The N-terminal region of Arabidopsis cystathionine gamma-synthase plays an important regulatory role in methionine metabolism

Cystathionine gamma-synthase (CGS) is a key enzyme of Met biosynthesis in bacteria and plants. Aligning the amino acid sequences revealed that the plant enzyme has an extended N-terminal region that is not found in the bacterial enzyme. However, this region is not essential for the catalytic activity of this enzyme, as deduced from the complementation test of an Escherichia coli CGS mutant. To determine the function of this N-terminal region, we overexpressed full-length Arabidopsis CGS and its truncated version that lacks the N-terminal region in transgenic tobacco (Nicotiana tabacum) plants. Transgenic plants expressing both types of CGS had a significant higher level of Met, S-methyl-Met, and Met content in their proteins. However, although plants expressing full-length CGS showed the same phenotype and developmental pattern as wild-type plants, those expressing the truncated CGS showed a severely abnormal phenotype. These abnormal plants also emitted high levels of Met catabolic products, dimethyl sulfide and carbon disulfide. The level of ethylene, the Met-derived hormone, was 40 times higher than in wild-type plants. Since the alien CGS was expressed at comparable levels in both types of transgenic plants, we further suggest that post-translational modification(s) occurs in this N-terminal region, which regulate CGS and/or Met metabolism. More specifically, since the absence of the N-terminal region leads to an impaired Met metabolism, the results further suggest that this region plays a role in protecting plants from a high level of Met catabolic products such as ethylene.     

The neuronal class 2 TSR proteins F-spondin and Mindin: a small family with divergent biological activities

F-spondin and Mindin are members of a subgroup of the thrombospondin type 1 (TSR) class molecules, defined by two domains of homology, the FS1/FS2 and TSR domains. The TSRs of F-spondin proteins are typical of class 2 TSRs. F-spondin and Mindin are evolutionarily conserved proteins. The embryonic expression of the vertebrate genes is enriched in the nervous system, mainly at the floor plate and the hippocampus. Similar to thrombospondin, F-spondin and Mindin are extracellular matrix attached molecules that promote neurite outgrowth and inhibit angiogenesis. Analysis of gain and loss of function experiments reveal that F-spondin is required for accurate pathfinding of embryonic axons. F-spondin plays a dual role in patterning axonal trajectories: it promotes the outgrowth of commissural and inhibits the outgrowth of motor axons. Macrophages of Mindin-deficient mice exhibit defective responses to a broad spectrum of microbial stimuli. This may implicate Mindin and F-spondin in inflammatory processes in the nervous system.     

A structure-based approach for prediction of MHC-binding peptides

Identification of immunodominant peptides is the first step in the rational design of peptide vaccines aimed at T-cell immunity. The advances in sequencing techniques and the accumulation of many protein sequences without the purified protein challenge the development of computer algorithms to identify dominant T-cell epitopes based on sequence data alone. Here, we focus on antigenic peptides recognized by cytotoxic T cells. The selection of T-cell epitopes along a protein sequence is influenced by the specificity of each of the processing stages that precede antigen presentation. The most selective of these processing stages is the binding of the peptides to the major histocompatibility complex molecules, and therefore many of the predictive algorithms focus on this stage. Most of these algorithms are based on known binding peptides whose sequences have been used for the characterization of binding motifs or profiles. Here, we describe a structure-based algorithm that does not rely on previous binding data. It is based on observations from crystal structures that many of the bound peptides adopt similar conformations and placements within the MHC groove. The algorithm uses a structural template of the peptide in the MHC groove upon which peptide candidates are threaded and their fit to the MHC groove is evaluated by statistical pairwise potentials. It can rank all possible peptides along a protein sequence or within a suspected group of peptides, directing the experimental efforts towards the most promising peptides. This approach is especially useful when no previous peptide binding data are available.     

Structure-function relations of interactions between Na,K-ATPase,the gamma subunit,and corticosteroid hormone-induced factor

Corticosteroid hormone-induced factor (CHIF) and the gamma subunit of the Na,K-ATPase (gamma) are two members of the FXYD family whose function has been elucidated recently. CHIF and gamma interact with the Na+ pump and alter its kinetic properties, in different ways, which appear to serve their specific physiological roles. Although functional interactions with the Na,K-ATPase have been clearly demonstrated, it is not known which domains and which residues interact with the alpha and/or beta subunits and affect the pump kinetics. The current study provides the first systematic analysis of structure-function relations of CHIF and gamma. It is demonstrated that the stability of detergent-solubilized complexes of CHIF and gamma with alpha and/or beta subunits is determined by the trans-membrane segments, especially three residues that may be involved in hydrophobic interactions. The transmembrane segments also determine the opposite effects of CHIF and gamma on the Na+ affinity of the pump, but the amino acids involved in this functional effect are different from those responsible for stable interactions with alpha.     

Subcloning,expression, purification,and characterization of recombinant human leptin-binding domain

A subdomain of the human leptin receptor encoding part of the extracellular domain (amino acids 428 to 635) was subcloned, expressed in a prokaryotic host, and purified to homogeneity, as evidenced by SDS-PAGE, with over 95% monomeric protein. The purified leptin-binding domain (LBD) exhibited the predicted beta structure, was capable of binding human, ovine, and chicken leptins, and formed a stable 1:1 complex with all mammalian leptins. The binding kinetics, assayed by surface plasmon resonance methodology, showed respective k(on) and k(off) values (mean +/- S.E.) of 1.20 +/- 0.23 x 10(-5) mol(-1) s(-1) and 1.85 +/- 0.30 x 10(-3) s(-1) and a K(d) value of 1.54 x 10(-8) m. Similar results were achieved with conventional binding experiments. LBD blocked leptin-induced, but not interleukin-3-induced, proliferation of BAF/3 cells stably transfected with the long form of human leptin receptor. The modeled LBD structure and the known three-dimensional structure of human leptin were used to construct a model of 1:1 LBD.human leptin complex. Two main residues, Phe-500, located in loop L3, and Tyr-441, located in L1, are suggested to contribute to leptin binding.     

The COP9 signalosome is vital for timely repair of DNA double-strand breaks

The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ring ubiquitin ligase (CRL) complexes by removing the ubiquitin-like protein, NEDD8, from their cullin scaffold. We find that the CSN is physically recruited to DSB sites in a neddylation-dependent manner, and is required for timely repair of DSBs, affecting the balance between the two major DSB repair pathways—nonhomologous end-joining and homologous recombination repair (HRR). The CSN is essential for the processivity of deep end-resection—the initial step in HRR. Cullin 4a (CUL4A) is recruited to DSB sites in a CSN- and neddylation-dependent manner, suggesting that CSN partners with CRL4 in this pathway. Furthermore, we found that ATM-mediated phosphorylation of CSN subunit 3 on S410 is critical for proper DSB repair, and that loss of this phosphorylation site alone is sufficient to cause a DDR deficiency phenotype in the mouse. This novel branch of the DSB response thus significantly affects genome stability.