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.

Synchronization and interaction of proline, ascorbate and oxidative stress pathways under abiotic stress combination in tomato plants

ABSTRACTAdverse environmental conditions have a devastating impact on plant productivity. In nature, multiple abiotic stresses occur simultaneously, and plants have evolved unique responses to cope against this combination of stresses. Here, we coupled genome-wide transcriptional profiling and untargeted metabolomics with physiological and biochemical analyses to characterize the effect of salinity and heat applied in combination on the metabolism of tomato plants. Our results demonstrate that this combination of stresses causes a unique reprogramming of metabolic pathways, including changes in the expression of 1,388 genes and the accumulation of 568 molecular features. Pathway enrichment analysis of transcript and metabolite data indicated that the proline and ascorbate pathways act synchronously to maintain cellular redox homeostasis, which was supported by measurements of enzymatic activity and oxidative stress markers. We also identified key transcription factors from the basic Leucine Zipper Domain (bZIP), Zinc Finger Cysteine-2/Histidine-2 (C2H2) and Trihelix families that are likely regulators of the identified up-regulated genes under salinity+heat combination. Our results expand the current understanding of how plants acclimate to environmental stresses in combination and unveils the synergy between key cellular metabolic pathways for effective ROS detoxification. Our study opens the door to elucidating the different signaling mechanisms for stress tolerance.HIGHLIGHTSThe combination of salinity and heat causes a unique reprogramming of tomato metabolic pathways by changing the expression of specific genes and metabolic features.Proline and ascorbate pathways act synchronously to maintain cellular redox homeostasisKey transcription factors from the basic Leucine Zipper Domain (bZIP), Zinc Finger Cysteine-2/Histidine-2 (C2H2) and Trihelix families were identified as putative regulators of the identified up-regulated genes under salinity and heat combination.

Large Maf Transcription Factors: Cousins of AP-1 Proteins and Important Regulators of Cellular Differentiation

A large number of mammalian transcription factors possess the evolutionary conserved basic and leucine zipper domain (bZIP). The basic domain interacts with DNA while the leucine zipper facilitates homo- and hetero- dimerization. These factors can be grouped into at least seven families: AP-1, ATF/CREB, CNC, C/EBP, Maf, PAR, and virus-encoded bZIPs. Here, we focus on a group of four large Maf proteins: MafA, MafB, c-Maf, and NRL. They act as key regulators of terminal differentiation in many tissues such as bone, brain, kidney, lens, pancreas, and retina, as well as in blood. The DNA-binding mechanism of large Mafs involves cooperation between the basic domain and an adjacent ancillary DNA-binding domain. Many genes regulated by Mafs during cellular differentiation use functional interactions between the Pax/Maf, Sox/Maf, and Ets/Maf promoter and enhancer modules. The prime examples are crystallin genes in lens and glucagon and insulin in pancreas. Novel roles for large Mafs emerged from studying generations of MafA and MafB knockouts and analysis of combined phenotypes in double or triple null mice. In addition, studies of this group of factors in invertebrates revealed the evolutionarily conserved function of these genes in the development of multicellular organisms.

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly

ABSTRACTHIV-1 immature particle (virus-like particle [VLP]) assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We previously investigated the role of SP1, a “spacer” between CA and NC, in VLP assembly. We found that small changes in SP1 drastically disrupt assembly and that a peptide representing the sequence around the CA-SP1 junction is helical at high but not low concentrations. We suggested that by virtue of such a concentration-dependent change, this region could act as a molecular switch to activate HIV-1 Gag for VLP assembly. A leucine zipper domain can replace NC in Gag and still lead to the efficient assembly of VLPs. We find that SP1 mutants also disrupt assembly by these Gag-Zip proteins and have now studied a small fragment of this Gag-Zip protein, i.e., the CA-SP1 junction region fused to a leucine zipper. Dimerization of the zipper places SP1 at a high local concentration, even at low total concentrations. In this context, the CA-SP1 junction region spontaneously adopts a helical conformation, and the proteins associate into tetramers. Tetramerization requires residues from both CA and SP1. The data suggest that once this region becomes helical, its propensity to self-associate could contribute to Gag-Gag interactions and thus to particle assembly. There is complete congruence between CA/SP1 sequences that promote tetramerization when fused to zippers and those that permit the proper assembly of full-length Gag; thus, equivalent interactions apparently participate in VLP assembly and in SP1-Zip tetramerization.IMPORTANCEAssembly of HIV-1 Gag into virus-like particles (VLPs) appears to require an interaction with nucleic acid, but replacement of its principal nucleic acid-binding domain with a dimerizing leucine zipper domain leads to the assembly of RNA-free VLPs. It has not been clear how dimerization triggers assembly. Results here show that the SP1 region spontaneously switches to a helical state when fused to a leucine zipper and that these helical molecules further associate into tetramers, mediated by interactions between hydrophobic faces of the helices. Thus, the correct juxtaposition of the SP1 region makes it “association competent.” Residues from both capsid and SP1 contribute to tetramerization, while mutations disrupting proper assembly in Gag also prevent tetramerization. Thus, this region is part of an associating interface within Gag, and its intermolecular interactions evidently help stabilize the immature Gag lattice. These interactions are disrupted by proteolysis of the CA-SP1 junction during virus maturation.