Bowman-Birk inhibitors in Lens: identification and characterization of two paralogous gene classes in cultivated lentil and wild relatives

Allele mining through TILLING and EcoTILLING approaches in vegetable crops

MAIN CONCLUSION

The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops. Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.

Lens culinaris Medik. seed proteome: analysis to identify landrace markers

Unlike modern cultivars selected for their growth performances in specific environmental conditions, local landraces have a high genetic variability that is an important resource for plant breeding. Consequent to their high adaptation to different environmental conditions, these landraces may have evolved adaptive gene complexes To promote the survival of endangered lentil landraces, we previously investigated the genetic relationship between two ancient landraces cultivated in the Molise region (Capracotta and Conca Casale, south-central Italy) and widely spread commercial varieties using an integrated approach consisting of morphological, DNA and protein characterization. In the present study, we used a proteomic approach to compare the mature seed proteomes of the Capracotta and Conca Casale lentil landraces. Multivariate analysis of 145 differentially expressed protein spots demonstrated that 52 proteins are required to discriminate among the two landraces. Therefore, these 52 proteins can be considered "landrace markers". The results of this study show that the combination of proteomics and multivariate analysis can be used to identify physiological and/or environmental markers, and is thus a powerful tool that complements the analysis of biodiversity in plant ecotypes.

Isolation and characterization of novel variants of BBI coding genes from the legume Lathyrus sativus

A pool of twelve cDNA sequences coding for Bowman-Birk inhibitors (BBIs) was identified in the legume grass pea (Lathyrus sativus L.). The corresponding amino acid sequences showed a canonical first anti-trypsin domain, predicted according to the identity of the determinant residue P(1). A more variable second binding loop was observed allowing to identify three groups based on the identity of residue P(1): two groups (Ls_BBI_1 and Ls_BBI_2) carried a second reactive site specific for chymotrypsin, while a third group (Ls_BBI_3) was predicted to inhibit elastase. A fourth variant carrying an Asp in the P(1) position of the second reactive site was identified only from genomic DNA. A phylogenetic tree constructed using grass pea BBIs with their homologs from other legume species revealed grouping based on taxonomy and on specificity of the reactive sites. Five BBI sequences, representing five different second reactive sites, were heterologously expressed in the yeast Pichia pastoris. The recombinant proteins demonstrated to be active against trypsin, while three of them were also active against chymotrypsin, and one against human leukocyte elastase. Comparative modeling and protein docking were used to further investigate interactions between two grass pea BBI isoforms and their target proteases. Thus two reliable 3D models have been proposed, representing two potential ternary complexes, each constituted of an inhibitor and its target enzymes.

The cytotoxic effect of Bowman-Birk isoinhibitors, IBB1 and IBBD2, from soybean (Glycine max) on HT29 human colorectal cancer cells is related to their intrinsic ability to inhibit serine proteases

Bowman-Birk inhibitors (BBI) from soybean and related proteins are naturally occurring protease inhibitors with potential health-promoting properties within the gastrointestinal tract. In this work, we have investigated the effects of soybean BBI proteins on HT29 colon adenocarcinoma cells, compared with non-malignant colonic fibroblast CCD-18Co cells. Two major soybean isoinhibitors, IBB1 and IBBD2, showing considerable amino acid sequence divergence within their inhibitory domains, were purified in order to examine their functional properties, including their individual effects on the proliferation of HT29 colon cancer cells. IBB1 inhibited both trypsin and chymotrypsin whereas IBBD2 inhibited trypsin only. Despite showing significant differences in their enzyme inhibitory properties, the median inhibitory concentration values determined for IBB1 and IBBD2 on HT29 cell growth were not significantly different (39.9+/-2.3 and 48.3+/-3.5 microM, respectively). The cell cycle distribution pattern of HT29 colon cancer cells was affected by BBI treatment in a dose-dependent manner, with cells becoming blocked in the G0-G1 phase. Chemically inactive soybean BBI had a weak but non-significant effect on the proliferation of HT29 cells. The anti-proliferative properties of BBI isoinhibitors from soybean reveal that both trypsin- and chymotrypsin-like proteases involved in carcinogenesis should be considered as potential targets of BBI-like proteins.

Inhibitory properties and solution structure of a potent Bowman-Birk protease inhibitor from lentil (Lens culinaris, L) seeds

Bowman-Birk serine protease inhibitors are a family of small plant proteins, whose physiological role has not been ascertained as yet, while chemopreventive anticarcinogenic properties have repeatedly been claimed. In this work we present data on the isolation of a lentil (Lens culinaris, L., var. Macrosperma) seed trypsin inhibitor (LCTI) and its functional and structural characterization. LCTI is a 7448 Da double-headed trypsin/chymotrypsin inhibitor with dissociation constants equal to 0.54 nM and 7.25 nM for the two proteases, respectively. The inhibitor is, however, hydrolysed by trypsin in a few minutes timescale, leading to a dramatic loss of its affinity for the enzyme. This is due to a substantial difference in the kon and k*on values (1.1 microM-1.s-1 vs. 0.002 microM-1.s-1), respectively, for the intact and modified inhibitor. A similar behaviour was not observed with chymotrypsin. The twenty best NMR structures concurrently showed a canonical Bowman-Birk inhibitor (BBI) conformation with two antipodal beta-hairpins containing the inhibitory domains. The tertiary structure is stabilized by ion pairs and hydrogen bonds involving the side chain and backbone of Asp10-Asp26-Arg28 and Asp36-Asp52 residues. At physiological pH, the final structure results in an asymmetric distribution of opposite charges with a negative electrostatic potential, centred on the C-terminus, and a highly positive potential, surrounding the antitryptic domain. The segment 53-55 lacks the anchoring capacity found in analogous BBIs, thus rendering the protein susceptible to hydrolysis. The inhibitory properties of LCTI, related to the simultaneous presence of two key amino acids (Gln18 and His54), render the molecule unusual within the natural Bowman-Birk inhibitor family.

A continent of plant defense peptide diversity: cyclotides in Australian Hybanthus (Violaceae)

Cyclotides are plant-derived miniproteins that have the unusual features of a head-to-tail cyclized peptide backbone and a knotted arrangement of disulfide bonds. It had been postulated that they might be an especially large family of host defense agents, but this had not yet been tested by field data on cyclotide variation in wild plant populations. In this study, we sampled Australian Hybanthus (Violaceae) to gain an insight into the level of variation within populations, within species, and between species. A wealth of cyclotide diversity was discovered: at least 246 new cyclotides are present in the 11 species sampled, and 26 novel sequences were characterized. A new approach to the discovery of cyclotide sequences was developed based on the identification of a conserved sequence within a signal sequence in cyclotide precursors. The number of cyclotides in the Violaceae is now estimated to be >9000. Cyclotide physicochemical profiles were shown to be a useful taxonomic feature that reflected species and their morphological relationships. The novel sequences provided substantial insight into the tolerance of the cystine knot framework in cyclotides to amino acid substitutions and will facilitate protein engineering applications of this framework.