CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES

CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHAPTER 14 – INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES

279 14 CHAPTER INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES CHRISTOPH SCHÜLLER, BETTINA E BAUER AND KARL KUCHLER INTRODUCTION The baker’s yeast Saccharomyces cerevisiae was the first eukaryotic organism to have its complete genome sequence determined, revealing 30 distinct genes encoding ATP-binding cassette (ABC) proteins (Bauer et al., 1999; Decottignies and Goffeau, 1997; Taglicht and Michaelis, 1998) ABC proteins are ubiquitous and form one of the largest gene families known with more than 2000 distinct ABC genes present in various current databases, e.g Interpro (www.ebi.ac.at/interpro/) or Prosite (www.expasy.ch/Prosite) All known ABC proteins share a common hallmark domain, the highly conserved ABC domain, also known as the nucleotide-binding domain (NBD) The NBD contains signature motifs found in all ABC proteins operating from bacteria to man (Higgins, 1992) Membrane-bound ABC proteins also contain variable numbers of membrane-spanning domains arranged in certain membrane architectures Many ABC proteins transport a variety of compounds across cellular membranes by an active process that is coupled to ATP hydrolysis These ABC proteins are therefore referred to as ABC transporters or pumps While some pumps seem to transport various xenobiotics, others exhibit a rather narrow substrate spectrum Notably, for many ABC proteins no defined substrates or even physiological roles are known Interestingly, ABC proteins not only function as simple membrane translocators ABC Proteins: From Bacteria to Man ISBN 0-12-352551-9 for molecules, they can also act as receptors, sensors, proteases, channels, channel regulators and even signal-ing components (Higgins, 1995) The question of how the highly conserved molecular architecture of ABC proteins entertains such a functional diversity remains elusive Hence, the functions of many ABC proteins may hold surprises and many important issues remain to be discovered In this chapter, we will discuss the structure, function and properties of fungal ABC proteins, focusing on the inventory of ABC genes in S cerevisiae Because the functional annotation of the yeast genome is fairly advanced, we will also compare the yeast ABC inventory to those from fungal pathogens (Candida albicans and Aspergillus fumigatus) whose genomes have been sequenced or are close to being sequenced THE INVENTORY AND MOLECULAR ARCHITECTURE OF FUNGAL ABC PROTEINS Based on their molecular architecture, one can distinguish two types of yeast ABC proteins The first type contains at least one transmembrane domain (TMD), while the second type lacks any obvious MSD (Figure 14.1) The Copyright 2003 Elsevier Science Ltd All rights of reproduction in any form reserved 280 ABC PROTEINS: FROM BACTERIA TO MAN Figure 14.1 Molecular architecture and predicted membrane topology of yeast ABC proteins The cartoon depicts the predicted membrane topologies and architecture present in distinct subfamilies of yeast ABC proteins architecture of yeast ABC proteins also includes one or two highly conserved ABC domains or NBDs, encompassing roughly 200 amino acids The most conserved features found in any given NBD are the Walker A and B motifs [AG]-X(4)-G-K-[ST] and [RK]-X(3)-G-X(3)-Lhydrophobic(4)-D, which are present in all ATP-binding proteins (Walker et al., 1982), and the ABC signature motif [LIVMFYC]-[SA][SAPGLVFYKQH]-G-[DENQMW]-[KRQASPCLIMFW]-[KRNQSTAVM]-[KRACLVM]-[LIV MFYPAN]-{PHY}-[LIVMFW]-[SAGCLIVP]{FYWHP}-{KRHP}-[LIVMFYWSTA] – (Prosite PS00211) Moreover, two additional regions provide diagnostic sequences for ABC proteins – the center motif located between Walker A and B, and the sequences found downstream of Walker B (Michaelis and Berkower, 1995) The molecular architecture of eukaryotic ABC proteins arranges NBDs with TMDs in two possible ways Yeast ABC proteins come in a duplicated TMD1-NBD1-TMD2-NBD2 forward or a mirror image NBD1-TMD1-NBD2-TMD2 reverse topology The reverse architecture of such full-size transporters is found mainly in the PDR subfamily (Table 14.1), while the forward orientation is similar to the one present in mammalian P-glycoproteins (Gros et al., 1986) However, so-called half-size transporters of both the TMD-NBD and NBD-TMD topologies are also known (Figure 14.1) Half-size ABC transporters are believed to dimerize to form functional transporter molecules The recent elucidation of a high-resolution 3-D crystal structure of the Escherichia coli MsbA protein nicely illustrates this interaction (Chang and Roth, 2001) In bacteria, each domain of a given ABC protein is encoded by a single gene, although many variations on this theme also exist in prokaryotes (Young and Holland, 1999; Chapter 8) Each TMD usually contains six predicted ␣-helical transmembrane-spanning segments (TMSs), although in some cases four to eight predicted TMSs per TMD are also known In sharp contrast to NBDs encompassing the hallmark domains, only limited homology can be found within the TMDs of different ABC proteins (Decottignies and Goffeau, 1997; Michaelis and Berkower, 1995) The NBDs serve to bind and hydrolyze ATP or other NTPs, thereby fueling transport processes However, numerous studies and genetic analyses have shown that NBDs not only serve as the fueling domains, but they appear intimately linked to the function and/or structure of individual ABC proteins Importantly, the functions of N-terminal and C-terminal NBDs are not necessarily equivalent and thus each NBD of a eukaryotic ABC protein is indispensable The analysis of the evolutionary sequence relationships between individual NBDs of yeast ABC proteins revealed five distinct clusters of homology Hence, the yeast ABC gene inventory comprises 30 genes subdivided into the PDR, MDR, ALDP, MRP/CFTR, and YEF3/RLi families (Bauer et al., 1999; Decottignies and Goffeau, 1997; Michaelis and Berkower, 1995) THE PLEIOTROPIC DRUG RESISTANCE (PDR) SUBFAMILY This subfamily includes the Pdr5p, Pdr10p, Pdr15p, Pdr11p, Pdr12p, Snq2p, Ynr070p, Adp1p and Aus1p/YOR011w ABC proteins Their function might be linked to cellular detoxification, although in several cases no substrates have been identified The overexpression of Pdr5p, Snq2p and Yor1p confers pleiotropic drug resistance (PDR) phenotypes These genes confer resistance to hundreds of chemically unrelated INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES TABLE 14.1 THE INVENTORY OF ABC PROTEINS IN SACCHAROMYCES CEREVISIAE ABC pump Substrates Length Topology Localization MDR family Ste6p Atm1p a-factor pheromone Fe/S proteins 1290 694 (TMS6-ABC)2 TMS6-ABC PM, GV, ESM Mdl1p Mdl2p PDR family Pdr5p Pdr10p Pdr15p Snq2p Pdr12p Pdr11p Aus1p/YOR011c Adp1p YNR070w YOL075c MRP/CFTR family Yor1p Ycf1p Ybt1p Bpt1p YHL035c YKR103w/YKR104c ALDp family Pxa1p Pxa2p YEF3/RLI family Yef3p Gcn20p Hef3p New1p/YPL226w Kre30p/YER036c Rli1p/YDR091c Non-classified YDR061w Caf16p/YFL028c ? ? 696 820 TMS6-ABC TMS6-ABC Mito IM Mito IM Mito IM Drugs, steroids, antifungals, PL ? ? Mutagens, drugs Weak organic acids ? ? ? ? ? 1511 1564 1529 1501 1511 1411 1394 1049 1333 1095 (ABC-TMS6)2 (ABC-TMS6)2 (ABC-TMS6)2 (ABC-TMS6)2 (ABC-TMS6)2 (ABC-TMS6)2 (ABC-TMS6)2 TMS2-ABC-TMS7 (ABC-TMS6)2 (ABC-TMS6)2 PM PM PM PM PM PM ? ? ? Oligo, revero, PL GS-conjugates, Cd2+, UCB, BA BA UCB ? 1477 1515 1661 1559 1592 1524 TMD0(TMS6-ABC)2 TMD0(TMS6-R-ABC)2 TMD0(TMS6-ABC)2 TMD0(TMS6-ABC)2 TMD0(TMS6-ABC)2 (TMS6-ABC)2 PM Vacuole Vacuole Vacuole, ERM? ? ? 870 853 TMS6-ABC TMS6-ABC Peroxisomes Peroxisomes 1044 752 1044 1196 610 608 ABC2 ABC2 ABC2 TMS3-ABC2 ABC2 ABC2 Ribo?, Cyt? Polysomes Cytosol? ? ? ? ABC ABC ? ? LCFA LCFA Hygromycin, paro 539 289 ? ABC, ATP-binding cassette; TMD0, transmembrane domain; TMS, transmembrane segment; GS, glutathione S; UCB, unconjugated bilirubin; BA, bile acids; PL, phospholipids; oligo, oligomycin; revero, reveromycin A; paro, paromomycin; LCFA, long chain fatty acids; PM, plasma membrane; ERM, endoplasmic reticulum membrane; ESM, endosomal membranes; Cyt, cytoplasm; Ribo, ribosome; Mito IM, mitochondrial inner membrane drugs, including agricultural fungicides, benzimidazoles, dithiocarbamates, azoles, mycotoxins, herbicides, cycloheximide, sulfometuron, nigericin and anticancer drugs (Balzi et al., 1987; Bissinger and Kuchler, 1994; Cui et al., 1996; Hirata et al., 1994; Katzmann et al., 1995; Kralli et al., 1995; Servos et al., 1993) These ABC genes and their regulation are described in great detail in Chapter 15 The Pdr12p pump seems to have a distinct physiological role, as it does not transport hydrophobic drugs, but confers resistance to weak organic acids Pdr12p mediates the energydependent extrusion of carboxylate anions (Piper et al., 1998), such as those used as food preservatives, including benzoate, sorbate and propionate, as well as C1–C7 weak organic acids, some of which are produced during normal 281 282 ABC PROTEINS: FROM BACTERIA TO MAN cellular metabolism Notably, PDR12 mRNA synthesis is dramatically induced by sorbic acid stress and by exposure of yeast cells to low pH stress (Piper et al., 1998), demonstrating that Pdr12 in fact represents a stress response gene Aus1p (YOR011w) is closely related to Pdr11p, sharing more than 65% sequence identity Non-essential Aus1p appears to be involved in the uptake of sterols, as a ⌬aus1 deletion mutant exhibits a reduced accumulation of cholesterol, while no obvious phenotypes are discernible under standard growth conditions (SGD http://genomewww.stanford.edu/ Saccharomyces/) The function of other members of the PDR subfamily such as Pdr11p, Pdr10p, Pdr15p, Adp1p and Ynr070p remains unknown and no data are currently available regarding their substrates or physiological roles Because Pdr10p and Pdr15p are tightly regulated by adverse conditions such as high osmolarity and heat shock, respectively, their functions might also be linked to a cellular response (Wolfger et al., in preparation) With the exception of Adp1p, all members of this group display a predicted NBD1-TMD1NBD2-TMD2 structure with usually 12 predicted TMSs Adp1p exhibits a slightly different architecture, replacing the first NBD with a large soluble domain, followed by a TMD1-NBD2TMD2 topology (Figure 14.1) It is noteworthy that all PDR members localize to the plasma membrane as shown in Figure 14.2 This cell surface localization further supports their purported function in cellular detoxification and cellular stress responses, although their precise roles and cellular substrates remain an enigma Finally, a substantial number of PDR subfamily members have been identified in other fungal species, including fungal pathogens All PDR homologues linked to multidrug resistance are extensively discussed in Chapter 15 These ABC proteins currently total almost 50 fungal PDR genes For many related PDR family members, a cellular function has not been established beyond the one known for the corresponding counterpart in baker’s yeast Examples for members of this impressive and growing group of fungal detoxification proteins are Candida krusei Abc1p, Schizosaccharomyces pombe bfr1+/Hba2p (Turi and Rose, 1995), Candida glabrata Cgr1p/ Pdh1p (Miyazaki et al., 1998), Penicillium digitatum Pmr1p (Nakaune et al., 1998), Emericella nidulans AtrAp/ANPGP1p (Del Sorbo et al., 1997) and AtrBp/ANPGP2p (Andrade et al., 2000), A fumigatus AtrFp, C albicans Cdr1p (Prasad et al., 1995), Cdr2p (Sanglard et al., 1997), Cdr3p (Balan Figure 14.2 Subcellular localization of yeast ABC proteins The cartoon depicts the subcellular localization of yeast ABC proteins in various cellular membranes or compartments For a list of ABC proteins and further details see text and Table 14.1 et al., 1997) and Cdr4p (Franz et al., 1998), Botrytis cinerea BCPGP1p, Cryptococcus neoformans eCdr1p and Magnaporte grisea Abc1p (Urban et al., 1999) This incomplete list illustrates the diversity of this ABC transporter family and hence underscores its importance, with more members surfacing at a rapid pace The interested reader is referred to publicly accessible databases such as Swissprot (www.expasy.ch) or Interpro (www.ebi.ac.uk/Interpro) to obtain continuously updated information THE MULTIDRUG RESISTANCE-RELATED PROTEIN MRP/CFTR SUBFAMILY Members of this class exhibit a membrane topology such as TMD0-TMD1-NBD1-TMD2-NBD2 (Tusnady et al., 1997) The C-terminal TMD comprises 11 predicted TMSs, interrupted by a small cytoplasmic domain Yeast MRP/CFTRlike pumps include Yor1p, Ycf1p, Bpt1p, Ybt1p, YHL035w and YKR103/YKR104w The YKR103/YKR104w open reading frames (ORFs) include a stop codon between MSD2 and NBD2 and thus represent perhaps a pseudogene or a sequencing error INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES Yor1p is probably among the best-studied members of the MRP family The gene was initially isolated in a genetic screen for genes conferring resistance to oligomycin (Katzmann et al., 1995) Yor1p is localized to the plasma membrane and has overlapping functions with PDR pumps such as Pdr5p, Snq2p and even Pdr12p, although Yor1p exhibits quite unique substrate specificities (Table 14.1) The ⌬yor1 null mutant is viable, but displays increased sensitivity to a variety of compounds, including azoles, antibiotics such as tetracycline, erythromycin and oligomycin, as well as anticancer drugs like daunorubicin and doxorubicin, carboxylic acids such as acetic, propionic and benzoic acids, and heavy metals such as cadmium (Cui et al., 1996) In contrast, Yor1p overproduction confers resistance to many of these compounds (Ogawa et al., 1998) The function of Yor1p and its regulation is also extensively discussed in Chapter 15 In contrast to Yor1p, Ycf1p is localized to the vacuolar membrane (Figure 14.2) Nevertheless, like Yor1p, Ycf1p confers resistance to cadmium (Szczypka et al., 1994) Besides vacuolar Cd2ϩ sequestration, Ycf1p is also involved in vacuolar transport of reduced glutathione and glutathione S-conjugates such as glutathioneconjugated arsenite A homologue of Ycf1p, Bpt1p, mediates transport of unconjugated bilirubin into the vacuole A ⌬ycf1 ⌬bpt1 double mutant is blocked for vacuolar transport of unconjugated bilirubin Ycf1p is related to the human multidrug resistance proteins MRP1 and MRP2, and has 45% overall similarity to human CFTR (cystic fibrosis transmembrane conductance regulator) based on a ClustalW 1.4 alignment It is interesting to note that yeast sequesters heavy metals to the vacuole, rather than extruding them Such a ‘social’ behavior of a unicellular organism might be explained by a beneficial effect on immediate neighbors Finally, Ybt1p, the yeast bile transporter (formerly Bat1p) mediates vacuolar uptake of bile acids such as taurocholate (Ortiz et al., 1997) Another close homologue of Ybt1p, the YHL035w gene product, has not been studied and its physiological cargo and cellular localization has not been elucidated as yet ABC proteins of the MRP/CFTR family have also been identified in other fungi However, in contrast to the large PDR family, substantially less information is available on fungal genes of this family In S pombe, YAWB (also SPAC3F10.11C) and ABC1 (Christensen et al., 1997b) have been identified as MRP/CFTR family members, as well as a gene from Neurospora crassa (B7A16.190) and a Yor1p homologue in C albicans (Ogawa et al., 1998) THE ALDP ADRENOLEUKODYSTROPHY PROTEIN SUBFAMILY This small subfamily contains only two halfsize transporters, Pxa1p and Pxa2p, displaying a TMD-NBD membrane topology Pxa1p/ Pxa2p are yeast orthologues of human Pmp70/ABCD3/ PXMP1, ALD/ALDR/ABCD2 and ABCD4/ PXMP1L/PMP69 peroxisomal disease genes associated with neurodegenerative diseases such as adrenoleukodystrophy and Zellweger syndrome (Gartner and Valle, 1993; Holzinger et al., 1997, 1999; Kamijo et al., 1992) Indeed, both Pxa1p and Pxa2p localize to the peroxisomal membrane and might function as heterodimers (Shani et al., 1996; Swartzman, et al., 1996) They are thought to mediate peroxisomal uptake of very long chain fatty acids to undergo degradation through ␤-oxidation (Watkins et al., 2000), which is consistent with the presence of a fatty acid-binding domain in Pxa1p/Pxa2p The null mutants fail to grow on fatty acids such as palmitate or oleate as the sole carbon source Although the Pxa1p/Pxa2p complex is required for peroxisome function, it is dispensable for peroxisome biogenesis or for import of peroxisomal matrix proteins While the PXA1 gene is only expressed when cells grow on oleate, the PXA1 and PXA2 promoters lack any consensus oleate-response elements, yet PXA1, but not PXA2, is oleateinduced and transcription is Oaf1p/Pip2pdependent (Bossier et al., 1994; Swartzman et al., 1996) The regulators Oaf1p and Pip2p represent the two key transcription factors for peroxisome biogenesis in yeast In contrast to the situation with the PDR family, only a few ALDP homologues have been described in other fungi, mostly from genomic sequencing approaches of other fungal genomes (Figure 14.3 A, B) THE MDR SUBFAMILY This subfamily contains the ABC proteins Mdl1p, Mdl2p, Atm1p and Ste6p The Ste6p 283 284 ABC PROTEINS: FROM BACTERIA TO MAN MDR MRP/ CFTR A B Figure 14.3 Similarity relationships of fungal ABC proteins A, A dendrogram in which the entire yeast inventory is compared with sequences from the Aspergillus genome project, including the apparent classification into yeast subfamilies Preliminary sequence data was obtained from The Institute for Genomic Research website at http://www.tigr.org B, The same dendrogram for the Candida albicans genome Sequence data for C albicans was obtained from the Stanford Genome Technology Center website at http://www-sequence.stanford.edu/group/candida Sequencing of C albicans was accomplished with the support of the NIDR and the Burroughs Welcome Fund a-factor pheromone transporter is a full-size transporter displaying the duplicated (TMDNBD)2 topology Ste6p is localized in Golgi vesicles, the plasma membrane and perhaps endocytic vesicles (Kölling and Hollenberg, 1994; Kuchler, 1993; Michaelis, 1993) Ste6p is a haploid-specific transporter required for the export of farnesylated a-factor, a pheromone absolutely required for mating in yeast Ste6p was the first ABC transporter identified in yeast (Kuchler et al., 1989; McGrath and Varshavsky, 1989), closing an evolutionary gap between the E coli hemolysin transport system (Wang et al., 1991) and mammalian Mdr1p P-glycoprotein mediating multidrug resistance (Chen et al., 1986; Gros et al., 1986) Interestingly, the steady state concentration of Ste6p was found to be highest in the Golgi vesicles, although its function is clearly required in the plasma membrane (Berkower et al., 1994; Kuchler et al., 1993) Because Ste6p travels through all exo- and endocytic compartments, it serves as a useful model membrane protein for intracellular trafficking, proteolytic degradation, endocytosis, and even vacuolar sorting studies (Berkower et al., 1994; Kölling and Hollenberg, 1994; Kuchler, 1993; Kuchler et al., 1989) Moreover, Ste6p has been subjected to extensive molecular studies to unravel the molecular mechanisms of ABC transporter-mediated peptide transport Ste6p function can be easily tested through convenient assays such as mating (Kuchler and Egner, 1997) Notably Ste6p, although an MDR family member, does not confer typical multidrug resistance phenotypes Extracellular a-factor pheromone is essential for the sexual reproduction cycle of haploid yeast cells Ste6p functions at the plasma membrane, providing the ratelimiting step in a-factor export After pheromone extrusion, Ste6p is rapidly removed from the cell surface through ubiquitin-mediated endocytosis, and delivered to the vacuole for terminal degradation (Egner et al., 1995; Kölling and Hollenberg, 1994) Pheromone export INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES occurs through a non-classical route, bypassing the vesicular secretory pathway (Kuchler, 1993) Interestingly, severing experiments demonstrate that both Ste6p halves, when coexpressed as individual half-size transporters, mediate pheromone export (Berkower et al., 1996) This indicates that both Ste6p halves are required for function and that they can interact in vivo to form a functional a-factor transporter The transport substrate, a-factor, is extremely hydrophobic due to its C-terminal lipid modification and carboxy-methylation While mutations in the structural gene encoding a-factor not dramatically affect its secretion, a lack of a-factor farnesylation or methylation debilitates its release (Sapperstein et al., 1994) Hence, the lipid moiety or its hydrophobicity may represent an essential recognition determinant for Ste6p As with many other eukaryotic ABC transporters, Ste6p is powered by ATP hydrolysis, because many NBD mutations destroy function (Browne et al., 1996), and because Ste6p binds photoactivatable ATP analogues (Kuchler et al., 1993) Interestingly, Ste6p might also play a role in cell fusion, since ste6 mutants were isolated that still mediate a-factor export, but fail to complete fusion of haploid mating partners (Elia and Marsh, 1996) Taken together, the precise mechanism by which the Ste6p ABC transporter mediates the actual pheromone translocation across the plasma membrane is somewhat mysterious, but it appears as if intracellular a-factor precursor processing and translocation across the plasma membrane are tightly coupled (Kuchler and Egner, 1997; Michaelis, 1993) The half-size molecules Mdl1p, Mdl2p and Atm1p display a similar TMD-NBD topology and localize to the mitochondrial inner membrane (Figure 14.2) Mdl1p is related to mammalian P-glycoproteins and to a greater extent to the mammalian peptide transporter of antigen presentation, TAP (Dean and Allikmets, 1995) It is required for efficient mitochondrial export of rather long peptides of 2100–2600 Da molecular mass These peptides are proteolytic degradation products of inner membrane proteins generated by mAAA proteases Afg3p and Yta12p However, Mdl1p fails to transport short peptides or free methionine (Young et al., 2001) Notably, Mdl2p seems to play a different role in mitochondrial function, since it has not been implicated in peptide transport processes It is therefore likely that Mdl1p and Mdl2p may form functional homodimers, which contrasts with the situation of peroxisomal Pxa1p and Pxa2p Furthermore, Mdl1p and Mdl2p co-purify at molecular masses of approximately 200 kDa and 300 kDa, respectively, suggesting that they are part of distinct oligomeric protein complexes (Young et al., 2001) The third member of the yeast MDR group, Atm1p, is related to the human ABCB7/ABC7 protein, which is implicated in the mitochondrial X-linked sideroblastic anemia and ataxia (Allikmets et al., 1999) Atm1p is required for mitochondrial DNA maintenance or stability, but this function might be an indirect phenotypic effect observed in the ⌬atm1 mutant The atm1-1 mutant displays a high level of damage and even loss of mitochondrial DNA during growth on rich medium Interestingly, the ATM1 mRNA localizes in close proximity to mitochondria in living cells, as demonstrated using a GFP fusion protein that binds to a heterologous sequence in a reporter ATM1 mRNA (Corral-Debrinski et al., 2000) Atm1p is also required for the assembly of iron–sulfur clusters of cytoplasmic iron–sulfur-containing proteins, and thus may be involved in the export of mitochondrial heme required for cluster assembly (Pelzer et al., 2000) ABC proteins of the MDR family have also been identified in other fungal species For example S pombe Mam1p is similar in length and domain structure to Ste6p and shares about 30% sequence identity, thus representing the Ste6p orthologue in fission yeast (Christensen et al., 1997a) The C albicans Hst6p transporter can also functionally complement a ⌬ste6 mutant (Raymond et al., 1998) Further, MDR family homologues have been identified in A fumigatus (Mdr2p) (Tobin et al., 1997), C albicans Mdl1p (Swissprot ID: P97998), S pombe (YFX9 C9B6.09c) and Rhizomucor racemosus (Trembl ID: Q9C163/ Pgy1p) THE NON-TRANSPORTER YEF3/RLI SUBFAMILIES AND NON-CLASSIFIED ABC PROTEINS This S cerevisiae subfamily includes Yef3p, Hef3p, Rli1p, Gcn20p, Kre30p, Caf16p and New1p Except for New1p, these ABC proteins lack any predicted TMSs normally present in other ABC transporters Surprisingly, three ABC 285 286 ABC PROTEINS: FROM BACTERIA TO MAN proteins from this class, Yef3p, Kre30p and Rli1p, are essential for viability under standard growth conditions These proteins are involved in cellular functions that appear unrelated to transport events, and the functional role of the NBDs is in most cases not clear Yef3p perhaps localizes to the cytoplasm or even to ribosomes It is also known as translation elongation factor EF-3A, which has a function in tRNA binding and dissociation from the ribosome (Chakraburtty, 1999) Yef3p displays basal ATPase activity, which is stimulated by the presence of ribosomes by two orders of magnitude, suggesting that Yef3p might at least interact with ribosomes or in fact localize to ribosomes (Gontarek et al., 1998) A ribosomebinding site and a putative tRNA-binding domain is located near the C-terminus of Yef3p ATP hydrolysis facilitates EF-3 dissociation from the ribosome In eukaryotes only fungal homologues are known, suggesting that Yef3p is a unique fungal translation elongation factor (Sarthy et al., 1998) Whole-genome transcriptome profiling of a conditional null-mutant indicates a gene expression pattern that resembles that of wild-type cells treated with cycloheximide, suggesting a role for Yef3p in blocking ribosomes in vivo (Hughes et al., 2000) The YEF3 mRNA levels are modulated by a variety of conditions It is repressed by rapamycin and peroxide or heat shock stress conditions (Causton et al., 2001), while hyperexpressed in high density cultures and during diauxic shift Notably, overexpression of Yef3p renders cells hypersensitive to paromomycin and hygromycin B, two translational inhibitors (Sandbaken et al., 1990) Hef3p (also known as Yef3Bp) shares 84% overall identity with Yef3p, implying a similar or overlapping function Indeed, Hef3p can rescue a yef3 null mutant when expressed from the YEF3 or ADH1 promoter (Sarthy et al., 1998) In striking contrast to loss of Yef3p, however, a ⌬hef3 null mutant has no obvious growth defect This might be explained by the fact that Hef3p is not expressed under normal culture conditions and its promoter is therefore inactive (Maurice et al., 1998) Interestingly, HEF3 mRNA levels are highly upregulated by limiting zinc concentration in the growth medium (Yuan, 2000) The HEF3 mRNA abundance increases during nitrogen starvation and during stationary phase, but is repressed by a shift to high osmolarity (Causton et al., 2001) It will be interesting to uncover the role of Hef3p under these conditions Like Yef3p, and perhaps Hef3p, Gcn20p has a functional role in translation Gcn20p is a component of a protein complex required for the response to amino acid starvation, glucose limitation and osmotic stress (Marton et al., 1997) Together with Gcn1p, Gcn20p is probably involved in detection of uncharged tRNA and transmission of this signal to Gcn2p, a protein kinase which phosphorylates eIF2alpha Gcn1p, Gcn2p and Gcn20p form a complex and the apparent role of Gcn20p is to activate Gcn2p, through the stabilization of the interaction between Gcn1p and Gcn2p (Garcia-Barrio et al., 2000) The gcn20 mutant phenotype is similar to a gcn1 mutant, in that the null mutant is viable under normal conditions and inviable under starvation conditions (Vazquez de Aldana et al., 1995) The C-terminal region of Gcn20p containing the ABC domain is dispensable for complex formation with Gcn1p and for the stimulation of Gcn2p kinase activity (Marton et al., 1997), and the role of the Gcn20p NBD remains obscure The physiological roles of the following nontransporter ABC proteins are largely unknown and they may therefore provide some surprises in the future Kre30p is required for viability and was initially isolated in a genetic screen for Killer toxin-resistant mutants The cellular function of Kre30p is not known, but it seems to interact with other proteins as determined by two-hybrid assays Interactions with several proteins, including Sma1p (spore membrane assembly) and Cbk1p (an S/T kinase required for sporulation) were discovered, but the physiological relevance of these interactions, if any, remains to be established The N-terminal domain of New1p, which is especially rich in glutamine and asparagine residues, is able to support prion inheritance when fused to SUP35 Sup35p is a translational release factor, eRF3, which interacts with Sup45p (eRF1) to form a translational release factor complex Moreover, Sup35p is also a prion-like molecule responsible for the [PSIϩ] determinant (Tuite et al., 1981) Although the cellular function of New1p remains elusive, it may behave as an epigenetic switch (Santoso et al., 2000) The New1p sequence also includes three predicted TMSs, although they are not clustered within a classical TMD Finally, NEW1 mRNA levels are repressed under stress conditions such as changes in temperature, oxidation, nutrients, pH and osmolarity (Causton et al., 2001; Jelinsky et al., 2000) INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES The Caf16p and Ydr061w ABC proteins contain only a single NBD While nothing is known about YDR061w, Caf16p seems to have a role in PoIII-dependent transcription of some, but not all, promoters Caf16p forms a dimer and interacts with the RNA polymerase II holoenzyme components Srb9p, Ssn3p, and Ssn8p Finally, Rli1p is similar to the human RNase L inhibitor (RLI) Its precise function has not been established, although a ⌬rli1 null mutation in yeast is lethal Human RLI is probably a regulator of the 2Ј,5Ј-oligoadenylatedependent RNase L, which is involved in the antiviral activity of interferons Some viruses developed strategies to bypass the antiviral activity of RNase L by virus-induced expression of RLI (Martinand et al., 1999) Interestingly, the C-terminal tail domain of yeast Ire1p displays sequence similarity to mammalian RNase L (Sidrauski and Walter, 1997) Ire1p is a regulator of the unfolded protein response pathway (UPR), which signals from the ER to the nucleus (Cox et al., 1993) A direct role for Rli1p in the UPR is possible but untested as yet EVOLUTIONARY RELATIONSHIPS OF ABC GENES IN FUNGI Numerous homologues of yeast ABC genes have also been identified in other fungal species through functional complementation approaches More importantly, genome sequencing of fungal pathogens such as C albicans and A fumigatus provided complete sequence datasets from their genomes and the data are publicly available (TIGR: http://www.tigr.org/; Stanford Genome Technology Center: http:// sequence-www.stanford.edu/) Although functional annotation of ABC genes in these fungal pathogens has been a difficult task, the comparison of various fungal ABC inventories has become possible Because a global picture of the evolutionary relationships of ABC genes from various fungi has not been reported, we have compared the inventory of baker’s yeast ABC genes to various fungal genomes Yeast ABC genes guided a search to detect and identify homologous sequences in other fungal species, including C albicans and A fumigatus (Figure 14.3 A, B) Previous work demonstrated that all S cerevisiae NBDs generate clusters of five subfamilies (Table 14.1) In a first round of comparison, NBDs were identified using a translated pattern search against the nucleotide sequence databases The patterns were generated by alignment of the respective subgroups of S cerevisiae NBD sequences The comparison of amino acid sequence patterns with a translated nucleotide sequence minimizes the effect of sequencing errors causing truncations or frameshift mutations In addition, the sequences were searched with the Prosite patterns for ABC proteins In the next step, the regions surrounding hits were analyzed in detail by extracting putative NBDs In cases where truncations due to frameshift mutations had occurred, ORFs were appropriately edited to allow for the generation of meaningful dendrograms Next we generated an alignment using the entire set of NBDs including S cerevisiae NBDs The A fumigatus candidate genes were first identified through a tblast at TIGR (http://www.tigr.org/) The dendrograms shown in Figure 14.3 represent a graphical display of the sequence homologies as detected through the alignment, although it should be noted that this is not a phylogenetic tree Furthermore, we intended to include a dendrogram showing the relationships to C neoformans ABC genes, the sequence data of which can be publicly accessed at http://wwwsequence.stanford.edu/group/C.neoformans/ However, because of the confidentiality policies of the sequencing consortium, we were prohibited from doing so As shown in Figure 14.3, each subfamily from baker’s yeast has an equivalent family in other fungi Thus, ABC proteins from other fungi form similar evolutionary relationships, and can thus be classified into similar subfamilies The PDR subfamily contains five Candida homologues (Cdr1p, Cdr2p, Cdr3p, Cdr4p and Cdr99p) of Pdr5p, all of which are more similar to each other than to other yeast members of the Pdr5p-family (Figure 14.3A) As in yeast, not all CDR genes are implicated in drug resistance While Cdr1p and Cdr2p mediate clinical antifungal resistance, the function of Cdr3p and Cdr4p has not been linked to drug efflux Homozygous deletion of CDR4 did not confer hypersensitivity to fluconazole (Franz et al., 1998) Interestingly, the CDR3 gene is regulated in a cell-type-specific manner, as it appears important in morphology switching, and it is not expressed in the standard laboratory strain CAI4 However, in a WO-1 genetic strain background that switches between two 287 288 ABC PROTEINS: FROM BACTERIA TO MAN morphological states, white and opaque, the CDR3 mRNA is only present in the opaque form Here, overexpression of Cdr3p did not result in increased resistance to known drug substrates of the PDR family (Balan et al., 1997) Substantially less information is available on the PDR family homologues in A fumigatus (Figure 14.3), although in general, a clear species-specific clustering becomes immediately apparent in this family As expected, the yeast ALDP subfamily has equivalent orthologues in all other fungal pathogens In C albicans a homologue to both Pxa1p and Pxa2p is detectable, while in A fumigatus only one close match could be identified Concerning the MDR subfamily, single nearest matches to each Atm1p, Mdl1p, Mdl2p and Ste6p were found in C albicans The situation seems to be somewhat more complicated in A fumigatus The A fumigatus MDR members cluster together and not allow even a tentative assignment The C albicans orthologue of Ste6p has been previously described as Hst6p (Raymond et al., 1992) Surprisingly, despite the diploid nature of C albicans, Hst6p is able to functionally complement a ste6 null mutant for a-factor transport in S cerevisiae The MRP subfamily indicates some differences between S cerevisiae and C albicans No close homologue to Ste6 was identified in A fumigatus Furthermore, we not find a close neighbor of Ybt1p and YHL035c, a fact that could also be the consequence of incomplete databases While single orthologues to Ycf1p and Yor1p are present, two Candida ORFs are similar to Bpt1p Thus, further experimental evidence will be necessary to establish the roles of the two Candida Bpt1ps, whether or not one of them represents a functional homologue of Ybt1p In the A fumigatus alignments we find a Yor1p and Ycf1p homologue but several candidates for Ybt1p remain Finally, the nontransporter ABC genes from the YEF3/RLI subfamilies, as well as non-classified ABC genes, all have corresponding genes in other fungal species For instance, both Yef3p and Hef3p cluster with the C albicans homologue Tef3p The Candida Eif3p, however, appears more similar to New1p than to Hef3p Both Gcn20p and Kre30p also have close homologues in Candida, and Caf16p and Rli1p also have a single counterpart in Candida Taken together, the inventory of ABC proteins from fungal pathogens is quite similar to the one present in baker’s yeast, with similar subfamilies of close evolutionary relationships TRANSCRIPTOMES AND YEAST ABC GENE MRNA PROFILES The completion of the entire yeast genome, and the availability of genomic tools such as whole-genome DNA microarrays, permitted the transcriptional profiling of many metabolic pathways It is therefore not surprising that expression regulation of yeast ABC genes was observed in numerous studies that investigated genome-wide expression of yeast genes For example, PDR5, SNQ2, YOR1, PDR10, PDR11 and PDR15 share common transcriptional regulators, such as the zinc-finger proteins Pdr1p, Pdr3p or Yrr1p (Del Sorbo et al., 1997) These regulators, also instrumental for PDR development, control a number of genes of both the ABC family and non-ABC genes (DeRisi et al., 2000; Wolfger et al., 2001) A detailed transcriptome analysis revealed the identification of numerous potential Pdr1p/Pdr3p target genes (DeRisi et al., 2000) Moreover, PDR target genes were also identified simply by the presence of potential PDRE cis-acting motifs in yeast gene promoters However, a Pdr1p/Pdr3p-dependent regulation has only been experimentally verified for certain ABC genes and two MFS permeases (Wolfger et al., 1997) It should be emphasized that the molecular signals, including the transduction pathways affecting transcriptional activities of Pdr1p, Pdr3p or Yrr1p, remain elusive A specific activation of these factors by drugs has not been reported It is tempting to speculate that PDR could evolve through increased mutation rate upon drug challenge or other adverse conditions Apart from other regulatory influences, the mRNA levels of several ABC genes show dependencies on carbon and/or nitrogen source, stress regulation as well as cell cycle-dependent fluctuations A closer inspection of the available literature on yeast ABC gene expression leads to the conclusion that individual mRNAs display a distinctive expression pattern Even closely related proteins such as the PDR group display striking differences under various conditions In many cases, the transcription factors involved remain unknown but a functional link between stress response and drug resistance is evident Whole genome transcriptome analysis suggested that Snq2p is induced by heat shock, H2O2 and rapamycin, whereas PDR5 mRNA is INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES only upregulated during cold shock, but not by heat shock (Causton et al., 2001; Gasch et al., 2000) Further, Pdr12p protein levels are specifically induced by weak organic acids (Piper et al., 1998), by an as yet unknown stress response pathway Notably, Pdr15p is upregulated in mitochondrial DNA mutants and it appears to be under general stress control through Msn2p and Msn4p (Wolfger et al., in preparation) Likewise, fluctuations in PDR12 and YOR1 mRNAs during the cell cycle, with a peak in early G1 phase, remain unexplained, as well as the observation that PDR5 mRNA and those of several other membrane proteins, most of them involved in nutrient metabolism, peak in the G2/M phase It is thus not clear what the common regulatory principle affecting these genes is, but relevant hints might emerge once more physiological roles of ABC genes are established The following chapter is devoted to comprehensive and detailed discussions on fungal ABC proteins and regulators implicated in pleiotropic or multidrug resistance phenomena To come full circle, additional chapters in this part of the book will address the functions of plant ABC proteins, as well as ABC proteins from parasitic organisms ACKNOWLEDGMENTS We are indebted to our colleagues Agnés Delahodde, Christophe D’énfert, Bertrand Favre, André Goffeau, Scott Moye-Rowley, Peter Piper, Elisabeth Presterl, Neil Ryder, Dominique Sanglard, Julius Subik, Friederike Turnowsky, Marten de Waard and Birgit Willinger for sharing unpublished information, materials, and strains as well as for many stimulating discussions Special thanks to the Vienna EMBnet manager Martin Grabner for help with database searches Thanks to all group members for critical comments on the manuscript Our research is supported by grants from the ‘Fonds zur Förderung der wissenschaftlichen Forschung’ (FWF, P12661-BIO), by funds from the Austrian National Bank (OeNB #7421), grants from Novartis Pharma Inc., DSM Bakery Ingredients, the ‘Hygiene-Fonds’ of the Medical Faculty of the University of Vienna and the ‘Herzfelder Foundation’ Sequence data for Candida albicans was obtained from the Stanford Genome Technology Center website at http://www-sequence stanford.edu/group/candida Sequencing of Candida albicans was accomplished with the support of the NIDR and the Burroughs Welcome Fund Aspergillus fumigatus preliminary sequence data was retrieved from The Institute for Genomic Research website at http://www tigr.org Sequencing of Aspergillus fumigatus was funded by the National Institute of Allergy and Infectious Disease U01 AI 48830 to David Denning and William Nierman REFERENCES Allikmets, R., Raskind, W.H., Hutchinson, A., Schueck, N.D., Dean, M and Koeller, D.M (1999) Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked 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These genes confer resistance to hundreds of chemically unrelated INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES TABLE 14. 1 THE INVENTORY OF ABC PROTEINS IN SACCHAROMYCES CEREVISIAE ABC pump... oxidation, nutrients, pH and osmolarity (Causton et al., 2001; Jelinsky et al., 2000) INVENTORY AND EVOLUTION OF FUNGAL ABC PROTEIN GENES The Caf16p and Ydr061w ABC proteins contain only a single... (1995) Evolution of ATP-binding cassette transporter genes Curr Opin Genet Dev 5, 77 9–7 85 Decottignies, A and Goffeau, A (1997) Complete inventory of the yeast ABC proteins Nat Genet 15, 137 145