The genus Yersinia includes species with a wide range of eukaryotic hosts (from fish, insects, and plants to mammals and humans). One of the major outer membrane proteins, the porin OmpC, is preferentially expressed in the host gut, where osmotic pressure, temperature, and the concentrations of nutrients and toxic products are relatively high. We consider here the molecular evolution and phylogeny of Yersinia ompC. The maximum likelihood gene tree reflects the macroevolution processes occurring within the genus Yersinia. Positive selection and horizontal gene transfer are the key factors of ompC diversification, and intraspecies recombination was revealed in two Yersinia species. The impact of recombination on ompC evolution was different from that of another major porin gene, ompF, possibly due to the emergence of additional functions and conservation of the basic transport function. The predicted antigenic determinants of OmpC were located in rapidly evolving regions, which may indicate the evolutionary mechanisms of Yersinia adaptation to the host immune system.
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http://dx.doi.org/10.4137/EBO.S40346 | DOI Listing |
In this study, we performed a comparative analysis based on a total of 255 spider mitogenomes and four outgroups, of which the mitogenomes of 39 species were assembled de novo, to explore the phylogenetic relationships and the adaptive evolution of mitogenomes. Results showed that had the longest mitochondrial length and the most pronounced codon preference to be UUA, followed by CCU. Codon usage frequencies were similar between families and codon usage in the mitogenome of spiders was mainly influenced by natural selection pressures rather than G/C mutation bias.
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January 2025
Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy 27100.
Redox enzymes, mostly equipped with metal or organic cofactors, can vary their reactivity with oxygen by orders of magnitudes. Understanding how oxygen reactivity is controlled by the protein milieu remains an open issue with broad implications for mechanistic enzymology and enzyme design. Here, we address this problem by focusing on a widespread group of flavoenzymes that oxidize phenolic compounds derived from microbial lignin degradation, using either oxygen or a cytochrome c as electron acceptors.
View Article and Find Full Text PDFNPJ Antimicrob Resist
January 2025
Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, G1V 0A6 Canada.
Faced with the burden of increasing resistance to antifungals in many fungal pathogens and the constant emergence of new drug-resistant strains, it is essential to assess the importance of various resistance mechanisms. Fungi have relatively plastic genomes and can tolerate genomic copy number variation (CNV) caused by aneuploidy and gene amplification or deletion. In many cases, these genomic changes lead to adaptation to stressful conditions, including those caused by antifungal drugs.
View Article and Find Full Text PDFJ Fish Biol
January 2025
Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon (INPA), Manaus, Brazil.
The tambaqui (Colossoma macropomum, G. Cuvier 1818) thrives both in the ion-poor waters of the Amazon and in commercial aquaculture. In both, environmental conditions can be harsh due to low ion levels, occasional high salt challenges (in aquaculture), low pH, extreme PO levels (hypoxia and hyperoxia), high PCO levels (hypercapnia), high ammonia levels (in aquaculture), and high and low temperatures.
View Article and Find Full Text PDFGenome Biol Evol
January 2025
ISEM, Univ. Montpellier, CNRS, IRD, Montpellier, France.
Ant-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, and hypertrophied salivary glands producing large amounts of saliva. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase acidic gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites.
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