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The moss is used both as an evo-devo model and biotechnological production system for metabolites and pharmaceuticals. Strong expression of genes of interest is important for production of recombinant proteins, e.g., selectable markers, fluorescent proteins, or enzymes. In this regard, the choice of the promoter sequence as well as codon usage optimization are two important inside factors to consider in order to obtain optimum protein accumulation level. To reliably quantify fluorescence, we transfected protoplasts with promoter:GFP fusion constructs and measured fluorescence intensity of living protoplasts in a plate reader system. We used the red fluorescent protein mCherry under 2x promoter control as second reporter to normalize for different transfection efficiencies. We derived a novel endogenous promoter and compared deletion variants with exogenous promoters. We used different codon-adapted green fluorescent protein (GFP) genes to evaluate the influence of promoter choice and codon optimization on protein accumulation in , and show that the promoter of the gene of chlorophyll a/b binding protein drives expression of GFP in protoplasts significantly (more than twofold) better than the commonly used 2x promoter or the rice promoter. We identified a shortened 677 bp version of the promoter that retains full activity in protoplasts. The codon optimized GFP yields significantly (more than twofold) stronger fluorescence signals and thus demonstrates that adjusting codon usage in can increase expression strength. In combination, new promotor and codon optimized GFP conveyed sixfold increased fluorescence signal.
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http://dx.doi.org/10.3389/fpls.2017.01842 | DOI Listing |
Eur J Clin Microbiol Infect Dis
September 2025
School of Bioengineering and Biosciences, Department of Biochemistry, Lovely Professional University, Punjab, 144411, India.
Purpose: This study investigates codon usage and amino acid usage bias in the genus Acinetobacter to uncover the evolutionary forces shaping these patterns and their implications for pathogenicity and biotechnology.
Methods: Codon usage patterns were examined in representative genomes of the genus Acinetobacter using standard codon bias indices, including GC content, relative synonymous codon usage (RSCU), effective number of codons (ENC), and codon adaptation index (CAI). Neutrality and parity plots were employed to evaluate the relative influence of mutational pressure and natural selection on codon preferences.
Planta
September 2025
Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy.
The first complete plastid genome of the critically endangered species Valeriana trinervis was sequenced, assembled and compared with other published Valeriana plastomes. In this study, we assembled the plastid genome of the critically endangered, endemic species Valeriana trinervis (= Centranthus trinervis) and compare it with all published plastomes of Valeriana. We found not only differences in the inverted repeats boundaries, in the type and abundance of repeats, but also similarities in codon usage and microsatellite numbers.
View Article and Find Full Text PDFJ Appl Stat
February 2025
Department of Mathematics and State Key Laboratory of Novel Software Technology, Nanjing University, Nanjing, People's Republic of China.
We conduct gene mutation rate estimations via developing mutual information and Ewens sampling based convolutional neural network (CNN) and machine learning algorithms. More precisely, we develop a systematic methodology through constructing a CNN. Meanwhile, we develop two machine learning algorithms to study protein production with target gene sequences and protein structures.
View Article and Find Full Text PDFISME Commun
January 2025
Department of Environmental Engineering, National Cheng Kung University, Tainan City 70101, Taiwan.
Global salinization increasingly threatens ecosystem integrity and the regulation of biogeochemical cycles. Our study reveals novel insights into the microbial contributions to the organohalide decomposition in saline environments, demonstrating the unprecedented ability of organohalide-respiring bacteria and to completely dechlorinate trichloroethene to non-toxic ethene under hypersaline conditions (up to 31.3 g/L) in long-term operations.
View Article and Find Full Text PDFMol Biol Rep
September 2025
ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400061, India.
Background: Labeo fimbriatus (Bloch, 1795) is a medium-sized South Asian minor carp with ecological significance and emerging aquaculture potential, particularly in polyculture systems with Indian major carps. Despite its wide distribution, it remains underrepresented in phylogenetic studies, and limited genomic resources are available. Here, we report the complete mitochondrial genome sequence of L.
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