Convergent evolution of cysteine residues in sperm protamines of one genus of marsupials, the Planigales

A characteristic feature of the sperm P1 protamines of eutherian mammals is the constant presence of six to nine cysteine residues per molecule. During spermiogenesis these residues become oxidized to form a three-dimensional network of disulfide bridges between, and within, protamine molecules in the sperm chromatin. This covalent cross linking strongly stabilizes eutherian sperm nuclei. In contrast, protamines sequenced from teleost fish, birds, monotremes, and marsupials all lack cysteine residues and their sperm nuclei, without the stabilizing cross links, are easily decondensed in vitro. We have now found that one genus of tiny, shrewlike dasyurid marsupials, the Planigales, possess P1 protamines containing five to six cysteine residues. These residues appear to have evolved since the divergence of Planigales from other members of the family Dasyuridae, such as the marsupial mouse, Sminthopsis crassicaudata. We believe this constitutes a case of convergent evolution in a subfamily of dasyurid marsupials toward the cysteine-rich eutherian form of sperm protamine P1.      

Evidence for independent recruitment of zeta-crystallin/quinone reductase (CRYZ) as a crystallin in camelids and hystricomorph rodents

Zeta-crystallin/quinone reductase (CRYZ) is an NADPH oxidoreductase expressed at very high levels in the lenses of two groups of mammals: camelids and some hystricomorph rodents. It is also expressed at very low levels in all other species tested. Comparative analysis of the mechanisms mediating the high expression of this enzyme/crystallin in the lens of the Ilama (Lama guanacoe) and the guinea pig (Cavia porcellus) provided evidence for independent recruitment of this enzyme as a lens crystallin in both species and allowed us to elucidate for the first time the mechanism of lens recruitment of an enzyme- crystallin. The data presented here show that in both species such recruitment most likely occurred through the generation of new lens promoters from nonfunctional intron sequences by the accumulation of point mutations and/or small deletions and insertions. These results further support the idea that recruitment of CRYZ resulted from an adaptive process in which the high expression of CRYZ in the lens provides some selective advantage rather than from a purely neutral evolutionary process.      

Matching the crystallographic structure of ribosomal protein S7 to a three-dimensional model of the 16S ribosomal RNA.

Two recently published but independently derived structures, namely the X-ray crystallographic structure of ribosomal protein S7 and the "binding pocket" for this protein in a three-dimensional model of the 16S rRNA, have been correlated with one another. The known rRNA-protein interactions for S7 include a minimum binding site, a number of footprint sites, and two RNA-protein crosslink sites on the 16S rRNA, all of which form a compact group in the published 16S rRNA model (despite the fact that these interactions were not used as primary modeling constraints in building that model). The amino acids in protein S7 that are involved in the two crosslinks to 16S rRNA have also been determined in previous studies, and here we have used these sites to orient the crystallographic structure of S7 relative to its rRNA binding pocket. Some minor alterations were made to the rRNA model to improve the fit. In the resulting structure, the principal positively charged surface of the protein is in contact with the 16S rRNA, and all of the RNA-protein interaction data are satisfied. The quality of the fit gives added confidence as to the validity of the 16S rRNA model. Protein S7 is furthermore known to be crosslinked both to P site-bound tRNA and to mRNA at positions upstream of the P site codon; the matched S7-16S rRNA structure makes a prediction as to the location of this crosslink site within the protein molecule.     

Xenopus laevis 18S ribosomal RNA: experimental determination of secondary structural elements, and locations of methyl groups in the secondary structure model.

18S ribosomal RNA from X. laevis was subjected to partial digestion with ribonucleases A or T1 under a variety of conditions, and base-paired fragments were isolated. Sequence analysis of the fragments enabled five base-paired secondary structural elements of the 18S RNA to be established. Four of these elements (covering bases 221-256, 713-757, 1494-1555 and 1669-1779) confirm our previous secondary structure predictions, whereas the fifth (comprising bases 1103-1125) represents a phylogenetically conserved "switch" structure, which can also form in prokaryotic 16S RNA. The results are incorporated into a refined model of the 18S RNA secondary structure, which also includes the locations of the many methyl groups in X. laevis 18S RNA. In general the methyl groups occur in non-helical regions, at hairpin loop ends, or at helix boundaries and imperfections. One large cluster of 2'-O-methyl groups occurs in a region of complicated secondary structure in the 5'-one third of the molecule.     

The three-dimensional folding of ribosomal RNA; localization of a series of intra-RNA cross-links in 23S RNA induced by treatment of Escherichia coli 50S ribosomal subunits with bis-(2-chloroethyl)-methylamine.

Intact 50S ribosomal subunits from E.coli were cross-linked with the symmetrical bifunctional reagent bis-(2-chloroethyl)-methylamine. After deproteinization, selected regions of the 23S RNA were excised by treatment with ribonuclease H in the presence of appropriate complementary decadeoxynucleotides, and screened for the presence of intra-RNA cross-links by two-dimensional gel electrophoresis. Individual isolated cross-linked RNA fragments were analysed by our established procedures. Sixteen intra-RNA cross-links were identified, three of which corresponded to those previously published. The thirteen 'new' cross-links were localized in the 23S RNA at positions 774-78 linked to 792-94, 876-79 linked to 899-900, 979-81 or 983-84 to 2029, 1715 to 1743-46, 1911-21 to 1964, 1933 to 1966, 2032 to 2054-55, 2112 to 2169-71, 2116-17 to 2163-67, 2128-32 to 2156-59, 2392-93 to 2422-23, 2737-38 to 2763-66, and 2791 to 2890. These results are discussed in the context of three-dimensional model-building studies with the 23S RNA, with particular reference to the environment of the 'active centre' of the 50S subunit.     

Precise localisation of three intra-RNA cross-links in 23S RNA and one in 5S RNA, induced by treatment of Escherichia coli 50S ribosomal subunits with bis-(2-chloroethyl)-methylamine.

Treatment of E. coli 50S ribosomal subunits with low doses of bis-(2-chloroethyl)-methylamine ("nitrogen mustard") leads to formation of a number of intra-RNA and RNA-protein cross-links. After partial digestion of the cross-linked subunits with cobra venom nuclease, followed by destruction of the protein moiety with proteinase K, complexes containing the intra-RNA cross-links were isolated by two-dimensional gel electrophoresis. The individual complexes were subjected to oligonucleotide analysis, either directly or after a second partial digestion procedure using ribonuclease T1, and the cross-link sites determined. In 23S RNA, the cross-links found were between bases 763 and 1567, 1210 and 1236, 1482 and 1501; in 5S RNA, base 69 was cross-linked to base 107. The significance of these cross-links in relation to the three-dimensional organization of the ribosomal RNA is discussed.     

An approach to the synthesis of branched-chain amino sugars from c-methylene sugars

The reaction of 1,2:5,6-di-O-isopropylidene-3-C-methylene-α-D-ribo-hexofuranose (4) with mercuric azide in hot 50% aqueous tetrahydrofuran yielded, after reductive demercuration, 3-azido-3-deoxy-1,2:5,6-di-O-isopropylidene-3-C-methyl-α-D-glucofuranose (5). Partial, acid hydrolysis of5 afforded the diol7, which gave 3-azido-3-deoxy-1,2-O-isopropylidene-5,6-di-O-methanesulphonyl-3-C-methyl-α-D-glucofuranose (8) on sulphonylation. On hydrogenation over a platinum catalyst and N-acetylation, the dimethanesulphonate 8 furnished 3,6-acetylepimino-3,6-dideoxy-1,2-O-isopropylidene-5-O-methanesulphonyl-3-C-methyl-α-D-glucofuranose (9), which was also prepared by an analogous sequence of reactions on 3-azido-3-deoxy-1,2-O-isopropylidene-5-O-methanesulphonyl-3-C-methyl-6-O-toluene-p-sulphonyl-α-D-glucofuranose (13). The formation of the N-acetylepimine 9 establishes the D-gluco configuration for 5.1,2-O-Isopropylidene-3-C-methylene-α-D-ribo-hexofuranose (20) reacted with mercuric azide in aqueous tetrahydrofuran at ≈85° to give 3,6-anhydro-1,2-O-isopropylidene-3-C-methyl-α-D-glucofuranose (22) as a result of intramolecular participation by the C-6 hydroxyl group in the initial intermediate.     

Nucleophilic displacements of methyl 2,3-O-isopropylidene-4-O-toluene-p-sulphonyl-α-d-lyxo- and -β-l-ribo-pyranosides,and deamination of the corresponding 4-amino sugars

Reinvestigation of the reaction of methyl 2,3-O-isopropylidene-4-O-toluene-p-sulphonyl-α-d-lyxopyranoside (4) with azide ion has shown that methyl 4-deoxy-2,3-O-isopropylidene-β-l-erythro-pent-4-enopyranoside (8, ～51.5%) is formed, as well as the azido sugar 7 (～48.5%) of an S_N2 displacement. The unsaturated sugar 8 was more conveniently prepared by heating the sulphonate 4 with 1,5-diazabicyclo-[5.4.0]undec-5-ene. An azide displacement on methyl 2,3-O-isopropylidene-4-O-toluene-p-sulphonyl-β-l-ribopyranoside (12) furnished methyl 4-azido-4-deoxy-2,3-O-isopropylidene-α-d-lyxopyranoside (13, ～66%) and the unsaturated sugar 14 (～28.5%), which was also prepared by heating the sulphonate with 1,5-diazabicyclo[5.4.0]undec-5-ene. Deamination of methyl 4-amino-4-deoxy-2,3-O-isopropylidene-α-d-lyxopyranoside (5), prepared by reduction of 13, with sodium nitrite in 90% acetic acid at ～0°, yielded methyl 2,3-O-isopropylidene-α-d-lyxopyranoside (10a, 26.2%), methyl 2,3-O-isopropylidene-β-l-ribofuranoside (21a, 18.4%), and the corresponding acetates 10b (34.5%) and 21b (21.3%). These products are considered to arise by solvolysis of the bicyclic oxonium ion 29, formed as a consequence of participation by the ring-oxygen atom in the deamination reaction. Similar deamination of methyl 4-amino-4-deoxy-2,3-O-isopropylidene-β-l-ribopyranoside (6) afforded, exclusively, the products 10a (34.4%) and 10b (65.6%) of inverted configuration. Deamination of methyl 5-amino-5-deoxy-2,3-O-isopropylidene-β-d-ribofuranoside (20) gave 22ab, but no other products. An alternative synthesis of the amino sugars 5 and 6 is available by conversion of 10a into methyl 2,3-O-isopropylidene-β-l-erythro-pentopyranosid-4-ulose (11), followed by reduction of the derived oxime 15 with lithium aluminium hydride.