Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
Correspondence
Julia M. Inamine
jinamine{at}colostate.edu
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ABSTRACT |
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The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are AF125999 and AF143772.
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INTRODUCTION |
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The ser2 gene cluster should be highly conserved among strains containing the serovar-2-specific GPL; however, previous studies demonstrated restriction fragment length polymorphisms in the ser2 region of the genomes of M. avium strains 2151 and TMC 724 (Belisle et al., 1993b). In the present study, the ser2 gene cluster and the flanking regions of these two strains were sequenced and compared with the homologous regions of M. avium strain 104 (serovar 1), M. avium subsp. paratuberculosis and M. avium subsp. silvaticum. In addition, the genetic basis for a rough colony variant of strain 104 was determined to be the deletion of 10 kb of DNA that includes several GPL biosynthetic genes. The results support a proposed pathway for ssGPL biosynthesis in M. avium serovar 2 in which serovar-2-specific GPLs are synthesized from nsGPLs via a serovar-1-specific GPL intermediate, and raise interesting questions about the evolutionary mechanism for creating the different serovars.
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METHODS |
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M. avium strain 104 and its rough derivative (104Rg) were from J. Torrelles and D. Chatterjee (Torrelles et al., 2002). These strains were grown on Middlebrook 7H11 agar (Difco) containing 10 % oleic acid-albumin-glucose-catalase (OADC). After 2 weeks growth at 37 °C, a single colony was used to inoculate Middlebrook 7H9 broth (Difco) containing 10 % OADC. The 10 ml starting culture was up-scaled several times to a final volume of 200 ml. Cells were harvested by centrifugation at 3000 g for 30 min. For isolation of genomic DNA, harvested cells were resuspended in TES buffer (50 mM Tris, pH 8·0; 10 mM EDTA, pH 8·0; 100 mM NaCl) and stored on ice. Cells were lysed by vortexing with 0·5 mm zirconium beads for 2 min. SDS (final concentration 1 %) was added to the lysed cells and kept on ice for 15 min. The lysate was treated with proteinase K (final concentration 100 µg ml-1) at 55 °C for 15 min and then extracted with phenol/chloroform/isoamyl alcohol (25 : 24 : 1). The aqueous phase was loaded on an equilibrated Genomic Tip 100 (Qiagen) and the genomic DNA was eluted with TE (10 mM Tris, pH 8·0; 1 mM EDTA, pH 8·0), according to the manufacturer's instructions.
Cloning, restriction endonuclease mapping and sequencing of ser2 and flanking regions from M. avium strains 2151 and TMC 724.
The recombinant plasmids used in this study and the procedures used for their derivation are shown in Table 1. These plasmids were characterized by digestion with restriction endonucleases SmaI, KpnI, PstI, EcoRI, EcoRV, SacI, NotI and BamHI (Invitrogen), and subclones were constructed by ligation of restriction fragments into the respective sites of the pBluescript II SK(-) vector (Stratagene) using T4 DNA ligase (Invitrogen). These subclones were used as double-stranded DNA templates for DNA sequencing with the pBluescript T3 and M1320 primers. Custom primers were synthesized as necessary to resolve sequence ambiguities. Sequencing of DNA was performed by Macromolecular Resources Facility, Colorado State University. Contiguous DNA sequences, ORF analysis and codon usage were determined with Sequencher 3.0 software (Gene Codes Corporation) and FramePlot 2.3beta (http://www.nih.go.jp/
jun/cgi-bin/frameplot.pl) (Ishikawa & Hotta, 1999
). Identification of the putative function of each ORF was achieved via similarity searches between the deduced amino acid sequences and known proteins using BLAST (http://www.ncbi.nlm.nih.gov/BLAST/) and multi-alignments were generated using MultAlin (http://www.toulouse.inra.fr/multalin.html) (Corpet, 1988
).
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The 3690 bp PCR product was purified from the gel using the QIAquick Gel Extraction Kit (Qiagen), according to the manufacturer's instructions, cloned into pGEM-TEasy (Promega) and the insert was sequenced using the SP6 and T7 primers. Subclones for DNA sequencing were generated with SstI, NcoI and HincII (Invitrogen). Sequencing of DNA was performed by the Macromolecular Resources Facility at Colorado State University. DNA sequence alignments, ORFs and codon usage were determined with Sequencher 3.0 software (Gene Codes Corporation). The site of the genomic deletion was facilitated by comparing the sequence data to the genome sequence data from M. avium strain 104 provided by The Institute for Genomic Research (http://www.tigr.org).
Nucleotide sequence accession numbers.
The sequence data presented in this article are available in GenBank at AF143772 (M. avium 2151) and AF125999 (M. avium TMC 724). The previously published rtfA sequence data (Eckstein et al., 1998) at AF060183 are included in AF125999, and the previously published IS1601 sequence data (Eckstein et al., 2000
) at AF060182 are included in AF143772.
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RESULTS |
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Definition and proposed role for the ser1 subcluster
The lipopeptide cores of all MAC GPLs are glycosylated at two positions: the C-terminal L-alaninol is glycosylated with a mono- or dimethylated Rha (it can also be trimethylated Rha in Mycobacterium smegmatis), and the D-allo-threonine is glycosylated with 6-dTal. This is the structure of nsGPLs. The simplest of the ssGPLs is that of serovar 1 (Table 3) which contains a single Rha residue linked to 6-dTal. This basic oligosaccharide structure is in all other ssGPLs except for those of serovars 5 and 10/11 (Aspinall et al., 1995
) and so the genes for its glycosylation and methylation should be present in all the relevant serovars. The ser1 region (indicated by the solid black box in Fig. 1
) was common to both serovar 1 (strain 104) and serovar 2 (strains 2151 and TMC 724), and the ORFs encompassed by this region are proposed to participate in the biosynthesis of the serovar-1-specific GPL.
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The roles for GtfA and GtfB proposed above and the order in which these glycosylation steps occur were further examined by genetic analysis of strain 104Rg, a naturally occurring rough derivative of M. avium strain 104. Torrelles et al. (2002) determined that 104Rg produces truncated GPLs that lack the 6-dTal attached to D-allo-threonine, but retain the methylated Rha on the L-alaninol. In the present study, PCR analysis of 104Rg genomic DNA in comparison to that of the parental strain indicated that 104Rg contains gtfB, but not gtfA (data not shown). Given the presence of two copies of IS999 flanking the gtfA region in strain 104 (Fig. 1a
), we reasoned that the absence of gtfA in 104Rg might be due to deletion, based on our previous finding that homologous recombination between direct repeats of IS1601 resulted in the deletion of the ser2 gene cluster to produce the Rg-1 morphotype of strain 2151 (Eckstein et al., 2000
). However, these particular copies of IS999 are inverted repeats rather than direct repeats in the genome sequence of strain 104 (http://www.tigr.org) and homologous recombination between them should result in inversion rather than deletion. Nevertheless, based on the PCR results, the deletion hypothesis was tested by using primers based on orfA and rtfA sequences flanking the left and right (Fig. 1a
) copies of IS999, respectively, to amplify 104Rg genomic DNA. A 3690 bp PCR product was obtained and this was cloned and sequenced. The DNA sequence indicates that 104Rg lost the 10 kb region containing orfBgtfA while retaining one copy of IS999 (the left copy in Fig. 1a
). It is possible that the 28 bp inverted repeats at the ends of IS999 mediated the deletion event since Mahairas et al. (1996)
identified 24 and 12 bp repeats that were involved in the deletion of the RD2 and RD3 regions, respectively, in Mycobacterium bovis BCG. The region deleted from strain 104 includes three genes (mtfA and mtfB as well as gtfA) from the ser1 subcluster. Since 104Rg produces a lipopeptide core with methylated Rha on the L-alaninol (Torrelles et al., 2002
), and we found that it has lost gtfA while retaining gtfB, it follows that GtfB is likely to transfer Rha to the C-terminal L-alaninol of the lipopeptide core before gtfa adds 6-dtal to the D-allo-threonine. Thus, the proposed biosynthetic scheme begins with GtfB (Fig. 2
).
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The anomalous ser3' gene cluster
The ser3' subcluster (indicated by the white box in Fig. 1) was so-named because it encodes a putative D-glucose dehydrogenase that would be needed to make the D-glucuronic acid found in the ssGPLs of M. avium serovars 3 or 9 (Table 3
). The deduced amino acid sequence demonstrated a high degree of similarity (69 and 65 %) to known D-glucose dehydrogenases of Bacillus subtilis (Hilt et al., 1991
) and Pseudomonas aeruginosa (van Schie et al., 1985
), respectively. The presence of this subcluster in the serovar 2 strains is anomalous because D-glucuronic acid is not found in the serovar-2-specific GPL.
Proposed role for the fbt subcluster in the de novo biosynthesis and transfer of L-fucose (L-Fuc)
The presence of dimethylfucose is the only difference between the serovar-2-specific and serovar-1-specific GPLs (Table 3), and so the genes for Fuc synthesis and addition should be present in serovar 2 strains, but not serovar 1. The region defined as fbt (Fuc biosynthesis and transfer; indicated by the grey box in Fig. 1
) fulfils this criterion and appears to contain the genes needed for the de novo biosynthesis and transfer of L-Fuc. The deduced amino acid sequences of gtfC, mdhA, merA, mtfF and gtfD demonstrated a high degree of similarity (52 % identity, 67 % similarity) to proteins involved in the de novo synthesis and transfer of L-Fuc in E. coli (Stevenson et al., 1996
; Andrianopoulous et al., 1998
). Interestingly, this gene cluster is identical to the GS element of M. avium subsp. paratuberculosis and subsp. silvaticum (Tizard et al., 1998
; Bull et al., 2000
) although neither of these subspecies expresses GPLs (see Discussion).
It is possible that one of the two putative glycosyltransferase genes (gtfC and gtfD) belongs to the ser3' rather than the fbt gene cluster because a transferase would be needed for the glucuronic acid found in the ssGPLs of serovars 3 or 9. However, mtfE is clearly part of the fbt subcluster, despite its physical separation from the other fbt genes, based on the earlier work of Mills et al. (1994). In that study, transposon mutants of the cloned ser2 region from M. avium strain 724 were analysed in M. smegmatis to identify genes involved in ssGPL biosynthesis (the M. avium genes required for nsGPL synthesis could not be characterized because M. smegmatis makes nsGPLs). The loci responsible for making 2-O-Me-Fuc and 3-O-Me-Fuc map to the mtfF and mtfE genes, respectively.
Comparison of the ser2 regions of strains 2151 and TMC 724
Comparison of the two ser2 gene clusters and their flanking regions revealed that the nucleotide sequences and gene organization were strongly conserved and only a few nucleotide differences were observed. Most were silent mutations, but some affected the deduced amino acid sequences of gtfB, mtfE and gdhA (4, 2 and 2 aa, respectively). Besides these highly conserved characteristics, there were three major differences between the organization of the ser2 gene clusters in M. avium TMC 724 and 2151. First, two ORFs encoding a putative dehydrogenase (dhgA) and a putative haemolytic protein (hlpA) are disrupted by IS1245 and IS1348, respectively, in M. avium 2151, but not in M. avium TMC 724. Second, a potential hot spot for insertion sequences was observed downstream of the fbt gene cluster in both M. avium strains, but IS1601 was found in 2151 while IS2534 was found in TMC 724. The site of integration of these two IS elements in the two strains differs by only 133 bp. Finally, M. avium TMC 724 contained a putative O-acetyltransferase gene (atfA) downstream of the fbt subcluster that is not present in the region sequenced for M. avium 2151.
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DISCUSSION |
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Both ser2 gene clusters have the same organization of genes encoding the enzymic machinery for the biosynthesis of the ssGPL, and this type of genetic conservation has been observed in other systems, such as the gene clusters responsible for expression of E. coli group 1 K-antigens (Rahn et al., 1999). The nucleotide and deduced amino acid sequences of the ORFs in the ser2 regions of both strains are identical, with three exceptions (gtfB, mtfE and gdhA) as noted earlier. Given the similarity in structure of Rha, Fuc and 6-dTal, one would expect a high degree of similarity in the enzymes transferring these 6-deoxyhexose sugars. Indeed, RtfA, GtfA and GtfB are very similar to one another. However, the putative fucosyltransferases GtfC and GtfD are not related to one another or the other three glycosyltransferases. None of the five glycosyltransferases contains the E-x(7)-E-A-x(18)-E hexosyltransferase motif identified by Henderson & Nataro (1999)
. However, this motif was based on the analysis of glucosyl-, galactosyl- and mannosyltransferases, and not 6-deoxyhexosyltransferases, suggesting that the loss of the hydroxyl group on the sixth carbon might be the reason for the mismatch. Multi-alignment of putative 6-deoxyhexosyltransferases yielded two new motifs (Fig. 3
a, b). The first motif, G-[TS]-R-G-D-x-[EQ]-P-x-x-A-x(4)-L-x(3)-G-x-x-V (Fig. 3a
), is in the N-terminal 60 aa of the transferase, and the second motif, [DE]-x(18)-[AG]-[VI]-[VI]-H-H-G-G-x-G-[TS]-T (Fig. 3b
), is about 200 aa away. Interestingly, NovM, an enzyme that transfers a Rha that is C-methylated at the fifth carbon, does not exhibit the first motif, but contains the second one. This suggests that the fifth and the sixth carbons of the 6-deoxyhexoses play a major role in binding to the first motif. RtfA, GtfA and GtfB contain both of the proposed 6-deoxyhexosyltransferase motifs while GtfC and GtfD do not. This supports our biosynthetic model (see below) in which GtfC or GtfD transfer methylated Fuc molecules and would thus have different binding and transfer motifs than the 6-deoxyhexosyltransferases.
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The proposed pathway is similar to the biosynthetic cascades for other cell-wall surface markers. Stevenson et al. (1996) described a biosynthetic pathway for the extracellular colanic acid of E. coli K-12 in which the four sugars are synthesized de novo in the cytosol and then transferred to the lipid carrier in the inner membrane. Polymerization and acetylation are then performed in the outer membrane of the cell wall. Similar pathways have been proposed by Arakawa et al. (1995)
for the biosynthesis of the serotype K2 capsular polysaccharide of Klebsiella pneumoniae, and by Hashimoto et al. (1993)
for the synthesis of the Vi antigen in Salmonella typhi. The transport of the cell surface markers to the final destination is usually mediated by an ABC transporter system (Hashimoto et al., 1993
; Stevenson et al., 1996
). We could not identify the genes for such a transport system for the GPLs within the ser2 gene clusters of M. avium 2151 or TMC 724. However, a second transport mechanism was discussed by Stevenson et al. (1996)
in which the lipid carrier involved in the synthesis of colanic acid acts as a transporter. They proposed that the lipid carrier is flipped from the cytoplasm into the periplasm. Further work is needed to determine whether this transport mechanism or the ABC transporter system is responsible for the transfer of the GPLs to the outer surface of the cell wall of M. avium. In this regard, it should be noted that Recht et al. (2000)
have suggested that tmtpC may be involved in both the biosynthesis and transport of GPLs in M. smegmatis.
Downstream of the ser2 gene cluster of M. avium TMC 724 is an ORF (atfA) encoding a putative O-acetyltransferase. AtfA contains all three of the acetyltransferase motifs proposed by Slauch et al. (1996). The atfA gene is not found in the analogous regions of strains 2151 or 104, but it is present within the GS gene cluster of M. avium subsp. paratuberculosis and subsp. silvaticum. Although AtfA is not necessary for the biosynthesis of ssGPLs, it might be involved in GPL modification since ssGPLs can sometimes be acetylated, methylated or sulfated (Aspinall et al., 1995
; Chatterjee & Khoo, 2001
). Recht & Kolter (2001)
recently showed that the atf1 gene of M. smegmatis encodes an acetyltransferase that acetylates one or two sites on the 6-dTal of nsGPL. The nucleotide sequences on either side of IS2534-atfA in strain 724 are identical to those surrounding the right copy of IS1601 (Fig. 1
) in strain 2151. This suggests that atfA may have been inserted along with the IS element, although IS2534-atfA is not flanked by direct repeats.
The presence of repetitive elements in the ser regions raises interesting possibilities with regard to the evolution of the different serovars. The ser2 region is flanked by IS1601 in strain 2151, and the ser1 region is flanked by IS999 and RE (a repetitive element containing portions of IS999) in strain 104, suggesting that these gene clusters together with the flanking IS elements form biosynthetic islands. A similar gene organization was found for the cap gene cluster of H. influenzae (Kroll, 1992) and the K10 capsule gene cluster in E. coli (Clarke et al., 1999
). The IS elements flanking the cap genes generated a duplication of the gene cluster resulting in enhanced production of the capsule polysaccharide (Kroll, 1992
). Clarke et al. (1999)
found that the K10 capsule genes are flanked by IS3 and prophage elements, leading them to speculate that these elements were involved in the acquisition of the capsule gene cluster at its present chromosomal location. Two observations from the present work suggest that the acquisition or loss of such biosynthetic islands has occurred in the MAC. First, the anomalous ser3' gene subcluster contains gdhA, a gene encoding a putative D-glucose dehydrogenase. This enzyme produces D-glucuronic acid, which is found only in the ssGPLs of M. avium serovars 3 or 9 (Aspinall et al., 1995
) (Table 3
). Thus, the ser2 gene cluster in M. avium TMC 724 and 2151 might represent an intermediate step in which a serovar 2 strain acquired new genetic information to produce serovars 3 and 9. The second observation is that the fbt gene cluster of M. avium 2151 and TMC 724 is identical to the GS element, an 8·9 kb genomic region reported to be present in M. avium subsp. paratuberculosis and M. avium subsp. silvaticum, but absent from some strains of M. avium subsp. avium (Tizard et al., 1998
; Bull et al., 2000
). Interestingly, the GS region from M. avium subsp. silvaticum contains exactly the same IS element in exactly the same site as in M. avium strain TMC 724 (IS1612 is identical to IS2534). This suggests that M. avium subsp. silvaticum might have been derived from a serovar 2 strain of M. avium such as strain TMC 724, or vice versa.
In summary, this work represents a comprehensive analysis of the genes responsible for the glycosylation of the GPLs of M. avium. The data presented show a strong conservation of gene sequences and organization together with significant differences among strains that suggests that the acquisition or deletion of genes has resulted in different serovars with specific haptenic oligosaccharides as well as different subspecies. This work also provides a template for future research to confirm gene function in the pathway for GPL biosynthesis and the role of GPLs in the biology of M. avium. One obstacle to these types of studies is the poor transformability of M. avium subspecies avium. Thus far, we have not been able to transform strain 2151 and so the genetic analyses of GPL biosynthesis in M. avium have been restricted to naturally occurring deletion mutants. However, J. N. Maslow, S.-W. Lee, T. M. Eckstein, J. M. Inamine and J. T. Belisle (unpublished) have recently used a transformation frequency of 4 [4 c.f.u. (µg DNA)-1] with strain 724 to successfully carry out allelic exchange mutagenesis, and so it should be possible to test individual genes in the proposed GPL biosynthesis pathway in future studies.
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ACKNOWLEDGEMENTS |
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Received 29 May 2003;
accepted 26 June 2003.