WRKY transcription factors: evolution,regulation, and functional diversity in plants

Protoplasma - The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues...     

The evolution of extracellular fibrillins and their functional domains

Fibrillins constitute the major backbone of multifunctional microfibrils in elastic and non-elastic extracellular matrices, and are known to interact with several binding partners including tropoelastin and integrins. Here, we study the evolution of fibrillin proteins. Following sequence collection from 39 organisms representative of the major evolutionary groups, molecular evolutionary genetics and phylogeny inference software were used to generate a series of evolutionary trees using distance-based and maximum likelihood methods. The resulting trees support the concept of gene duplication as a means of generating the three vertebrate fibrillins. Beginning with a single fibrillin sequence found in invertebrates and jawless fish, a gene duplication event, which coincides with the appearance of elastin, led to the creation of two genes. One of the genes significantly evolved to become the gene for present-day fibrillin-1, while the other underwent evolutionary changes, including a second duplication, to produce present-day fibrillin-2 and fibrillin-3. Detailed analysis of several sequences and domains within the fibrillins reveals distinct similarities and differences across various species. The RGD integrin-binding site in TB4 of all fibrillins is conserved in cephalochordates and vertebrates, while the integrin-binding site within cbEGF18 of fibrillin-3 is a recent evolutionary change. The proline-rich domain in fibrillin-1, glycine-rich domain in fibrillin-2 and proline-/glycine-rich domain in fibrillin-3 are found in all analyzed tetrapod species, whereas it is completely replaced with an EGF-like domain in cnidarians, arthropods, molluscs and urochordates. All collected sequences contain the first 9-cysteine hybrid domain, and the second 8-cysteine hybrid domain with exception of arthropods containing an atypical 10-cysteine hybrid domain 2. Furin cleavage sites within the N- and C-terminal unique domains were found for all analyzed fibrillin sequences, indicating an essential role for processing of the fibrillin pro-proteins. The four cysteines in the unique N-terminus and the two cysteines in the unique C-terminus are also highly conserved.     

Transcription dynamics of Saltol QTL localized genes encoding transcription factors,reveals their differential regulation in contrasting genotypes of rice

Functional & Integrative Genomics - Salinity is one of the major environmental factors affecting the growth and yield of rice crop. Salinity stress response is a multigenic trait and numerous...     

转录因子与造血调控

血细胞生成是一个极其复杂的过程,转录因子在这个过程中起到了重要的调控作用。而转录因子的表达具有阶段和细胞系特异性。在造血干细胞的增殖和分化、髓系和淋巴系细胞等的成熟过程中,众多转录因子既相互作用又表现出各自的特异性。转录因子数目较多,该文仅就一些与造血细胞分化、成熟相关的转录因子近年来的研究进展作一介绍。     

Cell cycle regulation in higher plants

The isolation of plant genes homologous to cdk and cyclin components from yeast and animals proves the existence of a basic cell cycle machinery in all eukaryotes. cdk and cyclin expression has been shown to be involved in the spatial and temporal control of cell division in a variety of developmental processes. In plants, cell division and development are closely interlinked processes that are regulated by phytohormones. cdks and cyclins were found to be under control of phytohormones underscoring their integral role in mediating different developmental pathways. Furthermore, studies on cdk and cyclin expression not only correlate with actual cell cycle activity but also with cell division competence providing a working model to understand regeneration capacity at the molecular level.     

Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution

Background  

Non-ribosomal peptide synthetases (NRPSs) are large multimodular enzymes that synthesize a wide range of biologically active natural peptide compounds, of which many are pharmacologically important. Peptide bond formation is catalyzed by the Condensation (C) domain. Various functional subtypes of the C domain exist: An^LC_L domain catalyzes a peptide bond between two L-amino acids, a^DC_L domain links an L-amino acid to a growing peptide ending with a D-amino acid, a Starter C domain (first denominated and classified as a separate subtype here) acylates the first amino acid with a β -hydroxy-carboxylic acid (typically a β -hydroxyl fatty acid), and Heterocyclization (Cyc) domains catalyze both peptide bond formation and subsequent cyclization of cysteine, serine or threonine residues. The homologous Epimerization (E) domain flips the chirality of the last amino acid in the growing peptide; Dual E/C domains catalyze both epimerization and condensation.     

Auxin biosynthetic intermediate genes and their role in developmental growth and plasticity in higher plants

Auxins are a group of phytohormones that regulate several aspects of plant growth and development. Indole-3-acetic acid (IAA) is the predominant form of auxin in plants and several IAA biosynthetic pathways have been previously proposed but remain genetically uncharacterized. One of the proposed pathways is the indole-3-pyruvic acid (IPyA) pathway, which is inferred to regulate key developmental processes such as apical hook formation and shade avoidance. Recent molecular evidence suggests the existence of the pathway in higher plants but remains unverified due to the elusive nature of IPyA in vitro. Extending on these recent advances, this research was aimed at investigating aspects of IPyA-dependent auxin biology in Pisum sativum (pea) using reverse genetics, expression profiling, and analytical techniques. As a result the genes PsTAR2, PsTAR 5g Mt 80, and PsTAR 5g Mt 90, which are inferred to encode key enzymes in the IPyA pathway, were cloned. On expression analysis PsTAR2 was found to be slightly heightened in response to IPyA-inducing conditions (shade) while IAA levels remained unaltered contrary to previous reports. Moreover, the inferred homologs PsTAR 5g Mt 80 and PsTAR 5g Mt 90 appeared down-regulated in the same conditions suggesting functional divergence in the gene family. Thus, PsTAR2 was thought to be solely responsible for regulating IPyA-dependent auxin synthesis. Consequently, using a reverse genetic approach, called TILLING, the PsTAR2 gene was mutated in order to study the down-stream effects of IPyA deficiency. The procedure is currently underway and in the process of isolating two novel pstar2 (IPyA) mutant lines consisting of a missense mutation (pstar2 4280) and a highly desired knockout mutation (pstar2 918). On completion the novel mutants are anticipated to be indispensable to future IPyA-auxin investigations in higher plants. In light of the unstable nature of IPyA, a protocol has been formulated using UPLC for fractioning followed by MS/MS analysis. This technique appears to be very promising as a robust IPyA detection protocol in plant extracts.     

Selective uptake of mineral ions and their concentration factors in aquatic higher plants

A comparative review of the elementary chemical composition of aquatic vascular plants is presented together with the author’s own results. Attention is focussed on the specific genotypic, onthogenetic and between-organs variability of the selective uptake and accumulation of mineral ions in macrophytes in relation to trophic conditions of habitat. The concentration factors and atomic ratios are also considered. Numerical tables presenting comparative data are arranged alphabetically according to plant species, with indications of geographical situation, phenology, part of plant tissues analyzed, nutrient status in biotopes and appropriate bibliography. *** DIRECT SUPPORT *** A01DO054 00003     

Structural and functional domains in human tumour necrosis factors.

Human tumour necrosis factors (hTNFs) alpha and beta are related pleiotropic cytokines which share many activities and compete with each other for binding to two receptor components on many cell types. Although structural and biological data indicate that the active form of hTNF-alpha may be a symmetrical trimer, the manner in which hTNFs interact with their receptors to trigger a myriad of cell type-dependent responses is not clear. A combination of chemical modification, epitope mapping and site-directed mutagenesis approaches suggest that at least four distinct peptide sequences are important for the biological activity of hTNF-alpha. In particular, certain peptide sequences between amino acid positions 11 and 35 in hTNF-alpha appear to be critical for receptor binding and triggering biological responses. The recent cloning of the two hTNF-alpha/beta receptors opens the way for precise mapping of the functional domains in hTNFs.