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Journal of Bacteriology, September 2006, p. 6217-6223, Vol. 188, No. 17
0021-9193/06/$08.00+0 doi:10.1128/JB.00766-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
Received 28 May 2006/ Accepted 19 June 2006
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Modified carotenoids are synthesized by such a variety of organisms that it is impossible to infer a function(s) from their distribution. They are found in both aerobic (33) and anaerobic (32, 36, 37, 38) photosynthetic bacteria as well as in the flowers and fruits of a few plant species (9). Among nonphotosynthetic bacteria, glycosylated and acylated carotenoids have also been identified in aerobes (22) and facultative aerobes (25) as well as in halophiles (23), psychrophiles (11), and thermophiles (41, 42).
The thermophilic filamentous anoxygenic phototroph (FAP) Chloroflexus aurantiacus produces OH-
-carotene glucoside esters, for which the major fatty acids are hexadecanoate and hexadecenoate (37). Thermus thermophilus has also been shown to produce thermozeaxanthins, which are zeaxanthin glucoside esters (42). Deinococcus spp., which are phylogenetically related to Thermus spp., are red pigmented as a result of carotenoid production, and at least two species of glycosylated xanthophyll carotenoids are produced by these organisms (4). Finally, acylated carotenoids also occur in Myxococcus xanthus, which synthesizes these carotenoids in response to blue light (6, 8), nutrient status (12), or copper stress (28).
The enzymatic pathway for modification of carotenoids has been elucidated for a few species. In Erwinia herbicola and related bacteria, the glucosyltransferase is CrtX, a membrane-associated protein that transfers glucose from UDP-glucose to zeaxanthin (20, 26). Staphylococcus aureus has an unrelated carotenoid glycosyltransferase, which converts the C30 carotenoid 4,4'-diaponeurosporenic acid to glycosyl 4,4'-diaponeurosporenoate (29). Acylation of this compound produces staphyloxanthin, or ß-D-glucopyranosyl 1-O-(4,4'-diaponeurosporen-4-oate)-6-O-(12-methyltetradecanoate). The genes encoding the glycosyltransferase and acyltransferase in S. aureus have been named crtQ and crtO, respectively (29). However, in this paper, we will refer to the S. aureus enzymes by their locus tags, SA2350 and SA2352, in order to avoid confusion with
-carotene desaturase, which is also named CrtQ (2), and ß-carotene ketolase, also named CrtO (19).
The green sulfur bacterium Chlorobium tepidum produces a small amount of OH-chlorobactene glucoside laurate (35, 38), which is found in the cytoplasmic membrane rather than associated with the chlorosomes (35). The genes in the chlorobactene biosynthetic pathway up to OH-chlorobactene have previously been identified (Fig. 1) (14, 24), but no homologs of the E. herbicola glycosyltransferase, CrtX, could be found in the predicted open reading frames (ORFs) in the C. tepidum genome (10). In this study, a comparative genomics approach was used to identify possible carotenoid-specific glycosyltransferases and acyltransferases in C. tepidum and other carotenogenic organisms. This approach identified single genes as candidates to encode the glycosyltransferase and the acyltransferase, both of which were insertionally inactivated in C. tepidum to confirm the roles of their products in carotenogenesis. The identification of these genes, which have now been named cruC and cruD, completes the identification of genes encoding the enzymes of the carotenoid biosynthetic pathway in C. tepidum (Fig. 1).
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FIG. 1. Biosynthetic pathway of carotenoids in C. tepidum. All genes identified in this pathway have been insertionally inactivated, and the resulting mutant strains have been biochemically and physiologically characterized (14, 24; this work).
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Identification of candidate genes and phylogenetic comparisons. All ORFs in the C. tepidum genome that had been annotated as either glycosyltransferases or acyltransferases were compared to proteins in the nonredundant databases in the Comprehensive Microbial Resources (CMR; The Institute for Genomic Research, Rockville, MD; http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi) and the Integrated Microbial Genomes (IMG; Joint Genome Institute, Walnut Grove, CA; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) sites by use of the BLASTP algorithm (1). The genome neighborhoods of the best hits were inspected for the presence of nearby ORFs predicted to be involved in carotenoid biosynthesis. For construction of phylogenetic trees, amino acid sequences were aligned by use of the ClustalW tool in MacVector 7.2.3 (Accelrys, San Diego, CA) and neighbor-joining trees were generated from the alignments with Paup 4.0 (Sinauer Associates, Inc., Sunderland, MA).
Inactivation of cruC and cruD. The left and right flanks of genes selected for inactivation were amplified by PCR from wild-type C. tepidum genomic DNA with the primers described in Table 1. The reverse primers for the left flanks and forward primers for the right flanks contained KpnI and SalI restriction sites, respectively. PCR products were digested with the appropriate restriction enzymes and purified from agarose gels by use of an Eppendorf Perfectprep gel cleanup kit (catalog number 0032 007.759; Westbury, NY). The aadA gene, conferring resistance to streptomycin and spectinomycin, was excised from plasmid pSRA81 (14) with SalI and KpnI and purified in the same manner. The fragments were mixed in a 1:1:1 ratio and ligated. The ligation products were separated on an agarose gel, and the products of the appropriate size were excised, purified, and used to transform wild-type C. tepidum as described previously (13, 15). Antibiotic-resistant colonies appeared after approximately 1 week and were transferred to fresh plates amended with spectinomycin and streptomycin. After three successive transfers, PCR across the site of insertion, using primers CT1987 F1 and CT1987 R1 for CT1987 and primers CT0967 F3 and CT0967 R3 for CT0967 (Table 1), confirmed that the wild-type and mutant alleles for both mutants had completely segregated. Two representative transformants from each mutant strain were selected for further analysis.
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TABLE 1. Sequences of primers used for construction of mutants and confirmation of segregation
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FIG. 2. Genome neighborhood comparisons. CT0967 (cruD) in C. tepidum and orthologs in other organisms are striped; CT1987 (cruC) in C. tepidum and homologs in other organisms are solid black. Other genes predicted to be involved in carotenoid biosynthesis are light gray; all other genes are white. In two species, orthologs of both CT1987 and CT0967 appear in a genomic region with at least one other carotenoid biosynthesis gene. This arrangement of genes suggests that these two ORFs might encode proteins that function in carotenoid biosynthesis.
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FIG. 3. Restriction maps of constructions used to inactivate CT1987 and CT0967 and confirmation of segregated mutants. (A) Restriction maps and primer locations of constructions used to inactivate CT1987 and CT0967. (B) Electrophoretic analysis of PCR products to evaluate putative mutants. The CT1987 and CT0967 loci were amplified by PCR with the primers indicated in Table 1. The DNA templates were derived from wild-type C. tepidum (lanes 2 and 4), from a CT1987::aadA transformant (lane 3), and from a CT0967::aadA transformant (lane 5). The amplicons from the two transformants are 0.9 kb larger than the corresponding amplicon from the wild type. This demonstrates that wild-type and mutant alleles had segregated fully in both transformants. Lanes 1 and 6 contain DNA size markers (Ladder I; GeneChoice, Frederick, MD).
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-carotene (peak 5), and 1',2'-dihydrochlorobactene (peak 6). As shown in Fig. 4, peaks 1, 2, and 3 were all missing when the crtC gene, encoding chlorobactene 2'-hydroxylase, is inactivated. The CT1987::aadA mutant no longer produced OH-chlorobactene glucoside or OH-chlorobactene glucoside laurate but still produced a carotenoid (peak 2) with an absorption spectrum identical to that for chlorobactene (absorption maxima at 461 and 491 nm; data not shown) and with the mass of OH-chlorobactene (550.4 Da). The CT0967::aadA mutant could no longer synthesize OH-chlorobactene glucoside laurate (peak 3) but could still produce OH-chlorobactene glucoside (peak 1) and OH-chlorobactene (peak 2). The carotenoid analyses of the two mutants confirm that CT1987 encodes the OH-chlorobactene glucosyltransferase while CT0967 encodes the OH-chlorobactene glucoside lauroyltransferase. These two ORFs have been renamed cruC and cruD, respectively.
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FIG. 4. HPLC elution profiles of the C. tepidum wild type (WT) and mutants unable to synthesize various modified carotenoids. Peak 1, OH-chlorobactene (550.4 Da); peak 2, OH-chlorobactene glucoside (729.4 Da); peak 3, OH-chlorobactene glucoside laurate (894.6 Da); peak 4, chlorobactene (532.4 Da); peak 5, -carotene (536.4 Da); peak 6, 1',2'-dihydrochlorobactene (534.5 Da). Elution of carotenoid species was monitored at 491 nm.
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-carotene, or chlorobactene (Fig. 1) can grow at rates similar to that of the wild type (14). The crtC mutant, which cannot hydroxylate chlorobactene and therefore makes no glycosylated carotenoids (Fig. 4), grows at a rate
90% of that of the wild type at 70 µmol photons m2 s1 and at the same rate as the wild type at high light intensity (14). In contrast, the cruC and cruD mutants grow at the same rate as the wild type at both intermediate and high light intensities (Fig. 5).
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FIG. 5. Growth rates for the wild type (WT) and cruC and cruD mutant strains of C. tepidum at different light intensities. The rates are the averages from three independent determinations, and standard errors are indicated.
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FIG. 6. Neighbor-joining tree showing phylogenetic relationships among carotenoid glycosyltransferases. Amino acid sequences were aligned and used to reconstruct the phylogeny; all labels are the automatically assigned locus tags for that ORF. Only C. tepidum CruC and S. aureus SA2350 have been genetically characterized. Another class II glycosyltransferase, CT0362, from C. tepidum was used as the outgroup for this comparison. Numbers for open reading frames in C. aggregans, H. aurantiacus, R. castenholzii, and Roseiflexus sp. strain (R. strain) RS-1 are the numbers currently assigned in the draft genome sequences.
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FIG. 7. Neighbor-joining tree showing phylogenetic relationships among various acyltransferases. Amino acid sequences were aligned and used to reconstruct the phylogeny. Bold lines indicate proteins whose functions have been genetically or biochemically confirmed. Numbers for open reading frames in C. aggregans, H. aurantiacus, R. castenholzii, and Roseiflexus sp. strain RS-1 are the numbers currently assigned in the draft genome sequences. E. coli, Escherichia coli.
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For C. tepidum, the presence of a population of carotenoids anchored in the cytoplasmic membrane most likely protects the membrane from radicals generated by the reaction centers, from reactive oxygen species, from chlorophyll triplet states, or from all of these. Although GSB are not oxygenic, the strong reductants generated by their reaction center can readily react with O2 to form reactive oxygen species (16), which have the potential to damage membrane lipids. Given their absolute dependence upon light for growth, many GSB inhabit the upper parts of anoxic zones, where periodic disturbance of the chemocline by wind or tides can result in transient exposure to molecular oxygen. Because homologs of both CruC and CruD are found in the genomes of all sequenced GSB, it is likely that these specialized carotenoids play an important role(s) in these organisms. Additionally, although inactivation of crtC, which encodes the enzyme that acts immediately before CruC and CruD, reduces the growth rate of C. tepidum under saturating-light intensity, neither the cruC nor the cruD mutant has a growth defect under optimal laboratory conditions. This suggests that the modified carotenoid may be more important under stress conditions such as low temperature or oxic conditions.
Because glycosylated and acylated carotenoids are widespread among both photosynthetic and nonphotosynthetic bacteria, it is unlikely that they are principally involved in light harvesting and the conversion of light energy to chemical energy. Instead, they most likely serve other structural or protective functions in the membrane, absorbing and dissipating the energy from reactive oxygen species, UV light, or chlorophyll triplet states. Polar modifications of carotenoids, such as the introduction of hydroxyl or keto groups, tend to facilitate interactions with the phosphate head groups of lipids, thereby orienting the carotenoids within membranes (7, 31). The acyl group should anchor these molecules within the membrane and could also provide structural interactions with particular membrane proteins. In some cases, specific lipids are known to play important roles in the biogenesis of some membrane proteins (5) or to have specific binding sites on membrane proteins associated with photosynthesis (17, 21). In light of the observations that chlorobactene glucoside esters are found in the cytoplasmic membrane rather than the chlorosome and that they copurify with reaction centers (35), it is also possible that in GSB, these modified carotenoids play some role, albeit nonessential, either in biogenesis of the photosystem proteins or in photoprotection of the reaction centers in the membrane.
The S. aureus carotenoid glycosyltransferase SA2350 can be aligned with CruC glycosyltransferases, but its sequence is not more similar to the carotenoid glycosyltransferases than to other glycosyltransferases; several outgroup sequences were tested, and SA2350 always grouped with that sequence (data not shown). The large sequence differences between SA2350 and CruC may be due to the fact that the substrates for SA2350 are C30 carotenoids rather than the C40 compounds synthesized by other species. Because the S. aureus acyltransferase, SA2352, also seems to be unrelated to other putative carotenoid acyltransferases (see below), it appears likely that the similarity of the SA2350 carotenoid glycosyltransferase to the other carotenoid glycosyltransferases may have arisen by convergent evolution from a nonorthologous glycosyltransferase subfamily.
The putative carotenoid acyltransferases orthologous to CruD form a coherent phylogenetic group when aligned and compared with lipid O-specific or N-specific acyltransferases. This grouping, in conjunction with gene neighborhood analysis, allows us to predict confidently that the ORFs RB11942 (in Rhodopirellula baltica) and Der0090 (in Deinococcus radiodurans), as well as ORF 9 in the M. xanthus carotenoid biosynthesis operon, also encode carotenoid acyltransferases. However, the S. aureus acyltransferase SA2352 cannot be aligned with these carotenoid acyltransferases. Thus, CruD appears to be the first characterized member of a new family of carotenoid acyltransferases.
The five sequenced FAP species, Chloroflexus aurantiacus, Chloroflexus aggregans, Roseiflexus sp. strain RS-1, and R. castenholzii, and the nonphotosynthetic Chloroflexus strain Herpetosiphon aurantiacus also have homologs of both cruC and cruD. As shown in Fig. 6, the glycosyltransferases of these Chloroflexi cluster together within the group of carotenoid glycosyltransferases, but their sequences are not very similar to those of the GSB and their lineage is deeply divergent from the GSB clade (Fig. 6). The CruD sequences, which form a distinct clade among the larger family of acyltransferases, exhibit a similar pattern, in which the sequences derived from the Chloroflexi and Chlorobi form distinct clades that are deeply divergent. Interestingly, the CruD sequence most divergent from the Chloroflexi species is that of the nonphototrophic H. aurantiacus; the sequences from the two Chloroflexus spp. and Roseiflexus spp. are more similar (Fig. 7). These relationships are similar to those inferred from comparisons of the 16S rRNA sequences of these organisms (data not shown).
The identification of cruC and cruD, and the distribution of these genes in other bacteria, highlights the chimeric nature of the carotenoid biosynthetic pathway in GSB. The enzymes for the conversion of phytoene to
-carotene in Chlorobi are similar to those for the conversion of phytoene to ß-carotene in cyanobacteria, and they differ from the enzymes found in Chloroflexi and most other bacteria (14, 24). However, the enzymes involved in modification of the cyclized carotenoids (ring modification,
-end hydroxylation, glycosylation, and acylation) are more similar to those in FAPs and nonphotosynthetic bacteria (14). This raises interesting questions about the acquisition and evolution of carotenoid biosynthesis genes in GSB. It seems plausible that the majority of the carotenoid biosynthesis pathway was inherited vertically from a common ancestor of GSB and cyanobacteria, while the genes encoding the final three steps for chlorobactene modification may have been acquired laterally at a later stage from another organism. Considering the prevalence of lateral gene transfer in the evolutionary history of carotenoid biosynthesis (18, 30), this is perhaps the rule rather than the exception.
This research was funded by grant DE-FG02-94ER20137 from the U.S. Department of Energy to D.A.B.
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-l-fucoside), not rhamnoside. Plant Cell Physiol. 42:756-762.
-carotene, 1',2'-dihydrochlorobactene, and OH-chlorobactene glucoside ester, and the carotenoid composition of different strains. Arch. Microbiol. 168:270-276.[CrossRef][Medline]This article has been cited by other articles:
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