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PubMed1997

Role of the X2 box in activated transcription from the DRA promoter in B cells.

We investigated the function of the evolutionary conserved X2 box in the promoter of the HLA-DRA gene from the human major histocompatibility complex (MHC) in resting and activated B cells. NF-X2, which contains members of the AP-1/ATF/CREB families of transcription factors, interacts with the X2 box (5'-TGCGTCA-3') from positions -97 to -91 in the DRA promoter. In resting Raji cells, little to no binding to the X2 box was observed. In sharp contrast, in B cells treated with the phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA), strong interactions between the X2 box and NF-X2 containing c-Fos were observed. As determined by transient expression and RNA analyses, the activation of protein kinase C (PKC) also increased rates of transcription from the wild-type DRA promoter but not from a DRA promoter bearing clustered point mutations in the X2 box. Since the co-expression with a dominant negative c-Fos abolished the responsiveness to TPA, we conclude that activated transcription of the DRA gene depends on interactions between the X2 box and NF-X2, which contains c-Fos.

Animals↗

PubMed2005

Nutritional regulation of ANR1 and other root-expressed MADS-box genes in Arabidopsis thaliana.

The ANR1 MADS-box gene in Arabidopsis thaliana (L.) Heynh. has previously been identified as a key regulator of lateral root growth in response to signals from external nitrate (NO3(-)). We have used quantitative real-time PCR to investigate the responsiveness of ANR1 and 11 other root-expressed MADS-box genes to fluctuations in the supply of N, P and S. ANR1 expression in roots of hydroponically grown Arabidopsis plants was specifically regulated by changes in the N supply, being induced by N deprivation and rapidly repressed by N re-supply. This pattern of N responsiveness differs from the NO3(-)-inducibility of ANR1 previously observed in Arabidopsis root cultures [H.M. Zhang and B.G. Forde (1998) Science 279:407-409]. Seven of the other MADS-box genes responded to N in a manner similar to ANR1, but less strongly, while four (AGL12, AGL17, AGL18 and AGL79) were unaffected. Six of the N-regulated genes (ANR1, AGL14, AGL16, AGL19, SOC1 and AGL21) belong to just two clades within the type II MADS-box lineage, while the other two (AGL26 and AGL56) belong to the poorly characterized type I lineage. Only SOC1 was additionally found to respond to changes in the P and S supply, suggesting a possible role in a general response to nutrient stress. Studies with an ANR1 transposon-insertion mutant provided no evidence for regulatory interactions between ANR1 and the other root-expressed MADS-box genes. The implications of the current data for our understanding of the role of ANR1 and other MADS box genes in the nutritional regulation of lateral root growth are discussed.

Anion Transport Proteins↗

PubMed2006

CENP-B box and pJalpha sequence distribution in human alpha satellite higher-order repeats (HOR).

Using our Key String Algorithm (KSA) to analyze Build 35.1 assembly we determined consensus alpha satellite higher-order repeats (HOR) and consensus distributions of CENP-B box and pJalpha motif in human chromosomes 1, 4, 5, 7, 8, 10, 11, 17, 19, and X. We determined new suprachromosomal family (SF) assignments: SF5 for 13mer (2211 bp), SF5 for 13mer (2214 bp), SF2 for 11mer (1869 bp), SF1 for 18mer (3058 bp), SF3 for 12mer (2047 bp), SF3 for 14mer (2379 bp), and SF5 for 17mer (2896 bp) in chromosomes 4, 5, 8, 10, 11, 17, and 19, respectively. In chromosome 5 we identified SF5 13mer without any CENP-B box and pJalpha motif, highly homologous (96%) to 13mer in chromosome 19. Additionally, in chromosome 19 we identified new SF5 17mer with one CENP-B box and pJalpha motif, aligned to 13mer by deleting four monomers. In chromosome 11 we identified SF3 12mer, homologous to 12mer in chromosome X. In chromosome 10 we identified new SF1 18mer with eight CENP-B boxes in every other monomer (except one). In chromosome 4 we identified new SF5 13mer with CENP-B box in three consecutive monomers. We found four exceptions to the rule that CENP-B box belongs to type B and pJalpha motif to type A monomers.

Algorithms↗

PubMedDate not supplied

Box-Cox transformation for QTL mapping.

The maximum likelihood method of QTL mapping assumes that the phenotypic values of a quantitative trait follow a normal distribution. If the assumption is violated, some forms of transformation should be taken to make the assumption approximately true. The Box-Cox transformation is a general transformation method which can be applied to many different types of data. The flexibility of the Box-Cox transformation is due to a variable, called transformation factor, appearing in the Box-Cox formula. We developed a maximum likelihood method that treats the transformation factor as an unknown parameter, which is estimated from the data simultaneously along with the QTL parameters. The method makes an objective choice of data transformation and thus can be applied to QTL analysis for many different types of data. Simulation studies show that (1) Box-Cox transformation can substantially increase the power of QTL detection; (2) Box-Cox transformation can replace some specialized transformation methods that are commonly used in QTL mapping; and (3) applying the Box-Cox transformation to data already normally distributed does not harm the result.

Chromosome Mapping↗

PubMed1985

Expression of homologous homeo-box-containing genes in differentiated human teratocarcinoma cells and mouse embryos.

Human chromosome 17 contains a cluster of at least three distinct homeo box regions, Hu1, Hu2, and Hu5, within a 20 kb stretch of DNA. A mouse homeo box region, Mu1, which maps to chromosome 11, was isolated and found to contain extensive nucleotide homology with a 4 kb region encompassing the Hu1 homeo box. The conservation of these chromosomal regions between man and mouse was confirmed by nucleotide sequence analysis: approximately 380 bp of DNA are more than 90% homologous and the 61 amino acids of the homeo box domain are perfectly conserved. We found that a human teratocarcinoma cell line expresses high levels of Hu1 homeo-box-containing mRNA only after differentiation of the cells following treatment with retinoic acid. In contrast, mouse teratocarcinoma cells did not express Mu1 homeo-box-containing mRNA at any stage of differentiation, whereas the expression of such transcripts was detected in mouse embryos from 10 to 17 days of gestation.

Amino Acid Sequence↗

PubMed1985

Clustered homeo boxes are differentially expressed during murine development.

A murine homeo box (m6-12) known to be expressed during differentiation of embryonal carcinoma cells lies within a cluster of homeo boxes located in 30 kilobase pairs of genomic DNA. We have established the organization of the boxes within this complex, as well as the nucleotide sequence of a second box, m5-4. Similar to the m6-12 box, expression of novel m5-4 transcripts is induced upon differentiation of embryonal carcinoma cells. Transcripts of genes containing m6-12 were found in embryonic tissue during almost all stages of prenatal development studied, whereas expression of m5-4 was detected only in 12 day embryonic tissue. Finally, we have described the differential expression of these homeo-box-containing regions in various adult tissues.

Amino Acid Sequence↗

PubMed1989

Replication properties of mini-Rts1 derivatives deleted for DnaA boxes in the replication origin.

Mini-Rts1 was found to be unable to replicate in a dnaA-null mutant. However, a mini-Rts1 derivative lacking entire tandem DnaA boxes in the replication origin retained the replication ability in a dnaA+ host although its copy number was about half that of the mini-Rts1 having complete DnaA boxes. Mini-Rts1cop1 that contains a high copy number mutation in repA was found to replicate more efficiently than mini-Rts1 of wild repA when DnaA boxes were deleted. In addition, the copy number of mini-Rts1cop1 without DnaA boxes increased 1.5-fold upon removal of incI iterons, whereas that of mini-Rts1 without DnaA boxes did not increase after the iterons were deleted. These indicate that the RepAcop1 protein can initiate the replication of mini-Rts1 efficiently even when DnaA boxes are absent from the origin of replication.

Bacterial Proteins↗

PubMed1991

Importance of the CArG box in regulation of beta-actin-encoding genes.

The beta-actin-encoding gene (Act) in carp is regulated by several cis-acting regulatory elements including the evolutionarily conserved CC(A/T)6GG (CArG box or serum-response element) sequences positioned in the promoter region between the CAAT and TATA boxes and in the first intron. To address the roles of the two CArG boxes on gene expression, we replaced them with linker sequences. The CArG box in the proximal promoter was not required for promoter activity in tissue-cultured cells, but was required in conjunction with a second CArG box in the first intron to give full expression in transgenic embryos. Likewise, the geometry of cis-acting transcriptional elements in the proximal promoter was more important for expression of transgenic constructs in developing embryos than in tissue-cultured fibroblasts. Mobility-shift and exonuclease mapping experiments indicated that the same or similar protein factors bind around the two CArG boxes, suggesting that interactions between the promoter and the first intron are involved in Act regulation.

Actins↗

PubMed1992

A protein binding to CArG box motifs and to single-stranded DNA functions as a transcriptional repressor.

A CArG box motif [CC(A+T-rich)6GG] is one of the DNA elements required for muscle-specific gene transcription. Nuclear factors in mouse C2 myogenic cells strongly bind to the CArG box in the first intron of the gene (Sm alpha-A) encoding human smooth muscle alpha-actin. To clone cDNAs of the CArG box-binding factor (CBF), lambda gt11 cDNA expression libraries from C2 cells were screened for in situ DNA binding specific for this CArG box sequence. The 1.6-kb cDNA (CBF-A) encoding 285 amino acids (aa) was obtained, and a beta-galactosidase fusion protein, bacterially produced from the cDNA, bound to DNA fragments containing several CArG boxes. When the expression level of CBF-A in C2 cells increased by transfection of CBF-A expression plasmids, Sm alpha-A transcription was repressed. The deduced aa sequence of CBF-A is similar to some single-stranded (ss) nucleic acid-binding proteins. The fusion protein could bind to ssDNA, whereas CBF in C2 cell nuclear extracts could not. From these results, CBF-A is a novel CArG box-, ssDNA- and RNA-binding protein, as well as a repressive transcriptional factor.

Actins↗

PubMed1994

The mouse creatine kinase paired E-box element confers muscle-specific expression to a heterologous promoter.

E-box elements, with the CANNTG sequence motif, occur in numerous promoters and enhancers. We evaluated the tissue-specific expression properties of the paired murine E-box element from the mouse muscle creatine kinase (MCK) enhancer in a minimal heterologous promoter construct. A 46-bp fragment containing the paired E-box element in its wild-type (wt) configuration conferred high levels of muscle-specific expression in transfected embryonic chicken cell cultures. The expression from this paired E-box element was similar to that of the simian virus 40 (SV40) promoter/enhancer, but a 21-bp fragment containing a single E-box was inactive. We conclude that the paired E-box element from the MCK enhancer is sufficient for high levels of muscle-specific expression when placed upstream from a non-muscle TATA element.

Actins↗

PubMed1987

Sequence analysis of the murine Hox-2.2, -2.3, and -2.4 homeo boxes: evolutionary and structural comparisons.

We have determined the nucleotide sequences and deduced the amino acid sequences of three tandemly arranged murine boxes of the Hox-2 homeo box gene complex on mouse chromosome 11 (Hox-2.2, -2.3, and -2.4). The type and position of differences with other sequenced homeo boxes were analyzed. Hox-2.2 is nearly identical with its cognate human homeo box Hu-2. Hox-2.3 shares 59 of 61 amino acids with the Antennapedia homeo domain of Drosophila and the MM-3 homeo domain of Xenopus and shows 60 of 61 amino acid identity with human HuC1. Hox-2.3, MM-3, and HuC1 also share a stretch of six glutamic acid residues followed by a stop codon 15-20 amino acids 3' of the homeo domain. Hox-2.4 is relatively divergent from most of the other homeo boxes sequenced to date; however, it matches the Hox-3.1 murine homeo domain at 60 of 61 positions. Sequence comparisons with other murine homeo domains, together with previous studies of their genomic organization and chromosomal location, provide support for the hypothesis of a large-scale duplication resulting in the two major murine homeo box gene complexes Hox-1 and Hox-2.

Amino Acid Sequence↗

PubMed2004

A W-box is required for full expression of the SA-responsive gene SFR2.

Transcripts of SFR2, a member of the S family of receptor kinase genes, accumulate rapidly in Brassica oleracea leaves in response to wounding, bacterial infection and following treatment with salicylic acid (SA). Expression of a chimeric gene consisting of the SFR2 5' flanking sequence fused to the gusA reporter gene is also induced in wounded and SA-treated Arabidopsis plants indicating that the observed response is conferred by the SFR2 promoter. We show here that, in Arabidopsis plants carrying the salicylate hydroxylase (NahG) transgene, wound induction of the SFR2 promoter-gusA reporter fusion was abolished, indicating that, as has previously been shown for the response to bacterial infection, SA is required for the response to wounding. Deletion analysis of the SFR2 promoter identified a region necessary for full expression following SA treatment. This region, which includes two putative W-boxes, is conserved in the promoter of the Arabidopsis SFR2 homologue, ARK3. Deletion of a 12 bp region containing the two W-box motifs reduced the response to SA treatment. Tandem repeats of the W-box-containing element fused upstream of a CaMV 35S minimal promoter enhanced reporter gene expression in transgenic Arabidopsis both in the absence and presence of SA. Gel-mobility shift assays showed that Arabidopsis leaf extracts contained factors that bound to a fragment of the promoter spanning the putative W-boxes and that a fragment in which these motifs were mutated was unable to compete for binding. In summary, induction of the SFR2 promoter in response to bacterial infection and wounding requires SA, and full expression of the induced gene requires the presence of a functional element containing W-box motifs in the SFR2 promoter. The involvement of two W-boxes indicates that transcription factors of the WRKY family may play a key role in mediating these responses.

Arabidopsis↗

PubMed2006

The evolution of High Mobility Group Box (HMGB) chromatin proteins in multicellular animals.

Mammalian HMGB proteins are abundant chromatin components, and are characterized by the presence of 2 HMG-box domains and an acidic tail. HMG boxes are present in a large number of DNA-binding proteins, and HMGB chromatin proteins represent a small and specific subset of HMG-box proteins. The comparison of DNA sequences that code for HMG-box proteins suggests that the ancestral HMG box was coded by an intronless gene, which picked up one or more introns during its radiation. Canonical HMGB proteins are only present in multicellular animals, from sponges onwards, and appear to have arisen through the fusion of two different genes, each coding for one of the boxes. The organization of HMGB genes was very conserved during Metazoan evolution, with the only deviations appearing in Caenorhabditis and Dipteran (Drosophila and Anopheles) species.

Amino Acid Sequence↗

PubMed2004

Different expression strategy: multiple intronic gene clusters of box H/ACA snoRNA in Drosophila melanogaster.

The high degree of rRNA pseudouridylation in Drosophila melanogaster provides a good model for studying the genomic organization, structural and functional diversity of box H/ACA small nucleolar RNAs (snoRNAs). Accounting for both conserved sequence motifs and secondary structures, we have developed a computer-assisted method for box H/ACA snoRNA searching. Ten snoRNA clusters containing 42 box H/ACA snoRNAs were identified from D.melanogaster. Strikingly, they are located in the introns of eight protein-coding genes. In contrast to the mode of one snoRNA per intron so far observed in all animals, our results demonstrate for the first time a novel polycistronic organization that implies a different expression strategy for a box H/ACA snoRNA gene when compared to box C/D snoRNAs in D.melanogaster. Mutiple isoforms of the box H/ACA snoRNAs, from which most clusters are made up, were observed in D.melanogaster. The degree of sequence similarity between the isoforms varies from 99% to 70%, implying duplication events in different periods and a trend of enlarging the intronic snoRNA clusters. The variation in the functional elements of the isoforms could lead to partial alternation of snoRNA's function in loss or gain of rRNA complementary sequences and probably contributes to the great diversity of rRNA pseudouridylation in D.melanogaster.

Animals↗

PubMed2006

Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling.

Archaeal dual-guide box C/D small nucleolar RNA-like RNAs (sRNAs) bind three core proteins in sequential order at both terminal box C/D and internal C'/D' motifs to assemble two ribonuclear protein (RNP) complexes active in guiding nucleotide methylation. Experiments have investigated the process of box C/D sRNP assembly and the resultant changes in sRNA structure or "remodeling" as a consequence of sRNP core protein binding. Hierarchical assembly of the Methanocaldococcus jannaschii sR8 box C/D sRNP is a temperature-dependent process with binding of L7 and Nop56/58 core proteins to the sRNA requiring elevated temperature to facilitate necessary RNA structural dynamics. Circular dichroism (CD) spectroscopy and RNA thermal denaturation revealed an increased order and stability of sRNA folded structure as a result of L7 binding. Subsequent binding of the Nop56/58 and fibrillarin core proteins to the L7-sRNA complex further remodeled sRNA structure. Assessment of sR8 guide region accessibility using complementary RNA oligonucleotide probes revealed significant changes in guide region structure during sRNP assembly. A second dual-guide box C/D sRNA from M. jannaschii, sR6, also exhibited RNA remodeling during temperature-dependent sRNP assembly, although core protein binding was affected by sR6's distinct folded structure. Interestingly, the sR6 sRNP followed an alternative assembly pathway, with both guide regions being continuously exposed during sRNP assembly. Further experiments using sR8 mutants possessing alternative guide regions demonstrated that sRNA folded structure induced by specific guide sequences impacted the sRNP assembly pathway. Nevertheless, assembled sRNPs were active for sRNA-guided methylation independent of the pathway followed. Thus, RNA remodeling appears to be a common and requisite feature of archaeal dual-guide box C/D sRNP assembly and formation of the mature sRNP can follow different assembly pathways in generating catalytically active complexes.

Amino Acid Sequence↗

PubMed2004

Autoregulation of subtilin biosynthesis in Bacillus subtilis: the role of the spa-box in subtilin-responsive promoters.

The production of the type I antimicrobial peptide (AMP) subtilin by Bacillus subtilis is regulated in a cell-density-dependent manner [Kleerebezem M, de Vos WM, Kuipers OP. The lantibiotics nisin and subtilin act as extracellular regulators of their own biosynthesis. In: Dunny GM, Winans SC, editors. Cell-cell signaling in bacteria. Washington, D.C., USA: ASM Press; 1999. p. 159-74; Stein T, Borchert S, Kiesau P, Heinzmann S, Kloss S, Klein C, Helfrich M, Entian KD. Dual control of subtilin biosynthesis and immunity in Bacillus subtilis. Mol Microbiol 2002;44:403-16; Stein T, Heinzmann S, Kiesau P, Himmel B, Entian KD. The spa-box for transcriptional activation of subtilin biosynthesis and immunity in Bacillus subtilis. Mol Microbiol 2003;47:1627-36]. Three subtilin-responsive promoter elements within the spaBTCSIFEGRK are controlled by the specific cis-acting sequence element called the spa-box, which represents the binding site of the subtilin regulator SpaR [Stein T, Heinzmann S, Kiesau P, Himmel B, Entian KD. The spa-box for transcriptional activation of subtilin biosynthesis and immunity in Bacillus subtilis. Mol Microbiol 2003;47:1627-36]. Here, we describe the functional characterization of the spaB, spaS and spaI promoters by transcriptional fusion with a promoterless beta-glucuronidase encoding gusA gene. Within these gusA fusion constructs, transcription initiation start sites of the spaS and spaI promoters were mapped to be located downstream of the spa-box, which is in contrast to previous reports [Banerjee S, Hansen JN. Structure and expression of a gene encoding the precursor of subtilin, a small protein antibiotic. J Biol Chem 1988;263:9508-14; Stein T, Heinzmann S, Kiesau P, Himmel B, Entian KD. The spa-box for transcriptional activation of subtilin biosynthesis and immunity in Bacillus subtilis. Mol Microbiol 2003;47:1627-36]. Nevertheless, all spa-promoters displayed typical cell-density-dependent activity in a subtilin-producing strain B. subtilis ATCC6633. Moreover, analysis of beta-glucuronidase activities in a spaB mutant of B. subtilis ATCC6633 and a derivative of strain 168 that harbors the spaRK genes integrated in the chromosomal amyE locus, confirmed that these promoters are activated by subtilin-triggered, SpaRK-mediated, quorum-sensing control. Quantitative analysis showed that the spaS promoter strength at a given subtilin concentration appeared to be approximately five-fold higher than the spaB promoter, which in turn is approximately two-fold higher than the spaI promoter. Finally, it is shown that the elementary components involved in subtilin-mediated regulation are the two-component system, SpaRK, and a spa-box containing promoter.

Anti-Bacterial Agents↗

PubMed1998

The isoenzyme-diagnostic regions of muscle-type creatine kinase, the M-260 and M-300 box, are not responsible for its binding to the myofibrillar M-band.

Muscle-type creatine kinase is known for its unique interaction with the myofibrillar M-band, but the molecular origin for this structural relationship is not well understood. A systematic sequence comparison between the highly homologous cytosolic isoforms, muscle-type and brain-type creatine kinase, yielded two isoenzyme-specific regions in the muscle-type creatine kinases, the M-260 box (residues 258-270) and the M-300 box (residues 300-315). These particular regions were conspicuous for the specific interaction of this CK isoenzyme, but not of brain-type creatine kinase, with the sarcomeric M-band. In situ diffusion assays with fluorescently labeled native, as well as mutated muscle-type creatine kinase variants, were used to study by laser confocal microscopy their association with the M-band of chemically skinned muscle fibers. Neither a set of charge mutants of the M-260 box and/or the M-300 box nor a hybrid construct of both isoforms with the entire C-terminal region derived from the brain-type isoform showed any significant alteration in the in situ M-band-binding properties when compared to the wild-type form of muscle-type creatine kinase. This indicates that in the intact protein of muscle type creatine kinase, these C-terminal isoenzyme-specific regions are not important for M-band interaction and that the actual M-band interaction domain(s) lay mostly within the N-terminal half of the molecule. The highly conserved motives (M-260 box and M-300 box) may serve an isoenzyme-specific purpose yet to be identified.

Amino Acid Sequence↗

PubMed1997

Oct-1, silencer sequence, and GC box regulate thyroid hormone receptor beta1 promoter.

Thyroid hormone, acting through thyroid hormone receptors (TRs), plays a crucial role in brain development and its insufficiency results in irreversible brain damage. TR alpha mRNA is expressed continuously from early embryonic stages, but the level of TR beta1 mRNA in brain is more abundant in adult than in fetus. To identify important factors which regulate TR beta1 expression, we compared mouse fetal and adult brain nuclear extracts by DNase I footprinting and electrophoretic gel mobility shift assays (EMSA) of the TR beta1 promoter. We carried out transient transfection studies in COS 1 cells using the TR beta1 promoter fused to Luciferase gene, and used mutated promoter vectors and various expression vectors. In DNase I footprinting using the fragment -950 to -717, fetal brain nuclear extracts protected the areas -910 to -884 and -815 to -800 more than did adult extracts. In EMSA, proteins in fetal nuclear extracts bound to a silencer sequence (-924 to -916), GC box (-901 to -887), and E box (-810 to -805), more strongly than did proteins in adult brain extracts. The bands formed on GC box were not supershifted by Sp-1, Sp-2, Sp-3, Sp-4, EGR-1, or EGR-2 antibodies. Three bands were detected on the octamer binding site probe (-913 to -906) and one protein was supershifted by Oct-1 antibody. Adult brain extracts appear to contain more Oct-1 protein than do fetal extracts. The other two bands were more intense in fetal extracts than in adult extracts, but were not supershifted by either Oct-1 or Oct-2 antibodies. Mutation of the silencer response element, mutation of the GC box, and Oct-1 over expression in COS 1 cells increased TR beta1 promoter function as assayed by Luciferase reporter. Mutation of the octamer binding site, to which only Oct-1 bound in COS 1 cells, decreased Luciferase reporter activity. Thus the TR beta1 promoter was regulated negatively by the proteins bound to the silencer sequence and the GC box, and positively by Oct-1. Silencer and GC box binding proteins are more abundant in fetal brain, and Oct-1 is more abundant in adult brain. The results may be responsible for increased amounts of TR beta1 present in late fetal and adult brain.

Animals↗