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Plant Biotechnology Journal May 2024
PubMed: 38803087
DOI: 10.1111/pbi.14369 -
BMC Genomics May 2024MeFtsZ2-1 is a key gene for plant plastid division, but the mechanism by which MeFtsZ2-1 affects pigment accumulation in cassava (Manihot esculenta Crantz) through...
MeFtsZ2-1 is a key gene for plant plastid division, but the mechanism by which MeFtsZ2-1 affects pigment accumulation in cassava (Manihot esculenta Crantz) through plastids remains unclear. We found that MeFtsZ2-1 overexpression in cassava (OE) exhibited darker colors of leaves, with increased levels of anthocyanins and carotenoids. Further observation via Transmission Electron Microscopy (TEM) revealed no apparent defects in chloroplast structure but an increase in the number of plastoglobule in OE leaves. RNA-seq results showed 1582 differentially expressed genes (DEGs) in leaves of OE. KEGG pathway analysis indicated that these DEGs were enriched in pathways related to flavonoid, anthocyanin, and carotenoid biosynthesis. This study reveals the role of MeFtsZ2-1 in cassava pigment accumulation from a physiological and transcriptomic perspective, providing a theoretical basis for improving cassava quality.
Topics: Manihot; Plant Leaves; Plant Proteins; Gene Expression Regulation, Plant; Gene Expression Profiling; Transcriptome; Anthocyanins; Carotenoids; Chloroplasts; Plastids
PubMed: 38802758
DOI: 10.1186/s12864-024-10165-w -
Nature Plants Jun 2024The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA...
The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications.
Topics: Nicotiana; Gene Dosage; Genome, Plastid; Inverted Repeat Sequences; Plastids; Genome Size; DNA Copy Number Variations; Genome, Plant
PubMed: 38802561
DOI: 10.1038/s41477-024-01709-9 -
Nature Plants Jun 2024
Topics: Plastids
PubMed: 38802560
DOI: 10.1038/s41477-024-01710-2 -
International Journal of Molecular... May 2024In plants, nucleotide-binding site and leucine-rich repeat proteins (NLRs) play pivotal roles in effector-triggered immunity (ETI). However, the precise mechanisms...
Unveiling the Role of RNA Recognition Motif Proteins in Orchestrating Nucleotide-Binding Site and Leucine-Rich Repeat Protein Gene Pairs and Chloroplast Immunity Pathways: Insights into Plant Defense Mechanisms.
In plants, nucleotide-binding site and leucine-rich repeat proteins (NLRs) play pivotal roles in effector-triggered immunity (ETI). However, the precise mechanisms underlying NLR-mediated disease resistance remain elusive. Previous studies have demonstrated that the NLR gene pair confers resistance to rice blast disease by interacting with the transcription factor OsBIHD1, consequently leading to the upregulation of hormone pathways. In the present study, we identified an RNA recognition motif (RRM) protein, OsRRM2, which interacted with Pik-H4 and Pik-H4 in vesicles and chloroplasts. OsRRM2 exhibited a modest influence on -mediated rice blast resistance by upregulating resistance genes and genes associated with chloroplast immunity. Moreover, the RNA-binding sequence of OsRRM2 was elucidated using systematic evolution of ligands by exponential enrichment. Transcriptome analysis further indicated that OsRRM2 promoted RNA editing of the chloroplastic gene . Collectively, our findings uncovered a chloroplastic RRM protein that facilitated the translocation of the NLR gene pair and modulated chloroplast immunity, thereby bridging the gap between ETI and chloroplast immunity.
Topics: Chloroplasts; Plant Immunity; Plant Proteins; Gene Expression Regulation, Plant; Oryza; Leucine-Rich Repeat Proteins; Binding Sites; RNA Recognition Motif Proteins; Plant Diseases; Disease Resistance; NLR Proteins; RNA Editing
PubMed: 38791594
DOI: 10.3390/ijms25105557 -
International Journal of Molecular... May 2024ROS-dependent induction of oxidative damage can be used as a trigger initiating genetically determined non-specific protection in plant cells and tissues. Plants are...
ROS-dependent induction of oxidative damage can be used as a trigger initiating genetically determined non-specific protection in plant cells and tissues. Plants are potentially able to withstand various specific (toxic, osmotic) factors of abiotic effects, but do not have sufficient or specific sensitivity to form an adequate effective response. In this work, we demonstrate one of the possible approaches for successful cold acclimation through the formation of effective protection of photosynthetic structures due to the insertion of the heterologous gene into the tobacco genome under the control of the constitutive promoter and equipped with a signal sequence targeting the protein to plastid. The increased enzymatic activity of superoxide dismutase in the plastid compartment of transgenic tobacco plants enables them to tolerate the oxidative factor of environmental stresses scavenging ROS. On the other hand, the cost of such resistance is quite high and, when grown under normal conditions, disturbs the arrangement of the intrachloroplastic subdomains leading to the modification of stromal thylakoids, probably significantly affecting the photosynthesis processes that regulate the efficiency of photosystem II. This is partially compensated for by the fact that, at the same time, under normal conditions, the production of peroxide induces the activation of ROS detoxification enzymes. However, a violation of a number of processes, such as the metabolism of accumulation, and utilization and transportation of sugars and starch, is significantly altered, which leads to a shift in metabolic chains. The expected step for further improvement of the applied technology could be both the use of inducible promoters in the expression cassette, and the addition of other genes encoding for hydrogen peroxide-scavenging enzymes in the genetic construct that are downstream in the metabolic chain.
Topics: Nicotiana; Oxidative Stress; Plastids; Superoxide Dismutase; Plants, Genetically Modified; Reactive Oxygen Species; Cold Temperature; Photosynthesis; Plant Proteins
PubMed: 38791585
DOI: 10.3390/ijms25105544 -
International Journal of Molecular... May 2024To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat ( L.) cultivar, miRNA transcriptome...
To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat ( L.) cultivar, miRNA transcriptome sequencing of the flag leaves of Zhengmai 1860, drought-sensitive variety Zhoumai 18, and drought-resistant variety Bainong 207 was performed during the grain filling stage. We also observed changes in the chloroplast ultrastructure, phytohormone levels, and antioxidant- and photosynthesis-related physiological indicators in three wheat varieties. The results showed that the flag leaves of the drought-tolerant variety Zhengmai 1860 had higher chlorophyll contents and net photosynthetic rates than those of Zhoumai 18 under drought stress during the grain filling stage; in addition, the chloroplast structure was more complete. However, there was no significant difference between Zhengmai 1860 and Bainong 207. MiRNA transcriptome analysis revealed that the differential expression of the miRNAs and mRNAs exhibited variable specificity. The KEGG pathway enrichment results indicated that most of the genes were enriched in the MAPK signaling pathway, plant hormone signal transduction, photosynthetic antennae protein, and amino acid and carbohydrate metabolism. In the drought-tolerant cultivar Zhengmai 1860, tae-miR408 was targeted to regulate the allene oxide synthase (AOS) gene, inhibit its expression, reduce the AOS content, and decrease the synthesis of jasmonic acid (JA) and abscisic acid (ABA). The results of this study suggest that Zhengmai 1860 could improve the photosynthetic performance of flag leaves by inhibiting the expression of genes involved in the JA pathway through miRNAs under drought conditions. Moreover, multiple miRNAs may target chlorophyll, antioxidant enzymes, phytohormone signal transduction, and other related pathways; thus, it is possible to provide a more theoretical basis for wheat molecular breeding.
Topics: MicroRNAs; Triticum; Photosynthesis; Gene Expression Regulation, Plant; Droughts; Stress, Physiological; Gene Expression Profiling; Transcriptome; Plant Growth Regulators; Edible Grain; Chloroplasts; Plant Leaves
PubMed: 38791558
DOI: 10.3390/ijms25105518 -
Genes Apr 2024Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been...
Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes were identified, including 87 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The base composition analysis showed that the overall GC content was 36.36% of the complete chloroplast genome sequence. Relative synonymous codon usage frequency (RSCU) analysis showed that most codons with values greater than 1 ended with A or U, while most codons with values less than 1 ended with C or G. Thirty-five scattered repeats were identified and most of them were distributed in the large single-copy (LSC) region. A total of 290 simple sequence repeats (SSRs) were found and 188 of them were distributed in the LSC region. Phylogenetic relationship analysis showed that five subspecies were clustered into one group and the kohlrabi chloroplast genome was closely related to that of var. Our results provide a basis for understanding chloroplast-dependent metabolic studies and provide new insight for understanding the polyploidization of Brassicaceae species.
Topics: Genome, Chloroplast; Phylogeny; Brassica; Microsatellite Repeats; Base Composition; Codon Usage; Chloroplasts; Whole Genome Sequencing
PubMed: 38790180
DOI: 10.3390/genes15050550 -
Genes Apr 2024is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on is lacking. To resolve the genetic... (Comparative Study)
Comparative Study
is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on is lacking. To resolve the genetic composition of within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in , with some genes (, , ) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed , , , and to have a close monophyletic relationship. By sequencing the chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.
Topics: Genome, Chloroplast; Phylogeny; Amaranthaceae; Codon Usage; Microsatellite Repeats; Evolution, Molecular; Chloroplasts; China; Molecular Sequence Annotation
PubMed: 38790176
DOI: 10.3390/genes15050546 -
Genes Apr 2024is considered the closest relative to the invasive weed in China, making it an important native species for studying the invasive mechanisms and adaptations of .... (Comparative Study)
Comparative Study
is considered the closest relative to the invasive weed in China, making it an important native species for studying the invasive mechanisms and adaptations of . Chloroplasts play a crucial role in a plant's environmental adaptation, with their genomes being pivotal in the evolution and adaptation of both invasive and related species. However, the chloroplast genome of has remained unknown until now. In this study, we sequenced and assembled the complete chloroplast genome of using high-throughput sequencing. The chloroplast genome is 151,935 base pairs long, comprising two inverted repeat regions, a large single copy region, and a small single copy region. This chloroplast genome contains 128 genes, including 8 rRNA-coding genes, 37 tRNA-coding genes, 4 pseudogenes, and 83 protein-coding genes. When compared to the chloroplast genome of the invasive weed and other Amaranthaceae species, we observed significant variations in the , , and regions in the chloroplast genome. Moreover, two genes, and , were found to be undergoing rapid evolution due to positive selection pressure. The phylogenetic trees were constructed for the Amaranthaceae family, estimating the time of independent species formation between and to be approximately 3.5186-8.8242 million years ago. These findings provide a foundation for understanding the population variation within invasive species among the genus.
Topics: Genome, Chloroplast; Amaranthaceae; Phylogeny; Introduced Species; Plant Weeds; Chloroplasts; High-Throughput Nucleotide Sequencing; Evolution, Molecular
PubMed: 38790173
DOI: 10.3390/genes15050544