Abstract
Secondary metabolites (SMs) produced by filamentous fungi are well known for having a broad range of bioactivities that have detrimental, as well as beneficial, impacts on human affairs. With the grouping of SM biosynthetic genes into clusters it is possible for regulatory elements, such as individual transcription factors or multiprotein complexes, to modulate metabolite expression individually or at a larger, more global scale. In this chapter, we survey some key transcriptional players in the regulation of secondary metabolism including cluster-specific Zn(II)2Cys6, Cys2His2, and winged helix proteins, bZIP factors associated with stress and SM, environmental monitoring Cys2His2 proteins (AreA, CreA, and PacC) and two global regulatory complexes—the velvet complex and the CCAAT-binding complex.
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Introduction
Beyond their environmental ubiquity and critical roles in nearly every ecological niche as primary decomposers, fungi are well known for producing a wealth of low molecular weight molecules called secondary metabolites, which are also known as natural products. Although the true ecological function of most secondary metabolites (SMs) is still unknown, their roles as biotic and abiotic protectants or defensive metabolites is emerging [1–4]. Furthermore, their significant impact on human well-being, both positive and negative, makes them attractive study targets.
With a broad spectrum of biological activity, SMs can have major influences on human health. For example, subsets of SMs known as mycotoxins are responsible for millions of dollars in crop loss annually just in the USA alone [5]. When mycotoxin contamination of consumables goes undetected, the resulting mycotoxicoses have additional health and economic consequences, which has been documented throughout recorded history [6]. Crop losses and health consequences are especially devastating in developing countries where testing for toxin contamination is either not well established or is nonexistent [7]. Conversely, the diverse pharmacodynamics of medically relevant SMs such as the β(beta)-lactam antibiotics penicillin and cephalosporin, and the popular cholesterol-lowering agent lovastatin, are examples of how fungal SMs have had positive impacts on human well-being.
At the genomic level, one of the defining hallmarks of SM is the grouping of biosynthetic genes into discreet clusters [8] and general localization to subtelomeric regions of the chromosome [9]. Many, but not all, clusters contain cluster-specific transcription factors that regulate expression of the biosynthetic genes for their respective metabolites. This clustering, coupled with unique chromosomal location, allows for multiple regulatory layers giving the producing fungus precise spatial and temporal control over metabolite expression and likely contributes to intra-, and possibly inter-kingdom, horizontal cluster transfer [10–12]. Additionally, SM production is often tightly correlated with growth and development [13], and oftentimes disruption of one process will have a significant effect on the other.
The study of fungal SMs has established several model fungal systems and particular metabolites with facile laboratory characterization allowing clear study of their expression and regulation. Yet, as an increasing number of fungal genomes become available, it has become clear that the number of metabolites observed under routine laboratory conditions is a paltry representation of the theoretic yield based on predicted in silico genomic regions containing signature SM biosynthetic cluster motifs [14]. Resulting from these observations, endeavors to unlock these “cryptic” gene clusters have shed light on SM regulators working at the level of individual metabolites or at a larger, global scale.
In this chapter, we review the general mechanisms of key players in the regulation of fungal SM . As will become evident in the following paragraphs, fungal SM regulation does not follow a strict hierarchical regime and is composed of overlapping and interconnected pathways making regulatory classifications of regulators less amenable to simple progressional delineations. As such, we will group and present key players based on the largely cluster-specific Zn(II)2Cys6 family of transcription factors, then investigate additional families that possess more pleiotropic regulatory characteristics, and finish with global regulators and multiprotein complexes that respond to environmental cues.
ZN(II)2CYS6
The grouping of SM biosynthetic genes into discreet and contiguous clusters is a distinguishing feature of SM in fungi [8]. In-cluster transcription factors are commonly found that exhibit regulatory control over their respective cluster’s transcription of biosynthetic genes. As the production and regulation of SMs in fungi are replete with diversity, it is not surprising that multiple families of transcription factors regulate these processes. Therefore, we will begin with the largest cluster-specific family of fungal transcription factors (Table 2.1) [15–35].
Unique to fungi are the Zn(II)2Cys6 family of transcription factors. Some distinguishing features of these proteins are the binding of two zinc atoms to six cysteine residues and their ability to bind DNA as monomers, homodimers, or heterodimers [36]. Common nomenclatures for Zn(II)2Cys6 transcription factors include: C6, Zn2C6, zinc binuclear cluster, as well as zinc cluster. Compared to other families of transcription factors, Zn(II)2Cys6 proteins are the most common family of dedicated cluster regulators for fungal SM.
To date, the most well-characterized cluster-specific transcription factor is the aflatoxin (AF)/sterigmatocystin (ST) regulator AflR. As the paradigm for Zn(II)2Cys6-mediated cluster regulation, AflR has unequivocally established the importance of studying transcriptional regulators in the context of SM expression and regulation. Deletion of aflR in Aspergillus nidulans produced a condition in which ST production was suppressed at the transcriptional level, even under ST-stimulating conditions [37] and, conversely, increasing expression of aflR in normally non-AF producing conditions resulted in concomitant expression of AF biosynthetic genes [18].
Many of the SM clusters characterized in A. nidulans contain Zn(II)2Cys6 proteins including AfoA and CtnR, ApdR, and MdpE required for asperfuranone, aspyridone, and monodictyphenone gene expression, respectively [19, 20, 30]. Overexpression of Zn(II)2Cys6 proteins can be sufficient to activate silent SM clusters as was first reported for ApdR, thus representing a critical proof-of-principle for fungal genome mining in the postgenomic era [20]. This technique, however, does not always work, resulting in the development of alternative methods to bypass Zn(II)2Cys6 regulation altogether and target individual keystone SM genes [38]. Cluster-specific Zn(II)2Cys6 transcription factors regulating SM production in plant pathogenic fungi include CTB8 for cercosporin, DEP6 for depudecin, FUM21 and ZFR1 for fumonisin, GIP2 for aurofusarin, ORFR for AK-toxin, and SirZ for sirodesmin PL in Cercospora nicotianae, Alternaria brassicicola, Fusarium verticillioides, Gibberella zeae, Alternaria alternata, and Leptosphaeria maculans, respectively [22, 24, 26, 27, 33–35]. Additionally, Bik5 controls synthesis of the mycelial pigment bikaverin in Fusarium fujikuroi [21]. Understanding Zn(II)2Cys6 cluster regulation is also critical in biotechnologically relevant fungi given that this family of transcription factors can also control production of the important antihypercholesterolemic agents lovastatin and monacolin K, as well as the pravastatin sodium precursor compactin, regulated by LovE, MokH, and MlcR in Aspergillus terreus, Monascus pilosus, and Penicillium citrinum , respectively [29, 31, 32, 39]. Recently, an interesting new twist to the canonical view of a Zn(II)2Cys6 regulating a single SM came with the finding of the transcription factor FapR that simultaneously regulates biosynthetic genes of the intertwined fumagillin and pseurotin cluster in Aspergillus fumigatus [25]. Table 2.1 provides a few additional examples of these types of transcription factors [15–35].
CYS2HIS2
Common to fungi (Table 2.2) and all other eukaryotes are the Cys2His2 family of transcription factors [21, 40–69]. Defining features of this family include two or more of the conserved, repeating amino acid zinc finger units that bind a single zinc atom [36]. Cys2His2 proteins bind DNA as monomers and can also be referred to as C2H2 and classical zinc finger transcription factors.
For surviving a multitude of environmental challenges, fungi often require structural pigments for withstanding biotic and abiotic stresses [70]. A unique group of orthologous Cys2His2 transcription factors has been found in several plant pathogenic fungi , all positively regulating biosynthesis of the structural pigment melanin. The proteins Cmr1p, Pig1p, Cmr1, and BMR1 are found in Colletrichum lagenarium, Magnaporthe grisea, Cochliobolus heterostrophus, and Bipolaris oryzae, respectively [43, 45, 46]. In addition to two Cys2His2 motifs, these four proteins also possess a Zn(II)2Cys6 sequence. The earliest recorded examples of SM regulation by Cys2His2 proteins are MRTRI6 and Tri6 regulating trichothecene mycotoxin gene clusters in the plant pathogenic fungi Myrothecium roridum and Fusarium sporotrichioides , respectively [50, 58]. In one of the few cases of an SM-specific regulator gene lying outside of the cluster it controls, the Cys2His2 transcription factor ScpR on chromosome II was shown to activate the asperfuranone cluster in A. nidulans, likely through binding the promoter region of afoA, embedded in the asperfuranone cluster located on chromosome VIII [57].
Recently, the characterization of two new Cys2His2 transcription factors has shown regulation of other physiological processes beyond SM. Exhibiting positive regulation over the toxins botrydial and botcinic acid in Botrytis cinerea, BcYOH1 exhibited a more global regulatory role as it also affects mechanisms in detoxification, virulence , and carbohydrate metabolism [44], whereas sda1 knockout strains of F. verticillioides had excessive fumonisin B1 biosynthesis, reduced capacity to form conidia, and an inability to grow on selected carbon sources [56].
bZIP
Found in all eukaryotic organisms, basic leucine zipper (bZIP) transcription factors are characterized by basic and leucine zipper regions. The basic region dictates sequence-specific DNA-binding whereas the leucine zipper region mediates dimerization of the protein. As dimers, bZIPs target palindromic DNA sequences. Many fungal bZIPs (Table 2.2 [21, 40–69]) have been characterized as stress response transcription factors, responding to a variety of environmental stresses that appears to link them to SM production [60, 71, 72]. bZIPs associated with SM regulation and stress include RsmA regulating sterigmatocystin and asperthecin in A. nidulans and gliotoxin in A. fumigatus [64, 65], AtfB regulating aflatoxin in Aspergillus parasiticus [60], and Aoyap1 regulating ochratoxin in Aspergillus ochraceus [59]. The bZIP protein MeaB, involved in nitrogen regulation, has also been associated with regulation of SMs including bikaverin in F. fujikuroi and AF in A. flavus [62, 63].
In the plant pathogen Cochliobolus carbonum, HC-toxin biosynthetic genes are regulated by the hybrid bZIP/ankyrin repeat transcription factor ToxE [73]. Despite having the basic region characteristic of bZIPS, ToxE lacks the leucine zipper sequence but possesses four ankyrin repeats. Both the basic region and ankyrin repeat region mediate DNA binding to promoter regions of all HC-toxin biosynthesis genes [67]. ToxE, together with the putative transcription factor Bap1 from the tomato pathogen Cladosporium fulvum, represent a potentially novel class of fungal-specific hybrid transcription factors possessing bZIP and ankyrin repeat characteristics [66].
Winged Helix
Winged helix proteins are found in all organisms and belong within the general helix-turn-helix structural group of proteins. Broadly speaking, the structure of a winged helix protein consists of two wings, three α(alpha) helices, and three β(beta) strands [74]. The industrially relevant fungus Acremonium chrysogenum is well known for production of the antibiotic cephalosporin C. Cluster-specific regulation of cephalosporin C production in A. chrysogenum was first shown to be controlled by the transcription factor CPCR1, which belongs to the winged helix subfamily of regulatory factor X (RFX) proteins [69]. Another regulator of cephalosporin C, AcFKH1 belongs to a subfamily of winged helix proteins possessing a forkhead associated domain (FHA) and a forkhead DNA-binding domain (FKH) [68]. Consistent with the observation that SM production is often inextricably linked to morphological development, it was shown that CPCR1 is not only required for cephalosporin C production, but also for the formation of arthrospores and whereas AcFKH1 deletion strains still retained the ability to form arthrospores despite possessing swollen and highly septate hyphae [75]. To the best of our knowledge, cephalosporin C is the only fungal SM currently known to be regulated by winged helix proteins (Table 2.2 [21, 40–69]).
Global Regulators
AreA—Nitrogen
So far we have reviewed transcription factors largely characterized as cluster-specific and will now move into global regulators that translate environmental cues into SM and concomitant physiological responses. In A. nidulans an increase in ST, and an increase in the rate of sexual development, is observed when grown on nitrate, whereas an opposite response for both phenotypes is observed on ammonium media [76]. Conversely, ammonium stimulates AF biosynthesis in A. parasiticus and nitrate inhibits its production [77]. Comparing the SM response to varying nitrogen sources between these two Aspergillus species suggests a highly dynamic interplay between environment, SM adaptation, and developmental regime.
Among fungi , the highly conserved global transcription factor AreA is responsible for repression of nitrogen metabolism in the presence of glutamine or ammonium, and is a member of the GATA family of transcription factors, which are conserved among eukaryotes and are characterized by their Cys2Hys2 zinc finger DNA binding domains [78]. Beyond its regulatory role in primary metabolism, AreA modulates morphological development and SM regulation in filamentous fungi and is likely responsible for the aforementioned species-specific mycotoxin responses based on the observation of multiple GATA sequences in the aflatoxin and sterigmatocystin regulatory genes aflR and aflJ, and subsequent AreA binding to these regions in A. parasiticus [40]. The rice pathogen Gibberella fujikuroi exhibits decreased transcript levels for nearly all structural genes for the SM gibberellin in an areA deletion mutant, showing direct regulation of this cluster by AreA [41]. Additionally, AreA in the maize pathogen F. verticillioides is a positive regulator of the toxic SM fumonisin [42].
PacC—pH
Beyond nutritional requirements, another environmental parameter essential for growth and development is pH. The global regulator PacC is a conserved Cis2His2 zinc finger transcription factor among fungi [79], capable of regulating a suite of physiological processes, including SM production, in response to environmental pH [80]. Studies investigating PacC regulation of SM have shown that this alkali-activated transcription factor dynamically controls metabolites to be expressed in a pH environment most suitable for compound bioactivity and maximum niche exploitation [81]. In A. nidulans, penicillin production was shown to be increased in an alkaline environment [51, 82], possibly as an ecological adaptation by the fungus to outcompete increased bacterial competition in high pH environments [81]. Also in A. nidulans, and in contrast to penicillin production, ST synthesis was repressed by alkaline pH as was AF synthesis in A. parasiticus [52]. Expression of another important β(beta)-lactam, cephalosporin, by A. chrysogenum was shown to be regulated by PacC through binding to promoter regions of structural genes [53]. Expression of the mycelial pigment bikaverin from the rice pathogen F. fujikuroi also exhibits PacC regulation through inhibition of its synthesis in a high pH environment [21]. Production of the mycotoxin fumonisin is also downregulated under elevated pH conditions by the maize pathogen F. verticillioides [54]. Interestingly, a recent study provides evidence for a dynamic role of PacC in tree fruit spoilage by the phytopathogen Penicillium expansum such that mechanisms of acidification after initial colonization, via secretion of organic acids such as gluconic acid, are mediated by PacC to control subsequent expression of the mycotoxin patulin [55]. Like other strains deficient in global regulators of SM, PacC deletion strains exhibit developmental phenotypes such as reduced conidiation [79] or growth inhibitions [21, 54], illustrating a pivotal role for pH sensing and homeostasis in proper growth, development, and SM expression.
CreA—Carbon
When grown in media rich in glucose, filamentous fungi downregulate genes required for metabolizing other carbon sources via a phenomenon called carbon catabolite repression [83], mediated largely by the Cys2His2 zinc finger transcription factor CreA [84]. Some examples of CreA-mediated regulation of SM include an overproducing cephalosporin strain of A. chrysogenum, obtained by classical mutagenesis techniques, which appeared to have deregulation of the CreA homologue Cre1 compared to wild-type strains [48]. Additionally, putative Cre1 binding sites found within the promoter regions of two cephalosporin biosynthetic genes suggest carbon catabolite repression of this metabolite [49]. In A. nidulans, glucose represses antibiotic production independent of a mutated CreA binding site in the penicillin biosynthetic gene ipnA promoter region [82] and was still unaffected by a CreA mutant background [85]. Although the role of CreA in regulating SM is less clear-cut compared to AreA and PacC, it is important to acknowledge the role of this global regulator in environmental sensing and the concomitant physiological response and consider how SMs might be affected. For example, the stringency of glucose repression, likely mediated by CreA, on a cryptic SM cluster in A. terreus was recently shown to be insurmountable even by overexpression of a putative in-cluster transcription factor [47].
Velvet Complex—Light
Like most organisms, filamentous fungi sense and respond to light. Conserved throughout the filamentous and dimorphic ascomycetes and possibly basidiomycetes [86] is the light-sensing heterotrimeric velvet complex consisting of LaeA, and the velvet proteins VeA and VelB [87]. The velvet complex links sexual development with SM production in response to light and accomplishes this through tightly regulated spatial compartmentalization of velvet complex components. VelB has nuclear and cytoplasmic localization regardless of illumination status [87], whereas VeA is cytoplasmic under light conditions and migrates to the nucleus in the absence of light [88] as a heterodimer with VelB, and LaeA is constitutively nuclear [89]. Consequently, the three velvet complex proteins are only colocalized to the nucleus under dark conditions, allowing formation of the fully functional heterotrimeric velvet complex. The mechanism of velvet complex regulation of SMs is best studied in A. nidulans but increasingly well known in other fungi [90–97]. Once assembled in the nucleus of A. nidulans, the velvet complex drives sexual development and production of SMs, whereas these processes are repressed under illuminating conditions resulting from a dissociated velvet complex [81]. Consequently, when localization of members of this complex is compromised, such as with VeA via interacting with the newly described LaeA-like methyltransferase LlmF, neither sexual development nor SM production can proceed normally [98]. The LlmF mechanism of VeA control appears conserved in other ascomycetes as well [99].
The finding that LaeA exhibited some similarity to methyltransferases involved in histone modification, coupled with the observation that SM clusters were most frequently found in subtelomeric regions of the genome [9], led to the hypothesis that SM clusters could be under epigenetic regulation [100]. This indeed has proved to be the case and for detailed coverage of histone modifications and their influence on SM production, we direct the reader to Chap. 3 for chromatin-based regulation of secondary metabolism.
CBC—Iron
Beyond the velvet complex, which is required for coordinating sexual development and SM production in response to light, another well-characterized global regulatory complex in filamentous fungi is the CCAAT-binding complex (CBC). Unlike velvet components, which are only conserved among filamentous fungi, CBC complexes are found in all eukaryotic organisms [101]. AnCF, the CBC in A. nidulans formerly known as PENR1 [101] is composed of the proteins HapB, HapC, and HapE. The AnCF is a positive regulator of genes required for penicillin biosynthesis including ipnA and aatA [102], is a negative autoregulator of hapB [103], and coordinates physiological processes in response to cellular redox state [104] and environmental iron [105]. With respect to iron depletion, CBC-mediated upregulation of sidC in A. nidulans is dependent upon physical interaction with the bZIP protein HapX [105] with SidC being a core enzyme for synthesis of ferricrocin, an SM siderophore that is essential for intracellular iron homeostasis and morphological development [61].
Conclusion
The study of SM in fungi originated primarily for two reasons: (1) to understand the regulation of mycotoxin gene clusters with the goal of using this knowledge to ameliorate the deleterious costs of crop contamination with mycotoxins and (2) to identify compounds with novel bioactivities applicable for pharmaceutical, medicinal, and agricultural uses. Since then, affecting all aspects of fungal biology, the integrated and critical roles of SMs have emerged as being greater than anticipated. SM regulators originally characterized as cluster-specific transcription factors have later been shown to have regulatory functions beyond their native cluster. For example, the canonical AF/ST regulator and Zn(II)2Cys6 transcription factor aflR was shown in A. parasiticus to regulate several genes beyond the defined boundaries of the cluster [64, 106]. Additionally, the Cys2Hys2 transcription factor Tri6 from F. graminearum was shown to regulate 192 genes, ranging from central metabolism to virulence , beyond the known targets within the trichothecene gene cluster [107], leading the authors to propose characterizing Tri6 as a global regulator much like the other known global Cys2Hys2 regulators AreA, PacC, and CreA.
Beyond expanding the roles of well-established regulators, research aimed toward elucidating new biosynthetic pathways and compounds has also benefited from exploiting the tight interplay of primary and SM. In one particular study, carbon catabolite repression was so stringent over a cryptic cluster, the authors utilized a suite of growth media containing various carbon sources to define nutrient conditions favorable for cluster activation, eventually identifying the compounds hydroisoflavipucin and dihydroisoflavipucin [47].
One of the greatest challenges in studying fungal SM will be to make sense of how key regulators fit into an ever-expanding network of global interactions linking primary and secondary metabolism with growth and development and how this modulates in response to nutrient availability, biotic and abiotic stresses, and niche exploitation. Taken together, it is apparent that ongoing and future studies will necessarily approach fungal SMs not from the standpoint that they are “accessory” molecules, but rather integrated members of a complex metabolic network affecting every facet of fungal biology.
References
Cho Y, Srivastava A, Ohm R, Lawrence CB, Wang K-H, Grigoriev IV et al (2012) Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola. PLoS Pathog 8:e1002974
Ortiz SC, Trienens M, Rohlfs M (2013) Induced fungal resistance to insect grazing: reciprocal fitness consequences and fungal gene expression in the Drosophila-Aspergillus model system. PLoS ONE 8:e74951
Mousa WK, Raizada MN (2013) The diversity of anti-microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective. Front Microbiol 4:1–18
Subramani R, Kumar R, Prasad P, Aalbersberg W (2013) Cytotoxic and antibacterial substances against multi-drug resistant pathogens from marine sponge symbiont: citrinin, a secondary metabolite of Penicillium sp. Asian Pac J Trop Biomed 3:291–296
Robens J, Cardwell K (2003) The costs of mycotoxin management to the USA: management of aflatoxins in the United States. Toxin reviews. J Toxicol-Toxin Rev 22:139–152
Bryden WL (2012) Mycotoxin contamination of the feed supply chain: implications for animal productivity and feed security. Anim Feed Sci Technol 173:134–158
Gieseker KE and Centers for Disease Control and Prevention (2004) Outbreak of aflatoxin poisoning—eastern and central provinces, Kenya, January-July 2004. Public Health Fac Publ 53:790–792
Hoffmeister D, Keller NP (2006) Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep 24:393–416
Palmer JM, Keller NP (2010) Secondary metabolism in fungi: does chromosomal location matter? Curr Opin Microbiol 13:431–436
Khaldi N, Collemare J, Lebrun M-H, Wolfe KH (2008) Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol 9(1):1–10
Schmitt I, Lumbsch HT (2009) Ancient horizontal gene transfer from bacteria enhances biosynthetic capabilities of fungi. PLoS ONE 4:e4437
Slot JC, Rokas A (2011) Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr Biol 21:134–139
Calvo AM, Wilson RA, Bok JW, Keller NP (2002) Relationship between secondary metabolism and fungal development. Microbiol Mol Biol Rev 66:447–459
Andersen MR, Nielsen JB, Klitgaard A, Petersen LM, Zachariasen M, Hansen TJ, Blicher LH, Gotfredsen CH, Larsen TO, Nielsen KF, Mortensen UH (2013) Accurate prediction of secondary metabolite gene clusters in filamentous fungi. Proc Natl Acad Sci USA 110:E99–E107
Yin W, Keller NP (2011) Transcriptional regulatory elements in fungal secondary metabolism. J Microbiol 49:329–339
Brown DW, Yu JH, Kelkar HS, Fernandes M, Nesbitt TC, Keller NP, Adams TH, Leonard TJ (1996) Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans. Proc Natl Acad Sci USA 93:1418–1422
Woloshuk CP, Foutz KR, Brewer JF, Bhatnagar D, Cleveland TE, Payne GA (1994) Molecular characterization of aflR, a regulatory locus for aflatoxin biosynthesis. Appl Environ Microbiol 60:2408–2414
Chang P-K, Ehrlich KC, Yu J, Bhatnagar D, Cleveland TE (1995) Increased expression of Aspergillus parasiticus aflR, encoding a sequence-specific DNA-binding protein, relieves nitrate inhibition of aflatoxin biosynthesis. Appl Environ Microb 61:2372–2377
Chiang Y-M, Szewczyk E, Davidson AD, Keller N, Oakley BR, Wang CCC (2009) A gene cluster containing two fungal polyketide synthases encodes the biosynthetic pathway for a polyketide, asperfuranone, in Aspergillus nidulans. J Am Chem Soc 131:2965–2970
Bergmann S, Schümann J, Scherlach K, Lange C, Brakhage AA, Hertweck C (2007) Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol 3:213–217
Wiemann P, Willmann A, Straeten M, Kleigrewe K, Beyer M, Humpf H-U, Tudzynski B (2009) Biosynthesis of the red pigment bikaverin in Fusarium fujikuroi: genes, their function and regulation. Mol Microbiol 72:931–946
Chen H, Lee M-H, Daub ME, Chung K-R (2007) Molecular analysis of the cercosporin biosynthetic gene cluster in Cercospora nicotianae. Mol Microbiol 64:755–770
Shimizu T, Kinoshita H, Nihira T (2007) Identification and in vivo functional analysis by gene disruption of ctnA, an activator gene involved in citrinin biosynthesis in Monascus purpureus. Appl Environ Microbiol 73(16):5097–5103
Wight WD, Kim K-H, Lawrence CB, Walton JD (2009) Biosynthesis and role in virulence of the histone deacetylase inhibitor depudecin from Alternaria brassicicola. Mol Plant Microbe Interact 22:1258–1267
Wiemann P, Guo CJ, Palmer JM, Sekonyela R, Wang CCC, Keller NP (2013) Prototype of an intertwined secondary metabolite supercluster. Proc Natl Acad Sci USA 110(42):17065–17070
Brown DW, Butchko R, Busman M, Proctor R (2007) The Fusarium verticillioides FUM gene cluster encodes a Zn(II)2Cys6 protein that affects FUM gene expression and fumonisin production. Eukaryot Cell 6:1210–1218
Kim J-E, Jin J, Kim H, Kim J-C, Yun S-H, Lee Y-W (2006) GIP2, a putative transcription factor that regulates the aurofusarin biosynthetic gene cluster in Gibberella zeae. Appl Environ Microbiol 72:1645–1652
Bok JW, Chung D, Balajee SA, Marr K, Andes D, Nielsen KF, Frisvad JC, Kirby KA, Keller NP (2006b) GliZ, a transcriptional regulator of gliotoxin biosynthesis, contributes to Aspergillus fumigatus virulence. Infect Immun 74:6761–6768
Kennedy J, Auclair K, Kendrew SG, Park C, Vederas JC, Hutchinson CR (1999) Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284:1368–1372
Chiang Y-M, Szewczyk E, Davidson AD, Entwistle R, Keller NP, Wang CCC, Oakley BR (2010) Characterization of the Aspergillus nidulans monodictyphenone gene cluster. Appl Environ Microbiol 76:2067–2074
Abe Y, Ono C, Hosobuchi M, Yoshikawa H (2002b) Functional analysis of mlcR, a regulatory gene for ML-236B (compactin) biosynthesis in Penicillium citrinum. Mol Genet Genomics 268:352–361
Chen Y-P, Yuan G-F, Hsieh S-Y, Lin Y-S, Wang W-Y, Liaw L-L et al (2010) Identification of the mokH gene encoding transcription factor for the upregulation of monacolin K biosynthesis in Monascus pilosus. J Agric Food Chem 58:287–293
Tanaka A, Tsuge T (2000) Structural and functional complexity of the genomic region controlling AK-toxin biosynthesis and pathogenicity in the Japanese pear pathotype of Alternaria alternata. Mol Plant Microbe Interact 13:975–986
Fox EM, Gardiner DM, Keller NP, Howlett BJ (2008) A Zn(II)2Cys6 DNA binding protein regulates the sirodesmin PL biosynthetic gene cluster in Leptosphaeria maculans. Fungal Genet Biol 45:671–682
Flaherty JE, Woloshuk CP (2004) Regulation of fumonisin biosynthesis in Fusarium verticillioides by a zinc binuclear cluster-type gene, ZFRI. Appl Environ Microbiol 70:2653–2659
MacPherson S, Larochelle M, Turcotte B (2006) A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 70:583–604
Yu J-H, Butchko RAE, Fernandes M, Keller NP, Leonard TJ, Adams TH (1996) Conservation of structure and function of the aflatoxin regulatory gene aflR from Aspergillus nidulans and A. flavus. Curr Genet 29:549–555
Ahuja M, Chiang Y-M, Chang S-L, Praseuth MB, Entwistle R, Sanchez JF, Lo H-C, Yeh H-H, Oakley BR, Wang CCC (2012) Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc 134:8212–8221
Abe Y, Suzuki T, Ono C, Iwamoto K, Hosobuchi M, Yoshikawa H (2002a) Molecular cloning and characterization of an ML-236B (compactin) biosynthetic gene cluster in Penicillium citrinum. Mol Genet Genomics 267:636–646
Chang P-K, Yu J, Bhatnagar D, Cleveland TE (2000) Characterization of the Aspergillus parasiticus major nitrogen regulatory gene, areA. Biochim Biophys Acta 1491:263–266
Mihlan M, Homann V, Liu T-WD, Tudzynski B (2003) AREA directly mediates nitrogen regulation of gibberellin biosynthesis in Gibberella fujikuroi, but its activity is not affected by NMR. Mol Microbiol 47:975–991
Kim H, Woloshuk CP (2008) Role of AREA, a regulator of nitrogen metabolism, during colonization of maize kernels and fumonisin biosynthesis in Fusarium verticillioides. Fungal Genet Biol 45:947–953
Kihara J, Moriwaki A, Tanaka N, Tanaka C, Ueno M, Arase S (2008) Characterization of the BMR1 gene encoding a transcription factor for melanin biosynthesis genes in the phytopathogenic fungus Bipolaris oryzae. FEMS Microbiol Lett 281:221–227
Simon A, Dalmais B, Morgant G, Viaud M (2013) Screening of a Botrytis cinerea one-hybrid library reveals a Cys2His2 transcription factor involved in the regulation of secondary metabolism gene clusters. Fungal Genet Biol 52:9–19
Eliahu N, Igbaria A, Rose MS, Horwitz BA, Lev S (2007) Melanin biosynthesis in the maize pathogen Cochliobolus heterostrophus depends on two mitogen-activated protein kinases, Chk1 and Mps1, and the transcription factor Cmr1. Eukaryot Cell 6:421–429
Tsuji G, Kenmochi Y, Takano Y, Sweigard J, Farrall L, Furusawa I, Horino O, Kubo Y (2000) Novel fungal transcriptional activators, Cmr1p of Colletotrichum lagenarium and pig1p of Magnaporthe grisea, contain Cys2His2 zinc finger and Zn(II)2Cys6 binuclear cluster DNA-binding motifs and regulate transcription of melanin biosynthesis genes in a developmentally specific manner. Mol Microbiol 38:940–954
Gressler M, Zaehle C, Scherlach K, Hertweck C, Brock M (2011) Multifactorial induction of an orphan PKS-NRPS gene cluster in Aspergillus terreus. Chem 18:198–209
Jekosch K, Kück U (2000a) Glucose dependent transcriptional expression of the cre1 gene in Acremonium chrysogenum strains showing different levels of cephalosporin C production. Curr Genet 37:388–395
Jekosch K, Kück U (2000b) Loss of glucose repression in an Acremonium chrysogenum beta-lactam producer strain and its restoration by multiple copies of the cre1 gene. Appl Microbiol Biotechnol 54:556–563
Trapp SC, Hohn TM, McCormick S, Jarvis BB (1998) Characterization of the gene cluster for biosynthesis of macrocyclic trichothecenes in Myrothecium roridum. Mol Gen Genet 257:421–432
Bergh KT, Brakhage AA (1998) Regulation of the Aspergillus nidulans penicillin biosynthesis gene acvA (pcbAB) by amino acids: implication for involvement of transcription factor PACC. Appl Environ Microbiol 64:843–849
Keller NP, Nesbitt C, Sarr B, Phillips TD, Burow GB (1997) pH regulation of sterigmatocystin and aflatoxin biosynthesis in Aspergillus spp. Phytopathology 87:643–648
Schmitt EK, Kempken R, Kuck U (2001) Functional analysis of promoter sequences of cephalosporin C biosynthesis genes from Acremonium chrysogenum: specific DNA-protein interactions and characterization of the transcription factor PACC. Mol Genet Genomics 265:508–518
Flaherty JE, Pirttilä AM, Bluhm BH, Woloshuk CP (2003) PAC1, a pH-regulatory gene from Fusarium verticillioides. Appl Environ Microbiol 69:5222–5227
Barad S, Horowitz S, Kobiler I, Sherman A, Prusky DB (2013) Accumulation of the mycotoxin patulin in the presence of gluconic acid contributes to pathogenicity of Penicillium expansum. Mol Plant-Microbe Interact 27:66–77
Malapi-Wight M, Smith J, Campbell J, Bluhm BH, Shim W-B (2013) Sda1, a Cys2-His2 zinc finger transcription factor, is involved in polyol metabolism and fumonisin B1 production in Fusarium verticillioides. PLoS ONE 8:e67656
Bergmann S, Funk AN, Scherlach K, Schroeckh V, Shelest E, Horn U, Hertweck C, Brakhage AA (2010) Activation of a silent fungal polyketide biosynthesis pathway through regulatory cross talk with a cryptic nonribosomal peptide synthetase gene cluster. Appl Environ Microbiol 76(24):8143–8149
Hohn TM, Krishna R, Proctor RH (1999) Characterization of a transcriptional activator controlling trichothecene toxin biosynthesis. Fungal Genet Biol 26:224–235
Reverberi M, Gazzetti K, Punelli F, Scarpari M, Zjalic S, Ricelli A, Fabbri AA, Fanelli C (2012) Aoyap1 regulates OTA synthesis by controlling cell redox balance in Aspergillus ochraceus. Appl Microbiol Biotechnol 95:1293–1304
Roze LV, Chanda A, Wee J, Awad D, Linz JE (2011) Stress-related transcription factor AtfB integrates secondary metabolism with oxidative stress response in aspergilli. J Biol Chem 286:35137–35148
Eisendle M, Schrettl M, Kragl C, Müller D, Illmer P, Haas H (2006) The intracellular siderophore ferricrocin is involved in iron storage, oxidative-stress resistance, germination, and sexual development in Aspergillus nidulans. Eukaryot Cell 5:1596–1603
Wagner D, Schmeinck A, Mos M, Morozov IY, Caddick MX, Tudzynski B (2010) The bZIP transcription factor MeaB mediates nitrogen metabolite repression at specific loci. Eukaryot Cell 9:1588–1601
Amaike S, Affeldt KJ, Yin W-B, Franke S, Choithani A, Keller NP (2013) The bZIP protein MeaB mediates virulence attributes in Aspergillus flavus. PLoS ONE 8:e74030
Yin W-B, Amaike S, Wohlbach DJ, Gasch AP, Chiang Y-M, Wang CCC, Bok JW, Rohlfs M, Keller NP (2012) An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR. Mol Microbiol 83:1024–1034
Sekonyela R, Palmer JM, Bok J-W, Jain S, Berthier E, Forseth R, Schroeder F, Keller NP (2013) RsmA regulates Aspergillus fumigatus gliotoxin cluster metabolites including cyclo(L-Phe-L-Ser), a potential new diagnostic marker for invasive aspergillosis. PLoS ONE 8:e62591
Bussink HJ, Clark A, Oliver R (2001) The Cladosporium fulvum Bap1 gene: evidence for a novel class of Yap-related transcription factors with ankyrin repeats in phytopathogenic fungi. Eur J plant Pathol 107:655–659
Pedley KF, Walton JD (2001) Regulation of cyclic peptide biosynthesis in a plant pathogenic fungus by a novel transcription factor. Proc Natl Acad Sci USA 98:14174–14179
Schmitt EK, Hoff B, Kück U (2004) AcFKH1, a novel member of the forkhead family, associates with the RFX transcription factor CPCR1 in the cephalosporin C-producing fungus Acremonium chrysogenum. Gene 342:269–281
Schmitt EK, Kuck U (2000) The fungal CPCR1 protein, which binds specifically to β-lactam biosynthesis genes, is related to human regulatory factor X transcription factors. J Biol Chem 275:9348–9357
Atanasova L, Knox BP, Kubicek CP, Druzhinina IS, Baker SE (2013) The polyketide synthase gene pks4 of Trichoderma reesei provides pigmentation and stress resistance. Eukaryot Cell 12:1499–1508
Hong S-Y, Roze LV, Linz JE (2013) Oxidative stress-related transcription factors in the regulation of secondary metabolism. Toxins 5:683–702
Temme N, Oeser B, Massaroli M, Heller J, Simon A, Collado IG, Viaud M, Tudzynski P (2012) BcAtf1, a global regulator, controls various differentiation processes and phytotoxin production in Botrytis cinerea. Mol Plant Pathol 13:704–718
Ahn JH, Walton JD (1998) Regulation of cyclic peptide biosynthesis and pathogenicity in Cochliobolus carbonum by TOXEp, a novel protein with a bZIP basic DNA-binding motif and four ankyrin repeats. Mol Gen Genet 260:462–469
Gajiwala KS, Burley SK (2000) Winged helix proteins. Curr Opin Struct Biol 10:110–116
Hoff B, Schmitt EK, Kück U (2005) CPCR1, but not its interacting transcription factor AcFKH1, controls fungal arthrospore formation in Acremonium chrysogenum. Mol Microbiol 56:1220–1233
Bayram O, Braus GH (2012) Coordination of secondary metabolism and development in fungi: the velvet family of regulatory proteins. FEMS Microbiol Rev 36(1):1–24
Feng GH, Leonard TJ (1998) Culture conditions control expression of the genes for aflatoxin and sterigmatocystin biosynthesis in Aspergillus parasiticus and A. nidulans. Appl Environ Microbiol 64:2275–2277
Wilson R, Arst H (1998) Mutational analysis of AREA, a transcriptional activator mediating nitrogen metabolite repression in Aspergillus nidulans and a member of the “streetwise” GATA family. Microbiol Mol Biol Rev 62:586–596
Tilburn J, Sarkar S, Widdick D, Espeso E, Orejas M, Mungroo J, Peñalva MA, Arst HN Jr (1995) The Aspergillus PacC zinc finger transcription factor mediates regulation of both acid- and alkaline-expressed genes by ambient pH. EMBO J 14:779–790
Trushina N, Levin M, Mukherjee PK, Horwitz BA (2013 Jan) PacC and pH-dependent transcriptome of the mycotrophic fungus Trichoderma virens. BMC Genomics 14(138):1–21
Brakhage AA (2013) Regulation of fungal secondary metabolism. Nat Rev Microbiol 11:21–32
Espeso EA, Tilburn J, Arst HN, Peñalva MA (1993) pH regulation is a major determinant in expression of a fungal penicillin biosynthetic gene. EMBO J 12:3947–3956
Ronne H (1995) Glucose repression in fungi. Trends Genet 11:12–17
Dowzer CEA, Kelly JM (1991) Analysis fo the creA gene, a regulator of carbon catabolite repression in Aspergillus nidulans. Mol Cell Biol 11:5701–5709
Brakhage AA, Browne P, Turner G (1992) Regulation of Aspergillus nidulans penicillin biosynthesis and penicillin biosynthesis genes acvA and ipnA by glucose. J Bacteriol 174:3789–3799
Ni M, Yu J-H (2007) A novel regulator couples sporogenesis and trehalose biogenesis in Aspergillus nidulans. PLoS ONE 2:e970
Bayram O, Krappmann S, Ni M, Bok JW, Helmstaedt K, Valerius O, Braus-Stronmeyer S, Kwon N-J, Keller NP, Yu J-H, Braus GH (2008) VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism. Science 320:1504–1506
Stinnett SM, Espeso E, Cobeño L, Araújo-Bazán L, Calvo AM (2007) Aspergillus nidulans VeA subcellular localization is dependent on the importin alpha carrier and on light. Mol Microbiol 63:242–255
Bok JW, Keller NP (2004) LaeA, a regulator of secondary metabolism in Aspergillus spp. Eukaryot Cell 3:527–535
Chettri P, Calvo AM, Cary JW, Dhingra S, Guo Y, McDougal RL, Bradshaw RE (2012) The veA gene of the pine needle pathogen Dothistroma septosporum regulates sporulation and secondary metabolism. Fungal Genet Biol 49:141–151
Hoff B, Kamerewerd J, Sigl C, Mitterbauer R, Zadra I, Kürnsteiner H, Kück U (2010) Two components of a velvet-like complex control hyphal morphogenesis, conidiophore development, and penicillin biosynthesis in Penicillium chrysogenum. Eukaryot Cell 9:1236–1250
Kopke K, Hoff B, Bloemendal S, Katschorowski A, Kamerewerd J, Kück U (2013) Members of the Penicillium chrysogenum velvet complex play functionally opposing roles in the regulation of penicillin biosynthesis and conidiation. Eukaryot Cell 12:299–310
López-Berges MS, Hera C, Sulyok M, Schäfer K, Capilla J, Guarro J, Di Pietro A (2013) The velvet complex governs mycotoxin production and virulence of Fusarium oxysporum on plant and mammalian hosts. Mol Microbiol 87:49–65
Veiga T, Nijland JG, Driessen AJM, Bovenberg RAL, Touw H, van den Berg MA, Pronk JT, Daran J-M (2012) Impact of velvet complex on transcriptome and penicillin G production in glucose-limited chemostat cultures of a β-lactam high-producing Penicillium chrysogenum strain. OMICS 16:320–333
Wiemann P, Brown DW, Kleigrewe K, Bok JW, Keller NP, Humpf H-U, Tudzynski B (2011) FfVel1 and FfLae1, components of a velvet-like complex in Fusarium fujikuroi, affect differentiation, secondary metabolism and virulence. Mol Microbiol 77:972–994
Wu D, Oide S, Zhang N, Choi MY, Turgeon BG (2012) ChLae1 and ChVel1 regulate T-toxin production, virulence, oxidative stress response, and development of the maize pathogen Cochliobolus heterostrophus. PLoS Pathog 8(2):e1002542
Yang Q, Chen Y, Ma Z (2013) Involvement of BcVeA and BcVelB in regulating conidiation, pigmentation and virulence in Botrytis cinerea. Fungal Genet Biol 50:63–71
Palmer JM, Theisen JM, Duran RM, Grayburn WS, Calvo AM, Keller NP (2013) Secondary metabolism and development is mediated by LlmF control of VeA subcellular localization in Aspergillus nidulans. PLoS Genet 9:e1003193
Bi Q, Wu D, Zhu X, Gillian Turgeon B (2013) Cochliobolus heterostrophus Llm1– a Lae1-like methyltransferase regulates T-toxin production, virulence, and development. Fungal Genet Biol 51:21–33
Bok JW, Noordermeer D, Kale SP, Keller NP (2006a) Secondary metabolic gene cluster silencing in Aspergillus nidulans. Mol Microbiol 61:1636–1645
Brakhage AA, Andrianopoulos A, Kato M, Steidl S, Davis MA, Tsukagoshi N, Hynes MJ (1999) HAP-like CCAAT-binding complexes in filamentous fungi: implications for biotechnology. Fungal Genet Biol 27:243–252
Brakhage AA, Thön M, Spröte P, Scharf DH, Al-Abdallah Q, Wolke SM, Hortschansky P (2009) Aspects on evolution of fungal β-lactam biosynthesis gene clusters and recruitment of trans-acting factors. Phytochemistry 70:1801–1811
Steidl S, Hynes MJ, Brakhage AA (2001) The Aspergillus nidulans multimeric CCAAT binding complex AnCF is negatively autoregulated via its hapB subunit gene. J Mol Biol 306:643–653
Thön M, Abdallah Q A, Hortschansky P, Scharf DH, Eisendle M, Haas H, Brakhage AA (2010) The CCAAT-binding complex coordinates the oxidative stress response in eukaryotes. Nucleic Acids Res 38:1098–1113
Hortschansky P, Eisendle M, Al-Abdallah Q, Schmidt AD, Bergmann S, Thön M, Kniemeyer O, Abt B, Seeber B, Werner ER, Kato M, Brakhage AA, Haas H (2007) Interaction of HapX with the CCAAT-binding complex—a novel mechanism of gene regulation by iron. EMBO J 26:3157–3168
Price MS, Yu J, Nierman WC, Kim HS, Pritchard B, Jacobus CA, Bhatnagar D, Cleveland TE, Payne GA (2006) The aflatoxin pathway regulator AflR induces gene transcription inside and outside of the aflatoxin biosynthetic cluster. FEMS Microbiol Lett 255:275–279
Nasmith CG, Walkowiak S, Wang L, Leung WWY, Gong Y, Johnston A, Harris LJ, Guttman DS, Subramaniam R (2011) Tri6 is a global transcription regulator in the phytopathogen Fusarium graminearum. PLoS Pathog 7:e1002266
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Knox, B., Keller, N. (2015). Key Players in the Regulation of Fungal Secondary Metabolism. In: Zeilinger, S., Martín, JF., García-Estrada, C. (eds) Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites, Volume 2. Fungal Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2531-5_2
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