Background: Endophytic fungi are known plant symbionts. They produce a variety of beneficial metabolites for plant growth and survival, as well as defend their hosts from attack of certain pathogens. Coastal dunes are nutrient deficient and offer harsh, saline environment for the existing flora and fauna. Endophytic fungi may play an important role in plant survival by enhancing nutrient uptake and producing growth-promoting metabolites such as gibberellins and auxins. We screened roots of Ixeris repenes (L.) A. Gray, a common dune plant, for the isolation of gibberellin secreting endophytic fungi.

The proteins harboring RING finger motif(s) have been shown to mediate protein-protein interactions that are relevant to a variety of cellular processes. In an effort to elucidate the evolutionary dynamics of the rice RING finger protein family, we have attempted to determine their genomic locations, expression diversity, and co-expressed genes via in silico analysis and semi-quantitative RT-PCR. A total of 425 retrieved genes appear to be distributed over all 12 of the chromosomes of rice with different distributions, and are reflective of the evolutionary dynamics of the rice genome. A genome-wide dataset harboring 155 gene expression omnibus sample plates evidenced some degree of differential evolutionary fates between members of RING-H2 and RING-HC types. Additionally, responses to abiotic stresses, such as salinity and drought, demonstrated that some degree of expression diversity existed between members of the RING finger protein genes. Interestingly, we determined that one RING-H2 finger protein gene (Os04g51400) manifested striking differences in expression patterns in response to abiotic stresses between leaf and culm-node tissues, further revealing responses highly similar to the majority of randomly selected co-expressed genes. The gene network of genes co-expressed with Os04g51400 may suggest some role in the salt response of the gene. These findings may shed further light on the evolutionary dynamics and molecular functional diversity of these proteins in complex cellular regulations.

Flowering time is an important factor determining yield and seed quality in maize. A change in flowering time is a strategy used to survive abiotic stresses. Among abiotic stresses, drought can increase anthesis-silking intervals (ASI), resulting in negative effects on maize yield. We have analyzed the correlation between flowering time and drought stress using RNA-seq and bioinformatics tools. Our results identified a total of 619 genes and 126 transcripts whose expression was altered by drought stress in the maize B73 leaves under short-day condition. Among drought responsive genes, we also identified 20 genes involved in flowering times. Gene Ontology (GO) enrichment analysis was used to predict the functions of the drought-responsive genes and transcripts. GO categories related to flowering time included reproduction, flower development, pollen–pistil interaction, and post-embryonic development. Transcript levels of several genes that have previously been shown to affect flowering time, such as PRR37, transcription factor HY5, and CONSTANS, were significantly altered by drought conditions. Furthermore, we also identified several drought-responsive transcripts containing C2H2 zinc finger, CCCH, and NAC domains, which are frequently involved in transcriptional regulation and may thus have potential to alter gene expression programs to change maize flowering time. Overall, our results provide a genome-wide analysis of differentially expressed genes (DEGs), novel transcripts, and isoform variants expressed during the reproductive stage of maize plants subjected to drought stress and short-day condition. Further characterization of the drought-responsive transcripts identified in this study has the potential to advance our understanding of the mechanisms that regulate flowering time under drought stress.

Duplicate genes are believed to be a major source of new gene functions over evolutionary time. In order to evaluate the evolutionary dynamics of rice duplicate genes, formed principally by paleoployploidization prior to the speciation of the Poaceae family, we have employed a public microarray dataset including 155 gene expression omnibus sample plates and bioinformatics tools. At least 57.4% of old »70 million years ago (MYA) duplicate gene pairs exhibit divergences in expression over the given experimental set, whereas at least 50.9% of young »7.7-MYA duplicate gene pairs were shown to be divergent. When grouping the rice duplicate genes according to functional categories, we noted a striking and signiWcant enrichment of divergent duplicate metabolism-associated genes, as compared to that observed in non-divergent duplicate genes. While both non-synonymous substitution (Ka) and synonymous substitution (Ks) values between nonand divergent duplicate gene pairs evidenced signiWcant diVerences, the Ka/Ks values between them exhibited no signiWcant diVerences. Interestingly, the average numbers of conserved motifs of the duplicate gene pairs revealed a pattern of decline along with an increase in expression diversity, partially supporting the subfunctionalization model with degenerative complementation in regulatory motifs. Duplicate gene pairs with high local similarity (HLS) segments, which might be formed via conversion between rice paleologs, evidenced higher expression correlations than were observed in the gene pairs without the HLS segments; this probably resulted in an increased likelihood of gene conversion in promoters of the gene pairs harboring HLS segments. More than 60% of the rice gene families exhibited similar high expression diversity between members as compared to that of randomly selected gene pairs. These Wndings are likely reXective of the evolutionary dynamics of rice duplicate genes for gene retention.

BackgroundThe PLAnt co-EXpression database (PLANEX) is a new internet-based database for plant gene analysis. PLANEX (http://planex.plantbioinformatics.org) contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI). PLANEX is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. It can be used for the characterization of genes for functional identification and analysis of a gene’s dependency among other genes. Gene co-expression databases have been developed for other species, but gene co-expression information for plants is currently limited.DescriptionWe constructed PLANEX as a list of co-expressed genes and functional annotations for Arabidopsis thaliana, Glycine max, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Triticum aestivum, Vitis vinifera and Zea mays. PLANEX reports Pearson’s correlation coefficients (PCCs; r-values) that distribute from a gene of interest for a given microarray platform set corresponding to a particular organism. To support PCCs, PLANEX performs an enrichment test of Gene Ontology terms and Cohen’s Kappa value to compare functional similarity for all genes in the co-expression database. PLANEX draws a cluster network with co-expressed genes, which is estimated using the k-mean method. To construct PLANEX, a variety of datasets were interpreted by the IBM supercomputer Advanced Interactive eXecutive (AIX) in a supercomputing center.ConclusionPLANEX provides a correlation database, a cluster network and an interpretation of enrichment test results for eight plant species. A typical co-expressed gene generates lists of co-expression data that contain hundreds of genes of interest for enrichment analysis. Also, co-expressed genes can be identified and cataloged in terms of comparative genomics by using the ‘Co-expression gene compare’ feature. This type of analysis will help interpret experimental data and determine whether there is a common term among genes of interest.

Wild-type p53-induced phosphatase (Wip1) is induced by p53 in response to stress, which results in the dephosphorylation of proteins (i.e. p38 MAPK, p53, and uracil DNA glycosylase) involved in DNA repair and cell cycle checkpoint pathways. p38 MAPK-p53 signaling is a unique way to induce Wip1 in response to stress. Here, we show that c-Jun directly binds to and activates the Wip1 promoter in response to UV irradiation. The binding of p53 to the promoter occurs earlier than that of c-Jun. In experiments, mutation of the p53 response element (p53RE) or c-Jun consensus sites reduced promoter activity in both non-stressed and stressed A549 cells. Overexpression of p53 significantly decreased Wip1 expression in HCT116 p53 As a master cell regulator, p53 activates genes involved in DNA repair, cell cycle control, and apoptosis to mediate cellular responses to agents that cause stress and DNA damage (1, 2). Wild-type p53-induced phosphatase 1 (Wip1) 2 is a recently identified member of the protein phosphatase type 2C and p53 target gene families (3, 4). Once induced by p53, Wip1 directly dephosphorylates checkpoint kinase 1 (Chk1), checkpoint kinase 2 (Chk2), p38 MAPK, uracil DNA glycosylase, ataxia-telangiectasia-mutated (ATM) kinase, mdm2, and p53, so that cells can return to normal after DNA repair (5-9). The Wip1 gene is frequently amplified or overexpressed in human cancers, including ϳ11% to 16% of breast cancers, 40% of ovarian clear cell adenocarcinomas, 40% of neuroblastomas, and 36% of pancreatic cancers, which rarely contain the p53 mutation (10 -14). Overexpressed Wip1 promotes tumor growth by switching off major checkpoint kinases and p53; facilitates cell proliferation; and transforms primary fibroblasts together with Ras, Myc, and Neu (15). Wip1 can promote unrestricted entry into the cell cycle in response to DNA damage via dephosphorylation of ATM/ATR and p38 MAPK through a mechanism similar to that used by protein phosphatase 5 and protein phosphatase 1 (16 -18). Wip1-null mouse embryonic fibroblast (MEF) cells exhibit increased expression of p53, p21, p16, and p19; severe proliferation defects; and vulnerability to replicative senescence (19,20). Although the exact mechanism by which Wip1 controls the cell cycle is unknown, Wip1 likely plays a conserved role in the progression of the normal cell cycle in eukaryotic cells.The search for a Wip1-specific chemical inhibitor has been undertaken by Belova et al. and Rayter et al. (21,22). A major factor influencing the use of Wip1 as a therapeutic target is that loss of Wip1 promotes apoptosis in response to external stresses. Wip1 Ϫ/Ϫ MEF cells exhibit increased caspase-3 and PARP cleavage and sustained activation of p38 MAPK and c-Jun N-terminal kinase (JNK), whereas wild-type MEF cells exhibit strong G 2 /M arrest upon etoposide treatment (23). Thus, p53 activation is necessary; however, the p53 downstream target, Wip1, should not be activated in cancer therapies.Mitogen-activated protein kinases (MAPKs), including extracellular signal-regulated kinase...

The root plays an important role during plant development and growth, i.e., the plant body maintenance, nutrient storage, absorption of water, oxygen and nutrient from the soil, and storage of water and carbohydrates, etc. The objective of this study was attempted to determine root-specific genes at the initial developmental stages of maize by using network-based transcriptome analysis. The raw data obtained using RNA-seq were filtered for quality control of the reads with the FASTQC tool, and the filtered reads were pre-proceed using the TRIMMOMATIC tool. The enriched BINs of the DEGs were detected using PageMan analysis with the ORA_FISHER statistical test, and genes were assigned to metabolic pathways by using the MapMan tool, which was also used for detecting transcription factors (TFs). For reconstruction of the co-expression network, we used the algorithm for the reconstruction of accurate cellular networks (ARACNE) in the R package, and then the reconstructed co-expression network was visualized using the Cytoscape tool. RNA-seq. was performed using maize shoots and roots at different developmental stages of root emergence (6-10 days after planting, VE) and 1 week after plant emergence (V2). A total of 1286 differentially expressed genes (DEGs) were detected in both tissues. Many DEGs involved in metabolic pathways exhibited altered mRNA levels between VE and V2. In addition, we observed gene expression changes for 113 transcription factors and found five enriched cis-regulatory elements in the 1-kb upstream regions of both DEGs. The network-based transcriptome analysis showed two modules as co-expressed gene clusters differentially expressed between the shoots and roots during plant development. The DEGs of one module exhibited gene expressional coherence in the maize root tips, suggesting that their functional relationships are associated with the initial developmental stage of the maize root. Finally, we confirmed reliable mRNA levels of the hub genes in the potential sub-network related to initial root development at the different developmental stages of VE, V2, and 2 weeks after plant emergence.

This study investigated the alteration of seed storage proteins in soybean mutants induced by γ-irradiation. Five soybean cultivars and four landraces were irradiated with 250 Gy of γ rays to induce variability. The seed storage protein profiles of 414 genetic fixed mutants (M(12)-M(20)) having excellent agricultural traits were analyzed by SDS-PAGE. Among the 414 mutants, 58 were identifed as lacking lipoxygenase, 89 lacking the α' subunit, 113 lacking the α subunit, and 40 with an altered β subunit. One hundred and forty-nine mutants lacked the A(3) subunit of glycinin. Fifty-four mutants showed higher trypsin inhibitor (TIA) activity, whereas 139 showed lower TIA activity compared to their original cultivars. The selected mutants with low amounts of antinutritional factors such as trypsin inhibitor, lipoxygenase, and α subunit will constitute genetic resources for improving soybean protein quality.