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The cytokinin response factors (CRFs) take crucial part in mediating plant development and stress response processes. However, hardly any information is known about CRF genes in the main crop plant soybean at present. Here, we carried out genome-wide dissection of CRF family in soybean and identified 26 members, which locate on 18 chromosomes of soybean. Sequence information was first observed to gain insight into the soybean CRF genes. Then, the gene duplication, phylogenetic relationships, protein motifs, and gene structure were analyzed in depth to better understand the CRF family in soybean. Cis-regulatory elements analysis showed that these CRFs contain many hormone- and stress-related elements on promoter regions, indicating their potential involvement in response to these factors. In addition, through investigating the public transcriptome data, we studied the expression patterns of those CRFs in different tissues/organs and various environments. The results revealed that expression of soybean CRFs not only exhibited spatial-diversity, but also differs in response to cold, drought, and salt stress. Our research offers new insights into soybean CRFs as well as useful information for future functional analysis of this gene family. [ABSTRACT FROM AUTHOR]

Background: Salt stress is often associated with excessive production of reactive oxygen species (ROS). Oxidative stress caused by the accumulation of ROS is a major factor that negatively affects crop growth and yield. Root is the primary organ that senses and transmits the salt stress signal to the whole plant. How oxidative stress affect redox sensitive proteins in the roots is not known. Results: In this study, the redox proteome of sugar beet M14 roots under salt stress was investigated. Using iTRAQ reporters, we determined that salt stress caused significant changes in the abundance of many proteins (2305 at 20 min salt stress and 2663 at 10 min salt stress). Using iodoTMT reporters, a total of 95 redox proteins were determined to be responsive to salt stress after normalizing again total protein level changes. Notably, most of the differential redox proteins were involved in metabolism, ROS homeostasis, and stress and defense, while a small number play a role in transport, biosynthesis, signal transduction, transcription and photosynthesis. Transcription levels of 14 genes encoding the identified redox proteins were analyzed using qRT-PCR. All the genes were induced by salt stress at the transcriptional level. Conclusions: Based on the redox proteomics results, we construct a map of the regulatory network of M14 root redox proteins in response to salt stress. This study further refines the molecular mechanism of salt resistance at the level of protein redox regulation. [ABSTRACT FROM AUTHOR]

Protein phosphatase 2Cs (PP2Cs) belong to the largest protein phosphatase family in plants. Some members have been described as being negative modulators of plant growth and development, as well as responses to hormones and environmental stimuli. However, little is known about the members of PP2C clade D, which may be involved in the regulation of signaling pathways, especially in response to saline and alkali stresses. Here, we identified 13 PP2C orthologs from the wild soybean (Glycine soja) genome. We examined the sequence characteristics, chromosome locations and duplications, gene structures, and promoter cis-elements of the PP2C clade D genes in Arabidopsis and wild soybean. Our results showed that GsPP2C clade D (GsAPD) genes exhibit more gene duplications than AtPP2C clade D genes. Plant hormone and abiotic stress-responsive elements were identified in the promoter regions of most PP2C genes. Moreover, we investigated their expression patterns in roots, stems, and leaves. Quantitative real-time PCR analyses revealed that the expression levels of representative GsPP2C and AtPP2C clade D genes were significantly influenced by alkali and salt stresses, suggesting that these genes might be associated with or directly involved in the relevant stress signaling pathways. Our results established a foundation for further functional characterization of PP2C clade D genes in the future. [ABSTRACT FROM AUTHOR]

DnaJ/Hsp40, one of molecular chaperones heat shock proteins (Hsps), is a kind of key components to contribute in cellular homeostasis under adverse growth conditions. However, until now, only few researches focus on its functions under alkaline stress response which tremendously inhibit plant growth and development, especially the DnaJ genes from wild soybean. In this study, we identified and characterized 196 DnaJ genes in soybean genome. We determined sequence information, conserve domains, gene structure, evolutionary relationship and chromosomal location of all the family members. Then, we investigated the expression profiles of DnaJ family genes in wild soybean under alkaline stress. According to heat map and our previous RNA-seq data, GsJ11, significantly induced by NaHCO treatment, was further selected. Moreover, we determined the temporal and spatial expression patterns of GsJ11 in wild soybean and characterized its physiological functions by using transgenic Arabidopsis and atj11 mutant Arabidopsis. Our results suggest that GsJ11 was moderately expressed in roots of wild soybean and could highly be induced by NaHCO in 3 h, and its Arabidopsis overexpression lines exhibited higher but the atj11 mutant lines showed lower tolerance to NaHCO than the WT line. Furthermore, we found that the transcript levels of stress-inducible genes were up-regulated in GsJ11 overexpression lines. Taken together, our results demonstrate that GsJ11 acts as a positive regulator in plant responses to bicarbonate alkaline stress. [ABSTRACT FROM AUTHOR]

Main conclusion : This is an original study focus on ERF gene response to alkaline stress. GsERF6 functions as transcription factor and significantly enhanced plant tolerance to bicarbonate (HCO ) in transgenic Arabidopsis . Alkaline stress is one of the most harmful, but little studied environmental factors, which negatively affects plant growth, development and yield. The cause of alkaline stress is mainly due to the damaging consequence of high concentration of the bicarbonate ion, high-pH, and osmotic shock to plants. The AP2/ERF family genes encode plant-specific transcription factors involved in diverse environmental stresses. However, little is known about their physiological functions, especially in alkaline stress responses. In this study, we functionally characterized a novel ERF subfamily gene, GsERF6 from alkaline-tolerant wild soybean ( Glycine soja). In wild soybean, GsERF6 was rapidly induced by NaHCO treatment, and its overexpression in Arabidopsis enhanced transgenic plant tolerance to NaHCO challenge. Interestingly, GsERF6 transgenic lines also displayed increased tolerance to KHCO treatment, but not to high pH stress, implicating that GsERF6 may participate specifically in bicarbonate stress responses. We also found that GsERF6 overexpression up-regulated the transcription levels of bicarbonate-stress-inducible genes such as NADP- ME, H - Ppase and H - ATPase, as well as downstream stress-tolerant genes such as RD29A, COR47 and KINI. GsERF6 overexpression and NaHCO stress also altered the expression patterns of plant hormone synthesis and hormone-responsive genes. Conjointly, our results suggested that GsERF6 is a positive regulator of plant alkaline stress by increasing bicarbonate ionic resistance specifically, providing a new insight into the regulation of gene expression under alkaline conditions. [ABSTRACT FROM AUTHOR]

It is widely accepted that CaATPase family proteins play important roles in plant environmental stress responses. However, up to now, most researches are limited in the reference plants Arabidopsis and rice. The function of CaATPases from non-reference plants was rarely reported, especially its regulatory role in carbonate alkaline stress responses. Hence, in this study, we identified the P-type II CaATPase family genes in soybean genome, determined their chromosomal location and gene architecture, and analyzed their amino acid sequence and evolutionary relationship. Based on above results, we pointed out the existence of gene duplication for soybean CaATPases. Then, we investigated the expression profiles of the ACA subfamily genes in wild soybean ( Glycine soja) under carbonate alkaline stress, and functionally characterized one representative gene GsACA1 by using transgenic alfalfa. Our results suggested that GsACA1 overexpression in alfalfa obviously increased plant tolerance to both carbonate alkaline and neutral salt stresses, as evidenced by lower levels of membrane permeability and MDA content, but higher levels of SOD activity, proline concentration and chlorophyll content under stress conditions. Taken together, for the first time, we reported a P-type II CaATPase from wild soybean, GsACA1, which could positively regulate plant tolerance to both carbonate alkaline and neutral salt stresses. [ABSTRACT FROM AUTHOR]

Soil alkalinity is an important environmental problem limiting agricultural productivity. Wild soybean ( Glycine soja) shows strong alkaline stress tolerance, so it is an ideal plant candidate for studying the molecular mechanisms of alkaline tolerance and identifying alkaline stress-responsive genes. However, limited information is available about G. soja responses to alkaline stress on a genomic scale. Therefore, in the present study, we used RNA sequencing to compare transcript profiles of G. soja root responses to sodium bicarbonate (NaHCO) at six time points, and a total of 68,138,478 pairs of clean reads were obtained using the Illumina GAIIX. Expression patterns of 46,404 G. soja genes were profiled in all six samples based on RNA-seq data using Cufflinks software. Then, t12 transcription factors from MYB, WRKY, NAC, bZIP, C2H2, HB, and TIFY families and 12 oxidation reduction related genes were chosen and verified to be induced in response to alkaline stress by using quantitative real-time polymerase chain reaction (qRT-PCR). The GO functional annotation analysis showed that besides 'transcriptional regulation' and 'oxidation reduction,' these genes were involved in a variety of processes, such as 'binding' and 'response to stress.' This is the first comprehensive transcriptome profiling analysis of wild soybean root under alkaline stress by RNA sequencing. Our results highlight changes in the gene expression patterns and identify a set of genes induced by NaHCO stress. These findings provide a base for the global analyses of G. soja alkaline stress tolerance mechanisms. [ABSTRACT FROM AUTHOR]

The microRNA156 (miR156) family ‘has’ been well demonstrated to regulate plant growth and development. However, no reports focused on the roles of miR156s in environmental stress responses. In previous studies, we identified 18 cold stress responsive microRNAs in rice by using microarray analysis. Here, in the present study, we focused on the biological function of one of these cold responsive microRNAs, OsmiR156k. We generated the transgenic rice overexpressing OsmiR156k under the control of CaMV35S promoter, and verified the presence of OsmiR156k by using Southern blot analysis. We found that overexpression of OsmiR156k inhibited the seedling growth at the very early seedling stage under cold stress. Furthermore, OsmiR156k overexpression decreased plant cold tolerance at the young seedling growth stage, as evidenced by lower survival rates, chlorophyll contents and proline contents. As expected, we also suggested the down-regulated expression of the cold stress responsive genes, 01g22249 and OsP5CS, and OsmiR156k-tagated SPL genes, SPL3, SPL14 and SPL17, in the OsmiR156k transgenic lines. Taken together, our findings suggest that overexpression of OsmiR156k decreased the tolerance to cold stress in rice. [ABSTRACT FROM AUTHOR]

Recent discoveries showed that hybrid proline rich type proteins were involved in plant responses to several environmental stresses. However, little is known about their roles in plant alkali stress adaptation, especially in wild soybean. Here, we isolated and characterized GsEARLI17, a novel the hybrid proline-rich protein type EARLI family gene from Glycine soja. Bioinformatic analysis showed that GsEARLI17 protein contained a conserved N-terminus hybrid proline-rich domain in and a C-terminus 8CM domain. Transcript abundance of GsEARLI17 was higher in young tissues than that in old tissues, and induced following exposure to salt and alkali treatments. GsEARLI17 overexpression in Arabidopsis influenced cuticles formation, as evidenced by thicker cuticles of transgenic lines, and enhanced plant tolerance to salt stress. Further observation was found that compared to the wild type Arabidopsis, overexpression of GsEARLI17 in Arabidopsis improved seed germination with higher leaf opening and greening rate during the early stages under alkali stress. GsEARLI17 exhibited enhanced alkaline tolerance with higher chlorophyll content, and lower malondialdehyde content at the adult developmental stage, and the expression levels of some alkali stress response marker genes NADP- ME, H Ppase were higher in the GsEARLI17 overexpression lines than in wild-type plants. Taken together we suggest that GsEARLI17 reveal a positive role in enhancing plant tolerance of alkali stress in Arabidopsis. [ABSTRACT FROM AUTHOR]

Plant SKP1-like family proteins, components of the SCF complex E3 ligases, are involved in the regulation of plant development and stress responses. Little is known about the precise function of SKP genes in plant responses to environmental stresses. GsSKP21 was initially identified as a potential stress-responsive gene based on the transcriptome sequencing of Glycine soja. In this study, we found that GsSKP21 protein contains highly conserved SKP domains in its N terminus and an extra unidentified domain in its C terminus. The transcript abundance of GsSKP21, detected by quantitative real-time PCR, was induced under the treatment of alkali and salt stresses. Overexpression of GsSKP21 in Arabidopsis dramatically increased plant tolerance to alkali stress. Furthermore, we found that overexpression of GsSKP21 resulted in decreased ABA sensitivity during both the seed germination and early seedling growth stages. GsSKP21 mediated ABA signaling by altering the expression levels of the ABA signaling-related and ABA-induced genes. We also investigated the tissue expression specificity and subcellular localization of GsSKP21. These results suggest that GsSKP21 is important for plant tolerance to alkali stress and plays a critical regulatory role in the ABA-mediated stress response. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) are one type of the human genetic variations and are pervasive in the human genome. It has been confirmed that they can play a causal role in complex diseases. Previous studies of CNVs focused more on identifying the disease-specific CNV regions or candidate genes on these CNV regions, but less on the synergistic actions between genes on CNV regions and other genes. Our research combined the CNVs with related gene co-expression to reconstruct gene co-expression network by using single nucleotide polymorphism microarray datasets and gene microarray datasets of breast cancer, and then extracted the modules which connected densely inside and analyzed the functions of modules. Interestingly, all of these modules' functions were related to breast cancer according to our enrichment analysis, and most of the genes in these modules have been reported to be involved in breast cancer. Our findings suggested that integrating CNVs and gene co-expressed relations was an available way to analyze the roles of CNV genes and their synergistic genes in breast cancer, and provided a novel insight into the pathological mechanism of breast cancer. [ABSTRACT FROM AUTHOR]