In silico identification and expression of SLC30 family genes: An expressed sequence tag data mining strategy for the characterization of zinc transporters' tissue expression

Background: The protozoan Giardia duodenalis, which causes giardiasis, is an intestinal parasite that commonly affects humans, mainly pre-school children. Although there are asymptomatic cases, the main clinical features are chronic and acute diarrhea, nausea, abdominal pain, and malabsorption syndrome. Little is currently known about the virulence of the parasite, but some cases of chronic gastrointestinal alterations post-infection have been reported even when the infection was asymptomatic, suggesting that the cathepsin L proteases of the parasite may be involved in the damage at the level of the gastrointestinal mucosa. Objective: The aim of this study was the in silico identification and characterization of extracellular cathepsin L proteases in the proteome of G. duodenalis. Methods: The NP_001903 sequence of cathepsin L protease from Homo sapienswas searched against the Giardia duodenalisproteome. The subcellular localization of Giardia duodenaliscathepsin L proteases was performed in the DeepLoc-1.0 server. The construction of a phylogenetic tree of the extracellular proteins was carried out using the Molecular Evolutionary Genetics Analysis software (MEGA X). The Robetta server was used for the construction of the three-dimensional models. The search for possible inhibitors of the extracellular cathepsin L proteases of Giardia duodenaliswas performed by entering the three-dimensional structures in the FINDSITEcomb drug discovery tool. Results: Based on the amino acid sequence of cathepsin L from Homo sapiens, 8 protein sequences were identified that have in their modular structure the Pept_C1A domain characteristic of cathepsins and two of these proteins (XP_001704423 and XP_001704424) are located extracellularly. Threedimensional models were designed for both extracellular proteins and several inhibitory ligands with a score greater than 0.9 were identified. In vitrostudies are required to corroborate if these two extracellular proteins play a role in the virulence of Giardia duodenalisand to discover ligands that may be useful as therapeutic targets that interfere in the mechanism of pathogenesis generated by the parasite. Conclusion: In silicoanalysis identified two proteins in the Giardia duodenalisprotein repertoire whose characteristics allowed them to be classified as cathepsin L proteases, which may be secreted into the extracellular medium to act as virulence factors. Three-dimensional models of both proteins allowed the identification of inhibitory ligands with a high score. The results suggest that administration of those compounds might be used to block the endopeptidase activity of the extracellular cathepsin L proteases, interfering with the mechanisms of pathogenesis of the protozoan parasite Giardia duodenalis.

Download Full-text

Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species

Botany ◽

10.1139/b10-019 ◽

2010 ◽

Vol 88 (5) ◽

pp. 537-543 ◽

Cited By ~ 11

Author(s):

Yong-Bi Fu ◽

Gregory W. Peterson

Keyword(s):

Simple Sequence Repeat ◽

Expressed Sequence Tag ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Linum Usitatissimum L ◽

Evolutionary Studies ◽

Expressed Sequence ◽

Simple Sequence ◽

Cultivated Flax

One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.

Download Full-text

Dissecting the sugarcane expressed sequence tag (SUCEST) database: unraveling flower-specific genes

Genetics and Molecular Biology ◽

10.1590/s1415-47572001000100012 ◽

2001 ◽

Vol 24 (1-4) ◽

pp. 77-84 ◽

Cited By ~ 4

Author(s):

R.C. Figueiredo ◽

M.S. Brito ◽

L.H.M. Figueiredo ◽

A.C. Quiapin ◽

P.M. Vitorelli ◽

...

Keyword(s):

Expressed Sequence Tag ◽

Tissue Expression ◽

Reproductive Organs ◽

Cdna Libraries ◽

Computer Assisted ◽

Transcript Accumulation ◽

Gene Encoding ◽

Assisted Analysis ◽

Expressed Sequence ◽

Different Tissues

There are almost 260,000 independent clones sequenced from the 5’ end in the Sugarcane Expressed Sequence Tag (SUCEST) database, which have been obtained from 37 cDNA libraries prepared from different tissues. This large number of expressed sequence tags (ESTs) provides an opportunity, unprecedented in plants, to perform ‘digital differential screening’ on selected cDNA libraries. In general, the frequency of a particular EST correlates with transcript accumulation in the tissues from which the cDNA libraries were constructed, so it is possible to compare the whole transcriptome from different tissues using computer-assisted analysis of an EST database. In our research we analyzed sugarcane ESTs according to tissue expression and identified more than 1,000 putative flower-specific genes. The fact that using this technique we were able to identify sugarcane homologues of several genes previously described as pollen-specific justifies this method of assessing tissue specificity. In addition, ESTs similar to genes specific to reproductive organs were detected e.g. a sugarcane gene encoding a meiotic protein essential for assembly of the synaptonemal complex and normal synapsis. This approach also allowed the identification of many flower-specific anonymous sequences that are good candidates for being novel genes involved in plant reproduction. This paper describes the analysis of the gene expression levels of 24 EST clusters during flower development using a ‘digital northern blot’ constructed from direct EST counts made on the non-normalized sugarcane cDNA libraries.

Download Full-text

In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.

Scientific Reports ◽

10.1038/s41598-018-34982-8 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 2

Author(s):

Wuhe Jike ◽

Gaurav Sablok ◽

Giorgio Bertorelle ◽

Mingai Li ◽

Claudio Varotto

Keyword(s):

In Silico ◽

Arundo Donax ◽

Bioenergy Crop ◽

In Silico Identification ◽

Identification And Characterization ◽

Arundo Donax L

Download Full-text

In silico identification and characterization of sensory motifs in the transcriptional regulators of the ArsR-SmtB family

Metallomics ◽

10.1039/c8mt00082d ◽

2018 ◽

Vol 10 (10) ◽

pp. 1476-1500 ◽

Cited By ~ 4

Author(s):

Rima Roy ◽

Saikat Samanta ◽

Surajit Patra ◽

Nav Kumar Mahato ◽

Rudra P. Saha

Keyword(s):

In Silico ◽

Transcriptional Regulators ◽

Transcriptional Repressors ◽

Structural Elements ◽

In Silico Identification ◽

Metal Efflux ◽

Identification And Characterization ◽

Secondary Structural Elements ◽

Efflux Proteins

The ArsR-SmtB family of transcriptional repressors regulates the transcription of metal-efflux proteins by binding specific metals at a variety of secondary structural elements, called motifs, on the surface of the proteins.

Download Full-text

Identification of metalloprotease gene families in sugarcane

Genetics and Molecular Biology ◽

10.1590/s1415-47572001000100037 ◽

2001 ◽

Vol 24 (1-4) ◽

pp. 285-290 ◽

Cited By ~ 12

Author(s):

O.H.P. Ramos ◽

H.S. Selistre-de-Araujo

Keyword(s):

Expressed Sequence Tag ◽

Gene Families ◽

Data Bank ◽

Matrix Metalloproteases ◽

Sequence Motifs ◽

Dna Library ◽

Physiological Processes ◽

Expressed Sequence ◽

Enzyme Class

Metalloproteases play a key role in many physiological processes in mammals such as cell migration, tissue remodeling and processing of growth factors. They have also been identified as important factors in the patho-physiology of a number of human diseases, including cancer and hypertension. Many bacterial pathogens rely on proteases in order to infect the host. Several classes of metalloproteases have been described in humans, bacteria, snake venoms and insects. However, the presence and characterization of plant metalloproteases have rarely been described in the literature. In our research, we searched the sugarcane expressed sequence tag (SUCEST) DNA library in order to identify, by homology with sequences deposited in other databases, metalloprotease gene families expressed under different conditions. Protein sequences from Arabidopsis thaliana and Glycine max were used to search the SUCEST data bank. Conserved regions corresponding to different metalloprotease domains and sequence motifs were identified in the reads to characterize each group of enzymes. At least four classes of sugarcane metalloproteases have been identified, i.e. matrix metalloproteases, zincins, inverzincins, and ATP-dependent metalloproteases. Each enzyme class was analyzed for its expression in different conditions and tissues.

Download Full-text