In vitro methods for processing lignin and other aromatic compounds
Enzymes for depolymerizing lignin. The enzymes include dehydrogenases, β-etherases, and glutathione lyases. The dehydrogenases can comprise one or more or LigD, LigO, LigN, and LigL. The β-etherases can comprise one or more of LigE, LigF, LigP, and BaeA. The glutathione lyases can comprise any one or more of LigG and a number of non-stereospecific, optionally recombinant glutathione lyases derived from Sphingobium sp. SYK-6, Novosphingobium aromaticivorans, Escherichia coli, Streptococcus sanguinis, Phanerochaete chrysosporium , and other microorganisms. The enzymes can be combined in compositions and/or used in methods of processing lignin or other aromatic compounds in vitro.
1. A method of processing lignin, comprising contacting lignin comprising β-O-4 ether linkages in vitro with:
a dehydrogenase comprising at least one of LigD, LigO, LigN, and LigL;
a β-etherase comprising at least one of LigE, LigF, LigP, and an enzyme comprising a first polypeptide having an amino acid sequence of SEQ ID NO:40 or an amino acid sequence at least about 95% identical thereto and a second polypeptide having an amino acid sequence of SEQ ID NO:42 or an amino acid sequence at least about 95% identical thereto; and
a non-stereospecific glutathione lyase comprising an amino acid sequence at least about 80% identical to any of:
SEQ ID NO:18 (NaGST Nu );
residues 21-313 of SEQ ID NO:20 (recombinant NaGST Nu );
SEQ ID NO:22 (SYK6GST Nu );
residues 21-324 of SEQ ID NO:24 (recombinant SYK6GST Nu );
SEQ ID NO:26 (ecYghU);
residues 21-313 of SEQ ID NO:28 (recombinant ecYghU); and
SEQ ID NO:32 (ssYghU),
wherein the non-stereospecific glutathione lyase comprises at least four of:
threonine or a conservative variant of threonine at a position corresponding to position 51 of SEQ ID NO:18 (NaGST Nu );
asparagine or a conservative variant of asparagine at a position corresponding to position 53 of SEQ ID NO:18 (NaGST Nu );
glutamine or a conservative variant of glutamine at a position corresponding to position 86 of SEQ ID NO:18 (NaGST Nu );
lysine, a conservative variant of lysine, arginine, or a conservative variant of arginine at a position corresponding to position 99 of SEQ ID NO:18 (NaGST Nu );
isoleucine or a conservative variant of isoleucine at a position corresponding to position 100 of SEQ ID NO:18 (NaGST Nu );
glutamate or a conservative variant of glutamate at a position corresponding to position 116 of SEQ ID NO:18 (NaGST Nu );
serine, threonine, a conservative variant of serine, or a conservative variant of threonine at a position corresponding to position 117 of SEQ ID NO:18 (NaGST Nu ); and
arginine or a conservative variant of arginine at a position corresponding to position 177 of SEQ ID NO:18 (NaGST Nu ).
2. The method of claim 1 , wherein the non-stereospecific glutathione lyase comprises an amino acid sequence at least about 85% identical to any of:
SEQ ID NO:18 (NaGST Nu );
residues 21-313 of SEQ ID NO:20 (recombinant NaGST Nu );
SEQ ID NO:22 (SYK6GST Nu );
residues 21-324 of SEQ ID NO:24 (recombinant SYK6GST Nu );
SEQ ID NO:26 (ecYghU);
residues 21-313 of SEQ ID NO:28 (recombinant ecYghU); and
SEQ ID NO:32 (ssYghU).
3. The method of claim 1 , wherein the non-stereospecific glutathione lyase comprises an amino acid sequence at least about 90% identical to any of:
SEQ ID NO:18 (NaGST Nu );
residues 21-313 of SEQ ID NO:20 (recombinant NaGST Nu );
SEQ ID NO:22 (SYK6GST Nu );
residues 21-324 of SEQ ID NO:24 (recombinant SYK6GST Nu );
SEQ ID NO:26 (ecYghU); and
residues 21-313 of SEQ ID NO:28 (recombinant ecYghU).
4. The method of claim 1 , wherein the non-stereospecific glutathione lyase comprises an amino acid sequence at least about 95% identical to any of:
SEQ ID NO:18 (NaGST Nu );
residues 21-313 of SEQ ID NO:20 (recombinant NaGST Nu );
SEQ ID NO:22 (SYK6GST Nu );
residues 21-324 of SEQ ID NO:24 (recombinant SYK6GST Nu );
SEQ ID NO:26 (ecYghU); and
residues 21-313 of SEQ ID NO:28 (recombinant ecYghU).
5. The method of claim 1 , wherein the non-stereospecific glutathione lyase comprises at least seven of:
asparagine or a conservative variant of asparagine at a position corresponding to position 25 of SEQ ID NO:18 (NaGST Nu );
threonine or a conservative variant of threonine at a position corresponding to position 51 of SEQ ID NO:18 (NaGST Nu );
asparagine or a conservative variant of asparagine at a position corresponding to position 53 of SEQ ID NO:18 (NaGST Nu );
glutamine or a conservative variant of glutamine at a position corresponding to position 86 of SEQ ID NO:18 (NaGST Nu );
lysine, a conservative variant of lysine, arginine, or a conservative variant of arginine at a position corresponding to position 99 of SEQ ID NO:18 (NaGST Nu );
isoleucine or a conservative variant of isoleucine at a position corresponding to position 100 of SEQ ID NO:18 (NaGST Nu );
glutamate or a conservative variant of glutamate at a position corresponding to position 116 of SEQ ID NO:18 (NaGST Nu );
serine, threonine, a conservative variant of serine, or a conservative variant of threonine at a position corresponding to position 117 of SEQ ID NO:18 (NaGST Nu );
tyrosine or a conservative variant of tyrosine at a position corresponding to position 166 of SEQ ID NO:18 (NaGST Nu );
arginine or a conservative variant of arginine at a position corresponding to position 177 of SEQ ID NO:18 (NaGST Nu ); and
tyrosine or a conservative variant of tyrosine at a position corresponding to position 224 of SEQ ID NO:18 (NaGST Nu ).
6. The method of claim 1 , wherein the contacting occurs in the presence of a glutathione (GSH) reductase that catalyzes reduction of glutathione disulfide (GSSG).
7. The method of claim 6 , wherein the GSH reductase comprises an amino acid sequence at least about 95% identical to SEQ ID NO:38 (AvGR).
8. The method of claim 1 , wherein the contacting releases at least one of a monomeric phenylpropanoid unit and a monomeric flavone.
9. The method of claim 1 , wherein the contacting releases at least one of a monomeric guaiacyl phenylpropanoid unit, a monomeric syringyl phenylpropanoid unit, a monomeric p-hydroxyphenyl phenylpropanoid unit, and a monomeric tricin unit.
10. The method of claim 1 , wherein the lignin comprises an average molecular weight (MW) of from about 600 to about 20,000.
11. The method of claim 1 , wherein the dehydrogenase comprises at least one of LigD and LigO and at least one of LigL and LigN.
12. The method of claim 1 , wherein the dehydrogenase comprises LigD and LigN.
13. The method of claim 1 , wherein the β-etherase comprises LigF and at least one of LigE, LigP, and the enzyme comprising the first polypeptide having the amino acid sequence of SEQ ID NO:40 or the amino acid sequence at least about 95% identical thereto and the second polypeptide having the amino acid sequence of SEQ ID NO:42 or the amino acid sequence at least about 95% identical thereto.
14. The method of claim 1 , wherein the β-etherase comprises LigF and LigE.
15. The method of claim 1 , wherein the non-stereospecific glutathione lyase comprises an amino acid sequence at least about 95% identical to SEQ ID NO:18 (NaGST Nu ).
16. The method of claim 1 , wherein:
the dehydrogenase comprises at least one of LigD and LigO and at least one of LigL and LigN;
the β-etherase comprises LigF and at least one of LigE, LigP, and the enzyme comprising the first polypeptide having the amino acid sequence of SEQ ID NO:40 or the amino acid sequence at least about 95% identical thereto and the second polypeptide having the amino acid sequence of SEQ ID NO:42 or the amino acid sequence at least about 95% identical thereto;
the non-stereospecific glutathione lyase comprises an amino acid sequence at least about 95% identical to SEQ ID NO:18 (NaGST Nu ); and
the contacting occurs in the presence of a glutathione (GSH) reductase that catalyzes reduction of glutathione disulfide (GSSG) and comprises an amino acid sequence at least about 95% identical to SEQ ID NO:38 (AvGR).
17. The method of claim 1 , wherein:
the dehydrogenase comprises LigD and LigN;
the β-etherase comprises LigF and LigE;
the non-stereospecific glutathione lyase comprises an amino acid sequence at least about 95% identical to SEQ ID NO:18 (NaGST Nu ); and
the contacting occurs in the presence of a glutathione (GSH) reductase that catalyzes reduction of glutathione disulfide (GSSG) and comprises an amino acid sequence at least about 95% identical to SEQ ID NO:38 (AvGR).