Compositions and methods comprising sequences having meganuclease activity

Abstract

Compositions and methods comprising polynucleotides and polypeptides having meganuclease activity are provided. Further provided are nucleic acid constructs, yeast, plants, plant cells, explants, seeds and grain having the meganuclease sequences. Various methods of employing the meganuclease sequences are provided. Such methods include, for example, methods for producing a meganuclease with increased activity at a wide range of temperatures, methods for producing a yeast, plant, plant cell, explant or seed comprising a meganuclease with increased activity.

1 . An isolated or recombinant polynucleotide encoding a meganuclease polypeptide, wherein said meganuclease polypeptide has at least 80% sequence identity to SEQ ID NO: 282, comprises a tyrosine (Y) at position 66 of SEQ ID NO:282, and further comprises:
 a) at least one amino acid modification at an amino acid position corresponding to a position of SEQ ID NO: 282 selected from the group consisting of positions 12, 16, 19, 22, 31, 50, 54, 56, 59, 62, 81, 98, 103, 105, 116, 118, 121, 132, 153, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 244, 258, 281, 308, 312, 316, 319, and combinations thereof; or,   b) an amino acid sequence having at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, or 57 of any of the amino acid modifications of (a);   
     
     
         2 . (canceled) 
     
     
         3 . The isolated or recombinant polynucleotide of  claim 1 , wherein said at least one amino acid modification comprises;
 a) a histidine (H) at a position corresponding to amino acid position 12 in SEQ ID NO: 282;   b) an isoleucine (I) at a position corresponding to amino acid position 16 in SEQ ID NO: 282;   c) a serine (S) at a position corresponding to amino acid position 19 in SEQ ID NO:282   d) a cysteine (C) at a position corresponding to amino acid position 22 in SEQ ID NO: 282;   e) an arginine (R) at a position corresponding to amino acid position 31 in SEQ ID NO: 282;   f) an arginine (R) or lysine (K) at a position corresponding to amino acid position 50 in SEQ ID NO: 282;   g) a leucine (L) at a position corresponding to amino acid position 56 in SEQ ID NO: 282;   h) an isoleucine (I) at a position corresponding to amino acid position 54 in SEQ ID NO: 282;   i) a histidine (H) at a position corresponding to amino acid position 59 in SEQ ID NO: 282;   j) a valine (V) at a position corresponding to amino acid position 62 in SEQ ID NO: 282;   k) a lysine (K) at a position corresponding to amino acid position 81 in SEQ ID NO: 282;   l) an arginine (R) at a position corresponding to amino acid position 98 in SEQ ID NO: 282;   m) a valine (V) at a position corresponding to amino acid position 103 in SEQ ID NO: 282;   n) a valine (V) at a position corresponding to amino acid position 105 in SEQ ID NO: 282;   o) an arginine (R) at a position corresponding to amino acid position 116 in SEQ ID NO: 282;   p) a threonine (T) at a position corresponding to amino acid position 118 in SEQ ID NO: 282;   q) a glycine (G) at a position corresponding to amino acid position 121 in SEQ ID NO: 282;   r) a threonine (T) or valine (V) at a position corresponding to amino acid position 132 in SEQ ID NO: 282;   s) a leucine (L) or a methionine (M) at a position corresponding to amino acid position 153 in SEQ ID NO: 282;   t) a glutamic acid (E) at a position corresponding to amino acid position 160 in SEQ ID NO: 282;   u) a valine (V) at a position corresponding to amino acid position 161 in SEQ ID NO: 282;   v) a tyrosine (Y) at a position corresponding to amino acid position 162 in SEQ ID NO: 282;   w) an arginine (R) at a position corresponding to amino acid position 163 in SEQ ID NO: 282;   x) a histidine (H) at a position corresponding to amino acid position 164 in SEQ ID NO: 282;   y) a leucine (L) at a position corresponding to amino acid position 165 in SEQ ID NO: 282;   z) an arginine (R) at a position corresponding to amino acid position 166 in SEQ ID NO: 282;   aa) a histidine (H) at a position corresponding to amino acid position 167 in SEQ ID NO: 282;   bb) a proline (P) at a position corresponding to amino acid position 168 in SEQ ID NO: 282;   cc) an alanine (A) at a position corresponding to amino acid position 169 in SEQ ID NO: 282;   dd) a proline (P) at a position corresponding to amino acid position 170 in SEQ ID NO: 282;   ee) a histidine (H) at a position corresponding to amino acid position 171 in SEQ ID NO: 282;   ff) a proline (P) at a position corresponding to amino acid position 172 in SEQ ID NO: 282;   gg) an arginine (R) at a position corresponding to amino acid position 173 in SEQ ID NO: 282;   hh) a leucine (L) at a position corresponding to amino acid position 174 in SEQ ID NO: 282;   ii) a proline (P) at a position corresponding to amino acid position 175 in SEQ ID NO: 282;   jj) a glutamine (Q) at a position corresponding to amino acid position 176 in SEQ ID NO: 282;   kk) an alanine (A) at a position corresponding to amino acid position 177 in SEQ ID NO: 282;   ll) an arginine (R) at a position corresponding to amino acid position 178 in SEQ ID NO: 282;   mm a valine (V) at a position corresponding to amino acid position 179 in SEQ ID NO: 282;   nn a glutamine (Q) at a position corresponding to amino acid position 180 in SEQ ID NO: 282;   oo) a serine (S) at a position corresponding to amino acid position 182 in SEQ ID NO: 282;   pp) a proline (P) at a position corresponding to amino acid position 183 in SEQ ID NO: 282;   qq) a lysine (K) at a position corresponding to amino acid position 184 in SEQ ID NO: 282;   rr) a threonine (T) or a histidine (H) at a position corresponding to amino acid position 185 in SEQ ID NO: 282;   ss) a serine (S) at a position corresponding to amino acid position 186 in SEQ ID NO: 282;   tt) a glutamic acid (E) at a position corresponding to amino acid position 187 in SEQ ID NO: 282;   uu) a leucine (L) at a position corresponding to amino acid position 188 in SEQ ID NO: 282;   vv) a glutamic acid (E) at a position corresponding to amino acid position 189 in SEQ ID NO: 282;   ww) a proline (P) at a position corresponding to amino acid position 190 in SEQ ID NO: 282;   xx) a lysine (K) at a position corresponding to amino acid position 191 in SEQ ID NO: 282;   yy) a glutamine acid € at a position corresponding to amino acid position 244 in SEQ ID NO: 282;   zz) a serine (S) at a position corresponding to amino acid position 258 in SEQ ID NO: 282;   aaa) a tyrosine (Y) at a position corresponding to amino acid position 281 in SEQ ID NO: 282;   bbb) a glycine (G) at a position corresponding to amino acid position 308 in SEQ ID NO: 1;   ccc) an alanine (A) at a position corresponding to amino acid position 312 in SEQ ID NO: 282;   ddd) an alanine (A) at a position corresponding to amino acid position 316 in SEQ ID NO: 1;   eee) a valine (V) at a position corresponding to amino acid position 319 in SEQ ID NO: 282;   or,   xxxx) any combination of a) to eee).   
     
     
         4 . The isolated or recombinant polynucleotide of  claim 1 , wherein said nucleotide sequence encodes a meganuclease polypeptide, wherein said polypeptide further comprises:
 a) a histidine (H) or tyrosine (Y) at a position corresponding to amino acid position 12 in SEQ ID NO: 282;   b) an isoleucine (I) or phenylalanine (F) at a position corresponding to amino acid position 16 in SEQ ID NO: 282;   c) a serine (S) or a glycine (G) at a position corresponding to amino acid position 19 in SEQ ID NO: 282;   d) a cysteine (C) or a serine (S) at a position corresponding to amino acid position 22 in SEQ ID NO: 282;   e) an arginine (R) or glutamine (Q) at a position corresponding to amino acid position 31 in SEQ ID NO: 282;   f) an arginine (R), glutamine (Q), or lysine (K) at a position corresponding to amino acid position 50 in SEQ ID NO: 1;   g) an isoleucine (I) or a phenylalanine at a position corresponding to amino acid position 54 in SEQ ID NO: 282;   h) a leucine (L) or aspartic acid (D) at a position corresponding to amino acid position 56 in SEQ ID NO: 282;   i) a histidine (H) or valine (V) at a position corresponding to amino acid position 59 in SEQ ID NO: 282;   j) a valine (V) or isoleucine (I) at a position corresponding to amino acid position 62 in SEQ ID NO: 282;   k) a lysine (K) or isoleucine (I) at a position corresponding to amino acid position 81 in SEQ ID NO: 282;   l) an arginine (R) or lysine (K) at a position corresponding to amino acid position 98 in SEQ ID NO: 282;   m) a valine (V) or asparagine (N) at a position corresponding to amino acid position 103 in SEQ ID NO: 282;   n) an alanine (A) or valine (V) at a position corresponding to amino acid position 105 in SEQ ID NO: 282;   o) an arginine (R) or lysine (K) at a position corresponding to amino acid position 116 in SEQ ID NO: 282;   p) a threonine (T) or serine (S) at a position corresponding to amino acid position 118 in SEQ ID NO: 282;   q a glycine (G) or lysine (K) at a position corresponding to amino acid position 121 in SEQ ID NO: 282;   r) a valine (V), threonine (T), or isoleucine (I) at a position corresponding to amino acid position 132 in SEQ ID NO: 282;   s) a leucine (L), aspartic acid (D), or a methionine (M) at a position corresponding to amino acid position 153 in SEQ ID NO: 282;   t) a glutamic acid (E) or glycine (G) at a position corresponding to amino acid position 160 in SEQ ID NO: 282;   u) a valine (V) or glycine (G) at a position corresponding to amino acid position 161 in SEQ ID NO: 282;   v) a tyrosine (Y) or leucine (L) at a position corresponding to amino acid position 162 in SEQ ID NO: 282;   w) an arginine (R) or serine (S) at a position corresponding to amino acid position 163 in SEQ ID NO: 282;   x) a histidine (H) or proline (P) at a position corresponding to amino acid position 164 in SEQ ID NO: 282;   y) a leucine (L) or serine (S) at a position corresponding to amino acid position 165 in SEQ ID NO: 282;   z) an arginine (R) or glutamine (Q) at a position corresponding to amino acid position 166 in SEQ ID NO: 1;   aa) a histidine (H) or alanine (A) at a position corresponding to amino acid position 167 in SEQ ID NO: 282;   bb) a proline (P) or serine (S) at a position corresponding to amino acid position 168 in SEQ ID NO: 282;   cc) an alanine (A) or serine (S) at a position corresponding to amino acid position 169 in SEQ ID NO: 282;   dd) a proline (P) or alanine (A) at a position corresponding to amino acid position 170 in SEQ ID NO: 282;   ee) a histidine (H) or alanine (A) at a position corresponding to amino acid position 171 in SEQ ID NO: 282;   ff) a proline (P) or serine (S) at a position corresponding to amino acid position 172 in SEQ ID NO: 282;   gg) an arginine (R) or serine (S) at a position corresponding to amino acid position 173 in SEQ ID NO: 282;   hh) a leucine (L) or alanine (A) at a position corresponding to amino acid position 174 in SEQ ID NO: 282;   ii) a proline (P) or serine (S) at a position corresponding to amino acid position 175 in SEQ ID NO: 282;   jj) a glutamine (Q) or serine (S) at a position corresponding to amino acid position 176 in SEQ ID NO: 282;   kk) an alanine (A) or serine (S) at a position corresponding to amino acid position 177 in SEQ ID NO: 282;   ll) an arginine (R) or proline (P) at a position corresponding to amino acid position 178 in SEQ ID NO: 282;   mm) a valine (V) or glycine (G) at a position corresponding to amino acid position 179 in SEQ ID NO: 282;   nn) a glutamine (Q) or serine (S) at a position corresponding to amino acid position 180 in SEQ ID NO: 282;   oo) a serine (S) or isoleucine (I) at a position corresponding to amino acid position 182 in SEQ ID NO: 282;   pp) a proline (P) or serine (S) at a position corresponding to amino acid position 183 in SEQ ID NO: 282;   qq) a lysine (K) or glutamic acid (E) at a position corresponding to amino acid position 184 in SEQ ID NO: 282;   rr) an alanine (A) or a histidine (H) at a position corresponding to amino acid position 185 in SEQ ID NO: 282;   ss) a serine (S) or leucine (L) at a position corresponding to amino acid position 186 in SEQ ID NO: 282;   tt) a glutamic acid (E) or arginine (R) at a position corresponding to amino acid position 187 in SEQ ID NO: 282;   uu) a leucine (L) or alanine (A) at a position corresponding to amino acid position 188 in SEQ ID NO: 282;   vv) a glutamic acid (E) or glycine (G) at a position corresponding to amino acid position 189 in SEQ ID NO: 282;   ww) a proline (P) or alanine (A) at a position corresponding to amino acid position 190 in SEQ ID NO: 282;   xx) a threonine (T) or lysine (K) at a position corresponding to amino acid position 191 in SEQ ID NO: 282;   yy) an amino acid deletion at a position corresponding to amino acid position 192 in SEQ ID NO: 282;   zz) a glutamic acid (E) or lysine (K) at a position corresponding to amino acid position 244 in SEQ ID NO: 282;   aaa) a serine (S) or glycine (G) at a position corresponding to amino acid position 258 in SEQ ID NO: 282;   bbb) a tyrosine (Y) or phenylalanine (F) at a position corresponding to amino acid position 281 in SEQ ID NO: 282;   ccc) a glycine (G) or lysine (K) at a position corresponding to amino acid position 308 in SEQ ID NO: 282;   ddd) an alanine (A) or valine (V) at a position corresponding to amino acid position 312 in SEQ ID NO: 282;   eee) an alanine (A) or valine at a position corresponding to amino acid position 316 in SEQ ID NO: 282;   fff) a valine (V) or isoleucine (I) at a position corresponding to amino acid position 319 in SEQ ID NO: 1;   or,   rrrrr) any combination of a) to fff).   
     
     
         5 . The isolated or recombinant polynucleotide of  claim 1 , wherein said nucleotide sequence encodes a meganuclease polypeptide selected from the group consisting of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, and 298. 
     
     
         6 . The isolated or recombinant polynucleotide of  claim 1 , wherein said nucleotide sequence encodes a meganuclease polypeptide, wherein the polypeptide is capable of recognizing and cleaving a meganuclease recognition sequence of SEQ ID NO: 281. 
     
     
         7 . The isolated or recombinant polynucleotide of  claim 1  wherein said polypeptide has an increased meganuclease activity when compared to a control meganuclease that lacks said amino acid modification. 
     
     
         8 . The isolated or recombinant polynucleotide of  claim 7 , wherein said control meganuclease is selected from the group of SEQ ID NO: 282 and SEQ ID NO: 283. 
     
     
         9 . The isolated or recombinant polynucleotide of  claim 7 , wherein the increased meganuclease activity is evidenced by:
 a) a higher yeast assay score when compared to the control meganuclease that lacks said amino acid modification; or,   b) a higher target site mutation rate when compared to the control meganuclease that lacks said amino acid modification; or,   c) a higher in-vitro cutting when compared to the control meganuclease that lacks said amino acid modification; or,   d) any combination of (a), (b) and (c).   
     
     
         10 . The isolated or recombinant polynucleotide of  claim 7 , wherein the increased meganuclease activity is determined at 16° C., 24° C., 28° C., 30° C. or 37° C. 
     
     
         11 . A recombinant DNA construct, comprising the isolated or recombinant polynucleotide of  claim 1 . 
     
     
         12 . A cell comprising at least one polynucleotide of  claim 1  or the recombinant DNA construct of  claim 11 , wherein said polynucleotide is heterologous to the cell. 
     
     
         13 . The cell of  claim 12 , wherein said cell is a plant cell. 
     
     
         14 . The cell of  claim 12 , wherein said plant cell is from a monocot. 
     
     
         15 . The cell of  claim 12 , wherein said plant cell is from a dicot. 
     
     
         16 . A plant comprising a plant cell of  claim 13 . 
     
     
         17 . A transgenic seed produced by the plant of  claim 16 , wherein said transgenic seed comprises the heterologous polynucleotide of  claim 1  or the recombinant construct of  claim 11 . 
     
     
         18 . A method for producing a meganuclease having increased activity over a range of temperatures, the method comprising:
 (a) producing a variant meganuclease, wherein the variant meganuclease has at least 80% sequence identity to SEQ ID NO:282 and comprises a tyrosine (Y) at an amino acid position corresponding to position 66 of SEQ ID NO:282, by modifying at least one amino acid at an amino acid position corresponding to a position of SEQ ID NO: 282 selected from the group consisting of positions 12, 16, 19, 22, 31, 50, 54, 56, 59, 62, 81, 98, 103, 105, 116, 118, 121, 132, 153, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 244, 258, 281, 308, 312, 316, 319, and combinations thereof;   (b) screening said variant meganuclease for the ability to cleave a DNA target sequence over a range of temperatures between and including 16 degrees Celsius and 37 degrees Celsius; and,   selecting a variant meganuclease from step (b) that is able to cleave a DNA target sequence over said temperature range.   
     
     
         19 . The method of  claim 18 , wherein said range of temperatures comprises:
 a) 16° C.;   b) 18° C.;   c) 20° C.;   d) 24° C.;   e) 28° C.;   f) 30° C.;   g) 37° C.; or,   h) any combination of a), b), c), d), e), f), and g).   
     
     
         20 . A method for producing a meganuclease having an increased meganuclease activity when compared to a control meganuclease, the method comprising:
 (a) producing a variant meganuclease by modifying at least one amino acid at an amino acid position corresponding to a position of SEQ ID NO: 282 selected from the group consisting of positions 12, 16, 19, 22, 31, 50, 54, 56, 59, 62, 81, 98, 103, 105, 116, 118, 121, 132, 153, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 244, 258, 281, 308, 312, 316, 319, and combinations thereof;   (b) screening said variant for increased meganuclease activity when compared to a control meganuclease; and,   (c) selecting a variant meganuclease from step (b) that is able to cleave a DNA target sequence.   
     
     
         21 . The method of  claim 20 , wherein the increased meganuclease activity is evidenced by:
 a) a higher yeast assay score when compared to the control meganuclease that lacks said amino acid modification; or,   b) a higher target site mutation rate when compared to the control meganuclease that lacks said amino acid modification; or,   c) a higher in-vitro cutting when compared to the control meganuclease that lacks said amino acid modification; or,   d) any combination of (a), (b) and (c).   
     
     
         22 . A composition comprising at least one polynucleotide of  claim 1 .