Chloroplast gene expression: Recent advances and perspectives

Zhang, Yi; Lin, Tao; Lu, Congming

doi:10.1016/j.xplc.2023.100611

Cited by 25 publications

(12 citation statements)

References 229 publications

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“…The chloroplast genome generally ranges in size from 120 to 160 kb and exhibits a highly conserved structure 26 . The sequencing, assembly, and analysis of chloroplast genomes can identify common features or differences between species, which can be used as DNA barcodes.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Xiao,

Zhao,

Wang

et al. 2024

Sci Rep

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The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8–75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as “rps16-trnQ”, “trnT-trnL”, “ndhG-ndhI”, and "rpl32-trnL” in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.

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Section: Discussionmentioning

confidence: 99%

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Xiao,

Zhao,

Wang

et al. 2024

Sci Rep

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“…Albino Lethal 13, a Chloroplast Imported Protein Required for Chloroplast Development in Rice Xiaoqiong Guo 1,6, † , Chunli Wang 1 † , Qian Zhu 1,2,3 , Wenhua Dongchen 4 , Xiaoling Zhang 5 , Wei Li…”

Section: Articlementioning

confidence: 99%

“…Chloroplasts are the main site of photosynthesis, which not only convert light energy into chemical energy, but also synthesize biologically essential compounds such as fatty acids, vitamins, amino acids, and tetrapyridine [1]. However defects of chloroplast development will affect leaf color, seeding survival or crop yield [2][3]. Therefore, the new rice leaf color mutants provide not only ideal materials for studying chloroplast development, but also important germplasm resources for high photosynthetic efficiency breeding in rice.…”

Section: Introductionmentioning

confidence: 99%

Albino Lethal 13, a Chloroplast Imported Protein Required for Chloroplast Development in Rice

Guo,

Wang,

Zhu

et al. 2024

Preprint

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The chloroplast is important organelle responsible for photosynthesis and various bio- synthetic functions essential to green plants. However, the regulatory mechanism of chloroplast development remains elusive. Here, we characterized a mutant with defective chloroplasts in rice (Oryza sativa L.) named it albino and lethal 13(osal13), which exhibited a distinct albino phenotype in leaves, eventually leading to seedling lethality. Molecular cloning revealed that OsAL13 encodes a novel protein in rice for which no homologous gene or known conserved domain was found. Analysis of the biological characteristics showed that the RNAi2 leaf was completely albino phenotype, the root and shoot lengths were significantly inhibited compared with wild type. Transmission electron microscopy indicated that RNAi2 were defective in chloroplast development. Overexpression of OsAL13 resulted the photosynthetic rate increase, So the total grain number per panicle also would be significantly increase. Besides, OsAL13 was located in chloroplast and constitutively expressed in various tissues, including green and non-green tissues. In addition, disruption of OsAL13 resulted in altered expression of plastid-encoded polymerases and nuclear-encoded chloroplast genes, OsAL13 also affected hormone levels in plant tissues. Therefore, our results provide new insights into the role of OsAL13 in regulating chloroplast development in rice.

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“…Since most plastid proteins are encoded in the nucleus, it exerts anterograde control over the plastids. For example, the process of PGE necessitates the involvement of diverse nuclear-encoded proteins that promote the transcription, splicing, trimming, and editing of RNA in organelles, while simultaneously regulating their translation (4)(5)(6)(7). On the other hand, nuclear gene expression, such as the expression of the so-called photosynthesisassociated nuclear genes (PhANGs), is controlled by plastid-to-nucleus retrograde signaling (8,9), which is thought to be mediated by multiple factors and sources.…”

Section: Introductionmentioning

confidence: 99%

“…PPR proteins belong to a large family, with an estimated 106 of these proteins targeted to chloroplasts (6). They participate in various PGE steps, including RNA cleavage, splicing, editing, stabilization, and translation (6,7). Thus far, no other ppr mutant has been identified as a gun mutant, indicating that GUN1 is a special component of an anterograde-retrograde axis.…”

Section: Introductionmentioning

confidence: 99%

Arabidopsis GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation

Tang,

Xu,

Lenzen

et al. 2024

Preprint

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Plastid biogenesis and the coordination of plastid and nuclear genome expression through anterograde and retrograde signaling are essential for plant development. GENOMES UNCOUPLED1 (GUN1) plays a central role in retrograde signaling during early plant development. The putative function of GUN1 has been extensively studied, but its molecular function remains controversial. Here, we evaluate published transcriptome data and generate our own data from gun1 mutants grown under signaling relevant conditions to show that editing and splicing are not relevant for GUN1-dependent retrograde signaling. Our study of the plastid (post)-transcriptome of gun1 seedlings with white and pale cotyledons demonstrates that GUN1 deficiency significantly alters the entire plastid transcriptome. By combining this result with a PPR code-based prediction and experimental validation by RNA immunoprecipitation experiments, several targets of GUN1 were identified, including 23S rRNA, tRNAs and RNAs derived from ycf1.2 and the ndhH-ndhA-ndhI-ndhG-ndhE-psaC-ndhD gene cluster. The absence of plastid rRNAs and the significant reduction of almost all plastid transcripts in white gun1 mutants account for the cotyledon phenotype. Our study identifies RNA binding and maturation as the long-sought molecular function of GUN1 and resolves long-standing controversies. We anticipate that our findings will serve as a basis for subsequent studies investigating the mechanism of plastid gene expression and will facilitate the elucidation of GUN1's function in retrograde signaling.

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Chloroplast gene expression: Recent advances and perspectives

Cited by 25 publications

References 229 publications

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Albino Lethal 13, a Chloroplast Imported Protein Required for Chloroplast Development in Rice

Arabidopsis GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation

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