Journal of Molecular Evolution最新文献

The origin of proteins is a fundamental question in the study of the origin of life. Peptides, as the building blocks of proteins, necessarily preceded the first proteins in prebiotic chemical evolution. Prebiotic peptides may have also played crucial roles in early life's evolution, contributing to self-catalysis, interacting with nucleic acids, and stabilizing primitive cell compartments. Longer and more complicated prebiotic peptides often have greater structural flexibility and functional potential to support the emergence and evolution of early life. Since the Miller-Urey experiment demonstrated that amino acids can be synthesized in a prebiotic manner, the prebiotic synthesis route of peptides has garnered increasing attention from researchers. However, it is difficult for amino acids to condense into peptides in aqueous solutions spontaneously. Over the past few decades, researchers have explored various routes of prebiotic peptide synthesis in the plausible prebiotic Earth environment, such as thermal polymerization, clay mineral catalysis, wet-dry cycles, condensing agents, and lipid-mediated. This paper reviews advancements in prebiotic peptide synthesis research and discusses the conditions that may have facilitated the emergence of longer peptides.

A-to-I mRNA editing resembles A-to-G mutations. Functional mRNA editing, representing only a corner of total editing events, can be inferred from the experimental removal of editing. However, it is intuitive to ask why evolution chose RNA editing rather than directly (and simply) changing the genomic sequence to G? If G is better than A, then drift or constructive neutral evolution (CNE) theory can explain the emergence of such editing, but it is still unclear why the exemplified conserved editing is perfectly maintained without observing any subsequent A-to-G DNA mutations? Virtually every functional and conserved mRNA editing site faces this ultimate question until one justifies that being editable is better than a hardwired genomic allele. While the advantage of editability has been validated in fungi, this ultimate question has not been answered for any functional editing sites in animals. By providing several conceptual arguments and specific examples, we propose that proving the evolutionary adaptiveness of an editing site is far more difficult than revealing its function.

Due to the COVID-19 pandemic and the uncertainty about aspects of its origin, in recent years there has been an increased interest in investigating coronaviruses in wild animals. Bats are hosts of the greatest diversity of coronaviruses to date, including the ancestors of viruses that have caused outbreaks in humans. Although in Brazil, information on coronaviruses in bats has expanded, still they remain unrepresentative. To help shed some light on this matter, we collected 175 samples from bats of different species from two Brazilian states. Here, we report the previously unknown presence of an alphacoronavirus in a bat (Molossus sp.) from Ceará. The phylogenetic analysis showed close relationships with alphacoronaviruses from Brazil and Argentina, but it was not possible to determine the subgenus or species of this virus using RNA-dependent RNA-polymerase (RdRp) domain of the nsp12 protein-coding sequence as it was distant from the specimens considered by the International Committee on Taxonomy of Viruses (ICTV). Finally, by performing High-Throughput Sequencing, we were able to find contigs mostly belonging to domains of the replicase of bat coronaviruses related to American bats of the Molossidae and Vespertilionidae families.

Monocyte chemoattractant proteins (MCPs) are involved in monocyte trafficking during severe inflammation by modulating the chemokine-glycosaminoglycan-receptor signaling axis. MCPs comprise a family of four chemokines (CCL2, CCL7, CCL8, and CCL13/12) that exhibit differential expression patterns in mammals, functional diversity, and receptor/glycosaminoglycan (GAG) binding promiscuity. In this context, the evolution-structure-function paradigm of MCP chemokines in mammals was established by assessing phylogeny, functional divergence, selection pressure, and coevolution in correlation with structural and surface characteristics. Comprehensive analyses were performed using an array of evolutionary and structural bioinformatic methods including molecular dynamics simulations. Our findings demonstrate that substitutions in receptor/GAG-interacting residues mediate episodic diversification and functional diversity in MCP chemokines. Additionally, a balanced interplay of selection pressures has driven the functional changes observed among MCP paralogs, with positive selection at various receptor/GAG-binding sites contributing to their promiscuous receptor/GAG interactions. Meanwhile, processes like purifying selection and coevolution maintain the classical chemokine structure and preserve the ancestral functions of MCP chemokines. Overall, this study suggests that selection pressure on sites within the N-terminal region [N-loop and 3₁₀-helix] and 40S loop of MCP chemokines alters surface properties to fine-tune the molecular interactions and functional characteristics without altering the overall chemokine structure.

One of the most important and difficult challenges in the research of molecular evolution is modeling the process of amino acid substitutions. Although single-matrix models, such as the LG model, are popular, their capability to properly capture the heterogeneity of the substitution process across sites is still questioned. Several mixture models with multiple matrices have been introduced and shown to offer advantages over single-matrix models. Current general mixture models assume the reversibility of the evolutionary process, implying that substitution rates between any two amino acids are equal in both forward and backward directions. This assumption is not based on biological properties but rather on computational simplicity. The well-known hypothesis is that more realistic models can yield more accurate evolutionary inferences; therefore, our aim is to estimate more biologically realistic models. To this end, we relax the assumption of reversibility and introduce two new general non-reversible 4-matrix mixture models, called nT4M and nT4X. Using alignments from HSSP and TreeBASE databases as data, our newly estimated models outperformed all single-matrix models and almost all reversible mixture models. Moreover, the new non-reversible mixture models enable us to infer rooted trees.

Expansion and losses of gene families are important drivers of molecular evolution. A recent survey of Fox genes in flatworms revealed that this superfamily of multifunctional transcription factors, present in all animals, underwent extensive losses and expansions during platyhelminth evolution. In this paper, I analyzed Fox gene complement in four additional species of platyhelminths, that represent early-branching lineages in the flatworm phylogeny: catenulids (Stenostomum brevipharyngium and Stenostomum leucops) and macrostomorphs (Macrostomum hystrix and Macrostomum cliftonense). Phylogenetic analysis of Fox genes from this expanded set of species provided evidence for multiple independent expansions of Fox gene families within flatworms. Notably, FoxG, a panbilaterian brain-patterning gene, appears to be the least susceptible to duplication, while FoxJ1, a conserved ciliogenesis factor, has undergone extensive expansion in various flatworm lineages. Analysis of the single-cell atlas of S. brevipharyngium, combined with RNA in situ hybridization, elucidated the tissue-specific expression of the selected Fox genes: FoxG is expressed in the brain, three of the Fox genes (FoxN2/3-2, FoxO4 and FoxP1) are expressed in the pharyngeal cells of likely glandular function, while one of the FoxQD paralogs is specifically expressed in the protonephridium. Overall, the evolution of Fox genes in flatworms appears to be characterized by an early contraction of the gene complement, followed by lineage-specific expansions that have enabled the co-option of newly evolved paralogs into novel physiological and developmental functions.

PIWI-interacting RNAs (piRNAs) are the most diverse small RNAs in animals. These small RNAs have been known to play an important role in the suppression of transposable elements (TEs). Protein-coding genes (PCGs) are the most well-recognized functional genes in genomes. In the present study, we designed and performed a set of statistics-based evolutionary analyses to reveal nonrandom phenomena in the evolution of human piRNA-PCG targeting relationships. Through analyzing the occurrence of single nucleotide variants (SNVs) in potential piRNA target sites in human PCGs, we provide evidence that there exists a mutational force biased to strengthen piRNA-PCG targeting relationships. Through analyzing the allele frequencies of SNVs in potential piRNA target sites in human PCGs, we provide evidence that there exists a piRNA-dependent selective force acting on potential piRNA target sites in human PCGs. Because of these nonrandom evolutionary forces, human piRNAs and their potential target sites in PCGs are not independent in evolution. Additionally, we found evidence that potential piRNA target sites in human PCGs are particularly likely to be present in regions derived from Alu elements. This finding suggests that the aforementioned evolutionary forces acting on piRNA-PCG targeting relationships could be particularly prone to affect Alu-derived regions in human PCGs. Collectively, our findings provide new insights into the evolutionary interplay between piRNAs, PCGs, and Alu elements in the evolution of the human genome.

Recently, certain studies have claimed that cognitive features and pathologies unique to humans can be traced to certain changes in the nervous system. These are caused by genes that have likely evolved "from scratch," not having any coding precursors. The translated proteins would not appear outside of the human lineage and any orthologs in other species should be non-coding. This contrasts with research that has identified a decisive role for duplication, and modifications to regulatory sequences, for such phenotypic traits. Closer examination, however, reveals that the inferred lineage-specific emergence of at least two of these genes is likely a misinterpretation owing to a lack of peptide verification, experimental oversights, and insufficient species comparisons. A possible pseudogenic origin is proposed for one of them. The implications of these claims for the study of molecular evolution are discussed.

The major histocompatibility complex (MHC) is a cluster of functionally related genes encoding proteins which, among other functions, mediate immune system activation. While the MHC of many vertebrates has been extensively studied, less is known about the amphibian MHC. This represents an important knowledge gap because amphibians mark the evolutionary transition from an aquatic to a terrestrial lifestyle and often maintain a biphasic lifestyle. Hence, they tend to be exposed to both aquatic and terrestrial pathogen communities, providing opportunities to gain fundamental insights into how the immune system responds to different environmental challenges. Moreover, amphibians are globally threatened by invasive pathogens and the MHC may play a role in combating population decline. In this review, we summarize the current state of knowledge regarding the amphibian MHC and identify the major differences with other vertebrates. We also review how the number of MHC gene copies varies across amphibian groups and how MHC-based variation relates to amphibian ontogeny, behaviour, disease, and phylogeography. We conclude by identifying knowledge gaps and proposing priorities for future research.