Enriching the viral–host interactomes with interactions mediated by SH3 domains

Protein–protein interactions play an essential role in the regulation of most cellular processes. The process of viral infection is no exception and many viral pathogenic strategies involve targeting and perturbing host–protein interactions. The characterization of the host protein subnetworks disturbed by invading viruses is a major goal of viral research and may contribute to reveal fundamental biological mechanisms and to identify new therapeutic strategies. To assist in this approach, we have developed a database, VirusMINT, which stores in a structured format most of the published interactions between viral and host proteome. Although SH3 are the most ubiquitous and abundant class of protein binding modules, VirusMINT contains only a few interactions mediated by this domain class. To overcome this limitation, we have applied the whole interactome scanning experiment approach to identify interactions between 15 human SH3 domains and viral proline-rich peptides of two oncogenic viruses, human papillomavirus type 16 and human adenovirus A type 12. This approach identifies 114 new potential interactions between the human SH3 domains and proline-rich regions of the two viral proteomes.     

Can the IUCN criteria be effectively applied to peripheral isolated plant populations?

The IUCN criteria 2001 are considered one of the best methods to evaluate species extinction risk at the global and regional levels. The aim of this work is to test the applicability of the IUCN criteria to peripheral isolated plant populations (PIPPs). PIPPs have been a topic of scientific debate in Conservation Biology for about 15 years and international conventions such as ESPC address the issue of their conservation. Conservation measures often rely on Red Lists based on IUCN criteria, but there is little evidence supporting their application to PIPPs. In this work, we tested the hypothesis that PIPPs’ intrinsic restricted range and rarity lead to the overestimation of their extinction risk. We compared and analyzed four IUCN criteria (A, B, C, D), considering 17 species with PIPPs in different Italian administrative regions. Special attention must be given to the spatial scale at which PIPPs are assessed, the evaluation of the threats affecting the populations, and their decline. PIPPs should not be assessed within political boundaries and we propose a new area designation that better corresponds to the characteristics of PIPPs. Criterion B is strongly biased by restricted range and overestimates the extinction risk of PIPPs, particularly when the population decline is only suspected and not observed. In this case, criterion D more accurately assesses the status of PIPPs. Criterion A is also suitable for assessing PIPPs, because it is not affected by their phytogeographic rarity. The proposed statements could also be valid for the global assessment of narrow endemic species.     

Climate change,biological invasions,and the shifting distribution of Mediterranean fishes: A large‐scale survey based on local ecological knowledge

Climate change and biological invasions are rapidly reshuffling species distribution, restructuring the biological communities of many ecosystems worldwide. Tracking these transformations in the marine environment is crucial, but our understanding of climate change effects and invasive species dynamics is often hampered by the practical challenge of surveying large geographical areas. Here, we focus on the Mediterranean Sea, a hot spot for climate change and biological invasions to investigate recent spatiotemporal changes in fish abundances and distribution. To this end, we accessed the local ecological knowledge (LEK) of small‐scale and recreational fishers, reconstructing the dynamics of fish perceived as “new” or increasing in different fishing areas. Over 500 fishers across 95 locations and nine different countries were interviewed, and semiquantitative information on yearly changes in species abundance was collected. Overall, 75 species were mentioned by the respondents, mostly warm‐adapted species of both native and exotic origin. Respondents belonging to the same biogeographic sectors described coherent spatial and temporal patterns, and gradients along latitudinal and longitudinal axes were revealed. This information provides a more complete understanding of the shifting distribution of Mediterranean fishes and it also demonstrates that adequately structured LEK methodology might be applied successfully beyond the local scale, across national borders and jurisdictions. Acknowledging this potential through macroregional coordination could pave the way for future large‐scale aggregations of individual observations, increasing our potential for integrated monitoring and conservation planning at the regional or even global level. This might help local communities to better understand, manage, and adapt to the ongoing biotic transformations driven by climate change and biological invaders.     

Partner-Mediated Polymorphism of an Intrinsically Disordered Protein

Intrinsically disordered proteins (IDPs) recognize their partners through molecular recognition elements (MoREs). The MoRE of the C-terminal intrinsically disordered domain of the measles virus nucleoprotein (N_TAIL) is partly pre-configured as an α-helix in the free form and undergoes α-helical folding upon binding to the X domain (XD) of the viral phosphoprotein. Beyond XD, N_TAIL also binds the major inducible heat shock protein 70 (hsp70). So far, no structural information is available for the N_TAIL/hsp70 complex. Using mutational studies combined with a protein complementation assay based on green fluorescent protein reconstitution, we have investigated both N_TAIL/XD and N_TAIL/hsp70 interactions. Although the same N_TAIL region binds the two partners, the binding mechanisms are different. Hsp70 binding is much more tolerant of MoRE substitutions than XD, and the majority of substitutions lead to an increased N_TAIL/hsp70 interaction strength. Furthermore, while an increased and a decreased α-helicity of the MoRE lead to enhanced and reduced interaction strength with XD, respectively, the impact on hsp70 binding is negligible, suggesting that the MoRE does not adopt an α-helical conformation once bound to hsp70. Here, by showing that the α-helical conformation sampled by the free form of the MoRE does not systematically commit it to adopt an α-helical conformation in the bound form, we provide an example of partner-mediated polymorphism of an IDP and of the relative insensitiveness of the bound structure to the pre-recognition state. The present results therefore contribute to shed light on the molecular mechanisms by which IDPs recognize different partners.     

Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies

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Bovine testis acylphosphatase: Purification and amino acid sequence

Two acylphosphatase molecular forms have been isolated from bovine testis. Their amino acid sequence was determined. One (ACY1) consists of 98 amino acid residues, while the other one (ACY2) consists of 100 amino acid residues. Both molecular forms are N-acetylated and differ only in the amino terminus. ACY2 has an additional Ser-Met tail with respect to ACY1. Both ACY1 and ACY2 are organ-common type isoenzymes and thus differ for about half of the amino acid positions from the previously sequenced bovine muscle isoenzyme.     

Genetic structure of Rhamnus glaucophylla Sommier endemic to Tuscany

Rhamnus glaucophylla Sommier is an endemic small tree or shrub belonging to sect. Eurhamnus. It grows on cliffs of the Apuan Alps and of the Lucca Apennine in Tuscany (Italy). ISSRs were used to detect the genetic diversity within and among five populations representative of the species distribution range. Moderate levels of genetic diversity were revealed as percentage of polymorphic band (PPB) both at the population (PPB?=?22.63%, H _S?=?0.0801, Sh?=?0.1193) and species level (PPB?=?48.68%, H _T?=?0.1155, Sh?=?0.1837). The correlation between genetic and geographic distances was not significant (Mantel test, r?=?0.17; P?<?0.26). The information on the pattern of genetic variation obtained in this work bears important implications for conservation management, and in particular for ex situ conservation programmes involving long-term seed storage in seed banks.