Characterization of BTBD1 and BTBD2, two similar BTB-domain-containing Kelch-like proteins that interact with Topoisomerase I
- Lixin Xu†1,
- Lihong Yang†1, 2,
- Keiko Hashimoto1,
- Melvin Anderson1,
- Glenda Kohlhagen3,
- Yves Pommier3 and
- Peter D'Arpa1Email author
© Xu et al; licensee BioMed Central Ltd. 2002
Received: 17 October 2001
Accepted: 07 January 2002
Published: 07 January 2002
Two-hybrid screening for proteins that interact with the core domain of human topoisomerase I identified two novel proteins, BTBD1 and BTBD2, which share 80% amino acid identities.
The interactions were confirmed by co-precipitation assays demonstrating the physical interaction of BTBD1 and BTBD2 with 100 kDa topoisomerase I from HeLa cells. Deletion mapping using two-hybrid and GST-pulldown assays demonstrated that less than the C-terminal half of BTBD1 is sufficient for binding topoisomerase I. The topoisomerase I sequences sufficient to bind BTBD2 were mapped to residues 215 to 329. BTBD2 with an epitope tag localized to cytoplasmic bodies. Using truncated versions that direct BTBD2 and TOP1 to the same cellular compartment, either the nucleus or the cytoplasm, co-localization was demonstrated in co-transfected Hela cells. The supercoil relaxation and DNA cleavage activities of topoisomerase I in vitro were affected little or none by co-incubation with BTBD2. Northern analysis revealed only a single sized mRNA for each BTBD1 and BTBD2 in all human tissues tested. Characterization of BTBD2 mRNA revealed a 255 nucleotide 90% GC-rich region predicted to encode the N-terminus. BTBD1 and BTBD2 are widely if not ubiquitously expressed in human tissues, and have two paralogs as well as putative orthologs in C. elegans and D. melanogaster.
BTBD1 and BTBD2 belong to a small family of uncharacterized proteins that appear to be specific to animals. Epitope-tagged BTBD2 localized to cytoplasmic bodies. The characterization of BTBD1 and BTBD2 and their interaction with TOP1 is underway.
DNA topoisomerase I (TOP1) is a ubiquitously expressed protein that relaxes DNA supercoils generated during many transactions of DNA including replication, transcription, repair, and chromatin condensation and remodeling. TOP1 has been shown to interact with many proteins including components of the holo TFIIIC complex , TFIID , p53 , SV-40 large T antigen , nucleolin , the RING finger protein topors , the RNA splicing factors PSF/p54nrb and SF2/ASF , the cell cycle regulatory protein ARF , RNA pol II complex [10, 11], and HTLV type 1 tax oncoprotein . TOP1 also interacts with a variety of unidentified proteins involved in its phosphorylation, ubiquitination and sumoylation [13–17].
We used the core domain of TOP1 lacking the N-terminal highly charged region, the coiled-coil linker domain and the C-terminal active site domain as bait in two hybrid screens for TOP1 interacting proteins. We obtained multiple independent cDNA clones coding for BTBD1 and BTBD2, two uncharacterized, BTB domain-containing, kelch-like proteins. The interactions of HeLa cell TOP1 with the BTBD proteins was confirmed using GST-pulldown and was further suggested by their intracellular co-localization.
Identification of TOP1-interacting proteins using two-hybrid assays
The core domain of human TOP1 from residue 198 to 651 was used as the bait in two-hybrid screens [18–20]. This region of TOP1 lacks the N-terminal ~25% of the protein that is highly charged and the C-terminal domain containing the active site and the coiled-coil linker. The resulting polypeptide comprises 60% of the TOP1 sequence. A screen of a HeLa cell library yielded 56 colonies that tested positive in the two hybrid assays (growth on plates lacking histidine or uracil, lack of growth on plates containing 5-fluoroorotic acid; and induction of lacZ resulting in blue color when assayed with X-gal). Nucleotide sequence analysis of 34 of these clones revealed two cDNA contigs of 15 and 19 that predict proteins whose sequences are 80% identical. The proteins were named BTBD1 and BTBD2 according to a recent analysis of their genomic sequences . The clones of each contig differed in the amount of 5' sequence present: 11/15 and 15/19 of BTBD1 and BTBD2, respectively, had different 5' ends. In the two-hybrid growth assays and β-galactosidase assays, each of the clones tested as positive as the control for strongly interacting proteins (the interaction of c-Fos with c-Jun, ProQuest, Life Technologies). Another two-hybrid screen using a different two-hybrid system (Matchmaker, Clontech) also yielded 2 clones identical to the contig of 15 clones (BTBD1).
Characterization of BTBD1 and BTBD2 mRNA
The longest BTBD1 cDNA clone obtained from two-hybrid screening (3196 bp) contains an ORF that encodes a 482 aa protein starting with an ATG that is preceded by an in-frame stop codon. Sequences in GenBank confirmed our sequence. One was obtained by the oligo-capping method (FLJ20724), and another assembled from partial cDNA and RACE fragments .
Northern blotting and in silico expression analysis
BTBD1 and BTBD2 cDNA were found in libraries from the following tissues: amniotic, aorta, bone, brain, bone marrow, colon, ear, embryo, foreskin, gall bladder, germ, heart, kidney, lung, muscle, ovary, pancreas, parathyroid, placenta, skin, spleen, stomach, testis, thymus, tonsil and uterus (LocusID 53339 and 55643, respectively ). BTBD1 and BTBD2 was also expressed in a large number of tumor types and normal tissues present in SAGE (serial analysis of gene expression) libraries (SAGEmap, ).
Mapping of the regions of TOP1 and the BTBDs that interact
Two-hybrid analysis was also used to map regions of the TOP1 core domain that interact with BTBD2. The region upstream of aa 215 and downstream of aa 329 were not required for binding BTBD2 (Fig. 3C). The fragment of TOP1 from amino acid 215 to 331 was capable of binding to BTBD2. This region includes 18 aa of core subdomain I, all of core subdomain II and 10 amino acids of the second section of core subdomain I.
GST-pulldown assays confirm two-hybrid deletion mapping
Effect of GST-BTBD2 on TOP1 activity
Cellular localization of BTBD2 and co-localization with TOP1
The localization of full length BTBD2 to cytoplasmic bodies was surprising because the cytoplasm is separated from the nucleus where endogenous TOP1 resides and transfected GFP-TOP1 localizes [26–30]. Because TOP1 and BTBD2 are not predominantly found in the same compartments, they may interact transiently, or they may interact only under specific conditions when they may be in the same compartment. We therefore analyzed mitotic cells, but did not observe co-localization of TOP1 and the BTBDs (not shown). We then tested for co-localization in transfected cells. Though the truncated m-BTBD2T localized to distinct nuclear bodies, its co-localization with endogenous TOP1 could not be determined against the background of endogenous TOP1 diffuse nuclear staining. However, in cells co-transfected with GFP-TOP1 and m-BTBD2T, the m-BTBD2T staining was nuclear diffuse as well as in nuclear bodies, indicating that m-BTBD2T interacts with GFP-TOP1, which localizes throughout the nucleus (not shown).
To determine if TOP1 co-localizes with BTBD2 in the cytoplasm, GFP-TOP1 lacking an NLS  was co-transfected with full length BTBD2 (m-BTBD2F) or truncated BTBD2 (m-BTBD2T). GFP-TOP1 lacking a NLS (GFP-pTI-6) localizes diffusely within the cytoplasm (Fig. 6A and ). In cells transfected with both GFP-pTI-6 and full length m-BTBD2F, the diffuse cytoplasmic GFP-pTI-6 significantly decreased, and GFP-pTI-6 co-localized with m-BTBD2F to cytoplasmic bodies (Fig. 6D). In cells transfected with GFP-pTI-6 and truncated m-BTBD2T, truncated m-BTBD2T was not in nuclear bodies as when transfected alone, rather it co-localized with GFP-pTI-6 to cytoplasmic bodies (Fig. 6E). Thus, when co-transfected with GFP-TOP1 lacking a NLS, both full length and the N-terminal deleted BTBD2 co-localized with TOP1 to cytoplasmic bodies.
Two-hybrid screens have identified BTBD1 and BTBD2 as proteins that interact with the core domain of TOP1. BTBD1 and BTBD2 were isolated as 15 and 19 independent clones, respectively, and in two-hybrid assays they interacted as strongly as the control for strongly interacting proteins (c-Fos with c-Jun). BTBD1 and BTBD2 also bound HeLa cell TOP1 (100 kDa) in nuclear extracts by GST-pulldown assays. N-terminal truncation studies showed the C-terminal 37% to 45% of the BTBD proteins are sufficient for binding TOP1. C-terminal deletions of either protein eliminated binding to TOP1 (C-terminal truncation of 112 aa of BTBD1 or 33 aa of BTBD2 in the two-hybrid assay; or a C-terminal truncation of 40 aa of BTBD2 in GST-pulldown). Truncation of the BTB domains demonstrated that they were not required for interaction with TOP1. The region of TOP1 sufficient for binding BTBD2 was narrowed to residues 215 – 329 in the "cap" region (core subdomain II) . Catalytic activities of TOP1 were affected slightly or not at all by co-incubation with GST-BTBD2 suggesting that the interaction does not regulate enzyme activity directly.
We cloned the full length BTBD1 cDNA from a HeLa cell library. This sequence is 3196 bp, and the start codon is preceded by a stop codon 6 nucleotides upstream (GenBank, FLJ20724). Our sequence is comparable to two others in GenBank, one of which was obtained by the oligo-capping method suggesting that it begins at the 5' cap [21, 32].
Our repeated attempts to clone the 5' end of the BTBD2 by library screening and the RACE method were unsuccessful. We tested sequences directly upstream of the longest cDNA in the BTBD2 gene for their presence on the mRNA. RT-PCR and sequencing of the RT-PCR product demonstrated that this 255 nucleotide, 89% GC-rich sequence is present on the BTBD2 mRNA and that it shares predicted polypeptide sequence with BTBD homologues and orthologs.
The BTBD proteins contain an amino terminal BTB/POZ domain as well as a C-terminal region that is related to proteins that contain the kelch domain. Neither of these regions yields unequivocal information for functional classification. The BTB domain is a highly conserved 120 amino acid, hydrophobic-rich, protein-protein interaction domain that mediates homodimerization and heterodimerization of a large number of proteins with diverse functions . The three dimensional structure of one BTB domain  has been characterized through structure-function studies . Proteins containing BTB domains are currently categorized into three groups : 1) DNA-binding proteins often containing zinc fingers in the C-terminal region, 2) actin binding proteins that contain a kelch repeat of ~50 residues that terminate in a pair of glycine residues  and 3) proteins that have neither an actin-binding domain nor a DNA-binding domain. The BTBD proteins belong to the last category, although they are distantly related to kelch proteins (~25% identical over ~250 aa), they lack the residues that are characteristic of kelch repeats, a double glycine sequence and a tyrosine separated from a tryptophan by precisely 6 residues [35, 37].
BTBD1 and BTBD2 are closely related sharing 80% identical amino acid sequence. They are one of eleven genes in 19p13.3 → p12 with close homology to genes in 15q24 → q26 that have apparently resulted from duplications of a common ancestral gene . Both BTBD1 and BTBD2 are widely if not ubiquitously expressed in human tissues. The predicted promoter regions are highly GC-rich and lack canonical TATA boxes, suggesting that they may be housekeeping genes [39, 40].
Close mammalian relatives of BTBD1 and BTBD2 include the mouse orthologs that are 98% and 95% identical respectively, as well as highly similar rat and bovine partial sequences . Sequence relatives in lower organisms include a C. elegans sequence with 58% identities with BTBD2 (429 residues; 2% gaps, F38H4.7), and a D. melanogaster sequence with 46% identities (437 residues, 3% gaps, CG5319). The human genome encodes two proteins with 46% (436 residues, 3% gaps, CAC22147) and 45% (497 residues, 5% gaps, AF353674) identities compared with BTBD2. These proteins comprise a small family whose members have not been functionally characterized and are evidently specific to animals because putative orthologs are not present in available fungi and plant sequence databases.
We have demonstrated an interaction between BTBD2 and TOP1 by two-hybrid, GST-pull down and intracellular co-localization analyses. Studies are underway to functionally characterize BTBD1 and BTBD2 and understand their interaction with TOP1.
• Fifteen and nineteen independent cDNA clones of BTBD1 and BTBD2, respectively, were isolated from two-hybrid screens and found to interact as strongly as c-Fos interacted with c-Jun in the two-hybrid assays.
• The interactions of TOP 1 with BTBD1 and BTBD2 were confirmed by deletion mapping using two-hybrid and GST-pulldown assays.
• Less than the C-terminal half of each BTBD protein lacking the BTB domain is sufficient for binding to TOP1. TOP1 from aa 215 to 329 interacted with BTBD2.
• GFP-BTBD2 localized to cytoplasmic bodies.
• BTBD2 had little effect on the supercoil relaxation or DNA cleavage activity of TOP1 in vitro.
• Co-transfected BTBD2 and TOP1 co-localized.
• The BTBD2 message contains 255 nucleotides that are 89% GC-rich and are predicted to encode the N-terminus of a 525 amino acid protein.
• BTBD1 and BTBD2 mRNA were detected in all human tissues tested. BTBD1 mRNA was highly expressed in testes, heart and skeletal muscle. BTBD2 was more highly expressed in skeletal muscle. Only a single mRNA species was present for each BTBD1 and BTBD2.
• Putative orthologs of BTBD1 and BTBD2 are found in C. elegans (58% identities, 429 residues; 2% gaps, F38H4.7) and D. melanogaster (46% identities, 437 residues, 3% gaps, CG5319).
• Two paralogs of BTBD1 and BTBD2 are present in the human genome (CAC22147 and AF353674).
Materials and Methods
To construct the bait expression plasmid (pGBD-cTOP1), the core domain of TOP1 (cTOP1, amino acids 198–651) was amplified by PCR (sense primer: 5'-CGGAATTCGAAGAGGAACAGAAGTGGAAATGG-3'; antisense primer: 5'-CGGGATCCTTAAATCTTAGTTTGCAAGTTCATCAT-3') and inserted into the vector pGBD (Clontech) cut with EcoRI and BamHI. To construct the cTOP1 expression vector (pDBleu-TOP1c), cTOP1 was excised from pGBD-cTOP1 with EcoRI and BamHI and inserted into the same sites in pDBleu (ProQuest, Life Technologies).
To construct the GST-fusion protein expression vectors, the BTBD inserts from the prey vector pPC86 were amplified using primers complementary to the BTBD coding regions with additional Sma I and EcoR I restriction sites for insertion into these sites in pGEX-2TK (Pharmacia). These primer sequences can be found below under the Two Hybrid Screens section. All constructs were confirmed by sequencing using pGEX sequencing primers (Pharmacia Cat# 27-1410-01 and 27-1411-01).
To construct the expression plasmid encoding C-terminal-myc-tagged, full length BTBD2 (m-BTBD2F), the entire coding region of BTBD2 (1–1575 bp) was amplified with primers (Upper primer: 5' ATGGCGGCGGGTGGGAGCGGCGGGCGTGCGTCGTG-3', Lower primer: 5'-GGTGTAGAAGATGACCTCGGGGATCTGGCCGTCCTCCAC-3') containing BamH I and Hind III cleavage sites and inserted into pCMV-Tag 5 vector (Stratagene) cut with BamH I and Hind III. To construct the expression plasmid encoding C-terminal-myc-tagged truncated BTBD2 having the N-terminal half the BTB domain deleted (m-BTBD2T), the coding region of BTBD2 from the second ATG to almost the end of the 3'-UTR (445–2542 bp) was amplified with primers (Upper primer: 5'-ATGTTCAACGGGGGAATGGCCACAACATC-3', Lower primer: 5'-GGGGAGGACGCAGGTTCCAGGAGT-3') containing BamH I and Hind III cleavage sites and inserted into pCMV-Tag 3 vector (Stratagene) cut with BamH I and Hind III.
Two hybrid screens
pGBD-cTOP1 was co-transfected with the HeLa cell library (Clontech, Cat. no. HL4000AA) into strain PJ69-4A (MAT a, trp 1-190 leu2-3, 112 ura3-52 his3-200 gal4 gal80 LYS2::GAL1-HIS3 GAL2-ADE2 met2::GAL7-lacZ). Strong expression of full length GALDB-TOP1 in PJ69-4A was verified by Western blotting with antibodies to both TOP1 and GALDB (not shown). Additionally, the ProQuest two-hybrid system was used because the low copy CEN plasmids may decrease the probability of obtaining weakly interacting false positives that could result from high concentrations of the two-hybrid proteins. In the ProQuest screens, pDBleu-TOP1c was co-transfected with a HeLa cell cDNA library (Life Technologies Cat. No. 11287-018) according the manufacturer protocols. Clones that tested positive in the two-hybrid assays were sequenced across the GAL4AD-prey junction into the coding regions of the prey inserts. Sequences were grouped into cDNA contigs using the SeqMan II program of DNASTAR (LASERGENE).
C-terminal deletions for mapping the interactions using two-hybrid assays were constructed using the exonuclease III/mung bean nuclease method (C-terminal deletions, Exonuclease III/Mung Bean Nuclease Deletion kit, Cat#460, NEW ENGLAND BioLabs company). N-terminal deletions, in addition to the series obtained through two-hybrid screening, were constructed by amplifying the two-hybrid cDNA clones using primers containing Sma I and EcoR I at the N- and C-terminus, respectively, and inserting them into both pPC86 and pGEX-2TK vectors. The sense primer sequences are as follows: BTBD1: U1 (395-482aa) 5'-GACCCCGGGGAATGATACCGGCTTTAGTTGTGA-3', U2 (342-482aa) 5'-GACCCCGGGCTGGGGTTACAGTGGGACGAGT-3', U3 (213-482aa) 5'-GACCCCGGGAAGTGCAGAAGGGTTTACT-3', U4 (303-482aa) 5'-GACCCCGGGAAACCTCTTTCTTCATTTTACTGT-3', The same antisense primer was used for all amplifications: 5'-CGGAATTCTTTGTGGCCATTTATGTTTTTGAC-3'. The sense primers for amplification of truncated BTBD2 fragments were: U1 (504-525aa) 5'-GACCCCGGGCTACGCGGCCGGGAACAACAATG-3', U2 (460-525aa) 5'-GACCCCGGGGGTGCTGCCCAACGTCAACTACAC-3', U3 (404-525aa) 5'-GACCCCGGGCGTGGTGGGATTTGGGCTGTATGG-3', U4 (289-525aa) 5'-GACCCCGGGCCGCTGGTCCGAGGCCGAGTGTC-3'. The same antisense primer was used for all amplifications: 5'-CGGAATTCAACCCCGTCCTGATGCTGAGAAAG-3'
Multiple tissue Northern blots containing 2 μg poly (A) + RNA (Human Multiple Tissue Northern Blot IV and Human Multiple Tissue Northern Blot; Catalog numbers: 7766-1 and 7760-1; CLONTECH) were hybridized with 32P-labeled human cDNA probes for TOP1(nucleotides 212–1661, GenBank accession number J03250), BTBD1 (nucleotides 84–3196, GenBank accession number AF355402) or BTBD2 (nucleotides 1229–2668, GenBank accession number AF355797) in Rapid-hyb buffers (Amersham Life Science, RPN1635). Hybridization and washing was carried out according to the manufacturer instructions.
Isolation of the BTBD2 coding region
The longest BTBD2 cDNA obtained from two-hybrid screening (2413 bp) contained an ORF starting at the 5' end. To obtain the full coding region, four independent cDNA libraries were screened using a nested PCR strategy with upper primers complementary to the vectors and two nested lower primers complementary to BTBD2 (5'-TCGTCCGAGTAGAGAAAC-3' and 5'-TCCACGTCGGGCAGCTCAATCTCC-3'). 5'-RACE (Life Technologies) was also used to try to identify longer clones using several different lower primers. Reverse transcription was also performed at 70°C using the thermophilic Tth polymerase with magnesium as the cofactor to enable it to use mRNA as a template. None of these strategies was successful.
To determine whether the mRNA contained the BTBD2 gene sequences directly upstream of the longest cDNA clone, RT-PCR was used with a sense primer complementary to the predicted start codon. The primers for reverse transcription were complementary to exon 2 (LO and LI, see below). PolyA+ RNA was reverse transcribed using Tth polymerase (Promega) at 70°C for 20 min. The resulting products were amplified using nested PCR with the Advantage-GC 2 PCR kit (CLONTECH, Cat# K-1913-Y) and two 30 cycle rounds with each cycle having two steps (denaturation 94°C, 30 sec.; annealing and extension 68°C, 3 min; UO: 5'-ATGGCGGCGGGTGGGAGCGGCGGGCGTGCGTCGTG-3'; UI: 5'-CGGGCCCCGGGACAGACG-3'; LO: 5'-CGGGCAGCTCAATCTCCGTGGATG-3'; LI: 5'-TTGTGGCCATTCCCCCGTTGAACA-3'). To amplify the 306 bp fragment, two rounds of PCR were used: the first round used the LO and UO primers, and the second round used the LO and UI. To amplify the 460 bp fragment, two rounds of PCR were also used, the LO and UO in the first round, and the LI and the UO in the second round.
GST Pull Down Assay
E. coli containing plasmids encoding GST-BTBD1 or GST-BTBD2 were grown to an O.D. of 0.3 at 25°C, and 2% EtOH was added just prior to induction with 0.1 mM IPTG for 8 hrs. E. coli extracts were prepared using a French Pressure Cell Press (American Instrument Company, Silver Spring, MD). For the GST-pull-down assay 5 μg of GST or the GST-fusion proteins were mixed with 150 μl HeLa cell nuclear extracts (5 × 106 cells/ml) and incubated for 2 hr at 4°C (0.25 M NaCl). The bead pellets were then washed 3 times with ice cold PBS before solubilization in SDS-PAGE sample buffer.
Supercoil relaxation assay
HeLa nuclear extract (5 ng) in reaction buffer (100 mM Tris.HCl, pH 7.5, 50 mM KCl, 5 mM MgCl2, 0.1 mM EDTA, 15 μg/ml BSA) was incubated with 5 μg of purified GST or GST-BTBD2 on ice for 15 min before the addition of 0.25 μg plasmid and incubation at 30°C for 0–24 min. Reactions were stopped by adding SDS (1% final) and proteinase K (0.5 mg/reaction).
DNA cleavage assays
Purified TOP1 was pre-incubated with GST or GST-BTBD2 for 20 min before addition of the DNA substrate, which was either an end-labeled 36 bp fragment containing a single strong TOP1 cleavage site , or a 161 bp PvuII-HindIII fragment of pBluescript (Stratagene) ). End labeling of the DNA substrates was as previously described [24, 25]. Cleavage reactions were continued for 20 min before stopping with 0.5% SDS.
Broad-Complex, Tramtrack and Bric-a-brac
nuclear localization signal
open reading frame
reverse transcription – polymerase chain reaction
DNA topoisomerase I.
We thank Dr's Yin-Yuan Mo and Bill Beck for providing the GFP-TOP1 expression plasmids and Dr. Todd Martensen for critical comments on the manuscript.
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