Two high-mobility group box domains act together to underwind and kink DNA.

High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1-DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

Spermiogenesis and biflagellate spermatozoon of the teleost fish Lampanyctus crocodilus (Myctophiformes, Myctophidae): ultrastructure and characterisation of its sperm basic nuclear proteins.

We undertook an ultrastructural study of the spermiogenesis of the lanternfish Lampanyctus crocodilus (Myctophiformes, Myctophidae) with special emphasis on the condensation of chromatin and the biochemical characterisation of its sperm nuclear basic proteins (SNBPs). The round head of the early spermatid of L. crocodilus develops into a curved conical-shaped head in the spermatozoon. Two flagella, present even in the spermatid, are inserted laterally at the convex side of the sperm head. Both flagella possess an axoneme with a 9 + 0 instead of the typical 9 + 2 axonemal structure. Mitochondria undergo a characteristic redistribution during spermiogenesis. A reduced number of them are present lying away from the centrioles at both ends of the concave side of the sperm head. During the chromatin condensation stages in spermiogenesis, fibrogranular structures with granules of 25 ± 5 and 50 ± 5 nm can be observed in the early spermatid and develop into larger granules of about 150 ± 50 nm in the middle spermatid. The latter granules coalesce during the transition to the advanced spermatid and spermatozoon giving rise to highly condensed chromatin in the sperm cell. Protamines are the main SNBPs associated with this chromatin; however, they are unusually large and correspond to the largest protamines described in fish to date. Small stoichiometric amounts of histones and other basic proteins coexist with these protamines in the spermatozoon.

Complex chromatin condensation patterns and nuclear protein transitions during spermiogenesis: examples from mollusks.

In this paper we review and analyze the chromatin condensation pattern during spermiogenesis in several species of mollusks. Previously, we had described the nuclear protein transitions during spermiogenesis in these species. The results of our study show two types of condensation pattern: simple patterns and complex patterns, with the following general characteristics: (a) When histones (always present in the early spermatid nucleus) are directly replaced by SNBP (sperm nuclear basic proteins) of the protamine type, the spermiogenic chromatin condensation pattern is simple. However, if the replacement is not direct but through intermediate proteins, the condensation pattern is complex. (b) The intermediate proteins found in mollusks are precursor molecules that are processed during spermiogenesis to the final protamine molecules. Some of these final protamines represent proteins with the highest basic amino acid content known to date, which results in the establishment of a very strong electrostatic interaction with DNA. (c) In some instances, the presence of complex patterns of chromatin condensation clearly correlates with the acquisition of specialized forms of the mature sperm nuclei. In contrast, simple condensation patterns always lead to rounded, oval or slightly cylindrical nuclei. (d) All known cases of complex spermiogenic chromatin condensation patterns are restricted to species with specialized sperm cells (introsperm). At the time of writing, we do not know of any report on complex condensation pattern in species with external fertilization and, therefore, with sperm cells of the primitive type (ect-aquasperm). (e) Some of the mollusk an spermiogenic chromatin condensation patterns of the complex type are very similar (almost identical) to those present in other groups of animals. Interestingly, the intermediate proteins involved in these cases can be very different.In this study, we discuss the biological significance of all these features and conclude that the appearance of precursor (intermediate) molecules facilitated the development of complex patterns of condensation and, as a consequence, a great diversity of forms in the sperm cell nuclei

Physicochemical and functional comparison of Xenopus laevis nucleoplasmin obtained from oocytes and from overexpression in bacteria.

We compare the physicochemical and functional characteristics of nucleoplasmin obtained from Xenopus laevis oocytes and by bacterial overexpression of a plasmid containing the nucleoplasmin gene. The comparison shows that, while the secondary structure of the protein is not affected by the method used to obtain this protein, the bacterial expressed form exhibits a marked tendency to form large aggregates and an impaired ability to displace protamines from sperm nuclei. These results add a word of caution to the indiscriminate use, in functional or structural (crystallographic) studies, of bacterially overproduced proteins that have been end-terminally tagged with polyhistidine.

Primary structure of scombrine alpha: two different species with an identical protamine.

We have studied the protamine scombrine alpha from the mackerel Scomber scombrus. Scombrine alpha is found phosphorylated in spermatid nuclei, but not in nuclei of ripe sperm. It is a typical fish protamine, made up of two distinct molecular species, each of 34 amino acid residues. The primary structure of the main component of scombrine alpha is 100% identical to scombrine gamma, the nonmicroheterogeneous protamine from Scomber australasicus (11). The second component of scombrine alpha is a very minor molecular species that has an isoleucine instead of a valine in position 11. Nuclear sperm-specific basic proteins display an enormous interspecific variability and it is very surprising that two different species show identical protamines. In this work we suggest that evolutionary changes in primary structure of protamines are restricted by several constitutive factors, especially when protamines either lack or have a low degree of microheterogeneity.

Sperm nuclear basic proteins (SNBPs) of agnathans and chondrichthyans: variability and evolution of sperm proteins in fish.

We have characterized for the first time SNBPs from the hagfish Eptatratus stouti (Myxini) and the lamprey Lampetra tridentatus (Cephalaspidomorphi) and have found that histones are the major protein components of the sperm of these agnathans. We have also conducted a systematic analysis of SNBPs from different groups of chondrichthyan fishes, including the skate Raja rhina and seven species of sharks. Together with our previous data showing the sporadic nature of SNBP evolution in bony fish (Saperas, N., Ausio, J., Lloris, D. and Chiva, M. [1994] J. Mol. Evol. 39: 282-295), the present study provides a unique insight into the overall evolutionary complexity and variability of the nuclear sperm proteins of fishes. It would appear that despite the discontinuous evolution of these proteins, the macroevolutionary pattern of histone (H type) --> protamine-like (PL type) --> protamine (P type) has been conserved in fish evolution, as it has in the evolution of other Deuterostomes.

The primary structure of a chondrichthyan protamine: a new apparent contradiction in protamine evolution.

We have determined the primary structure of protamine R3 from ratfish (Hydrolagus colliei), a species belonging to the order Chimaeriformes (an old phylogenetic line among the chondrichthyes). Protamine R3 contains 48 residues organized as follows: ARRRH SMKKK RKSVR RRKTR KNQRK RKNSL GRSFK (Q/A)HGFL KQPPR FRP. Comparison of this sequence with both protamine Z3 from Scyliorhinus canicula (a chondrichthyan) and typical protamines from bony fish generates an apparent contradiction: Two relatively close species (H. colliei and S. canicula, both chondichthyes) display different protamines, whereas species more distant in evolution (S. canicula and bony fish) contain very similar protamine molecules. We note that this is not an isolated case in the evolution of sperm nuclear basic proteins (SNBPs) and discuss the possible significance of this fact.

On the evolution of protamines in bony fish: alternatives to the "retroviral horizontal transmission" hypothesis.

Fish protamines are highly specialized molecules which are responsible for chromatin condensation during the last stages of spermatogenesis (spermiogenesis). However, not all fish contain protamines in their sperm nuclei; rather, there seems to be a random distribution of protamines within this group. The origin of this sporadic presence of protamines in the sperm and its significance have not yet been precisely determined. In this paper we have conducted an exhaustive survey of the literature available on the different types of nuclear protein composition of the sperm of teleost fish in order to try to correlate these data with what is presently known about the taxonomy of this group. The results of this analysis have allowed us to make the following observations. The divergence between protamines and histones has occurred several times during the evolution of the bony fish. However, the relative frequency of this divergence is almost negligible during the differentiation of genera and species (intrafamily variation) and is very small during the differentiation of families (interfamily variation). Nevertheless, the divergence is very noticeable among the different orders. It is therefore possible to conclude from all this that the sporadic distribution of protamines in bony fish is not a random event as initially believed. Furthermore, such a heterogeneous distribution of protamines cannot be easily accounted for by a mechanism of horizontal retroviral transmission through repeated and independent acquisition of a protamine gene as has been recently proposed (Jankowski, Stater, Dixon (1986) J Mol Evol 23:1-10). Rather, it could possibly be explained by a repeated and independent loss of the expression of the protamine gene (or loss of the gene itself) which mainly occurred during the diversification of the orders of this group.

Chromosomal Proteins of the Sperm of a Cephalochordate (Branchiostoma floridae) and an Agnathan (Petromyzon marinus): Compositional Variability of the Nuclear Sperm Proteins of Deuterostomes.

We have isolated and characterized for the first time the chromosomal proteins from the nucleus of the sperm of a lancelet (amphioxus) Branchiostoma floridae (Hubbs, 1922) (Phylum Chordata: Subphylum Cephalochordata) and of a lamprey Petromyzon marinus (Linnaeus, 1758) (Phylum Chordata: Subphylum Vertebrata: Class Agnatha). In the first case, the major protein component of the sperm-chromatin of a lancelet is a highly specialized protamine-like (PL) protein that has structural and compositional features similar to those of PL-III from bivalve mollusks. In contrast, the chromatin of the sperm of the lamprey has a structural arrangement and protein composition (histones) very similar to that found in the somatic cells of all eukaryotic organisms. Among the deuterostomes, chromosomal protein variability is considerably greater in representatives of the Phylum Chordata than in echinoderms. The possible evolutionary significance of these findings is discussed.

Sperm-Specific Basic Proteins in the Holocephalan Fish Hydrolagus colliei (Chondrichthyes, Chimaeriformes) and Comparison with Protamines from an Elasmobranch.

Seven basic proteins can be isolated from sperm nuclei of the holocephalan ratfish Hydrolagus colliei. Two of these proteins (R3 and m0) are devoid of cysteine, whereas five of them (R1, R2, m1, m2, and m3) contain low levels of this amino acid residue. The proteins R1, R2, and R3 are major ones in the sperm nuclei of H. colliei, and they are analogous to basic proteins Z1, Z2, and Z3 (scylliorhinines) from the sperm of the elasmobranch Scyliorhinus canicula. However, taking into account the partial sequence of R3 protein and the number of cysteines in R1 and R2, these proteins do not seem to be homologous to the scylliorhinines. A comparison of sperm basic proteins between H. colliei (a holocephalan) and S. canicula (an elasmobranch) suggests a remarkable divergence of these proteins from a common ancestral pattern during the evolution of Chondrichthyes.

Differences in chromatin condensation during spermiogenesis in two species of fish with distinct protamines.

The sperm cells of Mullus surmuletus (family Mullidae, order Perciformes) and Dicentrarchus labrax (family Percichthyidae, order Perciformes) belong respectively to "type I" and "type II" spermiogenesis categorized by Mattei ('70). The protein content in their sperm nuclei consists of two histone-like proteins (Mullus surmuletus) and one typical protamine (D. labrax). In order to correlate the molecular characteristics of these proteins with their function, we have analyzed the molecules in detail and studied at the ultrastructural level the condensation of chromatin during the spermiogenesis in both species. D. labrax has a true protamine of 34 amino acid residues and its sequence (PR4QASRPVR5TR2STAER5V2R4) contains four arginine clusters. The sperm proteins of M. surmuletus contain 110 and 115 amino acid residues and , by their composition (23-24% Lys, 21-22% Arg, 11-12% Ala), they are similar to protamine-like molecules from sperm of molluscs. During the spermiogenesis of D. Labrax, chromatin condensation progresses from small fibro-granular structures (25 +/- 5 nm in diameter), to larger granules (150 +/- 50 nm diameter). M. surmuletus accumulates 25 +/- 5 nm diameter structures in the basal pole of the nucleus; these structures grow till they reach a diameter of 50 +/- 10 nm and finally go through a process of fusion that changes the condensation of chromatin in sperm nuclei, acquiring a homogeneous aspect. These observations show that during spermiogenesis in the studied types, the last stages of chromatin condensation are dependent on the type of nuclear proteins.