1
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Li X, Ren Q, Sun Z, Wu Y, Pan H. Resuscitation Promotion Factor: A Pronounced Bacterial Cytokine in Propelling Bacterial Resuscitation. Microorganisms 2024; 12:1528. [PMID: 39203370 PMCID: PMC11356341 DOI: 10.3390/microorganisms12081528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
While confronted with unfavorable growth conditions, bacteria may transform into the dormant state, such as viable but nonculturable (VBNC) state, which is a reversible state characterized by low metabolic activity and lack of division. These dormant cells can be reactivated through the influence of the resuscitation promoting factor (Rpf) family, which are classified as autocrine growth factors and possess peptidoglycan hydrolase activities. To date, with the significant resuscitation or growth promotion ability of Rpf, it has been extensively applied to increasing bacterial diversity and isolating functional microbial species. This review provides a comprehensive analysis of the distribution, mode of action, and functional mechanisms of Rpf proteins in various bacterial species. The aim is to create opportunities for decoding microbial communities and extracting microbial resources from real samples across different research fields.
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Affiliation(s)
| | | | | | | | - Hanxu Pan
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (X.L.); (Q.R.); (Z.S.); (Y.W.)
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2
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Guo H, Lei T, Yang J, Wang Y, Wang Y, Ji Y. New Insights into the Biological Functions of Essential TsaB/YeaZ Protein in Staphylococcus aureus. Antibiotics (Basel) 2024; 13:393. [PMID: 38786122 PMCID: PMC11117223 DOI: 10.3390/antibiotics13050393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
TsaB/YeaZ represents a promising target for novel antibacterial agents due to its indispensable role in bacterial survival, high conservation within bacterial species, and absence of eukaryotic homologs. Previous studies have elucidated the role of the essential staphylococcal protein, TsaB/YeaZ, in binding DNA to mediate the transcription of the ilv-leu operon, responsible for encoding key enzymes involved in the biosynthesis of branched-chain amino acids-namely isoleucine, leucine, and valine (ILV). However, the regulation of ILV biosynthesis does not account for the essentiality of TsaB/YeaZ for bacterial growth. In this study, we investigated the impact of TsaB/YeaZ depletion on bacterial morphology and gene expression profiles using electron microscopy and deep transcriptomic analysis, respectively. Our results revealed significant alterations in bacterial size and surface smoothness upon TsaB/YeaZ depletion. Furthermore, we pinpointed specific genes and enriched biological pathways significantly affected by TsaB/YeaZ during the early and middle exponential phases and early stationary phases of growth. Crucially, our research uncovered a regulatory role for TsaB/YeaZ in bacterial autolysis. These discoveries offer fresh insights into the multifaceted biological functions of TsaB/YeaZ within S. aureus.
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Affiliation(s)
- Haiyong Guo
- School of Life Science, Jilin Normal University, Siping 136000, China; (H.G.)
| | - Ting Lei
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (T.L.)
| | - Junshu Yang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (T.L.)
| | - Yue Wang
- School of Life Science, Jilin Normal University, Siping 136000, China; (H.G.)
| | - Yifan Wang
- School of Life Science, Jilin Normal University, Siping 136000, China; (H.G.)
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (T.L.)
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3
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Pan H, Ren Q. Wake Up! Resuscitation of Viable but Nonculturable Bacteria: Mechanism and Potential Application. Foods 2022; 12:82. [PMID: 36613298 PMCID: PMC9818539 DOI: 10.3390/foods12010082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022] Open
Abstract
The viable but nonculturable (VBNC) state is a survival strategy for bacteria when encountered with unfavorable conditions. Under favorable environments such as nutrient supplementation, external stress elimination, or supplementation with resuscitation-promoting substances, bacteria will recover from the VBNC state, which is termed "resuscitation". The resuscitation phenomenon is necessary for proof of VBNC existence, which has been confirmed in different ways to exclude the possibility of culturable-cell regrowth. The resuscitation of VBNC cells has been widely studied for the purpose of risk control of recovered pathogenic or spoilage bacteria. From another aspect, the resuscitation of functional bacteria can also be considered a promising field to explore. To support this point, the resuscitation mechanisms were comprehensively reviewed, which could provide the theoretical foundations for the application of resuscitated VBNC cells. In addition, the proposed applications, as well as the prospects for further applications of resuscitated VBNC bacteria in the food industry are discussed in this review.
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Affiliation(s)
| | - Qing Ren
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
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4
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Su C, Jin M, Zhang W. Conservation and Diversification of tRNA t 6A-Modifying Enzymes across the Three Domains of Life. Int J Mol Sci 2022; 23:13600. [PMID: 36362385 PMCID: PMC9654439 DOI: 10.3390/ijms232113600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification occurs at position 37 of tRNAs that decipher codons starting with adenosine. Mechanistically, t6A stabilizes structural configurations of the anticodon stem loop, promotes anticodon-codon pairing and safeguards the translational fidelity. The biosynthesis of tRNA t6A is co-catalyzed by two universally conserved protein families of TsaC/Sua5 (COG0009) and TsaD/Kae1/Qri7 (COG0533). Enzymatically, TsaC/Sua5 protein utilizes the substrates of L-threonine, HCO3-/CO2 and ATP to synthesize an intermediate L-threonylcarbamoyladenylate, of which the threonylcarbamoyl-moiety is subsequently transferred onto the A37 of substrate tRNAs by the TsaD-TsaB -TsaE complex in bacteria or by the KEOPS complex in archaea and eukaryotic cytoplasm, whereas Qri7/OSGEPL1 protein functions on its own in mitochondria. Depletion of tRNA t6A interferes with protein homeostasis and gravely affects the life of unicellular organisms and the fitness of higher eukaryotes. Pathogenic mutations of YRDC, OSGEPL1 and KEOPS are implicated in a number of human mitochondrial and neurological diseases, including autosomal recessive Galloway-Mowat syndrome. The molecular mechanisms underscoring both the biosynthesis and cellular roles of tRNA t6A are presently not well elucidated. This review summarizes current mechanistic understandings of the catalysis, regulation and disease implications of tRNA t6A-biosynthetic machineries of three kingdoms of life, with a special focus on delineating the structure-function relationship from perspectives of conservation and diversity.
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Affiliation(s)
| | | | - Wenhua Zhang
- School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou 730030, China
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5
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Debnath A, Miyoshi SI. The Impact of Protease during Recovery from Viable but Non-Culturable (VBNC) State in Vibrio cholerae. Microorganisms 2021; 9:microorganisms9122618. [PMID: 34946219 PMCID: PMC8707003 DOI: 10.3390/microorganisms9122618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Vibrio cholerae can survive cold stress by entering into a viable but non-culturable (VBNC) state, and resuscitation can be induced either by temperature upshift only or the addition of an anti-dormancy stimulant such as resuscitation-promoting factors (Rpfs) at suitable temperature. In this study, the role of proteinase K was analyzed as an Rpf in V. cholerae. A VBNC state was induced in V. cholerae AN59 in artificial seawater (ASW) media at 4 °C, and recovery could be achieved in filtered VBNC microcosm, called spent ASW media, merely by a temperature upshift to 37 °C. The resuscitation ability of spent ASW was further enhanced by the addition of proteinase K. The mode of action of proteinase K was investigated by comparing its effect on the growth of the VBNC and culturable state of V. cholerae in ASW and spent ASW media. The presence of proteinase K allowed culturable cells to grow faster in ASW by reducing the generation time. However, this effect of proteinase K was more pronounced in stressed VBNC cells. Moreover, proteinase K-supplemented spent ASW could also accelerate the transition of VBNC into recovered cells followed by rapid growth. Additionally, we found that dead bacterial cells were the substrate on which proteinase K acts to support high growth in spent ASW. So, the conclusion is that the proteinase K could efficiently promote the recovery and growth of dormant VBNC cells at higher temperatures by decreasing the duration of the initial lag phase required for transitioning from the VBNC to recovery state and increasing the growth rate of these recovered cells.
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6
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Zhang XH, Ahmad W, Zhu XY, Chen J, Austin B. Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:189-203. [PMID: 37073345 PMCID: PMC10077291 DOI: 10.1007/s42995-020-00041-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 03/25/2020] [Indexed: 05/03/2023]
Abstract
Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in the late nineteenth century. However, even today, the majority of microorganisms in the marine environment remain uncultivated. There are various explanations for the inability to culture bacteria in the laboratory, including lack of essential nutrients, osmotic support or incubation conditions, low growth rate, development of micro-colonies, and the presence of senescent or viable but nonculturable (VBNC) cells. In the marine environment, many bacteria have been associated with dormancy, as typified by the VBNC state. VBNC refers to a state where bacteria are metabolically active, but are no longer culturable on routine growth media. It is apparently a unique survival strategy that has been adopted by many microorganisms in response to harsh environmental conditions and the bacterial cells in the VBNC state may regain culturability under favorable conditions. The resuscitation of VBNC cells may well be an important way to cultivate the otherwise uncultured microorganisms in marine environments. Many resuscitation stimuli that promote the restoration of culturability have so far been identified; these include sodium pyruvate, quorum sensing autoinducers, resuscitation-promoting factors Rpfs and YeaZ, and catalase. In this review, we focus on the issues associated with bacterial culturability, the diversity of bacteria entering the VBNC state, mechanisms of induction into the VBNC state, resuscitation factors of VBNC cells and implications of VBNC resuscitation stimuli for cultivating these otherwise uncultured microorganisms. Bringing important microorganisms into culture is still important in the era of high-throughput sequencing as their ecological functions in the marine environment can often only be known through isolation and cultivation.
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Affiliation(s)
- Xiao-Hua Zhang
- College of Marine Life Sciences and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Waqar Ahmad
- College of Marine Life Sciences and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xiao-Yu Zhu
- College of Marine Life Sciences and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050 China
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA Scotland, UK
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7
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Chandravanshi M, Samanta R, Kanaujia SP. Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function. FEBS J 2021; 288:4614-4636. [PMID: 33599038 DOI: 10.1111/febs.15774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/15/2021] [Accepted: 02/15/2021] [Indexed: 11/27/2022]
Abstract
Substrate (or solute)-binding proteins (SBPs) selectively bind the target ligands and deliver them to the ATP-binding cassette (ABC) transport system for their translocation. Irrespective of the different types of ligands, SBPs are structurally conserved. A wealth of structural details of SBPs bound to different types of ligands and the physiological basis of their import are available; however, the uptake mechanism of nucleotides is still deficient. In this study, we elucidated the structural details of an SBP endogenously bound to a novel ligand, a derivative of uridylyl-3'-5'-phospho-guanosine (U3G); thus, we named it a U3G-binding protein (U3GBP). To the best of our knowledge, this is the first report of U3G (and a dinucleotide) binding to the SBP of ABC transport system, and thus, U3GBP is classified as a first member of subcluster D-I SBPs. Thermodynamic data also suggest that U3GBP can bind phospholipid precursor sn-glycerophosphocholine (GPC) at a site other than the active site. Moreover, a combination of mutagenic and structural information reveals that the protein U3GBP follows the well-known 'Venus Fly-trap' mechanism for dinucleotide binding. DATABASES: Structural data are available in RCSB Protein Data Bank under the accession number(s) 7C0F, 7C0K, 7C0L, 7C0O, 7C0R, 7C0S, 7C0T, 7C0U, 7C0V, 7C0W, 7C0X, 7C0Y, 7C0Z, 7C14, 7C15, 7C16, 7C19, and 7C1B.
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Affiliation(s)
- Monika Chandravanshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Reshama Samanta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
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8
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Zhao R, Chen J, Wang Y, Li Y, Kong X, Han Y. Proteolytic activity of Vibrio harveyi YeaZ is related with resuscitation on the viable but non-culturable state. Lett Appl Microbiol 2020; 71:126-133. [PMID: 32349168 DOI: 10.1111/lam.13304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/27/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023]
Abstract
The YeaZ protein of Vibrio harveyi was expressed in Escherichia coli and purified. The purified recombinant protein YeaZ exhibited the protease activity. The proteolytic activities with azocasein as substrate were 39 130 U mg-1 . The mutation of the amino acid in active sites such as Asp88 , Ser185 and Trp169 was performed. The enzyme activities of the purified mutant proteins with Asp88 -Ala, Ser185 -Leu and Trp169 -Glu were decreased to 24·28, 35·27 and 41·66%, respectively. The mutant protein with two amino acid residues (Asp88 -Ala/Ser185 -Leu) lost the protease activity completely. Addition of the purified recombinant YeaZ increased resuscitation of the viable but non-culturable state (VBNC) cells to culturable state, and the culturable cell count increased from 1·35 × 102 to 3·10 × 106 CFU per ml. While addition of the mutant YeaZ without protease activities did not show obvious promoting effect on resuscitation of VBNC cells. Moreover, the purified YeaZ also showed lower muralytic activity, and the activities of proteins with single amino acids mutation (Thr71 and Asp112 ) were reduced from 7·05 to 4·75 and 2·50 U mg-1 , the resuscitation-promoting effect on VBNC cells was not affected by these mutant proteins. These results implied that resuscitation-promoting effect of YeaZ on VBNC cell was partly related to its protease activities, but not with the muralytic activity. SIGNIFICANCE AND IMPACT OF THE STUDY: Vibrio harveyi is a major pathogen of marine animals. The bacterium could enter into a viable but non-culturable state (VBNC) state when exposed to harsh conditions, and retains its pathogenicity after resuscitation. In this work, we analysed the enzyme activities of a resuscitation-promoting factor YeaZ and the relationship of protease activities with its promoting effect on the resuscitation of VBNC cells. The results partly revealed the promoting mechanism of the YeaZ on the bacterial resuscitation from VBNC state. The protein could be used as a new drug target and vaccine candidate.
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Affiliation(s)
- R Zhao
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - J Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Y Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Y Li
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, Chongqing University of Arts and Sciences, Chongqing, China
| | - X Kong
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Y Han
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
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9
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Luthra A, Paranagama N, Swinehart W, Bayooz S, Phan P, Quach V, Schiffer JM, Stec B, Iwata-Reuyl D, Swairjo MA. Conformational communication mediates the reset step in t6A biosynthesis. Nucleic Acids Res 2020; 47:6551-6567. [PMID: 31114923 PMCID: PMC6614819 DOI: 10.1093/nar/gkz439] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 11/16/2022] Open
Abstract
The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC–AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-Å crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-ATP in the ATPase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t6A cycle. Further, SAXS analysis of the TmTsaB2D2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC–AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system.
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Affiliation(s)
- Amit Luthra
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Naduni Paranagama
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - William Swinehart
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA
| | - Susan Bayooz
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Phuc Phan
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Vanessa Quach
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Jamie M Schiffer
- Schrödinger, 10201 Wateridge Cir Suite 220, San Diego, CA 92121, USA
| | - Boguslaw Stec
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.,The Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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10
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Britton TA, Guo H, Ji Y. Interaction between two essential, conserved bacterial proteins YeaZ and glycoprotease as a potential antibacterial target in multi-drug-resistant Staphylococcus aureus. Sci Prog 2020; 103:36850419890521. [PMID: 31829791 PMCID: PMC10452758 DOI: 10.1177/0036850419890521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein-protein interactions among highly conserved and essential proteins can serve as new targets for antibacterial therapies. One protein-protein interaction between two widely conserved and essential bacterial proteins, YeaZ and its paralog, a putative glycoprotease, is being looked into for its antimicrobial drug potential. These two proteins possess tandem functions, including repression of the branched-chain amino acids biosynthesis and induction of a tRNA modification important in enhancing translation fidelity through anticodon-codon base pairing. Heterodimer formation between these two proteins is essential for Staphylococcus aureus, and other bacterial species including Escherichia coli and Salmonella typhimurium. Such YeaZ-glycoprotease interaction could thus be a target for antimicrobial drugs designed for multi-drug-resistant S. aureus. In this review, we discuss the function, structure, and interaction between these two proteins and their orthologs in other bacteria.
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Affiliation(s)
- Timmie A Britton
- College of Biomedical Science, University of Minnesota, Minneapolis, MN, USA
| | - Haiyong Guo
- College of Life Science, Jilin Normal University, Siping, China
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN, USA
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11
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Missoury S, Plancqueel S, Li de la Sierra-Gallay I, Zhang W, Liger D, Durand D, Dammak R, Collinet B, van Tilbeurgh H. The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res 2018; 46:5850-5860. [PMID: 29741707 PMCID: PMC6009658 DOI: 10.1093/nar/gky323] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/25/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.
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Affiliation(s)
- Sophia Missoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Stéphane Plancqueel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Raoudha Dammak
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR7590 CNRS/Sorbonne-Université, UPMC, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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12
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Luthra A, Swinehart W, Bayooz S, Phan P, Stec B, Iwata-Reuyl D, Swairjo MA. Structure and mechanism of a bacterial t6A biosynthesis system. Nucleic Acids Res 2018; 46:1395-1411. [PMID: 29309633 PMCID: PMC5814804 DOI: 10.1093/nar/gkx1300] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 11/12/2022] Open
Abstract
The universal N(6)-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs is central to translational fidelity. In bacteria, t6A biosynthesis is catalyzed by the proteins TsaB, TsaC/TsaC2, TsaD and TsaE. Despite intense research, the molecular mechanisms underlying t6A biosynthesis are poorly understood. Here, we report biochemical and biophysical studies of the t6A biosynthesis system from Thermotoga maritima. Small angle X-ray scattering analysis reveals a symmetric 2:2 stoichiometric complex of TsaB and TsaD (TsaB2D2), as well as 2:2:2 complex (TsaB2D2E2), in which TsaB acts as a dimerization module, similar to the role of Pcc1 in the archaeal system. The TsaB2D2 complex is the minimal platform for the binding of one tRNA molecule, which can then accommodate a single TsaE subunit. Kinetic data demonstrate that TsaB2D2 alone, and a TsaB2D2E1 complex with TsaE mutants deficient in adenosine triphosphatase (ATPase) activity, can catalyze only a single cycle of t6A synthesis, while gel shift experiments provide evidence that the role of TsaE-catalyzed ATP hydrolysis occurs after the release of product tRNA. Based on these results, we propose a model for t6A biosynthesis in bacteria.
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Affiliation(s)
- Amit Luthra
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - William Swinehart
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Susan Bayooz
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Phuc Phan
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Boguslaw Stec
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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13
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Li Y, Chen J, Zhao M, Yang Z, Yue L, Zhang X. Promoting resuscitation of viable but nonculturable cells of Vibrio harveyi by a resuscitation-promoting factor-like protein YeaZ. J Appl Microbiol 2016; 122:338-346. [PMID: 27966258 DOI: 10.1111/jam.13342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 12/16/2022]
Abstract
AIMS To demonstrate the resuscitation-promoting activities of recombinant YeaZ from Vibrio harveyi SF-1. METHODS AND RESULTS The gene of resuscitation-promoting factor YeaZ was cloned from genomic DNA of V. harveyi SF-1. The gene was expressed in Escherichia coli, and the expressed protein was purified by Ni2+ -affinity chromatography. A yeaZ mutant was constructed by using the suicide plasmid pNQ705 with homologous recombination. Disruption of yeaZ did not affect cell growth significantly in 2216 E broth at 28°C. The wild-type and mutant viable but nonculturable (VBNC) cells could be resuscitated by temperature upshift method. In addition, the recombinant YeaZ increased the culturable counts from 1·27 × 104 CFU per ml and 1·99 × 104 CFU per ml to 2·88 × 105 CFU per ml and 4·59 × 105 CFU per ml, respectively. After the VBNC cells of wild-type and mutant cells were maintained at 4°C for 120 days, no resuscitation was obtained by temperature upshift method, but addition of the recombinant YeaZ promoted the resuscitation of the wild-type and mutant cells, with the culturable cell counts of 1·13 × 103 and 1·44 × 103 CFU per ml, respectively. Disruption of yeaZ decreased the virulence of V. harveyi in zebrafish. The lethal dose 50% of the yeaZ null mutant was more than 10-fold higher than that of the wild-type cells. CONCLUSIONS The recombinant YeaZ could efficiently promote resuscitation of the wild-type and mutant cells of V. harveyi from VBNC to culturable state. The protein also promoted resuscitation of the VBNC wild-type and mutant cells, which were maintained at 4°C for 120 days and not recovered by temperature upshift method. Disruption of yeaZ decreased the virulence of V. harveyi in zebrafish. SIGNIFICANCE AND IMPACT OF THE STUDY Here, we show clear evidence of a resuscitation-promoting factor YeaZ of V. harveyi and the roles in resuscitation of the VBNC cells and its pathogenicity.
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Affiliation(s)
- Y Li
- College of Energy and Power Engineering, Lanzhou University of Technology, Lanzhou, China.,School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - J Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - M Zhao
- Department of Marine Biology, College of marine Life Science, Ocean University of China, Qingdao, China
| | - Z Yang
- College of Energy and Power Engineering, Lanzhou University of Technology, Lanzhou, China.,School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - L Yue
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - X Zhang
- Department of Marine Biology, College of marine Life Science, Ocean University of China, Qingdao, China
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14
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Lei T, Yang J, Ji Y. Determination of essentiality and regulatory function of staphylococcal YeaZ in branched-chain amino acid biosynthesis. Virulence 2016; 6:75-84. [PMID: 25517685 DOI: 10.4161/21505594.2014.986415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The staphylococcal YeaZ is highly conserved in prokaryotic cells and critical for growth of many bacterial pathogens. However, the essentiality for Staphylococcus aureus growth and the biological function of YeaZ behind its essentiality remain undefined. In this study, we created and characterized a defined Pspac-regulated yeaZ expression mutant in S. aureus and demonstrated the indispensability of YeaZ for S. aureus growth. Moreover, we conducted complementation studies, not only confirmed the requirement of YeaZ for S. aureus growth, but also revealed a similarity of essential function between staphylococcal YeaZ and its E. coli homolog. On the other hand, we explored the biological functions of YeaZ and found that YeaZ is involved in the regulation of the transcription of ilv-leu operon that encodes key enzymes responsible for the biosynthesis of the branched-chain amino acids, including isoleucine, leucine, and valine (ILV). qPCR analysis showed that the 6-fold downregulation of YeaZ dramatically elevated approximately 17- to 289-fold RNA levels of ilvD, leuA and ilvA. We further confirmed the transcriptional regulation of the ilv-leu operon by YeaZ using an ilv-promoter-lux reporter system and gel-shift assays and revealed that YeaZ is able to bind the promoter region of ilv. Furthermore, we established that the regulation of ILV biosynthesis isn't associated with YeaZ's essentiality, as the deletion of the ilv-leu operon did not affect the requirement of YeaZ for growth in culture. Our results demonstrate the essentiality of YeaZ for S. aureus growth and suggest that the staphylococcal YeaZ possesses regulatory function.
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Affiliation(s)
- Ting Lei
- a Department of Veterinary and Biomedical Sciences ; College of Veterinary Medicine; University of Minnesota ; St. Paul , MN USA
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15
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Vecchietti D, Ferrara S, Rusmini R, Macchi R, Milani M, Bertoni G. Crystal structure of YeaZ from Pseudomonas aeruginosa. Biochem Biophys Res Commun 2016; 470:460-465. [PMID: 26768361 DOI: 10.1016/j.bbrc.2016.01.008] [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] [Received: 12/24/2015] [Accepted: 01/03/2016] [Indexed: 10/22/2022]
Abstract
The Pseudomonas aeruginosa PA3685 locus encodes a conserved protein that shares 49% sequence identity with Escherichia coli YeaZ, which was recently reported as involved in the biosynthesis of threonylcarbamoyl adenosine (t(6)A), a universal modified tRNA nucleoside. Many YeaZ orthologues were reported as "essential for life" among various bacterial species, suggesting a critical role for both these proteins and for the t(6)A biosynthetic pathway. We provide here evidences that PA3685 protein (PaYeaZ) is essential. Additionally, we describe its purification, crystallization, and crystallographic structure. The crystal structure shows that PaYeaZ is composed of two domains one of which is the platform to form protein-protein interaction involved either in homodimeric assembly or in the formation of the multiprotein complex required for the synthesis of t(6)A. These features make the PaYeaZ protein a potential target candidate for the design of novel inhibitors able to hinder the complex formation and expected to abolish the crucial activity of t(6)A synthesis.
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Affiliation(s)
- Davide Vecchietti
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Ruggero Rusmini
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Raffaella Macchi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Mario Milani
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy.
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
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16
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Zhang W, Collinet B, Perrochia L, Durand D, van Tilbeurgh H. The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli. Nucleic Acids Res 2015; 43:1804-17. [PMID: 25578970 PMCID: PMC4330362 DOI: 10.1093/nar/gku1397] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The essential and universal N6-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon–anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t6A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD–YeaZ at 2.3 Å, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD–YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD–YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD–YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD–YeaZ–YjeE complex is required for the in vitro biosynthesis of t6A but not its ATPase activity.
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Affiliation(s)
- Wenhua Zhang
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France
| | - Bruno Collinet
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France Sorbonne Universités, UPMC Univ Paris 06, UFR 927, Sciences de la vie, F-75005 Paris, France
| | - Ludovic Perrochia
- Institut de Génétique et de Microbiologie, Université Paris-Sud, UMR8621-CNRS, 91405 Orsay, France
| | - Dominique Durand
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France
| | - Herman van Tilbeurgh
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France
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17
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Ramamurthy T, Ghosh A, Pazhani GP, Shinoda S. Current Perspectives on Viable but Non-Culturable (VBNC) Pathogenic Bacteria. Front Public Health 2014; 2:103. [PMID: 25133139 PMCID: PMC4116801 DOI: 10.3389/fpubh.2014.00103] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/15/2014] [Indexed: 11/07/2022] Open
Abstract
Under stress conditions, many species of bacteria enter into starvation mode of metabolism or a physiologically viable but non-culturable (VBNC) state. Several human pathogenic bacteria have been reported to enter into the VBNC state under these conditions. The pathogenic VBNC bacteria cannot be grown using conventional culture media, although they continue to retain their viability and express their virulence. Though there have been debates on the VBNC concept in the past, several molecular studies have shown that not only can the VBNC state be induced under in vitro conditions but also that resuscitation from this state is possible under appropriate conditions. The most notable advance in resuscitating VBNC bacteria is the discovery of resuscitation-promoting factor (Rpf), which is a bacterial cytokines found in both Gram-positive and Gram-negative organisms. VBNC state is a survival strategy adopted by the bacteria, which has important implication in several fields, including environmental monitoring, food technology, and infectious disease management; and hence it is important to investigate the association of bacterial pathogens under VBNC state and the water/foodborne outbreaks. In this review, we describe various aspects of VBNC bacteria, which include their proteomic and genetic profiles under the VBNC state, conditions of resuscitation, methods of detection, antibiotic resistance, and observations on Rpf.
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Affiliation(s)
| | - Amit Ghosh
- National Institute of Cholera and Enteric Diseases (NICED) , Kolkata , India
| | - Gururaja P Pazhani
- National Institute of Cholera and Enteric Diseases (NICED) , Kolkata , India
| | - Sumio Shinoda
- Collaborative Research Center of Okayama University for Infectious Diseases in India, NICED , Kolkata , India
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18
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Nichols CE, Lamb HK, Thompson P, El Omari K, Lockyer M, Charles I, Hawkins AR, Stammers DK. Crystal structure of the dimer of two essential Salmonella typhimurium proteins, YgjD & YeaZ and calorimetric evidence for the formation of a ternary YgjD-YeaZ-YjeE complex. Protein Sci 2013; 22:628-40. [PMID: 23471679 DOI: 10.1002/pro.2247] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/22/2013] [Accepted: 03/01/2013] [Indexed: 11/07/2022]
Abstract
YgjD from COG0533 is amongst a small group of highly conserved proteins present in all three domains of life. Various roles and biochemical functions (including sialoprotease and endonuclease activities) have been ascribed to YgjD and orthologs, the most recent, however, is involvement in the post transcriptional modification of certain tRNAs by formation of N6-threonyl-adenosine (t⁶A) at position 37. In bacteria, YgjD is essential and along with YeaZ, YjeE, and YrdC has been shown to be 'necessary and sufficient' for the tRNA modification. To further define interactions and possible roles for some of this set of proteins we have undertaken structural and biochemical studies. We show that formation of the previously reported heterodimer of YgjD-YeaZ involves ordering of the C-terminal region of YeaZ which extends along the surface of YgjD in the crystal structure. ATPγS or AMP is observed in YgjD while no nucleotide is bound on YeaZ. ITC experiments reveal previously unreported binary and ternary complexes which can be nucleotide dependent. The stoichiometry of the YeaZ-YgjD complex is 1:1 with a K(D) of 0.3 µM. YgjD and YjeE interact only in the presence of ATP, while YjeE binds to YgjD-YeaZ in the presence of ATP or ADP with a K(D) of 6 µM. YgjD doesn't bind the precursors of t⁶A, threonine, and bicarbonate. These results show a more complex set of interactions than previously thought, which may have a regulatory role. The understanding gained should help in deriving inhibitors of these essential proteins that might have potential as antibacterial drugs.
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Affiliation(s)
- C E Nichols
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
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19
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Berthelot JM, de la Cochetière MF, Potel G, Le Goff B, Maugars Y. Evidence supporting a role for dormant bacteria in the pathogenesis of spondylarthritis. Joint Bone Spine 2013; 80:135-40. [PMID: 23473929 DOI: 10.1016/j.jbspin.2012.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2012] [Indexed: 12/18/2022]
Abstract
Spondylarthritis is still viewed as a reaction to infectious agents, as opposed to an infection by persistent bacteria, for several reasons: (a) an infection is considered proven only when the organism can be cultured; (b) no studies have identified dormant bacteria in the tissues targeted by spondylarthritis; (c) the bacterial persistence hypothesis has no therapeutic implications at the time being, since antibiotics are effective neither on dormant bacteria nor on the manifestations of spondylarthritis; and (d) the high prevalence of borderline disorders combining features of spondylarthritis and of psoriatic arthritis, or even rheumatoid arthritis (RA), would indicate a role for dormant bacteria in these last two diseases. However, recent data on dormant bacteria have rekindled interest in the bacterial persistence hypothesis. Dormant bacteria cannot be cultured, because they express only a small group of genes, known as the regulon, which includes genes for transcription factors that block the expression of the usual bacterial genes. Certain forms of cell stress, such as molecule misfolding, promote the entry of bacteria into a state of dormancy, which induces the low-level release by the host cells of cytokines such as TNF. Whether HLA-B27 misfolding facilitates the persistence of dormant bacteria within spondylarthritis tissue targets remains to be determined. If it does, then treatments that reactivate dormant bacteria might make these organisms susceptible to appropriate antibiotics and might therefore serve as useful adjuncts to nonsteroidal anti-inflammatory drugs and TNFα antagonists. TNFα antagonists rarely reactivate dormant bacteria, with the exception of Mycobacterium tuberculosis, which, together with metastatic cells, is the most extensively studied latency model to date.
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Affiliation(s)
- Jean-Marie Berthelot
- Service de Rhumatologie, Hôtel-Dieu, CHU de Nantes, place Alexis-Ricordeau, 44093 Nantes cedex 01, France.
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20
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Onodera T, Satoh K, Ohta T, Narumi I. Deinococcus radiodurans YgjD and YeaZ are involved in the repair of DNA cross-links. Extremophiles 2012; 17:171-9. [DOI: 10.1007/s00792-012-0506-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/29/2012] [Indexed: 12/29/2022]
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21
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Hoefman S, Van Hoorde K, Boon N, Vandamme P, De Vos P, Heylen K. Survival or revival: long-term preservation induces a reversible viable but non-culturable state in methane-oxidizing bacteria. PLoS One 2012; 7:e34196. [PMID: 22539945 PMCID: PMC3335116 DOI: 10.1371/journal.pone.0034196] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/23/2012] [Indexed: 11/18/2022] Open
Abstract
Knowledge on long-term preservation of micro-organisms is limited and research in the field is scarce despite its importance for microbial biodiversity and biotechnological innovation. Preservation of fastidious organisms such as methane-oxidizing bacteria (MOB) has proven difficult. Most MOB do not survive lyophilization and only some can be cryopreserved successfully for short periods. A large-scale study was designed for a diverse set of MOB applying fifteen cryopreservation or lyophilization conditions. After three, six and twelve months of preservation, the viability (via live-dead flow cytometry) and culturability (via most-probable number analysis and plating) of the cells were assessed. All strains could be cryopreserved without a significant loss in culturability using 1% trehalose in 10-fold diluted TSB (TT) as preservation medium and 5% DMSO as cryoprotectant. Several other cryopreservation and lyophilization conditions, all of which involved the use of TT medium, also allowed successful preservation but showed a considerable loss in culturability. We demonstrate here that most of these non-culturables survived preservation according to viability assessment indicating that preservation induces a viable but non-culturable (VBNC) state in a significant fraction of cells. Since this state is reversible, these findings have major implications shifting the emphasis from survival to revival of cells in a preservation protocol. We showed that MOB cells could be significantly resuscitated from the VBNC state using the TT preservation medium.
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Affiliation(s)
- Sven Hoefman
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Koenraad Van Hoorde
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- Faculty of Applied Bioscience Engineering, University College Ghent, Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Ghent University, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
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