Organization and nucleotide sequence of rainbow trout histone H2A and H3 genes

Gordon H. Dixon's trace in my personal career and the quantic jump experienced in regulatory information

Even before Rosalin Franklin had discovered the DNA double helix, in her impressive X-ray diffraction image pattern, Erwin Schröedinger, described, in his excellent book, What is Life, how the finding of aperiodic crystals in biological systems surprised him (an aperiodic crystal, which, in my opinion is the material carrier of life). In the 21st century and still far from being able to define life, we are attending to a quick acceleration of knowledge on regulatory information. With the discovery of new codes and punctuation marks, we will greatly increase our understanding in front of an impressive avalanche of genomic sequences. Trifonov et al. defined a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology. These patterns are largely captured in transcribed messages that give meaning and identity to the particular cells. In this review, I will go through my personal career in and after my years of work in the laboratory of Gordon H. Dixon, extending toward the impressive acquisition of new knowledge on regulatory information and genetic codes provided by remarkable scientists in the field. Abbreviations: CA II: carbonic anhydridase II (chicken); Car2: carbonic anhydridase 2 (mouse); CpG islands: short (>0.5 kb) stretches of DNA with a G+C content ≥55%; DNMT1: DNA methyltransferases 1; DNMT3b: DNA methyltransferases 3B; DSB: double-strand DNA breaks; ERT: endogenous retrotransposon; ERV: endogenous retroviruses; ES cells: embryonic stem cells; GAPDH: glyceraldehide phosphate dehydrogenase; H1: histone H1; HATs: histone acetyltransferases; HDACs: histone deacetylases; H3K4me3: histone 3 trimethylated at lys 4; H3K79me2: histone 3 dimethylated at lys 79; HMG: high mobility group proteins; HMT: histone methyltransferase; HP1: heterochromatin protein 1; HR: homologous recombination; HSE: heat-shock element; ICRs: imprinted control regions; IRF: interferon regulatory factor; LDH-A/-B: lactate dehydrogenase A/B; LTR: long terminal repeats; MeCP2: methyl CpG binding protein 2; OCT4: octamer-binding transcription factor 4; PAF1: RNA Polymerase II associated factor 1; piRNA: PIWI-interacting RNA; poly(A) tails: poly-adenine tails; PRC2: polycomb repressive complex 2; PTMs: post-translational modifications; SIRT 1: sirtuin 1, silent information regulator; STAT3: signal transducer and activator of transcription; tRNAs: transfer RNA; tRFs: tRNA-derived fragments; TSS: transcription start site; TE: transposable elements; UB I: polyubiquitin I; UB II: polyubiquitin II; UBE 2N: ubiquitin conjugating enzyme E2N; 5'-UTR: 5'-untranslated sequences; 3'-UTR: 3'-untranslated sequences.

The growth hormone-encoding gene isolated and characterized from Labeo rohita Hamilton is expressed in CHO cells under the control of constitutive promoters in 'autotransgene' constructs

The growth hormone (GH) gene along with its regulatory sequences has been isolated from the blood and pituitary gland of Labeo rohita. This GH gene is approximately 2.8 kb long and consists of five exons and four introns of varying sizes with AG/TA in its exon-intron junctions. The promoter has a single cyclic AMP response unit (CRE) element, TATA, CAT and several Pit 1 binding sequences. The 1169-bp gene transcript starts 54 bp upstream of the ATG initiation codon and has two polyadenylation signals, ATTAAA, after the TAG stop codon. The mature mRNA has the poly (A) tail inserted 16 bp downstream of the second polyadenylation signal. Four chimeric 'autotransgenes' were constructed having either histone 3 or beta-actin promoter and cDNA or the total GH gene. The functionality of the individual components of the autotransgene was determined in the Chinese hamster ovary (CHO) cells by transfection experiments. Based on the results, the transcription of the GH gene is initiated at the transcription start signal of the respective promoters and terminates at the 3' regulatory sequence of the GH gene. Expression of GH in CHO cells shows that the fish promoters are active, the splicing signal is recognized, and the mRNA produced is stable and translated. The GH protein produced is effectively translocated and secreted into the medium. These results indicate the usefulness of CHO cells in determining the property of individual components of autotransgenes constructed from L. rohita and overall functional commonality between fish and mammal.

The isoelectric point, a key to understanding a variety of biochemical problems: a minireview

We address the importance of the isoelectric point (IEP) of proteins and membrane components such as phospholipids for our understanding and interpretation of isoforms and opposite charge interactions in the formation of complexes. Five examples drawn from the literature are newly approached from the IEP point of view to clarify general principles.

Molecular evolutionary characterization of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of five histone genes containing an H1 subtype with "orphon" features

The present work represents the first characterization of a clustered histone repetitive unit containing an H1 gene in a bivalve mollusk. To complete the knowledge on the evolutionary history of the histone multigene family in invertebrates, we undertake its characterization in five mussel Mytilus species, as an extension of our previous work on the H1 gene family. We report the quintet H4-H2B-H2A-H3-H1 as the major organization unit in the genome of Mytilus galloprovincialis with two 5S rRNA genes with interspersed nontranscribed spacer segments linked to the unit, which is not justified by their cotranscription with histone genes. Surprisingly, 3' UTR regions of histone genes show two different mRNA termination signals, a stem-loop and a polyadenylation signal, both related to the evolution of histone gene expression patterns throughout the cell cycle. The clustered H1 histones characterized share essential features with "orphon" H1 genes, suggesting a common evolutionary origin for both histone subtypes which is supported by the reconstructed phylogeny for H1 genes. The characterization of histone genes in four additional Mytilus species revealed the presence of strong purifying selection acting among the members of the family. The chromosomal location of most of the core histone genes studied was identified by FISH close to telomeric regions in M. galloprovincialis. Further analysis on nucleotide variation would be necessary to assess if H1 proteins evolve according to the birth-and-death model of evolution and if the effect of the strong purifying selection maintaining protein homogeneity could account for the homologies detected between clustered and "orphon" variants.

Anti-microbial properties of histone H2A from skin secretions of rainbow trout, Oncorhynchus mykiss

Skin exudates of rainbow trout contain a potent 13.6 kDa anti-microbial protein which, from partial internal amino acid sequencing, peptide mass fingerprinting, matrix-associated laser desorption/ionization MS and amino acid analysis, seems to be histone H2A, acetylated at the N-terminus. The protein, purified to homogeneity by ion-exchange and reversed-phase chromatography, exhibits powerful anti-bacterial activity against Gram-positive bacteria, with minimal inhibitory concentrations in the submicromolar range. Kinetic analysis revealed that at a concentration of 0.3 microM all test bacteria lose viability after 30 min incubation. Weaker activity is also displayed against the yeast Saccharomyces cerevisiae. The protein is salt-sensitive and has no haemolytic activity towards trout erythrocytes at concentrations below 0.3 microM. Reconstitution of the protein in a planar lipid bilayer strongly disturbs the membrane but does not form stable ion channels, indicating that its anti-bacterial activity is probably not due to pore-forming properties. This is the first report to show that, in addition to its classical function in the cell, histone H2A has extremely strong anti-microbial properties and could therefore help contribute to protection against bacterial invasion.

Cathepsin D produces antimicrobial peptide parasin I from histone H2A in the skin mucosa of fish

Parasin I is a potent 19-residue antimicrobial peptide isolated from the skin mucus of wounded catfish (Parasilurus asotus). Here we describe the mechanism of parasin I production from histone H2A in catfish skin mucosa on epidermal injury. Cathepsin D is found to exist in the mucus as an inactive proenzyme (procathepsin D), and a metalloprotease, induced on injury, cleaves procathepsin D to generate active cathepsin D. This activated form of cathepsin D then cleaves the Ser19-Arg20 bond of histone H2A to produce parasin I. Immunohistochemical analysis reveals that unacetylated histone H2A, a precursor of parasin I, and procathepsin D are present in the cytoplasm of epithelial mucous cells and that parasin I is produced on the mucosal surface on epidermal injury. Western blot analysis shows that parasin I is also present in the skin mucus of other fish species. Furthermore, parasin I shows good antimicrobial activity against fish-specific bacterial pathogens. Taken together, these results indicate that cathepsin D and a metalloprotease participate in the production of parasin I from histone H2A and that parasin I contributes to the innate host defense of the fish against invading microorganisms.

Organization and chromosomal location of the major histone cluster in brown trout, Atlantic salmon and rainbow trout

The major histone cluster (hisDNA) was mapped by fluorescent in situ hybridization (FISH) to mitotic chromosomes of Atlantic salmon, brown trout, and rainbow trout. The data reveal that in the three species hisDNA is tandemly repeated in a single locus. Southern blots of genomic DNA indicate that these clusters are representative of the vast majority of the histone genes in these species. Similar reiteration values were found among the three species. Genetic variability in the hisDNA was found only in brown trout for an EcoRI site.

Analysis of the core histone gene cluster of the annelid Platynereis dumerilii

The arrangement of the polychaete annelid Platynereis dumerilii core histone gene cluster and nucleotide sequence has been reported (D. Sellos, S. A. Krawetz and G. H. Dixon, 1990). The H2B and H3 mRNAs are transcribed from one DNA strand, while the H2A and H4 histone mRNAs are transcribed from the other. The H1 gene is not contained as a member of this cluster. Computer assisted sequence analysis of this region was undertaken to define the organization and representation of the various sequence motifs embedded within this region. The analysis revealed that two large regions on opposite strands of the cluster were similar to one another. This organization is reminiscent of an ancient gene duplication event from which the various members independently evolved.

Organization and complete nucleotide sequence of the core-histone-gene cluster of the annelid Platynereis dumerilii

The arrangement of the core-histone genes, their transcriptional polarity and their nucleotide sequences have been determined for the polychaete annelid Platynereis dumerili. A clone containing the core-histone genes was isolated from a annelid genomic library constructed in the EMBL-4 phage vector, using a trout H3 genomic probe. This clone was found to contain two and a half repeats of a 6-kbp EcoRV fragment that contained one copy of each of the core-histone genes. The clusters are tandemly arrayed in the genome and the gene order within the core-histone cluster does not vary. Absolutely no differences were found in the nucleotide sequences comprising the same part of two adjacent clusters (bases -225 to 2776 and bases 5821 to 8825). The number of copies of the cluster appeared to be high: approximately 660 copies/diploid cell, as also observed in sea urchins and amphibians. There are also some additional subtypes of histone gene organization: multimers of tandemly arrayed genes and isolated genes; these are present at a much lower copy number (an average of 40-50 copies/diploid genome). Two mRNAs (for H2B and H3) are transcribed from one DNA strand and the two other histone mRNAs (for H2A and H4) from the other strand as is the case for some insects and certain vertebrates. No H1-coding sequence has been found in the completely sequenced four-membered cluster. The organization of histone genes in P. dumerilii is similar to the clustering found in Caenorhabditis elegans but in this nematode worm several different types of organization are observed with a low copy number for each.

Cloning and characterization of a histone gene family in Tilapia fish

Genomic organization and expression of a histone gene family in the Tilapia (Cichlidae) fish was determined. A genomic library was prepared; four clones containing the complete set of core histones were analyzed. These clones differed significantly in their restriction maps, although three of them revealed a uniform internal gene arrangement of the core histone genes. Differential expression between two of the cloned clusters was observed when the hybridization pattern of those clusters to various RNA preparations was compared. The copy number of histone genes was estimated to be 100 to 110 for haploid Tilapia genome.

Transitions, transversions, and the molecular evolutionary clock

Nucleotide substitutions in the form of transitions (purine-purine or pyrimidine-pyrimidine interchanges) and transversions (purine-pyrimidine interchanges) occur during evolution and may be compiled by aligning the sequences of homologous genes. Referring to the genetic code tables, silent transitions take place in third positions of codons in family boxes and two-codon sets. Silent transversions in third positions occur only in family boxes, except for A = C transversions between AGR and CGR arginine codons (R = A or G). Comparisons of several protein genes have been made, and various subclasses of transitional and transversional nucleotide substitutions have been compiled. Considerable variations occur among the relative proportions of transitions and transversions. Such variations could possibly be caused by mutator genes, favoring either transitions or, conversely, transversions, during DNA replication. At earlier stages of evolutionary divergence, transitions are usually more frequent, but there are exceptions. No indication was found that transversions usually originate from multiple substitutions in transitions.

A highly conserved sequence in H1 histone genes as an oligonucleotide hybridization probe: isolation and sequence of a duck H1 gene

A 3.5-kb HindIII fragment of a histone gene cluster was isolated from a recombinant phage out of a duck genomic library. This DNA contains a duck H1 gene and its flanking sequences. The hybridization probe, which was used to screen for the H1 gene, had been designed on the basis of a comparative analysis of available H1 gene and protein data. Most H1 histones contain repeated motifs in their C-terminal domain, and these form part of an octapeptide (ser pro lys lys ala lys lys pro) that is highly conserved in many H1 histone proteins. A comparison of the duck H1 described here with two different published chicken H1 histone sequences reveals conservative amino acid exchanges at 22 (of 217 and 218, respectively) positions. The homology is maintained at the flanking sequences, and includes the putative H1 histone gene-specific signal structures and the established 3' stem and loop structures and the CAAGA box. The duck H1 gene and its flanking sequence have been found in identical arrangements in two recombinant bacteriophages, but minor sequence variations and genomic Southern blotting after HindIII digestion suggest that we have either isolated alleles of this genome segment or that the gene described may occur twice per haploid duck genome.

Histones and their modifications

Histones constitute the protein core around which DNA is coiled to form the basic structural unit of the chromosome known as the nucleosome. Because of the large amount of new histone needed during chromosome replication, the synthesis of histone and DNA is regulated in a complex manner. During RNA transcription and DNA replication, the basic nucleosomal structure as well as interactions between nucleosomes must be greatly altered to allow access to the appropriate enzymes and factors. The presence of extensive and varied post-translational modifications to the otherwise highly conserved histone primary sequences provides obvious opportunities for such structural alterations, but despite concentrated and sustained effort, causal connections between histone modifications and nucleosomal functions are not yet elucidated.

Histone H4 and H2B genes in rainbow trout (Salmo gairdnerii)

The complete nucleotide sequence of the 3.0-kb BamH I-Sst I restriction fragment contained within the rainbow trout genomic clone lambda TH2 has been determined. This region contains the rainbow trout H4 and H2B histone genes and 5' and 3' flanking and spacer sequences, and represents the 5' half of the histone-gene cluster; the remaining half has been characterized previously. The genes are uninterrupted, and are transcribed from the same strand. The protein sequence of H4, as determined from the nucleic acid sequence, is the same as that derived for other vertebrate H4 proteins, although comparison of nucleotide sequences shows a great deal of sequence divergence, especially in the third base position. The amino acid sequence of H2B, though largely homologous to those of other vertebrate H2B proteins, displays some characteristic differences in primary structure. Consensus sequences noted in many other eukaryotic genes, as well as histone-specific consensus sequences, have been identified. An unusual feature of the spacer region between the H4 and H2B genes is the presence of a duplicated sequence 87 bp in length. The 5' and 3' ends of each repeat are complementary, and each repeat contains smaller repeated sequences internally, as well as a possible cruciform structure.

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

A specific oligonucleotide has been used to isolate a cDNA prepared from the mRNA for a trout High Mobility Group (HMG) protein closely related to trout HMG-T and bovine HMG 1 and 2 proteins. The sequence isolated more closely resembles bovine HMG-1 than the previously sequenced HMG-T protein in regions corresponding to the N terminal half of the protein. Northern blot analysis at low stringency indicated that 2 related sequences are expressed in total trout testis mRNA. Southern blots of total trout DNA indicate that several different forms of the homologous sequence are present in the trout genome and an estimate of copy number by dot-blot shows 4 HMG-T genes per trout sperm DNA equivalent. Analysis of mRNA from several trout tissues, including testis, liver and kidney indicates that expression of genes for histones and the larger HMG proteins in trout is not closely coupled.

An H1 histone gene from rainbow trout (Salmo gairdnerii)

A 1.7-kbp DNA region from the 10.2-kb cluster containing the five rainbow trout histone genes has been subcloned in pBR322 and completely sequenced. It contains a trout histone H1 gene together with its 5' and 3' flanking sequences. This H1 gene codes for a H1 variant different from the major trout testis H1 previously sequenced by Macleod et al. (1977). Northern blots of total RNA from trout testis, kidney, and liver indicate that this H1 gene is expressed in all three tissues but that the level of H1 mRNA is much higher in testis than in other tissues. The lack of heterogeneity in the sizes and 5' initiation sites of trout H1 mRNAs is surprising in view of the substantial heterogeneity of H1 variant proteins observed previously. The coding sequence of the H1 gene shows strong evidence of repeated partial duplications of a hexapeptide motif of the form Ala.Ala.Ala.Lys.Lys.Pro and of a pentapeptide phosphorylation-site sequence, Lys.Ser.Pro.Lys.Lys, during its evolution. Comparisons are drawn between this gene and the coding sequences of other vertebrate H1 genes from chicken and Xenopus, and a strong homology is seen in the region of amino acids 22-101, which form the hydrophobic "head" of the H1 molecule. The 5' and 3' regulatory signals in the trout H1 are also compared with those of H1 genes from other sequences.

Organization of the histone genes in the rainbow trout (Salmo gairdnerii)

Twelve clones containing histone genes were isolated from a genomic trout library constructed in the vector Charon 4A. Each of the clones was found to contain a conserved 10.2-kb Eco RI fragment that contained one copy of each of the histones in the order H4-H2B-H1-H2A-H3, all of which are transcribed from the same strand. Genomic Southern blots indicate that these clusters are representative of the vast majority of the histone genes in the trout. Tandemly linked clusters were not found. Approximately 145 copies of this cluster are present in a trout sperm cell. Sequence analysis has shown the genes to be without introns and to show strong selection for codons ending in C or G. Consensus signals similar to those found in other histone genes are present in the flanking regions.