulation mechanism.
Collapse
Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- * E-mail: (AB); (MH-H)
| | - Simanta S. Paul
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Huping Wang
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Nadine Wischnewski
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - F. Ulrich Hartl
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- * E-mail: (AB); (MH-H)
| |
Collapse
|
17
|
Semenyuk PI, Moiseenko AV, Sokolova OS, Muronetz VI, Kurochkina LP. Structural and functional diversity of novel and known bacteriophage-encoded chaperonins. Int J Biol Macromol 2020; 157:544-552. [PMID: 32344079 DOI: 10.1016/j.ijbiomac.2020.04.189] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 11/26/2022]
Abstract
A bioinformatics analysis of the currently predicted GroEL-like proteins encoded by bacteriophage genomes was carried out in comparison with the phage double-ring EL and single-ring OBP chaperonins, previously described by us, as well as with the known chaperonins of group I and group II. A novel GroEL-like protein predicted in the genome of phage AR9 Bacillus subtilis was expressed in E. coli cells, purified and characterised by various physicochemical methods. As shown by native electrophoresis, analytical ultracentrifugation and single-particle electron microscopy analysis, the putative AR9 chaperonin is a single-ring heptamer. Like the EL and OBP chaperonins, the new AR9 chaperonin possesses chaperone activity and does not require co-chaperonin to function. It was shown to prevent aggregation and provide refolding of the denatured substrate protein, endolysin, in an ATP-dependent manner. A comparison of its structural and biochemical properties with those of the EL and OBP chaperonins suggests outstanding diversity in this group of phage chaperonins.
Collapse
Affiliation(s)
- Pavel I Semenyuk
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 40, Moscow 119234, Russia
| | - Andrey V Moiseenko
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 12, Moscow 119234, Russia
| | - Olga S Sokolova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 12, Moscow 119234, Russia
| | - Vladimir I Muronetz
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 40, Moscow 119234, Russia
| | - Lidia P Kurochkina
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 40, Moscow 119234, Russia.
| |
Collapse
|
18
|
Lewis R, Clooney AG, Stockdale SR, Buttimer C, Draper LA, Ross RP, Hill C. Isolation of a Novel Jumbo Bacteriophage Effective Against Klebsiella aerogenes. Front Med (Lausanne) 2020; 7:67. [PMID: 32185177 PMCID: PMC7058600 DOI: 10.3389/fmed.2020.00067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/13/2020] [Indexed: 12/14/2022] Open
Abstract
Increasing levels of bacterial resistance to many common and last resort antibiotics has increased interest in finding new treatments. The low rate of approval of new antibiotics has led to the search for new and alternative antimicrobial compounds. Bacteriophages (phages) are bacterial viruses found in almost every environment. Phage therapy was historically investigated to control bacterial infections and is still in use in Georgia and as a treatment of last resort. Phage therapy is increasingly recognized as an alternative antimicrobial treatment for antibiotic resistant pathogens. A novel lytic Klebsiella aerogenes phage N1M2 was isolated from maize silage. Klebsiella aerogenes, a member of the ESKAPE bacterial pathogens, is an important target for new antimicrobial therapies. Klebsiella aerogenes can form biofilms on medical devices which aids its environmental persistence and for this reason we tested the effect of phage N1M2 against biofilms. Phage N1M2 successfully removed a pre-formed Klebsiella aerogenes biofilm. Biofilm assays were also carried out with Staphylococcus aureus and Phage K. Phage K successfully removed a preformed Staphylococcus aureus biofilm. Phage N1M2 and Phage K in combination were significantly better at removing a mixed community biofilm of Klebsiella aerogenes and Staphylococcus aureus than either phage alone.
Collapse
Affiliation(s)
- Rhea Lewis
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen R Stockdale
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
19
|
Abstract
This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is organized into various topics of physiology and mechanism, for each of which a chronologic order is generally followed. The text is liberally illustrated to provide firsthand inspection of the key pieces of experimental data that propelled this field. Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.
Collapse
|
20
|
Sharma R, Pielstick BA, Bell KA, Nieman TB, Stubbs OA, Yeates EL, Baltrus DA, Grose JH. A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia. Front Microbiol 2019; 10:1533. [PMID: 31428059 PMCID: PMC6690015 DOI: 10.3389/fmicb.2019.01533] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. Here we characterize eight lytic bacteriophages of E. amylovora that we isolated from the Wasatch front (Utah, United States) that are highly similar to vB_EamM_Ea35-70 which was isolated in Ontario, Canada. With the genome size ranging from 271 to 275 kb, this is a novel jumbo family of bacteriophages. These jumbo bacteriophages were further characterized through genomic and proteomic comparison, mass spectrometry, host range and burst size. Their proteomes are highly unstudied, with over 200 putative proteins with no known homologs. The production of 27 of these putative proteins was confirmed by mass spectrometry analysis. These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea.
Collapse
Affiliation(s)
- Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brittany A. Pielstick
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Kimberly A. Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Tanner B. Nieman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Olivia A. Stubbs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Edward L. Yeates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David A. Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| |
Collapse
|
21
|
Sauguet L. The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution. J Mol Biol 2019; 431:4167-4183. [PMID: 31103775 DOI: 10.1016/j.jmb.2019.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
DNA and RNA polymerases (DNAP and RNAP) play central roles in genome replication, maintenance and repair, as well as in the expression of genes through their transcription. Multisubunit RNAPs carry out transcription and are represented, without exception, in all cellular life forms as well as in nucleo-cytoplasmic DNA viruses. Since their discovery, multisubunit RNAPs have been the focus of intense structural and functional studies revealing that they all share a well-conserved active-site region called the two-barrel catalytic core. The two-barrel core hosts the polymerase active site, which is located at the interface between two double-psi β-barrel domains that contribute distinct amino acid residues to the active site in an asymmetrical fashion. Recently, sequencing and structural studies have added a surprising variety of DNA and RNA to the two-barrel superfamily, including the archaeal replicative DNAP (PolD), which extends the family to DNA-dependent DNAPs involved in replication. While all these polymerases share a minimal core that must have been present in their common ancestor, the two-barrel polymerase superfamily now encompasses a remarkable diversity of enzymes, including DNA-dependent RNAPs, RNA-dependent RNAPs, and DNA-dependent DNAPs, which participate in critical biological processes such as DNA transcription, DNA replication, and gene silencing. The present review will discuss both common features and differences among the extended two-barrel polymerase superfamily, focusing on the newly discovered members. Comparing their structures provides insights into the molecular mechanisms evolved by the contemporary two-barrel polymerases to accomplish their different biological functions.
Collapse
Affiliation(s)
- Ludovic Sauguet
- Institut Pasteur, Unité de Dynamique Structurale des Macromolécules, 75015 Paris, France.
| |
Collapse
|
22
|
Weintraub ST, Mohd Redzuan NH, Barton MK, Md Amin NA, Desmond MI, Adams LE, Ali B, Pardo S, Molleur D, Wu W, Newcomb WW, Osier MV, Black LW, Steven AC, Thomas JA. Global Proteomic Profiling of Salmonella Infection by a Giant Phage. J Virol 2019; 93:e01833-18. [PMID: 30541839 PMCID: PMC6384053 DOI: 10.1128/jvi.01833-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/19/2018] [Indexed: 11/20/2022] Open
Abstract
The 240-kb Salmonella phage SPN3US genome encodes 264 gene products, many of which are functionally uncharacterized. We have previously used mass spectrometry to define the proteomes of wild-type and mutant forms of the SPN3US virion. In this study, we sought to determine whether this technique was suitable for the characterization of the SPN3US proteome during liquid infection. Mass spectrometry of SPN3US-infected cells identified 232 SPN3US and 1,994 Salmonella proteins. SPN3US proteins with related functions, such as proteins with roles in DNA replication, transcription, and virion formation, were coordinately expressed in a temporal manner. Mass spectral counts showed the four most abundant SPN3US proteins to be the major capsid protein, two head ejection proteins, and the functionally unassigned protein gp22. This high abundance of gp22 in infected bacteria contrasted with its absence from mature virions, suggesting that it might be the scaffold protein, an essential head morphogenesis protein yet to be identified in giant phages. We identified homologs to SPN3US gp22 in 45 related giant phages, including ϕKZ, whose counterpart is also abundant in infected bacteria but absent in the virion. We determined the ϕKZ counterpart to be cleaved in vitro by its prohead protease, an event that has been observed to promote head maturation of some other phages. Our findings are consistent with a scaffold protein assignment for SPN3US gp22, although direct evidence is required for its confirmation. These studies demonstrate the power of mass spectral analyses for facilitating the acquisition of new knowledge into the molecular events of viral infection.IMPORTANCE "Giant" phages with genomes >200 kb are being isolated in increasing numbers from a range of environments. With hosts such as Salmonella enterica, Pseudomonas aeruginosa, and Erwinia amylovora, these phages are of interest for phage therapy of multidrug-resistant pathogens. However, our understanding of how these complex phages interact with their hosts is impeded by the proportion (∼80%) of their gene products that are functionally uncharacterized. To develop the repertoire of techniques for analysis of phages, we analyzed a liquid infection of Salmonella phage SPN3US (240-kb genome) using third-generation mass spectrometry. We observed the temporal production of phage proteins whose genes collectively represent 96% of the SPN3US genome. These findings demonstrate the sensitivity of mass spectrometry for global proteomic profiling of virus-infected cells, and the identification of a candidate for a major head morphogenesis protein will facilitate further studies into giant phage head assembly.
Collapse
Affiliation(s)
- Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | | | - Melissa K Barton
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Nur Amira Md Amin
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Maxim I Desmond
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Lily E Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Bazla Ali
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Sammy Pardo
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Dana Molleur
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Weimin Wu
- Laboratory of Structural Biology Research, National Institute for Arthritis, Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - William W Newcomb
- Laboratory of Structural Biology Research, National Institute for Arthritis, Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael V Osier
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Lindsay W Black
- Department of Biochemistry and Molecular Biology, The University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute for Arthritis, Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Julie A Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| |
Collapse
|
23
|
Saad AM, Soliman AM, Kawasaki T, Fujie M, Nariya H, Shimamoto T, Yamada T. Systemic method to isolate large bacteriophages for use in biocontrol of a wide-range of pathogenic bacteria. J Biosci Bioeng 2018; 127:73-78. [PMID: 30049605 DOI: 10.1016/j.jbiosc.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/18/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
Abstract
Large phages are characterized by genomes around 200 kbp or more. They can infect wide host ranges of bacteria and maintain long-lasting infection. There is no standard method for selective isolation of large phages. In this study, we developed a systemic method to isolate large phages and succeeded in isolating 11 large phages, named Escherichia phage E1∼E11. Electron microscopy observations revealed typical Myoviridae phages with big capsids and long contractile tails. Genome sizes of the isolated phages were determined by pulsed-field gel electrophoresis and found to be in two groups, those around 200 kbp for E1, E2, E5, E6, E7, E9 and E10 phages, and others of approximately 450 kbp for E3, E4, E8 and E11 phages. The isolated large phages had wide host ranges: for example, E9 was effective against Shigella sonnei SH05001, Shigella bydii SH00007, Shigella flexneri SH00006, Salmonella enterica serovar Enteritidis SAL01078 and Escherichia coli C3000 (K-12 derivative), as well as its original host E. coli BL21. Screening of these jumbo phages was performed with non-pathogenic E. coli strains as hosts. Therefore, this method opens a way to isolate jumbo phages infecting wide ranges of pathogenic bacteria in a typical laboratory with standard laboratory strains as the hosts. The isolated large phages will be good candidates for biocontrol of various pathogens.
Collapse
Affiliation(s)
- Alaaeldin Mohamed Saad
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan; Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmed Mahrous Soliman
- Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Takeru Kawasaki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Makoto Fujie
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Hirofumi Nariya
- Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan; Hiroshima Study Center, The Open University of Japan, Hiroshima 730-0053, Japan.
| |
Collapse
|
24
|
Bhatt JM, Enriquez AS, Wang J, Rojo HM, Molugu SK, Hildenbrand ZL, Bernal RA. Single-Ring Intermediates Are Essential for Some Chaperonins. Front Mol Biosci 2018; 5:42. [PMID: 29755985 PMCID: PMC5934643 DOI: 10.3389/fmolb.2018.00042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/13/2018] [Indexed: 11/20/2022] Open
Abstract
Chaperonins are macromolecular complexes found throughout all kingdoms of life that assist unfolded proteins reach a biologically active state. Historically, chaperonins have been classified into two groups based on sequence, subunit structure, and the requirement for a co-chaperonin. Here, we present a brief review of chaperonins that can form double- and single-ring conformational intermediates in their protein-folding catalytic pathway. To date, the bacteriophage encoded chaperonins ϕ-EL and OBP, human mitochondrial chaperonin and most recently, the bacterial groEL/ES systems, have been reported to form single-ring intermediates as part of their normal protein-folding activity. These double-ring chaperonins separate into single-ring intermediates that have the ability to independently fold a protein. We discuss the structural and functional features along with the biological relevance of single-ring intermediates in cellular protein folding. Of special interest are the ϕ-EL and OBP chaperonins which demonstrate features of both group I and II chaperonins in addition to their ability to function via single-ring intermediates.
Collapse
Affiliation(s)
- Jay M Bhatt
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Adrian S Enriquez
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Jinliang Wang
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Humberto M Rojo
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Sudheer K Molugu
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | | | - Ricardo A Bernal
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| |
Collapse
|
25
|
Abstract
Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages.
Collapse
|
26
|
Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology. ISME JOURNAL 2017; 11:2479-2491. [PMID: 28731469 PMCID: PMC5649160 DOI: 10.1038/ismej.2017.102] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/26/2017] [Accepted: 05/06/2017] [Indexed: 12/18/2022]
Abstract
Chaperonins are protein-folding machinery found in all cellular life. Chaperonin genes have been documented within a few viruses, yet, surprisingly, analysis of metagenome sequence data indicated that chaperonin-carrying viruses are common and geographically widespread in marine ecosystems. Also unexpected was the discovery of viral chaperonin sequences related to thermosome proteins of archaea, indicating the presence of virioplankton populations infecting marine archaeal hosts. Virioplankton large subunit chaperonin sequences (GroELs) were divergent from bacterial sequences, indicating that viruses have carried this gene over long evolutionary time. Analysis of viral metagenome contigs indicated that: the order of large and small subunit genes was linked to the phylogeny of GroEL; both lytic and temperate phages may carry group I chaperonin genes; and viruses carrying a GroEL gene likely have large double-stranded DNA (dsDNA) genomes (>70 kb). Given these connections, it is likely that chaperonins are critical to the biology and ecology of virioplankton populations that carry these genes. Moreover, these discoveries raise the intriguing possibility that viral chaperonins may more broadly alter the structure and function of viral and cellular proteins in infected host cells.
Collapse
|
27
|
Matsui T, Yoshikawa G, Mihara T, Chatchawankanphanich O, Kawasaki T, Nakano M, Fujie M, Ogata H, Yamada T. Replications of Two Closely Related Groups of Jumbo Phages Show Different Level of Dependence on Host-encoded RNA Polymerase. Front Microbiol 2017; 8:1010. [PMID: 28659872 PMCID: PMC5468394 DOI: 10.3389/fmicb.2017.01010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/22/2017] [Indexed: 11/13/2022] Open
Abstract
Ralstonia solanacearum phages ΦRP12 and ΦRP31 are jumbo phages isolated in Thailand. Here we show that they exhibit similar virion morphology, genome organization and host range. Genome comparisons as well as phylogenetic and proteomic tree analyses support that they belong to the group of ΦKZ-related phages, with their closest relatives being R. solanacearum phages ΦRSL2 and ΦRSF1. Compared with ΦRSL2 and ΦRSF1, ΦRP12 and ΦRP31 possess larger genomes (ca. 280 kbp, 25% larger). The replication of ΦRP12 and ΦRP31 was not affected by rifampicin treatment (20 μg/ml), suggesting that phage-encoded RNAPs function to start and complete the infection cycle of these phages without the need of host-encoded RNAPs. In contrast, ΦRSL2 and ΦRSF1, encoding the same set of RNAPs, did not produce progeny phages in the presence of rifampicin (5 μg/ml). This observation opens the possibility that some ΦRP12/ΦRP31 factors that are absent in ΦRSL2 and ΦRSF1 are involved in their host-independent transcription.
Collapse
Affiliation(s)
- Takeru Matsui
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Genki Yoshikawa
- Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyoto, Japan
| | - Tomoko Mihara
- Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyoto, Japan
| | - Orawan Chatchawankanphanich
- Plant Research Laboratory, National Center for Genetic Engineering and Biotechnology, NSTDAPathum Thani, Thailand.,Center for Agricultural Biotechnology, Kasetsart UniversityNakhon Pathom, Thailand
| | - Takeru Kawasaki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Miyako Nakano
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Makoto Fujie
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyoto, Japan
| | - Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| |
Collapse
|
28
|
Philosof A, Yutin N, Flores-Uribe J, Sharon I, Koonin EV, Béjà O. Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota. Curr Biol 2017; 27:1362-1368. [PMID: 28457865 PMCID: PMC5434244 DOI: 10.1016/j.cub.2017.03.052] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 03/09/2017] [Accepted: 03/21/2017] [Indexed: 12/16/2022]
Abstract
Marine group II Euryarchaeota (MG-II) are among the most abundant microbes in oceanic surface waters [1, 2, 3, 4]. So far, however, representatives of MG-II have not been cultivated, and no viruses infecting these organisms have been described. Here, we present complete genomes for three distinct groups of viruses assembled from metagenomic sequence datasets highly enriched for MG-II. These novel viruses, which we denote magroviruses, possess double-stranded DNA genomes of 65 to 100 kilobases in size that encode a structural module characteristic of head-tailed viruses and, unusually for archaeal and bacterial viruses, a nearly complete replication apparatus of apparent archaeal origin. The newly identified magroviruses are widespread and abundant and therefore are likely to be major ecological agents. A novel viral group, magroviruses, likely infects marine group II archaea Magroviruses are highly abundant in oceanic surface waters worldwide Magroviruses have linear, double-stranded DNA genomes of about 100 kilobases Magroviruses encode a near complete replication apparatus of apparent archaeal origin
Collapse
Affiliation(s)
- Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona 11016, Israel; Tel Hai College, Upper Galilee 12210, Israel
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| |
Collapse
|
29
|
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
|
30
|
Buttimer C, Hendrix H, Oliveira H, Casey A, Neve H, McAuliffe O, Ross RP, Hill C, Noben JP, O'Mahony J, Lavigne R, Coffey A. Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB. Front Microbiol 2017; 8:44. [PMID: 28174560 PMCID: PMC5259590 DOI: 10.3389/fmicb.2017.00044] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/06/2017] [Indexed: 11/30/2022] Open
Abstract
Enterobacteria phage vB_PcaM_CBB is a "jumbo" phage belonging to the family Myoviridae. It possesses highly atypical whisker-like structures along the length of its contractile tail. It has a broad host range with the capability of infecting species of the genera Erwinia, Pectobacterium, and Cronobacter. With a genome of 355,922 bp, excluding a predicted terminal repeat of 22,456 bp, phage CBB is the third largest phage sequenced to date. Its genome was predicted to encode 554 ORFs with 33 tRNAs. Based on prediction and proteome analysis of the virions, 29% of its predicted ORFs could be functionally assigned. Protein comparison shows that CBB shares between 33-38% of its proteins with Cronobacter phage GAP32, coliphages PBECO4 and 121Q as well as Klebsiella phage vB_KleM_Rak2. This work presents a detailed and comparative analysis of vB_PcaM_CBB of a highly atypical jumbo myoviridae phage, contributing to a better understanding of phage diversity and biology.
Collapse
Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU LeuvenLeuven, Belgium
| | - Hugo Oliveira
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of MinhoBraga, Portugal
| | - Aidan Casey
- Teagasc Food Research Centre, Moorepark Fermoy, Co.Cork, Ireland
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-InstitutKiel, Germany
| | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark Fermoy, Co.Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark Fermoy, Co.Cork, Ireland
| | - Colin Hill
- APC Microbiome Institute and School of Microbiology, University CollegeCork, Ireland
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt UniversityDiepenbeek, Belgium
| | - Jim O'Mahony
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| | - Rob Lavigne
- Laboratory of Gene Technology, KU LeuvenLeuven, Belgium
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| |
Collapse
|
31
|
Yuan Y, Gao M. Characteristics and complete genome analysis of a novel jumbo phage infecting pathogenic Bacillus pumilus causing ginger rhizome rot disease. Arch Virol 2016; 161:3597-3600. [PMID: 27619796 DOI: 10.1007/s00705-016-3053-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/05/2016] [Indexed: 01/22/2023]
Abstract
Tailed phages with genomes larger than 200 kbp are classified as jumbo phage and exhibit extremely high diversity. In this study, a novel jumbo phage, vB_BpuM_BpSp, infecting pathogenic Bacillus pumilus, the cause of ginger rhizome rot disease, was isolated. Notable features of phage vB_BpuM_BpSp are the large phage capsid of 137 nm and baseplate-attached curly tail fibers. The genome of the phage is 255,569 bp in size with G+C content of 25.9 %, and it shows low similarity to known biological entities. The phage genome contains 318 predicted coding sequences. Among these predicted coding sequences, 26 genes responsible for nucleotide metabolism were found, and seven structural genes could be identified. The findings of this study provide new understanding of the genetic diversity of phages.
Collapse
Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
| |
Collapse
|
32
|
Thomas JA, Benítez Quintana AD, Bosch MA, Coll De Peña A, Aguilera E, Coulibaly A, Wu W, Osier MV, Hudson AO, Weintraub ST, Black LW. Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly. J Virol 2016; 90:10284-10298. [PMID: 27605673 PMCID: PMC5105663 DOI: 10.1128/jvi.01492-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/26/2016] [Indexed: 01/20/2023] Open
Abstract
Giant tailed bacterial viruses, or phages, such as Pseudomonas aeruginosa phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica phage SPN3US could be a useful model phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241, which encodes an RNA polymerase β subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a "missing" β' subunit domain. These findings support SPN3US as an excellent model for giant phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution. IMPORTANCE In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant phages) can be found in many environments. A group of phages related to the prototype giant phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for biocontrol and phage therapy applications. Our understanding of the biology of these phages is limited, as a large proportion of their proteins have not been characterized and/or have been deemed putative without any experimental verification. In this study, we analyzed Salmonella phage SPN3US using a combination of genomics, genetics, and proteomics and in doing so revealed new information regarding giant phage head structure and assembly and virion RNA polymerase composition. Our findings demonstrate the suitability of SPN3US as a model phage for the growing group of phages related to ϕKZ.
Collapse
Affiliation(s)
- Julie A Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | | | - Martine A Bosch
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Adriana Coll De Peña
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Elizabeth Aguilera
- Natural and Physical Sciences, Baltimore City Community College, Baltimore, Maryland, USA
| | - Assitan Coulibaly
- Natural and Physical Sciences, Baltimore City Community College, Baltimore, Maryland, USA
| | - Weimin Wu
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael V Osier
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Susan T Weintraub
- University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Lindsay W Black
- University of Maryland School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
33
|
Skliros D, Kalatzis PG, Katharios P, Flemetakis E. Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell. Front Microbiol 2016; 7:1807. [PMID: 27895630 PMCID: PMC5107563 DOI: 10.3389/fmicb.2016.01807] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/27/2016] [Indexed: 01/21/2023] Open
Abstract
Sequencing and annotation was performed for two large double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage–host metabolic interactions and exploitation was studied by transcript profiling of selected viral and host genes. Comparative genomic analysis with other large Vibrio phages was also performed to establish the presence and location of homing endonucleases highlighting distinct features for both phages. Phylogenetic analysis revealed that they belong to the “schizoT4like” clade. Although many reports of newly sequenced viruses have provided a large set of information, basic research related to the shift of the bacterial metabolism during infection remains stagnant. The function of many viral protein products in the process of infection is still unknown. Genome annotation identified the presence of several viral open reading frames (ORFs) participating in metabolism, including a Sir2/cobB (sirtuin) protein and a number of genes involved in auxiliary NAD+ and nucleotide biosynthesis, necessary for phage DNA replication. Key genes were subsequently selected for detail study of their expression levels during infection. This work suggests a complex metabolic interaction and exploitation of the host metabolic pathways and biochemical processes, including a possible post-translational protein modification, by the virus during infection.
Collapse
Affiliation(s)
- Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens Athens, Greece
| | - Panos G Kalatzis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HeraklionCrete, Greece; Marine Biological Section, University of CopenhagenHelsingør, Denmark
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion Crete, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens Athens, Greece
| |
Collapse
|
34
|
Krylov V, Shaburova O, Pleteneva E, Bourkaltseva M, Krylov S, Kaplan A, Chesnokova E, Kulakov L, Magill D, Polygach O. Modular Approach to Select Bacteriophages Targeting Pseudomonas aeruginosa for Their Application to Children Suffering With Cystic Fibrosis. Front Microbiol 2016; 7:1631. [PMID: 27790211 PMCID: PMC5062033 DOI: 10.3389/fmicb.2016.01631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/30/2016] [Indexed: 01/21/2023] Open
Abstract
This review discusses the potential application of bacterial viruses (phage therapy) toward the eradication of antibiotic resistant Pseudomonas aeruginosa in children with cystic fibrosis (CF). In this regard, several potential relationships between bacteria and their bacteriophages are considered. The most important aspect that must be addressed with respect to phage therapy of bacterial infections in the lungs of CF patients is in ensuring the continuity of treatment in light of the continual occurrence of resistant bacteria. This depends on the ability to rapidly select phages exhibiting an enhanced spectrum of lytic activity among several well-studied phage groups of proven safety. We propose a modular based approach, utilizing both mono-species and hetero-species phage mixtures. With an approach involving the visual recognition of characteristics exhibited by phages of well-studied phage groups on lawns of the standard P. aeruginosa PAO1 strain, the simple and rapid enhancement of the lytic spectrum of cocktails is permitted, allowing the development of tailored preparations for patients capable of circumventing problems associated with phage resistant bacterial mutants.
Collapse
Affiliation(s)
- Victor Krylov
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Olga Shaburova
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Elena Pleteneva
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Maria Bourkaltseva
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Sergey Krylov
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Alla Kaplan
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Elena Chesnokova
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Leonid Kulakov
- Medical Biology Centre, School of Biological Sciences, Queen's University Belfast Belfast, UK
| | - Damian Magill
- Medical Biology Centre, School of Biological Sciences, Queen's University Belfast Belfast, UK
| | - Olga Polygach
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| |
Collapse
|
35
|
Bourrelle-Langlois M, Morrow G, Finet S, Tanguay RM. In Vitro Structural and Functional Characterization of the Small Heat Shock Proteins (sHSP) of the Cyanophage S-ShM2 and Its Host, Synechococcus sp. WH7803. PLoS One 2016; 11:e0162233. [PMID: 27643500 PMCID: PMC5028025 DOI: 10.1371/journal.pone.0162233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/21/2016] [Indexed: 11/22/2022] Open
Abstract
We previously reported the in silico characterization of Synechococcus sp. phage 18 kDa small heat shock protein (HspSP-ShM2). This small heat shock protein (sHSP) contains a highly conserved core alpha crystalline domain of 92 amino acids and relatively short N- and C-terminal arms, the later containing the classical C-terminal anchoring module motif (L-X-I/L/V). Here we establish the oligomeric profile of HspSP-ShM2 and its structural dynamics under in vitro experimental conditions using size exclusion chromatography (SEC/FPLC), gradient native gels electrophoresis and dynamic light scattering (DLS). Under native conditions, HspSP-ShM2 displays the ability to form large oligomers and shows a polydisperse profile. At higher temperatures, it shows extensive structural dynamics and undergoes conformational changes through an increased of subunit rearrangement and formation of sub-oligomeric species. We also demonstrate its capacity to prevent the aggregation of citrate synthase, malate dehydrogenase and luciferase under heat shock conditions through the formation of stable and soluble hetero-oligomeric complexes (sHSP:substrate). In contrast, the host cyanobacteria Synechococcus sp. WH7803 15 kDa sHSP (HspS-WH7803) aggregates when in the same conditions as HspSP-ShM2. However, its solubility can be maintained in the presence of non-ionic detergent Triton™X-100 and forms an oligomeric structure estimated to be between dimer and tetramer but exhibits no apparent inducible structural dynamics neither chaperon-like activity in all the assays and molar ratios tested. SEC/FPLC and thermal aggregation prevention assays results indicate no formation of hetero-oligomeric complex or functional interactions between both sHSPs. Taken together these in vitro results portray the phage HspSP-ShM2 as a classical sHSP and suggest that it may be functional at the in vivo level while behaving differently than its host amphitropic sHSP.
Collapse
Affiliation(s)
- Maxime Bourrelle-Langlois
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Intégrative et des Systémes (IBIS) and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Québec, Canada
| | - Geneviève Morrow
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Intégrative et des Systémes (IBIS) and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Québec, Canada
| | - Stéphanie Finet
- IMPMC UMR7590, CNRS/Sorbonne-Universités, UPMC/IRD/MNHN Paris 6, Paris, France
| | - Robert M. Tanguay
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Intégrative et des Systémes (IBIS) and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Québec, Canada
- * E-mail:
| |
Collapse
|
36
|
New GroEL-like chaperonin of bacteriophage OBP Pseudomonas fluorescens suppresses thermal protein aggregation in an ATP-dependent manner. Biochem J 2016; 473:2383-93. [DOI: 10.1042/bcj20160367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/31/2016] [Indexed: 11/17/2022]
Abstract
Recently, we discovered and studied the first virus-encoded chaperonin of bacteriophage EL Pseudomonas aeruginosa, gene product (gp) 146. In the present study, we performed bioinformatics analysis of currently predicted GroEL-like proteins encoded by phage genomes in comparison with cellular and mitochondrial chaperonins. Putative phage chaperonins share a low similarity and do not form a monophyletic group; nevertheless, they are closer to bacterial chaperonins in the phylogenetic tree. Experimental investigation of putative GroEL-like chaperonin proteins has been continued by physicochemical and functional characterization of gp246 encoded by the genome of Pseudomonas fluorescens bacteriophage OBP. Unlike the more usual double-ring architecture of chaperonins, including the EL gp146, the recombinant gp246 produced by Escherichia coli cells has been purified as a single heptameric ring. It possesses ATPase activity and does not require a co-chaperonin for its function. In vitro experiments demonstrated that gp246 is able to suppress the thermal protein inactivation and aggregation in an ATP-dependent manner, thus indicating chaperonin function. Single-particle electron microscopy analysis revealed the different conformational states of OBP chaperonin, depending on the bound nucleotide.
Collapse
|
37
|
Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B. mBio 2016; 7:mBio.00667-16. [PMID: 27302758 PMCID: PMC4916379 DOI: 10.1128/mbio.00667-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages. IMPORTANCE Filamentous cyanobacteria belonging to the genus Nostoc are widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.
Collapse
|
38
|
Lavysh D, Sokolova M, Minakhin L, Yakunina M, Artamonova T, Kozyavkin S, Makarova KS, Koonin EV, Severinov K. The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. Virology 2016; 495:185-96. [PMID: 27236306 DOI: 10.1016/j.virol.2016.04.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 11/17/2022]
Abstract
Bacteriophage AR9 and its close relative PBS1 have been extensively used to construct early Bacillus subtilis genetic maps. Here, we present the 251,042bp AR9 genome, a linear, terminally redundant double-stranded DNA containing deoxyuridine instead of thymine. Multiple AR9 genes are interrupted by non-coding sequences or sequences encoding putative endonucleases. We show that these sequences are group I and group II self-splicing introns. Eight AR9 proteins are homologous to fragments of bacterial RNA polymerase (RNAP) subunits β/β'. These proteins comprise two sets of paralogs of RNAP largest subunits, with each paralog encoded by two disjoint phage genes. Thus, AR9 is a phiKZ-related giant phage that relies on two multisubunit viral RNAPs to transcribe its genome independently of host transcription apparatus. Purification of one of PBS1/AR9 RNAPs has been reported previously, which makes AR9 a promising object for further studies of RNAP evolution, assembly and mechanism.
Collapse
Affiliation(s)
- Daria Lavysh
- Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Maria Sokolova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia.
| | - Leonid Minakhin
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.
| | - Tatjana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.
| | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Konstantin Severinov
- Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia; Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
| |
Collapse
|
39
|
Bhunchoth A, Blanc-Mathieu R, Mihara T, Nishimura Y, Askora A, Phironrit N, Leksomboon C, Chatchawankanphanich O, Kawasaki T, Nakano M, Fujie M, Ogata H, Yamada T. Two asian jumbo phages, ϕRSL2 and ϕRSF1, infect Ralstonia solanacearum and show common features of ϕKZ-related phages. Virology 2016; 494:56-66. [PMID: 27081857 DOI: 10.1016/j.virol.2016.03.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/26/2022]
Abstract
Jumbo phages infecting Ralstonia solanacearum were isolated in Thailand (ϕRSL2) and Japan (ϕRSF1). They were similar regarding virion morphology, genomic arrangement, and host range. Phylogenetic and proteomic tree analyses demonstrate that the ϕRSL2 and ϕRSF1 belong to a group of evolutionary related phages, including Pseudomonas phages ϕKZ, 201ϕ2-1 and all previously described ϕKZ-related phages. Despite conserved genomic co-linearity between the ϕRSL2 and ϕRSF1, they differ in protein separation patterns. A major difference was seen in the detection of virion-associated-RNA polymerase subunits. All β- and β'-subunits were detected in ϕRSF1, but one β'-subunit was undetected in ϕRSL2. Furthermore, ϕRSF1 infected host cells faster (latent period: 60 and 150min for ϕRSF1 and ϕRSL2, respectively) and more efficiently than ϕRSL2. Therefore, the difference in virion-associated-RNA polymerase may affect infection efficiency. Finally, we show that ϕRSF1 is able to inhibit bacterial wilt progression in tomato plants.
Collapse
Affiliation(s)
- Anjana Bhunchoth
- Plant Research Laboratory, National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani 12120, Thailand; Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoko Mihara
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yosuke Nishimura
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ahmed Askora
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Namthip Phironrit
- Plant Research Laboratory, National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani 12120, Thailand
| | - Chalida Leksomboon
- Department of Plant Pathology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Orawan Chatchawankanphanich
- Plant Research Laboratory, National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani 12120, Thailand
| | - Takeru Kawasaki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Miyako Nakano
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Makoto Fujie
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan.
| |
Collapse
|
40
|
Molugu SK, Hildenbrand ZL, Morgan DG, Sherman MB, He L, Georgopoulos C, Sernova NV, Kurochkina LP, Mesyanzhinov VV, Miroshnikov KA, Bernal RA. Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin. Structure 2016; 24:537-546. [PMID: 26996960 DOI: 10.1016/j.str.2016.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 01/05/2023]
Abstract
Chaperonins are ubiquitous, ATP-dependent protein-folding molecular machines that are essential for all forms of life. Bacteriophage φEL encodes its own chaperonin to presumably fold exceedingly large viral proteins via profoundly different nucleotide-binding conformations. Our structural investigations indicate that ATP likely binds to both rings simultaneously and that a misfolded substrate acts as the trigger for ATP hydrolysis. More importantly, the φEL complex dissociates into two single rings resulting from an evolutionarily altered residue in the highly conserved ATP-binding pocket. Conformational changes also more than double the volume of the single-ring internal chamber such that larger viral proteins are accommodated. This is illustrated by the fact that φEL is capable of folding β-galactosidase, a 116-kDa protein. Collectively, the architecture and protein-folding mechanism of the φEL chaperonin are significantly different from those observed in group I and II chaperonins.
Collapse
Affiliation(s)
- Sudheer K Molugu
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | | | - David Gene Morgan
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Lilin He
- Neutron Scattering Science Division, Oak Ridge National Laboratory, C23, Building 7964K, Oak Ridge, TN 37831-6430, USA
| | - Costa Georgopoulos
- Department of Biochemistry, University of Utah, 4100 EEJMRB, Salt Lake City, UT 84112-5650, USA
| | - Natalia V Sernova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Pereulok, 19, Moscow 127994, Russia
| | - Lidia P Kurochkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Vadim V Mesyanzhinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ricardo A Bernal
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA.
| |
Collapse
|
41
|
van Belkum A, Soriaga LB, LaFave MC, Akella S, Veyrieras JB, Barbu EM, Shortridge D, Blanc B, Hannum G, Zambardi G, Miller K, Enright MC, Mugnier N, Brami D, Schicklin S, Felderman M, Schwartz AS, Richardson TH, Peterson TC, Hubby B, Cady KC. Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa. mBio 2015; 6:e01796-15. [PMID: 26604259 PMCID: PMC4669384 DOI: 10.1128/mbio.01796-15] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates. IMPORTANCE P. aeruginosa is both an antibiotic-refractory pathogen and an important model system for type I CRISPR-Cas bacterial immune systems. By combining the genome sequences of 672 newly and previously sequenced genomes, we were able to provide a global view of the phylogenetic distribution, conservation, and potential targets of these systems. This analysis identified a new and putatively mobile P. aeruginosa CRISPR-Cas subtype, characterized the diverse distribution of known CRISPR-inhibiting genes, and provided a potential new use for CRISPR spacer libraries in accessory genome analysis. Our data demonstrated the importance of CRISPR-Cas systems in modulating the accessory genomes of globally distributed strains while also providing substantial data for subsequent genomic and experimental studies in multiple fields. Understanding why certain genotypes of P. aeruginosa are clinically prevalent and adept at horizontally acquiring virulence and antibiotic resistance elements is of major clinical and economic importance.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Mark C Enright
- Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Daniel Brami
- Synthetic Genomics, Inc., La Jolla, California, USA
| | | | | | | | | | | | - Bolyn Hubby
- Synthetic Genomics, Inc., La Jolla, California, USA
| | - Kyle C Cady
- Synthetic Genomics, Inc., La Jolla, California, USA
| |
Collapse
|
42
|
Non-structural proteins P17 and P33 are involved in the assembly of the internal membrane-containing virus PRD1. Virology 2015; 482:225-33. [PMID: 25880114 DOI: 10.1016/j.virol.2015.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/30/2014] [Accepted: 03/22/2015] [Indexed: 11/24/2022]
Abstract
Bacteriophage PRD1, which has been studied intensively at the structural and functional levels, still has some gene products with unknown functions and certain aspects of the PRD1 assembly process have remained unsolved. In this study, we demonstrate that the phage-encoded non-structural proteins P17 and P33, either individually or together, complement the defect in a temperature-sensitive GroES mutant of Escherichia coli for host growth and PRD1 propagation. Confocal microscopy of fluorescent fusion proteins revealed co-localisation between P33 and P17 as well as between P33 and the host chaperonin GroEL. A fluorescence recovery after photobleaching assay demonstrated that the diffusion of the P33 fluorescent fusion protein was substantially slower in E. coli than theoretically calculated, presumably resulting from intermolecular interactions. Our results indicate that P33 and P17 function in procapsid assembly, possibly in association with the host chaperonin complex GroEL/GroES.
Collapse
|
43
|
Magill DJ, Shaburova OV, Chesnokova EN, Pleteneva EA, Krylov VN, Kulakov LA. Complete nucleotide sequence of phiCHU: a Luz24likevirus infecting Pseudomonas aeruginosa and displaying a unique host range. FEMS Microbiol Lett 2015; 362:fnv045. [PMID: 25825475 DOI: 10.1093/femsle/fnv045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2015] [Indexed: 11/13/2022] Open
Abstract
A complete nucleotide sequence of the new Pseudomonas aeruginosa Luz24likevirus phiCHU was obtained. This virus was shown to have a unique host range whereby it grew poorly on the standard laboratory strain PAO1, but infected 26 of 46 clinical isolates screened, and strains harbouring IncP2 plasmid pMG53. It was demonstrated that phiCHU has single-strand interruptions in its genome. Analysis of the phiCHU genome also suggested that recombination event(s) participated in the evolution of the leftmost portion of the genome, presumably encoding early genes.
Collapse
Affiliation(s)
- Damian J Magill
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast BT9 7BL, Northern Ireland, UK
| | - Olga V Shaburova
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow 105064, Russia
| | - Elena N Chesnokova
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow 105064, Russia
| | - Elena A Pleteneva
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow 105064, Russia
| | - Victor N Krylov
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow 105064, Russia
| | - Leonid A Kulakov
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast BT9 7BL, Northern Ireland, UK
| |
Collapse
|
44
|
Semenyuk PI, Orlov VN, Kurochkina LP. Effect of chaperonin encoded by gene 146 on thermal aggregation of lytic proteins of bacteriophage EL Pseudomonas aeruginosa. BIOCHEMISTRY (MOSCOW) 2015; 80:172-9. [DOI: 10.1134/s0006297915020042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
45
|
Krylov V, Shaburova O, Pleteneva E, Krylov S, Kaplan A, Burkaltseva M, Polygach O, Chesnokova E. Selection of phages and conditions for the safe phage therapy against Pseudomonas aeruginosa infections. Virol Sin 2015; 30:33-44. [PMID: 25680443 PMCID: PMC8200895 DOI: 10.1007/s12250-014-3546-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 01/30/2015] [Indexed: 11/27/2022] Open
Abstract
The emergence of multidrug-resistant bacterial pathogens forced us to consider the phage therapy as one of the possible alternative approaches to treatment. The purpose of this paper is to consider the conditions for the safe, long-term use of phage therapy against various infections caused by Pseudomonas aeruginosa. We describe the selection of the most suitable phages, their most effective combinations and some approaches for the rapid recognition of phages unsuitable for use in therapy. The benefits and disadvantages of the various different approaches to the preparation of phage mixtures are considered, together with the specific conditions that are required for the safe application of phage therapy in general hospitals and the possibilities for the development of personalized phage therapy.
Collapse
Affiliation(s)
- Victor Krylov
- I.I. Mechnikov Research Institute for Vaccines & Sera, RAMS, Moscow, 105064, Russian,
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Abstract
Co-chaperonins function together with chaperonins to mediate ATP-dependant protein folding in a variety of cellular compartments. GroEL and its co-chaperonin GroES are the only essential chaperones in Escherichia coli and are the archetypal members of this family of protein folding machines. The unique mechanism used by GroEL and GroES to drive protein folding is embedded in the complex architecture of double-ringed complexes, forming two central chambers that undergo structural rearrangements as part of the folding mechanism. GroES forms a lid over the chamber, and in doing so dislodges bound substrate into the chamber, thereby allowing non-native proteins to fold in isolation. GroES also modulates allosteric transitions of GroEL. A significant number of bacteria and eukaryotes house multiple chaperonin and co-chaperonin proteins, many of which have acquired additional intracellular and extracellular biological functions. In some instances co-chaperonins display contrasting functions to those of chaperonins. Human Hsp60 continues to play a key role in the pathogenesis of many human diseases, in particular autoimmune diseases and cancer. A greater understanding of the fascinating roles of both intracellular and extracellular Hsp10, in addition to its role as a co-chaperonin, on cellular processes will accelerate the development of techniques to treat diseases associated with the chaperonin family.
Collapse
Affiliation(s)
- Aileen Boshoff
- Biomedical Biotechnology Research Unit (BioBRU), Biotechnology Innovation Centre, Rhodes University, PO Box 94, 6140, Grahamstown, South Africa,
| |
Collapse
|
47
|
Sokolova OS, Shaburova OV, Pechnikova EV, Shaytan AK, Krylov SV, Kiselev NA, Krylov VN. Genome packaging in EL and Lin68, two giant phiKZ-like bacteriophages of P. aeruginosa. Virology 2014; 468-470:472-478. [PMID: 25254945 DOI: 10.1016/j.virol.2014.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/01/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
Abstract
A unique feature of the Pseudomonas aeruginosa giant phage phiKZ is its way of genome packaging onto a spool-like protein structure, the inner body. Until recently, no similar structures have been detected in other phages. We have studied DNA packaging in P. aeruginosa phages EL and Lin68 using cryo-electron microscopy and revealed the presence of inner bodies. The shape and positioning of the inner body and the density of the DNA packaging in EL are different from those found in phiKZ and Lin68. This internal organization explains how the shorter EL genome is packed into a large EL capsid, which has the same external dimensions as the capsids of phiKZ and Lin68. The similarity in the structural organization in EL and other phiKZ-like phages indicates that EL is phylogenetically related to other phiKZ-like phages, and, despite the lack of detectable DNA homology, EL, phiKZ, and Lin68 descend from a common ancestor.
Collapse
Affiliation(s)
- O S Sokolova
- M.V. Lomonosov Moscow State University, Moscow, Russia; A.V. Shoubnikov Institute of Crystallography RAS, Moscow, Russia.
| | - O V Shaburova
- I.I. Mechnikov Research Institute of Vaccines and Sera, RAMS, Moscow, Russia
| | - E V Pechnikova
- A.V. Shoubnikov Institute of Crystallography RAS, Moscow, Russia
| | - A K Shaytan
- M.V. Lomonosov Moscow State University, Moscow, Russia
| | - S V Krylov
- I.I. Mechnikov Research Institute of Vaccines and Sera, RAMS, Moscow, Russia
| | - N A Kiselev
- A.V. Shoubnikov Institute of Crystallography RAS, Moscow, Russia
| | - V N Krylov
- I.I. Mechnikov Research Institute of Vaccines and Sera, RAMS, Moscow, Russia
| |
Collapse
|
48
|
Abstract
Bacteria Pseudomonas aeruginosa, being opportunistic pathogens, are the major cause of nosocomial infections and, in some cases, the primary cause of death. They are virtually untreatable with currently known antibiotics. Phage therapy is considered as one of the possible approaches to the treatment of P. aeruginosa infections. Difficulties in the implementation of phage therapy in medical practice are related, for example, to the insufficient number and diversity of virulent phages that are active against P. aeruginosa. Results of interaction of therapeutic phages with bacteria in different conditions and environments are studied insufficiently. A little is known about possible interactions of therapeutic phages with resident prophages and plasmids in clinical strains in the foci of infections. This chapter highlights the different approaches to solving these problems and possible ways to expand the diversity of therapeutic P. aeruginosa phages and organizational arrangements (as banks of phages) to ensure long-term use of phages in the treatment of P. aeruginosa infections.
Collapse
Affiliation(s)
- Victor N Krylov
- Mechnikov Research Institute for Vaccines & Sera, Russian Academy of Medical Sciences, Moscow, Russia.
| |
Collapse
|
49
|
Development of giant bacteriophage ϕKZ is independent of the host transcription apparatus. J Virol 2014; 88:10501-10. [PMID: 24965474 DOI: 10.1128/jvi.01347-14] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Pseudomonas aeruginosa bacteriophage ϕKZ is the type representative of the giant phage genus, which is characterized by unusually large virions and genomes. By unraveling the transcriptional map of the ∼ 280-kb ϕKZ genome to single-nucleotide resolution, we combine 369 ϕKZ genes into 134 operons. Early transcription is initiated from highly conserved AT-rich promoters distributed across the ϕKZ genome and located on the same strand of the genome. Early transcription does not require phage or host protein synthesis. Transcription of middle and late genes is dependent on protein synthesis and mediated by poorly conserved middle and late promoters. Unique to ϕKZ is its ability to complete its infection in the absence of bacterial RNA polymerase (RNAP) enzyme activity. We propose that transcription of the ϕKZ genome is performed by the consecutive action of two ϕKZ-encoded, noncanonical multisubunit RNAPs, one of which is packed within the virion, another being the product of early genes. This unique, rifampin-resistant transcriptional machinery is conserved within the diverse giant phage genus. IMPORTANCE The data presented in this paper offer, for the first time, insight into the complex transcriptional scheme of giant bacteriophages. We show that Pseudomonas aeruginosa giant phage ϕKZ is able to infect and lyse its host cell and produce phage progeny in the absence of functional bacterial transcriptional machinery. This unique property can be attributed to two phage-encoded putative RNAP enzymes, which contain very distant homologues of bacterial β and β'-like RNAP subunits.
Collapse
|
50
|
Eller MR, Vidigal PMP, Salgado RL, Alves MP, Dias RS, da Silva CC, de Carvalho AF, Kropinski A, De Paula SO. UFV-P2 as a member of the Luz24likevirus genus: a new overview on comparative functional genome analyses of the LUZ24-like phages. BMC Genomics 2014; 15:7. [PMID: 24384011 PMCID: PMC3890496 DOI: 10.1186/1471-2164-15-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/26/2013] [Indexed: 11/26/2022] Open
Abstract
Background Phages infecting spoilage microorganisms have been considered as alternative biocontrol agents, and the study of their genomes is essential to their safe use in foods. UFV-P2 is a new Pseudomonas fluorescens-specific phage that has been tested for its ability to inhibit milk proteolysis. Results The genome of the phage UFV-P2 is composed of bidirectional modules and presented 75 functionally predict ORFs, forming clusters of early and late transcription. Further genomic comparisons of Pseudomonas-specific phages showed that these viruses could be classified according to conserved segments that appear be free from genome rearrangements, called locally collinear blocks (LCBs). In addition, the genome organization of the phage UFV-P2 was shown to be similar to that of phages PaP3 and LUZ24 which have recently been classified as a Luz24likevirus. Conclusions We have presented the functional annotation of UFV-P2, a new Pseudomonas fluorescens phage. Based on structural genomic comparison and phylogenetic clustering, we suggest the classification of UFV-P2 in the Luz24likevirus genus, and present a set of shared locally collinear blocks as the genomic signature for this genus.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Sérgio O De Paula
- Laboratory of Molecular Immunovirology, Federal University of Viçosa, Av, PH Rolfs, s/n, Campus da UFV, Viçosa, Minas Gerais 36570-000, Brazil.
| |
Collapse
|