Autonomous cytoplasmic linear plasmid pPac1-1 of Pichia acaciae: molecular structure and expression studies.

The genome organization of the linear DNA-element pPac1-1 from Pichia acaciae was determined. It turned out to be the smallest autonomous cytoplasmic yeast plasmid known so far, consisting of only 12 646 bp, carrying the shortest terminal inverted repeats yet found (138 bp). As for other cytoplasmic linear yeast plasmids, it is characterized by a strikingly high A + T content (75.35%). Ten putative genes (open reading frames, ORFs) reside on the element, leaving only 2.9% of the sequence outside a coding region. Highest similarities of the predicted proteins were obtained for proteins encoded by the three hitherto known autonomous cytoplasmic linear yeast plasmids. Amino acid sequences correspond to predicted polypeptides encoded by ORFs 2-11 of the linear plasmids pGKL2 of Kluyveromyces lactis, pSKL of Saccharomyces kluyveri and pPE1B of Pichia etchellsii. As for the latter, ORF1 existing on the two other plasmids is lacking on pPac1-1. Consistent with cytoplasmic localization, a cytoplasmic promoter termed upstream conserved sequence (UCS) is located in front of each reading frame. RT-PCR transcript analyses for ORFs 8, 9 and 11 proved expression of such genes but functions could not be attributed. The genome organization of pPac1-1 and other autonomous linear elements was found to be almost congruent, irrespective of the accompanying smaller elements, which may or may not encode their own element-specific DNA polymerases. Copyright 2006 John Wiley & Sons, Ltd.