Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima.

Members of the periplasmic binding protein superfamily are involved in the selective passage of ligands through bacterial cell membranes. The hyperthermophilic eubacterium Thermotoga maritima was found to encode a highly stable and specific periplasmic arginine-binding protein (TM0593). Following signal sequence removal and overexpression in Escherichia coli, TM0593 was purified by thermoprecipitation and affinity chromatography. The ultra-stable protein with a monomeric molecular weight of 27.7 kDa was found to exist as both a homodimer and homotrimer at appreciable concentrations even under strongly denaturing conditions, with an estimated transition temperature of 116 degrees C. Its multimeric structure may provide further evidence of the importance of quaternary structure in the movement of nutrients across bacterial membranes. Purified and refolded TM0593 was further characterized by fluorescence spectroscopy, mass spectrometry, and circular dichroism to demonstrate the specificity of the protein for arginine and to elucidate structural changes associated with arginine binding. The protein binds arginine with a dissociation constant of 20 muM as determined by surface plasmon resonance measurements. Due to its high thermodynamic stability, TM0593 may serve as a scaffold for the creation of a robust fluorescent biosensor.

[1]  Robert Huber,et al.  Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C , 1986, Archives of Microbiology.

[2]  Yiling Fang,et al.  A Bacterial Arginine-Agmatine Exchange Transporter Involved in Extreme Acid Resistance* , 2007, Journal of Biological Chemistry.

[3]  J. Lakowicz Principles of fluorescence spectroscopy , 1983 .

[4]  H. Hellinga,et al.  Structural Analysis of a Periplasmic Binding Protein in the Tripartite ATP-independent Transporter Family Reveals a Tetrameric Assembly That May Have a Role in Ligand Transport* , 2008, Journal of Biological Chemistry.

[5]  G. Unden,et al.  A third periplasmic transport system for l‐arginine in Escherichia coli: molecular characterization of the artPIQMJ genes, arginine binding and transport , 1995, Molecular microbiology.

[6]  Marcus Fehr,et al.  Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering , 2005, Protein science : a publication of the Protein Society.

[7]  M. Marcus,et al.  Genetic Analysis of the Glutamate Permease in Escherichia coli K-12 , 1969, Journal of bacteriology.

[8]  T. Nohno,et al.  Cloning and complete nucleotide sequence of the Escherichia coli glutamine permease operon (glnHPQ) , 1986, Molecular and General Genetics MGG.

[9]  J. Pandit,et al.  Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand. , 1994, The Journal of biological chemistry.

[10]  I Gryczynski,et al.  Glucose sensor for low-cost lifetime-based sensing using a genetically engineered protein. , 1999, Analytical biochemistry.

[11]  S. Loefas,et al.  Immobilization of proteins to a carboxymethyldextran-modified gold surface for biospecific interaction analysis in surface plasmon resonance sensors. , 1991, Analytical biochemistry.

[12]  S. Daunert,et al.  A fluorescence-based sensing system for the environmental monitoring of nickel using the nickel binding protein from Escherichia coli , 2002, Analytical and bioanalytical chemistry.

[13]  M. Eftink,et al.  Dynamics of a protein matrix revealed by fluorescence quenching. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[14]  C. Higgins,et al.  ABC transporters: from microorganisms to man. , 1992, Annual review of cell biology.

[15]  H W Hellinga,et al.  The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[16]  G. F. Ames Bacterial periplasmic transport systems: structure, mechanism, and evolution. , 1986, Annual review of biochemistry.

[17]  David Pignol,et al.  Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding , 2020 .

[18]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[19]  Bryan S. Der,et al.  Analysis of ligand binding to a ribose biosensor using site‐directed mutagenesis and fluorescence spectroscopy , 2007, Protein science : a publication of the Protein Society.

[20]  G. Fields,et al.  Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids. , 2009, International journal of peptide and protein research.

[21]  S. d'Auria,et al.  Conformational stability and domain coupling in D-glucose/D-galactose-binding protein from Escherichia coli. , 2004, The Biochemical journal.

[22]  Loren L Looger,et al.  Computational design of receptors for an organophosphate surrogate of the nerve agent soman. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[23]  H. Hellinga,et al.  Periplasmic binding proteins: a versatile superfamily for protein engineering. , 2004, Current opinion in structural biology.

[24]  C. Ouzounis,et al.  Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools. , 2000, Nucleic acids research.

[25]  L. Looger,et al.  Construction of a fluorescent biosensor family , 2002, Protein science : a publication of the Protein Society.

[26]  M H Saier,et al.  Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria , 1993, Microbiological reviews.

[27]  J. Lakowicz,et al.  Optical determination of glutamine using a genetically engineered protein. , 2001, Analytical biochemistry.

[28]  Jue Chen,et al.  Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems , 2008, Microbiology and Molecular Biology Reviews.

[29]  S. Salzberg,et al.  Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima , 1999, Nature.

[30]  C. Woese,et al.  Were the original eubacteria thermophiles? , 1987, Systematic and applied microbiology.

[31]  Y. J. Sun,et al.  The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolution: comparisons with other amino acid binding proteins. , 1998, Journal of molecular biology.

[32]  H. Hellinga,et al.  Structure‐based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose‐binding protein , 2007, Protein science : a publication of the Protein Society.

[33]  K. Noll,et al.  Substrate Specificities and Expression Patterns Reflect the Evolutionary Divergence of Maltose ABC Transporters in Thermotoga maritima , 2005, Journal of bacteriology.

[34]  D. Swofford PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[35]  L. Looger,et al.  A novel analytical method for in vivo phosphate tracking , 2006, FEBS letters.

[36]  S Brunak,et al.  Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. , 2000, Nucleic acids research.

[37]  R. Daniel,et al.  An extremely thermostable xylanase from the thermophilic eubacterium Thermotoga. , 1991, The Biochemical journal.

[38]  J. Corrie,et al.  Direct, real-time measurement of rapid inorganic phosphate release using a novel fluorescent probe and its application to actomyosin subfragment 1 ATPase. , 1994, Biochemistry.

[39]  K. Nishikawa,et al.  Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. , 1999, Journal of molecular biology.

[40]  Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima. , 2008, Acta crystallographica. Section F, Structural biology and crystallization communications.

[41]  Bryan S. Der,et al.  Construction of a reagentless glucose biosensor using molecular exciton luminescence. , 2008, Analytical biochemistry.

[42]  Loren L Looger,et al.  Conversion of a Putative Agrobacterium Sugar-binding Protein into a FRET Sensor with High Selectivity for Sucrose* , 2006, Journal of Biological Chemistry.

[43]  A. Vahedi-Faridi,et al.  Crystal structures and mutational analysis of the arginine-, lysine-, histidine-binding protein ArtJ from Geobacillus stearothermophilus. Implications for interactions of ArtJ with its cognate ATP-binding cassette transporter, Art(MP)2. , 2008, Journal of molecular biology.

[44]  L. Looger,et al.  Computational design of receptor and sensor proteins with novel functions , 2003, Nature.

[45]  K. Nikaido,et al.  Purification and characterization of the periplasmic lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium. , 1992, The Journal of biological chemistry.

[46]  Matthew R. Johnson,et al.  Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. , 2006, FEMS microbiology reviews.

[47]  Construction and Characterization of Chimeric Proteins Composed of Type-1 and Type-2 Periplasmic Binding Proteins MglB and ArgT , 2004, Bioscience, biotechnology, and biochemistry.