Protein reservoirs of seeds are amyloid composites employed differentially for germination and seedling emergence.

Seed protein localization in seed storage protein bodies (SSPB) and their significance in germination are well recognized. SSPB are spherical and contain an assembly of water-soluble and salt-soluble proteins. Although the native structures of some SSPB proteins are explored, their structural arrangement to the functional correlation in SSPB remains unknown. SSPB are morphologically analogous to electron-dense amyloid-containing structures reported in other organisms. Here, we show that wheat, mungbean, barley, and chickpea SSPB exhibit a speckled pattern of amyloids interspersed in an amyloid-like matrix along with native structures, suggesting the composite nature of SSPB. This is confirmed by multispectral imaging methods, electron microscopy, infrared, and X-ray diffraction analysis, using in situ tissue sections, ex vivo protoplasts, and in vitro SSPB. Laser capture microdissection coupled with peptide fingerprinting has shown that globulin 1 and 3 in wheat, and 8S globulin and conglycinin in mungbean are the major amyloidogenic proteins. The amyloid composites undergo a sustained degradation during germination and seedling growth, facilitated by an intricate interplay of plant hormones and proteases. These results would lay down the foundation for understanding the amyloid composite structure during SSPB biogenesis and its evolution across the plant kingdom and have implications in both basic and applied plant biology.

Clinical proteomics of enervated neurons.

The dynamic field of neurosciences entails ever increasing search for molecular mechanisms of disease states, especially in the domain of neurodegenerative disorders. The previous century heralded the techniques in proteomics when indexing of the human proteomes relating to various disease conditions became important. Early stage research in certain diseases or pathological conditions requires a more holistic approach of first discovering the proteins of interest for the condition. Despite its limitations, proteomics is one of the most powerful techniques available to us today to dissect the molecular scenario in a particular disease situation. In this review we will discuss about the current clinical research in neurodegenerative disorders that employ proteomics techniques. We will specifically focus on our understanding of Alzheimer's disease, traumatic spinal cord injury and neuromyelitis optica. Discussions will include ongoing worldwide research in these areas, research in India and specifically our laboratory in these domains of neurodegenerative conditions.

Altered levels of amyloid precursor protein intracellular domain-interacting proteins in Alzheimer disease.

BACKGROUND: The amyloid precursor protein intracellular domain (AICD) is an intrinsically unstructured molecule with functional promiscuity that plays an important role in determining the fate of the neurons during its degeneration. Its association with Alzheimer disease (AD) recently played a key role in propelling scientists to choose AICD as a major molecule of interest. Although several studies have been conducted elucidating AICD's participation in inducing neurodegenerative outcomes in AD condition, much remains to be deciphered regarding the linkage of AICD with cellular pathways in the AD scenario. RESULTS: In the present study, we have pulled down interactors of nonphosphorylated AICD from the cerebrospinal fluid of AD subjects, identified them by matrix assisted laser desorption ionization mass spectrometry, and subsequently studied the differential expression of these interactors in AD and control cases by 2-dimensional difference gel electrophoresis. The study has yielded some AICD-interactors that are differentially expressed in the AD cases and are involved in diverse cellular functions. CONCLUSIONS: This proteomic-based approach highlights the first step in finding the possible cellular pathways engaged in AD pathophysiology on the basis of interaction of one or more of their members with AICD.

Differential expression of neuroblastoma cellular proteome due to AICD overexpression.

Amyloid-ß protein precursor intracellular domain (AICD), which exerts intracellular effects by interacting with proteins involved in a plethora of biological processes, is a key player behind the pathophysiology of Alzheimer's disease (AD). Keeping in mind that overwhelming presence of AICD would mimic AD-like conditions in neuroblastoma cell lines, we hypothesized alteration in the proteomic expression pattern in these cells in the presence of AICD compared to their normal proteome. The rationale behind the study was to distinguish between symptomatic pathophysiological effects as opposed to any artifactual consequence due to protein overload in the cell lines. Using 2D-DIGE analysis and MALDI-MS identifications in neuro2A (mouse) and SHSY5Y (human) cell lines, we have identified several proteins belonging to different functional classes and involved in several biological pathways including protein folding, cytoskeletal dynamics, metabolism, and stress. Many of these were being upregulated or downregulated due to AICD effects and could be correlated directly with AD phenotypes.

Effect of gamma irradiation on metallothionein protein expression in Plantago ovata Forsk.

PURPOSE: The effect of gamma rays on metallothionein (MT) expression was studied using the medicinal plant Plantago ovata as the test system. MATERIALS AND METHODS: Western blotting and Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) were used for this purpose. RESULTS: Western blot analysis showed significant induction of metallothionein protein following gamma exposure and that induction was highest at 20 Gy gamma dose. At higher gamma doses (100 Gy) MT expression level declined due to degeneration of cells. MALDI-TOF MS analysis indicated the presence of low molecular weight (7-8 kD) MT molecules following the lower radiation doses. CONCLUSION: It was concluded from the MALDI-TOF MS result that low gamma exposure leads to expression of MT-like protein. At high doses of gamma ray, MT homologues or MT-like protein were not identified, possibly because they might have precipitated due to uncontrolled cross-linking and non-specific aggregation.

Novel adaptors of amyloid precursor protein intracellular domain and their functional implications.

Amyloid precursor protein intracellular domain (AICD) is one of the potential candidates in deciphering the complexity of Alzheimer's disease. It plays important roles in determining cell fate and neurodegeneration through its interactions with several adaptors. The presence or absence of phosphorylation at specific sites determines the choice of partners. In this study, we identified 20 novel AICD-interacting proteins by in vitro pull down experiments followed by 2D gel electrophoresis and MALDI-MS analysis. The identified proteins can be grouped into different functional classes including molecular chaperones, structural proteins, signaling and transport molecules, adaptors, motor proteins and apoptosis determinants. Interactions of nine proteins were further validated either by colocalization using confocal imaging or by co-immunoprecipitation followed by immunoblotting. The cellular functions of most of the proteins can be correlated with AD. Hence, illustration of their interactions with AICD may shed some light on the disease pathophysiology.

"Patch"-ing up the neurons: revival or enervation?

Since its identification Patched1 (Ptch1) has gained importance for playing a cardinal role in developmental patterning through Hedgehog (Hh) pathway, acting as a transmembrane receptor. Involvement of this protein in diverse aspects of the neuronal system, from development to regeneration and protection, including uncontrolled proliferation in oncogenic perspectives, makes it an intriguing candidate for investigation in neurobiology. Stem cell population of adult nervous system is also found to be regulated by Ptch1. Though not elaborately studied, research in this field for the past one decade has suggested a new spectrum of Ptch1 function through an alternative route independent of Hh. In this chapter, the available knowledge about Ptch1 in neuronal system is critically reviewed and further functional insights about this protein are evaluated.

New motifs within the NB-ARC domain of R proteins: probable mechanisms of integration of geminiviral signatures within the host species of Fabaceae family and implications in conferring disease resistance.

The Gemini viruses are a group of plant infectious agents, of which mungbean yellow mosaic India virus (MYMIV) belongs to the bipartite subgroup of Gemini virus and causes serious yield penalty in the leguminous group of plants. In this investigation we have isolated two resistant gene homologues (RGHs; AY301990, AY301991) from two MYMIV-resistant lines of Vigna mungo and V. radiata that have high homology with a MYMIV-resistant linked marker, VMYR1 (AY 297425). These three resistance factors also have similarity with 221 reported R gene/RGH sequences in the NB-ARC domain of the family Fabaceae. NB-ARC domain is an ancient, highly conserved domain of a class of plant disease resistance genes/proteins. Out of 221 in silico translated protein sequences, multialignment of 188 sequences without large insertion or truncation, unlike that of the rest 33, illustrated presence of both TIR and non-TIR subfamilies of NB-ARC domain. A critical analysis of these sequences revealed eight new conserved motifs, in addition to the reported conserved motifs within the NB-ARC domains, which are hitherto not reported. Further analysis of these eight motifs with the aid of PRINTS and PROSITE databases revealed signatures of geminiviral coat protein (GVCP) within the favoured allele, R gene or RGHs. GVCP signatures are absent within the NB-ARC domain of three species of Medicago, which are non-host to Gemini virus. These observations tempted us to predict probable mechanism of integration of GVCP within the plant R gene/RGHs and their implications in conferring geminiviral disease resistance to the host plants. Our conjecture is that these signatures were integrated during plant pathogen interaction and are being maintained within this conserved domain through active selection of the favoured allele. We comprehensively addressed the biological significance of GVCP signatures, which probably provides additional defense against Gemini viruses through degradation of homologous transcript of the virus.