Genome-wide identification and structure-function studies of proteases and protease inhibitors in Cicer arietinum (chickpea)

Sharma, Ranu; Suresh, C.G.

doi:10.1016/j.compbiomed.2014.10.019

Cited by 9 publications

(4 citation statements)

References 36 publications

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“…The in silico research using bioinformatics tools are a rational approach to find interesting findings 23 – 25 . In silico searches of many plant genomes or proteomes was conducted to find abiotic stress responsive genes like NRAMP genes in Glycine max 26 , glutathione S-transferase genes in Vigna radiata L. 27 , proteases in Cicer arietinum 28 and so on.…”

Section: Discussionmentioning

confidence: 99%

Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)

Urwat

Ahmad

Masi

et al. 2021

Sci Rep

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Iron (Fe) and zinc (Zn) stress significantly affects fundamental metabolic and physiological processes in plants that results in reduction of plant growth and development. In the present study, common bean variety; Shalimar French Bean-1 (SFB-1) was used as an experimental material. Four different MGRL media i.e. normal MGRL medium (Control), media without Fe (0-Fe), media without Zn (0-Zn) and media with excess Zn (300-Zn) were used for growing seeds of SFB-1 under in vitro condition for three weeks under optimum conditions. Three week old shoot and root tissues were harvested from the plants grown in these four different in vitro conditions and were, subjected to Fe and Zn estimation. Further, extraction of total RNA for differential gene expression of ten candidate genes selected based on our in silico investigation and their classification, phylogeny and expression pattern was unraveled. Expression analysis of three candidate genes (OPT3, NRAMP2 and NRAMP3) in roots revealed possible cross talk among Fe/Zn stress that was further confirmed by observing less accumulation of Fe in roots under both these conditions. However, we observed, higher accumulation of Fe in shoots under 0-Fe condition compared to control that suggests precise sensing for priority based compartmentalization and partitioning leading to higher accumulation of Fe in shoots. Furthermore, the expression analysis of IRT1, FRO1 and Ferritin 1 genes under Fe/Zn stress suggested their role in uptake/transport and signaling of Fe and Zn, whereas the expression of ZIP2, NRAMP1, HA2 and GLP1 genes were highly responsive to Zn in Phaseolus vulgaris. The identified genes highly responsive to Fe and Zn stress condition can be potential candidates for overcoming mineral stress in dicot crop plants.

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Section: Discussionmentioning

confidence: 99%

Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)

Urwat

Ahmad

Masi

et al. 2021

Sci Rep

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“…However, we also noted some differences/discrepancies, particularly with respect to particular gene families that possess many members (e.g., A01, C01 and M12). This may relate to gene family expansions during the course of evolution [91][92][93], which would/could have facilitated adaptation to the unique parasitic lifestyle of H. contortus. Therefore, members of these families may be potential intervention targets, warranting future investigation.…”

Section: Key Protease Gene Families Associate With Key Biological Fun...mentioning

confidence: 99%

Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

Zheng,

Young,

Song

et al. 2023

IJMS

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Biodiversity within the animal kingdom is associated with extensive molecular diversity. The expansion of genomic, transcriptomic and proteomic data sets for invertebrate groups and species with unique biological traits necessitates reliable in silico tools for the accurate identification and annotation of molecules and molecular groups. However, conventional tools are inadequate for lesser-known organismal groups, such as eukaryotic pathogens (parasites), so that improved approaches are urgently needed. Here, we established a combined sequence- and structure-based workflow system to harness well-curated publicly available data sets and resources to identify, classify and annotate proteases and protease inhibitors of a highly pathogenic parasitic roundworm (nematode) of global relevance, called Haemonchus contortus (barber’s pole worm). This workflow performed markedly better than conventional, sequence-based classification and annotation alone and allowed the first genome-wide characterisation of protease and protease inhibitor genes and gene products in this worm. In total, we identified 790 genes encoding 860 proteases and protease inhibitors representing 83 gene families. The proteins inferred included 280 metallo-, 145 cysteine, 142 serine, 121 aspartic and 81 “mixed” proteases as well as 91 protease inhibitors, all of which had marked physicochemical diversity and inferred involvements in >400 biological processes or pathways. A detailed investigation revealed a remarkable expansion of some protease or inhibitor gene families, which are likely linked to parasitism (e.g., host–parasite interactions, immunomodulation and blood-feeding) and exhibit stage- or sex-specific transcription profiles. This investigation provides a solid foundation for detailed explorations of the structures and functions of proteases and protease inhibitors of H. contortus and related nematodes, and it could assist in the discovery of new drug or vaccine targets against infections or diseases.

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“…A single serpin gene was also reported in the Chlamydomonas reinhardtii (Location: Chlre3/ scaffold_28:1327628-1332277). However, 3 serpin genes were identified in chickpea genome database (Sharma et al 2015), whereas in cereals higher numbers of serpins were identified.In rice 14 serpin genes were identified, three of which encoded non inhibitory serpins but in Arabidopsis genome 7 serpin genes of inhibitory type were present (Francis et al 2012). A total of 189 serpin genes were reported in wheat genome database (Appels et al 2018, Ramirez Gonzalez et al 2018, Borrill et al 2016.…”

Section: Identification Of Serpin Membersmentioning

confidence: 99%

Identification and in-silico characterization of Serpin genes in legumes genomes

et al. 2020

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Serine protease inhibitors (serpins) are a unique family of protease inhibitor containing mobile reactive center loop. The availability of genome sequences of pigeonpea, soybean, commanbean, cowpea, mungbean and adzuki bean provided an opportunity to search for the serpin genes. A total of seven serpin genes were identified in the above legume genomes. Phylogenetic analysis of legume serpins, devided them into two major clades (Clade-I:VanSerpin, VraSerpin, VunSerpin, PvuSerpin and clade-II: GmaSerpin1, GmaSerpin2 and CcaSerpin) based on conserved reactive center (P2-P1’), domains and exon-intron boundary in the gene structure. The common reactive center of all the seven serpins indicated their ability to target cognate proteases and play an important role in response to insects, fungal pathogens and also the drought.

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Genome-wide identification and structure-function studies of proteases and protease inhibitors in Cicer arietinum (chickpea)

Cited by 9 publications

References 36 publications

Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)

Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)

Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

Identification and in-silico characterization of Serpin genes in legumes genomes

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