Engineered tyrosine ammonia lyase

Abstract

The present invention provides engineered tyrosine ammonia-lyase (TAL) polypeptides and compositions thereof. In some embodiments, the engineered TAL polypeptides have been optimized to provide enhanced catalytic activity while reducing sensitivity to proteolysis and increasing tolerance to acidic pH levels. The invention also provides methods for utilization of the compositions comprising the engineered TAL polypeptides for therapeutic and industrial purposes.

What is claimed is: 
     
         1 . A recombinant tyrosine ammonia lyase and/or biologically active recombinant tyrosine ammonia lyase fragment comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 2. 
     
     
         2 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution at position or set of positions selected from 79/95/107, 79/107, 79/107/410, 79/410, 95/107/184, 95/107/184/534, 95/184/534, 99/107/184, 107/184/534, and 107/401/534, wherein the positions are numbered with reference to SEQ ID NO: 2. 
     
     
         3 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 28, 29, 33, 33/34/37/46/279/554, 33/34/37/90/554, 33/34/46/66/90/289, 33/34/90/289/554, 33/34/279/289, 33/66, 33/66/289, 33/66/289/554, 34/37/46/289, 34/37/66/279/289, 34/46, 34/56/90, 34/56/90/289, 34/66/289, 34/90/289/554, 34/90/519, 36/70/234/302/461/500, 36/79, 36/79/304/407, 36/79/407/461/500/531, 36/111/304/461/531, 36/407/461/500/531, 37, 46, 46/66/289/519/554, 49, 56, 66, 66/90/279/289/554, 66/90/289/554, 69, 70/79/234/361/407, 70/111/461/500/531, 70/304/407/461, 72, 79/111/234/361/500, 79/111/234/531, 79/111/361, 79/111/531, 79/304/361, 79/304/461/531, 79/407/461, 88, 90/289/519, 90/289/554, 131, 142, 198, 201, 272, 278, 279/289/554, 289/519/554, 289/554, 295, 304/361, 305, 350, 361/500/531, 461/500, 490, 491, 499, 510, 518, 519, 521, 522, 523, 524, 531, 540, 541, 544, 547, 548, 554, 557, 558, and 560, wherein the positions are numbered with reference to SEQ ID NO: 14. 
     
     
         4 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 28/34/49/70/234/289/544/554, 33/34/49/234/531/547/554, 33/34/66/70/519/531, 33/34/66/289/522/531, 33/34/70/234/289/519, 33/34/70/234/518/519/547/554, 33/34/70/289/522/554, 33/34/289/522/531, 34/49/66/531, 34/49/234/531/554, 34/49/289/544/547, 34/66/70/234/518/519/547, 34/66/531/554, 34/66/554, 34/70/234/289/522, 34/70/234/554, 34/70/289/522, 34/234/522/554, 34/289, 34/289/522/531, 34/289/522/544/554, 34/522, 34/544, 66/70/234, and 234/531/544/547, wherein the positions are numbered with reference to SEQ ID NO: 86. 
     
     
         5 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 31, 37/49/56/66/111, 37/49/56/234/557, 37/49/56/500/524, 37/49/66/111/234, 37/49/111/524, 37/111, 37/111/361/500/557/558, 37/234, 43/59/93/506, 43/306, 43/306/506, 49/56/66/111/153/234/500/524, 49/66, 56/111/234, 56/234/500, 61, 65, 65/336, 66, 66/111/234/500, 93/506, 95, 103, 103/107/417/421, 103/306/506, 103/421, 104/105, 107, 107/417/421, 111/234/548/558, 111/361, 145, 146, 155, 172, 197, 211, 234, 234/524, 237/238/506, 286, 304, 306, 306/506, 328, 336, 361/524/557/558, 407, 417/421, 421, 471, 504, 506, 549, and 558, wherein the positions are numbered with reference to SEQ ID NO: 334. 
     
     
         6 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 31/61/95/286/328, 31/61/95/407/504, 31/61/95/471/504, 31/61/407/504, 31/95/155/286/504/549, 31/95/237/504/547/549, 31/95/286/504, 31/95/286/504/549, 31/95/328/504, 31/95/504, 31/95/549, 37/49/56/59/145, 37/103/111/145/421/500/524, 49/56/59/234/500, 49/59/66/111/145/234, 49/59/145/234/421, 56/59/66/234, 56/59/111/145, 56/59/111/145/234/421, 56/66/145/500, 56/103/111/145/234/500, 59/103/145/234/421/500, 59/103/234/421, 59/145, 59/234, 61, 61/95/155/286/407/471, 61/95/155/407, 61/95/286, 61/95/286/328/504, 61/95/328/407, 61/95/328/549, 61/95/407, 61/95/504/547, 61/286/407, 61/328, 61/328/504, 61/328/504/549, 61/407, 61/504, 66/103/145/234/421, 95/155/286/328/407/504, 95/155/286/549, 95/286, 95/286/328/407/504, 95/286/328/504, 95/286/547, 95/287/504/549, 95/328/504, 95/407, 95/407/504, 95/504/547, 95/549, 103/111/145/234/421, 111/145/234, 111/234, 145/234/500, 286/328/407/504/549, and 549, wherein the positions are numbered with reference to SEQ ID NO: 388. 
     
     
         7 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 14/56/114, 14/114/283/289, 14/114/283/289/291, 14/114/283/289/562, 14/114/291/518/562, 14/114/518, 14/234/283/291/305, 14/283/289/562, 29/66/111, 29/66/111/540, 29/111, 29/111/523, 33/46/49, 33/46/49/336/519/548/549, 33/46/49/549, 33/46/518/534/548/549, 33/46/519, 33/49/336, 33/336/519, 36/37/56/59/145/234/328, 36/37/59/131/531, 36/37/103/234, 36/37/131/145/234/328, 36/37/145/234, 36/37/145/234/328/471/531, 36/37/234/328/531, 36/56/145/234/328, 36/59/234/328, 36/59/531, 36/103/145/328/531, 36/131, 36/234/531, 37/56/59/103/145/234/328/471/531, 37/56/59/234/328/524/531, 37/56/59/234/531, 37/56/234/531, 37/59/234, 37/234/471, 46/49, 46/49/518/519/548/549, 46/49/519, 46/155, 46/548, 49/519, 56, 56/59/103/471/531, 56/59/471/531, 56/114/206/283, 56/114/291, 56/114/291/518/562, 56/114/518, 56/518, 59/328/524/531, 66/540, 111, 111/510/521/523/541/558, 111/523/557, 114, 114/206/283/289/562, 114/283/289/291, 114/283/289/305/518, 114/283/291, 114/289, 114/289/562, 114/291, 114/291/518, 114/518/562, 114/562, 131/234/328, 234, 234/328, 234/328/471, 234/531, 289/562, 305, 336/519, 518/519/548/549, 519, 521, 523, 531, 541, 548/549, and 549, wherein the positions are numbered with reference to SEQ ID NO: 604. 
     
     
         8 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 20/49/56/59/111/291, 20/59/234/518/549/562, 49/56/59/66/291/531/549, 49/56/59/111/549, 49/56/66/111/234/291/518, 49/56/66/234, 49/59/66/145/234, 49/59/66/289, 49/59/289/562, 49/66/111/234/291/518/562, 49/111/531, 49/234, 56/59/111/234/289, 56/59/111/234/531, 56/59/111/283/518/531, 56/59/111/291, 56/59/111/291/518/531, 56/59/145/289/518/562, 56/59/234, 56/59/234/518, 56/59/518, 56/111/145/234/289/531/562, 56/111/145/234/518/549/562, 56/111/518/549, 56/234/291, 59, 59/111, 59/145/234/291, 59/234/291, 59/234/291/387/549/562, 111/145, 111/145/234/291/562, 111/145/234/562, 111/234, 111/289, 111/291, 111/518, 234, 234/518/549, 291/518/549, 518, 518/531/549/562, 531, and 549, wherein the positions are numbered with reference to SEQ ID NO: 736. 
     
     
         9 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 33/37, 33/37/46/305, 33/37/103, 33/37/103/305, 33/37/103/305/336/541/548, 33/37/103/305/523/548, 33/37/103/305/548, 33/37/103/336/518/541/548, 33/37/103/471/519/548, 33/37/103/518/523/541, 33/37/103/519/523, 33/37/103/523, 33/37/103/540, 33/37/305, 33/37/305/328, 33/37/305/328/548, 33/37/305/336/471/541, 33/37/305/336/518/523, 33/37/305/336/521/523/548, 33/37/305/336/521/548, 33/37/305/336/541, 33/37/305/471/521/548, 33/37/305/523/540, 33/37/305/540, 33/37/305/541, 33/37/336, 33/37/336/540, 33/37/336/540/548, 33/37/471/523/540/548, 33/37/518/521/540, 33/37/518/521/548, 33/37/518/548, 33/37/521/548, 33/37/523, 33/37/523/540/548, 33/37/540, 33/37/548, 33/46, 33/46/66/305/521/523/540/548, 33/46/103/305/336/518/519/540, 33/46/103/305/336/548, 33/46/103/305/540, 33/46/103/540/548, 33/46/305, 33/46/305/336, 33/46/305/518/540/548, 33/46/336/471/519/523/548, 33/46/336/521, 33/46/336/521/523, 33/46/336/540, 33/46/336/540/548, 33/46/518/521/548, 33/46/521/548, 33/46/523, 33/46/541, 33/46/548, 33/103/336/518/521/548, 33/471/523/541, 37, 37/103, 37/103/305/336, 37/103/305/336/521/523/540/548, 37/103/305/336/523/540, 37/103/305/471, 37/103/305/471/540/548, 37/103/305/521/541/548, 37/103/305/540, 37/103/328/336/518/523/548, 37/103/328/521/541/548, 37/103/336, 37/103/336/521/541, 37/103/519/541/548, 37/103/540, 37/103/541/548, 37/305, 37/305/336, 37/305/336/521/540/548, 37/305/336/523/548, 37/305/336/540/548, 37/305/336/541/548, 37/305/471, 37/305/471/523/540/548, 37/305/471/540/548, 37/305/519/548, 37/305/521/523/540/548, 37/305/521/540, 37/305/521/541/548, 37/305/523/541/548, 37/305/541, 37/305/541/548, 37/305/548, 37/336, 37/336/471/541/548, 37/336/521/523, 37/336/521/523/548, 37/336/523/548, 37/336/540, 37/336/548, 37/471, 37/471/518, 37/471/518/519/523, 37/471/521/540/548, 37/519, 37/521/523/548, 37/521/540, 37/523/541, 37/523/548, 37/540, 37/540/548, 37/541, 37/548, 46, 46/49/59/111/523/531/549, 46/49/111/234/289/436/549, 46/49/111/234/289/531/549, 46/49/111/234/336, 46/49/111/234/336/523/549, 46/49/111/336/549, 46/49/234/289/336, 46/49/234/336/521/523/549, 46/49/234/540/549, 46/49/234/549, 46/49/289/523/531/549/562, 46/49/531/549, 46/59/234, 46/59/549/562, 46/103/305, 46/103/305/336/471/540/548, 46/103/305/336/523, 46/103/305/471/540/548, 46/103/305/520/540, 46/103/305/548, 46/103/523/548, 46/103/540/548, 46/103/541, 46/103/541/548, 46/103/548, 46/111/234/289/531/549, 46/111/234/521/549, 46/111/523/531/549, 46/234/289/549, 46/234/521/523/531/540/549, 46/234/549, 46/289/549, 46/305, 46/305/336, 46/305/336/518, 46/305/336/522, 46/305/336/548, 46/305/471, 46/305/523/548, 46/305/548, 46/336/521/523, 46/336/523/548, 46/336/540, 46/336/540/548, 46/521/523, 46/521/523/540, 46/521/523/549, 46/521/548, 46/523/540, 46/523/541/548, 46/541, 46/541/548, 46/548, 46/549, 49, 49/59/111/234/289/521, 49/59/111/289/523, 49/59/234/289/336, 49/59/234/289/336/523/531/549, 49/59/289/305/336, 49/59/289/336, 49/59/336, 49/59/521/531, 49/111, 49/111/234, 49/111/234/289/336/523/531/549, 49/111/234/289/521/523/531/549/562, 49/111/234/289/523/549, 49/111/234/336/521/523, 49/111/234/336/523/531, 49/111/234/523/531/549, 49/111/234/531, 49/111/234/549, 49/111/289, 49/111/289/336/521/549, 49/111/523/531/549, 49/111/531/549, 49/234, 49/234/289, 49/234/289/336/531/549, 49/234/289/523, 49/234/289/523/531/540, 49/234/289/523/549, 49/234/305/549, 49/234/521, 49/234/549, 49/289/305/336/523, 49/289/336, 49/289/336/521/531, 49/336/521/562, 49/521/531/549/562, 49/521/549, 49/523/549, 49/549, 59, 59/111/234/289/305/336/549, 59/111/234/289/305/549, 59/111/289, 59/111/336, 59/549, 103, 103/336/519/548, 103/521/523/540, 111/234/289, 111/234/289/523, 111/289/336/521, 111/289/336/523/549, 111/336/562, 111/521/523/549, 234, 234/289, 234/289/336/523, 234/289/523/531/549/562, 234/289/523/549, 234/289/531, 234/289/549, 234/336, 234/336/531/562, 234/521/523, 234/521/523/549, 234/523/531, 234/531/549, 234/540, 234/549, 234/562, 289, 289/336/549, 289/521/523, 289/521/523/540, 289/521/523/549, 289/523, 305/336/541/548, 336/548, 519/548, 521, 521/548, 521/549, 521/562, 523, 531/549, 540, and 549, wherein the positions are numbered with reference to SEQ ID NO: 736. 
     
     
         10 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 24/44/464, 24/201/202/351/507, 24/202/351, 33/37/46/56/103/523/540/548/549, 33/37/46/56/111/234/523, 33/37/46/56/111/523/540, 33/37/46/103/111/234, 33/37/46/103/111/548/549, 33/37/46/103/523, 33/37/46/111/234/328/523/540/548, 33/37/46/111/336/540, 33/37/46/234/523, 33/37/46/336, 33/37/46/548/549, 33/37/56/111/234/523/540/548, 33/37/56/234/523/540/548, 33/37/103/111/234/336/540/548, 33/37/103/336/523/540/548, 33/37/111/234/523/540/548, 33/37/111/523/540, 33/37/111/548, 33/37/234/336/523/548, 33/37/523/540/548, 33/46, 33/46/56/111/548, 33/46/56/234/248/549, 33/46/103/523/549, 33/56/103/111, 33/103/111/234, 33/103/111/234/336/523/548, 33/103/111/234/540/549, 33/103/111/336, 33/111/234/548, 33/234/328/523/540/549, 33/234/336/523/540/548/549, 33/234/523/540/548, 33/234/523/548, 33/234/540/548/549, 33/336, 33/336/523/540/548/549, 33/336/540/548, 33/336/549, 37, 37/46/56/523, 37/46/234, 37/46/336/523/540/548, 37/46/336/540/548, 37/56/234/336/523/540/548/549, 37/56/336/523/540/548, 37/103/336/548/549, 37/111/523, 37/234/328/336/523, 37/336, 37/548/549, 44, 46/103/328/336/523, 46/103/336, 46/234/336, 46/234/540/548, 46/336/540/549, 202, 202/332/408, 234/523/540/548/549, 336/523, 408, and 523/548, wherein the positions are numbered with reference to SEQ ID NO: 790. 
     
     
         11 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 74, 102, 210, 313, 391, 392, 402, 415, 417, 418, 420, 424, 506, and 530, wherein the positions are numbered with reference to SEQ ID NO: 790. 
     
     
         12 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 24, 24/44, 24/44/46/202/391, 24/44/111/202/464/506, 24/44/202/313/391/540, 24/44/549, 24/46/102/313/506, 24/46/103/111/464/506/549, 24/46/103/391/506, 24/46/111/313/391, 24/46/111/313/549, 24/46/111/506, 24/46/202/391/506, 24/46/549, 24/103/202, 24/202, 44/46/102/202/313/417, 44/46/103/111/391, 44/46/103/202/313/391, 44/46/103/202/417/464, 44/103/111/313/391/540, 44/111/464/506, 46/103/506, 46/111/417, 46/111/506, 46/202, 46/202/506/549, 46/313/391/540, 103/313/549, 111, 111/202, 111/202/313/391/464, 111/202/313/391/506, 111/202/313/417/540/549, 111/202/391, 111/202/391/540, 111/464/540/549, 202/313/391/549, 202/417/464/540/549, 202/464/506, 202/506/540, 202/506/540/549, 313/391/540/549, and 417, wherein the positions are numbered with reference to SEQ ID NO: 1454. 
     
     
         13 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 20/44/202/506, 20/103/111/471/506, 20/202/313/471/506, 24, 27, 33, 36, 41, 44, 44/111/202/464/471/506/549, 44/202/464/506, 46, 48, 50, 51, 55, 56/111/506, 56/506, 59, 66, 66/528, 103/111/202/464/471, 103/111/471, 103/202/540, 103/464/549, 103/471, 111, 111/202/313/316, 111/202/313/471/506, 111/202/471, 111/506, 197, 202, 202/313/464/471/506, 202/464/506, 202/464/506/549, 208, 272, 289, 292/553, 305, 312/559, 313/464/471/506, 331, 332, 432, 435, 464, 464/506, 470, 500, 504, 506, 506/549, 518, 519, 523, 540, 543, 547, 547/553, 555, 556, and 559, wherein the positions are numbered with reference to SEQ ID NO: 1578. 
     
     
         14 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 20, 20/44/208/272/519, 20/111/208/272/410/432, 20/197/432/519, 24, 24/46/410/435/518, 36/55/305/332/410, 36/66/197/305/332/457, 36/66/197/305/410, 36/66/305, 36/66/305/332/410, 36/66/305/500, 36/197/305, 36/197/305/332/410, 36/197/305/332/410/500, 36/197/305/332/410/559, 36/197/305/332/500, 36/197/305/410, 36/197/305/500, 36/305, 36/305/332, 36/305/332/410, 36/305/410, 41/44/46/111/272, 41/432/526, 44/46/111/208, 44/46/111/432/519, 44/111/432/519/526, 44/208/432/435, 46/111/208/272/435/526, 46/208/272/432/435/526, 46/432/471, 55/305, 55/305/332/457/543/547, 55/305/500/559, 66/305, 66/305/332, 111, 111/272/432/435, 111/272/471/526, 111/272/519, 111/432/435, 111/432/526, 111/526, 134/202/305, 197/305, 197/305/332/410, 197/305/332/500/543/547, 197/305/410, 197/305/500, 208, 208/272/432, 208/410/435, 208/435/519, 211/410, 272, 272/435/526, 298/410, 305, 305/332, 305/332/410, 305/332/410/500, 305/332/457, 305/332/457/500, 305/332/457/555, 305/332/500, 305/410, 305/500/543/547, 410, 432/526, 435, 435/518, 435/519/526, 471, 471/526, and 519, wherein the positions are numbered with reference to SEQ ID NO: 1660. 
     
     
         15 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 24/59/111/289/504, 24/111/289, 24/111/289/500/504, 24/111/432, 24/111/435/500, 24/289, 24/432/435/504, 41/44/208/547, 41/51/410/543, 41/208/410/543/547, 41/208/518/519/547, 41/208/547, 41/410/518/543, 41/410/518/547, 41/543, 44/208/518/547, 51/519, 59/66/111/289/432/500, 59/66/111/432/500, 59/66/111/432/504, 59/66/289/500/504/556, 59/111, 59/111/432/500, 59/289, 59/289/435, 59/432, 59/432/435/504/556, 66/111, 111, 111/289, 111/289/435, 111/289/435/500, 111/289/500, 111/331/432/504, 111/331/435/500, 111/432, 111/432/500, 111/500/504, 208, 208/211/410/519, 208/211/547, 211, 211/518/519/547, 211/547, 289, 289/432, 289/432/435, 289/435, 289/435/500/504, 289/435/504/556, 289/504, 410, 432, 435/504, 504, 504/556, 519, and 547, wherein the positions are numbered with reference to SEQ ID NO: 1844. 
     
     
         16 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 4, 8, 11, 13, 13/22/45/512, 13/45, 13/45/512, 17, 19, 45, 45/244/324/513, 45/436/512/513, 45/512, 144, 251, 324, 327, 341, and 428, wherein the positions are numbered with reference to SEQ ID NO: 2030. 
     
     
         17 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said tyrosine ammonia lyase comprises at least one substitution in at least one position or set of positions selected from 4/7/57/111, 4/7/111/114/437/547, 4/16/385/478, 4/57/111/437, 7/385/547, 10/16/437, 16, 16/41/57/111/385/547, 16/41/57/437/478, 16/41/437, 16/57, 16/241/437, 16/385, 16/385/437, 16/385/478/547, 16/437, 20/385/437/478/547, 57, 57/111/114, 57/111/478/547, 57/437, 111/114/202/234/289/305/313/324/332/336/410/432/435/464/504/512/519/523/548/549, 111/241/437/478, 111/478, 241, 241/385, 241/385/478, 241/385/478/547, 241/437, 385, 385/437, 385/437/478/547, 437, 437/478, and 478, wherein the positions are numbered with reference to SEQ ID NO: 2156. 
     
     
         18 . A recombinant tyrosine ammonia lyase comprising a sequence that is at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the polypeptide sequence of SEQ ID NO: 2, 14, 86, 334, 388, 604, 736, 790, 1454, 1578, 1660, 1844, 2030, and/or 2156. 
     
     
         19 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said recombinant tyrosine ammonia lyase is thermostable. 
     
     
         20 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said recombinant tyrosine ammonia lyase is resistant to proteolysis. 
     
     
         21 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said recombinant tyrosine ammonia lyase is acid stable. 
     
     
         22 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said recombinant tyrosine ammonia lyase is purified. 
     
     
         23 . The recombinant tyrosine ammonia lyase of  claim 1 , wherein said recombinant tyrosine ammonia lyase exhibits at least one improved property selected from: i) enhanced catalytic activity; ii) reduced sensitivity to proteolysis; iii) increased tolerance to acidic pH; iv) reduced aggregation; v) decreased Km for tyrosine; vi) decreased immunogenicity; or a combination of any of i), ii), iii), iv), v), and/or vi), as compared to a reference sequence selected from SEQ ID NO: 2, 14, 86, 334, 388, 604, 736, 790, 1454, 1578, 1660, 1844, 2030, 2114, and/or 2156. 
     
     
         24 . A composition comprising at least one recombinant tyrosine ammonia lyase of  claim 1 . 
     
     
         25 . A recombinant polynucleotide sequence encoding at least one recombinant tyrosine ammonia lyase set forth in  claim 1 . 
     
     
         26 . The recombinant polynucleotide sequence of  claim 25 , wherein said polynucleotide sequence is codon-optimized. 
     
     
         27 . An expression vector comprising a recombinant polynucleotide sequence encoding at least one recombinant tyrosine ammonia lyase of  claim 1 . 
     
     
         28 . The expression vector of  claim 27 , wherein said recombinant polynucleotide sequence is operably linked to a control sequence. 
     
     
         29 . A host cell comprising the expression vector of  claim 27 . 
     
     
         30 . The host cell of  claim 29 , wherein said host cell is selected from prokaryotic and eukaryotic cells. 
     
     
         31 . A method of producing a recombinant tyrosine ammonia lyase, comprising culturing said host cell of  claim 29 , under conditions that said recombinant tyrosine ammonia lyase encoded by said recombinant polynucleotide is produced. 
     
     
         32 . The method of  claim 31 , further comprising the steps of recovering and purifying said recombinant tyrosine ammonia lyase. 
     
     
         33 . A pharmaceutical composition for the treatment of tyrosinemia, comprising the composition of  claim 24 . 
     
     
         34 . The pharmaceutical composition of  claim 33 , further comprising a pharmaceutically acceptable carrier and/or excipient. 
     
     
         35 . The pharmaceutical composition of  claim 33 , wherein said composition is suitable for oral administration to a human. 
     
     
         36 . The pharmaceutical composition of  claim 33 , wherein said composition is suitable for parenteral injection into a human 
     
     
         37 . A method for treating and/or preventing the symptoms of tyrosinemia or alkaptonuria in a subject, comprising providing a subject having tyrosinemia or alkaptonuria, and providing the pharmaceutical composition of  claim 33 , to said subject. 
     
     
         38 . A method for the production of L-tyrosine and/or L-tyrosine derivatives comprising the steps of providing at least one recombinant tyrosine ammonia lyase of  claim 1 , and a suitable substrate, and combining said recombinant tyrosine ammonia lyase and said substrate under conditions such that L-tyrosine and/or at least one L-tyrosine derivative is produced. 
     
     
         39 . A method for the production of coumaric acid, comprising the steps of providing at least one recombinant tyrosine ammonia lyase of  claim 1 , and a suitable substrate, and combining said recombinant tyrosine ammonia lyase and said substrate under conditions such that coumaric acid is produced.