Functional characterization of Cyberlindnera jadinii carboxylate transporters in Saccharomyces cerevisiae

Introduction In Saccharomyces cerevisiae, two permeases are responsible for the uptake of carboxylates (CA) at the plasma membrane, Jen1p a monocarboxylate proton symporter (Major Facilitator Superfamily) and Ady2p an acetate permease (AceTr Family). In Cyberlindnera jadinii, different uptake systems for CAs were functionally characterized however until now the genes encoding these transporters remain unidentified. In this work, CA transporter homolog genes from C. jadinii were identified and expressed in S. cerevisiae. Materials and Methods The S. cerevisiae strain W303-1A jen1Δ ady2Δ, lacking carboxylate uptake capacity, was used to express C. jadinii ScJEN1 and ScADY2 homologs. Genes were identified through sequence alignment and homology prediction and cloned in the p416GPD vector, under the control of a GPD constitutive promoter. GFP-fusions versions were used to determine protein expression and localization. Transport activity was determined through growth on different carbon sources and measurement of the uptake of labelled CAs, namely D,L-[U-14C] lactic acid, [2,3-14C] succinic acid and [1-14C] acetic acid. Results In C. jadinii, 6 genes homolog to ScJEN1 (Cjj23088, Cjj21966, Cjj22358, Cjj21989, Cjj21602, Cjj25129) and 4 genes homolog to ScADY2 (Cja24587, Cja20823, Cja20690, Cja20822) were identified. All proteins were expressed and localized at the plasma membrane. Regarding transporter specificity CJJEN1-6 and CJAD3 encode lactate transporters, CJAD1 and 4, lactate and acetate transporters, and CJAD2 encodes a lactate, acetate and succinate transporter. Conclusions In this work, we identified 6 CjJEN1 and 4 CjADY2 homologs that are functional carboxylate transporters in S. cerevisiae. All the CjJEN1 homologs are lactate transporters and CjADY2 homologs present different specificities. Further studies are underway to fully characterize these ten new plasma membrane transporters from C. jadinii. References Soares-Silva, I., et al. (2007). Mol Membr Biol. 24(5-6), 464-474.PTDC/BIAMIC/5184/2014. NORTE-01-0145-FEDER-000009. NORTE-08-5369-FSE-00006

Characterization of Cyberlindnera jadinii carboxylate transporters by heterologous expression in S. cerevisiae

Concerning the global problems of resource scarcity and environmental damage, new technologies based on renewable biological sources are needed as the current model of natural resource exploitation is unsustainable. Cell factories with specific genetic and physiological traits, namely suitable protein transporters, may be key players in the bio-based production of organic acids, as an alternative approach to the production of these chemical building-blocks from petrochemical derivatives. The present work focused on the identification and characterization of novel organic acid transporters from the Cyberlindnera jadinii yeast. C. jadinii homologues of the monocarboxylate proton symporter Jen1p (Major Facilitator Superfamily) and the acetate permease Ady2p (AceTr Family) were identified and expressed in S. cerevisiae. The S. cerevisiae strain W303-1A jen1Δ ady2Δ, lacking carboxylate uptake capacity, was used as an expression host. Genes were identified through sequence alignment and homology prediction and cloned in the p416GPD vector, under the control of a GPD constitutive promoter. GFP-fusions versions were used to determine protein expression and localization. Transport activity was determined through growth on different carbon sources and measurement of the uptake of CAs, namely [1-14C] acetic acid, D,L-[U-14C] lactic acid and [2,3-14C] succinic acid. Molecular docking of these transporters was performed to unveil the amino acids that play a major role in the substrate binding of CAs tested. In this study, 4 CjADY2 and 6 CjJEN1 homologs were identified and revealed to be functional carboxylate transporters in S. cerevisiae. Further studies are underway to fully characterize these ten new plasma membrane transporters.PTDC/BIAMIC/5184/2014. NORTE-01-0145-FEDER-000009. NORTE-08-5369-FSE-00006

The Cyberlindnera jadinii carboxylate transporters Ady2 and Jen1 homologs are functional in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, two permeases are responsible for the uptake of carboxylates (CA) at the plasma membrane, Jen1p a monocarboxylate proton symporter (Major Facilitator Superfamily) and Ady2p an acetate permease (AceTr Family). In Cyberlindnera jadinii, different uptake systems for CAs were functionally characterized however until now the genes encoding these transporters remain unidentified. In this work, CA transporter homolog genes from C. jadinii were identified and expressed in S. cerevisiae. The S. cerevisiae strain W303-1A jen1Δ ady2Δ, lacking carboxylate uptake capacity, was used to express C. jadinii ScJEN1 and ScADY2 homologs. Genes were identified through sequence alignment and homology prediction and cloned in the p416GPD vector, under the control of a GPD constitutive promoter. GFP-fusions versions were used to determine protein expression and localization. Transport activity was determined through growth on different carbon sources and measurement of the uptake of labelled CAs, namely D,L-[U-14C] lactic acid, [2,3-14C] succinic acid and [1-14C] acetic acid. In C. jadinii, 6 genes homolog to ScJEN1 (Cjj23088, Cjj21966, Cjj22358, Cjj21989, Cjj21602, Cjj25129) and 4 genes homolog to ScADY2 (Cja24587, Cja20823, Cja20690, Cja20822) were identified. All proteins are being expressed to uncover their subcellular localization and the characterization of transporter specificity is currently underway. In this work, we identified 6 CjJEN1 and 4 CjADY2 homologs that are functional carboxylate transporters in S. cerevisiae. All the CjJEN1 homologs are lactate transporters and CjADY2 homologs present different specificities. Further studies are underway to fully characterize these ten new plasma membrane transporters from C. jadinii.PTDC/BIAMIC/5184/2014. NORTE-01-0145-FEDER-000009. NORTE-08-5369-FSE-00006

Expanding the knowledge on the skillful yeast Cyberlindnera jadinii

Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.This work was supported by the strategic program UID/BIA/04050/2019, funded by Portuguese funds through the FCT I.P., the projects: PTDC/BIAMIC/5184/2014, funded by national funds through the Fundação para a Ciência e Tecnologia (FCT) I.P. and by the European Regional Development Fund (ERDF) through the COMPETE 2020–Programa Operacional Competitividade e Internacionalização (POCI), and EcoAgriFood: Innovative green products and processes to promote AgriFood BioEconomy (operação NORTE-01–0145-FEDER-000009), supported by Norte Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). M.S.S. acknowledges the Norte2020 for the UMINHO/BD/25/2016 PhD grant with the reference NORTE-08–5369-FSE-000060

Characterization of novel plasma membrane carboxylate transporters from non-conventional yeasts

Carboxylic acids (CAs) are a group of organic compounds that play a central role in cellular metabolism of many organisms, using it as unique sources of carbon and energy [1]. In order to replace conventional petroleum-based methods for the obtainment of CAs, alternatives are required for more sustainable way of producing these compounds. The exploitation of yeast biodiversity has received great interest from food, pharmaceuticals and even fuels companies, due to the interesting properties of some microorganisms in producing these compounds in a “greener” trait [2]. Non-Saccharomyces yeasts, also called unconventional yeasts, have recently gained prominence in the biotech industry, and are increasingly being used for the heterologous production of valuable products [3]. New strategies for increasing the production of bio-based organic acids are based on the expression of carboxylate transporters in Saccharomyces cerevisiae strains. In this work, we focus on the identification of new carboxylate transporters present in several yeasts. The strategy involved the search of homologs to known carboxylate transporters characterized in several microorganisms from yeast, fungi and bacteria. The S. cerevisiae IMX1000 Δ25 strain, without carboxylate uptake capacity, was used as a host for the heterologous expression of putative genes encoding CAs transporters [4]. Transport activity was determined by growth phenotypes in different medias containing sole carbon and energy sources, namely mono, di and tricarboxylic acids. The full characterization of the newly identified putative CAs transporters is currently undergoing

Identification of novel carboxylate transporters encoded in the Cyberlindnera jadinii transportome by heterologous expression in S. cerevisiae

Novel strategies to boost bio-based production of organic acids are focused in the expression of specific transporter proteins, to improve adequate uptake and export mechanisms. This study focused on the identification and characterization of novel carboxylate (CA) transporters in the yeast Cyberlindnera jadinii. Transporters homologous to Jen1p and Ady2p, the lactate and acetate permeases from Saccharomyces cerevisiae, were identified and expressed in the S. cerevisiae W303-1A jen1Δ ady2Δ strain. Genes were identified by homology prediction and expressed under the control of a GPD constitutive promoter. GFP-fusions were used to determine protein expression and localization. The transformants were characterized physiologically by growth tests in different carbon sources, and evaluation of mediated transport systems for CAs. Molecular docking studies were performed, to unveil the residues involved in substrate binding in these transporters. We have identified 4 CjADY2 and 6 CjJEN1 homologs that are functional carboxylate transporters in S. cerevisiae. All permeases transport CAs, presenting different specificities. The full characterization of these plasma membrane transporters is underway.PTDC/BIAMIC/5184/2014. NORTE-01-0145-FEDER-000009. NORTE-08-5369-FSE-00006

Characterization of Cyberlindnera jadinii carboxylate permeases by heterologous expression in Saccharomyces cerevisiae

Background: The wide applicability of organic acids for direct use as commodity chemicals and as polymer building blocks has evidenced their importance in diverse types of industries. In Saccharomyces cerevisiae, two permeases are responsible for the uptake of carboxylates (CA) at the plasma membrane, Jen1p a monocarboxylate proton symporter (Major Facilitator Superfamily) and Ady2p an acetate permease (AceTr Family). Objectives: In Cyberlindnera jadinii, different uptake systems for CAs were functionally characterized however until now the genes encoding these transporters remain unidentified. In this study, CA transporter homolog genes from C. jadinii were identified and expressed in S. cerevisiae. Methods: The S. cerevisiae strain W303-1A jen1Δ ady2Δ, lacking carboxylate uptake capacity, was used to express C. jadinii ScADY2 homologs. Genes were identified through sequence alignment and homology prediction and cloned in the p416GPD vector, under the control of a GPD constitutive promoter. GFP-fusions versions were used to determine protein expression and localization. Transport activity was determined through growth on different carbon sources and measurement of the uptake of labelled CAs, namely D,L-[U14C] lactic acid, [2,3-14C] succinic acid and [1-14C] acetic acid. Results: In C. jadinii, 4 genes homolog to ScADY2 were identified. These are functional carboxylate transporters in S. cerevisiae, localized at the plasma membrane, presenting different specificities for the mono- and di-carboxylates. Further studies are underway to fully characterize these four new plasma membrane transporters, including molecular docking of these transporters to unveil the amino acids that play a major role in the substrate binding of CAs tested.PTDC/BIAMIC/5184/2014. NORTE-01-0145-FEDER-000009. UMINHO/BD/25/201

Exploring the Cyberlindnera jadinii yeast transportome to uncover novel carboxylate transporters for biotechnological applications

Due to global problems of resource scarcity and environmental damage, new technologies based on renewable biological sources are required, as the current model of natural resource exploitation is unsustainable. Novel strategies to boost bio-based production of organic acids are based on the expression of carboxylate transporters in microbial cell factories. In this work we have focused on the identification and characterization of novel carboxylate transporters in the yeast Cyberlindnera jadinii. C. jadinii transportome was analysed by two approaches. First, the C. jadinii homologs of the carboxylate transporters Jen1p (Major Facilitator Superfamily) and Ady2p (AceTr Family) were identified and expressed in Saccharomyces cerevisiae. The S. cerevisiae strain W303 1A jen1Δ ady2Δ was used for the heterologous expression. Genes were identified through sequence alignment and homology prediction. In a parallel bioinformatic approach, the proteome from C. jadinii NRRL 1542 was downloaded from the NCBI database and explored using a pipeline. This tool was designed to retrieve data from a specific database: a) that contains a single representative genome/proteome on the species level; b) where multiple matches within a species directly reflect the presence of homologs within the same genome, and c) e-values from BLAST searches that are statistically more reliable [1]. A set of genes were selected using this tool and expressed in the IMX1000 strain, which is deleted in 25 genes related to carboxylic acid transport [2]. Protein expression and localization was determined by microscopy evaluation of GFP- fused transporter proteins. Transporter activity was evaluated through growth on different carbon sources and measurement of the uptake of several radiolabelled CAs. The full characterization of the Ady2 and Jen1 homologs as well as other candidate CAs transporters from C. jadinii is ongoing

Exploring the Cyberlindnera jadinii transportome for the identification of novel carboxylate transporters

Considering the global problems of resource scarcity and environmental damage, new technologies based on renewable biological sources are needed as current model of natural resource exploitation is unsustainable. Novel strategies to boost bio-based production of organic acids are based on the expression of carboxylate transporters in microbial cell factories. In this work we have focused on the identification and characterization of novel carboxylate transporters in the Cyberlindnera jadinii yeast. The transportome of C. jadinii was analysed by two approaches. First, the C. jadinii homologs of the carboxylate transporters Jen1p (Major Facilitator Superfamily) and Ady2p (AceTr Family) were identified and expressed in Saccharomyces cerevisiae. The S. cerevisiae strain W303-1A jen1Δ ady2Δ, lacking carboxylate uptake capacity, was used for the heterologous expression. Genes were identified through sequence alignment and homology prediction. In a parallel bioinformatic approach, the proteome from C. jadinii NRRL-1542 was downloaded from NCBI database and explored using a pipeline developed together with the CBMA bioinformatic team. This tool was designed to retrieve data from a specific database: a) that contains a single representative genome/proteome on the species level; b) where multiple matches within a species directly reflect homologs within the same genome, and c) e-values from BLAST searches that are statistically more reliable. A set of genes were selected using this tool and expressed in the IMX1000 strain, which is deleted in 25 genes related to carboxylic acid transport [1]. GFP-fusions versions were used to determine protein expression and localization. Transport activity was determined through growth on different carbon sources and measurement of the uptake of several radiolabelled CAs. The full characterization of the Ady2 and Jen1 homologs as well as others candidate CAs transporters from C. jadinii is ongoing