Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice

<p>Abstract</p> <p>Background</p> <p>Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins in animals. To date, few plant CCCH proteins have been studied functionally.</p> <p>Results</p> <p>In this study, a comprehensive computational analysis identified 68 and 67 CCCH family genes in Arabidopsis and rice, respectively. A complete overview of this gene family in Arabidopsis was presented, including the gene structures, phylogeny, protein motifs, and chromosome locations. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. These results revealed that the CCCH families in Arabidopsis and rice were divided into 11 and 8 subfamilies, respectively. The gene duplication contributed to the expansion of the CCCH gene family in Arabidopsis genome. Expression studies indicated that CCCH proteins exhibit a variety of expression patterns, suggesting diverse functions. Finally, evolutionary analysis showed that one subfamily is higher plant specific. The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could have an effective role in stress tolerance.</p> <p>Conclusion</p> <p>Our comparative genomics analysis of CCCH genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of potential RNA-binding proteins.</p

Layered-Strip Fertilization Improves Nitrogen Use Efficiency by Enhancing Absorption and Suppressing Loss of Urea Nitrogen

Appropriate deep application of fertilizer is the key basis for improving nitrogen use efficiency (NUE). However, the effects of different deep application methods and fertilizer types on nutrient migration, NUE and biomass in wheat season are unclear. Therefore, in this study, a barrel planting test with multilayer fertilization (15N labeled urea (U) and coated urea (CU)) was conducted in a long-term positioning trial of winter wheat in the North China Plain (NCP). We quantified the migration of fertilizer N (Ndff) in soil–plant–atmosphere and its effects on wheat biomass and NUE based on surface (Usur, CUsur), layered-strip (Ustr, CUstr) and layered-mix fertilization (Umix, CUmix) of U and CU. Compared with surface fertilization, the concentration of mineral N in root zone (0–40 cm) was increased by Ustr and Umix (8.6–50.3%), and the concentration of ammonium N was decreased by CUstr and CUmix (49.6–76.0%), but there was no change in the nitrate N. The biomass and total N absorption of wheat tissues (straw and root) were increased by 12.3–38.9% under Ustr and CUstr. Meanwhile, the distribution of Ndff in the 0–10 cm soil was decreased under Ustr and CUstr, but it was increased in the 10–30 cm soil, thereby promoting the absorption of Ndff in wheat tissues by 12.3–28.7%. The rates of absorption and loss of Ndff were the highest (57.6–58.5%) and the lowest (4.5%) under Ustr and CUstr, respectively, compared with other treatments. Consequently, layered-strip fertilization optimized the migration and utilization of Ndff within the soil–plant–atmosphere system. This approach equalized distribution, enhanced absorption and minimized losses of Ndff, resulting in an increase in NUE by 9.6–16.7%. Under the same treatment, CU was more suitable for crop nutrient requirements than U, which was more conducive to the improvement of NUE. Our findings will provide a scientific basis for the precise directional fertilization of winter wheat in the NCP

<it>GhWRKY15</it>, a member of the WRKY transcription factor family identified from cotton (<it>Gossypium hirsutum</it> L.), is involved in disease resistance and plant development

Abstract Background As a large family of regulatory proteins, WRKY transcription factors play essential roles in the processes of adaptation to diverse environmental stresses and plant growth and development. Although several studies have investigated the role of WRKY transcription factors during these processes, the mechanisms underlying the function of WRKY members need to be further explored, and research focusing on the WRKY family in cotton crops is extremely limited. Results In the present study, a gene encoding a putative WRKY family member, GhWRKY15, was isolated from cotton. GhWRKY15 is present as a single copy gene, and a transient expression analysis indicated that GhWRKY15 was localised to the nucleus. Additionally, a group of cis-acting elements associated with the response to environmental stress and plant growth and development were detected in the promoter. Consistently, northern blot analysis showed that GhWRKY15 expression was significantly induced in cotton seedlings following fungal infection or treatment with salicylic acid, methyl jasmonate or methyl viologen. Furthermore, GhWRKY15-overexpressing tobacco exhibited more resistance to viral and fungal infections compared with wild-type tobacco. The GhWRKY15-overexpressing tobacco also exhibited increased RNA expression of several pathogen-related genes, NONEXPRESSOR OF PR1, and two genes that encode enzymes involved in ET biosynthesis. Importantly, increased activity of the antioxidant enzymes POD and APX during infection and enhanced expression of NtAPX1 and NtGPX in transgenic tobacco following methyl viologen treatment were observed. Moreover, GhWRKY15 transcription was greater in the roots and stems compared with the expression in the cotyledon of cotton, and the stems of transgenic plants displayed faster elongation at the earlier shooting stages compared with wide type tobacco. Additionally, exposure to abiotic stresses, including cold, wounding and drought, resulted in the accumulation of GhWRKY15 transcripts. Conclusion Overall, our data suggest that overexpression of GhWRKY15 may contribute to the alteration of defence resistance to both viral and fungal infections, probably through regulating the ROS system via multiple signalling pathways in tobacco. It is intriguing that GhWRKY15 overexpression in tobacco affects plant growth and development, especially stem elongation. This finding suggests that the role of the WRKY proteins in disease resistance may be closely related to their function in regulating plant growth and development.</p

Transcription Factor SiDi19-3 Enhances Salt Tolerance of Foxtail Millet and <i>Arabidopsis</i>

Salt stress is an important limiting factor of crop production. Foxtail millet (Setaria italica L.) is an important model crop for studying tolerance to various abiotic stressors. Therefore, examining the response of foxtail millet to salt stress at the molecular level is critical. Herein, we discovered that SiDi19-3 interacts with SiPLATZ12 to control salt tolerance in transgenic Arabidopsis and foxtail millet seedlings. SiDi19-3 overexpression increased the transcript levels of most Na+/H+ antiporter (NHX), salt overly sensitive (SOS), and calcineurin B-like protein (CBL) genes and improved the salt tolerance of foxtail millet and Arabidopsis. Six SiDi19 genes were isolated from foxtail millet. Compared with roots, stems, and leaves, panicles and seeds had higher transcript levels of SiDi19 genes. All of them responded to salt, alkaline, polyethylene glycol, and/or abscisic acid treatments with enhanced expression levels. These findings indicate that SiDi19-3 and other SiDi19 members regulate salt tolerance and other abiotic stress response in foxtail millet

BREVIPEDICELLUS Positively Regulates Salt-Stress Tolerance in <i>Arabidopsis thaliana</i>

Salt stress is one of the major environmental threats to plant growth and development. However, the mechanisms of plants responding to salt stress are not fully understood. Through genetic screening, we identified and characterized a salt-sensitive mutant, ses5 (sensitive to salt 5), in Arabidopsis thaliana. Positional cloning revealed that the decreased salt-tolerance of ses5 was caused by a mutation in the transcription factor BP (BREVIPEDICELLUS). BP regulates various developmental processes in plants. However, the biological function of BP in abiotic stress-signaling and tolerance are still not clear. Compared with wild-type plants, the bp mutant exhibited a much shorter primary-root and lower survival rate under salt treatment, while the BP overexpressors were more tolerant. Further analysis showed that BP could directly bind to the promoter of XTH7 (xyloglucan endotransglucosylase/hydrolase 7) and activate its expression. Resembling the bp mutant, the disruption of XTH7 gave rise to salt sensitivity. These results uncovered novel roles of BP in positively modulating salt-stress tolerance, and illustrated a putative working mechanism