The DNA binding properties of the parsley bZIP transcription factor CPRF4a are regulated by light

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet

As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.

Genome-Wide Identification and Expression Analysis of the Strawberry FvbZIP Gene Family and the Role of Key Gene FabZIP46 in Fruit Resistance to Gray Mold

A total of 54 FvbZIP genes were identified from the strawberry genome. These genes were found to be unevenly distributed on seven different chromosomes, and two of the genes had no matching chromosomal localization. FvbZIP genes were divided into 10 subfamilies according to protein sequence, and the structures of these genes were found to be highly conserved. Based on the bioinformatics analysis of FvbZIP genes, the expression of FabZIP genes changed during different stages of its growth and of its infection with gray mold disease. FabZIP46 was substantially upregulated, and its expression remained relatively high. FabZIP46 was cloned from cultivated strawberries by homologous cloning. The results of a transient transgenic assay revealed that the damage to the fruit tissue was markedly alleviated in strawberries overexpressing FabZIP46, with the incidence rate being substantially lower than that in the control group. By contrast, a brief silencing of FabZIP46 had the opposite effect. The results revealed that FabZIP46 played a positive role in the resistance of strawberries to Botrytis cinerea. The study findings provide valuable insights into the role of bZIP transcription factors as well as a theoretical reference for the regulation of resistance to gray mold disease in strawberry fruit.

A Cassava CPRF-2-like bZIP Transcription Factor Showed Increased Transcript Levels during Light Treatment

BACKGROUND

bZIP proteins participate in the regulation of gene expression, playing crucial roles in various biological processes in plants, including response to environmental changes. Luminosity is an environmental factor of extreme importance for plant metabolism, acting as a regulator of its growth and development. Despite advances in the identification of bZIP proteins in several plant species, studies on these transcription factors in cassava are lacking. Cassava (Manihot esculenta Crantz) is one of the most important food crops in tropical and subtropical regions, mainly in developing countries, where its storage root is a major source of calories for low-income people.

OBJECTIVES

Our main aim was the isolation of a cDNA sequence encoding a bZIP protein from cassava (MebZIP) as well as the in silico characterization of its nucleotide and deduced amino acid sequences. In addition, we evaluated the expression pattern of the MebZIP gene in response to light, and its possible relationship with regulation of the chalcone synthase (MeCHS) gene.

METHODS

RT-PCR and 3' and 5' RACE assays were used to isolate the full-length cDNA sequence of MebZIP. Bioinformatics tools were used to characterize the nucleotide and amino acid sequences of MebZIP. Semiquantitative RT-PCR assays were used to evaluate the expression levels of MebZIP and MeCHS genes.

RESULTS

We isolated the full-length cDNA sequence of MebZIP with a 1320-bp ORF encoding a deduced protein with a predicted molecular weight and isoelectric point of 47 kDa and 5.85, respectively. Comparative analyses with GenBank sequences showed high identity of MebZIP with bZIP CPRF-2 of Hevea brasiliensis (XP_021650934) and Petroselinum crispum (Q99090.2). Besides the basic region and leucine zipper domains, MebZIP contains putative conserved domains (D1- D4), found in parsley CPRF-2 and bZIP proteins closely related to this protein. Since CPRF proteins are known for their function in regulation of the CHS gene by light, we evaluated the expression levels of the MebZIP gene and the possible target gene to be regulated by MebZIP (the MeCHS gene) in cassava under light conditions. Semi-quantitative RT-PCR assays revealed that MebZIP transcription increased in response to white light, with maximum expression levels at 6 h of light exposure. On the other hand, the expression levels of the MeCHS gene were statistically constant in all samples, indicating that they were not influenced by the experimental conditions used here.

CONCLUSION

The putative MebZIP protein identified in this work contains the conserved domains (bZIP, D1-D4) that indicate its functionality, thus allowing it to be considered a new member of the bZIP transcription factor CPRF-2 family. The expression levels of the MebZIP gene increased during white light exposure, indicating a potential function in light-response in cassava.

Computational identification of anthocyanin-specific transcription factors using a rice microarray and maximum boundary range algorithm

This study identifies 2,617 candidate genes related to anthocyanin biosynthesis in rice using microarray analysis and a newly developed maximum boundary range algorithm. Three seed developmental stages were examined in white cultivar and two black Dissociation insertion mutants. The resultant 235 transcription factor genes found to be associated with anthocyanin were classified into nine groups. It is compared the 235 genes by transcription factor analysis and 593 genes from among clusters of COGs related to anthocyanin functions. Total 32 genes were found to be expressed commonly. Among these, 9 unknown and hypothetical genes were revealed to be expressed at each developmental stage and were verified by RT-PCR. These genes most likely play regulatory roles in either anthocyanin production or metabolism during flavonoid biosynthesis. While these genes require further validation, our results underline the potential usefulness of the newly developed algorithm.

A carrot G-box binding factor-type basic region/leucine zipper factor DcBZ1 is involved in abscisic acid signal transduction in somatic embryogenesis

Carrot (Daucus carota) somatic embryogenesis has been extensively used as an experimental system for studying embryogenesis. In maturing zygotic embryos, abscisic acid (ABA) is involved in acquisition of desiccation tolerance and dormancy. On the other hand, somatic embryos contain low levels of endogenous ABA and show desiccation intolerance and lack dormancy, but tolerance and dormancy can be induced by exogenous application of ABA. In ABA-treated carrot embryos, some ABA-inducible genes are expressed. We isolated the Daucus carota bZIP1 (DcBZ1) gene encoding a G-box binding factor-type basic region/leucine zipper (GBF-type bZIP) factor from carrot somatic embryos. The expression of DcBZ1 was detected in embryogenic cells, non-embryogenic cells, somatic embryos, developing seeds, seedlings, and true leaves. Notably, higher expression was detected in embryogenic cells, true leaves, and seedlings. The expression of DcBZ1 increased in seedlings and true leaves after ABA treatment, whereas expression was not affected by differences in light conditions. During the development of zygotic and somatic embryos, increased expression of DcBZ1 was commonly detected in the later phase of development. The recombinant DcBZ1 protein showed specific binding activity to the two ABA-responsive element-like motifs (motif X and motif Y) in the promoter region of the carrot ABA-inducible gene according to results from an electrophoretic mobility shift assay. Our findings suggest that the carrot GBF-type bZIP factor, DcBZ1, is involved in ABA signal transduction in embryogenesis and other vegetative tissues.

bZIP10-LSD1 antagonism modulates basal defense and cell death in Arabidopsis following infection

Plants use sophisticated strategies to balance responses to oxidative stress. Programmed cell death, including the hypersensitive response (HR) associated with successful pathogen recognition, is one cellular response regulated by reactive oxygen in various cellular contexts. The Arabidopsis basic leucine zipper (bZIP) transcription factor AtbZIP10 shuttles between the nucleus and the cytoplasm and binds consensus G- and C-box DNA sequences. Surprisingly, AtbZIP10 can be retained outside the nucleus by LSD1, a protein that protects Arabidopsis cells from death in the face of oxidative stress signals. We demonstrate that AtbZIP10 is a positive mediator of the uncontrolled cell death observed in lsd1 mutants. AtbZIP10 and LSD1 act antagonistically in both pathogen-induced HR and basal defense responses. LSD1 likely functions as a cellular hub, where its interaction with AtbZIP10 and additional, as yet unidentified, proteins contributes significantly to plant oxidative stress responses.

TCP34, a nuclear-encoded response regulator-like TPR protein of higher plant chloroplasts

We describe the identification of a novel chloroplast protein, designated TCP34 (tetratricopeptide-containing chloroplast protein of 34 kDa) due to the presence of three tandemly arranged tetratricopeptide repeat (TPR) arrays. The presence of the genes encoding this protein only in the genomes of higher plants but not in photosynthetic cyanobacterial prokaryotes suggests that TCP34 evolved after the separation of the higher plant lineage. The in vitro translated precursor could be imported into intact spinach chloroplasts and the processed products showed stable association with thylakoid membranes. Using a specific polyclonal antiserum raised against TCP34, three protein variants were detected. Two forms, T(1) and T(2), were associated with the thylakoid membranes and one, S(1), was found released in the stroma. TCP34 protein was not present in etioplasts and appeared only in developing chloroplasts. The ratio of membrane-bound and soluble forms was maximal at the onset of photosynthesis. The high molecular mass thylakoid TCP34 variant was found in association with a transcriptionally active protein/DNA complex (TAC) from chloroplasts and recombinant TCP34 showed specific binding to Spinacia oleracea chloroplast DNA. Two TCP34 forms, T(1) and S(1), were found to be phosphorylated. An as yet unidentified phosphorelay signal may modulate its capability for plastid DNA binding through the phosphorylation state of the putative response regulator-like domain. Based on the structural properties and biochemical analyses, we discuss the putative regulatory function of TCP34 in plastid gene expression.

bZIP transcription factors in Arabidopsis

In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development. The Arabidopsis genome sequence contains 75 distinct members of the bZIP family, of which approximately 50 are not described in the literature. Using common domains, the AtbZIP family can be subdivided into ten groups. Here, we review the available data on bZIP functions in the context of subgroup membership and discuss the interacting proteins. This integration is essential for a complete functional characterization of bZIP transcription factors in plants, and to identify functional redundancies among AtbZIP factors.

Arabidopsis GARP transcriptional activators interact with the Pro-rich activation domain shared by G-box-binding bZIP factors

The Pro-rich regions, found in a subset of plant bZIP transcription factors, including G-box-binding factors (GBFs) of Arabidopsis thaliana, are thought to be deeply involved in transcriptional regulation. However, the molecular mechanisms of the Pro-rich region-mediated transcriptional regulation are still largely unknown. Here we report evidence showing that two closely related Arabidopsis proteins, designated GPRI1 and GPRI2, containing a GARP DNA-binding domain, are likely partners of one or more GBFs. The results of yeast two-hybrid assays and in vitro binding assays indicated that GPRI1 can interact with the Pro-rich regions of GBF1 and GBF3. GPRI2 interacted with the Pro-rich region of GBF1. GPRI1 and GPRI2 transactivated transcription in yeast. In GPRI1 the region responsible for this activation was mapped in the N-terminal third of the protein. Transient assays showed that in Arabidopsis cells not only the N-terminal but also the C-terminal regions of GPRI1 can function as a separable activation domain. GPRI1 and GPRI2 may function in some promoters in concert with a GBF through interaction with its Pro-rich region to enhance the transcriptional level of the corresponding genes.