Post-translational modifications of bZIP transcription factors in abscisic acid signaling and drought responses

: Under drought stress, plants have developed various mechanisms to survive in the reduced water supply, of which the regulation of stress-related gene expression is responsible for several transcription factors. The basic leucine zippers (bZIPs) are one of the largest and most diverse transcription factor families in plants. Among the 10 Arabidopsis bZIP groups, group A bZIP transcription factors function as a positive or negative regulator in ABA signal transduction and drought stress response. These bZIP transcription factors, which are involved in the drought response, have also been isolated in various plant species such as rice, pepper, potato, and maize. Recent studies have provided substantial evidences that many bZIP transcription factors undergo the post-translational modifications, through which the regulation of their activity or stability affects plant responses to various intracellular or extracellular stimuli. This review aims to address the modulation of the bZIP proteins in ABA signaling and drought responses through phosphorylation, ubiquitination, and sumoylation.

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. Method: 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.

Version 4.3-12/08/20 Cotton bZIP Transcription Factors: Characterization of the bZIP Family From Gossypium Hirsutum, Gossypium Arboreum and Gossypium Raimondii

BackgroundCotton is an important commodity in the world economy. In this study we have carried out genome-wide identification and bioinformatics characterization of basic leucine zipper domain proteins (bZIPs) from cultivated cotton species G. hirsutum along with two subgenome species of allotetraploid cotton, G. arboreum and G. raimondii. Transcription factors (TFs) are the key regulators in plant development and stress adaptation. Understanding interactions of TFs in cotton crop is important for enhancing stress tolerance and yield enhancement. Among plant TFs, bZIPs plays a major role in seed germination, flower development, biotic and abiotic stress response. Most of the bZIP proteins from cotton remains uncharacterized and can be utilised for crop improvement. In this paper we performed genome-wide identification, phylogenetic analysis, structural characterization and functional role prediction of bZIPs from all three genome species of cotton.ResultsIn the present study genome-wide identification, phylogenetic analysis, structural characterization and functional role prediction of bZIP TFs from G. hirsutum (AADD) along with two subgenome species G. arboreum (A2) and G. raimondii (D5) were performed. A total of 228 bZIP genes of G. hirsutum, 91 bZIP genes of G. arboreum and 86 bZIP genes of G. raimondii were identified from CottonGen database. Cotton bZIP genes were annotated in standard pattern according to their match with Arabidopsis bZIPs. Multiple genes with similar bZIP designations were observed in cotton. Cotton bZIPs are distributed across all 13 chromosomes with varied density. Phylogenetic characterization of all three cotton species bZIPs with Arabidopsis bZIPs classified them into 12 subfamilies, namely A B, C, D, E, F, G, H, I, J, K and S and further into eight subgroups according to functional similarities, viz., A1, A2, A3, C1, C2, S1, S2 and S3.The classification was exclusively based on alignment with Arabidopsis bZIPs further supported by structural characteristics like exon number, amino acid length, common functional motifs shared among subfamilies and basic leucine zipper domain (BRLZ) alignment. Subfamily A and S are having maximum number of bZIP genes, subfamily B, H, J and K are single member families. Cotton is carrying only bZIP17 among the group of bZIP17, 28 and 49 which are known to be crucially worked under endoplasmic reticulum (ER) stress. Cotton bZIP protein functions were predicted from identified motifs and orthologs from varied species.MEME motif analysis identified MYND-Zinc binding domain, tetratricopeptide repeats motif, GluR7, DOG1, (DELAY OF GERMINATION 1) seed dormancy control motif, TGACG sequence specific motif, etc. specifically in some of the subfamily members and presence of bZIP signature domain in all identified bZIPs. Further we explored the BRLZ domain of G. raimondii bZIPs, conserved basic region motif N-X7-R/K is present in almost all subfamily members, variants are GrbZIP62 which is carrying N-X7-I motif and GrbZIP76 with K-X7-R motif. Leucine heptad repeats motif, L-X6-L-X6-L are also present in variant numbers from two to nine with leucine or other hydrophobic amino acid at designated position among 12 subfamily members.STRING protein interaction network analysis of G.raimondii bZIPs observed strong interaction between A-D subfamily members, C-S subfamily members and between GrbZIP17- GrbZIP60. NLS analysis of G. raimondii bZIPs observed conserved NLS sequences among subfamilies.ConclusionThis study analyzed, annotated and phylogenetically classified bZIP proteins from cultivated cotton species G. hirsutum along with two subgenome species G. arboreum and G. raimondii. Cotton bZIPs are classified into twelve subfamilies and eight subgroups. bZIP gene duplications are observed in all three cotton species. We have identified conserved functional motifs among different subfamilies of cotton bZIP proteins and correlated for the prediction of function along with reported function. Explored BRLZ domain structural analysis of G. raimondii bZIPs will be useful in further basic characterization of bZIP proteins of cultivated cotton species G. hirsutum. STRING protein interaction analysis of G. raimondii bZIPs resulted in prediction of interactions among A- D, B-K and C-S subfamily members. Phylogenetic analysis of this study will certainly help in the selection of specific cotton bZIP genes according to the close alignment with Arabidopsis orthologs or subgenome homolog.

Roles of C/EBP class bZip proteins in the growth and cell competition of Rp (‘Minute’) mutants in Drosophila

Reduced copy number of ribosomal protein (Rp) genes adversely affects both flies and mammals. Xrp1 encodes a reportedly Drosophila-specific AT-hook, bZIP protein responsible for many of the effects including the elimination of Rp mutant cells by competition with wild type cells. Irbp18, an evolutionarily conserved bZIP gene, heterodimerizes with Xrp1 and with another bZip protein, dATF4. We show that Irbp18 is required for the effects of Xrp1, whereas dATF4 does not share the same phenotype, indicating that Xrp1/Irbp18 is the complex active in Rp mutant cells, independently of other complexes that share Irbp18. Xrp1 and Irbp18 transcripts and proteins are upregulated in Rp mutant cells by auto-regulatory expression that depends on the Xrp1 DNA binding domains and is necessary for cell competition. We show that Xrp1 is conserved beyond Drosophila, although under positive selection for rapid evolution, and that at least one human bZip protein can similarly affect Drosophila development.

Nach Is a Novel Subgroup at an Early Evolutionary Stage of the CNC-bZIP Subfamily Transcription Factors from the Marine Bacteria to Humans

Normal growth and development, as well as adaptive responses to various intracellular and environmental stresses, are tightly controlled by transcriptional networks. The evolutionarily conserved genomic sequences across species highlights the architecture of such certain regulatory elements. Among them, one of the most conserved transcription factors is the basic-region leucine zipper (bZIP) family. Herein, we have performed phylogenetic analysis of these bZIP proteins and found, to our surprise, that there exist a few homologous proteins of the family members Jun, Fos, ATF2, BATF, C/EBP and CNC (cap’n’collar) in either viruses or bacteria, albeit expansion and diversification of this bZIP superfamily have occurred in vertebrates from metazoan. Interestingly, a specific group of bZIP proteins is identified, designated Nach (Nrf and CNC homology), because of their strong conservation with all the known CNC and NF-E2 p45 subunit-related factors Nrf1 and Nrf2. Further experimental evidence has also been provided, revealing that Nach1 and Nach2 from the marine bacteria exert distinctive functions, when compared with human Nrf1 and Nrf2, in the transcriptional regulation of antioxidant response element (ARE)-battery genes. Collectively, further insights into these Nach/CNC-bZIP subfamily transcription factors provide a novel better understanding of distinct biological functions of these factors expressed in distinct species from the marine bacteria to humans.

Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors

Three families of transcription factors have been reported to play key roles in light control of Arabidopsis seedling morphogenesis. Among them, bHLH protein PIFs and plant-specific protein EIN3/EIN3-LIKE 1 (EIN3/EIL1) accumulate in the dark to maintain skotomorphogenesis. On the other hand, HY5 and HY5 HOMOLOG (HYH), two related bZIP proteins, are stabilized in light and promote photomorphogenic development. To systemically investigate the transcriptional regulation of light-controlled seedling morphogenesis, we generated HY5ox/pifQein3eil1, which contained mutations of EIN3/EIL1 and four PIF genes (pifQein3eil1) and overexpression of HY5. Our results show that dark-grown HY5ox/pifQein3eil1 seedlings display a photomorphogenesis highly similar to that of wild-type seedlings grown in continuous light, with remarkably enhanced photomorphogenic phenotypes compared with the pifQ mutants. Consistent with the genetic evidence, transcriptome analysis indicated that PIFs, EIN3/EIL1, and HY5 are dominant transcription factors in collectively mediating a wide range of light-caused genome-wide transcriptional changes. Moreover, PIFs and EIN3/EIL1 independently control the expression of light-regulated genes such as HLS1 to cooperatively regulate apical hook formation, hypocotyl elongation, and cotyledon opening and expansion. This study illustrates a comprehensive regulatory network of transcription activities that correspond to specific morphological aspects in seedling skotomorphogenesis and photomorphogenesis.

Nach is a novel ancestral subfamily ofthe CNC-bZIP transcription factors selected during evolution from the marine bacteria to human

ABSTRACTAll living organisms have undergone the evolutionary selection under the changing natural environments to survive as diverse life forms. All life processes including normal homeostatic development and growth into organismic bodies with distinct cellular identifications, as well as their adaptive responses to various intracellular and environmental stresses, are tightly controlled by signaling of transcriptional networks towards regulation of cognate genes by many different transcription factors. Amongst them, one of the most conserved is the basic-region leucine zipper (bZIP) family. They play vital roles essential for cell proliferation, differentiation and maintenance in complex multicellular organisms. Notably, an unresolved divergence on the evolution of bZIP proteins is addressed here. By a combination of bioinformatics with genomics and molecular biology, we have demonstrated that two of the most ancestral family members classified into BATF and Jun subgroups are originated from viruses, albeit expansion and diversification of the bZIP superfamily occur in different vertebrates. Interestingly, a specific ancestral subfamily of bZIP proteins is identified and also designated Nach (Nrf and CNC homology) on account of their highly conservativity with NF-E2 p45 subunit-related factors Nrf1/2. Further experimental evidence reveals that Nach1/2 from the marine bacteria exerts distinctive functions from Nrf1/2 in the transcriptional ability to regulate antioxidant response element (ARE)-driven cytoprotective genes. Collectively, an insight into Nach/CNC-bZIP proteins provides a better understanding of distinct biological functions between these factors selected during evolution from the marine bacteria to human.SignificanceWe identified the novel ancestral subfamily (i.e. Nach) of CNC-bZIP transcription factors with highly conservativity from marine bacteria to human. Combination of bioinformatics with genomics and molecular biology demonstrated that two of the most ancestral family members classified into BATF and Jun subgroups are originated from viruses. The Jun and CNC subfamilies also share a common origin of these bZIP proteins. Further experimental evidence reveals that Nach1/2 from the marine bacteria exerts nuance functions from human Nrf1/2 in the transcriptional ability to regulate antioxidant response element (ARE)-driven genes, responsible for the host cytoprotection against inflammation and cancer. Overall, this study is of multidisciplinary interests to provide a better understanding of distinct biological functions between Nach/CNC-bZIPs selected during evolution.