Synthetic Core Promoters for <i>Pichia pastoris</i>

Synthetic promoters are commonly used tools for circuit design or high level protein production. Promoter engineering efforts in yeasts, such as <i>Saccharomyces cerevisiae</i> and <i>Pichia pastoris</i> have mostly been focused on altering upstream regulatory sequences such as transcription factor binding sites. In higher eukaryotes synthetic core promoters, directly needed for transcription initiation by RNA Polymerase II, have been successfully designed. Here we report the first synthetic yeast core promoter for <i>P. pastoris</i>, based on natural yeast core promoters. Furthermore we used this synthetic core promoter sequence to engineer the core promoter of the natural <i>AOX1</i> promoter, thereby creating a set of core promoters providing a range of different expression levels. As opposed to engineering strategies of the significantly longer entire promoter, such short core promoters can directly be added on a PCR primer facilitating library generation and are sufficient to obtain variable expression yields

Synthetic Core Promoters for <i>Pichia pastoris</i>

Synthetic promoters are commonly used tools for circuit design or high level protein production. Promoter engineering efforts in yeasts, such as <i>Saccharomyces cerevisiae</i> and <i>Pichia pastoris</i> have mostly been focused on altering upstream regulatory sequences such as transcription factor binding sites. In higher eukaryotes synthetic core promoters, directly needed for transcription initiation by RNA Polymerase II, have been successfully designed. Here we report the first synthetic yeast core promoter for <i>P. pastoris</i>, based on natural yeast core promoters. Furthermore we used this synthetic core promoter sequence to engineer the core promoter of the natural <i>AOX1</i> promoter, thereby creating a set of core promoters providing a range of different expression levels. As opposed to engineering strategies of the significantly longer entire promoter, such short core promoters can directly be added on a PCR primer facilitating library generation and are sufficient to obtain variable expression yields

A Toolbox of Diverse Promoters Related to Methanol Utilization: Functionally Verified Parts for Heterologous Pathway Expression in <i>Pichia pastoris</i>

The heterologous expression of biosynthetic pathways for pharmaceutical or fine chemical production requires suitable expression hosts and vectors. In eukaryotes, the pathway flux is typically balanced by stoichiometric fine-tuning of reaction steps by varying the transcript levels of the genes involved. Regulated (inducible) promoters are desirable to allow a separation of pathway expression from cell growth. Ideally, the promoter sequences used should not be identical to avoid loss by recombination. The methylotrophic yeast Pichia pastoris is a commonly used protein production host, and single genes have been expressed at high levels using the methanol-inducible, strong, and tightly regulated promoter of the <i>alcohol oxidase 1</i> gene (<i>P</i>_<i>AOX1</i>). Here, we have studied the regulation of the P. pastoris methanol utilization (MUT) pathway to identify a useful set of promoters that (i) allow high coexpression and (ii) differ in DNA sequence to increase genetic stability. We noticed a pronounced involvement of the pentose phosphate pathway (PPP) and genes involved in the defense of reactive oxygen species (ROS), providing strong promoters that, in part, even outperform <i>P</i>_<i>AOX1</i> and offer novel regulatory profiles. We have applied these tightly regulated promoters together with novel terminators as useful tools for the expression of a heterologous biosynthetic pathway. With the synthetic biology toolbox presented here, P. pastoris is now equipped with one of the largest sets of strong and co-regulated promoters of any microbe, moving it from a protein production host to a general industrial biotechnology host

A Toolbox of Diverse Promoters Related to Methanol Utilization: Functionally Verified Parts for Heterologous Pathway Expression in <i>Pichia pastoris</i>

The heterologous expression of biosynthetic pathways for pharmaceutical or fine chemical production requires suitable expression hosts and vectors. In eukaryotes, the pathway flux is typically balanced by stoichiometric fine-tuning of reaction steps by varying the transcript levels of the genes involved. Regulated (inducible) promoters are desirable to allow a separation of pathway expression from cell growth. Ideally, the promoter sequences used should not be identical to avoid loss by recombination. The methylotrophic yeast Pichia pastoris is a commonly used protein production host, and single genes have been expressed at high levels using the methanol-inducible, strong, and tightly regulated promoter of the <i>alcohol oxidase 1</i> gene (<i>P</i>_<i>AOX1</i>). Here, we have studied the regulation of the P. pastoris methanol utilization (MUT) pathway to identify a useful set of promoters that (i) allow high coexpression and (ii) differ in DNA sequence to increase genetic stability. We noticed a pronounced involvement of the pentose phosphate pathway (PPP) and genes involved in the defense of reactive oxygen species (ROS), providing strong promoters that, in part, even outperform <i>P</i>_<i>AOX1</i> and offer novel regulatory profiles. We have applied these tightly regulated promoters together with novel terminators as useful tools for the expression of a heterologous biosynthetic pathway. With the synthetic biology toolbox presented here, P. pastoris is now equipped with one of the largest sets of strong and co-regulated promoters of any microbe, moving it from a protein production host to a general industrial biotechnology host

A Toolbox of Diverse Promoters Related to Methanol Utilization: Functionally Verified Parts for Heterologous Pathway Expression in <i>Pichia pastoris</i>

The heterologous expression of biosynthetic pathways for pharmaceutical or fine chemical production requires suitable expression hosts and vectors. In eukaryotes, the pathway flux is typically balanced by stoichiometric fine-tuning of reaction steps by varying the transcript levels of the genes involved. Regulated (inducible) promoters are desirable to allow a separation of pathway expression from cell growth. Ideally, the promoter sequences used should not be identical to avoid loss by recombination. The methylotrophic yeast Pichia pastoris is a commonly used protein production host, and single genes have been expressed at high levels using the methanol-inducible, strong, and tightly regulated promoter of the <i>alcohol oxidase 1</i> gene (<i>P</i>_<i>AOX1</i>). Here, we have studied the regulation of the P. pastoris methanol utilization (MUT) pathway to identify a useful set of promoters that (i) allow high coexpression and (ii) differ in DNA sequence to increase genetic stability. We noticed a pronounced involvement of the pentose phosphate pathway (PPP) and genes involved in the defense of reactive oxygen species (ROS), providing strong promoters that, in part, even outperform <i>P</i>_<i>AOX1</i> and offer novel regulatory profiles. We have applied these tightly regulated promoters together with novel terminators as useful tools for the expression of a heterologous biosynthetic pathway. With the synthetic biology toolbox presented here, P. pastoris is now equipped with one of the largest sets of strong and co-regulated promoters of any microbe, moving it from a protein production host to a general industrial biotechnology host

MetR specifically regulates induction of autophagy.

<p>MET⁺, Δ<i>met15</i> and Δ<i>met2</i> strains from chronological aging experiments were analyzed for vacuolar ALP activity (with a fluorescent plate reader) (A) (n = 6), and GFP-Atg8p processing (by Western-blot analysis) (B). (C) GFP-Atg8p localization was determined by using fluorescent microscopy (white arrows indicate vacuolar localization or autophagosome formation) and statistical analysis thereof (330–600 cells of each GFP-Atg8p expressing strain were evaluated from two independent samples) (D). (E) <i>MET2</i> deletion strain (Δ<i>met2</i>) was grown to stationary phase in SCD (supplemented with all aa) and shifted to SCD media with given methionine concentrations. Autophagy was measured by means of ALP activity with a fluorescent plate reader (Tecan, Genios Pro) (n = 6). (F) ALP assays of chronological aging of MET⁺ strain, in SCD media supplemented with all aa except for methionine which was added at given concentrations (n = 2). See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004347#pgen.1004347.s003" target="_blank">Figure S3</a>.</p

Model of MetR-mediated longevity.

<p>MetR specifically enhances autophagy, either by interfering upstream of TOR-pathway or presumably by impinging on (metabolic) pathways that potentially target autophagy directly, downstream of the TOR-pathway. MetR-specific vacuolar acidification is dependent on autophagy and elongates CLS. High levels of methionine inhibit autophagy induction during early phases of chronological aging, enhancing ROS and diminishing acidic vacuoles in a cell population, which leads to cell death.</p

MetR enhancement of vacuolar acidification is autophagy-dependent and necessary for longevity.

<p>Fluorescent microscopy of acidic vacuoles during chronological aging of MET+, Δ<i>met2</i>, and Δ<i>met2</i>/Δ<i>atg5</i> strains, by means of quinacrine accumulation and statistical analysis thereof. (>1000 cells of each strain from 3 to 5 independent samples at each time point were evaluated. Only cells with acidic vacuoles without an additionally stained cytoplasm were counted as positive, resulting in cell counts that represent cells which have a clearly intact pH-homeostasis. Positively counted cells are indicated by white arrowheads) (A and B). (C) Statistical analysis of fluorescent microscopy of acidic vacuoles by means of quinacrine accumulation. Strains Δ<i>met2</i> and Δ<i>met2</i>/Δ<i>atg5</i> were grown to stationary phase under excess of methionine and shifted to media with the indicated amounts of methionine (>500 cells from each strain from 2 independent samples) and assayed for quinacrine accumulation after ∼20 hours (D) Chronological aging of the MET⁺ strain overexpressing Vma1p or Vph2p. Cell death was measured via propidium iodide staining of cells that have lost integrity and subsequent flow cytometry analysis (BD LSRFortessa) (n = 6 to 8). See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004347#pgen.1004347.s006" target="_blank">Figure S6</a>.</p

Methionine determines yeast chronological lifespan.

<p>(A) Chronological aging of methionine prototroph (MET⁺), semi-auxotroph (Δ<i>met15</i>) and auxotroph (Δ<i>met2</i>) isogenic yeast strains in SCD media supplemented with all amino acids (aa). Cell survival was estimated as colony formation of 500 cells plated at given time points, normalized to cell survival on day one (n = 4). (B) Chronological aging of Δ<i>met15</i> strain, in SCD media supplemented with all aa except for methionine which was added at given concentrations. Cell survival of 500 cells plated at given time points, normalized to cell survival on day one (n = 4). (C) <i>MET2</i> deletion strain (Δ<i>met2</i>) was grown to stationary phase in SCD (supplemented with all aa) and shifted to SCD media with different methionine concentrations. Cell survival of 500 cells plated at given time points, normalized to cell survival before the shift (n = 4). (D) Day 8 from experiment shown in C (n = 4). (E) Chronological aging of EUROSCARF BY4741 (also used above as Δ<i>met15</i> reference strain) and mating type α wild type strain BY4742, as well as a methionine semi-auxotrophic variant thereof (BY4742 Δ<i>met15</i>), in SCD media supplemented with all aa. Cell survival of 500 cells plated at given time points, normalized to cell survival on day one (n = 3). See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004347#pgen.1004347.s001" target="_blank">Figure S1</a>.</p

MetR is epistatic to other longevity treatments involving <i>TOR1</i> inhibition.

<p>(A and B) Chronological aging of <i>MET2</i> and <i>MET15</i> deletion strains deleted for <i>TOR1</i>. Cell survival of 500 cells plated at given time points, normalized to cell survival on day one (n = 6). Chronological aging of <i>MET2</i> (C) and <i>MET15</i> (D) deletion strains treated with indicated amounts of rapamycin (Rap). Cell survival of 500 cells plated at given time points, normalized to cell survival on day one (n = 3). Autophagy was measured by means of ALP activity with a fluorescent plate reader (Tecan, Genios Pro) and normalized to untreated controls at indicated time points (also compare to <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004347#pgen-1004347-g003" target="_blank">Figure 3C</a>) (E) (n = 4). See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004347#pgen.1004347.s005" target="_blank">Figure S5</a>.</p