Article
Plant Sciences
Hui Xu, Zhen Li, Peng-Fei Jiang, Li Zhao, Chang Qu, Yves Van de Peer, Yan-Jing Liu, Qing-Yin Zeng
Summary: Enzymes are essential for all living systems, and in plants, the glutaredoxin (GRX) family of enzymes plays important roles in development and stress tolerance. This study identified and classified 41 GRX genes in the poplar genome based on differences in gene structure, expression patterns, subcellular localization, enzymatic activity, and substrate specificity. Site-directed mutagenesis revealed that the divergence of active site motifs among different classes of GRX proteins led to substrate switches, providing new insights into the molecular evolution of these important plant enzymes.
Article
Plant Sciences
Hemeng Wang, Jin-Gui Chen, Ying Chang
Summary: OFPs are a family of plant growth regulators known to play diverse roles in physiological processes, with members like PtOFP1 having been shown to act as a transcriptional repressor. In Populus trichocarpa, 30 PtOFP genes were identified, grouped into four subfamilies, and found to be involved in hormonal responses and cellular processes. Overexpression of PtOFP1 in Arabidopsis enhanced tolerance to drought stress, highlighting its potential as a target for genetic modification in improving stress resistance in plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Chanaka Roshan Abeyratne, David Macaya-Sanz, Ran Zhou, Kerrie W. Barry, Christopher Daum, Kathy Haiby, Anna Lipzen, Brian Stanton, Yuko Yoshinaga, Matthew Zane, Gerald A. Tuskan, Stephen P. DiFazio
Summary: This study used genetic mapping and haplotype reconstruction to estimate fine-scale meiotic recombination events in a Populus trichocarpa cross. The results showed a large number of recombination events in the progeny, which were associated with gene density, GC content, and long-terminal repeats. Male individuals had higher rates of recombination in some chromosomes compared to female individuals. These findings have important implications for accelerating domestication of biomass feedstocks and studying various aspects of evolutionary history, wood formation, vegetative propagation, and dioecy.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Hila Behar, Yaseen Mottiar, Rohan Chandrasekhar, Allegra Corelli Grappadelli, Markus Pauly, A. Lacey Samuels, Shawn D. Mansfield, Harry Brumer
Summary: This study used a hybrid polar plant model, Populus alba x Populus grandidentata (P39), to investigate the expression, subcellular localization, and phenotypes and chemotypes of EG16-downregulated P39 plants. The results showed that Populus EG16 is strongly expressed in young tissues, but RNAi-mediated downregulation did not affect plant growth or the fine structure of hemicellulose xyloglucan, suggesting a restricted or currently unknown role in angiosperm physiology.
Article
Forestry
Yang Ye, Haodong Xin, Xiting Gu, Jianwen Ma, Lingli Li
Summary: This study identified 233 PtbHLHs and 10 PtFBHs in the newest version of Populus trichocarpa genome, and analyzed their classification, distribution, expression patterns, and evolutionary pressures. The results suggest that PtbHLHs may be involved in plant growth and development, providing valuable clues for further investigations on the physiological and molecular functions of these genes.
Article
Biochemistry & Molecular Biology
Ben E. Clifton, Muhammad A. Fariz, Gen-Ichiro Uechi, Paola Laurino
Summary: This study investigated the essential function of tRNA modification m(1)G37 introduced by TrmD in bacteria. Experimental evolution of trmD mutant strains of E. coli revealed that the loss of m(1)G37 could be tolerated due to rapid recovery of growth rate via duplication or mutation of the proline-tRNA ligase gene proS. The inefficient aminoacylation of tRNA(Pro) was identified as the main reason for growth defects in trmD mutant strains, and proS was suggested to act as a gatekeeper of translational accuracy.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Merve Seven, U. Cem Derman, Andrew J. Harvey
Summary: Xyloglucan endotransglycosylase/hydrolase (XTH) enzymes have been found to exhibit broad substrate specificities, including cellulose analogues and mixed-link beta-glucans, in addition to the standard xyloglucan. This discovery opens up a wide range of potential roles for these enzymes, both within plants and in various industries. Furthermore, genome screening and expression analyses suggest that the XTH genes in the "ancestral" clades are unique to angiosperms, predominantly expressed in reproductive tissues, leading to the proposal of renaming this phylogenetic group as the group-IV clade.
Article
Chemistry, Applied
Jingjing Shen, Guangning Chen, Yuying Zhang, Xuanwei Mei, Yaoguang Chang, Changhu Xue
Summary: In recent decades, there has been increasing research interest in sulfated fucans due to their various physiological activities. Fucanases are essential for studying sulfated fucans. In this study, a novel GH168 family endo1,3-fucanase was cloned from the genome of the marine bacterium Wenyingzhuangia fucanilytica. The enzyme, named Fun168D, was found to cleave specific bonds in sulfated fucans from Isostichopus badionotus and Holothuria tubulosa, revealing the presence of diversity within the GH168 family.
CARBOHYDRATE POLYMERS
(2023)
Article
Biochemistry & Molecular Biology
Joshua J. Hamey, Sinja Rakow, Caroline Bouchard, Johanna M. Senst, Peter Kolb, Uta-Maria Bauer, Marc R. Wilkins, Gene Hart-Smith
Summary: PRMT6 catalyzes the asymmetric dimethylation of arginines on substrate proteins, including histone H3, affecting gene regulation. This study systematically characterized PRMT6's substrate recognition motif, showing broad specificity and a preference for the RG motif. Despite efficient methylation at H3R2, PRMT6 tolerates various amino acid substitutions in the H3 peptide, with preference for positively charged and bulky residues near the target arginine.
Article
Evolutionary Biology
Xinhui Zhang, David Jacobs
Summary: This study investigated DNA methylation in Cnidaria and found that the pattern and function of gene body methylation differs from that of bilaterian vertebrates and invertebrates. Cnidarians have lower CpG frequencies on gene bodies, potentially indicating a compensatory mechanism. The GbM pattern in Cnidaria shows consistency within taxonomic groups and variation across different taxonomic ranks, and some GbM variation is associated with life history change and genome expansion.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
June H. Kim, Emily R. Hildebrandt, Anushka Sarkar, Wayland Yeung, La Ryel A. Waldon, Natarajan Kannan, Walter K. Schmidt
Summary: This study comprehensively evaluated all possible CXXX sequences as targets of farnesyltransferase (FTase) using the reporter Ydj1. It found that yeast FTase can farnesylate sequences outside the CaaX motif and that these sequences do not undergo the canonical 3-step pathway. The study also revealed that yeast FTase specificity is mainly influenced by restrictive amino acids at a(2) and X positions, rather than the resemblance of the CaaX motif.
G3-GENES GENOMES GENETICS
(2023)