Identification and Characterisation of a Novel Acylpeptide Hydrolase from Sulfolobus Solfataricus: Structural and Functional Insights

A novel acylpeptide hydrolase, named APEH-3Ss, was isolated from the hypertermophilic archaeon Sulfolobus solfataricus. APEH is a member of the prolyl oligopeptidase family which catalyzes the removal of acetylated amino acid residues from the N terminus of oligopeptides. The purified enzyme shows a homotrimeric structure, unique among the associate partners of the APEH cluster and, in contrast to the archaeal APEHs which show both exo/endo peptidase activities, it appears to be a “true” aminopeptidase as exemplified by its mammalian counterparts, with which it shares a similar substrate specificity. Furthermore, a comparative study on the regulation of apeh gene expression, revealed a significant but divergent alteration in the expression pattern of apeh-3Ss and apehSs (the gene encoding the previously identified APEHSs from S. solfataricus), which is induced in response to various stressful growth conditions. Hence, both APEH enzymes can be defined as stress-regulated proteins which play a complementary role in enabling the survival of S. solfataricus cells under different conditions. These results provide new structural and functional insights into S. solfataricus APEH, offering a possible explanation for the multiplicity of this enzyme in Archaea

Helinoto, a Helitron2 transposon from the icefish Chionodraco hamatus, contains a region with three deubiquitinase-like domains that exhibit transcriptional activity

Transposable elements have accompanied the evolution of the eukaryotic genome for millions of 26 years. The recently discovered Helitron order (class II, subclass 2 single-strand DNA transposons) 27 is common in eukaryotes and seems to play a highly active role in genome reshuffling. This study 28 provides novel insights into the characteristics of Helinoto, a helitron isolated in the genome of the 29 Antarctic fish Chionodraco hamatus. In particular, investigation of the structure of its 5‘ and 3' 30 ends, which are involved in the transposition process, enabled identification of the characteristic 31 motifs of the Helitron2 group. Moreover, identification of a deubiquitinating protease domain in the 32 region upstream two consecutive OTU domains extended and strengthened the ―deubiquitinase‖ 33 character of the N-terminal portion of Helinoto. Finally, Helinoto transcriptional activity was 34 detected in several C. hamatus tissues. Taken together, these data are particularly intriguing because 35 they document high transcription levels for genes involved in ubiquitination, which ensures protein 36 homeostasis in the extreme Antarctic environment

Adaptations and lifestyle in polar marine environments: a biological challenge for the study of fish evolution

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Laser microdissection-based analysis of the Y sex chromosome of the Antarctic fish Chionodraco hamatus (Notothenioidei, Channichthyidae)

Microdissection, DOP-PCR amplification and microcloning were used to study the large Y chromosome of Chionodraco hamatus, an Antarctic fish belonging to the Notothenioidei, the dominant component of the Southern Ocean fauna. The species has evolved a multiple sex chromosome system with digametic males showing an X1YX2 karyotype and females an X1X1X2X2 karyotype. Fluorescence in situ hybridization, performed with a painting probe made from microdissected Y chromosomes, allowed a deeper insight on the chromosomal rearrangement, which underpinned the fusion event that generated the Y. Then, we used a DNA library established by microdissection and microcloning of the whole Y chromosome of Ch. hamatus for searching sex-linked sequences. One clone provided preliminary information on the presence on the Y chromosome of the CHD1 gene homologue, which is sex-linked in birds but in no other vertebrates. Several clones from the Y-chromosome mini-library contained microsatellites and transposable elements, one of which mapped to the q arm putative fusion region of the Y chromosome. The findings confirm that interspersed repetitive sequences might have fostered chromosome rearrangements and the emergence of the Y chromosome in Ch. hamatus. Detection of the CHD1 gene in the Y sex-determining region could be a classical example of convergent evolution in action

Adaptations and lifestyle in polar marine environments: a biological challenge for the study of fish evolution

The climatic features of Antarctic waters are more extreme and constant than in the Arctic. The Antarctic has been isolated and cold longer than the Arctic. The polar ichthyofaunas differ in age, endemism, taxonomy, zoogeographic distinctiveness and physiological tolerance to environmental parameters. The Arctic is the connection between the Antarctic and the temperate-tropical systems. Paradigmatic comparisons of the pathways of adaptive evolution of fish from both poles address the oxygen-transport system and the antifreezes of northern and southern species, (i) Haemoglobin evolution has included adaptations at the biochemical, physiological and molecular levels. Within the study of the molecular bases offish cold adaptation, and taking advantage of the information on haemoglobin amino acid sequence, we analysed the evolutionary history of the ? and ? globins of Antarctic, Arctic and temperate haemoglobins as a basis for reconstructing phylogenetic relationships. In the trees, the constant physico-chemical conditions of the Antarctic waters are matched by clear grouping of globin sequences, whereas the variability typical of the Arctic ecosystem corresponds to high sequence variation, reflected by scattered intermediate positions between the Antarctic and non-Antarctic clades. (ii) Antifreeze (glyco)proteins and peptides allow polar fish to survive at sub-zero temperatures. In Antarctic Notothenioidei the antifreeze gene evolved from a trypsinogen-like serine protease gene. In the Arctic polar cod the genome contains genes which encode nearly identical proteins, but have evolved from a different genomic locus–a case of convergent evolution

Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish?

In this study, we investigated by in silico analysis the possible correlation between microRNAs (miRNAs) and Anamnia V-SINEs (a superfamily of short interspersed nuclear elements), which belong to those retroposon families that have been preserved in vertebrate genomes for millions of years and are actively transcribed because they are embedded in the 3' untranslated region (UTR) of several genes. We report the results of the analysis of the genomic distribution of these mobile elements in zebrafish (Danio rerio) and discuss their involvement in generating miRNA gene loci. The computational study showed that the genes predicted to bear V-SINEs can be targeted by miRNAs with a very high hybridization E-value. Gene ontology analysis indicates that these genes are mainly involved in metabolic, membrane, and cytoplasmic signaling pathways. Nearly all the miRNAs that were predicted to target the V-SINEs of these genes, i.e., miR-338, miR-9, miR-181, miR-724, miR-735, and miR-204, have been validated in similar regulatory roles in mammals. The large number of genes bearing a V-SINE involved in metabolic and cellular processes suggests that V-SINEs may play a role in modulating cell responses to different stimuli and in preserving the metabolic balance during cell proliferation and differentiation. Although they need experimental validation, these preliminary results suggest that in the genome of D. rerio, as in other TE families in vertebrates, the preservation of V-SINE retroposons may also have been favored by their putative role in gene network modulation

Oxidized Substrates of APEH as a Tool to Study the Endoprotease Activity of the Enzyme

APEH is a ubiquitous and cytosolic serine protease belonging to the prolyl oligopeptidase (POP) family, playing a critical role in the processes of degradation of proteins through both exo- and endopeptidase events. Endopeptidase activity has been associated with protein oxidation; however, the actual mechanisms have yet to be elucidated. We show that a synthetic fragment of GDF11 spanning the region 48–64 acquires sensitivity to the endopeptidase activity of APEH only when the methionines are transformed into the corresponding sulphoxide derivatives. The data suggest that the presence of sulphoxide-modified methionines is an important prerequisite for the substrates to be processed by APEH and that the residue is crucial for switching the enzyme activity from exo- to endoprotease. The cleavage occurs on residues placed on the C-terminal side of Met(O), with an efficiency depending on the methionine adjacent residues, which thereby may play a crucial role in driving and modulating APEH endoprotease activity