Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases

Yi, Lanbo; Liu, Bin; Nixon, Peter J.; Yu, Jianfeng; Chen, Feng

doi:10.3389/fpls.2022.837528

Cited by 26 publications

(13 citation statements)

References 186 publications

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“…In our study, miR9410 targeted a filamentation temperature sensitive protein H 1 ( FtsH7 ) gene copy encoding a protease that in turns degrades D 1 protein in photosystem II. FtsH genes have been reported in tomato, sorghum, Arabidopsis and B. napus (Xu et al 2021 ; Yi et al 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

et al. 2023

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Key message Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. Abstract The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F1 hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.

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Section: Discussionmentioning

confidence: 99%

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

et al. 2023

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“…FtsH genes have been reported in tomato, sorghum, Arabidopsis and B . napus (Xu et al, 2021; Yi et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…In our study, miR9410 targeted a filamentation temperature sensitive protein H 1 ( FtsH7 ) gene copy encoding a protease that in turns degrades D1 protein in photosystem II. FtsH genes have been reported in tomato, sorghum, Arabidopsis and B. napus (Xu et al, 2021; Yi et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Transgressive and parental dominant gene expression and cytosine methylation during seed development inBrassica napushybrids

Orantes-Bonilla

Wang

Lee

et al. 2022

Preprint

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The enhanced performance of hybrids though heterosis remains a key aspect in plant breeding; nonetheless, the transcriptomic and epigenomic mechanisms behind it are still not fully elucidated. In the present study, gene expression, small RNA abundance and genome-wide methylation patterns were evaluated in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next generation sequencing technologies. A total of 71217, 773, 79518 and 31825 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified respectively. Approximately 70% of the differential expression and methylation patterns observed could be explained due to parental dominance levels. Reproductive, developmental, and meiotic gene copies following transgressive and paternal dominance patterns were found through gene ontology enrichment and microRNA-target association analyses. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation which contrasts strikingly with the general maternal gamete demethylation occurring during gametogenesis in most plant species. Linkages between methylation and gene expression allowed the identification of putative genetic epialleles with diverse pivotal biological functions. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were found near gene flanking regions that had no differential expression, hence, indicating their potential role in conserving essential genomic and transcriptomic loci across the parents and offspring.

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“…In addition to the genomes of putative tryptorubin producers, genomes of frequently used bacterial heterologous host strains were likewise mined for all genes annotated as proteases or peptidases to identify suitable host strains for subsequent heterologous expression studies of the putative minimal trp BGC. Phylogenetic analyses revealed that putative producers of tryptorubin‐like peptides encode members of four conserved protease families, three of which (M41 family of unassigned peptidases, [13] S16 family of unassigned peptidases [14] and AA223 family of peptidases [13] ) belong to the superfamily of AAA+ proteases that are intracellular, membrane‐associated enzymes that catalyze the degradation of a wide range of proteins. Moreover, members of the family of M24B unassigned extracellular metallo‐peptidases [15] were identified in all putative tryptorubin producers and all commonly used Streptomyces host strains (Figure S3).…”

Section: Figurementioning

confidence: 99%

Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape

et al. 2022

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Biomacromolecules are known to feature complex three-dimensional shapes that are essential for their function. Among natural products, ambiguous molecular shapes are a rare phenomenon. The hexapeptide tryptorubin A can adopt one of two unusual atropisomeric configurations. Initially hypothesized to be a non-ribosomal peptide, we show that tryptorubin A is the first characterized member of a new family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) that we named atropopeptides. The sole modifying enzyme encoded in the gene cluster, a cytochrome P450 monooxygenase, is responsible for the atropospecific formation of one carbon-carbon and two carbon-nitrogen bonds. The characterization of two additional atropopeptide biosynthetic pathways revealed a two-step maturation process. Atropopeptides promote pro-angiogenic cell functions as indicated by an increase in endothelial cell proliferation and undirected migration. Our study expands the biochemical space of RiPPmodifying enzymes and paves the way towards the chemoenzymatic utilization of atropopeptide-modifying P450s.

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Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases

Cited by 26 publications

References 186 publications

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

Transgressive and parental dominant gene expression and cytosine methylation during seed development inBrassica napushybrids

Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape

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