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Hirano Y, Kimura Y, Suzuki H, Miki K, Wang ZY. Structure Analysis and Comparative Characterization of the Cytochrome c′ and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum. Biochemistry 2012; 51:6556-67. [DOI: 10.1021/bi3005522] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Hirano
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
- Department of Chemistry, Graduate
School of Science, Kyoto University, Sakyo-ku,
Kyoto 606-8502, Japan
| | - Yukihiro Kimura
- Organization
of Advanced Science
and Technology, Kobe University, Nada,
Kobe 657-8501, Japan
| | - Hideaki Suzuki
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate
School of Science, Kyoto University, Sakyo-ku,
Kyoto 606-8502, Japan
| | - Zheng-Yu Wang
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
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Hada N, Shida Y, Negishi N, Schweizer F, Takeda T. Syntheses of glycoclusters containing a phosphocholine residue related to a glycosphingolipid from the earthworm Pheretima hilgendorfi. Chem Pharm Bull (Tokyo) 2009; 57:1081-8. [PMID: 19801862 DOI: 10.1248/cpb.57.1081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three types of glycoclusters related to an amphoteric glycosphingolipid found in the earthworm Pheretima hilgendorfi were synthesized. The glycoclusters were prepared from a common precursor and a simple approach for the rational design of a glycocluster was developed.
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Affiliation(s)
- Noriyasu Hada
- Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan.
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Sonoda Y, Hada N, Kaneda T, Suzuki T, Ohshio T, Takeda T, Kasahara T. A synthetic glycosphingolipid-induced antiproliferative effect in melanoma cells is associated with suppression of FAK, Akt, and Erk activation. Biol Pharm Bull 2008; 31:1279-83. [PMID: 18520069 DOI: 10.1248/bpb.31.1279] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Numerous studies have demonstrated the participation of glicolipids in signal transduction and the regulation of melanoma cell growth and apoptosis. Hoping to discover new anticancer drugs, we have synthesized ten glycolipids found in various invertebrates that do not have sialic acids. These compounds were tested for antiproliferative effects on a melanoma cell line, B16F10. A synthetic compound, Manbeta(1-4)[Fucalpha(1-3)]Glcbeta1-Cer, (glycosphingolipid 7), which was identified in the millipede Parafontaria laminata armigera, had an antiproliferative effect on the melanoma cells. This compound suppressed the activation of the focal adhesion kinase (FAK)-Akt pathway as well as the activation of extracellular signal-regulated kinase (Erk)1/2 pathway involved in cell proliferation. Expression of the cell cycle proteins, cyclin D1 and CDK4, was suppressed by glycosphingolipid 7. From these results, glycosphingolipid 7 suppressed the activation of the FAK-Akt pathway and of Erk1/2, which resulted in a decrease in the expression of cyclin D1 and CDK4. Glycosphingolipid 7 might be a candidate for an inhibitor of cell proliferation in melanomas.
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Affiliation(s)
- Yoshiko Sonoda
- Department of Biochemistry and Pharmacognosy, Kyoritsu University of Pharmacy, Tokyo, Japan.
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Meyer TE, Tsapin AI, Vandenberghe I, de Smet L, Frishman D, Nealson KH, Cusanovich MA, van Beeumen JJ. Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2004; 8:57-77. [PMID: 15107237 DOI: 10.1089/153623104773547499] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Through pattern matching of the cytochrome c heme-binding site (CXXCH) against the genome sequence of Shewanella oneidensis MR-1, we identified 42 possible cytochrome c genes (27 of which should be soluble) out of a total of 4758. However, we found only six soluble cytochromes c in extracts of S. oneidensis grown under several different conditions: (1) a small tetraheme cytochrome c, (2) a tetraheme flavocytochrome c-fumarate reductase, (3) a diheme cytochrome c4, (4) a monoheme cytochrome c5, (5) a monoheme cytochrome c', and (6) a diheme bacterial cytochrome c peroxidase. These cytochromes were identified either through N-terminal or complete amino acid sequence determination combined with mass spectroscopy. All six cytochromes were about 10-fold more abundant when cells were grown at low than at high aeration, whereas the flavocytochrome c-fumarate reductase was specifically induced by anaerobic growth on fumarate. When adjusted for the different heme content, the monoheme cytochrome c5 is as abundant as are the small tetraheme cytochrome and the tetraheme fumarate reductase. Published results on regulation of cytochromes from DNA microarrays and 2D-PAGE differ somewhat from our results, emphasizing the importance of multifaceted analyses in proteomics.
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Affiliation(s)
- Terry E Meyer
- Department of Biochemistry and Molecular Biophysics University of Arizona, Tucson, Arizona 85721, USA.
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Miller GT, Mackay DQ, Standley MS, Fields SL, Clary WM, Timkovich R. Expression of Pseudomonas stutzeri Zobell cytochrome c-551 and its H47A variant in Escherichia coli. Protein Expr Purif 2003; 29:244-51. [PMID: 12767816 DOI: 10.1016/s1046-5928(03)00065-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nirM gene encoding cytochrome c-551 from Pseudomonas stutzeri Zobell (PZ) has been expressed in Escherichia coli at levels higher than those previously reported but only under strict anaerobic growth conditions. Expression yields for wild-type cytochrome in this study typically reached 0.6 micromol per liter of saturated E. coli culture (5.5mg/L). Culture conditions investigated are compared to obtained c-551 expression levels; the results may lead to a greater understanding of the challenges encountered when expressing c-type hemoproteins in E. coli. The nirM gene was mutated to produce a histidine-47-alanine mutation of c-551 that been heterologously expressed in E. coli using optimum culture conditions and had its physiochemical properties compared to those of the wild-type protein. In PZ, the histidine-47 residue is part of a conserved hydrogen-bonding network located at the bottom of the heme crevice that also involves tryptophan-56 and a heme propionate. Ionization events within this network are experimentally demonstrated to modulate c-551 oxidation-reduction potential and its observed dependence on pH around neutrality. The redox potential of the mutant cytochrome still displays pH-dependence; however, the midpoint potential is approximately 25mV lower with respect to wild-type c-551 at neutral pH while the pK at which the heme propionate (HP-17) ionizes is lowered by 1.3 pH units. Temperature and chemical denaturant studies also show that loss of the hydrogen-bond-donating imidazole leads to a large decrease in c-551 tertiary stability.
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Affiliation(s)
- Gregory T Miller
- Department of Chemistry, Southern Oregon University, Ashland, OR 97520, USA.
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6
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Bertsch M, Mayburd AL, Kassner RJ. The identification of hydrophobic sites on the surface of proteins using absorption difference spectroscopy of bromophenol blue. Anal Biochem 2003; 313:187-95. [PMID: 12605855 DOI: 10.1016/s0003-2697(02)00590-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrophobic sites on the surface of protein molecules are thought to have important functional roles. The identification of such sites can provide information about the function and mode of interaction with other cellular components. While the fluorescence enhancement of polarity-sensitive dyes has been useful in identifying hydrophobic sites on a number of targets, strong intrinsic quenching of Nile red and ANSA dye fluorescence is observed on binding to a cytochrome c('). Fluorescence quenching is also observed to take place in the presence of a variety of other biologically important molecules which can compromise the quantitative determination of binding constants. Absorption difference spectroscopy is shown not to be sensitive to the presence of fluorescence quenchers but sensitive enough to measure binding constants. The dye BPB is shown to bind to the same hydrophobic sites on proteins as polarity-sensitive fluorescence probes. The absorption spectrum of BPB is also observed to be polarity sensitive. A binding constant of 3x10(6)M(-1) for BPB to BSA has been measured by absorption difference spectroscopy. An empirical correlation is observed between the shape of the absorption difference spectrum of BPB and the polarity of the environment. The results indicate that absorption difference spectroscopy of BPB provides a valuable supplement to fluorescence for determining the presence of hydrophobic sites on the surface of proteins as well as a method for measuring binding constants.
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Affiliation(s)
- M Bertsch
- Department of Chemistry, University of Illinois at Chicago, Science and Engineering South 845 West Taylor Street, Rm. 4500, Chicago, IL 60607, USA
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AOKI K, SUGIYAMA S, DULANEY JT, ITONORI S, SUGITA M. Classification into a Novel Mollu-Series of Neutral Glycosphingolipids from the Lamp Shell, Lingula unguis. J Oleo Sci 2002. [DOI: 10.5650/jos.51.463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Tsapin AI, Vandenberghe I, Nealson KH, Scott JH, Meyer TE, Cusanovich MA, Harada E, Kaizu T, Akutsu H, Leys D, Van Beeumen JJ. Identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in Shewanella oneidensis strain MR1. Appl Environ Microbiol 2001; 67:3236-44. [PMID: 11425747 PMCID: PMC93006 DOI: 10.1128/aem.67.7.3236-3244.2001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two abundant, low-redox-potential cytochromes c were purified from the facultative anaerobe Shewanella oneidensis strain MR1 grown anaerobically with fumarate. The small cytochrome was completely sequenced, and the genes coding for both proteins were cloned and sequenced. The small cytochrome c contains 91 residues and four heme binding sites. It is most similar to the cytochromes c from Shewanella frigidimarina (formerly Shewanella putrefaciens) NCIMB400 and the unclassified bacterial strain H1R (64 and 55% identity, respectively). The amount of the small tetraheme cytochrome is regulated by anaerobiosis, but not by fumarate. The larger of the two low-potential cytochromes contains tetraheme and flavin domains and is regulated by anaerobiosis and by fumarate and thus most nearly corresponds to the flavocytochrome c-fumarate reductase previously characterized from S. frigidimarina to which it is 59% identical. However, the genetic context of the cytochrome genes is not the same for the two Shewanella species, and they are not located in multicistronic operons. The small cytochrome c and the cytochrome domain of the flavocytochrome c are also homologous, showing 34% identity. Structural comparison shows that the Shewanella tetraheme cytochromes are not related to the Desulfovibrio cytochromes c(3) but define a new folding motif for small multiheme cytochromes c.
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Affiliation(s)
- A I Tsapin
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA
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Mayburd AL, Tan Y, Kassner RJ. Complex formation between Chromatium vinosum ferric cytochrome c' and bromophenol blue. Arch Biochem Biophys 2000; 378:40-4. [PMID: 10871042 DOI: 10.1006/abbi.2000.1783] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An unusual complex has been observed between the common electrophoresis tracer bromophenol blue (BPB) and the cytochrome c' from Chromatium vinosum during polyacrylamide gel electrophoresis. Complex formation results in a shift and increase in the intensity of the visible absorption band of BPB. Differential spectrophotometric titration of BPB with cytochrome c' indicates that one BPB binds to each of the two subunits of cytochrome c' with a binding constant of 4.2(0.5) x 10(5). The absence of a significant effect of ionic strength on the binding constant and the effect of Triton X-100 on the spectrum of BPB suggest that hydrophobic interactions are important to binding. An analysis of the structure of C. vinosum cytochrome c' shows the presence of a surface hydrophobic patch which may participate in the binding interaction. Many of the hydrophobic amino acids in the patch are well conserved by type among all known sequences of cytochrome c' and are found in loop elements of the 3D structure, suggesting a functional basis for conservation. It is proposed that the binding of BPB may mimic a relevant interaction involving the cytochrome c' biological function.
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Affiliation(s)
- A L Mayburd
- Department of Chemistry, University of Illinois at Chicago, 60607, USA
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Cross R, Aish J, Paston SJ, Poole RK, Moir JW. Cytochrome c' from Rhodobacter capsulatus confers increased resistance to nitric oxide. J Bacteriol 2000; 182:1442-7. [PMID: 10671472 PMCID: PMC94437 DOI: 10.1128/jb.182.5.1442-1447.2000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the cloning and sequencing of the gene containing cytochrome c' (cycP) from the photosynthetic purple bacterium Rhodobacter capsulatus and the regions flanking that gene. Mutant strains unable to synthesize cytochrome c' had increased sensitivity to nitrosothiols and to nitric oxide (which binds to the heme moiety of cytochrome c').
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Affiliation(s)
- R Cross
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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Brüser T, Trüper HG, Dahl C. Cloning and sequencing of the gene encoding the high potential iron-sulfur protein (HiPIP) from the purple sulfur bacterium Chromatium vinosum. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1352:18-22. [PMID: 9177478 DOI: 10.1016/s0167-4781(97)00033-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The gene encoding the high potential iron-sulfur protein (HiPIP) of Chromatium vinosum strain D (DSM 180T) was cloned from an EcoRI-HindIII digest of genomic DNA. A nucleotide sequence of 648 bp length was determined which contained the coding region and putative promoter and termination sites. The gene codes for a 122 residue 12761 Da protein. The C-terminal 85 residues are those of the previously biochemically determined sequence, whereas the N-terminal 37 residues constitute a leader peptide which shows characteristics of the double arginine signal sequences of complex cofactor containing periplasmic proteins.
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Affiliation(s)
- T Brüser
- Institut für Mikrobiologie and Biotechnologie, Bonn, Germany
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