Four iertransform infrared(FTIR) microspectroscopy was used to investigate the effects of C-terminal acidic protein on the secondary structure of wheat α-thionin in the absence of signal pepti deduring the prokaryotic expression process. SDSPAGE analysis revealed that the presence of acidic protein gave rise to the form ation of inclusion body, however, the absence of acidic protein greatly enhanced the solubility of the heterogenous protein expressed in E. coli BL21(DE3) with the induction of 1 mmol·L^-1 IPTGat 37 ℃. Difference spectra in amide I region were obtained by subtraction between the spectra of intact cells containing S and Sc, which corresponds to the absence and presence of C-terminal acidic proteins, respectively. The second derivative of the difference spectra measured 2 h after induction showed one principal componentat～1630cm^-1, while no significant peak appeared at the same peak position when the spectra before induction were compared. Combined with SDSPAGE of recombinant protein, the authorspres umed that the peak absorption at～1630 cm^-1 is most likey to beassigned to protein aggregate within inclusion body. Gaussian curve-fitting was done on the Fourier self-deconvolution spectra within amide I region of intact cells containing S and Sc. The experimental data revealed that the relative content of aggregate absorption at(1629±1) cm^-1 gradually increased with induction time, which is consistent with the results of SDS-PAGE. Simutaneously, the formation of aggregate gave rise to the increase of α-helix, as well as thedecrease of β-turn and random coil in the case of Sc. It was not the case for S, however, where random coil experienced the increase in therelative average fractions, while β-turn and β-sheet at(1629±1) cm^-1 behaved in different ways. The above mentioned phenomenon indicated that β-sheet and random coil are most likely to transform into aggregate and α-helix with the introduction of C-terminal acidic protein.