HinT proteins and their putative interaction partners in Mollicutes and Chlamydiaceae
© Hopfe et al; licensee BioMed Central Ltd. 2005
Received: 24 November 2004
Accepted: 18 May 2005
Published: 18 May 2005
HinT proteins are found in prokaryotes and eukaryotes and belong to the superfamily of HIT proteins, which are characterized by an histidine-triad sequence motif. While the eukaryotic variants hydrolyze AMP derivates and modulate transcription, the function of prokaryotic HinT proteins is less clearly defined. In Mycoplasma hominis, HinT is concomitantly expressed with the proteins P60 and P80, two domains of a surface exposed membrane complex, and in addition interacts with the P80 moiety.
An cluster of hit ABL genes, similar to that of M. hominis was found in M. pulmonis, M. mycoides subspecies mycoides SC, M. mobile and Mesoplasma florum. RT-PCR analyses provided evidence that the P80, P60 and HinT homologues of M. pulmonis were polycistronically organized, suggesting a genetic and physical interaction between the proteins encoded by these genes in these species. While the hit loci of M. pneumoniae and M. genitalium encoded, in addition to HinT, a protein with several transmembrane segments, the hit locus of Ureaplasma parvum encoded a pore-forming protein, UU270, a P60 homologue, UU271, HinT, UU272, and a membrane protein of unknown function, UU273. Although a full-length mRNA spanning the four genes was not detected, amplification of all intergenic regions from the center of UU270 to the end of UU273 by RT-PCR may be indicative of a common, but unstable mRNA.
In Chlamydiaceae the hit gene is flanked upstream by a gene predicted to encode a metal dependent hydrolase and downstream by a gene putatively encoding a protein with ARM-repeats, which are known to be involved in protein-protein interactions. In RT-PCR analyses of C. pneumoniae, regions comprising only two genes, Cp265/Cp266 and Cp266/Cp267 were able to be amplified. In contrast to this in vivo interaction analysis using the yeast two-hybrid system and in vitro immune co-precipitation revealed an interaction between Cp267, which contains the ARM repeats, Cp265, the predicted hydrolase, and Cp266, the HinT protein.
In the Mollicutes HinT proteins were shown to be linked with membrane proteins while in the Chlamydiaceae they were genetically and physically associated with cytoplasmic proteins, one of which is predicted to be a metal-dependent phosphoesterase. Future work will elucidate whether these differing associations indicate that HinT proteins have evolved independently or are indeed two hotspots of a common sphere of action of bacterial HinT proteins.
The detection of an unusual, highly conserved sequence motif "His-phi-His-phi-His-phi-phi" (phi representing hydrophobic amino acids) in a variety of organisms of all kingdoms led to the definition of a new family of proteins named HIT (hi stidine triad) . This family has three main branches: the fragile histidine triad (FHit)-related proteins found in animals and fungi, which act as di-adenosine polyphosphate hydrolases and function as tumor suppressors in humans and mice  (although the tumor suppressing function is not dependent on ApppA hydrolysis ), the GalT (galactose 1 phosphate uridylytransferase) homologues, which have a modified "His-phi-His-phi-Gln" motif, which transfers nucleoside monophosphates to phosphorylated secondary substrates rather than hydrolyzing them , and the Hi stidine-t riad n ucleotide binding (HinT) homologues, which in eukaryotes are intracellular receptors and hydrolases of purine mononucleotides . Although HinT homologues are found in all kingdoms and this family is the most ancient and widespread branch of the HIT proteins, the cellular function, the substrates and the interaction partners of HinT proteins are largely unknown. In prokaryotes, knowledge of HinT proteins is generally restricted to sequence analyses. In the cell wall-less prokaryote Mycoplasma hominis, the cytoplasmic HinT protein interacts with a surface localized membrane complex by binding to the P80 moiety. Interestingly, the genes encoding P80 and P60, the domains of the membrane complex, form an operon with the HinT gene . The identification of a homologous hit locus in M. pulmonis and access to several sequenced prokaryotic genomes enabled us, in this study, to hypothetically identify interaction partners and thus propose a functional role for HinT in bacteria with small genomes.
To find out more about the function of prokaryotic HinT proteins we first analyzed the hit loci of bacteria with a restricted genome, with the view that they might represent a model for organisms possessing the minimal genetic make-up essential for life as a free-living organism. As polycistronically organized genes often encode proteins that are functionally related (e.g. in a protein-complex formation or as part of a common pathway) we ran a search of known genome sequences for genes closely neighbouring or overlapping the hit gene. Species from the Mollicutes and the Chlamydiaceae fulfill these requirements and were thus analyzed.
Mollicutes are phenotypically distinguished from other bacteria by their minute size and total lack of a cell wall. They have evolved as a branch of gram-positive bacteria by a process of reductive evolution. The significant genome "condensation" (for example the genome of M. genitalium is only 580 kbp) was made possible by adopting a parasitic behavior. The primary habitats of human and animal mycoplasmas are the mucous surfaces which they colonize during infection . While the intracellular localization of Mollicutes in insect tissues is well established, cell entry of human or animal mycoplasmas seems to be rare and possibly mediated by a site-directed, receptor-mediated event found in chlamydia . However, Chlamydiaceae have a number of features in common with mycoplasmas: their small genomes predict a limited metabolic capability, their major target tissue are mucous membranes and they also cause ocular and sexually transmitted diseases. In contrast, the chlamydia are obligate-intracellular bacteria that undergo a unique developmental cycle in which is an alteration in size between the small metabolically inactive infectious elementar body and the relatively large, metabolically active reticular body which is adapted for intracellular growth . Bearing in mind, that in M. hominis the HinT-interacting protein is a secreted antigen and thus predicted to play a role in the pathogenicity of mycoplasmas we expand this analysis to include a family of obligate-intracellular organisms known to secrete antigens in the inclusion body in the infected cell.
Organization of the hit-locus in Mollicutes
Hit loci with a different genomic organization were identified in the mollicutes Ureaplasma parvum,M. pneumoniae and M. genitalium (Figure 1B). While UU271 of U. parvum, the gene immediately upstream of hit L encoded a putative P60 homologue possessing the P60 consensus sequences CS1 (35.7 % identity) and CS2 (30% identity), it differed from all other P60 homologues in possessing a SPase I recognition sequence and two other transmembrane helices (AA 355 to AA 375 and AA 407 to AA 427). The UU273 gene, immediately downstream of hit L, encoded a protein with two transmembrane spanning helices, but with no significant similarity to other known proteins. The deduced protein sequence of UU270 did not have any sequence similarity with P80. With six transmembrane segments, it appeared more likely to form a pore than to be surface exposed. The organization of the hit locus of U. parvum appeared intermediate between the hit loci described above and those of M. pneumoniae and M. genitalium. The sequence identity between the ureaplasma HinT and the HinT proteins of M. pneumoniae (42.7 %) and M. genitalium (47.4 %) was higher than that between HinT of U. parvum and M. hominis (39.2 %), and the genes immediately upstream of hit L encoded proteins with seven (MPN_274) or five (MG_133) transmembrane domains (Figure 1B). MPN_274 is predicted to encode a permease of an ABC transporter  suggesting a comparable function in M. genitalium and probably also in U. parvum. Thus, these hit loci of Mollicutes analyzed appear to have a hit L gene flanked by genes that are predicted to encode membrane-anchored proteins.
As in M. gallisepticum, the hit L gene is not flanked by other genes on the same strand, also exceptions of a polycistronic organization of the hit L gene seem to exist within the Mollicutes.
Organization of the hit loci in Chlamydiaceae
In the obligately intra cellular Chlamydiaceae the order of genes within the hit loci and the function of the encoded proteins appeared to be highly conserved, but distinctly different from that of the Mollicutes (Figure 1C). In all chlamydial species analyzed, the gene upstream of hit L encoded a putative cytoplasmic protein with the signature sequence of a metal-dependent protein hydrolase and a large number of metal binding residues (IPR003226/UPF0160), probably indicative of a phosphoesterase function, and an o ligonucleotide/oligosaccharide-b inding OB fold (IPR008994). The deduced protein sequence of the gene located downstream of hit L contained a 37–47 AA long tandemly repeated ARM repeat fold (IPR008938), which forms a right-handed superhelix and has been implicated in the mediation of protein-protein interactions . Cp267 contained an RGD motif, which plays a role in cell adhesion . However, the presence of RGD in a sequence alone is not sufficient to suggest a biological function for this motif . The presence of two transmembrane helices (AA 314 to AA 334 and AA 428 to AA 448) suggested that it is more likely that Cp267 may interact with the bacterial cell membrane. In all other chlamydial species analyzed, the Cp267 homologues did not contain domains suggestive of membrane attachment.
Are the hit loci genes co-expressed?
In bacteria, overlapping genes on the same coding strand may indicate the polycistronic organization of these genes, and co-expressed proteins are often related in function.
Interactions between the proteins encoded by the hit locus of C. pneumoniae
HinT is known to dimerize [19, 20]. We introduced the coding region of M. hominis HinT into both pGADT7 and pGBKT7 and transformed the histidine dependent yeast strain AH109 with them. Quantification of transcriptional activation of the reporter gene was achieved using a liquid β-galactosidase assay measuring the hydrolysis of 4-methylumbelliferyl-β, D-galactopyranoside (MUG), yielding the fluorescent molecule 4-methylumbelliferone (4 MU). As expected, dimerization of the fused HinT peptides led to apposition of the AD and DB domains generating a functional transcription factor. The transcription of the reporter genes resulted in growth of the yeast on histidine-deficient agar plates (Fig. 5, top row, left plate) and production of β-galactosidase (Fig. 6C). Next we analyzed whether the proteins encoded by the hit locus of C. pneumoniae interacted. The coding regions of Cp265, Cp266 and Cp267 were introduced into pGADT7 and pGBKT7 and expressed in yeast in all possible combinations. As shown in Figure 5, large colonies, comparable in size to those of the positive control, were produced by yeast that expressed Cp265 fused to both the binding and the activation domain. This suggested a strong interaction between the molecules of the Cp265 protein. All other combinations of plasmids encoding Cp265, Cp266 and Cp267 only led to the growth of small colonies, a finding that was difficult to interpret. To differentiate between strong and weak interactions, the β-galactosidase assay was used. As shown in Fig. 6, the measurement of β-galactoside activity indicated an interaction between Cp267 and Cp265, Cp266 and Cp267 itself, independent of the fusion partner (the AD or DB domains of the GAL4 protein). Surprisingly, dimerization of Cp266 (HinT) was not detected, although Cp265 interacted strongly with itself. Cp267 did not activate transcription by itself (Fig. 6A. 267/BD and 267/AD) nor did it interact with the unrelated protein SV40 large T antigen (T/267) or murine tumor suppressor p53 (267/p53) to activate transcription, as in all these cases the β-galactosidase activity was at background levels (Fig. 6A).
Immune co-precipitation of Cp265, Cp266 and Cp267
Thus, we can conclude that the chlamydial proteins Cp265, Cp266 (HinT) and Cp267 have a tendency to dimerize and Cp267 interacts with both Cp265 and Cp266.
A remarkable feature of HinT proteins is their ubiquity. They are found in all kingdoms ranging from Mycoplasma genitalium, the smallest prokaryote, to one of the most complex eukaryotes, the human [1, 19]. However the function of this homo-dimer in the cytoplasm of these different organisms has only been closely examined in eukaryotes, where it has been characterized as an intracellular receptor for purine ribonucleotides [4, 5], especially for hydrolases of 5'-monophosphoramide substrates such as AMP-lysine , with the histidine triad motif forming the α-phosphate binding site . HinT has been shown to associate with the protein microphthalmia, an important transcription factor that controls growth and function in mast cells and melanocytes , to interact with the human cyclin-dependent kinase 7 (Cdk7), a subunit of the RNA polymerase II C-terminal domain kinase Cdk7/Kin28 , and to act as a positive regulator of the yeast Cdk7 homologue Kin28 . That it may not be the key regulator of Cdk7 activity was recently suggested by analysis of HinT-/- knock-out mice . This led to the hypothesis that eukaryotic HinT homologues are involved in the regulation of transcriptional processes by hydrolyzing related adenylyl-modified proteins .
The observation that HinT homologues are ubiquitous and that they are even encoded by the smallest bacterial genomes, suggests that HinT was present at the cellular root of the tree of life and that its preservation is advantageous for the survival of cells . However the function of bacterial HinT homologues seems to be quite different from those of eukaryotes. In M. hominis HinT had been demonstrated to interact both physically and genetically with a surface-localized membrane complex by binding to the P80 domain . The data presented here suggest that the co-expression of HinT with membrane proteins is prevalent within the Mollicutes. Comparable organization of the hit-loci was found in Mycoplasma hominis, M. pulmonis, M. mycoides subsp. mycoides SC, M. mobile and Mesoplasma florum. Analysis of further genomes will most likely lengthen this list. A genomic DNA fragment of M. bovis encoding the amino-terminal end of a P80 homologue has been sequenced and this homologue is predicted to possess an SPase I cleavage site. In M. hyorhinis, a nearly complete hit locus, encoding P80, P60 and HinT homologues has been found adjacent to a genomic region encoding the high affinity transport system (personal communication of Michael Calcutt, Columbia, MO, USA) . The organization of the hit ABL genes in an operon, as recently demonstrated for M. hominis  and shown here for M. pulmonis, suggests polycistronic expression of the hit loci genes. However, it remains to be elucidated whether the encoded proteins have comparable functions to those already shown in M. hominis. P80 of M. hominis was recently shown to reside in the membrane as a precursor protein and to be secreted into the extra cellular milieu as a 10 kDa smaller antigen. Processing of P80 was suggested to be initiated by SPase I cleavage . While the P80 homologues in M. mobile and M. bovis also contained signal sequences for SPase I cleavage, those in M. mycoides subsp. mycoides SC and Mesoplasma florum were putative pro-lipoproteins. Secretion of lipoproteins has been observed in M. hominis  and other bacteria , indicating that similar function may be still possible.
M. pneumoniae and M. genitalium each had only one gene adjacent to hit L encoding a pore-forming protein with homologies to ABC permeases, suggesting they are part of a distinct phylogenetic branch. Interestingly, in M. penetrans the gene upstream of hit L also encodes a protein of an ABC transporter, an ATPase . The hit locus of U. parvum, which contained a P60 homologue and a gene encoding a permease, may have functions that are a hybrid of those of M. hominis and the M. pneumoniae groups. RT-PCR analyses infer the presence of a mRNA encoding HinT and UU271, a P60-homologue, and a membrane protein of unknown function. Thus, the interaction of HinT with membrane proteins seems to be a common phenomenon in Mollicutes.
A quite different situation was detected in the Chlamydiaceae. Although we were not able to establish definitely the presence of a polycistronic mRNA derived from the three genes comprising hit locus, the overlap of the hit L gene with the upstream gene, as well as the conserved order of the three genes within the hit loci of Chlamydiaceae, suggested a relationship between the gene products. Analysis of Cp265, Cp266 (HinT) and Cp267 in the yeast two-hybrid system and immune co-precipitation assays confirmed our hypothesis that these proteins interacted and demonstrated that they form homo-dimers. Cp267, a protein with large areas of ARM repeats, which are known to mediate protein-protein interactions , was shown to interact with HinT, a protein known in eukaryotes to influence transcriptional activation, as well as with Cp265, a putative metal-dependent hydrolase with a binding fold for short, single stranded nucleic acids. These findings suggest that in Chlamydiaceae, the function of HinT may be more closely related to intracellular processes than to interactions with the extracellular milieu, as suggested by the findings on Mollicutes.
The data presented here demonstrate that HinT proteins of the Chlamydiaceae associate with probable cytosolic proteins likely to function in the regulation of cellular processes, such as nucleotide metabolism. This function would be similar to that of homologues in eukaryotes, where HinT has been shown to influence transcription. The finding that HinT proteins of the Mollicutes interact both physically and genetically with membrane proteins may reflect a phylogenic shift towards a different function in this group, or may indicate an additional function of bacterial HinT proteins. Our future work will focus on decoding the intra- and extra-cellular processes that bacterial HinT proteins are involved in.
All routine DNA manipulation techniques, including plasmid preparation, restriction endonuclease analysis, ligation and transformation of E. coli were performed as described by Sambrook et al.  or according to the manufacturers' recommendations (Qiagen, Hilden, Germany, and Roche Applied Science, Mannheim, Germany).
Bacterial strains and plasmids
The plasmids pXB (Roche Applied Science, Mannheim, Germany), pGADT7 and pGBKT7 (BD Bioscience Clontech, Palo Alto, USA) were used as expression vectors for the heterologous expression of Cp265, Cp266 and Cp267. The pXB plasmids were propagated in Escherichia coli DH5α F'(Life Technologies), pGADT7 and pGBKT7 in yeast AH109 cells (BD Biosciences Clontech, Palo Alto, CA USA).
Analysis of the DNA and protein sequences and the design of oligonucleotides were facilitated by the Lasergene software (DNA Star Inc., Madison Wisc.).
Organisms used for genome sequence analyses
Chlamydophila caviae GPIC
Chlamydophila pneumoniae AR39
Chlamydia trachomatis D/UW-3/CX
Mesoplasma florum L1
Mycoplasma gallisepticum R
Mycoplasma genitalium G-37
Mycoplasma mobile 163 K
Mycoplasma mycoides spp.mycoides SC str. PG1
Mycoplasma pneumoniae M129
Mycoplasma penetrans HF2
Mycoplasma pulmonis UAB CTIP
Parachlamydia sp. UWE25
Ureaplasma parvum serovar 3 str. ATCC 700970
Computer-based prediction of transcription termination was performed using the GeneBee service (online http://www.genebee.msu.su/services/rna2_reduced.html). Distant relation-ships between HinT protein sequences of the analyzed Mollicutes were determined by using the BLAST method through Molligen 1.4 . Conserved domains of proteins were predicted using the Conserved Domain Database (CDD) or the InterPro service (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, http://www.ebi.ac.uk/interpro/).
RNA was prepared from exponential phase cultures of M. pulmonis and U. parvum as described by Chomczynski and Sacchi . Chlamydophila pneumoniae respiratory isolate GiD was used for all experiments . Chlamydial RNA was prepared from HEp-2 cells 2 days post-infection as described by Mölleken et al. (Mölleken et al., manuscript in preparartion). Before use as a template for RT-PCR, contaminating traces of DNA were digested with DNase I as described previously . Overlapping regions of the Ureaplasma and Chlamydophila genes were amplified using the Expand Template PCR system (Roche Applied Science, Mannheim, Germany) by standard PCR conditions (initial cycle of 5 min at 95°C; 35 cycles of 1 min at 95°C, 1 min at 50°C (U. parvum) or 58°C (C. pneumoniae), 2.5 min at 68°C). The hit operon of M. pulmonis was amplified using the Expand Long Template PCR system by standard PCR conditions (initial cycle of 5 min at 95°C; 10 cycles of 1 min at 95°C, 1 min at 44°C, 4 min at 68°C; addition of 0.5 U polymerase; then 20 cycles of 1 min at 95°C, 30 sec at 44°C, 4 min (+ 20 sec per cycle) at 68 °C). Southern blot analysis was performed as described previously .
Construction of plasmids
Primers used in PCR
For heterologous expression of the protein-C tagged proteins, CP265C, Cp266C and Cp267C, in E. coli, the Cp inserts of the respective pGADT7 plasmids were digested with Sac I, the ends bluntened by incubation with 3 units S1 nuclease (Amersham Bioscience, Freiburg, Germany) for 30 min at 37°C and subsequently cut with Eco RI. The blunt-end/Eco RI digested Cp265, Cp266 and Cp267 fragments were cloned in-frame into the blunt-end/Eco RI digested plasmid pXB and propagated in E. coli Dh5α F'.
All plasmid constructs were confirmed by DNA sequencing (ABI 373 A machine) .
Expression and purification of Cp265C, Cp266C and Cp267C
One liter of LB broth (Gibco BRL, Life Technologies Inc., Gaithersburg, USA) containing ampicillin (100 μg/ml) was inoculated with the respective E. coli DH5α F' clone and incubated for 16 h at 37°C with vigorous shaking. The cells were harvested by centrifugation (15,000 × g, 20 min, 4°C) and frozen at -70°C. After thawing on ice, the cells were resuspended in 40 ml buffer A (120 mM NaCl, 1 mM CaCl2, 20 mM Tris-HCl pH 7.5) and disrupted by three repeated freeze-thaw cycles in liquid nitrogen, followed by three bursts of sonication on ice (5 min bursts at 95 W with a 1 min cooling period between each burst). Insoluble material was sedimented (15,000 × g, 20 min, 4°C) and the supernatant was transferred to an anti-Protein C affinity matrix (Roche Applied Science, Mannheim, Germany). Bound proteins were eluted from the anti-Protein C affinity matrix with 2 mM EDTA.
SDS-PAGE and immunostaining of proteins
Proteins were separated on 12 or 15 % polyacrylamide gels , transferred to nitrocellulose (Schleicher and Schüll, Dassel, Germany) using a semi-dry blotting apparatus (Phase, Mölln, Germany) , and immunostained using anti-Protein C peroxidase (Roche Applied Science, Mannheim, Germany), anti HA-antibody (pGADT7) or anti c-myc antibody (pGBKT7) (BD Bioscience Clontech, Palo Alto, USA).
Immune co-precipitation assay
The [35S]-labeled Cp265, Cp266 and Cp267 proteins were generated from pGADT7 and pGBKT7 fusion vectors by in vitro translation using a T7 coupled transcription/translation system in the presence of [35S]-methionine (Promega, Madison, USA). Two micrograms of purified Protein C-tagged protein were incubated with 10 μl of the [35S]-labeled protein in buffer B (20 mM Tris/HCl (pH 7.5), 75 mM KCl, 0.1 mM EDTA, 2.5 mM MgCl2, 0.05 (v/v) % Igepal, 2 mM DTT, 10 (v/v) % glycerol and 2 mM CaCl2) for 1 h . Thereafter, a 5 μl aliquot of a slurry of the anti-Protein C matrix, equilibrated in buffer B containing 5 μg BSA, was added to each sample and the mixture further incubated for 1 h. The Protein C-matrix was washed eight times in buffer B, resuspended in 20 μl of SDS-PAGE sample buffer and heated at 95°C for 5 min. The proteins were then analyzed by 15 % SDS-PAGE and autoradiography using a phosphorimager (Fujifilm FLA 3000).
Yeast two-hybrid assays
The MATCHMAKER Gal4 two-hybrid system (BD Bioscience Clontech, Palo Alto, USA) was used for interaction assays. AH109 cells were co-transformed with the Cp265, Cp266 or Cp267 expressing pGADT-T7 and pGBKT7 plasmids, grown in small scale cultures and plated onto histidine deficient agar plates, followed by a β-galactosidase colony lift filter assay. All procedures were carried out as outlined in the BD Bioscience Clontech protocol. The β-galactosidase assay was performed after the inoculation of 7.5 ml YPD Medium with 0.5 ml overnight culture in selective medium and incubation for five hours at 30°C until the culture reached an OD600 of 0.4 to 0.6. The cells were harvested by centrifugation at 14,000 × g for 1 min and re-suspended in 300 μl Buffer Z (Na2HPO4+ 7 × H2O, NaH2PO4 + 4 × H2O, KCl, MgSO4 × 7 H2O, pH7.0). Lysis of the cells was achieved with four cycles of freezing in liquid nitrogen and thawing at 37°C. Soluble and insoluble components were separated by centrifugation at 14000 × g for 2 min. The β-galactosidase activity was measured using a FluorAce™ β-galactosidase Reporter Assay kit (BioRad, Hercules, USA).
This work was supported by the Deutsche Forschungsgemeinschaft (DFG-HE 2028/3-2). We thank Michael Calcutt (Columbia, MO, USA) for information about the hit loci in M. bovis and M. hyorhinis, Marzena Wyschkon for excellent technical assistance and Colin MacKenzie for critically reading the manuscript. Katja Mölleken is thanked for preparation of C. pneumoniae RNA and genomic DNA.
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