This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

Metagenomic biomarker discovery and explanation

The WRKY gene family is among the largest families of transcription factors (TFs) in higher plants. By regulating the plant hormone signal transduction pathway, these TFs play critical roles in some plant processes in response to biotic and abiotic stress. Various bodies of research have demonstrated the important biological functions of WRKY TFs in plant response to different kinds of biotic and abiotic stresses and working mechanisms. However, very little summarization has been done to review their research progress. Not just important TFs function in plant response to biotic and abiotic stresses, WRKY also participates in carbohydrate synthesis, senescence, development, and secondary metabolites synthesis. WRKY proteins can bind to W-box (TGACC (A/T)) in the promoter of its target genes and activate or repress the expression of downstream genes to regulate their stress response. Moreover, WRKY proteins can interact with other TFs to regulate plant defensive responses. In the present review, we focus on the structural characteristics of WRKY TFs and the research progress on their functions in plant responses to a variety of stresses.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/jipb.12513

WRKY transcription factors in plant responses to stresses

Plants in their natural habitat have to face multiple stresses simultaneously. Evolutionary adaptation of developmental, physiological, and biochemical parameters give advantage over a single window of stress but not multiple. On the other hand transcription factors like WRKY can regulate diverse responses through a complicated network of genes. So molecular orchestration of WRKYs in plant may provide the most anticipated outcome of simultaneous multiple responses. Activation or repression through W-box and W-box like sequences is regulated at transcriptional, translational, and domain level. Because of the tight regulation involved in specific recognition and binding of WRKYs to downstream promoters, they have become promising candidate for crop improvement. Epigenetic, retrograde and proteasome mediated regulation enable WRKYs to attain the dynamic cellular homeostatic reprograming. Overexpression of several WRKYs face the paradox of having several beneficial affects but with some unwanted traits. These overexpression-associated undesirable phenotypes need to be identified and removed for proper growth, development and yeild. Taken together, we have highlighted the diverse regulation and multiple stress response of WRKYs in plants along with the future prospects in this field of research.

/pdf/wrky-transcription-factors-molecular-regulation-and-stress-2cpccsr1cr.pdf

WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants.

Agricultural production and quality are adversely affected by various abiotic stresses worldwide and this will be exacerbated by the deterioration of global climate. To feed a growing world population, it is very urgent to breed stress-tolerant crops with higher yields and improved qualities against multiple environmental stresses. Since conventional breeding approaches had marginal success due to the complexity of stress tolerance traits, the transgenic approach is now being popularly used to breed stress-tolerant crops. So identifying and characterizing the critical genes involved in plant stress responses is an essential prerequisite for engineering stress-tolerant crops. Far beyond the manipulation of single functional gene, engineering certain regulatory genes has emerged as an effective strategy now for controlling the expression of many stress-responsive genes. Transcription factors (TFs) are good candidates for genetic engineering to breed stress-tolerant crop because of their role as master regulators of many stress-responsive genes. Many TFs belonging to families AP2/EREBP, MYB, WRKY, NAC, bZIP have been found to be involved in various abiotic stresses and some TF genes have also been engineered to improve stress tolerance in model and crop plants. In this review, we take five large families of TFs as examples and review the recent progress of TFs involved in plant abiotic stress responses and their potential utilization to improve multiple stress tolerance of crops in the field conditions.

/pdf/recent-advances-in-utilizing-transcription-factors-to-jtq63eoee6.pdf

Recent Advances in Utilizing Transcription Factors to Improve Plant Abiotic Stress Tolerance by Transgenic Technology

Pathogenesis-related proteins and peptides as promising tools for engineering plants with multiple stress tolerance.

WRKY transcription factors constitute a very large family of proteins in plants and participate in modulating plant biological processes, such as growth, development and stress responses. However, the exact roles of WRKY proteins are unclear, particularly in non-model plants. In this study, Gossypium hirsutum WRKY41 (GhWRKY41) was isolated and transformed into Nicotiana benthamiana. Our results showed that overexpression of GhWRKY41 enhanced the drought and salt stress tolerance of transgenic Nicotiana benthamiana. The transgenic plants exhibited lower malondialdehyde content and higher antioxidant enzyme activity, and the expression of antioxidant genes was upregulated in transgenic plants exposed to osmotic stress. A β-glucuronidase (GUS) staining assay showed that GhWRKY41 was highly expressed in the stomata when plants were exposed to osmotic stress, and plants overexpressing GhWRKY41 exhibited enhanced stomatal closure when they were exposed to osmotic stress. Taken together, our findings demonstrate that GhWRKY41 may enhance plant tolerance to stress by functioning as a positive regulator of stoma closure and by regulating reactive oxygen species (ROS) scavenging and the expression of antioxidant genes.

/pdf/the-cotton-wrky-gene-ghwrky41-positively-regulates-salt-and-58k3kom95e.pdf

The Cotton WRKY Gene GhWRKY41 Positively Regulates Salt and Drought Stress Tolerance in Transgenic Nicotiana benthamiana

Our results indicate that overexpression of the
 GhWRKY39
 -
 1
 gene
 enhances resistance to pathogen infection and tolerance to high salt and oxidative
 stress in transgenic
 Nicotiana benthamiana.
 WRKY transcription factor genes play significant roles in the response to biotic and abiotic stresses. Cotton (Gossypium hirsutum) is an important fiber and oil crop worldwide. We isolated and characterized GhWRKY39-1, which is a group IId WRKY gene that is present as a single copy in the cotton genome. Quantitative PCR analyses indicated that GhWRKY39-1 was induced by pathogen infection, defense-related signaling molecules, and abiotic stresses, such as NaCl and methyl viologen. An analysis of the subcellular localization of the GhWRKY39-1 protein indicated that it localized to the nucleus. Furthermore, constitutive overexpression of GhWRKY39-1 in Nicotiana benthamiana conferred a greater resistance to infection by both the bacterial pathogen Ralstonia solanacearum and the fungal pathogen Rhizoctonia solani. The transgenic plants also exhibited elevated mRNA levels of several pathogen-related (PR) genes, including PR1c, PR2 and PR4. Moreover, transgenic plants displayed an enhanced tolerance to salt and oxidative stress and elevated expression of several oxidation-related genes, including APX, CAT, GST and SOD. Overall, these results indicate that GhWRKY39-1 functions as a positive regulator of plant defense against pathogen infection and responses to salt stress and reactive oxygen species.

The Gossypium hirsutum WRKY gene GhWRKY39 - 1 promotes pathogen infection defense responses and mediates salt stress tolerance in transgenic Nicotiana benthamiana

The diversified physiological responses in cyanobacteria under ultraviolet-B (UV-B) radiation have been broadly researched. The changes in the metabolic control mechanisms hidden behind these physiological traits still need to be further investigated. This research attempts to identify some of the internal mechanisms of several stressful phenotypes such as a decreased growth rate, an impaired photosystem, and the degradation of photosynthetic pigments. Different expression levels of proteins in the cytoplasm of Synechocystis sp. PCC 6803 under short-term and long-term UV-B stress were investigated by using a comparative proteomic approach. One hundred and twelve differentially expressed protein spots were identified by mass spectrometry to match 75 diverse protein species. They mainly focus on amino acid biosynthesis, photosynthesis and respiration, energy metabolism, protein biosynthesis, cell defence, and other functional groups. By focusing on these areas, the study reveals the correlation between UV-B stress-responsive proteins and the physiological changes listed above. The research, showing that short-term response-proteins are quite different from long-term response-proteins, helps to identify the change in homeostatic mechanisms in Synechocystis sp. PCC 6803. Related putative functions of these proteins and the physiological responses of cyanobacteria under UV-B stress, a UV-B responsive protein network in Synechocystis sp. PCC 6803 under long-term stress was successfully produced. Such a protein network helps to increase our understanding of the comprehensive functional network cyanobacteria use to adapt to UV-B stress. In addition, 30 novel proteins not previously found related to UV-B stress were identified. This opens up new areas for exploration to identify the response to UV-B stress in cyanobacteria.

/pdf/identification-of-the-proteomic-changes-in-synechocystis-sp-2fdn9w5ov4.pdf

Identification of the proteomic changes in Synechocystis sp. PCC 6803 following prolonged UV-B irradiation

WRKY transcription factors have been suggested to play crucial roles in the response to biotic and abiotic stresses. However, previous studies concerning WRKYs have primarily focused on model plants, and fairly limited research has been performed with cotton. In the present study, we functionally characterized a stress-responsive IId WRKY gene (GhWRKY39) from cotton. GhWRKY39 is present as a single copy gene, and subcellular localization analysis indicated that GhWRKY39 localizes to the nucleus. Additionally, some cis-acting elements associated with the environmental stress response were observed in the promoter region of this gene. Consistently, a β-glucuronidase activity assay and quantitative PCR analysis revealed that GhWRKY39 expression could be induced by bacterial and fungal infection or NaCl treatment. Furthermore, the constitutive overexpression of GhWRKY39 in Nicotiana benthamiana conferred greater resistance to bacterial and fungal pathogen infections, and the expression of several pathogenesis-related (PR) genes was significantly increased. The transgenic plants also exhibited less H2O2 accumulation than wild-type plants following pathogen infection. Moreover, GhWRKY39-overexpressing plants displayed enhanced tolerance to salt and oxidative stress and increased transcription of antioxidant enzyme genes, including ascorbate peroxidase (APX), catalase (CAT), glutathione-S-transferase (GST) and superoxide dismutase (SOD). Importantly, overexpression of GhWRKY39 improved the activities of the antioxidant enzymes SOD, POD and CAT after pathogen infection and salt stress treatment. Overall, our data suggest that the overexpression of GhWRKY39 may positively regulate the plant response against pathogen infection and salt stress, likely through the regulation of the reactive oxygen species system via multiple signaling pathway.

Han Li

Papers

The Cotton WRKY Gene GhWRKY41 Positively Regulates Salt and Drought Stress Tolerance in Transgenic Nicotiana benthamiana

The Gossypium hirsutum WRKY gene GhWRKY39 - 1 promotes pathogen infection defense responses and mediates salt stress tolerance in transgenic Nicotiana benthamiana

Identification of the proteomic changes in Synechocystis sp. PCC 6803 following prolonged UV-B irradiation

GhWRKY39, a member of the WRKY transcription factor family in cotton, has a positive role in disease resistance and salt stress tolerance

Characterization of a mitochondrial manganese superoxide dismutase gene from Apis cerana cerana and its role in oxidative stress