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Transcription Factors as Bioengineer for Tunable Gene Expression: Recent Advances...
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Transcription Factors as Bioengineer for Tunable Gene Expression: Recent Advances and Prospects

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (15 December 2022) | Viewed by 5234

Special Issue Editors

Dr. Muhammad Waseem

E-Mail Website
Guest Editor
Department of Botany, University of Narowal, Narowal, Pakistan
Interests: stress; fruit development; bioinformatics; gene family; transcriptome; hormones; non-coding genes
Dr. Vicent Arbona

E-Mail Website
Guest Editor
Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
Interests: abiotic stress; Arabidopsis; biochemistry; citrus; drought; flooding; metabolomics; plant physiology; tomato
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Transcription factors (TFs) are key components of transcriptional regulation machinery. The discovery of plant TFs as key regulators of plant growth, development, and responses to distinct biotic and abiotic stresses has opened up new horizons for plant scientists. In plants, TFs accompany the process of evolution from unicellular aquatic algae to complex flowering plants that dominate land environments. TFs perceive signals and switch certain stress-responsive genes on and off by binding to different cis-regulatory elements required for gene expression alteration, and they are important in the regulation of cell activities. Therefore, alterations in the expression of TF genes normally result in dramatic changes to a plant, and the structural changes to these genes may represent a significant evolutionary force. More than 50 families of plant TFs have been reported in nature. Among them, DREB, bZIP, MYB, NAC, zinc-finger, HSF, Dof, WRKY, bHLH, GRAS, ERF, AP2, and NF-Y genes serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. However, the potential of many TFs to improve crop quality is currently an unexplored topic. As a practical consequence, the engineering of TF genes provides a valuable means for the manipulation of plants, but success in such endeavors depends on how well the genes are understood. To this end, numerous plant TF genes and the proteins that they encode were characterized. In this Special Issue, we aim to compile the latest advances in the study of higher plant TF, with an emphasis on bioinformatic analysis; the analysis of molecular function; expression analysis; phenotype analysis; and network analysis for the description of entire transcriptional regulatory networks, and to relate this information to processes that control the synthesis and actions of these proteins. In plants, transcriptional regulation plays a major role in the control of gene expression, and a number of plant TFs are known to act as key regulators of various functions. The manipulation of a TF often induces drastic phenotype changes and alters the proteomes, metabolomes, phenomes, and transcriptomes of plants. By clarifying the complete functional network of TFs, it may be possible to predict events in the transcriptomes, metabolomes, and phenomes of plants induced by the manipulation of a gene of interest.

Dr. Muhammad Waseem
Dr. Vicent Arbona
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • transcription factors
  • expression
  • synthetic biology
  • metabolic engineering
  • transcriptomes
  • metabolomes
  • phenomes

Published Papers (2 papers)

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Research

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20 pages, 6960 KiB  
Article
Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri
by Mengna Wang, Muhammad Aamir Manzoor, Xinya Wang, Xiaofeng Feng, Yu Zhao, Jinling He and Yongping Cai
Int. J. Mol. Sci. 2022, 23(13), 7054; https://doi.org/10.3390/ijms23137054 - 24 Jun 2022
Cited by 4 | Viewed by 2033
Abstract
The SAUR (small auxin-up RNA) gene family is the biggest family of early auxin response genes in higher plants and has been associated with the control of a variety of biological processes. Although SAUR genes had been identified in several genomes, no systematic [...] Read more.
The SAUR (small auxin-up RNA) gene family is the biggest family of early auxin response genes in higher plants and has been associated with the control of a variety of biological processes. Although SAUR genes had been identified in several genomes, no systematic analysis of the SAUR gene family has been reported in Chinese white pear. In this study, comparative and systematic genomic analysis has been performed in the SAUR gene family and identified a total of 116 genes from the Chinese white pear. A phylogeny analysis revealed that the SAUR family could be classified into four groups. Further analysis of gene structure (introns/exons) and conserved motifs showed that they are diverse functions and SAUR-specific domains. The most frequent mechanisms are whole-genome duplication (WGD) and dispersed duplication (DSD), both of which may be important in the growth of the SAUR gene family in Chinese white pear. Moreover, cis-acting elements of the PbrSAUR genes were found in promoter regions associated with the auxin-responsive elements that existed in most of the upstream sequences. Remarkably, the qRT-PCR and transcriptomic data indicated that PbrSAUR13 and PbrSAUR52 were significantly expressed in fruit ripening. Subsequently, subcellular localization experiments revealed that PbrSAUR13 and PbrSAUR52 were localized in the nucleus. Moreover, PbrSAUR13 and PbrSAUR52 were screened for functional verification, and Dangshan pear and frandi strawberry were transiently transformed. Finally, the effects of these two genes on stone cells and lignin were analyzed by phloroglucinol staining, Fourier infrared spectroscopy, and qRT-PCR. It was found that PbrSAUR13 promoted the synthesis and accumulation of stone cells and lignin, PbrSAUR52 inhibited the synthesis and accumulation of stone cells and lignin. In conclusion, these results indicate that PbrSAUR13 and PbrSAUR52 are predominantly responsible for lignin inhibit synthesis, which provides a basic mechanism for further study of PbrSAUR gene functions. Full article
(This article belongs to the Special Issue Transcription Factors as Bioengineer for Tunable Gene Expression: Recent Advances and Prospects)
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Review

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23 pages, 1505 KiB  
Review
From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology
by Juan Manuel Acién, Eva Cañizares, Héctor Candela, Miguel González-Guzmán and Vicent Arbona
Int. J. Mol. Sci. 2023, 24(3), 2526; https://doi.org/10.3390/ijms24032526 - 28 Jan 2023
Cited by 1 | Viewed by 2271
Abstract
The selection of plant genotypes with improved productivity and tolerance to environmental constraints has always been a major concern in plant breeding. Classical approaches based on the generation of variability and selection of better phenotypes from large variant collections have improved their efficacy [...] Read more.
The selection of plant genotypes with improved productivity and tolerance to environmental constraints has always been a major concern in plant breeding. Classical approaches based on the generation of variability and selection of better phenotypes from large variant collections have improved their efficacy and processivity due to the implementation of molecular biology techniques, particularly genomics, Next Generation Sequencing and other omics such as proteomics and metabolomics. In this regard, the identification of interesting variants before they develop the phenotype trait of interest with molecular markers has advanced the breeding process of new varieties. Moreover, the correlation of phenotype or biochemical traits with gene expression or protein abundance has boosted the identification of potential new regulators of the traits of interest, using a relatively low number of variants. These important breakthrough technologies, built on top of classical approaches, will be improved in the future by including the spatial variable, allowing the identification of gene(s) involved in key processes at the tissue and cell levels. Full article
(This article belongs to the Special Issue Transcription Factors as Bioengineer for Tunable Gene Expression: Recent Advances and Prospects)
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