Plant and Cell Physiology最新文献_第10页

Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism. 水稻根尖转录组分析揭示了营养生长所依赖的辅助素、赤霉素和乙烯信号。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcae003

Kiyoshi Yamazaki, Yoshihiro Ohmori, Hirokazu Takahashi, Atsushi Toyoda, Yutaka Sato, Mikio Nakazono, Toru Fujiwara

{"title":"Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism.","authors":"Kiyoshi Yamazaki, Yoshihiro Ohmori, Hirokazu Takahashi, Atsushi Toyoda, Yutaka Sato, Mikio Nakazono, Toru Fujiwara","doi":"10.1093/pcp/pcae003","DOIUrl":"10.1093/pcp/pcae003","url":null,"abstract":"Nutritropism is a positive tropism toward nutrients in plant roots. An NH4+ gradient is a nutritropic stimulus in rice (Oryza sativa L.). When rice roots are exposed to an NH4+ gradient generated around nutrient sources, root tips bend toward and coil around the sources. The molecular mechanisms are largely unknown. Here, we analyzed the transcriptomes of the inside and outside of bending root tips exhibiting nutritropism to reveal nutritropic signal transduction. Tissues facing the nutrient sources (inside) and away (outside) were separately collected by laser microdissection. Principal component analysis revealed distinct transcriptome patterns between the two tissues. Annotations of 153 differentially expressed genes implied that auxin, gibberellin and ethylene signaling were activated differentially between the sides of the root tips under nutritropism. Exogenous application of transport and/or biosynthesis inhibitors of these phytohormones largely inhibited the nutritropism. Thus, signaling and de novo biosynthesis of the three phytohormones are necessary for nutritropism. Expression patterns of IAA genes implied that auxins accumulated more in the inside tissues, meaning that ammonium stimulus is transduced to auxin signaling in nutritropism similar to gravity stimulus in gravitropism. SAUR and expansin genes, which are known to control cell wall modification and to promote cell elongation in shoot gravitropism, were highly expressed in the inside tissues rather than the outside tissues, and our transcriptome data are unexplainable for differential elongation in root nutritropism.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139472119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease. 植物器官MSH1是一种置换环特异性核酸内切酶。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad112

Alejandro Peñafiel-Ayala, Antolin Peralta-Castro, Josue Mora-Garduño, Paola García-Medel, Angie G Zambrano-Pereira, Corina Díaz-Quezada, María Jazmín Abraham-Juárez, Claudia G Benítez-Cardoza, Daniel B Sloan, Luis G Brieba

{"title":"Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease.","authors":"Alejandro Peñafiel-Ayala, Antolin Peralta-Castro, Josue Mora-Garduño, Paola García-Medel, Angie G Zambrano-Pereira, Corina Díaz-Quezada, María Jazmín Abraham-Juárez, Claudia G Benítez-Cardoza, Daniel B Sloan, Luis G Brieba","doi":"10.1093/pcp/pcad112","DOIUrl":"10.1093/pcp/pcad112","url":null,"abstract":"MutS HOMOLOG 1 (MSH1) is an organellar-targeted protein that obstructs ectopic recombination and the accumulation of mutations in plant organellar genomes. MSH1 also modulates the epigenetic status of nuclear DNA, and its absence induces a variety of phenotypic responses. MSH1 is a member of the MutS family of DNA mismatch repair proteins but harbors an additional GIY-YIG nuclease domain that distinguishes it from the rest of this family. How MSH1 hampers recombination and promotes fidelity in organellar DNA inheritance is unknown. Here, we elucidate its enzymatic activities by recombinantly expressing and purifying full-length MSH1 from Arabidopsis thaliana (AtMSH1). AtMSH1 is a metalloenzyme that shows a strong binding affinity for displacement loops (D-loops). The DNA-binding abilities of AtMSH1 reside in its MutS domain and not in its GIY-YIG domain, which is the ancillary nickase of AtMSH1. In the presence of divalent metal ions, AtMSH1 selectively executes multiple incisions at D-loops, but not other DNA structures including Holliday junctions or dsDNA, regardless of the presence or absence of mismatches. The selectivity of AtMSH1 to dismantle D-loops supports the role of this enzyme in preventing recombination between short repeats. Our results suggest that plant organelles have evolved novel DNA repair routes centered around the anti-recombinogenic activity of MSH1.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Applications of Synthetic Pentatricopeptide Repeat Proteins. 合成五肽重复序列蛋白的应用。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad150

Farley Kwok van der Giezen, Suvi Honkanen, Catherine Colas des Francs-Small, Charles Bond, Ian Small

{"title":"Applications of Synthetic Pentatricopeptide Repeat Proteins.","authors":"Farley Kwok van der Giezen, Suvi Honkanen, Catherine Colas des Francs-Small, Charles Bond, Ian Small","doi":"10.1093/pcp/pcad150","DOIUrl":"10.1093/pcp/pcad150","url":null,"abstract":"RNA-binding proteins play integral roles in the regulation of essential processes in cells and as such are attractive targets for engineering to manipulate gene expression at the RNA level. Expression of transcripts in chloroplasts and mitochondria is heavily regulated by pentatricopeptide repeat (PPR) proteins. The diverse roles of PPR proteins and their naturally modular architecture make them ideal candidates for engineering. Synthetic PPR proteins are showing great potential to become valuable tools for controlling the expression of plastid and mitochondrial transcripts. In this review, by 'synthetic', we mean both rationally modified natural PPR proteins and completely novel proteins designed using the principles learned from their natural counterparts. We focus on the many different applications of synthetic PPR proteins, covering both their use in basic research to learn more about protein-RNA interactions and their use to achieve specific outcomes in RNA processing and the control of gene expression. We describe the challenges associated with the design, construction and deployment of synthetic PPR proteins and provide perspectives on how they might be assembled and used in future biotechnology applications.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138462204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction To: Root PRR7 Improves the Accuracy of the Shoot Circadian Clock through Nutrient Transport. Correction To：根部 PRR7 通过养分运输提高了萌芽昼夜节律钟的准确性

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcae026

引用次数: 0

Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis. 根原基缺陷 1 编码线粒体编码的 II 组内含子剪接和呼吸复合体 I 生物发生所需的重要 PORR 蛋白。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad101

Rana Edris, Laure D Sultan, Corinne Best, Ron Mizrahi, Ofir Weinstein, Stav Chen, Nina A Kamennaya, Nir Keren, Hagit Zer, Hongliang Zhu, Oren Ostersetzer-Biran

{"title":"Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis.","authors":"Rana Edris, Laure D Sultan, Corinne Best, Ron Mizrahi, Ofir Weinstein, Stav Chen, Nina A Kamennaya, Nir Keren, Hagit Zer, Hongliang Zhu, Oren Ostersetzer-Biran","doi":"10.1093/pcp/pcad101","DOIUrl":"10.1093/pcp/pcad101","url":null,"abstract":"Cellular respiration involves complex organellar metabolic activities that are pivotal for plant growth and development. Mitochondria contain their own genetic system (mitogenome, mtDNA), which encodes key elements of the respiratory machinery. Plant mtDNAs are notably larger than their counterparts in Animalia, with complex genome organization and gene expression characteristics. The maturation of the plant mitochondrial transcripts involves extensive RNA editing, trimming and splicing events. These essential processing steps rely on the activities of numerous nuclear-encoded cofactors, which may also play key regulatory roles in mitochondrial biogenesis and function and hence in plant physiology. Proteins that harbor the plant organelle RNA recognition (PORR) domain are represented in a small gene family in plants. Several PORR members, including WTF1, WTF9 and LEFKOTHEA, are known to act in the splicing of organellar group II introns in angiosperms. The AT4G33495 gene locus encodes an essential PORR protein in Arabidopsis, termed ROOT PRIMORDIUM DEFECTIVE 1 (RPD1). A null mutation of At.RPD1 causes arrest in early embryogenesis, while the missense mutant lines, rpd1.1 and rpd1.2, exhibit a strong impairment in root development and retarded growth phenotypes, especially under high-temperature conditions. Here, we further show that RPD1 functions in the splicing of introns that reside in the coding regions of various complex I (CI) subunits (i.e. nad2, nad4, nad5 and nad7), as well as in the maturation of the ribosomal rps3 pre-RNA in Arabidopsis mitochondria. The altered growth and developmental phenotypes and modified respiration activities are tightly correlated with respiratory chain CI defects in rpd1 mutants.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10278681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chloroplast Ribosome Biogenesis Factors. 叶绿体核糖体生物发生因子。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad082

Lisa-Marie Schmid, Nikolay Manavski, Wei Chi, Jörg Meurer

引用次数: 0

Plastid Inheritance Revisited: Emerging Role of Organelle DNA Degradation in Angiosperms. 再论质体遗传：被子植物细胞器 DNA 降解的新作用。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad104

Wataru Sakamoto, Tsuneaki Takami

{"title":"Plastid Inheritance Revisited: Emerging Role of Organelle DNA Degradation in Angiosperms.","authors":"Wataru Sakamoto, Tsuneaki Takami","doi":"10.1093/pcp/pcad104","DOIUrl":"10.1093/pcp/pcad104","url":null,"abstract":"Plastids are essential organelles in angiosperms and show non-Mendelian inheritance due to their evolution as endosymbionts. In approximately 80% of angiosperms, plastids are thought to be inherited from the maternal parent, whereas other species transmit plastids biparentally. Maternal inheritance can be generally explained by the stochastic segregation of maternal plastids after fertilization because the zygote is overwhelmed by the maternal cytoplasm. In contrast, biparental inheritance shows the transmission of organelles from both parents. In some species, maternal inheritance is not absolute and paternal leakage occurs at a very low frequency (∼10-5). A key process controlling the inheritance mode lies in the behavior of plastids during male gametophyte (pollen) development, with accumulating evidence indicating that the plastids themselves or their DNAs are eliminated during pollen maturation or at fertilization. Cytological observations in numerous angiosperm species have revealed several critical steps that mutually influence the degree of plastid transmission quantitatively among different species. This review revisits plastid inheritance from a mechanistic viewpoint. Particularly, we focus on a recent finding demonstrating that both low temperature and plastid DNA degradation mediated by the organelle exonuclease DEFECTIVE IN POLLEN ORGANELLE DNA DEGRADATION1 (DPD1) influence the degree of paternal leakage significantly in tobacco. Given these findings, we also highlight the emerging role of DPD1 in organelle DNA degradation.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10590749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages. ATAD3蛋白质：在不同真核谱系中对生命至关重要的独特线粒体蛋白质。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad122

Elizabeth R Waters, Magdalena Bezanilla, Elizabeth Vierling

{"title":"ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages.","authors":"Elizabeth R Waters, Magdalena Bezanilla, Elizabeth Vierling","doi":"10.1093/pcp/pcad122","DOIUrl":"10.1093/pcp/pcad122","url":null,"abstract":"ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49681587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome Editing of Plant Mitochondrial and Chloroplast Genomes. 植物线粒体和叶绿体基因组编辑。

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad162

Shin-Ichi Arimura, Issei Nakazato

{"title":"Genome Editing of Plant Mitochondrial and Chloroplast Genomes.","authors":"Shin-Ichi Arimura, Issei Nakazato","doi":"10.1093/pcp/pcad162","DOIUrl":"10.1093/pcp/pcad162","url":null,"abstract":"Plastids (including chloroplasts) and mitochondria are remnants of endosymbiotic bacteria, yet they maintain their own genomes, which encode vital components for photosynthesis and respiration, respectively. Organellar genomes have distinctive features, such as being present as multicopies, being mostly inherited maternally, having characteristic genomic structures and undergoing frequent homologous recombination. To date, it has proven to be challenging to modify these genomes. For example, while CRISPR/Cas9 is a widely used system for editing nuclear genes, it has not yet been successfully applied to organellar genomes. Recently, however, precise gene-editing technologies have been successfully applied to organellar genomes. Protein-based enzymes, especially transcription activator-like effector nucleases (TALENs) and artificial enzymes utilizing DNA-binding domains of TALENs (TALEs), have been successfully used to modify these genomes by harnessing organellar-targeting signals. This short review introduces and discusses the use of targeted nucleases and base editors in organellar genomes, their effects and their potential applications in plant science and breeding.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138805341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular Genetic Dissection of the Regulatory Network of Proton Motive Force in Chloroplasts. 叶绿体质子动力调控网络的分子遗传学剖析

IF 4.9 2区生物学

Plant and Cell Physiology Pub Date : 2024-05-14 DOI: 10.1093/pcp/pcad157

Toshiharu Shikanai

{"title":"Molecular Genetic Dissection of the Regulatory Network of Proton Motive Force in Chloroplasts.","authors":"Toshiharu Shikanai","doi":"10.1093/pcp/pcad157","DOIUrl":"10.1093/pcp/pcad157","url":null,"abstract":"The proton motive force (pmf) generated across the thylakoid membrane rotates the Fo-ring of ATP synthase in chloroplasts. The pmf comprises two components: membrane potential (∆Ψ) and proton concentration gradient (∆pH). Acidification of the thylakoid lumen resulting from ∆pH downregulates electron transport in the cytochrome b6f complex. This process, known as photosynthetic control, is crucial for protecting photosystem I (PSI) from photodamage in response to fluctuating light. To optimize the balance between efficient photosynthesis and photoprotection, it is necessary to regulate pmf. Cyclic electron transport around PSI and pseudo-cyclic electron transport involving flavodiiron proteins contribute to the modulation of pmf magnitude. By manipulating the ratio between the two components of pmf, it is possible to modify the extent of photosynthetic control without affecting the pmf size. This adjustment can be achieved by regulating the movement of ions (such as K+ and Cl-) across the thylakoid membrane. Since ATP synthase is the primary consumer of pmf in chloroplasts, its activity must be precisely regulated to accommodate other mechanisms involved in pmf optimization. Although fragments of information about each regulatory process have been accumulated, a comprehensive understanding of their interactions is lacking. Here, I summarize current knowledge of the network for pmf regulation, mainly based on genetic studies.","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139049184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0