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Applied and Environmental Microbiology, September 2004, p. 5589-5594, Vol. 70, No. 9
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.9.5589-5594.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
R&D Biology, Antibióticos S. A. and Vitatene, E-24009 León, Spain
Received 2 February 2004/ Accepted 15 May 2004
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The biosynthetic pathway for ß-carotene has been determined for fungi such as Phycomyces blakesleeanus and Neurospora crassa (12, 21). It contains three enzymatic activities: (i) phytoene synthase, which links two molecules of geranylgeranyl pyrophosphate to form phytoene; (ii) phytoene dehydrogenase, which introduces four double bonds in the phytoene molecule to yield lycopene; and (iii) lycopene cyclase, which sequentially converts the
acyclic ends of lycopene to ß rings to form
-carotene and ß-carotene. A similar biosynthetic pathway is known in all carotenogenic organisms (20). The accumulation of ß-carotene in B. trispora is associated with sexual interaction (18). Mating of two sexually compatible strains increases mycelial ß-carotene accumulation 5- to 15-fold, as does the addition of trisporic acids, compounds with hormonal activity formed upon mating (25, 35).
The carB and carRA (or carRP) genes, encoding phytoene dehydrogenase and lycopene cyclase/phytoene synthase, have been cloned from the zygomycetes P. blakesleeanus (3, 29) and Mucor circinelloides (36, 37), but there is no information on the ß-carotene biosynthetic genes of the commercially important B. trispora. The carRA genes have two domains: (i) the R domain, located near the 5' end, which encodes lycopene cyclase activity, and (ii) the A (or P) domain, which is downstream of the R domain and encodes phytoene synthase. The carB and carRA genes of M. circinelloides and P. blakesleeanus are closely linked, divergently transcribed, and coordinately induced by blue light, with a bidirectional promoter between them (3, 36).
The objectives of this study were to clone and characterize the ß-carotene biosynthetic genes of B. trispora and to determine whether these sequences were functional in M. circinelloides and could be used to increase the amount of ß-carotene it synthesizes. This report is the first description of ß-carotene biosynthetic genes of B. trispora, a fungus used industrially to produce ß-carotene and lycopene.
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GEM12 (Promega, Madison, Wis.) phage derivatives. E. coli DH5
(30) was the recipient for high-frequency plasmid transformation. DNA fragments were purified from agarose gels with the Qiaex II gel extraction kit (QIAGEN, Valencia, Calif.) and subcloned in pBluescript I KS(+) (Stratagene) and pBC KS(+) (Stratagene). pALBT3, pALBT11, pALBT12, and pALBT59 were sequenced (Fig. 1). pLeu4 (2, 27) and pEPM9 (8) were used as M. circinelloides shuttle vectors. General procedures for plasmid DNA purification, cloning, and transformation of E. coli were those of Sambrook et al. (30). |
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TABLE 1. Fungal strains used in this work
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FIG. 1. Restriction map of the B. trispora genomic region containing the carB and carRA genes. The ORFs and the direction of transcription are shown by large arrows. White boxes inside the arrows represent introns. Small arrows indicate the primers used for PCR amplification. Plasmids described in the text appear below the arrows. The thick lines represent the plasmids used to transform M. circinelloides. The 8,788-bp sequenced region is represented by the entire map, and the 2,430-bp HindIII fragment found in all four positive phages is represented by pALBT3/pALBT11.
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GEM12, and packaged with the Gigapack II Gold kit (Stratagene) to yield approximately 5 x 104 PFU. The library was amplified in E. coli LE392, plated to obtain
4 x 104 PFU, and hybridized with a [32P]dCTP-labeled probe consisting of a 560-bp internal fragment from the carRP gene of M. circinelloides (30). Four recombinant phages were isolated and amplified in liquid medium to purify their DNA (30).
Nucleic acid hybridization and sequencing.
Southern hybridizations were made with digoxigenin-labeled probes (Non-radioactive labeling and immunological detection kit, Roche Molecular Biochemicals, Mannheim, Germany) according to the recommendations of the manufacturer. A 778-bp BglII-NdeI fragment of the carB gene and a 526-bp BglII-SalI fragment of the carRA gene were used as probes. Clones to be sequenced were constructed with the Erase a base system (Promega) and sequenced with an ABI PRISM 377 DNA sequencer (Applied Biosystems, Foster City, Calif.). DNA sequences were analyzed with the Dnastar and Winstar packages (DNASTAR, Inc., Madison, Wis.) and compared to known sequences with the BLASTP and BLASTX programs (1). The codon-preference algorithm (16) was used to detect the presence of open reading frames (ORFs). Multiple protein alignments were made with the Clustal V algorithm, and pairwise alignments were made by the Lipman-Pearson method (MegAlign, Winstar). RNA secondary structures that can act as potential transcriptional terminators were predicted with the aid of the M-fold program (23).
PCR amplification.
Primers 61 (5'-CGCGCCGACTGCCATTGACT-3') and 62 (5'-CACGCACGCCGCCTTGACA-3') were designed to amplify a 560-bp internal fragment of the carRP gene of M. circinelloides (GenBank AJ238028). The carB gene of B. trispora NRRL2457 was amplified as a 2.6-kb fragment with primers 98 (5'-GGGTTTCTTTGTTTGAGCTGATTCTGATAC-3') and 99 (5'-GATACTGTCATCTCGAGAGCGTTG-3'). The carRA gene of B. trispora NRRL2457 was amplified in two fragments (overlapping 187 bp): a 1.3-kb fragment including the 5' region with primers 100 (5'-CATGCCTGACTTTCTTTTTCCATCG-3') and 48 (5'-CAGGCATTCTTCTACAGG-3') and a 1.5-kb fragment covering the 3' region with primers 110 (5'-TCTTTGGCTGGGTGCTGGTGAA-3') and 112 (5'-CCAGAAGCGGGGTGAACTCATTG-3'). Optimized amplification reaction mixtures (each 20 µl) were processed in a DNA Thermal Cycler 480 (Perkin-Elmer, Norwalk, Conn.) and contained about 50 ng of genomic DNA, 20 mM Tris-HCl (pH 8.8), 2 mM MgSO4, 10 mM KCl, 10 mM (NH4)2SO4, 0.1% Triton X-100, 0.1 mg of nuclease-free bovine serum albumin/ml, 0.25 µM each primer, 1.0 U of Turbo Pfu DNA polymerase (Stratagene), and 200 µM each deoxynucleoside triphosphates. The reaction mixtures were overlaid with mineral oil and subjected to 25 PCR cycles as follows: (i) for primers 61 and 62, 94°C for 30 s (120 s for the first cycle), 55°C for 60 s, and 72°C for 90 s; (ii) for primers 98 and 99, 94°C for 60 s (120 s for the first cycle), 45°C for 60 s, and 72°C for 180 s; (iii) for primers 100 and 48, 94°C for 60 s (120 s for the first cycle), 41°C for 60 s, and 72°C for 180 s; and (iv) for primers 110 and 112, 94°C for 60 s (120 s for the first cycle), 57°C for 60 s, and 72°C for 240 s. Total RNA from B. trispora F-744 was subjected to 35 PCR cycles as follows: 94°C for 10 s, 41°C for 30 s, and 68°C for 45 s (extending 5 s per cycle after the 11th repeat) with primers 90 (5'-CTTTTTATTTTATCTCTATGTCAATACTCAC-3') and 48, with the Titan One Tube RT-PCR system (Roche) used to amplify the cDNA from the 5'-region of the carRA gene as a 670-bp fragment. Amplified fragments were purified from agarose gels with the Qiaex II gel extraction kit (QIAGEN) and subcloned into EcoRV-digested pBluescript I KS(+).
Transcriptional analysis of the carB and carRA genes.
A pilot-scale (800-liter) fed-batch fermentation was carried out by mating the two sexual forms (+ and ) of B. trispora to maximize ß-carotene production (13). At 96 h, mycelium was frozen in liquid nitrogen, and total RNA was recovered (4). RNA was resolved by agarose-formaldehyde gel electrophoresis and blotted onto Hybond-N+ membranes (Amersham Biosciences, Little Chalfont, Buckinghamshire, United Kingdom) according to standard procedures (30). Two plasmids, pALBT132 (466-bp BglII-EcoRV of carRA) and pALBT133 (415-bp EcoRV-NdeI of carB) were constructed in pBluescript I KS(+) to be used as templates for the synthesis of an antisense digoxigenin-labeled RNA probe with the DIG RNA labeling kit (Roche). The filters were hybridized at 68°C overnight with DIG-Easy Hyb buffer (Roche) and subsequently washed for 15 min at room temperature in 2x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate)-0.1% sodium dodecyl sulfate, followed by two washes of 15 min each at 68°C in 0.1x SSC-0.1% sodium dodecyl sulfate. Immunological detection with CDP-Star chemiluminescent substrate (Roche) was carried out following the manufacturer's instructions.
Transformation of M. circinelloides.
Plasmids pLeu4 (2, 27), pEPM9 (8), pALBT119, and pALBT120 were used to transform M. circinelloides. pALBT119 (Fig. 1) was constructed by subcloning the carRA gene as a 3.6-kb NdeI fragment filled with Klenow into the SmaI site of pLeu4. Likewise, the introduction of a 3.0-kb XbaI fragment containing the carB gene in the XbaI site of pEPM9 generated pALBT120 (Fig. 1). M. circinelloides was transformed as previously described (28, 36) with a mixture of 1.5 mg of Caylase (Cayla, Toulouse, France)/ml and 4 to 12 U of Streptozyme/ml for protoplast preparation. Several transformants of each plasmid, prototrophic for leucine or uridine, were selected on yeast nitrogen base (YNB) minimal medium (19) osmotically stabilized with 0.55 M sorbitol.
Carotenoid analysis.
Carotenoid production was tested following growth on YNB plates for 4 days (36). Carotenoids were extracted with a mixture of methanol and dichloromethane (50/50 ratio) and redissolved in acetone. High-performance liquid chromatography analyses were performed with a Hypersil octyldecyl silane column (resin particle diameter, 5 µm; 100 by 4.6 mm) and acetonitrile-methanol-chloroform (47/47/6 ratio) with a flow rate of 1 ml/min as the mobile phase.
Nucleotide sequence accession number.
The carB-carRA DNA sequences of B. trispora NRRL2457 and B. trispora F-744 have been deposited as GenBank accession numbers AY176663 and AY176662, respectively.
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TABLE 2. Features of carB and carRA genes and deduced proteins from zygomycetes
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The carRA deduced protein was similar to fungal proteins with lycopene cyclase/phytoene synthase activity and had high similarity to lycopene cyclases/phytoene synthases from M. circinelloides (67%) (36), P. blakesleeanus (55%) (3), X. dendrorhous (31%) (39), F. fujikuroi (29%) (22), and N. crassa (28%) (31). The CarRA protein had two different domains, as described for P. blakesleeanus, M. circinelloides, and X. dendrorhous: a hydrophobic transmembrane domain (R), located near to the 5' end expressing lycopene cyclase (240 residues), and a hydrophilic domain, P, located downstream that expresses phytoene synthase (362 residues). A putative protease cleavage site, AQAILH (residues 241 to 246), that could split the polypeptide between residues 243 and 244 is present at the boundary between the two domains.
Wild-type carB and carRA genes from B. trispora (GenBank AY176663).
The B. trispora wild-type strain (NRRL2457) and mutant ß-carotene-overproducing strain (F-744) both had the same hybridization pattern in Southern blots, suggesting that carB and carRA are present at a single copy per genome. The carB and carRA mutant and wild-type genes differ from each other by two nucleotides per gene (four total differences). The A1791
C mutation in carB substitutes an arginine for the wild-type serine at position 528 (S528R). An A1958
G transition mutation occurred in the carB stop codon, changing the wild-type TAA to TAG but not affecting the protein sequence. The T497
C mutation in the carRA gene changes the wild-type proline at position 143 to a serine (P143S), while the C568
T mutation does not change the amino acid encoded (glycine at position 166). Transcripts of the carB (1.8-kb) and carRA (1.9-kb) genes were the expected size and were present at a constant level during fermentation (Fig. 2).
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FIG. 2. Transcription of carB (A) and carRA (B) genes. Northern analyses were done with total RNA purified at 96 h from pilot scale fermentation under ß-carotene production conditions (13). (C) Stained gel showing rRNAs and molecular weight markers used to estimate transcript size of carB (1.8-kb) and carRA (1.9-kb) genes.
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with total DNA from MS8/pALBT119, MS12/pALBT119, MS12/pALBT120, MS12/pALBT119/pALBT120, and MS23/pALBT120. Fifty independent clones of each type were analyzed, and most of them (>97%) had the expected restriction pattern for pALBT119 and pALBT120, confirming the extrachromosomal location of the plasmids in M. circinelloides and an almost total lack of rearrangements. Most of the E. coli transformants selected with DNA from MS12/pALBT119/pALBT120 (96%) had the pALBT119 pattern, implying a lower copy number of pALBT120 in M. circinelloides. The carotenoids accumulated by wild-type strains of M. circinelloides, mutants, and transformants were analyzed by high-performance liquid chromatography (Table 3). |
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TABLE 3. Carotenoids produced by M. circinelloidesa
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FIG. 3. Southern analysis of DNA from M. circinelloides MS8 (lanes 2 and 4) and MS8/pALBT119 (lanes 1, 3, and 5) with a 526-bp BglII-SalI fragment corresponding to the carRA gene of B. trispora as a probe. DNA was digested with BamHI (lanes 1 and 2), EcoRV (lanes 3 and 4), and PvuII (lane 5). Lane 6 contains the size markers.
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The three enzymatic activities needed to convert geranylgeranyl pyrophosphate to ß-carotene in B. trispora depend on the expression of two closely linked genes that are divergently transcribed. A similar arrangement, which permits expression of the whole pathway from a single promoter region, also is found in P. blakesleeanus (3) and M. circinelloides (36). The promoter regions of B. trispora, M. circinelloides, and P. blakesleeanus differ significantly in both length and regulatory signals. APE elements probably involved in light regulation are located in the 5' upstream region of N. crassa al-3 (11) and also are present with minor modifications in the carB-carRA promoter region of M. circinelloides (36), P. blakesleeanus (29), and B. trispora, even though ß-carotene biosynthesis in B. trispora is not stimulated by blue light (34).
Other regulatory signals present in the promoter region of B. trispora and P. blakesleeanus include putative TR box binding sites for the Ste11 transcription factor, an HMG box protein essential for induction of sexual development in S. pombe (17). ß-Carotene accumulation in B. trispora is strongly linked to sexual interaction and increases 5- to 15-fold during mating (18), which is consistent with the presence of the three putative TR boxes in the promoter region of the carB-carRA genes, if sexual development is mediated by an Ste11-like transcription factor in B. trispora. Two putative TR boxes are present in the carB-carRA promoter of P. blakesleeanus, but they are absent in this promoter of M. circinelloides.
The carB-carRA region of wild-type and overproducing strains differed at only four point mutations in the coding sequence. The S528R mutation of CarB is located in a poorly conserved region, while the P143S mutation of CarRA occurred in a conserved region. The effect of these mutations on enzymatic activities is not known.
There is no transformation system for B. trispora, so the function of the cloned sequences was tested indirectly with M. circinelloides. Heterologous expression of the P. blakesleeanus carB gene in a mutant of M. circinelloides lacking phytoene dehydrogenase only partially restores the enzymatic activity and ß-carotene production and may be due to the formation of a poorly functional heterologous enzyme complex, improper recognition of the heterologous gene promoter, or the dilution of a fixed number of transcription factors across additional promoters. Transformation of M. circinelloides with autonomously replicating plasmids containing a homologous wild-type copy of the carB gene silences the carB function in 3% of transformants. This reduction in carB function is not due to differences in transcription levels but to the biosynthesis of two size classes of small antisense RNAs (26). Either inefficient heterologous expression or antisense RNA could explain the behavior of transformant MS23/pALBT120, in which ß-carotene biosynthesis is partially restored and there is some accumulation of phytoene and neurosporene.
The expression of the carRA gene in mutant strain MS8, deficient in lycopene cyclase/phytoene synthase activities, partially complements this mutation and restores a minimal amount of ß-carotene production. In MS12 transformants, the accumulation of lycopene and
-carotene at levels three to seven times higher than in ATCC 1216b suggests that carB and carRA expression is in some manner different. Extra copies of carB do not increase carotenoid production, but additional copies of carRA do. This effect could be due to a pALBT119 (carRA)/pALBT120 (carB) ratio of 20:1.
At present, ß-carotene is produced commercially by chemical synthesis. We are now using a new industrial process with B. trispora to produce ß-carotene. Although neither gene number nor gene sequence in B. trispora can yet be altered by transformation, the carB and carRA sequences described here can be used to guide the development of overproducing strains that are altered either in these genes themselves or in other genes that affect their expression.
We thank A. P. Eslava for M. circinelloides strains and pEPM9, S. Torres-Martínez for pLeu4, and M. Sandoval, P. Merino, C. Alonso, and E. G. Quiñones for technical assistance.
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rulff, S., D. Dooijes, H. Clevers, and O. Nielsen. 1997. Cell differentiation by interaction of two HMG-box proteins: Mat1-Mc activates M cell-specific genes in S. pombe by recruiting the ubiquitous transcription factor Ste11 to weak binding sites. EMBO J. 16:4021-4033.[CrossRef][Medline]
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