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Although PII signal transduction proteins have been described in bacteria, archaea and plants, only one PII homolog has so far been characterized in green algae. Using a specific antibody to the PII protein from Chlamydomonas (CrPII), we provide the evidence that the model plant organism Chlorella variabilis NC64A (NC64A) possesses a protein that is immunologically related to the CrPII. The coding region of the CvGLB1 gene was sequenced, and it contained six introns and seven exons. In comparison to PII proteins from plants and cyanobacteria, the predicted amino acid sequence showed its highest degree of identity with proteins from Chlamydomonas (55.2%) and cyanobacteria, Synechococcus PCC 7942 (52.3%) and Synechocystis sp PCC 6803 (51.8%). Here, we demonstrated that like its plant PII homologs, the C. variabilis PII protein (CvPII) is appeared to be localized in the chloroplast. Expression analysis indicated that CvGLB1 transcription was independent on growth rates or nitrogen availability. The results of this study will facilitate not only characterization of PII signaling network but also the transcriptional analysis in this alga.