An overview of RNA splicing and functioning of splicing factors in land plant chloroplasts

RNA splicing refers to a process by which introns of a pre-mRNA are excised and the exons at both ends are joined together. Chloroplast introns are inherently self-splicing ribozymes, but over time, they have lost self-splicing ability due to the degeneration of intronic elements. Thus, the splicing of chloroplast introns relies heavily on nuclear-encoded splicing factors, which belong to diverse protein families. Different splicing factors and their shared intron targets are supposed to form ribonucleoprotein particles (RNPs) to facilitate intron splicing. As characterized in a previous review, around 14 chloroplast intron splicing factors were identified until 2010. However, only a few genetic and biochemical evidence has shown that these splicing factors are required for the splicing of one or several introns. The roles of splicing factors are generally believed to facilitate intron folding; however, the precise role of each protein in RNA splicing remains ambiguous. This may be because the precise binding site of most of these splicing factors remains unexplored. In the last decade, several new splicing factors have been identified. Also, several splicing factors were found to bind to specific sequences within introns, which enhanced the understanding of splicing factors. Here, we summarize recent progress on the splicing factors in land plant chloroplasts and discuss their possible roles in chloroplast RNA splicing based on previous studies.</p

Specific Ion Effect on the “Water Bridge” Interaction at an Interface: A New Understanding into the Extraction and Separation Selectivity Based upon Competitive Diffusion and Adsorption

Understanding the essence of a specific ion effect on the intermolecular interaction at the near-interface boundary layer during solvent extraction is crucial for developing new approaches to achieve enhanced extraction and separation of various valuable metals from complex aqueous solutions. The present work aims to detect the microscopic effect from competitive diffusion and adsorption of various salt cations in the near-interface boundary layer on their interaction with amphiphilic model molecules, 2-ethylhexylphosphonic acid mono-(2-ethylhexyl) ester (P507), at the air–water interface by using the Langmuir–Blodgett (LB) monolayer technique. It was found that the interaction between cations and P507 molecules through a long-range hydrogen bond “water bridge” confined in the near-interface boundary layer plays a crucial role in determining the difference in the diffusion mass transfer rate of ions with different hydration abilities. Conventional understanding about competitive extraction of various metal cations controlled mainly by their thermodynamic difference in the interaction intensity with the P–O and PO groups in P507 molecules cannot explain such a kind of specific ion effect on the mass transfer kinetics via ion hydration. Molecular dynamics simulation revealed that the hydration ability of ions is the key factor determining the mass transfer rate and interaction intensity. In the low salt concentration region, the interaction intensity of salt cations with the P–O and PO groups in P507 molecules is one of the determinants of the competitive adsorption behavior at the interface. However, in a higher salt concentration region, the specific ion salting-out effect via ion hydration becomes significant, causing a decrease in hydration of the target salt cation; therefore, it dominated the diffusion mass transfer rate of ions. This work provides a new insight to understand the kinetic role of competitive diffusion and adsorption of ions in the near-interface boundary layer and their effect on extraction and separation selectivity. It lays the foundation for achieving controllable separation of target metal ions by adjusting the coexisting ion species and their concentrations

Table_1_Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum.docx

Long non-coding RNAs (lncRNAs) can enhance plant stress resistance by regulating the expression of functional genes. Sweet sorghum is a salt-tolerant energy crop. However, little is known about how lncRNAs in sweet sorghum respond to salt stress. In this study, we identified 126 and 133 differentially expressed lncRNAs in the salt-tolerant M-81E and the salt-sensitive Roma strains, respectively. Salt stress induced three new lncRNAs in M-81E and inhibited two new lncRNAs in Roma. These lncRNAs included lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929, and lncRNA14798, which potentially function as competitive endogenous RNAs (ceRNAs) that influence plant responses to salt stress by regulating the expression of target genes related to ion transport, protein modification, transcriptional regulation, and material synthesis and transport. Additionally, M-81E had a more complex ceRNA network than Roma. This study provides new information regarding lncRNAs and the complex regulatory network underlying salt-stress responses in sweet sorghum.</p

Image_3_Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum.TIF

Long non-coding RNAs (lncRNAs) can enhance plant stress resistance by regulating the expression of functional genes. Sweet sorghum is a salt-tolerant energy crop. However, little is known about how lncRNAs in sweet sorghum respond to salt stress. In this study, we identified 126 and 133 differentially expressed lncRNAs in the salt-tolerant M-81E and the salt-sensitive Roma strains, respectively. Salt stress induced three new lncRNAs in M-81E and inhibited two new lncRNAs in Roma. These lncRNAs included lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929, and lncRNA14798, which potentially function as competitive endogenous RNAs (ceRNAs) that influence plant responses to salt stress by regulating the expression of target genes related to ion transport, protein modification, transcriptional regulation, and material synthesis and transport. Additionally, M-81E had a more complex ceRNA network than Roma. This study provides new information regarding lncRNAs and the complex regulatory network underlying salt-stress responses in sweet sorghum.</p

Image_1_Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum.TIF

Long non-coding RNAs (lncRNAs) can enhance plant stress resistance by regulating the expression of functional genes. Sweet sorghum is a salt-tolerant energy crop. However, little is known about how lncRNAs in sweet sorghum respond to salt stress. In this study, we identified 126 and 133 differentially expressed lncRNAs in the salt-tolerant M-81E and the salt-sensitive Roma strains, respectively. Salt stress induced three new lncRNAs in M-81E and inhibited two new lncRNAs in Roma. These lncRNAs included lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929, and lncRNA14798, which potentially function as competitive endogenous RNAs (ceRNAs) that influence plant responses to salt stress by regulating the expression of target genes related to ion transport, protein modification, transcriptional regulation, and material synthesis and transport. Additionally, M-81E had a more complex ceRNA network than Roma. This study provides new information regarding lncRNAs and the complex regulatory network underlying salt-stress responses in sweet sorghum.</p

Image_4_Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum.pdf

Long non-coding RNAs (lncRNAs) can enhance plant stress resistance by regulating the expression of functional genes. Sweet sorghum is a salt-tolerant energy crop. However, little is known about how lncRNAs in sweet sorghum respond to salt stress. In this study, we identified 126 and 133 differentially expressed lncRNAs in the salt-tolerant M-81E and the salt-sensitive Roma strains, respectively. Salt stress induced three new lncRNAs in M-81E and inhibited two new lncRNAs in Roma. These lncRNAs included lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929, and lncRNA14798, which potentially function as competitive endogenous RNAs (ceRNAs) that influence plant responses to salt stress by regulating the expression of target genes related to ion transport, protein modification, transcriptional regulation, and material synthesis and transport. Additionally, M-81E had a more complex ceRNA network than Roma. This study provides new information regarding lncRNAs and the complex regulatory network underlying salt-stress responses in sweet sorghum.</p

NADP-Malate Dehydrogenase of Sweet Sorghum Improves Salt Tolerance of <i>Arabidopsis thaliana</i>

Sweet sorghum is a C₄ crop that shows high salt tolerance and high yield. NADP-malate dehydrogenase (<i>NADP-ME</i>) is a crucial enzyme of the C₄ pathway. The regulatory mechanism of NADP-ME remains unclear. In this study, we isolated <i>SbNADP-ME</i> from sweet sorghum. The open reading frame of <i>SbNADP-ME</i> is 1911 bp and 637 amino acid residues. Quantitative real-time PCR analysis showed that <i>SbNADP-ME</i> transcription in sweet sorghum was enhanced by salt stress. The <i>SbNADP-ME</i> transcript level was highest under exposure to 150 mM NaCl. <i>Arabidopsis</i> overexpressing <i>SbNADP-ME</i> showed increased germination rate and root length under NaCl treatments. At the seedling stage, physiological photosynthesis parameters, chlorophyll content, PSII photochemical efficiency, and PSI oxidoreductive activity in the wild type decreased more severely than in the overexpression lines but less than in T-DNA insertion mutants under salt stress. Overexpression of <i>SbNADP-ME</i> in <i>Arabidopsis</i> may also increase osmotic adjustment and scavenging activity on DPPH and decrease membrane peroxidation. These results suggest that <i>SbNADP-ME</i> overexpression in <i>Arabidopsis</i> increases salt tolerance and alleviates PSII and PSI photoinhibition under salt stress by improving photosynthetic capacity

Image_2_Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum.TIF

Long non-coding RNAs (lncRNAs) can enhance plant stress resistance by regulating the expression of functional genes. Sweet sorghum is a salt-tolerant energy crop. However, little is known about how lncRNAs in sweet sorghum respond to salt stress. In this study, we identified 126 and 133 differentially expressed lncRNAs in the salt-tolerant M-81E and the salt-sensitive Roma strains, respectively. Salt stress induced three new lncRNAs in M-81E and inhibited two new lncRNAs in Roma. These lncRNAs included lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929, and lncRNA14798, which potentially function as competitive endogenous RNAs (ceRNAs) that influence plant responses to salt stress by regulating the expression of target genes related to ion transport, protein modification, transcriptional regulation, and material synthesis and transport. Additionally, M-81E had a more complex ceRNA network than Roma. This study provides new information regarding lncRNAs and the complex regulatory network underlying salt-stress responses in sweet sorghum.</p

Table_1_C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants.docx

Abiotic stresses such as drought and salinity are major environmental factors that limit crop yields. Unraveling the molecular mechanisms underlying abiotic stress resistance is crucial for improving crop performance and increasing productivity under adverse environmental conditions. Zinc finger proteins, comprising one of the largest transcription factor families, are known for their finger-like structure and their ability to bind Zn2+. Zinc finger proteins are categorized into nine subfamilies based on their conserved Cys and His motifs, including the Cys2/His2-type (C2H2), C3H, C3HC4, C2HC5, C4HC3, C2HC, C4, C6, and C8 subfamilies. Over the past two decades, much progress has been made in understanding the roles of C2H2 zinc finger proteins in plant growth, development, and stress signal transduction. In this review, we focus on recent progress in elucidating the structures, functions, and classifications of plant C2H2 zinc finger proteins and their roles in abiotic stress responses.</p