Reciprocal regulation of the tandemly duplicated PHO5/PHO3 gene cluster within the acid phosphatase multigene family of Saccharomyces cerevisiae

Dynamic Changes in Yeast Phosphatase Families Allow for Specialization in Phosphate and Thiamine Starvation

Convergent evolution is often due to selective pressures generating a similar phenotype. We observe relatively recent duplications in a spectrum of Saccharomycetaceae yeast species resulting in multiple phosphatases that are regulated by different nutrient conditions – thiamine and phosphate starvation. This specialization is both transcriptional and at the level of phosphatase substrate specificity. In Candida glabrata, loss of the ancestral phosphatase family was compensated by the co-option of a different histidine phosphatase family with three paralogs. Using RNA-seq and functional assays, we identify one of these paralogs, CgPMU3, as a thiamine phosphatase. We further determine that the 81% identical paralog CgPMU2 does not encode thiamine phosphatase activity; however, both are capable of cleaving the phosphatase substrate, 1-napthyl-phosphate. We functionally demonstrate that members of this family evolved novel enzymatic functions for phosphate and thiamine starvation, and are regulated transcriptionally by either nutrient condition, and observe similar trends in other yeast species. This independent, parallel evolution involving two different families of histidine phosphatases suggests that there were likely similar selective pressures on multiple yeast species to recycle thiamine and phosphate. In this work, we focused on duplication and specialization, but there is also repeated loss of phosphatases, indicating that the expansion and contraction of the phosphatase family is dynamic in many Ascomycetes. The dynamic evolution of the phosphatase gene families is perhaps just one example of how gene duplication, co-option, and transcriptional and functional specialization together allow species to adapt to their environment with existing genetic resources.

The phosphatase system in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae has at least six species of acid and alkaline phosphatases with different cellular localizations, as well as inorganic phosphate (Pi) transporters. Most of the genes encoding these enzymes are coordinately repressed and derepressed depending on the Pi concentration in the growth medium. The Pi signals are conveyed to these genes through a regulatory circuit consisting of a set of positive and negative regulatory proteins. This phosphatase system is interested as one of the best systems for studying gene regulation in S. cerevisiae due to the simplicity of phenotype determination in genetic analysis. With this methodological advantage, considerable amounts of genetic and molecular evidence in phosphatase regulation have been accumulated in the past twenty-five years. This article summarizes the current progress of research into this subject.

Two tandemly arrayed genes encode the (histidine) secretory acid phosphatases of Leishmania donovani

Leishmania donovani promastigotes constitutively secrete a glycosylated and phosphorylated acid phosphatase activity. This secretory acid phosphatase (SAcP) was purified from L. donovani culture supernatants and amino-acid sequence was obtained from both the N-terminus and a tryptic peptide fragment derived from the isolated protein. A polymerase chain reaction (PCR)-based strategy, using degenerate oligo primers designed from the amino-acid sequence data, identified two single-copy, tandemly arrayed open reading frames (ORFs) capable of encoding the L. donovani SAcP (SAcP-1, 2052 bp and SAcP-2, 2124 bp). Both SAcP-1 and -2 were shown to be actively transcribed by L. donovani promastigotes by reverse transcription (RT) and PCR amplification. The deduced amino-acid sequences of SAcP-1 and SAcP-2 show high conservation to each other in four regions: a 23-amino-acid signal peptide; a catalytic domain containing several potential N-linked glycosylation sites; a Ser/Thr-rich repeat region containing multiple potential phosphorylation sites and a common C-terminus. Within the catalytic domain, the L. donovani SAcPs possess two conserved consensus sequences characteristic of histidine acid phosphatases (AcPs). Furthermore, antisera to native L. donovani SAcP immunoprecipitated in vitro transcription/translation products of both SAcP-1 and SAcP-2. Cumulatively, these data indicate that the acid phosphatase activity constitutively secreted by L. donovani promastigotes is composed of two (histidine) AcP isoforms that are encoded by SAcP-1 and SAcP-2, respectively.

Upstream activation element of the PH03 gene encoding for thiamine-repressible acid phosphatase in Saccharomyces cerevisiae

The PH03 gene of Saccharomyces cerevisiae encodes thiamine-repressible acid phosphatase and requires the positively acting regulatory protein THI2 for its expression. Deletion analysis of the 5'-flanking region of PH03 gene revealed that an activating region located at nucleotide position -234 to -215 relative to the translation initiation codon is required for the expression and sensitivity to thiamine. A chemically synthesized DNA fragment covering -234 to -215 showed a significant level of expression when inserted in front of the PH03 promoter lacking the activating region. Electrophoretic mobility shift assay demonstrated the presence of proteins that bound to the above DNA fragment in the nuclear extract from cells grown in thiamine-free medium. These findings suggested that this region between -234 and -215 acts as an upstream activation element of the PH03 gene that can interact with regulatory proteins.

Construction of versatile Escherichia coli--yeast shuttle vectors for promoter testing in Saccharomyces cerevisiae

The promoterless PHO5 gene of the yeast Saccharomyces cerevisiae, encoding the repressible acid phosphatase (AP) was utilized as a reporter gene for the construction of a novel vector system for selection and functional analysis of yeast promoters. The Escherichia coli-yeast shuttle plasmids, pZHB81 and pZHB82, contain different arrays of unique restriction sites located upstream of the PHO5 coding region. Yeast promoters could be screened from random DNA fragments (cloned in the upstream sites) for their ability to direct the expression of the PHO5 gene in transformed (AP-deficient) yeast host cells. AP-expressing transformants were selected directly on agar plates by using a routine colony staining method. Relative promoter strength was assessed by direct assay for AP activity in cell lysates.