Glucose biosensors and uses thereof

Abstract

The present subject matter provides glucose biosensors as well as compositions, devices, and methods comprising such biosensors.

1 . A biosensor for a ligand, comprising a ligand-binding protein and a reporter group attached to said ligand-binding protein, wherein binding of said ligand to a ligand-binding domain of said ligand-binding protein causes a change in signaling by said reporter group,
 wherein said ligand comprises glucose or galactose, and   wherein if said ligand-binding protein is an  Escherichia coli  ( E. coli ) glucose-galactose binding protein, then said ligand-binding protein comprises a mutation other than a mutation of amino acid Y10, D14, N15, F16, N91, K92, E93, S112, S115, E149, H152, D154, A155, R158, M182, W183, N211, D236, L255, N256, D257, P294, or V296, wherein each amino acid position is numbered as in (SEQ ID NO: 17).   
     
     
         2 . (canceled) 
     
     
         3 . (canceled) 
     
     
         4 . The biosensor of  claim 1 , wherein said ligand-binding protein comprises a mutation compared to a naturally occurring protein, and wherein at least one amino acid of the ligand-binding protein has been substituted with a cysteine. 
     
     
         5 . The biosensor of  claim 1 , wherein said ligand-binding protein comprises a mutation compared to a naturally occurring protein, and wherein said ligand-binding protein has no deletions or insertions compared to the naturally occurring protein. 
     
     
         6 . The biosensor of  claim 1 , wherein said ligand-binding protein comprises a mutation compared to a naturally occurring protein, and wherein said ligand-binding protein comprises (i) less than about 5, 4, 3, 2, or 1 inserted amino acids, and/or (ii) less than about 5, 4, 3, 2, or 1 deleted amino acids compared to the naturally occurring protein. 
     
     
         7 . (canceled) 
     
     
         8 . The biosensor of  claim 1 , wherein said ligand-binding protein comprises a mutant of a microbial glucose-galactose binding protein, and wherein said mutant comprises a mutation that alters the mutant's affinity and/or specificity for glucose and/or galactose compared to the microbial glucose-galactose binding protein. 
     
     
         9 . The biosensor of  claim 1 , wherein said ligand-binding protein is or is a mutant of: an  Escherichia  sp. GGBP; a  Thermoanaerobacter  sp. GGBP; a  Clostridium  sp. GGBP; a  Salmonella  sp. GGBP; a  Caldicellulosiruptor  sp. GGBP; a  Paenibacillus  sp. GGBP; a  Butyrivibrio  sp. GGBP; a  Roseburia  sp. GGBP; a  Faecalibacterium  sp. GGBP; an  Erysipelothrix  sp. GGBP; or an  Eubacterium  sp. GGBP. 
     
     
         10 . The biosensor of  claim 1 , wherein said ligand-binding protein is or is a mutant of: an  Escherichia coli  GGBP (ecGGBP; SEQ ID NO: 1 or 16), a  Thermoanaerobacter thermosaccharolyticum  GGBP (ttGGBP; SEQ ID NO: 2 or 18), a  Salmonella typhimurium  GGBP (stGGBP; SEQ ID NO: 3 or 19), a  Caldicellulosiruptor hydrothermalis  GGBP (chyGGBP; SEQ ID NO: 4 or 20), a  Caldicellulosiruptor obsidiansis  GGBP (cobGGBP; SEQ ID NO: 5 or 21), a  Paenibacillus  sp. GGBP (pspGGBP; SEQ ID NO: 6 or 22); a  Clostridium saccharolyticum  GGBP (csaGGBP; SEQ ID NO: 7 or 23); a  Clostridium autoethanogenum  GGBP (cauGGBP; SEQ ID NO: 12 or 28); a  Clostridium ljungdahlii  GGBP (clj GGBP; SEQ ID NO: 11 or 27); a  Butyrivibrio proteoclasticus  GGBP (bprGGBP; SEQ ID NO: 8 or 24); a  Roseburia intestinalis  GGBP (finGGBP_A; SEQ ID NO: 9 or 25 or rinGGBP_B; SEQ ID NO: 13 or 29); a  Faecalibacterium prausnitzii  GGBP (fprGGBP; SEQ ID NO: 10 or 26); a  Erysipelothrix rhusiopathiae  GGBP (erhGGBP; SEQ ID NO: 14 or 30); or a  Eubacterium rectale  GGBP (ereGGBP; SEQ ID NO: 15 or 31). 
     
     
         11 . The biosensor of  claim 1 , wherein said glucose-galactose binding protein comprises an amino acid sequence that is between 10% and 100% identical to the amino acid sequence of ecGGBP (SEQ ID NO: 1 or 16), ttGGBP (SEQ ID NO: 2 or 18), stGGBP (SEQ ID NO: 3 or 19), chyGGBP (SEQ ID NO: 4 or 20), pspGGBP (SEQ ID NO: 6 or 22); csaGGBP (SEQ ID NO: 7 or 23); bprGGBP (SEQ ID NO: 8 or 24); rinGGBP A (SEQ ID NO: 9 or 25); rinGGBP B (SEQ ID NO: 13 or 29); fprGGBP (SEQ ID NO: 10 or 26); cljGGBP (SEQ ID NO: 11 or 27); cauGGBP (SEQ ID NO: 12 or 28); erhGGBP (SEQ ID NO: 14 or 30); and/or ereGGBP (SEQ ID NO: 15 or 31). 
     
     
         12 . The biosensor of  claim 1 , wherein said ligand-binding protein comprises
 (a) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 10 of ecGGBP;   (b) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 14 of ecGGBP;   (c) a stretch of at least 5 amino acids having at least about 50%, 55%, 60%, 65%, 75%, 80%, 85%, 90%, or 95% identity to a stretch of consecutive amino acids including position 91 of ecGGBP;   (d) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 149 of ecGGBP;   (e) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 150 of ecGGBP;   (f) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 155 of ecGGBP;   (g) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 160 of ecGGBP;   (h) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 183 of ecGGBP;   (i) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 210 of ecGGBP;   (j) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 235 of ecGGBP;   (k) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 240 of ecGGBP;   (l) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 255 of ecGGBP; or   (m) a stretch of at least 5 amino acids having at least about 50% identity to a stretch of consecutive amino acids including position 260 of ecGGBP,   wherein each ecGGBP amino acid position is numbered as in SEQ ID NO: 17.   
     
     
         13 . (canceled) 
     
     
         14 . The biosensor of  claim 1 , wherein when said ligand-binding protein shares a primary complementary surface (PCS) with ecGGBP, wherein the PCS of ecGGBP comprises positions 14, 16, 91, 152, 154, 158, 183, 211, 236, and 256, wherein each position is counted as in SEQ ID NO: 17, and wherein when the amino acid sequence of said ligand-binding protein is aligned with ecGGBP (SEQ ID NO: 17), then said amino acid sequence comprises
 (i) D or N at the position that aligns with position 14 of ecGGBP;   (ii) F, Y, or W at the position that aligns with position 16 of ecGGBP;   (iii) N or D at the position that aligns with position 91 of ecGGBP;   (iv) H, N, or Q at the position that aligns with position 152 of ecGGBP;   (v) D or N at the position that aligns with position 154 of ecGGBP;   (vi) R at the position that aligns with position 158 of ecGGBP;   (vii) W, F, or Y at the position that aligns with position 183 of ecGGBP;   (viii) N or D at the position that aligns with position 211 of ecGGBP;   (ix) D or N at the position that aligns with position 236 of ecGGBP; and   (x) N or D at the position that aligns with position 256 of ecGGBP.   
     
     
         15 . (canceled) 
     
     
         16 . (canceled) 
     
     
         17 . The biosensor of  claim 1 , wherein the C α  root-mean-square deviation (RMSD) between the backbone of the ligand-binding polypeptide and ecGGBP, ttGGBP, stGGBP, chyGGBP, cobGGBP, pspGGBP, csaGGBP, bprGGBP, rinGGBP_A, rinGGBP_B, fprGGBP, cljGGBP, cauGGBP, erhGGBP, ereGGBP, and/or chyGGBP is between about 0.1-3, 0.5-1, 0.5-1.5, or 0.5-2, or less than about 0.1 Å, 0.2 Å, 0.3 Å, 0.4 Å, 0.5 Å, 0.6 Å, 0.7 Å, 0.8 Å, 0.9 Å, 1.0 Å, 1.5 Å, 1.6 Å, 1.7 Å, 1.8 Å, 1.9 Å, 2.0 Å, 2.5 Å, or 3 Å. 
     
     
         18 . The biosensor of  claim 1 , wherein said ligand-binding protein is a mutant of ecGGBP comprising one or more of the following substitutions: Y10X, D14X, N15X, F16X, P70X, N91X, K92X, S112X, S115X, E149X, H152X, P153X, D154X, A155X, R158X, M182X, W183X, N211X, D212X, D236X, L238X, D257X, P294X, and V296X, where X is any amino acid, an amino acid that results in a conservative substitution, or a cysteine, and where each position is counted in ecGGBP without including the signal peptide (SEQ ID NO: 17). 
     
     
         19 . (canceled) 
     
     
         20 . The biosensor of  claim 1 , wherein said reporter group is covalently attached to said ligand-binding protein. 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . The biosensor of  claim 1 , wherein said reporter group is conjugated to a cysteine of the ligand-binding protein. 
     
     
         24 . (canceled) 
     
     
         25 . The biosensor of  claim 1 , wherein said reporter group comprises a fluorophore, and wherein said signal comprises a fluorescent signal. 
     
     
         26 . (canceled) 
     
     
         27 . (canceled) 
     
     
         28 . (canceled) 
     
     
         29 . The biosensor of  claim 25 , wherein an emission spectrum of said fluorophore exhibits hypsochromicity or bathochromicity upon ligand binding to the ligand-binding domain of said ligand-binding protein. 
     
     
         30 . (canceled) 
     
     
         31 . The biosensor of  claim 25 , wherein said fluorophore comprises 5-iodoacetamidofluorescein (5IAF) or 6-iodoacetamidofluorescein (6IAF), rhodamine, Oregon Green, eosin, Texas Red, indocarbocyanine, oxacarbocyanine, thiacarbocyanine, merocyanine, Badan, Acrylodan, IAEDANS, comprising 3-cyano-7-hydroxycoumarin, 7-hydroxycoumarin-3-carboxylic acid, 6,8-difluoro-7-hydroxy-4-methylcoumarin, or 7-amino-4-methylcoumarin, pyridyloxazole, nitrobenzoxadiazole, benzoxadiazole, DRAQS, DRAQ7, or CyTRAK Orange, cascade blue, Nile red, Nile blue, cresyl violet, oxazine 170, proflavin, acridine orange, acridine yellow, auramine, crystal violet, malachite green, porphin, phthalocyanine, bilirubin, pyrene, N,N′-dimethyl-N-(iodoacetyl)-N′-(7-nitrobenz-2-ox-a-1,3-diazol-4-yl)ethylenediamide (NBD), N-((2-(iodoacetoxy)ethyl)-N-methy-1)amino-7-nitrobenz-2-oxa-1,3-diazole (NBDE), Acrylodan, JPW4039, JPW4042, JPW4045, Oregon Green, Pacific Blue, N,N′-Dimethyl-N-(Iodoacetyl)-N′-(7-Nitrobenz-2-Oxa-1,3-Diazol-4-yl)Ethylenediamine (IANBD), 7-diethylamino-3-(4′-maleimidylphenyl)-4-methylcoumarin (CPM), BODIPY 499, BODIPY 507, Alexa488, Alexa532, Alexa546, Cy5, or 1-(2-maleimidylethyl)-4-(5-(4-methoxyphenyl)oxazol-2-yl)pyridinium methanesulfonate (PyMPO maleimide) (PyMPO). 
     
     
         32 . The biosensor of  claim 25 , comprising Acrylodan (6-acryloy 1-2-dimethylaminonaphthalene) or Badan (6-bromo-acetyl-2-dimethylamino-naphthalene) or a derivative thereof. 
     
     
         33 . The biosensor of  claim 32 , wherein said derivative comprises a replacement of the two-ring naphthalene of Acrylodan or Badan with a three-ring anthracene, a fluorene, or a styrene. 
     
     
         34 . (canceled) 
     
     
         35 . (canceled) 
     
     
         36 . A method of detecting the presence of a ligand in a sample, the method comprising:
 (a) contacting the biosensor of  claim 1  with the sample;   (b) measuring a signal from the biosensor; and   (c) comparing the signal to a ligand-free control, wherein a difference in signal indicates the presence of ligand in the sample, and   wherein the ligand comprises glucose, galactose, or combination thereof.   
     
     
         37 .- 51 . (canceled) 
     
     
         52 . A method for monitoring the level of a ligand in a subject, comprising
 (a) administering a biosensor according to  claim 1  or a device comprising a biosensor according to  claim 1  to said subject, wherein after administration the biosensor is in contact with a bodily fluid or surface of said subject, and   (b) detecting (i) a signal produced by a reporter group of said biosensor continuously or repeatedly at intervals less than about 30 minutes apart, and/or (ii) whether a signal is produced by a reporter group of said biosensor continuously or repeatedly at intervals less than about 30 minutes apart.   
     
     
         53 .- 82 . (canceled)