A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina

Diversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.

THE CONURBATION OF THE CENTER-EAST OF MONASTIR BETWEEN INDIVIDUALITY AND FUNCTIONAL COMPLEMENTARITY

The towns of central-eastern of Monastir have over time been able to form an urban complex, which is referred to as conurbation. The study shows that this form of urban growth is not simply due to the coalescence of urban fabrics, favored by the short distances that separate these cities. It is also the result of the complementarity already established between these centers, although they are originally individualized. The study of spatial structures shows that these cities have remained individualized and their respective structures are well characterized. They do not appear in a uniform mass; they each have a more or less complex structure comprising residential areas, various facilities, an industrial area, etc. Moreover, these agglomerations today have very strong links of interdependence and constitute a veritable urban complex where functional complementarities clearly appear; each city makes its contribution to the functioning of the whole system and it happens that some stand out in one sector or another.

Zooplankton functional complementarity between temporary and permanent environments

Aims This study aims to evaluate the functional complementarity of the zooplankton community between temporary ponds and permanent lagoons. We hypothesize that temporary environments will be functionally more diverse than permanent environments and will have different functional composition. Methods Five temporary ponds and five permanent lagoons were compared regarding their limnological characteristics, species richness, functional diversity indices and functional trait composition. Results No differences between ponds and lagoons were found regarding mean species richness and functional diversity. However, a larger number of species was found in the set of temporary environments i.e., although the mean richness was the same, the species' identity varied from one pond to another. Ponds showed greater variability in functional trait composition, resulting in significant differences in zooplankton functional dispersion. Ponds also presented a greater range of limnological characteristics. Conclusions Temporary and permanent environments present high limnological and functional complementarity, which make them important for maintaining biodiversity on a regional scale. Temporary environments seem to be refugees for species that do not settle in more stable environments because these species are more likely to colonize environments that periodically restart their successional trajectory. Therefore, actions that seek to preserve complementary environments are essential and urgent, especially those related to small and temporary environments.

Like wings of a bird: functional divergence and complementarity between HLA-A and HLA-B molecules

Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations worldwide are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence and linear modelling) on 2,909 common and rare HLA-A, HLA-B and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defence. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intra-protein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.

Spectral niches reveal taxonomic identity and complementarity in plant communities

SummaryPlants’ spectra provide integrative measures of their chemical, morphological, anatomical, and architectural traits. We posit that the degree to which plants differentiate in n-dimensional spectral space is a measure of niche differentiation and reveals functional complementarity.In both experimentally and naturally assembled communities, we quantified plant niches using hypervolumes delineated by either plant spectra or 10 functional traits. We compared the niche fraction unique to each species in spectral and trait spaces with increasing dimensionality, and investigated the association between the spectral space occupied, plant growth and community productivity.We show that spectral niches differentiated species better than their functional trait niches. The amount of spectral space occupied by individuals and plant communities increased with plant growth and community productivity, respectively. Further, community productivity was better explained by inter-individual spectral complementarity than by productive individuals occupying large spectral niches.The degree of differentiation in spectral space provides the conceptual basis for identifying plant taxa spectrally. Moreover, our results indicate that the size and position of plant spectral niches reflect ecological strategies that shape community composition and ecosystem function, with the potential to reveal insight in niche partitioning over large areas with spectroscopy.

Patterns of Autologous and Nonautologous Interactions between Core Nuclear Egress Complex (NEC) Proteins of α-, β- and γ-Herpesviruses

Nuclear egress is a regulated process shared by α-, β- and γ-herpesviruses. The core nuclear egress complex (NEC) is composed of the membrane-anchored protein homologs of human cytomegalovirus (HCMV) pUL50, murine cytomegalovirus (MCMV) pM50, Epstein–Barr virus (EBV) BFRF1 or varicella zoster virus (VZV) Orf24, which interact with the autologous NEC partners pUL53, pM53, BFLF2 or Orf27, respectively. Their recruitment of additional proteins leads to the assembly of a multicomponent NEC, coordinately regulating viral nucleocytoplasmic capsid egress. Here, the functionality of VZV, HCMV, MCMV and EBV core NECs was investigated by coimmunoprecipitation and confocal imaging analyses. Furthermore, a recombinant MCMV, harboring a replacement of ORF M50 by UL50, was analyzed both in vitro and in vivo. In essence, core NEC interactions were strictly limited to autologous NEC pairs and only included one measurable nonautologous interaction between the homologs of HCMV and MCMV. A comparative analysis of MCMV-WT versus MCMV-UL50-infected murine fibroblasts revealed almost identical phenotypes on the levels of protein and genomic replication kinetics. In infected BALB/c mice, virus spread to lung and other organs was found comparable between these viruses, thus stating functional complementarity. In conclusion, our study underlines that herpesviral core NEC proteins are functionally conserved regarding complementarity of core NEC interactions, which were found either virus-specific or restricted within subfamilies.