Genome-wide analysis of basic leucine zipper transcription factor families in Arabidopsis thaliana,Oryza sativa and Populus trichocarpa

The basic leucine zipper （bZIP） transcription factors form a large gene family that is important in pathogen defense, light and stress signaling, etc. The Completed whole genome sequences of model plants Arabidopsis （Arabidopsis thaliana）, rice （Oryza sativa） and poplar （Populus trichocarpa） constitute a valuable resource for genome-wide analysis and genomic comparative analysis, as they are representatives of the two major evolutionary lineages within the angiosperms： the monocotyledons and the dicotyledons. In this study, bioinformatics analysis identified 74, 89 and 88 bZIP genes respectively in Arabidopsis, rice and poplar. Moreover, a comprehensive overview of this gene family is presented, including the gene structure, phylogeny, chromosome distribution, conserved motifs. As a result, the plant bZIPs were organized into 10 subfamilies on basis of phylogenetic relationship. Gene duplication events during the family evolution history were also investigated. And it was further concluded that chromosomal/segmental duplication might have played a key role in gene expansion of bZIP gene family.

Contributions of a Position Amino Acid Residues to the Conformational Stability of GCN4 Leucine Zipper

The stability of GCN4 leucine zipper and its four mutants in guanidine hydrochloride was detected to verify the contributions of different a position amino acid residues in polypeptide sequences to the forming and stability of parallel coiled coils. The changes of the circular dichroism spectra show that the displace- ment of the a position polar asparagine and the increase of asparagine in the GCN4 leucine zipper can reduce the α-helix content of the coiled coil structure. The mutants are less stable than the natural peptide in guanidine hydrochloride. The results show that the interaction between the polar asparagine contributes to the conformational stability of the coiled coil. Both the conformation and the number of polar residues in the coiled coil also affect the α-helix content and its resistance to the denaturant. The conclusions provide evidence describing the folding process of proteins including coiled coils in vivo.

Assessment of pathogenicity and functional characterization of APPL1 gene mutations in diabetic patients

BACKGROUND Adaptor protein,phosphotyrosine interacting with PH domain and leucine zipper 1(APPL1)plays a crucial role in regulating insulin signaling and glucose metabolism.Mutations in the APPL1 gene have been associated with the development of maturity-onset diabetes of the young type 14(MODY14).Currently,only two mutations[c.1655T>A(p.Leu552*)and c.281G>A p.(Asp94Asn)]have been identified in association with this disease.Given the limited understanding of MODY14,it is imperative to identify additional cases and carry out comprehensive research on MODY14 and APPL1 mutations.AIM To assess the pathogenicity of APPL1 gene mutations in diabetic patients and to characterize the functional role of the APPL1 domain.METHODS Patients exhibiting clinical signs and a medical history suggestive of MODY were screened for the study.Whole exome sequencing was performed on the patients as well as their family members.The pathogenicity of the identified APPL1 variants was predicted on the basis of bioinformatics analysis.In addition,the pathogenicity of the novel APPL1 variant was preliminarily evaluated through in vitro functional experiments.Finally,the impact of these variants on APPL1 protein expression and the insulin pathway were assessed,and the potential mechanism underlying the interaction between the APPL1 protein and the insulin receptor was further explored.RESULTS A total of five novel mutations were identified,including four missense mutations(Asp632Tyr,Arg633His,Arg532Gln,and Ile642Met)and one intronic mutation(1153-16A>T).Pathogenicity prediction analysis revealed that the Arg532Gln was pathogenic across all predictions.The Asp632Tyr and Arg633His variants also had pathogenicity based on MutationTaster.In addition,multiple alignment of amino acid sequences showed that the Arg532Gln,Asp632Tyr,and Arg633His variants were conserved across different species.Moreover,in in vitro functional experiments,both the c.1894G>T(at Asp632Tyr)and c.1595G>A(at Arg532Gln)mutations were found to downregulate the expression of APPL1 on both protein and mRNA levels,indicating their pathogenic nature.Therefore,based on the patient’s clinical and family history,combined with the results from bioinformatics analysis and functional experiment,the c.1894G>T(at Asp632Tyr)and c.1595G>A(at Arg532Gln)mutations were classified as pathogenic mutations.Importantly,all these mutations were located within the phosphotyrosinebinding domain of APPL1,which plays a critical role in the insulin sensitization effect.CONCLUSION This study provided new insights into the pathogenicity of APPL1 gene mutations in diabetes and revealed a potential target for the diagnosis and treatment of the disease.

Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment

The Arabidopsis （Arabidopsis thaliana L.） genome encodes for four distinct classes of homeodomain leucinezipper （HD-ZIP） transcription factors （HD-ZIPI to HD-ZIPIV）, which are all organized in multi-gene families. HD-ZIP transcription factors act as sequence-specific DNA-binding proteins that are able to control the expression level of target genes. While HD-ZIPI and HD-ZIPII proteins are mainly associated with environmental responses, HD-ZIPIII and HD- ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD-ZlP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone-signaling networks.

Expression of a novel bHLH-Zip gene in human testis

<abstract>Aim: To identify specifically expressed genes in the adult and fetal testes. Methods: A human testis cDNA microarray was established. Then the mRNA of adult and fetal testis was purified and probes were prepared by a reverse transcription reaction with the testis mRNA as template. The microarray was hybridized with probes of adult and fetal testes. The nucleic sequences of differentially expressed genes were determined and homologies were searched in the databases of the GenBank. Results: When hybridized with adult or fetal testis probes, the positive clones were 96.8 % and 95.4 %, respectively. Among these genes, one was a new testis-specific gene, which was named TSP1. TSP1 was highly expressed in human adult testis. The cDNA of TSP1 was 1,484 bp in length. The cDNA sequence of this clone was deposited in the Genbank (AF333098). TSP1 was also determined as Interim Gen Symbol (Unigene, No. Hs.98266). Protein analysis showed that TSP1 contained two functional domains: an N-terminal basic helix-loop-helix (bHLH) and a C-terminal leucine zipper (Zip). Homologous analysis showed that the 430 amino acid sequences deduced from the 1,293 bp open reading frame (ORF) had a homology with the human gene FLJ2509 (AK098575). TSP1 had also a sequence homology with Spz 1 protein of mouse. Expression profiles showed that TSP1 was specifically and strongly expressed in the testis. Conclusion: TSP1 is a gene highly expressed in adult testis. It may play an important role in spermatogenesis in the humans.

OsbZIP72 Is Involved in Transcriptional Gene-Regulation Pathway of Abscisic Acid Signal Transduction by Activating Rice High-Affinity Potassium Transporter OsHKT1;1

We created CRISPR-Cas9 knock-out and overexpressing OsbZIP72 transgenic rice plants to gain a better understanding of the role and molecular mechanism of OsbZIP72 gene in stress tolerance,which has remained largely elusive.OsbZIP72 was expressed and integrated into rice transgenic plant genomes,and the OsbZIP72 transcript in overexpression lines was elicited by salinity,abscisic acid(ABA)and drought stresses.OsbZIP72 overexpressing plants showed higher tolerance to drought and salinity stresses,while knock-out transgenic lines showed higher sensitivity to these stresses.The differentially expressed genes(DEGs)from RNA-sequencing data encompassed several abiotic stress genes,and the functional classification of these DEGs demonstrated the robust transcriptome diversity in OsbZIP72.Yeast one-hybrid,along with luciferase assay,indicated that OsbZIP72 acted as a transcriptional initiator.Remarkably,electrophoresis mobility assay revealed that OsbZIP72 bound directly to the ABAresponsive element in the OsHKT1;1 promoter region and activated its transcription.Overall,our findings revealed that OsbZIP72 can act as a transcriptional modulator with the ability to induce the expression of OsHKT1;1 in response to environmental stress through an ABA-dependent regulatory pathway,indicating that OsbZIP72 can play a crucial role in the ABA-mediated salt and drought tolerance pathway in rice.

The identification of a new actin-binding region in p57

The actin-binding protein p57 is a member of mammalian coronin-like proteins. The roles of this protein in phagocytic processes conceivably depend on its interactions with F-actin. Two regions, p57^1-34 and p57^111-204, were previously reported to be actin-binding sites. In this study, we found that the C-terminal region of p57 ,p57^297-461 , also possessed F-actin binding activity. Furthermore, the leucine zipper domain at the C-terminus of p57^297-461 was essential for this actin-binding activity. The F-actin cross-linking assay revealed that the region contained in p57^297-461 was sufficient to cross-link actin filaments. Our results strongly suggested that there was a new actin-binding region at the C-terminus of p57.

Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments:The Influence of Force Field Polarisation and Capping

Coiled-coils are well known protein–protein interaction motifs,with the leucine zipper region of activator protein-1(AP-1)consisting of the c-Jun and c-Fos proteins being a typical example.Molecular dynamics(MD)simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins.The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge)were investigated.Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding,peptide capping has the largest influence on the predicted free energy of binding.Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.

Recent advances in plant membrane-bound transcription factor research: Emphasis on intracellular movement

Transcription factors constitute numerous signal transduction networks and play a central role in gene expression regulation. Recent studies have shown that a limited portion of transcription factors are anchored in the cellular membrane, storing as dormant forms. Upon exposure to environmental and developmental cues, these transcription factors are released from the membrane and translocated to the nucleus, where they regulate associated target genes. As this process skips both transcriptional and translational regulations, it guarantees prompt response to external and internal signals. Membrane- bound transcription factors （MTFs） undergo several unique steps that are not involved in the action of canonical nuclear transcription factors： proteolytic processing and intracellular movement. Recently, alternative splicing has also emerged as a mechanism to liberate MTFs from the cellular membranes, establishing an additional activation scheme independent of proteolytic processing. Multiple layers of MTF regulation add complexity to transcriptional regulatory scheme and ensure elaborate action of MTFs. In this review, we provide an overview of recent findings on MTFs in plants and highlight the molecular mechanisms underlying MTF liberation from cellular membranes with an emphasis on intracellular movement.