Journal of Molecular Evolution最新文献

Heavy metal-associated (HMA) proteins are mainly metal ion transporters and are involved in heavy metal homeostasis and detoxification processes. However, despite the importance of this protein family, their role in several plant species has not been identified nor studied. In the present work, a genome-wide identification methodology was used to identify HMA proteins in 13 plant species, in a representation of angiosperm species belonging to the clades of magnoliids, monocotyledons, and eudicotyledons, and non-angiosperms such as Physcomitrella patens and Selaginella moellendorffii. The identified proteins were analyzed for phylogenetic relationships, prediction of protein domains and motifs, physicochemical characteristics, gene structures, and cis-elements present in the promoters. We found that all plant species have HMA proteins, according to the analysis carried out, it allowed us to propose 5 HMA groups, each one with a different gene and protein structure. Among these subfamilies there are the copper chaperone for superoxide dismutase (CCS) and the P1B-ATPase groups. Furthermore, the cis-elements found in the promoters of these genes suggest mainly possible functions in abiotic stress scenarios, not only caused by the presence of heavy metals but also by the exposure to drought, salts, light, as well as by plant hormones, biotic stresses and developmental processes. Our results provide new knowledge about the possible HMA proteins that are present in Persea americana, Cinnamomum micranthum, and ancestral species such as S. moellendorffii and P. patens, and their possible characteristics and functions against phenomena like abiotic stress.

Methods for the probabilistic mapping of the history of state changes over a phylogeny have been available for the study of molecular evolution for over two decades. In spite of this, such methods have yet to be adopted at large by most molecular evolutionary biologists. Here, we re-emphasize the potential of these stochastic mappings with examples pertaining to the study of the amino acid replacement process. We show how the features targeted by today's top-performing models could have been highlighted in a full phylogenetic context with an amino acid-level Jukes-Cantor model. We also demonstrate how stochastic mappings could be used for detecting CpG hypermutability, a site-dependent feature. We hope for a larger project utilizing mapping-based methods to provide of more fulsome characterization of molecular evolution, and to prioritize and assess modeling efforts. Finally, we draw attention to the options available within the PhyloBayes(-MPI) software for producing mappings under a large set of evolutionary models.

Intron splicing is a critical step that pre-mRNA transcripts undergo to become mature mRNAs. Although long thought to occur in a single step, introns are now also known to be removed by a multi-step process called recursive splicing. In recursive splicing, the spliceosome removes the intron one segment at a time with segments defined by discreet sequences called recursive splice sites. As each segment is removed, the remaining downstream intronic sequence is brought into contact with the upstream exon. Recursive splicing can be detected through RNA-seq analysis because it produces a "sawtooth" pattern of read depth across intron length with peaks corresponding to sites in the ephemeral partially spliced introns where the remaining downstream intron segments contact the upstream exon. Recursive splicing can also be detected by RNA lariat sequencing and real-time imaging of single-cell transcriptional and splicing dynamics. These methods have been applied to fruit flies, humans, and mice, revealing that recursive splicing 1) increases in prevalence with intron length, and 2) increases splicing fidelity, particularly in long introns. However, intron lengths in the typically sized genomes of these model organisms fail to represent the diversity that exists across the tree of life. Species with gigantic genomes like salamanders and lungfishes have introns that are ten- to 50-fold longer. Future studies targeting recursive splicing in gigantic genomes will provide a unique perspective on its functional significance and will also reveal whether this splicing mechanism plays a role in overcoming constraints placed on transcriptional capacity and efficiency by enormous introns.

In most vertebrates, teeth are continuously shed and replaced throughout life, while mammals and several lineages of reptiles have reduced replacement to only one or two generations. In contrast to the vast majority of their living relatives, members of the lizard families Chamaeleonidae and Agamidae have dispensed with lifelong tooth replacement, instead developing acrodont dentition that fuses to the jawbone to be used for the lifetime of the animal. Though, the loss of tooth replacement has not come without a cost. In order to mitigate the consequences that come with tooth replacement loss, mammals and acrodont lizards have evolved adaptations that strengthen enamel structure and minimize wear and tear experienced during the life of the animal. While these physical adaptations are well documented, the effect that loss of tooth replacement has had on the molecular components of teeth has not received significant attention. Here, we analyze the coding and amino acid sequences of six tooth proteins (AMBN, AMEL, AMTN, ACP4, ENAM, and MMP20) from acrodont lizards, pleurodont lizards that replace teeth, and mammals. We show that the reduction of tooth generations has disproportionately affected the evolutionary trajectory of proteins associated with enamel structure, with a particularly magnified effect on the evolution of AMEL.

Vpu, an accessory protein of human immunodeficiency virus-1 (HIV-1), plays a crucial role in viral particle production and significantly contributes to HIV virulence. However, the evolution of the vpu gene remains poorly understood. We conducted a computational analysis of approximately 39,000 simian immunodeficiency virus (SIV) and HIV sequences, focusing on 141 representative Vpu proteins. Phylogenetic analysis classified the SIV and HIV strains into four major types based on their Vpu proteins: Vpu-type 1 (ancestral, found in SIVs such as SIVmon and SIVgsn), Vpu-type 2 (SIVgor and HIV-1 group O), Vpu-type 3 (SIVcpz), and Vpu-type 4 (HIV-1 group M and N). Notably, Vpu-type 1 exhibited variability in gene length, genome length, and the overlap between vpu and env compared with other Vpu-types. A phylogenetic tree was constructed using 426 nucleotide sequences from HIV-1, HIV-2, and SIVs focusing on the region between the pol and env genes. Vpu-type 1 was closely clustered with SIVasc and SIVsyk, lacking both vpu and vpx. The similarities observed between vpu and genes such as vpr and env suggest that vpu originated within the SIV genome. In addition, a phylogenetic tree constructed from 252 Vpu-type 4a sequences from the HIV pandemic strain and 135 sequences of circulating recombinant forms of HIV-1 revealed 18 distinct protein subtypes, exceeding the number of previously recognized subtypes. The systematic analysis of the sequences from large datasets has enabled a detailed characterization of the transition states of vpu, enhancing our understanding of the processes driving viral diversity.

Asexual reproduction often leads to loss of genetic diversity, but several mechanisms have evolved to maintain heterozygosity. The subterrestrial nematode, Halicephalobus mephisto, reproduces parthenogenetically, and here, we investigate how its genetic diversity $-$ 1.15% SNP heterozygosity-is retained from generation to generation. To test for loss of heterozygosity, we PCR-typed 56 individual animals at two different loci; no homozygotes were observed in the population. Furthermore, whole-genome analysis of parent and progeny demonstrated no transition from heterozygote to homozygote across over 620,000 SNPs. Surprisingly, these SNPs are not uniformly distributed throughout the genome, as we find multiple tracts of loss of heterozygosity (LOH) where no variation exists. Covering 4.3 million base pairs (Mb) genome-wide, these LOH tracts are most consistent with a recent meiotic recombination event or an error of chromosomal segregation. Supporting this, we observed chromosomal associations during reproduction that may reflect some degree of synapsis, potentially enabling recombination. However, full-genome analysis of parent-progeny pairs shows the current state of the genome remains stable, with no new LOH detectable, suggesting that history of H. mephisto is more dynamic than previously appreciated, and that heterozygosity has not always been retained with perfect fidelity. The potential functional and evolutionary consequences of this observation are discussed along with potential mechanisms contributing to this unusual genomic history.

Drd2 dopamine receptor mRNAs are alternatively spliced in rodents and primates by skipping exon 6 to produce the D2_S protein, or including exon 6 to produce the D2_L protein. These protein isoforms have differing roles in pre- vs. post-synaptic signaling, cytoplasmic vesicle processing, and calcium-mediated desensitization. Genetic alteration in the D2_S/D2_L ratio affects human behavior and cognition at multiple levels, including working memory. Here we show that exon 6 originated early in vertebrate evolution, after the duplication and divergence of D2 and D4 dopamine receptor genes, but before the duplication and divergence of D2 and D3 dopamine receptor genes. Exon 6 encodes a relatively conserved sequence in the third cytoplasmic loop of the D2-D3 receptor. Its amino acid sequence is relatively short (24-33 amino acids), and is not strictly necessary for dopamine signal transduction. Exon skipping of Drd2 exon 6 was not detectable in the brains of cyclostomes, sharks, fish, relatively primitive amphibians (Xenopus, Notophthalmus), relatively primitive reptiles (turtles), relatively primitive birds (ostrich), or relatively primitive mammals (monotremes and marsupials). However, exon skipping of Drd2 exon 6 did occur at significant levels in the brains of more derived amphibians, reptiles, birds and mammals. Thus, skipping of Drd2 exon 6 arose convergently and specifically in the more derived tetrapod lineages, none of which deleted this exon. In contrast, exon 6 was convergently deleted during Drd3 evolution in an apparently random subset of the species of sharks, fish, amphibians, reptiles, birds, and mammals.

Epigenetic modifications are one of the evolutionary mechanisms that allow individuals and populations to adapt to environmental changes. However, the relative importance of epigenetic versus genetic changes in adaptation and how they may interact remains poorly understood. Here, we investigate the role of DNA methylation in adaptation by studying a population of Allis shad (Alosa alosa) that evolved a completely freshwater life history approximately 70 years ago and the anadromous one that founded it. Using reduced representation bisulfite sequencing, we identified 227 differentially methylated regions (DMRs) between them, overlapping known important genes for freshwater adaptation, such as ATP2B4, PRLH2, and KCNF1A. Enrichment analysis of GO terms suggested that genes in the identified DMRs play key roles in neural, growth, and developmental functions, which is concordant with previous studies on adaptation to freshwater in this species and genus. Using pool-seq data from an earlier study, we then tested if the DMRs for freshwater shad found here overlapped genomic outlier regions that may be under genetic selection in three independently evolved, freshwater populations (including the one studied here). Our analysis showed that the DMRs identified here fall broadly outside genomic regions under natural selection. However, 45% of these were associated with CpG > TpG deamination events in DMRs, a mutation tightly linked with DNA methylation. Our study illustrates that both genetic and epigenetic mechanisms are important during the initial stages of adaptation in this system. It also supports the hypothesis that methylation may generate polymorphism that fuels adaptive evolution.

A new class of viroid-like RNAs, called Obelisks, was recently reported by Zheludev et al. (Cell 187:6521-6536.e6518, 2024). They found thousands of Obelisk sequences globally and identified a specific 1137 nt Obelisk, called Obelisk-S.s, in monoculture transcriptomes of Streptococcus sanguinis SK36, a commensal bacterium of the human oral microbiome. Here, we confirm that Obelisk-S.s is highly abundant in SK36, despite its absence from the SK36 genome (i.e., as DNA). In 11 out of 17 monoculture SK36 RNA-seq datasets examined, Obelisk-S.s is more abundant than any mRNA. Given its relative abundance, we hypothesized that multiple Obelisk-S.s variants could coexist within SK36. We found three Obelisk-S.s mutations at 5-10% allele frequency in some samples: a R162R synonymous mutation in one set of replicate transcriptomes, and an I48I synonymous mutation and an intergenic mutation in another set of replicate transcriptomes. A simple mathematical model shows how high Obelisk abundance can transiently stabilize intracellular Obelisk populations, and how extreme Obelisk abundances may stabilize intracellular Obelisk populations indefinitely. Evolution experiments with SK36 could test this theory and could shed light on how Obelisks function and evolve within their microbial hosts.

The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylum Nucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimeric RNA polymerases, and mRNA-capping enzymes to explore their evolutionary relationships. Our results show that viral enzymes form clades that are typically adjacent to eukaryotes, suggesting that they originate prior to the emergence of the Last Eukaryotic Common Ancestor (LECA). The machinery for viral DNA replication, transcription, and mRNA capping are all key processes needed for the maintenance of virus factories, which are complex structures formed by many nucleocytoviruses during infection, indicating that viruses capable of making these structures are ancient. These findings hint at a diverse and complex pre-LECA virosphere and indicate that large DNA viruses may encode proteins that are relics of extinct proto-eukaryotic lineages.