# Kluyveromyces lactis: A Suitable Yeast Model to Study Cellular Defense Mechanisms against Hypoxia-Induced Oxidative Stress

Authors: M. Isabel González Siso; M. Esperanza Cerdán
Journal: Oxidative Medicine and Cellular Longevity
 (2012)

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## Abstract

Studies about hypoxia-induced oxidative stress in human health disorders take advantage from the use of unicellular eukaryote models. A widely extended model is the fermentative yeastSaccharomyces cerevisiae. In this paper, we describe an overview of the molecular mechanisms induced by a decrease in oxygen availability and their interrelationship with the oxidative stress response in yeast. We focus on the differential characteristics between S. cerevisiae and the respiratory yeast Kluyveromyces lactis, a complementary emerging model, in reference to multicellular eukaryotes.


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## Body

## 1. Introduction

Interest in hypoxic and oxidative stress studies is increasing in recent years, mostly in relation to aging or diseases such as neurodegenerative disorders or cancer. These processes in human cell lines show a very complex regulation, and therefore the availability of simple models is extremely useful. Yeasts have demonstrated to be suitable unicellular eukaryotic models since, in addition to generalized culture facilities, global “omic” analysis is fully developed and molecular mechanisms are generally well conserved. For instance, although obviously without nervous system, most of the molecular signaling pathways and the proteins involved in human neurological diseases are functionally conserved in yeasts [1]. Besides, functional characterization of human genes is sometimes achieved by means of their heterologous expression in mutant yeasts.Most studies about the hypoxic and oxidative stress responses and their connections have been carried out hitherto onSaccharomyces cerevisiae, a yeast model with a predominantly fermentative metabolism [2]. In the same way, S. cerevisiae mutants have been frequently used as research models in aging [3] and in human pathologies [4]. Frequently, the mechanisms discovered with this yeast proved to be conserved in multicellular eukaryotes. However, human tissues such as the neuronal network have oxidative metabolism, and therefore the use of alternative yeast models has been suggested [5]. We analyze Kluyveromyces lactis from the perspective of an alternative eukaryote model in these studies  or similar studies, since this yeast has a predominantly respiratory metabolism.Molecular mechanisms that support the metabolic differences betweenS. cerevisiae and K. lactisand the specific responses to hypoxia or oxidative stress have been studied. Redox metabolism is a key differential point between S. cerevisiae and K. lactis, both thiol-redox and NAD(P)H-redox reactions. K. lactis is characterized, opposite to S. cerevisiae, by a higher glucose flow through the pentose phosphate pathway (PPP) than through glycolysis [6] and as a consequence by a higher production of NADPH in the cytosol. In fact, one of the molecular keys supporting the difference in the Crabtree phenotype (inhibition of respiration by fermentation) of the two yeast species lies in the mechanisms involved in the re-oxidation of the NADPH [7, 8]. A significant part of this reoxidation is carried out in K. lactis by mitochondrial external alternative dehydrogenases (NDEs), which use NADPH, the enzymes of S. cerevisiae being NADH-specific. Unlike S. cerevisiae, transcription of NDEs genes in K. lactis is not regulated by the carbon source. Since NDEs may compete with alcohol dehydrogenases for the cytosolic NADH, their repression at high glucose concentrations, as it occurs in S. cerevisiae, correlates with an increase of reoxidation of glycolytic NADH by the alcohol dehydrogenases and therefore with the prevalence of aerobic fermentation and the Crabtree-positive phenotype [9]. Interestingly, NDEs have been reported to influence ROS production and life span in S. cerevisiae [10, 11]. Moreover, the NADPH-dependent pathways of response to oxidative stress also contribute to NADPH reoxidation. In S. cerevisiae, they play a main role together with glutamate dehydrogenase and also operate, although to a lesser extent, in K. lactis, [8, 12, 13].In this paper, we focus on the complex interdependence of multiple mechanisms, which arise as a consequence of the decrease of oxygen availability and on the responses elicited to compensate this stress. A general overview of all the subjects analyzed is shown in Figure1. Along the text, special reference is made on the differences found between S. cerevisiae and K. lactis, looking for the potential advantages and disadvantages of these models in reference to each other and in comparison to multicellular eukaryotes.Figure 1
A panorama of the multiple connections between hypoxia, metabolic rerouting, oxidative stress response, and cell defense mechanisms. Erg: ergosterol; PPP: pentoses phosphate pathway; TF: transcriptional factors.The first intracellular signal sensing low levels of oxygen is the heme content. The biosynthesis of heme includes enzymes that directly use oxygen as electron acceptor during the catalysis, and, besides, several steps are regulated by oxygen availability. Other important pathway that directly uses oxygen is the biosynthesis of ergosterol, which is also regulated by oxygen availability. The intake of ergosterol from the media through the membrane is also regulated by oxygen levels. Downstream in these sensing strategies is heme and ergosterol dependent transcriptional factors, which act in the nucleus to regulate the transcription of more than 100 genes, those conditioning the “hypoxic response” and improving the use of the low levels of oxygen. Hypoxia signals the activation of mechanisms that regulate the transcription of genes involved in the oxidative stress response. Simultaneously, the decrease in oxygen levels causes a complete rerouting of nutrients through different metabolic pathways. This principally affects glucose and other sugars, which can follow fermentative or respiratory transformations and, in turn, condition the systems of redox exchange between cytoplasm and mitochondria and the mechanisms that produce ROS. Reoxidation of reduced NAD(P)H also has regulatory effects on the diverse metabolic routes that need the oxidized coenzyme forms to function. ROS also elicit other mechanisms of cell defense, including reoxidation of NAD(P)H and life span adjustment, programmed cell death, and mitophagy (Figure1).


## 2. The Hypoxic Response inK. lactis

During hypoxia, it is advantageous for cells to adapt the pattern of gene expression in order to improve oxygen utilization. The hypoxic response is well documented in the model yeastSaccharomyces cerevisiae,whose cells sense oxygen via the levels of heme and sterols [14–17]. The response of S. cerevisiae to hypoxia produces increased expression of genes related to ergosterol synthesis, cell wall composition, and glycolytic genes and reduced expression of components of the respiratory chain, ATP synthesis, and the citric acid cycle [14, 18, 19]. However, this knowledge is not directly applicable to other yeasts, even to those close-related in phylogeny, which became evident in the last years with the advances in the study of the hypoxic response in K. lactisand other yeasts. It has been proposed that a whole-genome duplication (WGD) contributed to yeast evolution from strict aerobes to facultatives/fermentatives [20–22]. Functional specialization between duplicated genes explains the existence in S. cerevisiae of homologous genes (COX5a/COX5b; CYC1/CYC7; HYP2/ANB1; AAC1/AAC2/AAC3) differentially expressed in aerobic and hypoxic conditions [14, 23–25]. Kluyveromyces lactis does not present duplication of genes with specialized aerobic, hypoxic transcription, but the unique copy is regulated by oxygen availability [26]. Probably, K. lactis and S. cerevisiae are diverged from one common ancestor yeast previously to the WGD event and this could explain the multiple differences observed when comparing the response to hypoxia in both yeasts, as explained below.AlthoughK. lactis is unable to grow under strictly anoxic conditions [27], probably due to the absence of expression of genes related to the import of sterols in this condition [28], this yeast ferments sugars and grows in hypoxic conditions defined as oxygen availability below 1% of fully aerobic levels [7, 29]. Several reports of genes upregulated during hypoxia in K. lactis have been published. A K. lactis heme-deficient strain, obtained by KlHEM1 disruption, was used to assess the functional significance of heme-directed regulation in K. lactis; KlHEM13, encoding the coproporphyrinogen oxidase (EC 1.3.3.3), an oxygen-requiring enzyme that catalyzes the sixth step of heme biosynthesis, was the first hypoxic gene functionally characterized in this yeast [30, 31]. Other gene from the heme biosynthetic pathway, KlHEM1, is upregulated during hypoxia in K. lactis [32]. The KlPDC1 gene, encoding for the enzyme pyruvate decarboxylase, is also induced by hypoxia [33]. After the completion of the Génolevures sequencing project [34], the availability of the complete sequence of the K. lactis genome allowed the design of specific DNA arrays containing selected DNA probes putatively related to the aerobic-hypoxic response by their similarity to the orthologs in S. cerevisiae [26]. The nature of the hypoxic transcriptional response in K. lactis, as revealed by using these arrays, differed notably from S. cerevisiae, but confirmed the existence of hypoxic upregulated genes in K. lactis such as KlOYE2 (KLLA0A09075g), KlGSH1 (KLLA0F14058g) and KlOLE1 [26]. Besides KlOLE1, the transcription of other lipid biosynthetic genes like KlERG1,KlFAS1,and KlATF1 is also induced by hypoxia [35].InS. cerevisiae, adaptation to hypoxia requires the transcriptional induction or derepression of multiple genes organized in regulons controlled by specific transcriptional regulators. Considering that in K. lactis the hypoxic response exists but the target genes are not coincident and are not equally regulated, the question arose about the functionality of sensors and transcriptional regulators. The principal sensors in the yeast response to hypoxia are heme and ergosterol. The heme biosynthetic pathway is well conserved in different organisms throughout evolution [36], and this is also true between S. cerevisiae and K. lactis.Both yeasts have eight highly homologous genes necessary for the biosynthesis of heme. For the three genes of the heme biosynthetic pathway characterized in K. lactis to date (KlHEM1,KlHEM12,andKlHEM13), functional equivalence with their S. cerevisiae homologs has been confirmed experimentally by cross-complementation [31, 32, 37]. As it happens in S. cerevisiae, the transcriptional regulation of KlHEM12 is not a key point for regulation of heme synthesis in K. lactis[38] and its transcriptional regulation in different carbon sources [38] is also similar to that reported for its homolog in S. cerevisiae [39, 40]. However, notable differences exist in the regulation of the other two characterized genes. In S. cerevisiae, the expression of HEM1 is constitutive [41], but in K. lactis the first step of the heme biosynthesis is under double-feedback regulation by heme, at the level of gene transcription [37] and mitochondrial import of the protein [42]. Although in S. cerevisiae the aerobic repression of HEM13 is mediated by the transcriptional regulator Rox1p, diverse data indicate that the mechanism is different in K. lactis and a similar repressor does not operate [43, 44].InS. cerevisiae, intracellular levels of heme regulate the activity of the transcriptional regulator Hap1 [14]. The CCAAT-binding complex Hap2/3/4/5, an evolutionarily conserved multimeric transcriptional activator in eukaryotes [45], is also necessary for the activation of many genes involved in respiratory metabolism [45], although its direct activation by heme has not been demonstrated. Targets of Hap1 include genes required for respiration and for controlling oxidative damage [46–48] and also the aerobic repressor Rox1. When the oxygen levels drop, heme does not bind to Hap1. Then, the interaction with Ssa1, Ydj1, and Sro9 maintains to Hap1 inactive [49, 50]. As a result, ROX1 is not expressed and no longer represses aerobic expression of genes involved in the hypoxic response. Moreover, Mot3 collaborates in the repression exerted by Rox1 in target promoters [51], and Ixr1 has been related to the hypoxic response of S. cerevisiae in cross-regulation with ROX1 [52–54]. Although several homologs to the components of the Hap2/3/4/5 complex have been cloned in K. lactis[55–57], the respiratory system of K. lactis, escapes from HAP2 control [56]. Contrary to data previously described for the homologous gene of S. cerevisiae, the function of the KlHAP1 gene does not affect growth in media with carbon sources used by fermentative or respiratory pathways in K. lactis and KlHap1 is not a transcriptional activator of the expression of genes related to respiration or sterol biosynthesis [58] but represses the expression of the major glucose transporter [59]. In a similar way, KlROX1 does not regulate the hypoxic response in K. lactis [60] and the KlROX1 promoter is not regulated by KlHap1 or KlRox1 in response to changes aerobiosis/hypoxia [44].Parallel, Hap1-Rox1-independent, oxygen response pathways exist in yeast. For instance, inS. cerevisiae, the transcription of the hypoxic gene OLE1 depends on cytochrome c oxidase [61] and requires the transcription factor Mga2 that is functional in hypoxia [62]. In K. lactis, this regulatory circuit is also different and, although KlMGA2shows homology to the MGA2gene from S. cerevisiae, KlMga2does not regulate KlOLE1hypoxic expression [35]. Sut1 and Sut2 are also involved in the transcriptional induction of hypoxic genes and in sterol uptake and synthesis in S. cerevisiae [63, 64].Another sensing pathway includes the regulators of sterol biosynthesis Upc2 and Ecm22 [65]. Sterol depletion leads to activation of the paralogous genes UPC2 and ECM22 [16], which control expression of a subset of hypoxic genes. Both bind to a sequence motif known as the sterol regulatory element (SRE) in the promoters of their target genes, but Ecm22 is an aerobic repressor and Upc2 an anaerobic activator, which is upexpressed during hypoxia. They regulate expression of ergosterol biosynthesis genes and the DAN/TIR family of cell wall proteins [65–67]. This regulatory circuit remains unstudied in K. lactis,although analysis of the genome sequence shows that the hypoxic genes from the sterol biosynthetic pathway are conserved in the two yeasts [26].Quantitation of the homology between proteins translated from verified or putative orthologous genes ofK. lactis and S. cerevisiae reveals that, with few exceptions, the proteins related to biosynthetic routes producing intracellular changes in heme and ergosterol are more conserved than the transcriptional factors, which are regulated by their levels and produce the hypoxic response (Figure 2).Figure 2
Homologies (percentage of identity calculated according to BLASTp in Génolevures) betweenK. lactis and S. cerevisiae proteins related to the pathways summarized in Figure 1. Red, 100–70% identity; green 69–40% identity; blue, <40% identity. (A) heme biosynthesis; (B) ergosterol biosynthesis and supply; (C) NAD(P)H consuming oxidative defense reactions; (D) other oxidative defense reactions; E, NAD(P)-dehydrogenases from the inner membrane of mitochondria; (F) heme/respiration-related transcriptional factors; (G) sterol-related transcriptional factors; (H) peroxide-related transcriptional factors; (I) life span-related proteins; (J) mitophagy-related proteins.


## 3. Oxidative Stress Response inK. lactis

The oxidative stress response inK. lactis is a mostly unexplored field. The number of published works is less than 1.5% compared to S. cerevisiae. Several studies based on comparative genomics have been performed, combining in silico and experimental approaches [26, 68, 69]. The search in the K. lactis genome of putative S. cerevisiae orthologs related to the oxidative stress response (genes coding for superoxide dismutases and their chaperones, catalases and peroxidases, proteins of the glutathione, and thioredoxin systems) has suggested that pathways and proteins are generally conserved, with a few exceptions mainly affecting gene redundancy or predicted subcellular location of the proteins [69]. These exceptions comprise the groups of genes encoding thioredoxin peroxidases, thioredoxin reductases, thioredoxins, glutaredoxins, and glutathione transferases (Figure 2). However, several functional differences affecting mainly connections between redox pathways related to carbohydrate metabolism, respiratory functions and oxidative stress response are observed [69]. In support of these results, a recent study about glutathione transferases, and synthetases in yeast species representatives of fermentative, respiratory, and oxidative metabolism [70] found significant differences in homology and predicted intracellular sorting.Among the reported differences, it is remarkable to outline the role of the thiol-redox pathways, specifically glutathione reductase (GLR), the enzyme that catalyzes the interconversion of oxidized (GSSG) and reduced glutathione (GSH) using NADPH as reducing power. Whereas inS. cerevisiae the expression of GLR increases in response to oxidative stress produced after addition of peroxides by a Yap1-mediated mechanism, this effect is absent in K. lactis [26, 71, 72]. Surprisingly, both S. cerevisiae and K. lactis GLR depletion mutants are more sensitive to oxidative stress [12, 13]. In such K. lactis GLR mutants, increase in ROS production, catalase, and thioredoxin reductase (TRR) activities are observed and the expression of a pool of other antioxidant enzymes and oxidoreductases is also upregulated [73]. It is likely that TRR and other NADPH-dependent oxidoreductases might replace GLR in maintaining the GSH/GSSG ratio. In fact, purified K. lactis TRR shows GLR activity in vitro (our unpublished results). In support of this explanation, it has been reported that the thioredoxin-TRR system can reduce GSSG in S. cerevisiae [74]. Other reported functional differences affecting the OS defense enzymes of K. lactis and S. cerevisiae are regarding the mechanism of cation handling of the superoxide dismutase Sod1 [75] and the transcriptional regulation of the SOD1 gene after a shift to hypoxia [26, 76]. Also the transcriptional regulation of the genes encoding catalases [12, 26, 77, 78] and glutathione synthetases [26, 79] under aerobic/hypoxic conditions and under peroxide-treatment is different in the two yeasts. About comparative analyses between the transcriptional factors related to the oxidative stress response in S. cerevisiae and K. lactis, Yap1 and Snk7 share, respectively, 33% and 50% identities (Figure 2), and KlYap1 has been functionally characterized in relation to the oxidative stress response induced by metals and peroxides [80].Several evidences support that inK. lactis the OS response has a regulatory role upon fermentation/respiration balance. Thus, there is a positive correlation between the increase of GLR activity and the glucose-6-phosphate-dehydrogenase activity (from PPP) when oxygen levels increase [12]. Besides, the glucose respiration rate, in K. lactis cells that metabolize all the monosaccharide through the PPP, increases upon GLR depletion and decreases upon GLR overexpression [13]. Proteome analysis reveals that there is a different response to H2O2-treatment, which is dependent on GLR in such a way that the expression of several enzymes of the glycolysis and the Krebs’ cycle decreases in the wild-type strain, while enzymes of these pathways and the PPP increase in the GLR depleted mutant [73]. Other indirect evidence is that K. lactis GLR activity decreases in a Gcr1-mutant [13] being Gcr1 at the same time a positive transcriptional regulator of KlNDI1 [9]; KlNDI1 is the gene encoding the internal mitochondrial alternative dehydrogenase (NDI), the enzyme that replaces the respiratory chain complex I found in other eukaryotes [81]. GLR depletion mutants grow better in glucose than the wild type, overall when all the glucose is metabolized through the PPP, which might be explained by rerouting the oxidation of the NADPH produced in the PPP from GLR to NDEs, thus increasing ATP production in the respiratory chain [12, 13].Yeasts alternative dehydrogenases of the mitochondrial inner membrane are also related to OS and are other point of connection with the response to metabolic changes produced by oxygen availability. The transcription of the twoK. lactis genes encoding NDEs decreases when cells are under oxidative stress and the NADPH-related defense mechanisms are activated [9, 82]. Regarding K. lactis NDI, we have proved that the transcription of the KlNDI1 gene is induced in nonfermentable carbon sources through a process mediated by the factor Adr1 and that the expression of the gene did not decrease after an hypoxic shift [9]. The homologous S. cerevisiae enzyme has been more widely studied and its role in aging and ROS production has been reported [83]. Differences found in yeasts NDI are of clinical interest since they have been used in gene therapy of diseases [84] such as Parkinson’s disease [85] or hereditary optic neuropathy [86, 87]. Heterologous expression of the S. cerevisiae NDI1 gene reduces the overproduction of ROS caused by mitochondrial complex I defects in multicellular eukaryotes [88].These connections between thiol-redox OS reactions and carbohydrate metabolism described above inK. lactis are also supported in other organisms. Ralser et al. [89] discovered that S. cerevisiae cells with reduced activity of the key glycolytic enzyme triose-phosphate isomerase exhibit an increased resistance to the thiol-oxidizing reagent diamide. This phenotype is conserved in Caenorhabditis elegans and the underlying mechanism is based on a redirection of the metabolic flux from glycolysis to the PPP, altering the redox equilibrium of the cytoplasmic NADP(H) pool. Another key glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), is known to be inactivated in response to various oxidant treatments, and this causes a similar redirection of the metabolic flux [89].


## 4. The Hypoxic-Induced Oxidative Stress Response inK. lactis

A connection between the hypoxic and oxidative stress responses has been reported in the fermentative yeastS. cerevisiae. Several S. cerevisiae genes that are induced during hypoxia are related to the oxidative stress response. CUP1 and CUP2, which are necessary for the removal of superoxide radicals, are upregulated 11.6-fold during hypoxia in a Rox1 and Srb10-dependent mechanism [18]. Other genes related to oxidative stress (HSP12, FMP46, and GRE1) DNA repair (ALK1) or mitochondrial genome maintenance (MGM1)also increase their expression during hypoxia [18]. The level of mitochondrial and cytosolic protein carbonylation, the level of mitochondrial and nuclear DNA damage measured by 8-OH-dG modification, and the expression of SOD1, encoding superoxide dismutase, increases transiently during a shift to anoxia [76]. Besides, the specific proteins, which become carbonylated during the shift to anoxia, are the same proteins that become carbonylated during peroxidative stress. These results demonstrate that yeast cells exposed to anoxia experience transient oxidative stress and suggest that ROS generated could also signal the variation in oxygen levels and trigger the nuclear response to hypoxia affecting transcription [76]. However, the specific connection between ROS production, protein, or DNA modifications and transcriptional regulation has not yet been elucidated in yeasts. The question about whether mitochondrial or cytosolic proteins, which are specifically oxidized in cells exposed to anoxia, play a role in signaling pathways from the mitochondrion to the nucleus that function to induce hypoxic genes remains unanswered.InK. lactis, after analyzing 30 genes related to oxidative stress, only two (KlGSH1 and KlOYE2) increased their expression after the hypoxic shift [26]. However, a whole-genome approach has not been carried out in this yeast and, therefore, a direct comparison of these data with those reported from S. cerevisiae is not accurate. An interesting observation, which suggests that also in K. lactis the hypoxic response might be triggered by ROS production, is that the hypoxic response is highly dependent on the relative flux of glucose through glycolysis or the pentose phosphate pathway (PPP). The predominant use of PPP versus glycolysis is accompanied by a higher expression of mitochondrial cytochrome c [7], which might be associated with the mitochondrial chain activation and changes in ROS production. Indeed, in a rag2 mutant, lacking phosphoglucose isomerase and committed to reroute the glucose-6-phosphate through PPP, in order to bypass the blocked glycolytic step, a more intense hypoxic response than the wild-type strain, and that affects the genes of heme metabolism and the oxidative stress response, is observed [26].A new link between oxidative stress and hypoxia comes from the analysis of multiple functions attributed to transcriptional regulators initially characterized in the aerobic/hypoxic response. InS. cerevisiae, Hap1 not only acts as an aerobic activator but has a regulatory function during hypoxia [17, 90]. Hap1 also controls the expression of genes related to sterol biosynthesis [14, 91–94] and SOD2,involved in the oxidative stress response [95].Although putative homologues of two of the principal regulators of the aerobic/hypoxic response inS. cerevisiae (Hap1 and Rox1) have been characterized in K. lactis, their sequence and function diverge notably from those described in S. cerevisiae [44, 58]. Remarkably, their functions in K. lactis are somehow related to the metal-induced oxidative-stress response. Deletion of KlHAP1 increases the resistance to oxidative stress or cadmium [58]. Moreover, the induction by 0.5 mM H2O2 of two genes related to the oxidative stress response, KlYAP1 andKlTSA1, is repressed by KlHap1p [58]. KlROX1 mediates the response to arsenate and cadmium [44]. KlRox1p binds to the KlYCF1 promoter, a gene related to cadmium detoxification, and causes its activation [44].


## 5. Adjustment of Cell Survival and the Oxidative Stress Response

Besides the transcriptional, proteomic, and metabolomic reorganization caused by the oxidative stress, ROS also elicit other mechanisms of cell defense, including life span adjustment, programmed cell dead, autophagy, and mitophagy. Mitochondria, being the major intracellular source of ROS, are involved in aging and life span regulation [96] Yeasts have been proved to be good models for studying these processes. In S. cerevisiae, a cross-regulation between glycolysis and PPP has been proposed in order to prevent oxidative stress when cells switch from anaerobic to oxidative metabolism. Low activity of the glycolytic enzyme pyruvate kinase causes accumulation of PEP and blocks the pathway diverting the glucose flux into the PPP [97]. This mechanism helps to balance the increased ROS production during oxidative metabolism [97]. Also in mammals, during oxidative damage in cancer cells, a similar redirection of metabolic fluxes contributes to ROS clearance [98]. Therefore, it is possible that the hypoxic and the oxidative stress responses, influenced by the reorganization of the utilization of different metabolic pathways, also contribute to modulate these cell defense mechanisms in yeasts and other cells.Studies pioneered inS. cerevisiae by measuring life span have revealed several molecular mechanisms underlying cellular aging and which are well conserved in eukaryotes. Two basic experimental approaches have been applied in unicellular organisms. Replicative life span (RLS) is defined as the number of daughters a single cell produces during its life [99]. Chronological life span (CLS) is defined as the time a population of cells survive in stationary phase [100]. In S. cerevisiae, a Crabtree-positive yeast, calorie restriction by glucose limitation increases both RLS and CLS, a feature that coincides with increased cytochrome content, and NADH-cytochrome c reductase activity [101]. In K. lactis, a Crabtree-negative yeast for which glucose limitation does not promote an enhancement of the respiratory capacity [2], the increase in CLS by glucose limitation is not produced [102]. These results suggest that calorie restriction-dependent increase in longevity may be due to mitochondrial control and more particularly the regulation of oxidative phosphorylation activity.An additional nexus between aging and the redox cell balance came from the discovery of sirtuins. They are NAD+-dependent enzymes and they belong to a highly conserved family of proteins that in yeasts, invertebrates, and mammals act in diverse functions related to longevity [103]. In S. cerevisiae, Sir2 is induced in cells treated with 4 mM H2O2 or 10 mM menadione [104] and these data suggest a connection between oxidative stress, Sir2 activation and longevity. The existence of complexes of Sir2 with other metabolic enzymes NAD+-dependent, like those formed with the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase Tdh3 or the alcohol dehydrogenase Adh1 [105], might indicate that the ratio NAD+/NADPH in the microenvironment surrounding Sir2 could act as its modulator. Recently, a third complex of Sir2 with Mdh1, the mitochondrial malate dehydrogenase, has been proposed based on multiple common network interactions involving also the proteins Rad53, Aat1, Fob1, and Hst1 [106], although not yet proved by physical interactions. Since Mdh1 is overexpressed under conditions of calorie restriction [107] and it causes extension of Sir2-dependent RLS [108], further investigation is promising. In K. lactis sirtuins or its regulators have not been studied but there is an ORF (KLLA0F14663g) with 62% identities to S. cerevisiae Sir2 (Figure 2). Considering the importance of sirtuins and their modulators in the etiology and treatment of human pathologies such as metabolic, cardiovascular, and neurodegenerative diseases or cancer [104, 109] and the similarities found between the high respiratory metabolism of K. lactis and certain human cell types like neurons [5], sirtuins and related proteins from K. lactis are good targets for study.About the signaling pathways that affect life span in yeast (reviewed in [103]), the serine threonine kinases Tor1, Sch9, and PKA that control nutrient signaling pathways also regulate aging in yeasts, and their homologs in animals share conserved functions in aging. Depletion of Tor1 kinase increases both RLS and CLS in budding yeast, flies, and C. elegans. Likewise, PKA kinase activation lengthens life span in budding yeast and longevity in mice. The kinase S6K1, which is known to be related to the control of aging in mice, Drosophila, C. elegans, and the yeast Sch9 kinase that controls RLS and CLS in yeast represent other group or orthologous genes. Purification of TOR from yeast and human cells revealed that TOR can exist in at least two multiprotein complexes, termed TORC1 and TORC2 [110]. Interestingly, it has been found that superoxide anions regulate the TORC1 complex and its ability to bind the Fpr1-rapamycin complex [111], thus establishing another link between OS and aging. In S. cerevisiae, 15 genes are functionally related to TORC1 function and Tor, Sch9, and PKA signaling are interconnected (Table 1). In S. cerevisiae, the genes TPK1 (alias PKA1, SRA3; ORF, YJL164C), TPK2 (alias PKA2, YKR1, PKA3; ORF, YPL203W), and TPK3 (YKL166C) encode for three forms of the cAMP-dependent protein kinase catalytic subunit of the cyclic AMP-dependent protein kinase (PKA) and BCY1 (YIL033C) for the regulatory subunit. In K. lactis,homologous genes of main participants in these signaling pathways are present (Table 1) and homology (recorded using BLASTp in Génolevures at http://www.genolevures.org/) is summarized in Figure 2 The most remarkable observation is that in K. lactis, there is only one ORF (KLLA0B13948g), which encodes for a protein with 71% identity to S. cerevisiae Tor2 and 68% identity to S. cerevisiae Tor1. This opens a question about the existence and composition of two TORC complexes in K. lactis as previously reported in S. cerevisiae [110] and outlines this issue as a differential point to study in relation to divergences in life span signaling. Besides, the K. lactis proteins in this group with less than 40% identity to their S. cerevisiae counterparts are also good targets for further studies.Table 1
Putative main actors of aging and its signaling pathways inK. lactis and S. cerevisiae. Degree of identity (%) between homologs is indicated in Figure 2.
Protein
ORFK. lactis
ORFS. cerevisiae
Function
Sir2
YDL042C
KLLA0F14663g
NAD+ -dependent histone deacetylase
Tpk1
YJL164C
KLLA0B12716g
PKA catalytic subunit
Tpk2
YPL203W
KLLA0D03190g
PKA catalytic subunit
Tpk3
YKL166C
KLLA0B07205g
PKA catalytic subunit
Bcy1
YIL033C
KLLA0E04181g
PKA regulatory subunit
Ypk3
YBR028C
KLLA0F24618g
An AGC kinase phosphorylated by cAMP-dependent protein kinase (PKA) in a TORC1-dependent manner
Asa1
YPR085C
KLLA0D09086g
Subunit of the ASTRA complex involved in the stability or biogenesis of PIKK*s such as TORC1
Tor1
YJR066W
KLLA0B13948g
PIK-related protein kinase and rapamycin target, subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport, and autophagy, involved in meiosis
Tor2
YKL203C
KLLA0B13948g
PIK-related protein kinase and rapamycin target, subunit of TORC1 and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton, involved in meiosis
Nnk1
YKL171W
KLLA0A06776g
Protein kinase, implicated in proteasome function, interacts with TORC1, Ure2, and Gdh2
Tco89
YPL180W
KLLA0E18855g
Subunit of TORC1 (Tor1 or Tor2-Kog1-Lst8-Tco89)
Kog1
YHR186C
KLLA0A09471g
Subunit of TORC1, it may act as a scaffold protein to couple TOR and its effectors
Tti1
YKL033W
KLLA0F25762g
Subunit of the ASTRA complex, involved in chromatin remodeling, telomere length regulator involved in the stability or biogenesis of PIKK*s such as TORC1
Tti2
YJR136C
KLLA0B04026g
Subunit of the ASTRA complex, involved in chromatin remodeling, telomere length regulator involved in the stability or biogenesis of PIKK*s such as TORC1
Sch9
YHR205W
KLLA0B03586g
AGC family protein kinase and functional ortholog of mammalian S6 kinase, phosphorylated by Tor1p and required for TORC1-mediated regulation of ribosome biogenesis, translation initiation, and entry into G0 phase, integrates nutrient signals and stress signals from sphingolipids to regulate life span
Maf1
YDR005C
KLLA0E17535g
Negative regulator of RNA polymerase III, binds to the N-terminal domain of the Rpc160 subunit of Pol III to prevent closed-complex formation, localization and activity are regulated by phosphorylation, mediated by TORC1, protein kinase A, and Sch9
Tel2
YGR099W
KLLA0D15158g
Subunit of the ASTRA complex, involved in the stability or biogenesis of PIKK*s such as TORC1
Sfp1
YLR403W
KLLA0B03047g
Regulates transcription of ribosomal protein, response to nutrients and stress, G2/M transitions during mitotic cell cycle, and DNA-damage response and modulates cell size, regulated by TORC1 and Mrs6 prion
Npr2
YEL062W
KLLA0D01067g
Npr2/3 complex mediates downregulation of TORC1 activity upon amino acid limitation
Npr3
YHL023C
KLLA0F18238g
Npr2/3 complex mediates downregulation of TORC1 activity upon amino acid limitation
*
PIKK phosphoinositide 3-kinase related kinase.Apoptosis is one type of programmed cell death (PCD) with great importance for the development and homeostasis of multicellular organisms. Basal apoptosis machinery exists also in yeast, unicellular fungus, and in some filamentous fungi [112]. Regarding the respiratory yeast K. lactis, once more the number of studies performed hitherto is very scarce [113]. A mutant in the essential gene KlLSM4, an ortholog to LSM4 of S. cerevisiae, which encodes an essential protein involved in both pre-mRNA splicing and mRNA decapping, shows phenotypic markers of apoptosis such as chromatin condensation, DNA fragmentation, accumulation of ROS, and increased sensitivity to different drugs. Mechanisms of Bax-induced [114, 115] and lactose-induced [116] cell death have also been described in K. lactis. We have recently investigated PCD in K. lactis, using the drugs staurosporine (STS) and phytosphingosine (PHS), which induce PCD in other organisms, and found that glutathione and GLR played an important role. While K. lactis seemed to be insensitive to STS, PHS induced PCD. The insensitivity of K. lactis to STS might be dependent upon the higher levels of GSH found in cells treated with STS. In human cells, PCD induced by STS causes GSH efflux, but GSH exporter proteins are absent in K. lactis. In addition, GLR appears to be involved in PHS-triggered PCD because cells lacking this enzyme are more resistant to the drug than the wild-type strain. Moreover, the addition of GSSG or GSH to the medium partially restores growth of the wild-type K. lactis strain on PHS [117].The strictly regulated removal of oxidized structures is a universal stress response of eukaryotic cells that targets damaged or toxic components for vacuolar or lysosome degradation. Autophagy stands at the crossroad between cell survival and death. It promotes survival by degrading proteins and organelles damaged during oxidative stress, but it is also activated as a part of death programs, when the damage cannot be overcome. Evidence is accumulating that the cellular sites of ROS production and signaling (including mitochondria) may be primary targets of autophagy [118]. The surplus ROS damage the mitochondria themselves and the damaged mitochondria produce more ROS in a vicious circle, ultimately leading to mitochondrial DNA deletion, a form of the so-called petite-mutant phenotype [119]. Selective mitochondria autophagy is called mitophagy and contributes to the maintenance of mitochondrial quality by eliminating damaged or excess mitochondria [120]. Although little is known about the mechanism, glutathione influences mitophagy [121, 122]. The interplay between mitochondria and autophagy seems to be evolutionarily conserved from yeast to higher eukaryotes. Defects in one of these elements could simultaneously impair the other, resulting in risk increments for various human diseases [123]. Autophagy is associated with tumor genesis, neurodegenerative diseases, cardiomyopathy, Crohn's disease, fatty liver, type 2 diabetes, defense against intracellular pathogens, antigen presentation, and longevity [121, 122, 124].Recent studies in yeast identified several mitophagy-related proteins, which have been characterized with regard to their function and regulation, allowing to compare the similarities and differences of this degradation process between yeast and mammalian cells [120]. Up to our knowledge, no studies at all about mitophagy or even autophagy have been published at present in K. lactis. We have performed a custom Blastp in Génolevures for the main actors of mitophagy [125] and its signaling pathways [126] in S. cerevisiae versus K. lactis and we found sequences with different degrees of similarity as shown in Table 2 and Figure 2. Further research is required to analyze if the sequence similarity corresponds to similarity of function or not. This is a new field of research in the respiratory yeast K. lactis. As occurs with other pathways, it is likely that functional differences exist according to fermentative or respiratory predominant metabolism in yeasts. K. lactis proteins in this group (Figure 2) are good targets for comparative studies in mitophagy.Table 2
Putative main actors of mitophagy and its signaling pathways inK. lactis and S.  cerevisiae.Degree of identity (%) between homologs is indicated in Figure 2.
Protein
ORFK. lactis
ORFS. cerevisiae
Function
Atg1
KLLA0C17160g
YGL180W
Autophagy-dedicated protein serine/threonine kinase
Atg11
KLLA0B12133g
YPR049C
Cytoplasm-to-vacuole targeting (Cvt) pathway and peroxisomal degradation (pexophagy)
Atg32
KLLA0A00660g
YIL146C
Mitochondrial receptor specific to mitophagy
Atg33
KLLA0A02695g
YLR356W
Detects or presents aged mitochondria for degradation at the stationary phase
Atg8
KLLA0E20593g
YBL078C
Component of autophagosomes and Cvt vesicles
Aup1
KLLA0F06985g
YCR079W
Mitochondrial protein phosphatase
Bck1
KLLA0F14190g
YJL095W
MAP kinase kinase kinase acting in the protein kinase C signaling pathway
Dnm1
KLLA0F12892g
YLL001W
Dynamin-related GTPase
Fmc1
KLLA0F04081g
YIL098C
Assembly at high temperature of mitochondrial ATP synthase
Hog1
KLLA0F20053g
YLR113W
MAP kinase involved in osmoregulation
Mdm38
KLLA0B11748g
YOL027C
Mitochondrial distribution and morphology
Mkk1
KLLA0D07304g
YOR231W
MAP kinase kinase acting in the protein kinase C signaling pathway
Mkk2
KLLA0D07304g
YPL140C
MAP kinase kinase acting in the protein kinase C signaling pathway
Pbs2
KLLA0E15313g
YJL128C
MAP kinase kinase in the osmosensing signal-transduction pathway
Pkc1
KLLA0E06447g
YBL105C
Protein kinase C
Rtg3
KLLA0E06513g
YBL103C
Transcription factor to activate the retrograde (RTG) and TOR pathways
Slt2
KLLA0B11902g
YHR030C
MPK1 MAP kinase
Uth1
KLLA0E14939g
YKR042W
Regulator outer membrane protein
Whi2
KLLA0F15972g
YOR043W
Full activation of the general stress response
Wsc1
KLLA0D14377g
YOR008C
Sensor transducer of the stress-activated PKC1-MPK1 kinase pathway
Yme1
KLLA0E06711g
YPR024W
Protease catalytic subunit for degradation of unfolded or misfolded mitochondrial gene products
Ynt1
KLLA0C06534g
YDR394W
Subunit of the 26S proteasome


## 6. Conclusions and Perspectives

K. lactisis proposed as a respiratory eukaryote model, complementary to the fermentative S. cerevisiae, for the study of the pathways of hypoxia-induced oxidative stress. The experimental studies carried so far reveal that there are many differences in all the steps analysed from a comparative perspective, even when high homology exists between the acting proteins from the two yeasts. Some of these differences are briefly summarized in Table 3, although they are probably much wider than here exposed and they will increase with future studies. Besides, in silico analysis reveals that transcriptional factors and several actors from the cell-defense response (life span and mitophagy) are among the poorly homologous proteins, and therefore those become good candidates for functional characterization.Table 3
Main differences reported hitherto betweenK. lactis and S. cerevisiae, two alternative unicellular eukaryote models for hypoxic and oxidative stress responses.
K. lactis
S. cerevisiae
Crabtree effect
Negative
Positive
Glucose catabolism in aerobic conditions
Mainly respiratory
Mainly fermentative
Ratio PPP/glycolysis for glucose catabolism
High
Low
Reoxidation of NADPH from PPP
Mainly by mitochondrial alternative external dehydrogenases
Mainly by cytosolic NADPH oxidoreductases
Catabolic repression of respiration
Low
High
Respiratory capacity
Unlimited
Limited
Petite phenotype
Positive in specific mutant genetic backgrounds
Positive
Caloric restriction increases longevity
No
Yes
Aerobic/hypoxic gene pairs
Absent
Present
Upregulated by hypoxia
Genes related to ergosterol synthesis, cell wall composition, and glycolytic genes. OS genes: CUP1 and CUP2, HSP12, FMP46 and GRE1, and SOD1.
Genes from the heme biosynthetic pathway, pyruvate decarboxylase, and lipid biosynthesis.OS genes: KlOYE2, KlGSH1. This response is highly dependent on the relative flux of glucose through glycolysis or PPP
Transcriptional regulators  Hap1 and Rox1
Not related to heme-mediated oxygen response
Related to heme-mediated oxygen responseMany yeast genes related to the hypoxic, oxidative, and cell-defense responses are related to human diseases [127]. Although most of the studies performed hitherto about K. lactis physiology are focused on the respiro-fermentative metabolism, and much less is known about other pathways, there are representative examples of differences between K. lactis and S. cerevisiae that might be of interest for their applications in therapy of human health disorders and in the potential use of K. lactis as a model for this research. Among the potential genes or proteins of interest, SOD1 is homolog of the human gene involved in amyotrophic lateral sclerosis [128]. NDI is involved in gene therapy of complex I defects [88, 129] and is important in neurological diseases [84–86]. Several genes of ergosterol biosynthesis are targets to look for pharmacological drugs (anticholesterol, antifungal, anticancer, etc.) [125]. Diamine oxidases and catalases have been used as therapeutic approaches for the treatment of inflammatory bowel diseases, intestinal cancers, or pseudoallergic reactions [130]. Hereditary coproporphyria (HCP), an autosomal dominant acute hepatic porphyria, results from mutations in the gene that encodes coproporphyrinogen III oxidase [131]. Sirtuins have been associated to diabetes type 2 [132] and Huntington disease [104] as well as cardiopathies or cancer [109].NeitherS. cerevisiae nor other currently used models, even multicellular, manifest the complex set of alterations associated to each health disorder in humans. This makes necessary the combination of the information obtained from several models, as representative as possible of the diversity of human cell types (S. cerevisiae, K. lactis, and others), in order to advance in puzzling out the molecular basis of the diseases and in developing new preventive and therapeutic tools.



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*Source: 634674-2012-08-14.xml*