Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from R1, only distantly related to previously described homologues and whose presence, along with a 3-hydroxybenzoate/gentisate pathway, correlated with the ability to grow on other meta-methoxylated aromatics, such as 3-methoxybenzoate and 5-methoxysalicylate. The complementation of catabolic abilities by heterologous expression in a host strain unable to grow on vanillate, and subsequent resting cell assays, suggest that the genes of R1 strain encode a proficient VanOD acting on different vanillate-like substrates; and also revealed that a methoxy group in the position and a carboxylic acid moiety in the aromatic ring are key for substrate recognition. Phylogenetic analysis of the oxygenase subunit of bacterial VanODs revealed three divergent groups constituted by homologues found in Proteobacteria (Type I), Actinobacteria (Type II), or Proteobacteria/Actinobacteria (Type III) in which the R1 VanOD is placed. These results suggest that VanOD from R1 strain, and its type III homologues, expand the range of methoxylated aromatics used as substrates by bacteria.
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http://dx.doi.org/10.3390/microorganisms11010078 | DOI Listing |
BMC Plant Biol
January 2025
Maize and Millet Research Institute, Yousafwala, Sahiwal, Pakistan.
Heat stress poses a significant challenge for maize production, especially during the spring when high temperatures disrupt cellular processes, impeding plant growth and development. The B-cell lymphoma-2 (Bcl-2) associated athanogene (BAG) gene family is known to be relatively conserved across various species. It plays a crucial role as molecular chaperone cofactors that are responsible for programmed cell death and tumorigenesis.
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January 2025
Guangxi University of Chinese Medicine School of Yao Medicine, Nanning, 530200, Guangxi, China.
Golden camellia species are endangered species with great ecological significance and economic value in the section Chrysantha of the genus Camellia of the family Theaceae. Literature shows that more than 50 species of golden camellia have been found all over the world, but the exact number remains undetermined due to the complex phylogenetic background, the non-uniform classification criteria, and the presence of various synonyms and homonyms; and phylogenetic relationships among golden camellia species at the gene level are yet to be disclosed. Therefore, it is necessary to investigate the divergence time and phylogenetic relationships between all golden camellia species at the gene level to improve their classification system and achieve accurate identification of them.
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January 2025
Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp genome data with nuclear DNA information offers a more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives.
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January 2024
Department of Biological Sciences, Ajou University, Suwon 16499, Republic of Korea.
Bacterial species adapt to cold environments with diverse molecular mechanisms enabling their growth under low ambient temperature. The emergence of cold-adapted species at macro-evolutionary scale, however, has not been systematically explored. In this study, we performed phylogenetic analysis on the growth temperature traits in the genera that occupy broad environmental and host niches and contain known cold-adapted species.
View Article and Find Full Text PDFMol Ecol
January 2025
Department of Biology and Wildlife, University of Alaska Museum, Fairbanks, Alaska, USA.
The application of high-throughput sequencing to phylogenetic analyses is allowing authors to reconstruct the true evolutionary history of species. This work can illuminate specific mechanisms underlying divergence when combined with analyses of gene flow, recombination and selection. We conducted a phylogenomic analysis of Catharus, a songbird genus with considerable potential for gene flow, variation in migratory behaviour and genomic resources.
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