In the physiological state, there appears to be a regulatory link between endoplasmic reticulum (ER) Ca(2+) homoeostasis and the initiation of neuronal protein synthesis. Exposing neuronal cell cultures to thapsigargin (Tg), an irreversible inhibitor of sarcoplasmic/ER Ca(2+)-ATPase (SERCA), induced an almost complete suppression of protein synthesis, which recovered to approx. 60% of control 24 h after Tg exposure. This is an experimental model where the regulatory link between the initiation of protein synthesis and ER Ca(2+) homoeostasis recovers, despite an irreversible suppression of SERCA activity [Doutheil, Treiman, Oschlies and Paschen (1999) Cell Calcium 25, 419--428]. The model was used to investigate the relationship between transcription and translation of various stress genes that respond to conditions causing graded suppression of protein synthesis. Expression patterns revealed three groups of genes. The mRNA levels of genes responding to conditions of ER stress (grp78, grp94, gadd34 and gadd153) were increased up to 200-fold after Tg exposure, whereas those coding for ER-resident proteins (SERCA 2b and Bcl-2) were increased up to 6-fold in treated cultures, and those coding for cytoplasmic proteins (heat-shock protein 70 and p67) were increased only 2--4-fold. Analysis of translation of these mRNAs suggests an imbalance in the synthesis of apoptosis-inducing (GADD153) and tolerance-activating (GRP78 and Bcl-2) proteins after blocking of the ER Ca(2+) pump. The observation that the relationship between Tg-induced changes in mRNA and protein levels varied considerably for the various genes studied implies that translation of the respective transcripts is differently regulated under conditions causing graded suppression of global protein synthesis. Detailed analysis of the response of neuronal cells to transient disturbance of ER Ca(2+) homoeostasis may help to elucidate the mechanisms underlying neuronal cell injury in those neurological disorders in which an impairment of ER function is thought to contribute to the pathological process of deterioration.