New Insights into the Evolution and Gene Structure of the Mitochondrial Carrier Family Unveiled by Analyzing the Frequent and Conserved Intron Positions.

Mitochondrial carriers (MCs) belong to a eukaryotic protein family of transporters that in higher organisms is called the solute carrier family 25 (SLC25). All MCs have characteristic triplicated sequence repeats forming a 3-fold symmetrical structure of a six-transmembrane α-helix bundle with a centrally located substrate-binding site. Biochemical characterization has shown that MCs altogether transport a wide variety of substrates but can be divided into subfamilies, each transporting a few specific substrates. We have investigated the intron positions in the human MC genes and their orthologs of highly diversified organisms. The results demonstrate that several intron positions are present in numerous MC sequences at the same specific points, of which some are 3-fold symmetry related. Many of these frequent intron positions are also conserved in subfamilies or in groups of subfamilies transporting similar substrates. The analyses of the frequent and conserved intron positions in MCs suggest phylogenetic relationships not only between close but also distant homologs as well as a possible involvement of the intron positions in the evolution of the substrate specificity diversification of the MC family members.

Modulation of Biological Activities in Glioblastoma Mediated by Curcumin.

Curcumin is an alkaloid with various pharmacologic properties; numerous investigations have suggested that in the Central Nervous System, Curcumin has anti-inflammatory, antimicrobial, antioxidant, and antitumor effects. Gliomas are the most common primary intracranial tumors in adults. The prognosis of glioblastoma is still dismal. In this review, we profile that Curcumin could suppress cell proliferation and induce apoptosis of cancer cells and genomic modulation. In particular, Curcumin could exert its therapeutic effect via modulating miRNA, affecting a variety of miRNAs involved in the response to cancer therapy. The combination of Curcumin with chemotherapeutic drugs or radiotherapy could prime the sensitivity of cancer cells to chemotherapy or radiotherapy. We also discuss the use of exosomes as Curcumin delivery vehicles. In this context, exosomes containing Curcumin may change the behavior of recipient cells by targeting a sequence of cellular and molecular pathways. Hence, the application of exosomes containing Curcumin may prove to be an emerging area of research in cancer therapy.

Conservation/Mutation in the Splice Sites of Mitochondrial Solute Carrier Genes of Vertebrates.

The "canonical" introns begin by the dinucleotide GT and end by the dinucleotide AG. GT, together with a few downstream nucleotides, and AG, with a few of the immediately preceding nucleotides, are thought to be the strongest splicing signals (5'ss and 3'ss, respectively). We examined the composition of the intronic initial and terminal hexanucleotides of the mitochondrial solute carrier genes (SLC25A's) of zebrafish, chicken, mouse, and human. These genes are orthologous and we selected the transcripts in which the arrangement of exons and introns was superimposable in the species considered. Both 5'ss and 3'ss were highly polymorphic, with 104 and 126 different configurations, respectively, in our sample. In the line of evolution from zebrafish to chicken, as well as in that from zebrafish to mammals, the average nucleotide conservation in the four variable nucleotides was about 50 % at 5' and 40 % at 3'. In the divergent evolution of mouse and human, the conservation was about 80 % at 5' and 70 % at 3'. Despite these changes, the splicing signals remain strong enough to operate at the same site. At both 5' and 3', the frequency of a nucleotide at a given position in the zebrafish sequence is positively correlated with its conservation in chicken and mammals, suggesting that selection continued to operate in birds and mammals along similar lines.

Pathogenic potential of SLC25A15 mutations assessed by transport assays and complementation of Saccharomyces cerevisiae ORT1 null mutant.

HHH syndrome is an autosomal recessive urea cycle disorder caused by alterations in the SLC25A15 gene encoding the mitochondrial ornithine carrier 1, which catalyzes the transport of cytosolic ornithine into the mitochondria in exchange for intramitochondrial citrulline. In this study the functional effects of several SLC25A15 missense mutations p.G27R, p.M37R, p.N74A, p.F188L, p.F188Y, p.S200K, p.R275Q and p.R275K have been tested by transport assays in reconstituted liposomes and complementation of Saccharomyces cerevisiae ORT1 null mutant in arginine-less synthetic complete medium. The HHH syndrome-causing mutations p.G27R, p.M37R, p.F188L and p.R275Q had impaired transport and did not complement ORT1∆ cells (except p.M37R slightly after 5 days in solid medium). The experimentally produced mutations p.N74A, p.S200K and p.R275K exhibited normal or considerable transport activity and complemented ORT1∆ cells after 3 days (p.N74A, p.S200K) or 5 days (p.R275K) incubation. Furthermore, the experimentally produced p.F188Y mutation displayed a substantial transport activity but did not complement the ORT1∆ cells in both liquid and solid media. In view of the disagreement in the results obtained between the two methods, it is recommended that the method of complementing the S. cerevisiae ORT1 knockout strain is used complimentary with the measurement of the catalytic activity, in order to distinguish HHH syndrome-causing mutations from isomorphisms.

5' and 3' splicing signals evolution in vertebrates: Analysis in a conserved gene family.

The mitochondrial solute carrier genes (SLC25) are highly conserved during vertebrate evolution. In most SLC25 genes of zebrafish, chicken, mouse, and human, the introns are located at exactly superimposable positions. In these topographically corresponding introns we studied the composition of the initial and terminal hexanucleotides (5'ss and 3'ss) which are instrumental in splicing signaling, focusing on the evolutionary conservation/mutation dynamics of these genetically related sequences. At each position, the per cent conservation of zebrafish individual nucleotides in chicken, mouse and human is proportional to their percent frequency in zebrafish; furthermore, nucleotide mutations are biased in favor of the more represented nucleotides, thus compensating for those highly represented zebrafish nucleotides which have not been conserved. As a result of these evolutionary dynamics, the general nucleotide composition at each position has remained relatively conserved throughout vertebrates. At 5'ss, following the canonical GT, A and G are largely prevailing at position +3, A at +4 and G at +5 (GT[A/G]AGx). At 3'ss, T and C are largely prevailing at positions -6, -5 and -3, preceding the canonical intron terminal AG ([C/T] [C/T]x[C/T]AG). However, the actual composition of the tetranucleotides at 5' and 3' often does not conform to the above scheme. At 5'ss the more canonical sequence is completely expressed in 63% of cases and partially (2 or 1 matches) in 37 % of cases. At 3'ss the more canonical sequence is completely expressed in 71 % of cases and partially (2 or 1 matches) in 29 % of cases. The nucleotide conservation loss (nucleotide mutation) is higher in the evolution from fish to the last common ancestor of birds and mammals (58 %), then diminishes in the successive evolution steps up to the mammalian common ancestor (10 %), and becomes still lower at the divergence of rodents and primates (5 %).

An analysis of the human chemokine CXC receptor 4 gene.

In this article we analyze some of the structural characteristics of the coding section and the intron of the human chemokine CXC receptor 4 (a 7-transmembrane receptor) pre-mRNA. In the coding sequence the frequencies of the individual nucleotides do not depart significantly from 0.25, while in the intron the frequencies of the As and Gs are significantly lower and higher, respectively, than expected from a random distribution. Analysis of the pattern of association of nucleotides into triplets or couples shows that some triplets or couples occur with frequencies significantly higher or lower than expected when assuming a random association of nucleotides. In particular, in the intron combinations of the same nucleotide are over-represented. 7-or-more nucleotide repeats occur in both the coding section and the intron with frequencies which exceed the confidence limits for a random distribution. For the coding sequence this is possibly explained by the alternans of relatively similar hydrophobic-coding sections and relatively similar intervening intracellular and extracellular hydrophilic-coding sections. 7-or-more nucleotide repeats in reverse order and in reverse/complemented order occur in the intron, but not in the coding section, with frequencies which significantly exceed a random distribution. The numerous intronic repeats in reverse/complemented order may be of relevance for the secondary structure of the intron and might be one important element of the integrated splicing code.

Mutation patterns in the chemokine CXC receptor 4 gene subfamily.

Six representative CXCR4 mRNAs of fish, amphibia, birds, and mammals were selected to study the pattern of conservation/mutation of the individual nt of the coding sequences. According to an arbitrary conservation index ranging from 1 to 6, the indexes of conservation were: 5.04 for the first nt of coding triplets; 5.34 for the second nt of triplets, and 3.75 for the third nt of triplets. The average conservation index of the individual triplets was 4.71. The conservation index of the seven hydrophobic transmembrane domains was 5.60, while the cumulative conservation index of the intracytoplasmic and extracellular domains was 4.63. Separate autocorrelation and power spectral analyses of the series of conservation indexes for the first nt, the second nt and the triplets demonstrated a modest "basic" positive correlation for about the first 20 lags and accordingly some power concentration at the lower frequencies (long periods). Within the triplets, the correlation was studied between the conservation indexes of nt 1 and 2, 1 and 3, and 2 and 3. Correlations of 1 with 3 and 2 with 3 were positive, but in the range of the basic local correlation, whereas the correlation between the first and second nt was significantly higher. This correlation, together with the higher conservation of the second nt as compared to the first (two patterns also found in the formyl peptide receptors), are likely to have been established by selection processes directed towards a functional conservation or a "functional repair."

Unusual structure and splicing pattern of the vertebrate mitochondrial solute carrier SLC25A3 gene.

The DNA sequence corresponding to the second exon of the SLC25A3 gene is duplicated in vertebrates. The second exon codes for the first transmembrane segment and parts of the immediately adjoining intermembrane and mitochondrial matrix segments. The two genomic exon 2 sequences are 84% similar in zebrafish (slc25a3b gene), 70% in chicken, 66% in mouse and 67% in human. The amino acid identity is 86% in zebrafish, 77% in chicken and 70% in mouse and human. The two copies of exon 2 are separated by an intronic interval. Translation of both exon 2 sequences would alter the reading frame of the downstream sequence, generating a modified aa sequence which would soon be truncated by a stop codon. As a matter of fact the splicing machinery is tuned in such a way that in some species only one of the two copies is expressed and the other is spliced out, while in other species both copies are expressed but only one at a time, generating two alternative protein products.

Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes.

In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor.

Neuroprotective effects of resveratrol in an MPTP mouse model of Parkinson's-like disease: possible role of SOCS-1 in reducing pro-inflammatory responses.

In the present study we used a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinson's disease (PD) mouse model to analyze resveratrol neuroprotective effects. The MPTP-induced PD model is characterized by chronic inflammation, oxidative stress and loss of the dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). We observed that resveratrol treatment significantly reduced glial activation, decreasing the levels of IL-1ß, IL-6 and TNF-α, as well as their respective receptors in the SNpc of MPTP-treated mice, as demonstrated by Western blotting, RT-PCR and quantitative PCR analysis. This reduction is related to possible neuroprotection as we also observed that resveratrol administration limited the decline of tyrosine hydroxylase-immunoreactivity induced in the striatum and SNpc by MPTP injection. Consistent with these data, resveratrol treatment up-regulated the expression of the suppressor of cytokine signaling-1 (SOCS-1), supporting the hypothesis that resveratrol protects DA neurons of the SNpc against MPTP-induced cell loss by regulating inflammatory reactions, possibly through SOCS-1 induction.

MC70 potentiates doxorubicin efficacy in colon and breast cancer in vitro treatment.

A major limitation of cancer treatment is the ability of cancer cells to develop resistance to chemotherapeutic drugs, by the establishment of multidrug resistance. Here, we characterize MC70 as ABC transporters inhibitor and anticancer agent, alone or with chemotherapy. MC70 was analyzed for its interaction with ABCB1, ABCG2 and ABCC1 by specific transport assays. In breast and colon cancer cell lines, cell growth and apoptosis were measured by MTT assay and DNA laddering Elisa kit, respectively. Cell cycle perturbation and cellular targets modulation were analyzed by Flow-cytometry and Western blotting, respectively. MC70 interacted with ABC transporters. In breast cancer cells, MC70 slightly inhibited cell proliferation strongly enhancing doxorubicin effectiveness. By contrast, MC70 was found to inhibit cell growth in colon cancer cells without affecting doxorubicin efficacy and in combination with topoisomerase I inhibitors it could be a promising therapeutic approach. What is more, it was also observed that MC70 induced apoptosis, canceled in favor of necrosis when given in combination with high doses of doxorubicin. MC70 inhibited cell migration probably through its interaction with sigma-1 receptor. Modulations of i) cell cycle, ii) pAkt and the phosphorylation of the three MAPKs were highlighted, while any activity was excluded at transcription level, thus accounting for the phenotypic effects observed. MC70 might be considered as a new potential anticancer agent capable to i) enhance chemotherapy effectiveness and ii) to play a contributory role in the treatment of chemotherapy resistant tumors.

Mutation, selection and the amino acid hydropathic character: a study on receptor genes involved in immune and non-immune functions.

In some mRNA sequences, namely those of formyl peptide receptors and chemokine CXC receptors 4, it has been observed that the second nucleotide (nt) of the coding triplets is significantly more highly conserved than the first nt and the correlation between the conservation indexes of the first two nt is positive and significantly higher than the "basic" correlation usually found between adjacent nt. A theoretical analysis demonstrated that random mutations in the first nt preserve hydrophobicity in 73 % of triplets coding for hydrophobic amino acids (aa) and hydrophilicity in 77 % of triplets coding for hydrophilic aa, while random mutations in the second nt preserve hydrophobicity in 18 % of triplets coding for hydrophobic aa and hydrophilicity in 53 % of triplets coding for hydrophilic aa. When the triplets which had changed their hydropathic aa coding character underwent a second random mutation in the previously unmutated first or second nt, an additional 11 % of the originally hydrophobic-coding triplets reverted to hydrophobicity and an additional 14 % of the originally hydrophilic-coding triplets reverted to hydrophilicity. This analysis provides a rationale for why a higher number of mutations in the second nt are presumably negatively selected and a number of double mutations in the first and second nt presumably are positively selected, in cases when a mutation in one of the two is not reverted.

The HIV-1 Rev binding family of proteins: the dog proteins as a study model.

Various proteins that are required for the building of new complete human immunodeficiency type 1 virions (HIV-1) are coded by unspliced or partly spliced virus-derived mRNAs. HIV-1 has developed special strategies for moving these mRNAs to the cytoplasm to be translated. In the nucleus of the infected cell the virus-derived protein Regulator of expression of viral proteins (Rev) can bind both the viral intron-containing mRNAs and the cellular co-factor HIV-1 Rev binding protein (HRB) and this complex may be shuttled through the nuclear pores. HRB genes have been relatively well conserved during evolution, from Drosophila to humans. However, as a consequence of reading-frame shifts due to nt insertions/deletions, the protein products generated may differ considerably from the prototypal HRB protein, which comprises one Arf-GAP zinc finger domain, several Phenylalanine-Glycine (FG) motifs and four Asparagine-Proline-Phenylalanine (NPF) motifs. This variability is best exemplified by four HRB proteins of the dog, which are discussed here in more detail. The hypothesis is advanced that atypical HRB proteins may not be able to bind Rev and possibly have other, still undetermined, functions. Since the cellular co-factor HRB is essential for viral replication and spread but is not required for cell viability and main bodily functions, it might be an attractive candidate for anti-HIV-1 drug targeting.

Canine leishmaniasis in Southern Italy: a role for nitric oxide released from activated macrophages in asymptomatic infection?

BACKGROUND: Human and canine leishmaniasis (CanL) by Leishmania infantum is endemic in Italy, with a high percentage of infected asymptomatic animals. However, the immune response mechanisms underlying the clinical presentation of CanL have not been fully investigated. Among leishmanicidal molecules produced by activated macrophages, nitric oxide (NO) produced by an inducible NO synthase seems to play an important protective role, but no conclusive data are available. Therefore, NO released by cultured macrophages from dogs with natural Leishmania infection living in an endemic area for CanL was evaluated. METHODS: On the basis of one year's clinical and laboratory follow-up, 22 dogs infected by Leishmania infantum were identified and grouped as: asymptomatic dogs (n = 13) and dogs with symptoms of leishmaniasis (n = 9). Each animal was bled twice at 4-month intervals and macrophage and lymphocyte cultures were obtained from peripheral blood mononuclear cells. Supernatants of L. infantum-infected macrophage cultures, with or without addition of autologous lymphocytes, were assayed for NO production by Griess reaction for nitrites. RESULTS: In the first months of the infection the levels of NO in supernatants of Leishmania-infected macrophages were higher in symptomatic than in asymptomatic dogs, but they were significantly increased in the latter group eight months after the diagnosis of infection. Furthermore, NO release significantly decreased in the presence of autologous lymphocytes in both groups of animals. CONCLUSION: These results suggest that NO may be involved in the long-term protection of dogs against natural Leishmania infection and in the clinical presentation of canine leishmaniasis in the Mediterranean area.