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Desiderato CK, Hasenauer KM, Reich SJ, Goldbeck O, Holivololona L, Ovchinnikov KV, Reiter A, Oldiges M, Diep DB, Eikmanns BJ, Riedel CU. Garvicin Q: characterization of biosynthesis and mode of action. Microb Cell Fact 2022; 21:236. [PMID: 36368990 PMCID: PMC9652874 DOI: 10.1186/s12934-022-01952-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteriocins are ribosomally synthesized antimicrobial peptides, that either kill target bacteria or inhibit their growth. Bacteriocins are used in food preservation and are of increasing interest as potential alternatives to conventional antibiotics. In the present study, we show that Lactococcus petauri B1726, a strain isolated from fermented balsam pear, produces a heat-stable and protease-sensitive compound. Following genome sequencing, a gene cluster for production of a class IId bacteriocin was identified consisting of garQ (encoding for the bacteriocin garvicin Q), garI (for a putative immunity protein), garC, and garD (putative transporter proteins). Growth conditions were optimized for increased bacteriocin activity in supernatants of L. petauri B1726 and purification and mass spectrometry identified the compound as garvicin Q. Further experiments suggest that garvicin Q adsorbs to biomass of various susceptible and insusceptible bacteria and support the hypothesis that garvicin Q requires a mannose-family phosphotransferase system (PTSMan) as receptor to kill target bacteria by disruption of membrane integrity. Heterologous expression of a synthetic garQICD operon was established in Corynebacterium glutamicum demonstrating that genes garQICD are responsible for biosynthesis and secretion of garvicin Q. Moreover, production of garvicin Q by the recombinant C. glutamicum strain was improved by using a defined medium yet product levels were still considerably lower than with the natural L. petauri B1726 producer strain.Collectively, our data identifies the genetic basis for production of the bacteriocin garvicin Q by L. petauri B1726 and provides insights into the receptor and mode of action of garvicin Q. Moreover, we successfully performed first attempts towards biotechnological production of this interesting bacteriocin using natural and heterologous hosts.
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Affiliation(s)
- Christian K. Desiderato
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Katharina M. Hasenauer
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Sebastian J. Reich
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Oliver Goldbeck
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Lalaina Holivololona
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kirill V. Ovchinnikov
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Alexander Reiter
- grid.8385.60000 0001 2297 375XInstitute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425 Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Marco Oldiges
- grid.8385.60000 0001 2297 375XInstitute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425 Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Dzung B. Diep
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Bernhard J. Eikmanns
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Christian U. Riedel
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Structural Basis of the Immunity Mechanisms of Pediocin-like Bacteriocins. Appl Environ Microbiol 2022; 88:e0048122. [PMID: 35703550 DOI: 10.1128/aem.00481-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pediocin-like bacteriocins, also designated class IIa bacteriocins, are ribosomally synthesized antimicrobial peptides targeting species closely related to the producers. They act on the cytoplasmic membrane of Gram-positive cells by dissipating the transmembrane electrical potential through pore formation with the mannose phosphotransferase system (man-PTS) as the target/receptor. Bacteriocin-producing strains also synthesize a cognate immunity protein that protects them against their own bacteriocins. Herein, we report the cryo-electron microscopy structure of the bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. The complex structure reveals that pediocin-like bacteriocins bind to the same position on the Core domain of man-PTS, while the C-terminal helical tails of bacteriocins delimit the opening range of the Core domain away from the Vmotif domain to facilitate transmembrane pore formation. Upon attack of bacteriocins from the extracellular side, man-PTS exposes its cytosolic side for recognition of the N-terminal four-helix bundle of the immunity protein. The C-terminal loop of the immunity protein then inserts into the pore and blocks leakage induced by bacteriocins. Elucidation of the toxicity and immunity mechanisms of pediocin-like bacteriocins could support the design of novel bacteriocins against antibiotic-resistant pathogenic bacteria. IMPORTANCE Pediocin-like bacteriocins, ribosomally synthesized antimicrobial peptides, are generally co-expressed with cognate immunity proteins to protect the bacteriocin-producing strain from its own bacteriocin. Bacteriocins are considered potential alternatives to conventional antibiotics in the context of the bacterial resistance crisis, but the immunity mechanism is unclear. This study uncovered the mechanisms of action and immunity of class IIa bacteriocins.
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Balandin SV, Sheremeteva EV, Ovchinnikova TV. Pediocin-Like Antimicrobial Peptides of Bacteria. BIOCHEMISTRY (MOSCOW) 2019; 84:464-478. [PMID: 31234762 DOI: 10.1134/s000629791905002x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacteriocins are bacterial antimicrobial peptides that, unlike classical peptide antibiotics, are products of ribosomal synthesis and usually have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like bacteriocins (PLBs) belong to the class IIa of the bacteriocins of Gram-positive bacteria. PLBs possess high activity against pathogenic bacteria from Listeria and Enterococcus genera. Molecular target for PLBs is a membrane protein complex - bacterial mannose-phosphotransferase. PLBs can be synthesized by components of symbiotic microflora and participate in the maintenance of homeostasis in various compartments of the digestive tract and on the surface of epithelial tissues contacting the external environment. PLBs could give a rise to a new group of antibiotics of narrow spectrum of activity.
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Affiliation(s)
- S V Balandin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - E V Sheremeteva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - T V Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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Acedo JZ, Chiorean S, Vederas JC, van Belkum MJ. The expanding structural variety among bacteriocins from Gram-positive bacteria. FEMS Microbiol Rev 2019; 42:805-828. [PMID: 30085042 DOI: 10.1093/femsre/fuy033] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteria use various strategies to compete in an ecological niche, including the production of bacteriocins. Bacteriocins are ribosomally synthesized antibacterial peptides, and it has been postulated that the majority of Gram-positive bacteria produce one or more of these natural products. Bacteriocins can be used in food preservation and are also considered as potential alternatives to antibiotics. The majority of bacteriocins from Gram-positive bacteria had been traditionally divided into two major classes, namely lantibiotics, which are post-translationally modified bacteriocins, and unmodified bacteriocins. The last decade has seen an expanding number of ribosomally synthesized and post-translationally modified peptides (RiPPs) in Gram-positive bacteria that have antibacterial activity. These include linear azol(in)e-containing peptides, thiopeptides, bottromycins, glycocins, lasso peptides and lipolanthines. In addition, the three-dimensional (3D) structures of a number of modified and unmodified bacteriocins have been elucidated in recent years. This review gives an overview on the structural variety of bacteriocins from Gram-positive bacteria. It will focus on the chemical and 3D structures of these peptides, and their interactions with receptors and membranes, structure-function relationships and possible modes of action.
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Affiliation(s)
- Jeella Z Acedo
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
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Pediocin-like bacteriocins: new perspectives on mechanism of action and immunity. Curr Genet 2017; 64:345-351. [PMID: 28983718 DOI: 10.1007/s00294-017-0757-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 01/26/2023]
Abstract
This review attempts to analyze the mechanism of action and immunity of class IIa bacteriocins. These peptides are promising alternative food preservatives and they have a great potential application in medical sciences. Class IIa bacteriocins act on the cytoplasmic membrane of Gram-positive cells dissipating the transmembrane electrical potential by forming pores. However, their toxicity and immunity mechanism remains elusive. Here we discuss the role of the mannose phosphotransferase system (man-PTS) as the receptor for class IIa bacteriocins and the influence of the membrane composition on the activity of these antimicrobial peptides. A model that is consistent with experimental results obtained by different researchers involves the non-specific binding of the bacteriocin to the negatively charged membrane of target bacteria. This step would facilitate a specific binding to the receptor protein, altering its functionality and forming an independent pore in which the bacteriocin is inserted in the membrane. An immunity protein could specifically recognize and block the pore. Bacteriocins function in bacterial ecosystems and energetic costs associated with their production are also discussed. Theoretical models based on solid experimental evidence are vital to understand bacteriocins mechanism of action and to promote new technological developments.
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Barraza DE, Ríos Colombo NS, Galván AE, Acuña L, Minahk CJ, Bellomio A, Chalón MC. New insights into enterocin CRL35: mechanism of action and immunity revealed by heterologous expression in Escherichia coli. Mol Microbiol 2017; 105:922-933. [PMID: 28692133 DOI: 10.1111/mmi.13746] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2017] [Indexed: 11/30/2022]
Abstract
The role of the class IIa bacteriocin membrane receptor protein remains unclear, and the following two different mechanisms have been proposed: the bacteriocin could interact with the receptor changing it to an open conformation or the receptor might act as an anchor allowing subsequent bacteriocin insertion and membrane disruption. Bacteriocin-producing cells synthesize an immunity protein that forms an inactive bacteriocin-receptor-immunity complex. To better understand the molecular mechanism of enterocin CRL35, the peptide was expressed as the suicidal probe EtpM-enterocin CRL35 in Escherichia coli, a naturally insensitive microorganism since it does not express the receptor. When the bacteriocin is anchored to the periplasmic face of the plasma membrane through the bitopic membrane protein, EtpM, E. coli cells depolarize and die. Moreover, co-expression of the immunity protein prevents the deleterious effect of EtpM-enterocin CRL35. The binding and anchoring of the bacteriocin to the membrane has demonstrated to be a sufficient condition for its membrane insertion. The final step of membrane disruption by EtpM-enterocin CRL35 is independent from the receptor, which means that the mannose PTS might not be involved in the pore structure. In addition, the immunity protein can protect even in the absence of the receptor.
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Affiliation(s)
- Daniela E Barraza
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI San Miguel de Tucumán, Argentina
| | - Natalia S Ríos Colombo
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI San Miguel de Tucumán, Argentina
| | - Adriana E Galván
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI San Miguel de Tucumán, Argentina
| | - Leonardo Acuña
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI San Miguel de Tucumán, Argentina
| | - Carlos J Minahk
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI San Miguel de Tucumán, Argentina
| | - Augusto Bellomio
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI San Miguel de Tucumán, Argentina
| | - Miriam C Chalón
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI San Miguel de Tucumán, Argentina
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7
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Kristiansen PE, Persson C, Fuochi V, Pedersen A, Karlsson GB, Nissen-Meyer J, Oppegård C. Nuclear Magnetic Resonance Structure and Mutational Analysis of the Lactococcin A Immunity Protein. Biochemistry 2016; 55:6250-6257. [DOI: 10.1021/acs.biochem.6b00848] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Per Eugen Kristiansen
- Department
of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O.
Box 1066, Blindern, 0316 Oslo, Norway
| | - Cecilia Persson
- Swedish
NMR Centre, University of Gothenburg, P.O. Box 465, 405 30 Gothenburg, Sweden
| | - Virginia Fuochi
- Department
of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O.
Box 1066, Blindern, 0316 Oslo, Norway
- Department
of Biomedical and Biotechnological Sciences (BIOMETEC), Microbiology
Section, University of Catania, via Androne 81, 95124 Catania, Italy
| | - Anders Pedersen
- Swedish
NMR Centre, University of Gothenburg, P.O. Box 465, 405 30 Gothenburg, Sweden
| | - Göran B. Karlsson
- Swedish
NMR Centre, University of Gothenburg, P.O. Box 465, 405 30 Gothenburg, Sweden
| | - Jon Nissen-Meyer
- Department
of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O.
Box 1066, Blindern, 0316 Oslo, Norway
| | - Camilla Oppegård
- Department
of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O.
Box 1066, Blindern, 0316 Oslo, Norway
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Ainsworth S, Stockdale S, Bottacini F, Mahony J, van Sinderen D. The Lactococcus lactis plasmidome: much learnt, yet still lots to discover. FEMS Microbiol Rev 2014; 38:1066-88. [PMID: 24861818 DOI: 10.1111/1574-6976.12074] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/17/2014] [Accepted: 05/07/2014] [Indexed: 01/20/2023] Open
Abstract
Lactococcus lactis is used extensively worldwide for the production of a variety of fermented dairy products. The ability of L. lactis to successfully grow and acidify milk has long been known to be reliant on a number of plasmid-encoded traits. The recent availability of low-cost, high-quality genome sequencing, and the quest for novel, technologically desirable characteristics, such as novel flavour development and increased stress tolerance, has led to a steady increase in the number of available lactococcal plasmid sequences. We will review both well-known and very recent discoveries regarding plasmid-encoded traits of biotechnological significance. The acquired lactococcal plasmid sequence information has in recent years progressed our understanding of the origin of lactococcal dairy starter cultures. Salient points on the acquisition and evolution of lactococcal plasmids will be discussed in this review, as well as prospects of finding novel plasmid-encoded functions.
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Affiliation(s)
- Stuart Ainsworth
- Department of Microbiology, University College Cork, Cork, Ireland
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Site-directed mutagenesis identifies the positively charged residue lysine-46 essential for the function of the immunity protein PedB. Curr Microbiol 2014; 69:423-8. [PMID: 24838664 DOI: 10.1007/s00284-014-0596-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
Abstract
The immunity proteins of pediocin-like bacteriocins possess a positively charged region which is located at the C-terminus in all three subclasses. It has been suggested that this region may be involved in directing the immunity protein to the surface of the bacterial cell membrane. The aim of this study was to determine whether the positively charged residue lysine-46 (K46) around the hydrophobic pocket played a key role for immunity activity of subgroup A immunity protein PedB. At first, heterologous expression of the immune gene pedB from Lactobacillus plantarum BM-1 rendered the sensitive Lactobacillus plantarum WQ0815 resistant to bacteriocin BM-1. Then, using site-directed mutagenesis, the residue K46 was replaced by five different amino-acid residues, including arginine (R), aspartate (D), glutamate (E), glutamine (Q), and threonine (T). Western blot analysis confirmed that all mutated pedB genes were successfully expressed in the host L. plantarum WQ0815. Bacteriocin activity assays subsequently showed that any substitution of the K46 residue significantly reduced its immunity activity. Our present results indicated that the positively charged residue K46 located near the hydrophobic pocket was essential for the functionality of the immunity protein PedB.
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The plasmid complement of Lactococcus lactis UC509.9 encodes multiple bacteriophage resistance systems. Appl Environ Microbiol 2014; 80:4341-9. [PMID: 24814781 DOI: 10.1128/aem.01070-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Lactococcus lactis subsp. cremoris strains are used globally for the production of fermented dairy products, particularly hard cheeses. Believed to be of plant origin, L. lactis strains that are used as starter cultures have undergone extensive adaptation to the dairy environment, partially through the acquisition of extrachromosomal DNA in the form of plasmids that specify technologically important phenotypic traits. Here, we present a detailed analysis of the eight plasmids of L. lactis UC509.9, an Irish dairy starter strain. Key industrial phenotypes were mapped, and genes that are typically associated with lactococcal plasmids were identified. Four distinct, plasmid-borne bacteriophage resistance systems were identified, including two abortive infection systems, AbiB and AbiD1, thereby supporting the observed phage resistance of L. lactis UC509.9. AbiB escape mutants were generated for phage sk1, which were found to carry mutations in orf6, which encodes the major capsid protein of this phage.
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Immunity to the Staphylococcus aureus leaderless four-peptide bacteriocin aureocin A70 is conferred by AurI, an integral membrane protein. Res Microbiol 2014; 165:50-9. [DOI: 10.1016/j.resmic.2013.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/22/2013] [Indexed: 11/22/2022]
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Nishie M, Nagao JI, Sonomoto K. Antibacterial peptides "bacteriocins": an overview of their diverse characteristics and applications. Biocontrol Sci 2012; 17:1-16. [PMID: 22451427 DOI: 10.4265/bio.17.1] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Bacteriocins are ribosomally synthesized antibacterial peptides produced by bacteria that inhibit the growth of similar or closely related bacterial strains. A number of bacteriocins from a wide variety of bacteria have been discovered, and their diverse structures have been reported. Growing evidence suggests that bacteriocins have diverse structures, modes of action, mechanisms of biosynthesis and self-immunity, and gene regulation. Bacteriocins are considered as an attractive compound in food and pharmaceutical industries to prevent food spoilage and pathogenic bacterial growth. Furthermore, elucidation of their biosynthesis has led to the use of bacteriocin-controlled gene-expression systems and the biosynthetic enzymes of lantibiotics, a class of bacteriocins, as tools to design novel peptides. In this review, we summarize and discuss currently known information on bacteriocins produced by Gram-positive bacteria and their applications.
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Affiliation(s)
- Mami Nishie
- Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
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Halami PM. Isolation and characterization of a nitrosoguanidine-induced Enterococcus faecium MTCC 5153 mutant defective in enterocin biosynthesis. Res Microbiol 2010; 161:590-4. [DOI: 10.1016/j.resmic.2010.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 05/21/2010] [Accepted: 05/21/2010] [Indexed: 10/19/2022]
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The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes. BMC STRUCTURAL BIOLOGY 2009; 9:75. [PMID: 20017931 PMCID: PMC2806384 DOI: 10.1186/1472-6807-9-75] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 12/17/2009] [Indexed: 11/10/2022]
Abstract
Background Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall structurally into three different classes, I, II, III, with class IIa being pediocin-like single entities and class IIb being two-peptide bacteriocins. Self-protective cognate immunity proteins are usually co-transcribed with these toxins. Several examples of cognates for IIa have already been solved structurally. Streptococcus pyogenes, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable. Results We have solved the crystal structure of the gene-product of locus Spy_2152 from S. pyogenes, (PDB:2fu2), and found it to comprise an anti-parallel four-helix bundle that is structurally similar to other bacteriocin immunity proteins. Sequence analyses indicate this protein to be a possible immunity protein protective against class IIa or IIb bacteriocins. However, given that S. pyogenes appears to lack any IIa pediocin-like proteins but does possess class IIb bacteriocins, we suggest this protein confers immunity to IIb-like peptides. Conclusions Combined structural, genomic and proteomic analyses have allowed the identification and in silico characterization of a new putative immunity protein from S. pyogenes, possibly the first structure of an immunity protein protective against potential class IIb two-peptide bacteriocins. We have named the two pairs of putative bacteriocins found in S. pyogenes pyogenecin 1, 2, 3 and 4.
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Attia AS, Sedillo JL, Hoopman TC, Liu W, Liu L, Brautigam CA, Hansen EJ. Identification of a bacteriocin and its cognate immunity factor expressed by Moraxella catarrhalis. BMC Microbiol 2009; 9:207. [PMID: 19781080 PMCID: PMC2761928 DOI: 10.1186/1471-2180-9-207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 09/25/2009] [Indexed: 12/23/2022] Open
Abstract
Background Bacteriocins are antimicrobial proteins and peptides ribosomally synthesized by some bacteria which can effect both intraspecies and interspecies killing. Results Moraxella catarrhalis strain E22 containing plasmid pLQ510 was shown to inhibit the growth of M. catarrhalis strain O35E. Two genes (mcbA and mcbB) in pLQ510 encoded proteins predicted to be involved in the secretion of a bacteriocin. Immediately downstream from these two genes, a very short ORF (mcbC) encoded a protein which had some homology to double-glycine bacteriocins produced by other bacteria. A second very short ORF (mcbI) immediately downstream from mcbC encoded a protein which had no significant similarity to other proteins in the databases. Cloning and expression of the mcbI gene in M. catarrhalis O35E indicated that this gene encoded the cognate immunity factor. Reverse transcriptase-PCR was used to show that the mcbA, mcbB, mcbC, and mcbI ORFs were transcriptionally linked. This four-gene cluster was subsequently shown to be present in the chromosome of several M. catarrhalis strains including O12E. Inactivation of the mcbA, mcbB, or mcbC ORFs in M. catarrhalis O12E eliminated the ability of this strain to inhibit the growth of M. catarrhalis O35E. In co-culture experiments involving a M. catarrhalis strain containing the mcbABCI locus and one which lacked this locus, the former strain became the predominant member of the culture after overnight growth in broth. Conclusion This is the first description of a bacteriocin and its cognate immunity factor produced by M. catarrhalis. The killing activity of the McbC protein raises the possibility that it might serve to lyse other M. catarrhalis strains that lack the mcbABCI locus, thereby making their DNA available for lateral gene transfer.
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Affiliation(s)
- Ahmed S Attia
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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16
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Jeon HJ, Noda M, Matoba Y, Kumagai T, Sugiyama M. Crystal structure and mutagenic analysis of a bacteriocin immunity protein, Mun-im. Biochem Biophys Res Commun 2008; 378:574-8. [PMID: 19061861 DOI: 10.1016/j.bbrc.2008.11.093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 11/18/2008] [Indexed: 10/21/2022]
Abstract
Bacteriocin-producing lactic acid bacteria (LAB) possess a self-protection factor, which is generally called an immunity protein. In this study, we determine the crystal structure of an immunity protein, designated Mun-im, which was classified into subgroup B immunity proteins for class IIa bacteriocins. The Mun-im protein takes a left-turning antiparallel four-helix bundle structure with the flexible N- and C-terminal parts. Although the amino acid sequences of the subgroup B immunity proteins are distinguished from those of the subgroup A, the core structure of Mun-im is well-superimposed with that of the subgroup A immunity protein, EntA-im, and the C-terminus of both proteins is flexible. However, the C-terminus of Mun-im is obviously shorter than that of the subgroup A. We found through mutagenic study of Mun-im that the C-terminus and the K86 residue on the helix 4 in the immunity protein molecule are important for expression of the immunity activity on the subgroup B immunity proteins.
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Affiliation(s)
- Hyung Joon Jeon
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
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Martin-Visscher LA, Sprules T, Gursky LJ, Vederas JC. Nuclear magnetic resonance solution structure of PisI, a group B immunity protein that provides protection against the type IIa bacteriocin piscicolin 126, PisA. Biochemistry 2008; 47:6427-36. [PMID: 18500825 DOI: 10.1021/bi8004076] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lactic acid bacteria produce and secrete bacteriocins. These bacteriocins are potent antimicrobial peptides that are active against other closely related bacteria. As a means of self-protection, producer organisms also express immunity proteins. Immunity proteins are generally located on the same genetic locus and are cotranscribed with the bacteriocin. Although some cross immunity between bacteriocins has been observed, immunity proteins are typically highly specific. Immunity proteins for the type IIa bacteriocins range from 81 to 115 amino acids in length and display substantial variation in their sequences. Nonetheless, such immunity proteins have been classified into three groupings (groups A, B, and C) according to sequence homology. The structures of a group C (ImB2) and two group A (EntA-im and PedB) immunity proteins have previously been reported. We herein report the nuclear magnetic resonance solution structure of the remaining class of the type IIa immunity proteins. PisI, a 98-amino acid protein, is a group B immunity protein conferring immunity against piscicolin 126 (PisA). Like ImB2, EntA-im, and PedB, PisI folds into a globular protein in aqueous solution and contains an antiparallel four-helix bundle. Compared to ImB2 and EntA-im, PisI has a substantially longer and more flexible N-terminus, but a shorter C-terminus. No direct interaction between the bacteriocin and immunity protein is observed by NMR in either aqueous or membrane mimicking environments. This further suggests that the mechanism that mediates immunity is not due to a direct bacteriocin-immunity protein interaction but rather is receptor-mediated. It has now been confirmed that the four-helix bundle is indeed a structural motif among the type IIa immunity proteins.
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High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins. BMC STRUCTURAL BIOLOGY 2007; 7:35. [PMID: 17537233 PMCID: PMC1904221 DOI: 10.1186/1472-6807-7-35] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 05/30/2007] [Indexed: 11/10/2022]
Abstract
BACKGROUND Pediocin-like bacteriocins, ribosomally-synthesized antimicrobial peptides, are generally coexpressed with cognate immunity proteins in order to protect the bacteriocin-producer from its own bacteriocin. As a step for understanding the mode of action of immunity proteins, we determined the crystal structure of PedB, a pediocin-like immunity protein conferring immunity to pediocin PP-1. RESULTS The 1.6 A crystal structure of PedB reveals that PedB consists of an antiparallel four-helix bundle with a flexible C-terminal end. PedB shows structural similarity to an immunity protein against enterocin A (EntA-im) but some disparity to an immunity protein against carnobacteriocin B2 (ImB2) in both the C-terminal conformation and the local structure constructed by alpha3, alpha4, and their connecting loop. Structure-inspired mutational studies reveal that deletion of the last seven residues of the C-terminus of PedB almost abolished its immunity activity. CONCLUSION The fact that PedB, EntA-im, and ImB2 share a four-helix bundle structure strongly suggests the structural conservation of this motif in the pediocin-like immunity proteins. The significant difference in the core structure and the C-terminal conformation provides a structural basis for the classification of pediocin-like immunity proteins. Our mutational study using C-terminal-shortened PedBs and the investigation of primary sequence of the C-terminal region, propose that several polar or charged residues in the extreme C-terminus of PedB which is crucial for the immunity are involved in the specific recognition of pediocin PP-1.
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Soliman W, Bhattacharjee S, Kaur K. Molecular dynamics simulation study of interaction between a class IIa bacteriocin and its immunity protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1002-13. [PMID: 17586105 DOI: 10.1016/j.bbapap.2007.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 04/18/2007] [Accepted: 05/15/2007] [Indexed: 11/17/2022]
Abstract
Molecular dynamics (MD) simulations of carnobacteriocin B2 (CbnB2), a structurally well-characterized class IIa bacteriocin, and its immunity protein (ImB2) in lipid bilayer environment have been conducted to explore the interaction between them. Six 30-ns simulations were conducted in DPPC or POPG bilayer systems. In these simulations, ImB2 was placed in the aqueous layer with different orientations facing CbnB2 to sample all the faces of ImB2. The MD results indicate that (i) while CbnB2 remained embedded in the bilayer, it tends to move toward the interface, and (ii) the presence of CbnB2 in the DPPC bilayer attracts ImB2 toward the bilayer. In one of the orientations in DPPC bilayer system (simulation 1), ImB2 penetrates the bilayer and interacts with CbnB2 by ion-pair interaction. At several instances toward the later half of the simulation (15-30 ns), ImB2 and CbnB2 were found to form salt-bridge between Arg95 of ImB2 and Glu24 of CbnB2. Simulation in POPG bilayer displayed strong interaction between the positively charged ImB2 and the negatively charged polar head groups of the POPG molecules at the lipid-water interface. However, ImB2 was not able to penetrate the bilayer thereby preventing any interaction between ImB2 and CbnB2.
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Affiliation(s)
- Wael Soliman
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2N8
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Van Reenen CA, Van Zyl WH, Dicks LMT. Expression of the immunity protein of plantaricin 423, produced by Lactobacillus plantarum 423, and analysis of the plasmid encoding the bacteriocin. Appl Environ Microbiol 2006; 72:7644-51. [PMID: 17056693 PMCID: PMC1694273 DOI: 10.1128/aem.01428-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plantaricin 423 is a class IIa bacteriocin produced by Lactobacillus plantarum isolated from sorghum beer. It has been previously determined that plantaricin 423 is encoded by a plasmid designated pPLA4, which is now completely sequenced. The plantaricin 423 operon shares high sequence similarity with the operons of coagulin, pediocin PA-1, and pediocin AcH, with small differences in the DNA sequence encoding the mature bacteriocin peptide and the immunity protein. Apart from the bacteriocin operon, no significant sequence similarity could be detected between the DNA or translated sequence of pPLA4 and the available DNA or translated sequences of the plasmids encoding pediocin AcH, pediocin PA-1, and coagulin, possibly indicating a different origin. In addition to the bacteriocin operon, sequence analysis of pPLA4 revealed the presence of two open reading frames (ORFs). ORF1 encodes a putative mobilization (Mob) protein that is homologous to the pMV158 superfamily of mobilization proteins. Highest sequence similarity occurred between this protein and the Mob protein of L. plantarum NCDO 1088. ORF2 encodes a putative replication protein that revealed low sequence similarity to replication proteins of plasmids pLME300 from Lactobacillus fermentum and pYIT356 from Lactobacillus casei. The immunity protein of plantaricin 423 contains 109 amino acids. Although plantaricin 423 shares high sequence similarity with the pediocin PA-1 operon, no cross-reactivity was recorded between the immunity proteins of plantaricin 423 and pediocin PA-1.
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Affiliation(s)
- C A Van Reenen
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
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Drider D, Fimland G, Héchard Y, McMullen LM, Prévost H. The continuing story of class IIa bacteriocins. Microbiol Mol Biol Rev 2006; 70:564-82. [PMID: 16760314 PMCID: PMC1489543 DOI: 10.1128/mmbr.00016-05] [Citation(s) in RCA: 430] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many bacteria produce antimicrobial peptides, which are also referred to as peptide bacteriocins. The class IIa bacteriocins, often designated pediocin-like bacteriocins, constitute the most dominant group of antimicrobial peptides produced by lactic acid bacteria. The bacteriocins that belong to this class are structurally related and kill target cells by membrane permeabilization. Despite their structural similarity, class IIa bacteriocins display different target cell specificities. In the search for new antibiotic substances, the class IIa bacteriocins have been identified as promising new candidates and have thus received much attention. They kill some pathogenic bacteria (e.g., Listeria) with high efficiency, and they constitute a good model system for structure-function analyses of antimicrobial peptides in general. This review focuses on class IIa bacteriocins, especially on their structure, function, mode of action, biosynthesis, bacteriocin immunity, and current food applications. The genetics and biosynthesis of class IIa bacteriocins are well understood. The bacteriocins are ribosomally synthesized with an N-terminal leader sequence, which is cleaved off upon secretion. After externalization, the class IIa bacteriocins attach to potential target cells and, through electrostatic and hydrophobic interactions, subsequently permeabilize the cell membrane of sensitive cells. Recent observations suggest that a chiral interaction and possibly the presence of a mannose permease protein on the target cell surface are required for a bacteria to be sensitive to class IIa bacteriocins. There is also substantial evidence that the C-terminal half penetrates into the target cell membrane, and it plays an important role in determining the target cell specificity of these bacteriocins. Immunity proteins protect the bacteriocin producer from the bacteriocin it secretes. The three-dimensional structures of two class IIa immunity proteins have been determined, and it has been shown that the C-terminal halves of these cytosolic four-helix bundle proteins specify which class IIa bacteriocin they protect against.
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Affiliation(s)
- Djamel Drider
- Laboratoire de Microbiologie Alimentaire et Industrielle, ENITIAA, Rue de la Géraudière, BP82225, 44322 Nantes Cedex, France.
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Fimland G, Pirneskoski J, Kaewsrichan J, Jutila A, Kristiansen PE, Kinnunen PKJ, Nissen-Meyer J. Mutational analysis and membrane-interactions of the β-sheet-like N-terminal domain of the pediocin-like antimicrobial peptide sakacin P. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1132-40. [PMID: 16762606 DOI: 10.1016/j.bbapap.2006.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Revised: 04/03/2006] [Accepted: 04/03/2006] [Indexed: 11/16/2022]
Abstract
To gain insight into how the N-terminal three-stranded beta-sheet-like domain in pediocin-like antimicrobial peptides positions itself on membranes, residues in the well-conserved (Y)YGNGV-motif in the domain were substituted and the effect of the substitutions on antimicrobial activity and binding of peptides to liposomes was determined. Peptide-liposome interactions were detected by measuring tryptophan-fluorescence upon exposing liposomes to peptides in which a tryptophan residue had been introduced in the N-terminal domain. The results revealed that the N-terminal domain associates readily with anionic liposomes, but not with neutral liposomes. The electrostatic interactions between peptides and liposomes facilitated the penetration of some of the peptide residues into the liposomes. Measuring the antimicrobial activity of the mutated peptides revealed that the Tyr2Leu and Tyr3Leu mutations resulted in about a 10-fold reduction in activity, whereas the Tyr2Trp, Tyr2Phe, Tyr3Trp and Tyr3Phe mutations were tolerated fairly well, especially the mutations in position 3. The Val7Ile mutation did not have a marked detrimental effect on the activity. The Gly6Ala mutation was highly detrimental, consistent with Gly6 being in one of the turns in the beta-sheet-like N-terminal domain, whereas the Gly4Ala mutation was tolerated fairly well. All mutations involving Asn5, including the conservative mutations Asn5Gln and Asn5Asp, were very deleterious. Thus, both the polar amide group on the side chain of Asn5 and its exact position in space were crucial for the peptides to be fully active. Taken together, the results are consistent with Val7 positioning itself in the hydrophobic core of target membranes, thus forcing most of the other residues in the N-terminal domain into the membrane interface region: Tyr3 and Asn5 in the lower half with their side chains pointing downward and approaching the hydrophobic core, Tyr2, Gly4 and His8 and 12 in the upper half, Lys1 near the middle of the interface region, and the side chain of Lys11 pointing out toward the membrane surface.
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Affiliation(s)
- Gunnar Fimland
- Department of Molecular Biosciences, University of Oslo, Post box 1041, Blindern, 0316 Oslo, Norway.
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Kim IK, Kim MK, Yim HS, Cha SS, Kang SO. Crystallization and preliminary X-ray crystallographic analysis of the pediocin immunity protein (PedB) from Pediococcus pentosaceus at 1.35 A resolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1751:205-8. [PMID: 16019271 DOI: 10.1016/j.bbapap.2005.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 05/31/2005] [Accepted: 06/01/2005] [Indexed: 10/25/2022]
Abstract
PedB, a bacterial immunity protein conferring immunity to a newly identified pediocin (pediocin PP-1), was crystallized by the hanging-drop vapor diffusion method at 296 K. A 1.35 A data set has been collected from a single crystal at 100 K using synchrotron-radiation source. The PedB crystals belong to the hexagonal space group P6(2) or P6(4), with unit cell parameters a = b = 62.2, c = 39.9 A. Analysis of the packing density shows that the asymmetric unit probably contains one molecule with a solvent content of 33.8%.
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Affiliation(s)
- In-Kwon Kim
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
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