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Chakraborty N, Das BK, Bera AK, Borah S, Mohanty D, Yadav AK, Kumar J, Koushlesh SK, Chanu TN, Panda SP, Vallangi R. Co-Prevalence of Virulence and Pathogenic Potential in Multiple Antibiotic Resistant Aeromonas spp. from Diseased Fishes with In Silico Insight on the Virulent Protein Network. Life (Basel) 2022; 12:life12121979. [PMID: 36556344 PMCID: PMC9781969 DOI: 10.3390/life12121979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Aeromonas species exhibit widespread presence in food, poultry, and aquaculture. They are major multi-drug-resistant fish pathogens. This study aims to identify Aeromonas species harbouring virulence genes aerolysin, flagellin, and lipase from diseased fishes of Assam wetlands with association with antibiotic resistance and in vivo pathogenicity. One hundred and thirty-four Aeromonas strains were isolated and thirty representative species identified using genus-specific 16S rRNA gene amplification. A. veronii was most prevalent (53.7%) followed by A. hydrophila (40.2%), A. caviae (4.47%), and A. dhakensis (1.49%). Ninety percent (90%) of strains harboured at least one of the studied virulence genes: aerA (73.3%), lip (46.6%), and flaA (26.6%). The highest multiple antibiotic resistance (MAR) index 0.8 corresponded to A. hydrophila DBTNE1 (MZ723069), containing all the studied genes. The lowest LD50 values (1.6 × 106 CFU/fish) corresponded to isolates having both aerA and lip. β-lactams showed utmost resistance and lowest for aminoglycosides. There was a significant (p < 0.05) Pearson chi-square test of association between the occurrence of virulence and antibiotic resistance. The in silico protein−protein interaction revealed important drug targets, such as σ28 transcription factor, aminoacyl-tRNA synthetase, and diacylglycerol kinase, with significant (p < 0.05) enrichment. This study suggests that fish-isolate Aeromonas strains represent potential threat to aquaculture with subsequent risk of transferring antibiotic resistance to human pathogens.
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Affiliation(s)
- Nabanita Chakraborty
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
| | - Basanta Kumar Das
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
- Correspondence: ; Tel.: +91-033-2592-1190; Fax: +91-033-2592-0388
| | - Asit Kumar Bera
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
| | - Simanku Borah
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
| | - Debasmita Mohanty
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
| | - Anil Kumar Yadav
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
| | - Jeetendra Kumar
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Prayagraj 211002, India
| | | | | | - Soumya Prasad Panda
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
| | - Ravali Vallangi
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
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Luo Q, Kong L, Dong J, Zhang T, Wang H, Zhang R, Lu Q, Chen H, Shao H, Jin M. Protection of chickens against fowl cholera by supernatant proteins of Pasteurella multocida cultured in an iron-restricted medium. Avian Pathol 2019; 48:221-229. [PMID: 30640510 DOI: 10.1080/03079457.2019.1568390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pasteurella multocida (P. multocida), a causative agent of fowl cholera, is an important pathogen in the poultry industry. In the present study, we found that the inactivated vaccine of P. multocida grown in an iron-restricted medium provided better protection than that grown in normal medium. Thus, we adopted a comparative proteomics approach, by using two-dimensional gel electrophoresis (2-DE), coupled with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/TOF MS), to profile the supernatant proteins associated with P. multocida under both conditions. Eleven upregulated proteins were identified, including aspartate ammonia-lyase (AspA), diacylglycerol kinase (DgK), 30S ribosomal protein S6 (RpsF), and eight outer membrane proteins (OMPs). To further characterize the three novel supernatant proteins identified under iron-restricted conditions, the AspA, DgK and RpsF proteins were expressed and purified, and used as immunogens to vaccinate chickens. The results showed that AspA, DgK and RpsF proteins induced 80.0%, 66.7%, and 80.0% immunity, respectively. These data indicate that the three novel proteins identified in the supernatant of the culture media might play important roles in the survival of bacteria under iron-restricted conditions, and thus protect chickens against P. multocida. These findings also suggest that the proteins identified can be used as subunit vaccines.
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Affiliation(s)
- Qingping Luo
- a State Key Laboratory of Agricultural Microbiology , Huazhong Agricultural University , Wuhan , People's Republic of China.,b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Lingyan Kong
- b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Jun Dong
- b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Tengfei Zhang
- b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China.,c Hubei Engineering Technology Center of Veterinary Diagnostic products , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Honglin Wang
- b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China.,c Hubei Engineering Technology Center of Veterinary Diagnostic products , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Rongrong Zhang
- b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China.,c Hubei Engineering Technology Center of Veterinary Diagnostic products , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Qin Lu
- b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China.,c Hubei Engineering Technology Center of Veterinary Diagnostic products , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Huanchun Chen
- a State Key Laboratory of Agricultural Microbiology , Huazhong Agricultural University , Wuhan , People's Republic of China
| | - Huabin Shao
- b Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China.,c Hubei Engineering Technology Center of Veterinary Diagnostic products , Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences , Wuhan , People's Republic of China
| | - Meilin Jin
- a State Key Laboratory of Agricultural Microbiology , Huazhong Agricultural University , Wuhan , People's Republic of China
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3
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Kawakami N, Fujisaki S. Undecaprenyl phosphate metabolism in Gram-negative and Gram-positive bacteria. Biosci Biotechnol Biochem 2018; 82:940-946. [DOI: 10.1080/09168451.2017.1401915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Undecaprenyl phosphate (UP) is essential for the biosynthesis of bacterial extracellular polysaccharides. UP is produced by the dephosphorylation of undecaprenyl diphosphate (UPP) via de novo synthetic and recycling pathways. Gram-positive bacteria contain remarkable amounts of undecaprenol (UOH), which is phosphorylated to UP, although UOH has not been found in Gram-negative bacteria. Here, current knowledge about UPP phosphatase and UOH kinase is reviewed. Dephosphorylation of UPP is catalyzed by a BacA homologue and a type-2 phosphatidic acid phosphatase (PAP2) homologue. The presence of one of these UPP phosphatases is essential for bacterial growth. The catalytic center of both types of enzyme is located outside the cytoplasmic membrane. In Gram-positive bacteria, an enzyme homologous to DgkA, which is the diacylglycerol kinase of Escherichia coli, catalyzes UOH phosphorylation. The possible role of UOH and the significance of systematic construction of Staphylococcus aureus mutants to determine UP metabolism are discussed.
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Affiliation(s)
- Naoki Kawakami
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Shingo Fujisaki
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
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Huang LY, Wang SC, Cheng TJR, Wong CH. Undecaprenyl Phosphate Phosphatase Activity of Undecaprenol Kinase Regulates the Lipid Pool in Gram-Positive Bacteria. Biochemistry 2017; 56:5417-5427. [PMID: 28872301 DOI: 10.1021/acs.biochem.7b00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria cell walls contain many repeating glycan structures, such as peptidoglycans, lipopolysaccharides, teichoic acids, and capsular polysaccharides. Their synthesis starts in the cytosol, and they are constructed from a glycan lipid carrier, undecaprenyl phosphate (C55P), which is essential for cell growth and survival. The lipid derivative undecaprenol (C55OH) is predominant in many Gram-positive bacteria but has not been detected in Gram-negative bacteria; its origin and role have thus remained unknown. Recently, a homologue of diacylglycerol kinase (DgkA) in Escherichia coli (E. coli) was demonstrated to be an undecaprenol kinase (UK) in the Gram-positive bacterium Streptococcus mutans (S. mutans). In this study, we found that S. mutans UK was not only an undecaprenol kinase but also a Mg-ADP-dependent undecaprenyl phosphate phosphatase (UpP), catalyzing the hydrolysis of C55P to C55OH and a free inorganic phosphate. Furthermore, the naturally undetectable C55OH was observed in E. coli cells expressing S. mutans dgkA, supporting the phosphatase activity of UK/UpP in vivo. These two activities were indispensable to each other and utilized identical essential residues binding to their substrates, suggesting that both activities share the same active site and might involve a direct phosphoryl transfer mechanism. This study revealed a unique membrane enzyme displaying bifunctional activities determined by substrate binding and C55OH production. The reciprocal conversion of C55P and the undecaprenol pool efficiently regulate cell wall synthesis, especially in Gram-positive bacteria.
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Affiliation(s)
- Lin-Ya Huang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
| | - Shih-Chi Wang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
| | | | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
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Abstract
Oral colonising bacteria are highly adapted to the various environmental niches harboured within the mouth, whether that means while contributing to one of the major oral diseases of caries, pulp infections, or gingival/periodontal disease or as part of a commensal lifestyle. Key to these infections is the ability to adhere to surfaces via a range of specialised adhesins targeted at both salivary and epithelial proteins, their glycans and to form biofilm. They must also resist the various physical stressors they are subjected to, including pH and oxidative stress. Possibly most strikingly, they have developed the ability to harvest both nutrient sources provided by the diet and those derived from the host, such as protein and surface glycans. We have attempted to review recent developments that have revealed much about the molecular mechanisms at work in shaping the physiology of oral bacteria and how we might use this information to design and implement new treatment strategies.
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6
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Manat G, Roure S, Auger R, Bouhss A, Barreteau H, Mengin-Lecreulx D, Touzé T. Deciphering the metabolism of undecaprenyl-phosphate: the bacterial cell-wall unit carrier at the membrane frontier. Microb Drug Resist 2014; 20:199-214. [PMID: 24799078 DOI: 10.1089/mdr.2014.0035] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
During the biogenesis of bacterial cell-wall polysaccharides, such as peptidoglycan, cytoplasmic synthesized precursors should be trafficked across the plasma membrane. This essential process requires a dedicated lipid, undecaprenyl-phosphate that is used as a glycan lipid carrier. The sugar is linked to the lipid carrier at the inner face of the membrane and is translocated toward the periplasm, where the glycan moiety is transferred to the growing polymer. Undecaprenyl-phosphate originates from the dephosphorylation of its precursor undecaprenyl-diphosphate, with itself generated by de novo synthesis or by recycling after the final glycan transfer. Undecaprenyl-diphosphate is de novo synthesized by the cytosolic cis-prenyltransferase undecaprenyl-diphosphate synthase, which has been structurally and mechanistically characterized in great detail highlighting the condensation process. In contrast, the next step toward the formation of the lipid carrier, the dephosphorylation step, which has been overlooked for many years, has only started revealing surprising features. In contrast to the previous step, two unrelated families of integral membrane proteins exhibit undecaprenyl-diphosphate phosphatase activity: BacA and members of the phosphatidic acid phosphatase type 2 super-family, raising the question of the significance of this multiplicity. Moreover, these enzymes establish an unexpected link between the synthesis of bacterial cell-wall polymers and other biological processes. In the present review, the current knowledge in the field of the bacterial lipid carrier, its mechanism of action, biogenesis, recycling, regulation, and future perspective works are presented.
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Affiliation(s)
- Guillaume Manat
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Université Paris Sud , Orsay Cedex, France
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A novel gene involved in the survival of Streptococcus mutans under stress conditions. Appl Environ Microbiol 2013; 80:97-103. [PMID: 24123744 DOI: 10.1128/aem.02549-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Streptococcus mutans mutant defective in aciduricity was constructed by random-insertion mutagenesis. Sequence analysis of the mutant revealed a mutation in gidA, which is known to be involved in tRNA modification in Streptococcus pyogenes. Complementation of gidA by S. pyogenes gidA recovered the acid tolerance of S. mutans. Although the gidA-inactivated S. pyogenes mutant exhibited significantly reduced expression of multiple extracellular virulence proteins, the S. mutans mutant did not. On the other hand, the gidA mutant of S. mutans showed reduced ability to withstand exposure to other stress conditions (high osmotic pressure, high temperature, and bacitracin stress) besides an acidic environment. In addition, loss of GidA decreased the capacity for glucose-dependent biofilm formation by over 50%. This study revealed that gidA plays critical roles in the survival of S. mutans under stress conditions, including lower pH.
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Abstract
Prokaryotic diacylglycerol kinase (DAGK) and undecaprenol kinase (UDPK) are the lone members of a family of multispan membrane enzymes that are very small, lack relationships to any other family of proteins-including water soluble kinases-and exhibit an unusual structure and active site architecture. Escherichia coli DAGK plays an important role in recycling diacylglycerol produced as a by-product of biosynthesis of molecules located in the periplasmic space. UDPK seems to play an analogous role in gram-positive bacteria, where its importance is evident because UDPK is essential for biofilm formation by the oral pathogen Streptococcus mutans. DAGK has also long served as a model system for studies of membrane protein biocatalysis, folding, stability, and structure. This review explores our current understanding of the microbial physiology, enzymology, structural biology, and folding of the prokaryotic DAGK family, which is based on over 40 years of studies.
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Affiliation(s)
- Wade D Van Horn
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
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Shibata Y, Kawada-Matsuo M, Shirai Y, Saito N, Li D, Yamashita Y. Streptococcus mutans diacylglycerol kinase homologue: a potential target for anti-caries chemotherapy. J Med Microbiol 2011; 60:625-630. [DOI: 10.1099/jmm.0.026070-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yukie Shibata
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Miki Kawada-Matsuo
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | | | - Naoaki Saito
- Biosignal Research Center, Kobe University, Kobe, Japan
| | - Dan Li
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Yoshihisa Yamashita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
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Lahiri S, Brehs M, Olschewski D, Becker CFW. Total Chemical Synthesis of an Integral Membrane Enzyme: Diacylglycerol Kinase fromEscherichia coli. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006686] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Lahiri S, Brehs M, Olschewski D, Becker CFW. Total chemical synthesis of an integral membrane enzyme: diacylglycerol kinase from Escherichia coli. Angew Chem Int Ed Engl 2011; 50:3988-92. [PMID: 21433227 DOI: 10.1002/anie.201006686] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 02/14/2011] [Indexed: 12/17/2022]
Affiliation(s)
- Sunanda Lahiri
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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12
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Kitagawa N, Shiota S, Shibata Y, Takeshita T, Yamashita Y. Characterization of MbrC involved in bacitracin resistance in Streptococcus mutans. FEMS Microbiol Lett 2011; 318:61-7. [PMID: 21306428 DOI: 10.1111/j.1574-6968.2011.02238.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Streptococcus mutans, a major etiological agent of dental caries, is resistant to bacitracin. Microarray analysis revealed that mbrA and mbrB, encoding a putative ATP-binding cassette transporter, are prominently induced in the presence of bacitracin. On the basis of the latest report that MbrC, a putative response regulator in a two-component signaling system, binds the promoter region of mbrA and thus regulates its transcription, we cut into the mechanism by generating a mutant MbrC (D(54) N-MbrC) that substituted asparagine for aspartate at position 54, the predicted phosphorylation site. MbrC, but not the mutant D(54) N-MbrC, showed affinity for a DNA probe that contained the hypothetical mbrA promoter sequence. Furthermore, we introduced a point mutation (D(54) N-MbrC) into UA159; this mutant strain exhibited neither mbrA induction nor resistance in the presence of bacitracin. These data suggest that the aspartate residue at position 54 of MbrC is a promising candidate for phosphorylation in a bacitracin-sensing system and indispensable for S. mutans bacitracin resistance.
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Affiliation(s)
- Norio Kitagawa
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
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Abstract
Since its discovery in 1924 by J Clarke, Streptococcus mutans has been the focus of rigorous research efforts due to its involvement in caries initiation and progression. Its ability to ferment a range of dietary carbohydrates can rapidly drop the external environmental pH, thereby making dental plaque inhabitable to many competing species and can ultimately lead to tooth decay. Acid production by this oral pathogen would prove suicidal if not for its remarkable ability to withstand the acid onslaught by utilizing a wide variety of highly evolved acid-tolerance mechanisms. The elucidation of these mechanisms will be discussed, serving as the focus of this review.
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Affiliation(s)
- Robert Matsui
- Room 449A Faculty of Dentistry, University of Toronto, 124 Edward St., Toronto, ON, M5G 1G6, Canada, Tel.: +1 416 979 4917 ext. 4592, Fax: +1 416 978 4936
| | - Dennis Cvitkovitch
- Room 449A Faculty of Dentistry, University of Toronto, 124 Edward St., Toronto, ON, M5G 1G6, Canada, Tel.: +1 416 979 4917 ext. 4592, Fax: +1 416 978 4936
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Van Horn WD, Beel AJ, Kang C, Sanders CR. The impact of window functions on NMR-based paramagnetic relaxation enhancement measurements in membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:140-9. [PMID: 19751702 DOI: 10.1016/j.bbamem.2009.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 08/25/2009] [Accepted: 08/31/2009] [Indexed: 11/24/2022]
Abstract
Though challenging, solution NMR spectroscopy allows fundamental interrogation of the structure and dynamics of membrane proteins. One major technical hurdle in studies of helical membrane proteins by NMR is the difficulty of obtaining sufficient long range NOEs to determine tertiary structure. For this reason, long range distance information is sometimes sought through measurement of paramagnetic relaxation enhancements (PRE) of NMR nuclei as a function of distance from an introduced paramagnetic probe. Current PRE interpretation is based on the assumption of Lorentzian resonance lineshapes. However, in order to optimize spectral resolution, modern multidimensional NMR spectra are almost always subjected to resolution-enhancement, leading to distortions in the Lorentizian peak shape. Here it is shown that when PREs are derived using peak intensities (i.e., peak height) and linewidths from both real and simulated spectra that were produced using a wide range of apodization/window functions, that there is little variation in the distances determined (<1 A at the extremes). This indicates that the high degree of resolution enhancement required to obtain well-resolved spectra from helical membrane proteins is compatible with the use of PRE data as a source of distance restraints. While these conclusions are particularly important for helical membrane proteins, they are generally applicable to all PRE measurements made using resolution-enhanced data.
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Affiliation(s)
- Wade D Van Horn
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-8725, USA
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Van Horn WD, Kim HJ, Ellis CD, Hadziselimovic A, Sulistijo ES, Karra MD, Tian C, Sönnichsen FD, Sanders CR. Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase. Science 2009; 324:1726-9. [PMID: 19556511 PMCID: PMC2764269 DOI: 10.1126/science.1171716] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Escherichia coli diacylglycerol kinase (DAGK) represents a family of integral membrane enzymes that is unrelated to all other phosphotransferases. We have determined the three-dimensional structure of the DAGK homotrimer with the use of solution nuclear magnetic resonance. The third transmembrane helix from each subunit is domain-swapped with the first and second transmembrane segments from an adjacent subunit. Each of DAGK's three active sites resembles a portico. The cornice of the portico appears to be the determinant of DAGK's lipid substrate specificity and overhangs the site of phosphoryl transfer near the water-membrane interface. Mutations to cysteine that caused severe misfolding were located in or near the active site, indicating a high degree of overlap between sites responsible for folding and for catalysis.
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Affiliation(s)
- Wade D. Van Horn
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Hak-Jun Kim
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
- Korea Polar Research Institute, Incheon, 406-840, Korea
| | - Charles D. Ellis
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Arina Hadziselimovic
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Endah S. Sulistijo
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Murthy D. Karra
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Changlin Tian
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Frank D. Sönnichsen
- Otto Diels Institute for Organic Chemistry, Christian Albrechts University of Kiel, Germany
| | - Charles R. Sanders
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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