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Pelosi B. Developing a bioinformatics pipeline for comparative protein classification analysis. BMC Genom Data 2022; 23:43. [PMID: 35668373 PMCID: PMC9172112 DOI: 10.1186/s12863-022-01045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted. RESULTS The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with "population analysis" to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1-11, 2015). CONCLUSIONS This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.
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Affiliation(s)
- Benedetta Pelosi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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La HV, Chu HD, Tran CD, Nguyen KH, Le QTN, Hoang CM, Cao BP, Pham ATC, Nguyen BD, Nguyen TQ, Van Nguyen L, Ha CV, Le HT, Le HH, Le TD, Tran LSP. Insights into the gene and protein structures of the CaSWEET family members in chickpea (Cicer arietinum), and their gene expression patterns in different organs under various stress and abscisic acid treatments. Gene 2022; 819:146210. [PMID: 35104577 DOI: 10.1016/j.gene.2022.146210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 12/21/2021] [Accepted: 01/13/2022] [Indexed: 11/30/2022]
Abstract
'Sugars Will Eventually be Exported Transporters' (SWEETs) are a group of sugar transporters that play crucial roles in various biological processes, particularly plant stress responses. However, no information is available yet for the CaSWEET family in chickpea. Here, we identified all putative CaSWEET members in chickpea, and obtained their major characteristics, including physicochemical patterns, chromosomal distribution, subcellular localization, gene organization, conserved motifs and three-dimensional protein structures. Subsequently, we explored available transcriptome data to compare spatiotemporal transcript abundance of CaSWEET genes in various major organs. Finally, we studied the changes in their transcript levels in leaves and/or roots following dehydration and exogenous abscisic acid treatments using RT-qPCR to obtain valuable information underlying their potential roles in chickpea responses to water-stress conditions. Our results provide the first insights into the characteristics of the CaSWEET family members and a foundation for further functional characterizations of selected candidate genes for genetic engineering of chickpea.
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Affiliation(s)
- Hong Viet La
- Faculty of Biology and Agricultural Technology, Hanoi Pedagogical University 2, Phuc Yen City, Vinh Phuc Province 280000, Viet Nam
| | - Ha Duc Chu
- Faculty of Agricultural Technology, University of Engineering and Technology, Vietnam National University Hanoi, Xuan Thuy Road, Cau Giay District, Hanoi City 122300, Viet Nam.
| | - Cuong Duy Tran
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong Road, North Tu Liem District, Hanoi City 122300, Viet Nam
| | - Kien Huu Nguyen
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong Road, North Tu Liem District, Hanoi City 122300, Viet Nam
| | - Quynh Thi Ngoc Le
- Faculty of Chemistry and Environment, Thuy loi University, Dong Da District, Hanoi City 122300, Viet Nam
| | - Chinh Minh Hoang
- Vietnam National University of Agriculture, Ngo Xuan Quang Road, Gia Lam District, Hanoi City 122300, Viet Nam
| | - Bang Phi Cao
- Hung Vuong University, Phu Tho Province 35000, Viet Nam
| | - Anh Tuyen Cong Pham
- Vietnam National University of Agriculture, Ngo Xuan Quang Road, Gia Lam District, Hanoi City 122300, Viet Nam
| | - Bach Duc Nguyen
- Vietnam National University of Agriculture, Ngo Xuan Quang Road, Gia Lam District, Hanoi City 122300, Viet Nam
| | - Trung Quoc Nguyen
- Vietnam National University of Agriculture, Ngo Xuan Quang Road, Gia Lam District, Hanoi City 122300, Viet Nam
| | - Loc Van Nguyen
- Vietnam National University of Agriculture, Ngo Xuan Quang Road, Gia Lam District, Hanoi City 122300, Viet Nam
| | - Chien Van Ha
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Hien Thi Le
- Faculty of Agricultural Technology, University of Engineering and Technology, Vietnam National University Hanoi, Xuan Thuy Road, Cau Giay District, Hanoi City 122300, Viet Nam
| | - Ham Huy Le
- Faculty of Agricultural Technology, University of Engineering and Technology, Vietnam National University Hanoi, Xuan Thuy Road, Cau Giay District, Hanoi City 122300, Viet Nam; Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong Road, North Tu Liem District, Hanoi City 122300, Viet Nam
| | - Thao Duc Le
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong Road, North Tu Liem District, Hanoi City 122300, Viet Nam.
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA; Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Viet Nam.
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Viet La H, Duc Chu H, Thi Ha Q, Huyen Tran TT, Van Tong H, Van Tran T, Ngoc Le QT, Thu Bui HT, Bang Cao P. SWEET Gene Family in Sugar Beet ( Beta vulgaris): Genome-Wide Survey, Phylogeny and Expression Analysis. Pak J Biol Sci 2022; 25:387-395. [PMID: 35638508 DOI: 10.3923/pjbs.2022.387.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
<b>Background and Objective:</b> The SWEET (Sugars Will Eventually be Exported Transporter) proteins play important roles in modulating the growth and development processes in plants. However, little information is available on the SWEET family in sugar beet (<i>Beta vulgaris</i>). The objectives of this present study were to genome-wide identify and characterize the BvSWEET family in sugar beet. <b>Materials and Methods:</b> Based on the available genome, proteome and transcriptome databases of sugar beet, various computational tools have been used to analyze the nucleotide and full-length protein sequences of members of the BvSWEET family. <b>Results:</b> A total of 16 members of the BvSWEET family has been identified in sugar beet at the genome-wide scale. Structural analysis indicated that the BvSWEET family exhibited variable characteristics. Furthermore, the BvSWEET family in sugar beet could be categorized into four distinct groups like in other plant species. Of our interest, we found that some <i>BvSWEET</i> genes exhibited strongly preferential expression in major organs/tissues under adverse environmental stimuli. <b>Conclusion:</b> The results provided a comprehensive foundation for further functional characterization of the <i>BvSWEET </i>gene family.
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Hussein HE, Scoles GA, Ueti MW, Suarez CE, Adham FK, Guerrero FD, Bastos RG. Targeted silencing of the Aquaporin 2 gene of Rhipicephalus (Boophilus) microplus reduces tick fitness. Parasit Vectors 2015; 8:618. [PMID: 26626727 PMCID: PMC4667534 DOI: 10.1186/s13071-015-1226-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ticks are blood-feeding arthropods that can affect human and animal health both directly by blood-feeding and indirectly by transmitting pathogens. The cattle tick Rhipicephalus (Boophilus) microplus is one of the most economically important ectoparasites of bovines worldwide and it is responsible for the transmission of the protozoan Babesia bovis, the etiological agent of bovine babesiosis. Aquaporins (AQPs) are water channel proteins implicated in physiological mechanisms of osmoregulation. Members of the AQP family are critical for blood-feeding arthropods considering the extreme osmoregulatory changes that occur during their feeding. We investigated the pattern of expression of a newly identified AQP2 gene of R. microplus (RmAQP2) in different tick tissues and stages. We also examined in vivo the biological implications of silencing expression of RmAQP2 silencing during tick feeding on either uninfected or B. bovis-infected cattle. METHODS In silico gene analyses were performed by multiple alignments of amino acid sequences and topology prediction. Levels of RmAQP2 transcripts in different tick tissues and stages were analyzed by reverse transcriptase quantitative PCR. Patterns of expression of RmAQP2 protein were investigated by immunoblots. Gene silencing was performed by RNA interference and in vivo functional analyses carried out by feeding ticks on either uninfected or B. bovis-infected cattle. RESULTS RmAQP2 transcripts were found in unfed larvae, engorged nymphs, and salivary glands and guts of partially engorged females; however, of all tick tissues and stages examined, RmAQP2 protein was found only in salivary glands of partially engorged females. RmAQP2 silencing significantly reduced tick fitness and completely abrogated protein expression. The effect of RmAQP2 silencing on fitness was more pronounced in females fed on a B. bovis-infected calf than in ticks fed on an uninfected calf and none of their larval progeny survived. CONCLUSIONS Collectively, considering the gene expression and tick fitness data, we conclude that RmAQP2 is critical for tick blood feeding and may be a suitable candidate target for the development of novel strategies to control R. microplus and tick-borne parasites.
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Affiliation(s)
- Hala E Hussein
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, 99164, USA. .,Department of Entomology, Faculty of Science, Cairo University, Giza, 12613, Egypt.
| | - Glen A Scoles
- Animal Disease Research Unit, USDA-ARS, Washington State University, 3003 ADBF, P.O. Box 646630, Pullman, WA, 99164, USA.
| | - Massaro W Ueti
- Animal Disease Research Unit, USDA-ARS, Washington State University, 3003 ADBF, P.O. Box 646630, Pullman, WA, 99164, USA.
| | - Carlos E Suarez
- Animal Disease Research Unit, USDA-ARS, Washington State University, 3003 ADBF, P.O. Box 646630, Pullman, WA, 99164, USA.
| | - Fatma K Adham
- Department of Entomology, Faculty of Science, Cairo University, Giza, 12613, Egypt.
| | - Felix D Guerrero
- USDA-ARS, Knipling Bushland US Livestock Insect Research laboratory, 2700 Fredericksburg Road, Kerrville, TX, 78028, USA. .,USDA-ARS Veterinary Pest Genomics Center, Kerrville, TX, USA.
| | - Reginaldo G Bastos
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA.
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