Molecular cloning and characterisation of a Rab-binding GDP-dissociation inhibitor from Medicago truncatula

Salt-induced expression of intracellular vesicle trafficking genes, CaRab-GTP, and their association with Na+ accumulation in leaves of chickpea (Cicer arietinum L.)

BACKGROUND

Chickpea is an important legume and is moderately tolerant to salinity stress during the growing season. However, the level and mechanisms for salinity tolerance can vary among accessions and cultivars. A large family of CaRab-GTP genes, previously identified in chickpea, is homologous to intracellular vesicle trafficking superfamily genes that play essential roles in response to salinity stress in plants.

RESULTS

To determine which of the gene family members are involved in the chickpea salt response, plants from six selected chickpea accessions (Genesis 836, Hattrick, ICC12726, Rupali, Slasher and Yubileiny) were exposed to salinity stress and expression profiles resolved for the major CaRab-GTP gene clades after 5, 9 and 15 days of salt exposure. Gene clade expression profiles (using degenerate primers targeting all members of each clade) were tested for their relationship to salinity tolerance measures, namely plant biomass and Na⁺ accumulation. Transcripts representing 11 out of the 13 CaRab clades could be detected by RT-PCR, but only six (CaRabA2, -B, -C, -D, -E and -H) could be quantified using qRT-PCR due to low expression levels or poor amplification efficiency of the degenerate primers for clades containing several gene members. Expression profiles of three gene clades, CaRabB, -D and -E, were very similar across all six chickpea accessions, showing a strongly coordinated network. Salt-induced enhancement of CaRabA2 expression at 15 days showed a very strong positive correlation (R² = 0.905) with Na⁺ accumulation in leaves. However, salinity tolerance estimated as relative plant biomass production compared to controls, did not correlate with Na⁺ accumulation in leaves, nor with expression profiles of any of the investigated CaRab-GTP genes.

CONCLUSION

A coordinated network of CaRab-GTP genes, which are likely involved in intracellular trafficking, are important for the salinity stress response of chickpea plants.

Intracellular Vesicle Trafficking Genes, RabC-GTP, Are Highly Expressed Under Salinity and Rapid Dehydration but Down-Regulated by Drought in Leaves of Chickpea (Cicer arietinum L.)

Intracellular vesicle trafficking genes, Rab, encoding small GTP binding proteins, have been well studied in medical research, but there is little information concerning these proteins in plants. Some sub-families of the Rab genes have not yet been characterized in plants, such as RabC - otherwise known as Rab18 in yeast and animals. Our study aimed to identify all CaRab gene sequences in chickpea (Cicer arietinum L.) using bioinformatics approaches, with a particular focus on the CaRabC gene sub-family since it featured in an SNP database. Five isoforms of the CaRabC gene were identified and studied: CaRabC-1a, -1b, -1c, -2a and -2a∗ . Six accessions of both Desi and Kabuli ecotypes, selected from field trials, were tested for tolerance to abiotic stresses, including salinity, drought and rapid dehydration and compared to plant growth under control conditions. Expression analysis of total and individual CaRabC isoforms in leaves of control plants revealed a very high level of expression, with the greatest contribution made by CaRabC-1c. Salinity stress (150 mM NaCl, 12 days in soil) caused a 2-3-fold increased expression of total CaRabC compared to controls, with the highest expression in isoforms CaRabC-1c, -2a∗ and -1a. Significantly decreased expression of all five isoforms of CaRabC was observed under drought (12 days withheld water) compared to controls. In contrast, both total CaRabC and the CaRabC-1a isoform showed very high expression (up-to eight-fold) in detached leaves over 6 h of dehydration. The results suggest that the CaRabC gene is involved in plant growth and response to abiotic stresses. It was highly expressed in leaves of non-stressed plants and was down-regulated after drought, but salinity and rapid dehydration caused up-regulation to high and very high levels, respectively. The isoforms of CaRabC were differentially expressed, with the highest levels recorded for CaRabC-1c in controls and under salinity stress, and for CaRabC-1a - in rapidly dehydrated leaves. Genotypic variation in CaRabC-1a, comprising eleven SNPs, was found through sequencing of the local chickpea cultivar Yubileiny and germplasm ICC7255 in comparison to the two fully sequenced reference accessions, ICC4958 and Frontier. Amplifluor-like markers based on one of the identified SNPs in CaRabC-1a were designed and successfully used for genotyping chickpea germplasm.

Involvement of SchRabGDI1 from Solanum chilense in endocytic trafficking and tolerance to salt stress

Physiological responses of plants to salinity stress requires the coordinated activation of many genes. A salt-induced gene was isolated from roots of the wild tomato species Solanum chilense and named SchRabGDI1 because it encodes a protein with high identity to GDP dissociation inhibitors of plants. These proteins are regulators of the RabGTPase cycle that play key roles in intracellular vesicular trafficking. The expression pattern of SchRabGDI1 showed an early up-regulation in roots and leaves under salt stress. Functional activity of SchRabGDI1 was shown by restoring the defective phenotype of the yeast sec19-1 mutant and the capacity of SchRabGDI1 to interact with RabGTPase was demonstrated through BiFC assays. Expression of SchRabGDI1 in Arabidopsis thaliana plants resulted in increased salt tolerance. Also, the root cells of transgenic plants showed higher rate of endocytosis under normal growth conditions and higher accumulation of sodium in vacuoles and small vesicular structures under salt stress than wild type. Our results suggest that in salt tolerant species such as S. chilense, bulk endocytosis is one of the early mechanisms to avoid salt stress, which requires the concerted expression of regulatory genes involved in vesicular trafficking of the endocytic pathway.

Bacterial-induced expression of RAB18 protein in Orzya sativa salinity stress and insights into molecular interaction with GTP ligand

In the present research, we have studied the inoculation effects of two root-associated plant growth-promoting rhizobacteria (PGPR) in rice and provide the pieces of evidence that the inoculation of the PGPR could potentially result in inducing the expression of the salt stress-related RAB18 plant gene under varying degrees of salinity stress. The sequenced putative gene of RAB18 of Oryza sativa in this study is 740 bp long, has a content of 44.4%, and a molecular weight of 492 102.00 Da. BLAST homology patterns revealed sequence similarity with the previously sequenced RAB in model plant species. We demonstrate the mode of action of this stress-related protein by performing comparative modeling of Q10RT8 (Os03g0146000 protein, homolog of the sequenced RAB18; O. sativa subsp. japonica) using energy minimization, molecular dynamic simulations, and molecular docking of a guanosine triphosphate (GTP) ligand with the protein. The docking results indicated that Ser21, Ala22, Lys25, Asp68, Ala70, Glu73, and Arg74 are important determinant residues for functional interaction with the GTP ligand. The present research contributes to the understanding of the PGPR inoculation in salinity stress. Additionally, it provides the layout of the understanding of the molecular interactions between RAB and GTP ligand.

Survey of the year 2005 commercial optical biosensor literature

We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.