Similarly, 1.0-kb 3′ flanking sequence of dhfr-ts

was amplified using primers attB2_3′UTR_dhfr_f and attB3_3′UTR_dhfr_r (Additional file 6: Table S2) and cloned into pDONR™P2R-P3 to generate pDONR_3′UTR_dhfr. Using plasmid pBSSK-hyg1f8 [27] as a template, the Hyg and its upstream 1f8 region was amplified with primers attB1_1F8_f and attB2_1F8Hyg_r (Additional file 6: Table S2) and cloned into Entry vector pDONR™221. The three Entry clones were then mixed with a Destination vector pDEST™R4-R3 in an LR reaction using the LR Clonase II Plus Enzyme Mix (Invitrogen) to generate a final plasmid pDEST/dhfr-ts_1F8Hyg (Additional file 2: Figure S2). The knockout DNA cassette was liberated from the plasmid backbone with AlwNI and PvuI enzymes, and purified Autophagy inhibitor as above. pDEST/ech_Neo-GAPDH and pDEST/ech_Hyg-GAPDH Trypanosoma cruzi ech1 and ech2 are click here tandemly arranged genes. To construct the pDEST/ech_Hyg-GAPDH plasmid, 1.0-kb 5′ sequence of ech2 was amplified with primers attB4_ech5′UTR_f and attB1_ech5′UTR_r (Additional file 6: Table S2), gel purified and cloned into the Entry clone pDONR-ech5′UTR. Similarly, 1.0-kb 3′ sequence of ech1 was amplified with primers attB2_ech3′UTR_f and attB3_ech3′UTR_r (Additional file 6:

Table S2) and cloned into pDONR™P2R-P3 to generate pDONR-ech3′UTR. Hyg and the downstream intergenic region of GAPDH (glyceraldehyde-3-phosphate L-NAME HCl dehydrogenase) (GAPDH-IR) was amplified from plasmid pTEX-Hyg.mcs [36] using primers attB1_Hyg_f and attB2_Hyg_r (Additional file 6: Table S2) and cloned into Entry vector pDONR™221. The three Entry clones were then mixed with a Destination vector pDEST™R4-R3 to generate pDEST/ech_Hyg-GAPDH (Additional file 4: Figure S3A) through a LR reaction. The final plasmid was digested with restriction enzymes PvuII and PciI and purified as above. Similarly, to construct pDEST/ech_Neo-GAPDH (Additional file 4: Figure

S3B), Neo and 3′UTR of GAPDH (GAPDH 3′UTR) was amplified from plasmid pTrex-YFP (modified from the backbone of pTrex [37]) with primers attB1_Neo_f and attB2_Neo_r (Additional file 6: Table S2) and cloned into Entry vector pDONR™221. The final plasmid was digested with restriction enzymes PvuI and PciI and purified as above. Construction of knockout DNA cassettes via one-step-PCR For the constructs for deletion of the dhfr-ts gene using one-step-PCR, Neo and Hyg was amplified with primers LP_dhfr_Neo_f and LP_dhfr_Neo_r, and LP_dhfr_Hyg_f and LP_dhfr_Hyg_r (Additional file 7: Table S3) from plasmids pTrex-YFP and pTEX-Hyg.mcs respectively.