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

Halomonas ventosae JPT10 promotes salt tolerance in foxtail millet (Setaria italica) by affecting the levels of multiple antioxidants and phytohormones

Abstract Plant growth‐promoting bacterias (PGPBs) can increase crop output under normal and abiotic conditions. However, the mechanisms underlying the plant salt tolerance‐promoting role of PGPBs still remain largely unknown. In this study, we demonstrated that Halomonas ventosae JPT10 promoted the salt tolerance of both dicots and monocots. Physiological analysis revealed that JPT10 reduced reactive oxygen species accumulation by improving the antioxidant capability of foxtail millet seedlings. The metabolomic analysis of JPT10‐inoculated foxtail millet seedlings led to the identification of 438 diversely accumulated metabolites, including flavonoids, phenolic acids, lignans, coumarins, sugar, alkaloids, organic acids, and lipids, under salt stress. Exogenous apigenin and chlorogenic acid increased the salt tolerance of foxtail millet seedlings. Simultaneously, JPT10 led to greater amounts of abscisic acid (ABA), indole‐3‐acetic acid (IAA), salicylic acid (SA), and their derivatives but lower levels of 12‐oxo‐phytodienoic acid (OPDA), jasmonate (JA), and JA‐isoleucine (JA‐Ile) under salt stress. Exogenous JA, methyl‐JA, and OPDA intensified, whereas ibuprofen or phenitone, two inhibitors of JA and OPDA biosynthesis, partially reversed, the growth inhibition of foxtail millet seedlings caused by salt stress. Our results shed light on the response of foxtail millet seedlings to H. ventosae under salt stress and provide potential compounds to increase salt tolerance in foxtail millet and other crops

<i>GhWRKY40</i>, a Multiple Stress-Responsive Cotton WRKY Gene, Plays an Important Role in the Wounding Response and Enhances Susceptibility to <i>Ralstonia solanacearum</i> Infection in Transgenic <i>Nicotiana benthamiana</i>

<div><p>WRKY transcription factors form one of the largest transcription factor families and function as important components in the complex signaling processes that occur during plant stress responses. However, relative to the research progress in model plants, far less information is available on the function of WRKY proteins in cotton. In the present study, we identified the <i>GhWRKY40</i> gene in cotton (<i>Gossypium hirsutum</i>) and determined that the GhWRKY40 protein is targeted to the nucleus and is a stress-inducible transcription factor. The <i>GhWRKY40</i> transcript level was increased upon wounding and infection with the bacterial pathogen <i>Ralstonia solanacearum</i>. The overexpression of <i>GhWRKY40</i> down-regulated most of the defense-related genes, enhanced the wounding tolerance and increased the susceptibility to <i>R. solanacearum</i>. Consistent with a role in multiple stress responses, we found that the <i>GhWRKY40</i> transcript level was increased by the stress hormones salicylic acid (SA), methyl jasmonate (MeJA) and ethylene (ET). Moreover, GhWRKY40 interacted with the MAPK kinase GhMPK20, as shown using yeast two-hybrid and bimolecular fluorescence complementation systems. Collectively, these results suggest that <i>GhWRKY40</i> is regulated by SA, MeJA and ET signaling and coordinates responses to wounding and <i>R. solanacearum</i> attack. These findings highlight the importance of WRKYs in regulating wounding- and pathogen-induced responses.</p></div

<i>GhWRKY40</i> overexpression enhances susceptibility to <i>R. Solanacearum</i> in transgenic plants.

<p>(A) Phenotype of WT and OE lines after 5 days of incubation with <i>R. solanacearum</i>. (B–C) Relative transcript levels of defense-related genes in non-infected and infected WT and OE plants were analyzed by qPCR. The data are presented as the mean ± standard error of three independent experiments. The values indicated by the different letters are significantly different at P<0.01, as determined using Duncan's multiple range tests.</p

Putative <i>cis</i>-elements in the <i>GhWRKY40</i> promoter.

<p>Putative <i>cis</i>-elements in the <i>GhWRKY40</i> promoter.</p

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice-2

Ng tree: The unrooted tree, constructed using ClustalX (1.83), summarizes the evolutionary relationship among the 68 members of CCCH families. The neighbor-joining tree was constructed using aligned full-length amino acid sequences. The proteins are named according to their gene name (see Table 2) with the CCCH zinc finger number of each protein. The tree shows the 11 major phylogenetic subfamilies (left column, numbered I to XI and marked with different alternating tones of a gray background to make subfamily identification easier) with high predictive value. The numbers beside the branches represent bootstrap values (≥500) based on 1000 replications that were used to class the major 11 subfamilies. Gene structure: The gene structure is presented by black exon(s) and spaces between the black boxes correspond to introns. The sizes of exons and introns can be estimated using the horizontal lines. Protein structure: Each black box represents the motif in the protein, as indicated in the table on the left side. The conserved motifs outside CCCH motif are highlighted with an arranged number, and the same number referred to the same motif. The length of the motif can be estimated using the scale at top. aa, amino acids.<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/9/44</p><p>BMC Genomics 2008;9():44-44.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2267713.</p><p></p