Development and function explain the modular evolution of phalanges in gecko lizards

Selective regimes favouring the evolution of functional specialization probably affect covariation among phenotypic traits. Phalanges of most tetrapods develop from a conserved module that constrains their relative proportions. In geckos, however, biomechanical specializations associated with adhesive toepads involve morphological variation in the autopodium and might reorganize such modular structures. We tested two hypotheses to explain the modular architecture of hand bones in geckos, one based on developmental interactions and another incorporating functional associations related to locomotion, and compared the empirical support for each hypothetical module between padded and padless lineages. We found strong evidence for developmental modules in most species, which probably reflects embryological constraints during phalangeal formation. Although padded geckos exhibit a functional specialization involving the hyperextension of the distal phalanges that is absent in padless species, the padless species are the ones that show a distal functional module with high integration. Some ancestrally padless geckos apparently deviate from developmental predictions and present a relatively weak developmental module of phalanges and a strongly integrated distal module, which may reflect selective regimes involving incipient frictional adhesion in digit morphology. Modularity of digit elements seems dynamic along the evolutionary history of geckos, being associated with the presence/absence of adhesive toepads.

Scaling of cellular proteome with ploidy

Ploidy changes are frequent in nature and contribute to evolution, functional specialization and tumorigenesis. Analysis of model organisms of different ploidies revealed that increased ploidy leads to an increase in cell and nuclear volume, reduced proliferation, metabolic changes, lower fitness, and increased genomic instability, but the underlying mechanisms remain poorly understood. To investigate how the gene expression changes with cellular ploidy, we analyzed isogenic series of budding yeasts from 1N to 4N. We show that mRNA and protein abundance scales allometrically with ploidy, with tetraploid cells showing only threefold increase in proteins compared to haploids. This ploidy-specific scaling occurs via decreased rRNA and ribosomal protein abundance and reduced translation. We demonstrate that the Tor1 activity is reduced with increasing ploidy, which leads to rRNA gene repression via a novel Tor1-Sch9-Tup1 signaling pathway. mTORC1 and S6K activity are also reduced in human tetraploid cells and the concomitant increase of the Tup1 homolog Tle1 downregulates the rDNA transcription. Our results revealed a novel conserved mTORC1-S6K-Tup1/Tle1 pathway that ensures proteome remodeling in response to increased ploidy.

The tandem repeat modules of Xist lncRNA: a swiss army knife for the control of X-chromosome inactivation

X-inactive-specific transcript (Xist) is a long non-coding RNA (lncRNA) essential for X-chromosome inactivation (XCI) in female placental mammals. Thirty years after its discovery, it is still puzzling how this lncRNA triggers major structural and transcriptional changes leading to the stable silencing of an entire chromosome. Recently, a series of studies in mouse cells have uncovered domains of functional specialization within Xist mapping to conserved tandem repeat regions, known as Repeats A-to-F. These functional domains interact with various RNA binding proteins (RBPs) and fold into distinct RNA structures to execute specific tasks in a synergistic and coordinated manner during the inactivation process. This modular organization of Xist is mostly conserved in humans, but recent data point towards differences regarding functional specialization of the tandem repeats between the two species. In this review, we summarize the recent progress on understanding the role of Xist repetitive blocks and their involvement in the molecular mechanisms underlying XCI. We also discuss these findings in the light of the similarities and differences between mouse and human Xist.

Sustainable Development in Middle Powers’ Governance Arrangements

Considering middle powers’ potential to address new demands worldwide and their propensity to contribute to new forms of institution-building in global governance, arrangements between them consist of interesting opportunities to promote sustainable development. However, some have shown to be more effective than others in this regard. When observing two of these partnerships’ outcomes between 2015 and 2018, India, Brazil, and South Africa (IBSA) Trilateral Forum has demonstrated more effectiveness than Mexico, Indonesia, South Korea, Turkey, and Australia (MIKTA) New Innovative Partnership. To understand why, this study analyses specialized literature, with special attention to Koenig-Archibugi’s (2002) framework on global governance arrangements’ effectiveness. Arguing that middle power arrangements that address sustainable development are more effective when benefiting from greater functional specialization and that diversified power access also plays a role, this study raises awareness about middle powers’ relevance in addressing new global demands. The study points out the nascent research on these informal partnerships and the causal relations between these arrangements’ structures and effectiveness.

Business development while transforming the economy on the example of the city of Perm

The purpose of the study is to identify the essence of digitalization for business. The theoretical and methodological relevance of the article consists in the fact that the issue of publicity of digitalization processes for small and medium-sized businesses have not until now considered by economists. The lack of development of these issues predetermined the relevance and practical significance of the study. The scenario of digitalization implementation has been considered on the example of Perm, where digitalization is carried out in accordance with the approved “Concept of digital economy development in the Perm Region”. The task of determining the economic effect of business processes digitalization in the city economy was solved. The following methods were used in the study: methods of statistical information processing, the general scientific method of cognition of the problem, the method of system analysis, the theory of digitalization of systems, computational and experimental methods for modeling the digitalization of property, as well as methods based on the theory of functional specialization and the theory of restructuring. It has been concluded that the introduction of digital technologies into public life allows businesses to take part in this and develop themselves.

Bend or break: how biochemically versatile molecules enable metabolic division of labor in clonal microbial communities

In fluctuating nutrient environments, isogenic microbial cells transition into “multicellular” communities composed of phenotypically heterogeneous cells, showing functional specialization. In fungi (such as budding yeast), phenotypic heterogeneity is often described in the context of cells switching between different morphotypes (e.g., yeast to hyphae/pseudohyphae or white/opaque transitions in Candida albicans). However, more fundamental forms of metabolic heterogeneity are seen in clonal Saccharomyces cerevisiae communities growing in nutrient-limited conditions. Cells within such communities exhibit contrasting, specialized metabolic states, and are arranged in distinct, spatially organized groups. In this study, we explain how such an organization can stem from self-organizing biochemical reactions that depend on special metabolites. These metabolites exhibit plasticity in function, wherein the same metabolites are metabolized and utilized for distinct purposes by different cells. This in turn allows cell groups to function as specialized, interdependent cross-feeding systems which support distinct metabolic processes. Exemplifying a system where cells exhibit either gluconeogenic or glycolytic states, we highlight how available metabolites can drive favored biochemical pathways to produce new, limiting resources. These new resources can themselves be consumed or utilized distinctly by cells in different metabolic states. This thereby enables cell groups to sustain contrasting, even apparently impossible metabolic states with stable transcriptional and metabolic signatures for a given environment, and divide labor in order to increase community fitness or survival. We speculate on possible evolutionary implications of such metabolic specialization and division of labor in isogenic microbial communities.

Evolution of Methyltransferase-Like (METTL) Proteins in Metazoa: A Complex Gene Family Involved in Epitranscriptomic Regulation and Other Epigenetic Processes

The methyltransferase-like (METTL) proteins constitute a family of seven-beta-strand methyltransferases with S-adenosyl methionine-binding domains that modify DNA, RNA, and proteins. Methylation by METTL proteins contributes to the epigenetic, and in the case of RNA modifications, epitranscriptomic regulation of a variety of biological processes. Despite their functional importance, most investigations of the substrates and functions of METTLs within metazoans have been restricted to model vertebrate taxa. In the present work, we explore the evolutionary mechanisms driving the diversification and functional differentiation of 33 individual METTL proteins across Metazoa. Our results show that METTLs are nearly ubiquitous across the animal kingdom, with most having arisen early in metazoan evolution (i.e., occur in basal metazoan phyla). Individual METTL lineages each originated from single independent ancestors, constituting monophyletic clades, which suggests that each METTL was subject to strong selective constraints driving its structural and/or functional specialization. Interestingly, a similar process did not extend to the differentiation of nucleoside-modifying and protein-modifying METTLs (i.e., each METTL type did not form a unique monophyletic clade). The members of these two types of METTLs also exhibited differences in their rates of evolution. Overall, we provide evidence that the long-term evolution of METTL family members was driven by strong purifying selection, which in combination with adaptive selection episodes, led to the functional specialization of individual METTL lineages. This work contributes useful information regarding the evolution of a gene family that fulfills a variety of epigenetic functions, and can have profound influences on molecular processes and phenotypic traits.

Overexpression of MsRCI2A, MsRCI2B, and MsRCI2C in Alfalfa (Medicago sativa L.) Provides Different Extents of Enhanced Alkali and Salt Tolerance Due to Functional Specialization of MsRCI2s

Rare cold-inducible 2/plasma membrane protein 3 (RCI2/PMP3) genes are ubiquitous in plants and belong to a multigene family whose members respond to a variety of abiotic stresses by regulating ion homeostasis and stabilizing membranes, thus preventing damage. In this study, the expression of MsRCI2A, MsRCI2B, and MsRCI2C under high-salinity, alkali and ABA treatments was analyzed. The results showed that the expression of MsRCI2A, MsRCI2B, and MsRCI2C in alfalfa (Medicago sativa L.) was induced by salt, alkali and ABA treatments, but there were differences between MsRCI2 gene expression under different treatments. We investigated the functional differences in the MsRCI2A, MsRCI2B, and MsRCI2C proteins in alfalfa (Medicago sativa L.) by generating transgenic alfalfa plants that ectopically expressed these MsRCI2s under the control of the CaMV35S promoter. The MsRCI2A/B/C-overexpressing plants exhibited different degrees of improved phenotypes under high-salinity stress (200 mmol.L–1 NaCl) and weak alkali stress (100 mmol.L–1 NaHCO3, pH 8.5). Salinity stress had a more significant impact on alfalfa than alkali stress. Overexpression of MsRCI2s in alfalfa caused the same physiological response to salt stress. However, in response to alkali stress, the three proteins encoded by MsRCI2s exhibited functional differences, which were determined not only by their different expression regulation but also by the differences in their regulatory relationship with MsRCI2s or H+-ATPase.