Complexity, connectivity, and duplicability as barriers to lateral gene transfer

Background

Lateral gene transfer is a major force in microbial evolution and a great source of genetic innovation in prokaryotes. Protein complexity has been claimed to be a barrier for gene transfer, due to either the inability of a new gene's encoded protein to become a subunit of an existing complex (lack of positive selection), or from a harmful effect exerted by the newcomer on native protein assemblages (negative selection).

Results

We tested these scenarios using data from the model prokaryote Escherichia coli. Surprisingly, the data did not support an inverse link between membership in protein complexes and gene transfer. As the complexity hypothesis, in its strictest sense, seemed valid only to essential complexes, we broadened its scope to include connectivity in general. Transferred genes are found to be less involved in protein-protein interactions, outside stable complexes, and this is especially true for genes recently transferred to the E. coli genome. Thus, subsequent to transfer, new genes probably integrate slowly into existing protein-interaction networks. We show that a low duplicability of a gene is linked to a lower chance of being horizontally transferred. Notably, many essential genes in E. coli are conserved as singletons across multiple related genomes, have high connectivity and a highly vertical phylogenetic signal.

Conclusion

High complexity and connectivity generally do not impede gene transfer. However, essential genes that exhibit low duplicability and high connectivity do exhibit mostly vertical descent.     

Spatial prioritisation of management zones in protected areas for the integration of multiple objectives

Biodiversity and Conservation - Biodiversity keeps declining in the European Union despite the large conservation effort done over the last decades. The Biodiversity Strategy for 2030 aims to...     

Cytogenetic characterization of the invasive mussel species Xenostrobus securis Lmk. (Bivalvia: Mytilidae)

The chromosomes of the invasive black-pigmy mussel (Xenostrobus securis (Lmk. 1819)) were analyzed by means of 4',6-diamidino-2-phenylindole (DAPI) / propidium iodide (PI) and chromomycin A3 (CMA) / DAPI fluorescence staining and fluorescent in situ hybridization using major rDNA, 5S rDNA, core histone genes, linker histone genes, and telomeric sequences as probes. The diploid chromosome number in this species is 2n = 30. The karyotype is composed of seven metacentric, one meta/submetacentric, and seven submetacentric chromosome pairs. Telomeric sequences appear at both ends of every single chromosome. Major rDNA clusters appear near the centromeres on chromosome pairs 1 and 3 and are associated with bright CMA fluorescence and dull DAPI fluorescence. This species shows five 5S rDNA clusters close to the centromeres on four chromosome pairs (2, 5, 6, and 8). Three of the four core histone gene clusters map to centromeric positions on chromosome pairs 7, 10, and 13. The fourth core histone gene cluster occupies a terminal position on chromosome pair 8, also bearing a 5S rDNA cluster. The two linker histone gene clusters are close to the centromeres on chromosome pairs 12 and 14. Therefore, the use of these probes allows the unequivocal identification of 11 of the 15 chromosome pairs that compose the karyotype of X. securis.     

Bivalent ligand approach on N-{2-[(3-methoxyphenyl)methylamino]ethyl}acetamide: synthesis, binding affinity and intrinsic activity for MT(1) and MT(2) melatonin receptors

We report the synthesis, binding properties and intrinsic activity at MT(1) and MT(2) melatonin receptors of new dimeric melatonin receptor ligands in which two units of the monomeric agonist N-{2-[(3-methoxyphenyl)methylamino]ethyl}acetamide (1) are linked together through different anchor points. Dimerization of compound 1 through the methoxy substituent leads to a substantial improvement in selectivity for the MT(1) receptor, and to a partial agonist behavior. Compound 3a, with a trimethylene linker, was the most selective for the MT(1) subtype (112-fold selectivity) and compound 3d, characterized by a hexamethylene spacer, had the highest MT(1) binding affinity (pK(iMT1)=8.47) and 54-fold MT(1)-selectivity. Dimerization through the aniline nitrogen of 1 abolished MT(1) selectivity, leading to compounds with either a full agonist or an antagonist behavior depending on the nature of the linker.     

Phylogenetic relationships of the genus Hoplia Illiger (Scarabaeidae: Hopliinae)

Results of phylogenetic analysis based on 34 morphological characters of 24 species of 11 genera of Hopliinae from Europe, Japan, South Africa, Madagascar, North and Central America, indicates that the genus Hoplia is a monophyletic group with species distributed in Europe, Japan and America. Based in this analysis the Asiatic genus Ectinohoplia is the closest relative of the genus Hoplia, and the South American genus Barybas (Melolonthinae: Macrodactylini) is the sister group of Hopliinae.     

Mitochondrial biogenesis related endurance genotype score and sports performance in athletes

We determined the probability of individuals having the ‘optimal’ mitochondrial biogenesis related endurance polygenic profile, and compared the endurance polygenic profile of Israeli (Caucasian) endurance athletes (n = 74), power athletes (n = 81), and non-athletes (n = 240). We computed a mitochondrial biogenesis related ‘endurance genotype score’ (EGS, scoring from 0 to 100) from the accumulated combination of six polymorphisms in the PPARGC1A-NRF-TFAM pathway. Some of the variant alleles of the polymorphisms studied were so infrequent, that the probability of possessing an ‘optimal’ EGS (= 100) was 0% in the entire study population. However, the EGS was significantly higher (P < 0.001) in endurance athletes (38.9 ± 17.1) compared with controls (30.6 ± 12.4) or power athletes (29.0 ± 11.2). In summary, although the probability of an individual possessing a theoretically ‘optimal’ genetic background for endurance sports is very low, in general endurance athletes have a polygenic profile that is more suitable for mitochondrial biogenesis.     

Reactive oxygen species participate in the p38-mediated apoptosis induced by potassium deprivation and staurosporine in cerebellar granule neurons

Apoptosis induced by low potassium (K5) or staurosporine in cerebellar granule neurons triggers an increase in reactive oxygen species (ROS) levels. ROS inhibition by antioxidants or inhibitors of the NADPH oxidase (NOX) activity reduces the apoptosis induced by both stimuli. It has been reported that JNK mediates the apoptosis induced by K5 but not by staurosporine. No information is available about the role of other signaling pathways such as p38 in staurosporine-induced apoptosis, and whether p38 activation could be related to ROS levels induced by both K5 and staurosporine. Here, we explored this possibility and found that K5 activates p38 and ATF2 and that the inhibition of p38 activity prevents the apoptosis induced by this treatment. We also found that p38 is downstream of ROS generation induced by K5. On the other hand, staurosporine promotes a sustained activation of p38. We found that p38 inhibition markedly decreases ROS generation, NOX activity and apoptosis induced by staurosporine. Furthermore, antioxidants inhibit p38 activation induced by staurosporine. These data indicate that apoptosis induced by both K5 and staurosporine is dependent on p38 activation, which is mediated by ROS. In addition, p38 activation by staurosporine induces a further production of ROS through NOX activation.     

The K153R polymorphism in the myostatin gene and muscle power phenotypes in young, non-athletic men

The Lys(K)153Arg(R) polymorphism in exon 2 (rs1805086, 2379 A>G replacement) of the myostatin (MSTN) gene is a candidate to influence skeletal muscle phenotypes. We examined the association between the MSTN K153R polymorphism and 'explosive' leg power, assessed during sprint (30 m) and stationary jumping tests [squat (SJ) and counter-movement jumps (CMJ)] in non-athletic young adults (University students) [n = 281 (214 men); age: 21-32 years]. We also genotyped the MSTN exonic variants E164K (rs35781413), I225T, and P198A, yet no subject carried any of these variant MSTN alleles. As for the K153R polymorphism, we found only one woman with the KR genotype; thus, we presented the results only for men. The results of a one-way ANCOVA (with age, weight and height entered as covariates) showed that men with the KR genotype (n = 15) had a worse performance in vertical jumps compared with those with the KK genotype [SJ: vertical displacement of center of gravity (CG) of 35.17 ± 1.42 vs. 39.06 ± 0.39 cm, respectively, P = 0.009; CMJ: vertical displacement of CG of 36.44 ± 1.50 vs. 40.63 ± 0.41 cm, respectively, P = 0.008]. The results persisted after adjusting for multiple comparisons according to Bonferroni. Performance in 30 m sprint tests did however not differ by K153R genotypes. In summary, the MSTN K153R polymorphism is associated with the ability to produce 'peak' power during muscle contractions, as assessed with vertical jump tests, in young non-athletic men. Although more research is still needed, this genetic variation is among the numerous candidates to explain, alone or in combination with other polymorphisms, individual variations in muscle phenotypes.