Isolation and sequence of cDNA clones coding for a member of the family of high mobility group proteins (HMG-T) in trout and analysis of HMG-T-mRNA's in trout tissues

Screening for beta-poly(L-malate) binding proteins by affinity chromatography

Poly(beta-L-malic acid) is a cell type-specific polymer of myxomycetes (true slime molds) with the physiological role to organize mobility of certain proteins over the giant multinucleated plasmodia. We have developed an affinity chromatography employing 1,6-diamino-n-hexane-Sepharose-coupled poly(malic acid) to identify such proteins in cellular extracts of Physarum polycephalum. Molecular masses were measured by SDS-PAGE and non-denaturing PAGE after silver staining and/or Western blotting. Protein complexes/subunits were detected by 2-dimensional non-denaturing PAGE/SDS-PAGE. A simplified gel shift experiment displayed binding to fragmented calf thymus DNA. Nuclei were richest in poly(malate) binding proteins followed by cytoplasm and membranes. A protein of 370 kDa dissociated into 11 subunits of 11-29 kDa, indicative of a highly complex protein. This and other proteins displayed binding to nucleic acid in gel shift experiments. Poly(malate) is considered a structural and functional equivalent of long contiguous aspartate repeats in proteins of eukaryotes.

The chicken genome contains no HMG1 retropseudogenes but a functional HMG1 gene with long introns

We have cloned the genomic sequence coding for the high mobility group 1 (HMG1) protein in chickens. Multiple sequence alignment shows that the chicken HMG1 gene is highly homologous to the human and the mouse HMG1 genes. The gene structure of chicken HMG1 is similar to that of the mouse and the human HMG1 genes, with the same exon-intron boundaries. However, in contrast to other avian genes that have shorter introns, the chicken HMG1 gene has introns that are twice as long as their mammalian homologues. In addition to the functional, intron-containing HMG1 gene, all mammalian genomes contain more than 50 copies of HMG1 retropseudogenes each, while in the chicken genome there are no HMG1 retropseudogenes. This finding suggests that the HMG1 retropseudogenes arose in mammals after their divergence away from the birds.

Evidence for a shared structural role for HMG1 and linker histones B4 and H1 in organizing chromatin

The high mobility group proteins 1 and 2 (HMG1/2) and histone B4 are major components of chromatin within the nuclei assembled during the incubation of Xenopus sperm chromatin in Xenopus egg extract. To investigate their potential structural and functional roles, we have cloned and expressed Xenopus HMG1 and histone B4. Purified histone B4 and HMG1 form stable complexes with nucleosomes including Xenopus 5S DNA. Both proteins associate with linker DNA and stabilize it against digestion with micrococcal nuclease, in a similar manner to histone H1. However, neither histone B4 nor HMG1 influence the DNase I or hydroxyl radical digestion of DNA within the nucleosome core. We suggest that HMG1/2 and histone B4 have a shared structural role in organizing linker DNA in the nucleosome.

cDNA sequence and structure of a trout HMG-2 gene. Evidence for a trout-specific 3'-untranslated region

A complete cDNA sequence (1026 bp) and a partial structure of a gene encoding the trout testis chromosomal HMG (high mobility group) 2 protein (HMG-T2) is presented. The deduced protein consists of 214 amino acids and shares over 80% similarity to the trout HMG-1 protein (HMG-T1) as well as to the mammalian or avian HMG-2 proteins. Northern blot analysis revealed two transcripts, a major one of 1.2 kb and a minor one of 1.6 kb. Southern analysis and polymerase chain reaction of trout genomic DNA indicated that the HMG-T2 gene is encoded by several introncontaining genes. The 5'-UTR (untranslated region) of the HMG-T2 is interrupted by an intron and the coding region of the HMG-T2 is divided into four exons by three relatively short introns (173, 91 and 78 bp). The exon/intron boundaries of trout HMG-2 are identical to those of human HMG-2, as reported earlier [Shirakawa and Yoshida, J. Biol. Chem. 267 (1992) 6641-6645], suggesting the evolution of the HMG-1/2 family genes from a common ancestor. Phylogenetic analysis indicated that the common ancestor of trout HMG-1/2 genes very likely diverged from the ancestor of the mammalian (or avian) HMG-1/2 genes before its separation into two distinct mammalian or (avian) HMG-1 and HMG-2 genes. Sequence comparisons of the 3'UTR of trout HMG-2 cDNA with the corresponding regions in the mammalian (or avian) HMG-2 revealed that the trout 3'-UTR was clearly distinct from the 3'-UTR of the mammalian or avian HMG-2 cDNAs which were otherwise remarkably well conserved.(ABSTRACT TRUNCATED AT 250 WORDS)

The HMG-1 box protein family: classification and functional relationships

The abundant and highly-conserved nucleoproteins comprising the high mobility group-1/2 (HMG-1/2) family contains two homologous basic domains of about 75 amino acids. These basic domains, termed HMG-1 boxes, are highly structured and facilitate HMG-DNA interactions. Many proteins that regulate various cellular functions involving DNA binding and whose target DNA sequences share common structural characteristics have been identified as having an HMG-1 box; these proteins include the RNA polymerase I transcription factor UBF, the mammalian testis-determining factor SRY and the mitochondrial transcription factors ABF2 and mtTF1, among others. The sequences of 121 HMG-1 boxes have been compiled and aligned in accordance with thermodynamic results from homology model building (threading) experiments, basing the alignment on structure rather than by using traditional sequence homology methods. The classification of a representative subset of these proteins was then determined using standard least-squares distance methods. The proteins segregate into two groups, the first consisting of HMG-1/2 proteins and the second consisting of proteins containing the HMG-1 box but which are not canonical HMG proteins. The proteins in the second group further segregate based on their function, their ability to bind specific sequences of DNA, or their ability to recognize discrete non-B-DNA structures. The HMG-1 box provides an excellent example of how a specific protein motif, with slight alteration, can be used to recognize DNA in a variety of functional contexts.

Molecular cloning, expression analysis, and chromosomal localization of mouse Hmg1-containing sequences

We isolated clones encoding the mouse high-mobility-group (Hmg) chromatin protein, Hmg1, from a 7.5-day mouse embryo cDNA library. The translated amino acid sequence encodes a protein of 24,890 daltons and is identical to previously characterized mouse, rat, and hamster Hmg1. However, comparison of the two mouse Hmg1 cDNA sequences revealed nine sequence alterations. This observation, together with the finding of a complex pattern of hybridizing bands in genomic Southern analysis, suggests that mouse Hmg1 is encoded by a multigene family. The expression of Hmg1 was examined by Northern analysis of RNA isolated from the early mouse embryo and revealed a predominant 1.5-kb transcript in conjunction with low levels of a 2.5-kb transcript. Further analysis of mouse embryos by in situ hybridization showed that Hmg1 transcripts are expressed in high abundance during early mouse embryogenesis. As development progresses, Hmg1 transcript abundance is modulated in a spatially restricted and developmentally regulated manner. Chromosomal localization with recombinant inbred strains revealed that Hmg1-related sequences are widely dispersed in the mouse genome. Here we also report the mapping of six Hmg1 loci to mouse Chromosomes (Chrs) 10, 13, 16, and 17.

Identification of genes encoding zinc finger proteins, non-histone chromosomal HMG protein homologue, and a putative GTP phosphohydrolase in the genome of Chilo iridescent virus

Five RNA transcripts of about 1.2 to 1.7 kilobases were mapped to a part of the genome of insect iridescent virus type 6 (Chilo iridescent virus; CIV) between genome coordinates 0.832 and 0.856 within the EcoRI DNA fragment F. The nucleotide sequence of this particular region (5702 base pairs) of the CIV genome was determined. The DNA sequence contains a number of perfect direct, inverted, and palindromic repeats including three clusters of tandemly organized repetitive DNA elements located between the nucleotide positions 1534 to 1566, 3720 to 3780, and 4350 to 4450. Eight long open reading frames (ORFs; EF1 to 8) were detected in the sequenced region of the CIV genome. ORF EF1 encodes a putative protein of 221 amino acid residues (aa) that is closely related to eukaryotic nonhistone chromosomal proteins of the high mobility group (HMG) superfamily. Virus encoded homologues of HMG proteins have not been reported so far. The EF2 gene product (145 aa) contains a specific zinc finger motif and belongs to a distinct group of identified and putative zinc finger proteins including a second putative protein (239 aa) of CIV encoded in the EcoRI DNA fragment Y (1984 bp; 0.381 to 0.391 viral map units). The product of EF6 (127 aa) is related to D250 ORF product of African swine fever virus (ASFV) and belongs to the recently described protein family sharing a highly conserved sequence motif with bacterial antimutator GTP phosphohydrolase MutT. Thus the sequenced region of the CIV genome encodes three putative proteins which may be directly involved in the replication and/or transcription of the viral DNA.

Phylogenetic relationships of HMG box DNA-binding domains

HMG boxes were initially identified as DNA-binding domains of the human RNA polymerase I (pol I) transcription factor hUBF and the animal high-mobility-group (HMG) protein family HMG1. Since then, numerous sequences of HMG-box-containing HMG proteins and other DNA-binding proteins from several species have become available. By sequence comparisons of a selected range of HMG boxes from these proteins and the construction of phylogenetic trees we show that the HMG box is highly conserved between DNA-binding proteins of organisms from all three eukaryotic kingdoms and that HMG boxes are linked by distinct evolutionary relationships. In addition, most HMG boxes display comparable hydropathy profiles and amino acid arrangements, which could serve as nuclear targeting sequences.

Solution structure of a DNA-binding domain from HMG1

We have determined the tertiary structure of box 2 from hamster HMG1 using bacterial expression and 3D NMR. The all alpha-helical fold is in the form of a V-shaped arrowhead with helices along two edges and one rather flat face. This architecture is not related to any of the known DNA binding motifs. Inspection of the fold shows that the majority of conserved residue positions in the HMG box family are those involved in maintaining the tertiary structure and thus all homologous HMG boxes probably have essentially the same fold. Knowledge of the tertiary structure permits an interpretation of the mutations in HMG boxes known to abrogate DNA binding and suggests a mode of interaction with bent and 4-way junction DNA.

Ancestry and diversity of the HMG box superfamily

The HMG box is a novel type of DNA-binding domain found in a diverse group of proteins. The HMG box superfamily comprises a.o. the High Mobility Group proteins HMG1 and HMG2, the nucleolar transcription factor UBF, the lymphoid transcription factors TCF-1 and LEF-1, the fungal mating-type genes mat-Mc and MATA1, and the mammalian sex-determining gene SRY. The superfamily dates back to at least 1,000 million years ago, as its members appear in animals, plants and yeast. Alignment of all known HMG boxes defined an unusually loose consensus sequence. We constructed phylogenetic trees connecting the members of the HMG box superfamily in order to understand their evolution. This analysis led us to distinguish two subfamilies: one comprising proteins with a single sequence-specific HMG box, the other encompassing relatively non sequence-specific DNA-binding proteins with multiple HMG boxes. By studying the extent of diversification of the superfamily, we found that the speed of evolution was very different within the various groups of HMG-box containing factors. Comparison of the evolution of the two boxes of ABF2 and of mtTF1 implied different diversification models for these two proteins. Finally, we provide a tree for the highly complex group of SRY-like ('Sox' genes), clustering at least 40 different loci that rapidly diverged in various animal lineages.

In situ hybridization for creatine kinase-B messenger RNA in rat uterus and brain

Creatine kinase-B (CKB) is present in both uterus and brain, and in uterus its synthesis (protein and mRNA) is regulated by estrogen. In the present study we have used in situ hybridization to detect CKB mRNA in uterus and brain, and to determine whether there is cell type specific induction of CKB by estrogen in these tissues. Tissue was taken from ovariectomized (ovx) rats that had been injected with either estrogen (17 beta-estradiol-3-benzoate and/or 17 beta-estradiol) or vehicle alone, 2, 8, 24 and 72 h previously. The brains and uteri were removed, frozen, cryostat-sectioned, and processed for in situ hybridization histochemistry. The uterine and brain sections were incubated with a tritiated DNA probe complementary to a 3' fragment of CKB mRNA, or a control sense probe to the same 3' fragment. In uterine smooth muscle cells, a 2.5- and 3.5-fold induction of CKB mRNA was observed 2 and 24 h after estrogen administration, respectively, and levels approached ovx controls at 72 h. A smaller induction (1.9-fold, 2 h) was observed in uterine epithelium, with little induction of CKB mRNA in stroma. In the brain CKB mRNA was detected in neurons, but not in clearly identified glia, and only occasionally in ependymal cells. In brain regions containing estrogen receptors there was no evidence of a significant estrogen effect on CKB mRNA levels. Some brain regions had higher neuronal expression than others (e.g. medial septum vs. preoptic area), but expression was widespread and not limited to neuroendocrine sites.

A retropseudogene for non-histone chromosomal protein HMG-1

Southern analysis of the human genome revealed that there are several sequences with homology to the nonhistone chromosomal protein HMG-1. The majority of the HMG-1 sequences are intronless as suggested from the polymerase chain reaction of HeLa DNA. Sequencing of a clone from a human placenta genomic library revealed that the clone was intronless and displayed 99% homology to the human HMG-1 cDNA. The 5' regulatory motif, CCAAT, is present in the clone but there is no TATA-box. Most of the differences between the HMG-1 cDNA sequence and the clone involve point mutations with no interruption of the reading frame. The sequence is flanked at 5' and 3' ends by a 15 nucleotide long direct repeat suggesting that the clone is a processed HMG-1 retropseudogene. Sequence differences between the reading frames of the HMG-1 pseudogene and HMG-1 cDNA indicated that the pseudogene arose relatively late in evolution, approximately one million years ago. The present paper is the first study on a genomic sequence related to HMG-1 genes.

A familial mutation in the testis-determining gene SRY shared by both sexes

A familial mutation in SRY, the gene coding for the testis-determining factor TDF, was identified in an XY female with gonadal dysgenesis, her father, her two brothers and her uncle. The mutation consists of a T to C transition in the region of the SRY gene coding for a protein motif known as the high mobility group (HMG) box, a protein domain known to confer DNA-binding specificity on the SRY protein. This point mutation results in the substitution, at amino acid position 109, of a serine residue for phenylalanine, a conserved aromatic residue in almost all HMG box motifs known. This F109S mutation was not found in 176 male controls. When recombinant wildtype SRY and SRYF109S mutant protein were tested in vitro for binding to the target site AAC AAAG, no differences in DNA-binding activity were observed. These results imply that the F109S mutation either is a rare neutral sequence variant, or produces an SRY protein with slightly altered in vivo activity, the resulting sex phenotype depending on the genetic background or environmental factors.

Sequence of a cDNA encoding chicken high-mobility-group protein-2

There are several members of the high-mobility-group (HMG) of DNA-binding proteins, including HMG-1, HMG-2, HMG-14 and HMG-17 [Johns: The HMG Chromosomal Proteins. Academic Press, London, 1982]. We report here sequences encoding the chicken HMG-2 protein of 207 amino acids (aa). This assignment is made on the basis of available data which indicate 89% homology of the chicken aa sequence to porcine HMG-2. This compares with 78-81% homology to the HMG-1 proteins of rat, hamster, human, porcine, and bovine origin.

Isolation of a chicken HMG2 cDNA clone and evidence for an HMG2-specific 3'-untranslated region

HMG1 and HMG2 (high-mobility group proteins) are two of the most abundant nonhistone chromosomal proteins in higher eukaryotes. Mammalian HMG1 cDNA sequences have the unusual feature of being conserved not only over their coding regions, but also over large segments of their 3'-untranslated regions (3' UTRs) as well. In contrast, the only reported mammalian HMG2 cDNA clone has a distinct 3' UTR. We now report the isolation of a chicken HMG2 cDNA clone and show that it is markedly similar to the mammalian HMG2 cDNA clone over both its coding regions and 3' UTRs. We therefore infer that the 3' UTRs of the HMG1 and HMG2 genes are subject to distinct evolutionary pressures. Our data, along with published data, also serve to highlight 26 amino acid positions where HMG1 and HMG2 are distinctly conserved, and we note that trout HMG-T conforms to the HMG1 paradigm at most of these diagnostic positions.

Characterization of a cDNA clone from the haemoparasite Babesia bovis encoding a protein containing an "HMG-Box"

The complete nucleotide sequence of a Babesia bovis cDNA clone encoding a protein containing an HMG-Box has been determined. The predicted protein of 97 amino acids has a molecular weight of 11,116. It exhibits approximately 45% overall amino acid identity with the Saccharomyces cerevisiae non-histone protein 6A (NHP6A) and approximately 57% identity in the HMG-Box. The B. bovis protein has been designated NHP1. Like HNP6A, and unlike most other HMG1 homologues, NHP1 does not have a basic or an acidic carboxy-terminal domain. The amino acid sequence of HNP1 is much less similar to HMG1 homologues of another protozoan, Tetrahymena thermophila, than to the HMG1 homologues identified in S. cerevisiae, plants and vertebrates. This suggests that the T. thermophila proteins may not be true HMG1 homologues, or that they may be evolving at a much faster rate.

Differential expression of two mRNAs from a single gene encoding an HMG1-like DNA binding protein of African trypanosomes

We have isolated cDNA clones expressing a member of the high mobility group (HMG) protein family by screening a Trypanosoma brucei rhodesiense expression cDNA library with multimerized oligonucleotides corresponding to an octamer transcriptional regulatory sequence motif. The trypanosome DNA binding protein (TDP-1) encoded by these cDNAs contains two domains that show striking sequence similarity to the consensus sequence for HMG1-like DNA binding domains (HMG boxes). Southern blot analysis is consistent with TDP-1 being encoded by a single copy gene. The cDNA clones are derived from 2 mature mRNA species of approximately 1.6 and 2.3 kb in length that are generated by differential polyadenylation at sites 563 nucleotides and 1113 nucleotides downstream from the stop codon. Stage specific differences exist in the steady state levels of the 2 mRNAs: bloodstream parasites contain predominantly the 1.6-kb mRNA, while procyclic culture forms express predominantly the 2.3-kb mRNA.

DNA binding activity of recombinant SRY from normal males and XY females

The protein encoded by the human testis determining gene, SRY, contains a high mobility group (HMG) box related to that present in the T cell-specific, DNA-binding protein TCF-1. Recombinant SRY protein was able to bind to the same core sequence AACAAAG recognized by TCF-1 in a sequence dependent manner. In five XY females point mutations were found in the region encoding the HMG box. In four cases DNA binding activity of mutant SRY protein was negligible; in the fifth case DNA binding was reduced. These results imply that the DNA binding activity of SRY is required for sex determination.

A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1

The SIN1 gene was initially identified because mutations in SIN1 bypass the need for SWI1 to activate transcription of the yeast HO gene. We show here that transcription of HO in swi1 sin1 cells efficiently utilizes the normal start site. We have cloned SIN1 and found that it is identical to the previously identified gene SPT2, mutations in which allow transcription from certain mutated regulatory regions. The predicted SIN1/SPT2 protein has a distinctive amino acid composition (45% charged residues, 25% basic and 20% acidic) and has similarity to the mammalian HMG1 protein, a nonhistone component of chromatin. We show that SIN1 is concentrated in the nucleus and binds to DNA with little or no sequence specificity in vitro. It thus exhibits properties of an HMG protein. Addition of random DNA segments to a test promoter alters regulation by SIN1 in a manner similar to addition of a segment from the HO upstream region. Functional analysis of certain SIN1 mutations suggests that SIN1 may be part of a multiprotein complex. On the basis of these results, we propose that SIN1 is a nonhistone component of chromatin which creates the proper context for transcription. Because sin1 mutants exhibit increased loss of chromosome III, SIN1 may also play a role in fidelity of chromosome segregation.

A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1

The SIN1 gene was initially identified because mutations in SIN1 bypass the need for SWI1 to activate transcription of the yeast HO gene. We show here that transcription of HO in swi1 sin1 cells efficiently utilizes the normal start site. We have cloned SIN1 and found that it is identical to the previously identified gene SPT2, mutations in which allow transcription from certain mutated regulatory regions. The predicted SIN1/SPT2 protein has a distinctive amino acid composition (45% charged residues, 25% basic and 20% acidic) and has similarity to the mammalian HMG1 protein, a nonhistone component of chromatin. We show that SIN1 is concentrated in the nucleus and binds to DNA with little or no sequence specificity in vitro. It thus exhibits properties of an HMG protein. Addition of random DNA segments to a test promoter alters regulation by SIN1 in a manner similar to addition of a segment from the HO upstream region. Functional analysis of certain SIN1 mutations suggests that SIN1 may be part of a multiprotein complex. On the basis of these results, we propose that SIN1 is a nonhistone component of chromatin which creates the proper context for transcription. Because sin1 mutants exhibit increased loss of chromosome III, SIN1 may also play a role in fidelity of chromosome segregation.

Isolation and characterization of maize cDNAs encoding a high mobility group protein displaying a HMG-box

cDNAs encoding a nonhistone chromosomal high mobility group (HMG) protein corresponding to the animal HMG1 family were isolated from a maize cDNA library using an immunoscreening approach. The cDNAs revealed an open reading frame of 471 base pairs together with 413 base pairs of flanking region, in agreement with the size of mRNA detected by Northern analysis of maize endosperm RNA. Like its animal counterparts the 17146 Da maize HMG protein contains a basic aminoterminus and an acidic carboxyterminus. The HMG-box region of this plant HMG protein shows striking sequence similarity to members of the vertebrate HMG1 family. Based on Southern blot hybridization analysis of genomic DNA, the isolated cDNA appears to be derived from a single or low copy gene.

Similarity of human mitochondrial transcription factor 1 to high mobility group proteins

Human mitochondrial transcription factor 1 (mtTF1) has been sequenced and is a nucleus-encoded DNA binding protein of 204 amino acids (24,400 daltons). Expression of human mtTF1 in bacteria yields a protein with correct physical properties and the ability to activate mitochondrial DNA promoters. Analysis of the protein's sequence reveals no similarities to any other DNA binding proteins except for the existence of two domains that are characteristic of high mobility group (HMG) proteins. Human mtTF1 is most closely related to a DNA binding HMG-box region in hUBF, a human protein known to be important for transcription by RNA polymerase I.

High-mobility-group proteins P1, I and Y as substrates of the M-phase-specific p34cdc2/cyclincdc13 kinase

All dividing cells entering the M phase of the cell cycle undergo the transient activation of an M-phase-specific histone H1 kinase which was recently shown to be constituted of at least two subunits, p34cdc2 and cyclincdc13. The DNA-binding high-mobility-group (HMG) proteins 1, 2, 14, 17, I, Y and an HMG-like protein, P1, were investigated as potential substrates of H1 kinase. Among these HMG proteins, P1 and HMG I and Y are excellent substrates of the M-phase-specific kinase obtained from both meiotic starfish oocytes and mitotic sea urchin eggs. Anticyclin immunoprecipitates, extracts purified on specific p34cdc2-binding p13suc1-Sepharose and affinity-purified H1 kinase display strong HMG I, Y and P1 phosphorylating activities, demonstrating that the p34cdc2/cyclincdc13 complex is the active kinase phosphorylating these HMG proteins. HMG I and P1 phosphorylation is competitively inhibited by a peptide mimicking the consensus phosphorylation sequence of H1 kinase. HMG I, Y and P1 all possess the consensus sequence for phosphorylation by the p34cdc2/cyclincdc13 kinase (Ser/Thr-Pro-Xaa-Lys/Arg). HMG I is phosphorylated in vivo at M phase on the same sites phosphorylated in vitro by H1 kinase. P1 is phosphorylated by H1 kinase on sites different from the sites of phosphorylation by casein kinase II. The three thermolytic phosphopeptides of P1 phosphorylated in vitro by purified H1 kinase are all present in thermolytic peptide maps of P1 phosphorylated in vivo in proliferating HeLa cells. These phosphopeptides are absent in nonproliferating cells. These results demonstrate that the DNA-binding proteins HMG I, Y and P1 are natural substrates for the M-phase-specific protein kinase. The phosphorylation of these proteins by p34cdc2/cyclincdc13 may represent a crucial event in the intense chromatin condensation occurring as cells transit from the G2 to the M phase of the cell cycle.

Macronuclei and micronuclei in Tetrahymena thermophila contain high-mobility-group-like chromosomal proteins containing a highly conserved eleven-amino-acid putative DNA-binding sequence

HMG (high-mobility-group protein) B and HMG C are abundant nonhistone chromosomal proteins isolated from Tetrahymena thermophila macronuclei with solubilities, molecular weights, and amino acid compositions like those of vertebrate HMG proteins. Genomic clones encoding each of these proteins have been sequenced. Both are single-copy genes that encode single polyadenylated messages whose amounts are 10 to 15 times greater in growing cells than in starved, nongrowing cells. The derived amino acid sequences of HMG B and HMG C contain a highly conserved sequence, the HMG 1 box, found in vertebrate HMGs 1 and 2, and we speculate that this sequence may represent a novel, previously unrecognized DNA-binding motif in this class of chromosomal proteins. Like HMGs 1 and 2, HMGs B and C contain a high percentage of aromatic amino acids. However, the Tetrahymena HMGs are small, are associated with nucleosome core particles, and can be specifically extracted from macronuclei by elutive intercalation, properties associated with vertebrate HMGs 14 and 17, not HMGs 1 and 2. Thus, it appears that these Tetrahymena proteins have features in common with both of the major subgroups of higher eucaryotic HMG proteins. Surprisingly, a linker histone found exclusively in transcriptionally inactive micronuclei also has several HMG-like characteristics, including the ability to be specifically extracted from nuclei by elutive intercalation and the presence of the HMG 1 box. This finding suggests that at least in T. thermophila, proteins with HMG-like properties are not restricted to regions of transcriptionally active chromatin.

Macronuclei and micronuclei in Tetrahymena thermophila contain high-mobility-group-like chromosomal proteins containing a highly conserved eleven-amino-acid putative DNA-binding sequence

HMG (high-mobility-group protein) B and HMG C are abundant nonhistone chromosomal proteins isolated from Tetrahymena thermophila macronuclei with solubilities, molecular weights, and amino acid compositions like those of vertebrate HMG proteins. Genomic clones encoding each of these proteins have been sequenced. Both are single-copy genes that encode single polyadenylated messages whose amounts are 10 to 15 times greater in growing cells than in starved, nongrowing cells. The derived amino acid sequences of HMG B and HMG C contain a highly conserved sequence, the HMG 1 box, found in vertebrate HMGs 1 and 2, and we speculate that this sequence may represent a novel, previously unrecognized DNA-binding motif in this class of chromosomal proteins. Like HMGs 1 and 2, HMGs B and C contain a high percentage of aromatic amino acids. However, the Tetrahymena HMGs are small, are associated with nucleosome core particles, and can be specifically extracted from macronuclei by elutive intercalation, properties associated with vertebrate HMGs 14 and 17, not HMGs 1 and 2. Thus, it appears that these Tetrahymena proteins have features in common with both of the major subgroups of higher eucaryotic HMG proteins. Surprisingly, a linker histone found exclusively in transcriptionally inactive micronuclei also has several HMG-like characteristics, including the ability to be specifically extracted from nuclei by elutive intercalation and the presence of the HMG 1 box. This finding suggests that at least in T. thermophila, proteins with HMG-like properties are not restricted to regions of transcriptionally active chromatin.

Ribosomal and chromosomal protein cDNA clones of Xenopus laevis thymus isolated with differential screening

1. Xenopus laevis is an excellent system for the study of the evolution and ontogeny of the immune system. But since only immunoglobulin genes have been isolated from this species, we undertook to isolate other genes expressed in an immunologically important organ, the thymus. 2. We used differential screening of a thymus cDNA library with cDNA probes made from thymus and from erythroblasts. 3. Approximately 50 clones which hybridized to the probe from thymus, but not from erythroblast, were isolated and sequenced from their termini. 4. Several clones were identified in data bank searches by their similarity to previously published sequences, and the partial sequences of these loci are reported here. 5. These include elongation factor 2, ribosomal protein S11, ribosomal protein S13, and the high mobility group protein. 6. Although these genes are not expected to be involved in an immune function, the availability of these sequences will facilitate the study of these loci in this species.

The RPC31 gene of Saccharomyces cerevisiae encodes a subunit of RNA polymerase C (III) with an acidic tail

The RPC31 gene encoding the C31 subunit of Saccharomyces cerevisiae RNA polymerase C (III) has been isolated, starting from a C-terminal fragment cloned on a lambda gt11 library. It is unique on the yeast genome and lies on the left arm of chromosome XIV, very close to a NotI site. Its coding sequence perfectly matches the amino acid sequence of two oligopeptides prepared from purified C31. It is also identical to the ACP2 gene previously described as encoding an HMG1-like protein (W. Haggren and D. Kolodrubetz, Mol. Cell. Biol. 8:1282-1289, 1988). Thus, ACP2 and RPC31 are allelic and encode a subunit of RNA polymerase C. The c31 protein has a highly acidic C-terminal tail also found in several other chromatin-interacting proteins, including animal HMG1. Outside this domain, however, there is no appreciable homology to any known protein. The growth phenotypes of a gene deletion, of insertions, and of nonsense mutations indicate that the C31 protein is strictly required for cell growth and that most of the acidic domain is essential for its function. Random mutagenesis failed to yield temperature-sensitive mutants, but a slowly growing mutant was constructed by partial suppression of a UAA nonsense allele of RPC31. Its reduced rate of tRNA synthesis in vivo relative to 5.8S rRNA supports the hypothesis that the C31 protein is a functional subunit of RNA polymerase C.

The RPC31 gene of Saccharomyces cerevisiae encodes a subunit of RNA polymerase C (III) with an acidic tail

The RPC31 gene encoding the C31 subunit of Saccharomyces cerevisiae RNA polymerase C (III) has been isolated, starting from a C-terminal fragment cloned on a lambda gt11 library. It is unique on the yeast genome and lies on the left arm of chromosome XIV, very close to a NotI site. Its coding sequence perfectly matches the amino acid sequence of two oligopeptides prepared from purified C31. It is also identical to the ACP2 gene previously described as encoding an HMG1-like protein (W. Haggren and D. Kolodrubetz, Mol. Cell. Biol. 8:1282-1289, 1988). Thus, ACP2 and RPC31 are allelic and encode a subunit of RNA polymerase C. The c31 protein has a highly acidic C-terminal tail also found in several other chromatin-interacting proteins, including animal HMG1. Outside this domain, however, there is no appreciable homology to any known protein. The growth phenotypes of a gene deletion, of insertions, and of nonsense mutations indicate that the C31 protein is strictly required for cell growth and that most of the acidic domain is essential for its function. Random mutagenesis failed to yield temperature-sensitive mutants, but a slowly growing mutant was constructed by partial suppression of a UAA nonsense allele of RPC31. Its reduced rate of tRNA synthesis in vivo relative to 5.8S rRNA supports the hypothesis that the C31 protein is a functional subunit of RNA polymerase C.

Amino acid sequence of chicken calsequestrin deduced from cDNA: comparison of calsequestrin and aspartactin

We have previously reported the amino terminal sequence of adult chicken calsequestrin, an intraluminal Ca2(+)-binding protein isolated from fast-twitch skeletal muscle. The partial sequence showed homology with mammalian calsequestrins contained in the PIR data bank and complete identity with the amino terminus of a putative laminin-binding protein of the extracellular matrix, aspartactin. Based on these data, oligonucleotide primers were synthesized for PCR amplification and direct DNA sequencing. We report herein the primary sequence of chicken calsequestrin, deduced from cDNA. The sequence has been verified by amino acid sequencing of internal tryptic peptides. Importantly, the data show the primary structure of calsequestrin to be identical to the amino acid sequence reported for aspartactin, with the exception of a single amino acid difference (ileu vs. val) which may be animal strain-related. Based on these data, calsequestrin and aspartactin are the same protein.

High mobility group proteins 1 and 2 function as general class II transcription factors

High mobility group (HMG) proteins 1 and 2 are thought to be associated with chromatin enriched in active gene sequences, to stimulate endogenous transcription of class II and III genes using HMG-depleted nuclei, and to bind specific DNA sequences upstream of the coding regions of trout HMG-T and human beta-globin genes. In testing the possibility that these proteins may act as general transcription factors, the run-off transcription of trout protamine, human beta-globin, adenovirus 2 major late promoter, and herpes simplex virus (HSV) thymidine kinase genes was found to be inhibited by affinity-purified HMG-1 and -2 antibodies. The inhibition was partially relieved by exogenously added HMG-1 or -2. A complementation assay showed that the 0.15 M KCl flowthrough of HeLa nuclear extract fractionated by anion-exchange chromatography (DE-52) could be replaced by purified HMG-1 and/or -2 to complement transcription of the trout protamine gene by the 0.5 M KCl eluate fraction. Inhibition studies with heparin showed that HMG-1 and -2 were required for initiation of transcription. These results indicate an absolute requirement of HMG-1 and -2 for class II gene transcription. Western blotting and transcription reconstituted with purified factors show a copurification of HMG-1 and -2 with factor II B, described earlier by Reinberg and Roeder [(1987) J. Biol. Chem. 262, 3310-3321].

The Caenorhabditis elegans genome contains monomorphic minisatellites and simple sequences

Many species have been shown to contain tandemly repeated short sequence DNA known as minisatellites and simple sequence motifs. Due to allelic variation in the copy number of the repeat unit these loci are usually highly polymorphic. Here we demonstrate the presence of sequences in the genome of the nematode Caenorhabditis elegans which are homologous to two sets of short sequence DNA. However, when two independent strains were compared no polymorphism for these sequences could be detected.

A human placental cDNA clone that encodes nonhistone chromosomal protein HMG-1

From a human placental lambda gt11 cDNA library, we have isolated a cDNA clone that encodes the entire 215-residue amino acid sequence of HMG-1. Analysis of an internal sequence similarity suggests that the DNA-binding domains of HMG-1 are separated by a rather long and flexible linker segment. Southern blotting of DNA digested with BamHI indicated a highly variable number of genes (or pseudogenes) for HMG-1 in different species. Characterization of HMG-1 mRNA expression by Northern blotting showed that three mRNA species of approximately 1.0, 1.4 and 2.4 kb were expressed in all mammalian organs and cell lines examined. These included several rat organs at different stages of development. Northern analysis also suggested the occurrence of HMG-1 mRNA in an invertebrate and a plant species.

Full length cDNA sequence for bovine high mobility group 1 (HMG1) protein

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Amino-terminal sequence of a Saccharomyces cerevisiae nuclear protein, NHP6, shows significant identity to bovine HMG1

Several nonhistone chromatin proteins (NHPs) have been isolated from Saccharomyces cerevisiae nuclei. They have molecular masses and amino acid compositions typical of the high mobility group (HMG) proteins from higher eukaryotic cells. Polyclonal antisera raised against two of the NHPs have been used in immunoblots of proteins from subcellular fractions of yeast to show that the NHPs are indeed nuclear. In addition, the amino-terminal amino acid sequences of several of the NHPs were determined. Importantly, the amino-terminal sequence of one of the proteins, NHP6, has significant (60%) identity with a stretch of amino acids in calf thymus HMG1.

Domain structure and functional analysis of the carboxyl-terminal polyacidic sequence of the RAD6 protein of Saccharomyces cerevisiae

The RAD6 gene of Saccharomyces cerevisiae, which is required for normal tolerance of DNA damage and for sporulation, encodes a 172-residue protein whose 23 carboxyl-terminal residues are almost all acidic. We show that this polyacidic sequence appends to RAD6 protein as a polyanionic tail and that its function in vivo does not require stoichiometry of length. RAD6 protein was purified to near homogeneity from a yeast strain carrying a RAD6 overproducing plasmid. Approximately the first 150 residues of RAD6 protein composed a structural domain that was resistant to proteinase K and had a Stokes radius typical of a globular protein of its calculated mass. The carboxyl-terminal polyacidic sequence was sensitive to proteinase K, and it endowed RAD6 protein with an aberrantly large Stokes radius that indicates an asymmetric shape. We deduce that RAD6 protein is monomeric and comprises a globular domain with a freely extending polyacidic tail. We tested the phenotypic effects of partial or complete deletion of the polyacidic sequence, demonstrating the presence of the shortened proteins in the cell by using antibody to RAD6 protein. Removal of the entire polyacidic sequence severely reduced sporulation but only slightly affected survival after UV irradiation or UV-induced mutagenesis. Strains with deletions of all but the first 4 or 15 residues of the polyacidic sequence were phenotypically almost wild type or wild type, respectively. We conclude that the intrinsic activity of RAD6 protein resides in the globular domain, that the polyacidic sequence has a stimulatory or modifying role evident primarily in sporulation, and that only a short section apparently functions as effectively as the entire polyacidic sequence.

The Saccharomyces cerevisiae ACP2 gene encodes an essential HMG1-like protein

The high-mobility-group (HMG) proteins, a group of nonhistone chromatin-associated proteins, have been extensively characterized in higher eucaryotic cells. To test the biological function of an HMG protein, we have cloned and mutagenized a gene encoding an HMG-like protein from the yeast Saccharomyces cerevisiae. A yeast genomic DNA library was screened with an oligonucleotide designed to hybridize to any yeast gene containing an amino acid sequence conserved in several higher eucaryotic HMG proteins. DNA sequencing and Northern (RNA) blot analysis revealed that one gene, called ACP2 (acidic protein 2), synthesizes a poly(A)+ RNA in S. cerevisiae which encodes a 27,000-molecular-weight protein whose amino acid sequence is homologous to those of calf HMG1 and HMG2 and trout HMGT proteins. Standard procedures were used to construct a diploid yeast strain in which one copy of the ACP2 gene was mutated by replacement with the URA3 gene. When this diploid was sporulated and dissected, only half of the spores were viable. About half of the nonviable spores proceeded through two or three cell divisions and then stopped dividing; the rest did not germinate at all. None of the viable spores contained the mutant ACP2 gene, thus proving that the protein encoded by ACP2 is required for cell viability. The results presented here demonstrate that an HMG-like protein has an essential physiological function.

The Saccharomyces cerevisiae ACP2 gene encodes an essential HMG1-like protein

The high-mobility-group (HMG) proteins, a group of nonhistone chromatin-associated proteins, have been extensively characterized in higher eucaryotic cells. To test the biological function of an HMG protein, we have cloned and mutagenized a gene encoding an HMG-like protein from the yeast Saccharomyces cerevisiae. A yeast genomic DNA library was screened with an oligonucleotide designed to hybridize to any yeast gene containing an amino acid sequence conserved in several higher eucaryotic HMG proteins. DNA sequencing and Northern (RNA) blot analysis revealed that one gene, called ACP2 (acidic protein 2), synthesizes a poly(A)+ RNA in S. cerevisiae which encodes a 27,000-molecular-weight protein whose amino acid sequence is homologous to those of calf HMG1 and HMG2 and trout HMGT proteins. Standard procedures were used to construct a diploid yeast strain in which one copy of the ACP2 gene was mutated by replacement with the URA3 gene. When this diploid was sporulated and dissected, only half of the spores were viable. About half of the nonviable spores proceeded through two or three cell divisions and then stopped dividing; the rest did not germinate at all. None of the viable spores contained the mutant ACP2 gene, thus proving that the protein encoded by ACP2 is required for cell viability. The results presented here demonstrate that an HMG-like protein has an essential physiological function.

Domain structure and functional analysis of the carboxyl-terminal polyacidic sequence of the RAD6 protein of Saccharomyces cerevisiae

The RAD6 gene of Saccharomyces cerevisiae, which is required for normal tolerance of DNA damage and for sporulation, encodes a 172-residue protein whose 23 carboxyl-terminal residues are almost all acidic. We show that this polyacidic sequence appends to RAD6 protein as a polyanionic tail and that its function in vivo does not require stoichiometry of length. RAD6 protein was purified to near homogeneity from a yeast strain carrying a RAD6 overproducing plasmid. Approximately the first 150 residues of RAD6 protein composed a structural domain that was resistant to proteinase K and had a Stokes radius typical of a globular protein of its calculated mass. The carboxyl-terminal polyacidic sequence was sensitive to proteinase K, and it endowed RAD6 protein with an aberrantly large Stokes radius that indicates an asymmetric shape. We deduce that RAD6 protein is monomeric and comprises a globular domain with a freely extending polyacidic tail. We tested the phenotypic effects of partial or complete deletion of the polyacidic sequence, demonstrating the presence of the shortened proteins in the cell by using antibody to RAD6 protein. Removal of the entire polyacidic sequence severely reduced sporulation but only slightly affected survival after UV irradiation or UV-induced mutagenesis. Strains with deletions of all but the first 4 or 15 residues of the polyacidic sequence were phenotypically almost wild type or wild type, respectively. We conclude that the intrinsic activity of RAD6 protein resides in the globular domain, that the polyacidic sequence has a stimulatory or modifying role evident primarily in sporulation, and that only a short section apparently functions as effectively as the entire polyacidic sequence.

Isolation of the human gene that complements a temperature-sensitive cell cycle mutation in BHK cells

We have cloned the human genomic DNA and the corresponding cDNA for the gene which complements the mutation of tsBN51, a temperature-sensitive (Ts) cell cycle mutant of BHK cells which is blocked in G1 at the nonpermissive temperature. After transfecting human DNA into TsBN51 cells and selecting for growth at 39.5 degrees C, Ts+ transformants were identified by their content of human AluI repetitive DNA sequences. Following two additional rounds of transfection, a genomic library was constructed from a tertiary Ts+ transformant and a recombinant phage containing the complementing gene isolated by screening for human AluI sequences. A genomic probe from this clone recognized a 2-kilobase mRNA in human and tertiary transformant cell lines, and this probe was used to isolate a biologically active cDNA from the Okayama-Berg cDNA expression library. Sequencing of this cDNA revealed a single open reading frame encoding a polypeptide of 395 amino acids. The deduced BN51 gene product has a high proportion of acidic and basic amino acids which are clustered in four hydrophilic domains spaced at 60- to 80-amino-acid intervals. These domains have strong sequence homology to each other. Thus, the tsBN51 protein consists of periodic repetitive clusters of acidic and basic amino acids.

Retropseudogenes for human chromosomal protein HMG-17

The human genome contains multiple copies of sequences homologous to the cDNA coding for non-histone chromosomal protein HMG-17. To study the mechanism of generation and dispersion of the HMG-17 multigene family a human genomic library was screened and 70 clones isolated and studied by Southern transfer and restriction site analysis. The results suggest that most of the clones contain unique sequences. Sequence analysis of two genomic clones indicates that they contain elements typical of processed retropseudogenes. Even though both sequences contained open reading frames the sequences lacked introns, were flanked by short, direct repeats and lacked elements associated with functional genes. The sequences of the two pseudogenes were 85% homologous to each other and each was 90% homologous to the human cDNA. Based on the sequence difference in the open reading frame between the pseudogenes and the cDNA it can be estimated that the sequences arose approximately ten million years ago from a common precursor. The present paper, which is the first study on genes coding for this nucleosomal binding protein, indicates that the HMG-17 multigene family is the largest known human retropseudogene family.

Isolation of the human gene that complements a temperature-sensitive cell cycle mutation in BHK cells

We have cloned the human genomic DNA and the corresponding cDNA for the gene which complements the mutation of tsBN51, a temperature-sensitive (Ts) cell cycle mutant of BHK cells which is blocked in G1 at the nonpermissive temperature. After transfecting human DNA into TsBN51 cells and selecting for growth at 39.5 degrees C, Ts+ transformants were identified by their content of human AluI repetitive DNA sequences. Following two additional rounds of transfection, a genomic library was constructed from a tertiary Ts+ transformant and a recombinant phage containing the complementing gene isolated by screening for human AluI sequences. A genomic probe from this clone recognized a 2-kilobase mRNA in human and tertiary transformant cell lines, and this probe was used to isolate a biologically active cDNA from the Okayama-Berg cDNA expression library. Sequencing of this cDNA revealed a single open reading frame encoding a polypeptide of 395 amino acids. The deduced BN51 gene product has a high proportion of acidic and basic amino acids which are clustered in four hydrophilic domains spaced at 60- to 80-amino-acid intervals. These domains have strong sequence homology to each other. Thus, the tsBN51 protein consists of periodic repetitive clusters of acidic and basic amino acids.

Characterization of cDNA sequences corresponding to three distinct HMG-1 mRNA species in line CHO Chinese hamster cells and cell cycle expression of the HMG-1 gene

We have isolated cDNA clones encoding the high mobility group (HMG) protein HMG-1 in line CHO Chinese hamster cells. The cDNA clones correspond to the three HMG-1 mRNA species detected on Northern blots. Three different polyadenylation sites are found to be used. The three mRNA species of sizes 1.05, 1.45 and 2.45 kb are generated by differential polyadenylation at sites 115 nucleotides, 513 nucleotides and 1515 nucleotides downstream from the stop codon. A perfectly conserved putative poly(A) signal AAUAAA is present upstream of only one of the three poly(A) sites. Two homologous but imperfect sequences exist upstream from the other two poly(A) sites. All three HMG-1 mRNA species maintain significant levels throughout the M, G1 and S phases of the cell cycle and the rate of large HMG protein (HMG-1 and HMG-2) synthesis increases approximately two-fold from G1 to S phase.