The role of active site arginines of sorghum NADP-malate dehydrogenase in thioredoxin-dependent activation and activity

Probing protein structure by amino acid-specific covalent labeling and mass spectrometry

For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies.

Thioredoxins in chloroplasts

Thioredoxins (TRXs) are small disulfide oxidoreductases of ca. 12 kDa found in all free living organisms. In plants, two chloroplastic TRXs, named TRX f and TRX m, were originally identified as light dependent regulators of several carbon metabolism enzymes including Calvin cycle enzymes. The availability of genome sequences revealed an unsuspected multiplicity of TRXs in photosynthetic eukaryotes, including new chloroplastic TRX types. Moreover, proteomic approaches and focused studies allowed identification of 90 potential chloroplastic TRX targets. Lately, recent studies suggest the existence of a complex interplay between TRXs and other redox regulators such as glutaredoxins (GRXs) or glutathione. The latter is involved in a post-translational modification, named glutathionylation that could be controlled by GRXs. Glutathionylation appears to specifically affect the activity of TRX f and other chloroplastic enzymes and could thereby constitute a previously undescribed regulatory mechanism of photosynthetic metabolism under oxidative stress. After summarizing the initial studies on TRX f and TRX m, this review will focus on the most recent developments with special emphasis on the contributions of genomics and proteomics to the field of TRXs. Finally, new emerging interactions with other redox signaling pathways and perspectives for future studies will also be discussed.

Use of the arginine-specific butanedione/phenylboronic acid tag for analysis of peptides and protein digests using matrix-assisted laser desorption/ionization mass spectrometry

We have applied an arginine-specific labeling technique to the study of peptides by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The reaction converts the guanidine group of the arginine side chain by reacting it with 2,3-butanedione and an arylboronic acid. Despite the general chemical lability of the tag under acidic conditions, it was possible to employ acidic matrices like alpha-cyano-4-hydroxycinnamic acid without adverse effects, using the thin-layer technique for preparation. After optimizing the method using arginine-containing model peptides--for which sensitivity down to the low fmol range was demonstrated--the procedure was applied to enzymatic digests of several model proteins in solution and to protein spots in gels obtained by two-dimensional electrophoretic separation of cell lysate samples. Information on the presence of arginine in peptides can be easily obtained from the mass spectra by the characteristic mass shift and the isotope pattern resulting from the incorporation of boron. This information might serve as a valuable additional search constraint for achieving a higher degree of confidence for protein identification by peptide mass fingerprinting.

Transferring redox regulation properties from sorghum NADP-malate dehydrogenase to Thermus NAD-malate dehydrogenase

NADP-dependent chloroplastic malate dehydrogenase (E.C.1.1.1.82) is regulated by thiol disulfide-interchange with thioredoxin. It displays two regulatory disulfides per subunit, located in specific sequence extensions respectively at the N- and C-terminal ends of each subunit. In the present study, attempts were made to transfer the regulatory properties of sorghum NADP-malate dehydrogenase to a constitutively active NAD-dependent malate dehydogenase (E.C.1.1.1.37) from the thermophilic bacteria Thermus flavus, by grafting the regulatory extensions of the former to the latter. The results demonstrate that a successful transfer of redox regulation properties requires the grafting of both full-length extensions, but also the introduction of specific hydrophobic residues in the core part of the protein. These residues are very likely involved in the interaction between monomers, and structural changes at the active site.

NADP-malate dehydrogenase gene evolution in Andropogoneae (Poaceae): gene duplication followed by sub-functionalization

BACKGROUND AND AIMS

Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C4 plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C3; Erhartoideae) and maize (C4; Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C4; Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C4 isoform has evolved over a broader range of panicoid grasses.

METHODS

Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios. Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach.

KEY RESULTS

Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II.

CONCLUSIONS

It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C4 isoform as previously suggested. Nevertheless, some C4 species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C4 photosynthesis but are not required in every case.

Calcium transport by sarcoplasmic reticulum Ca(2+)-ATPase. Role of the A domain and its C-terminal link with the transmembrane region

After treatment of sarcoplasmic reticulum Ca(2+)-ATPase with proteinase K (PK) in the presence of Ca(2+) and a protecting non-phosphorylated ligand (e.g. adenosine 5'-(beta,gamma-methylenetriphosphate), we were able to prepare in high yield an ATPase species that only differs from intact ATPase because of excision of the MAATE(243) sequence from the loop linking the A domain with the third transmembrane segment. The PK-treated ATPase was unable to transport Ca(2+) and to catalyze ATP hydrolysis, but it could bind two calcium ions with high affinity and react with ATP to form a classical ADP-sensitive phosphoenzyme, Ca(2)E1P, with occluded Ca(2+). The ability of Ca(2)E1P to become converted to the Ca(2+)-free ADP-insensitive form, E2P, was strongly reduced, as was the ability of PK-treated ATPase to react with orthovanadate or to form an E2P intermediate from inorganic phosphate in the absence of Ca(2+). PK-treated ATPase also reacted with thapsigargin to form a complex with altered properties, and the tryptic cleavage "T2" site in the A domain was no longer protected in the absence of Ca(2+). It is probable that disrupting the C-terminal link of the A domain with the transmembrane region severely compromises reorientation of A and P domains and the functionally critical cross-talk of these domains with the membrane-bound Ca(2+) ions.