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Microbial Engineering: Gene Expression Regulation and Its Application
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Microbial Engineering: Gene Expression Regulation and Its Application

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Biochemistry, Molecular and Cellular Biology".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 17867

Special Issue Editor

Dr. Naglis Malys

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Guest Editor
1. Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų pl. 19, LT-50254 Kaunas, Lithuania
2. Department of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų pl. 19, LT-50254 Kaunas, Lithuania
Interests: systems biology; synthetic biology; biotechnology; microbial metabolism; metabolic engineering; gene expression regulation; constitutive and inducible gene expression systems
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Substantial progress has been made in understanding mechanisms of gene expression regulation at the molecular level. This knowledge has been extended into different areas of cell biology and beyond, revealing its critical importance and complexity. Gene expression regulation is now considered a multidimensional process involving signaling pathways and epigenetics along with transcriptional, post-transcriptional and translational regulation. Comprising a large number of molecular and genetic components with an even larger number of their interactions, the process with such enormous complexity requires a systematic study approach.

This Special Issue focuses on research aimed at the identification and characterization of gene expression regulation features and mechanisms in biotechnologically relevant microorganisms. Synthetic biology approaches and metabolic engineering with application gene expression control tools and systems with the aim to develop highly performing biocatalysts are of particular interest.

The Special Issue welcomes submissions covering, but not limited to, the following themes:

  • Transcriptional and translational regulation;
  • Structure and function of regulatory elements such as gene promoters, operators, ribosome binding sites and other gene expression regulatory elements;
  • Mapping of regulatory elements;
  • Identification and development of gene expression control systems;
  • Regulatory network reconstruction;
  • Computational approaches for studying gene expression regulation and regulatory elements;
  • Gene expression in microbial engineering and synthetic biology;
  • Use of gene expression control elements for developing synthetic biology tools;
  • Application of gene expression control elements for developing biosynthetic pathways.

Dr. Naglis Malys
Guest Editor

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. Current Issues in Molecular Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gene expression regulation
  • transcription
  • translation
  • post-transcriptional regulation
  • transcription factors
  • promoters
  • riboswitches
  • ribosome binding sites
  • gene regulatory networks
  • molecular mechanisms
  • systems biology
  • synthetic biology
  • biosynthetic pathways
  • biocatalysts
  • microbial cell factories

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Published Papers (6 papers)

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Research

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12 pages, 2638 KiB  
Article
Screening of Tnfaip1-Interacting Proteins in Zebrafish Embryonic cDNA Libraries Using a Yeast Two-Hybrid System
by Shulan Huang, Hongning Zhang, Wen Chen, Jiawei Wang, Zhen Wu, Meiqi He, Jian Zhang, Xiang Hu and Shuanglin Xiang
Curr. Issues Mol. Biol. 2023, 45(10), 8215-8226; https://doi.org/10.3390/cimb45100518 - 10 Oct 2023
Viewed by 1608
Abstract
TNFAIP1 regulates cellular biological functions, including DNA replication, DNA repair, and cell cycle, by binding to target proteins. Identification of Tnfaip1-interacting proteins contributes to the understanding of the molecular regulatory mechanisms of their biological functions. In this study, 48 hpf, 72 hpf, and [...] Read more.
TNFAIP1 regulates cellular biological functions, including DNA replication, DNA repair, and cell cycle, by binding to target proteins. Identification of Tnfaip1-interacting proteins contributes to the understanding of the molecular regulatory mechanisms of their biological functions. In this study, 48 hpf, 72 hpf, and 96 hpf wild-type zebrafish embryo mRNAs were used to construct yeast cDNA library. The library titer was 1.12 × 107 CFU/mL, the recombination rate was 100%, and the average length of the inserted fragments was greater than 1000 bp. A total of 43 potential interacting proteins of Tnfaip1 were identified using zebrafish Tnfaip1 as a bait protein. Utilizing GO functional annotation and KEGG signaling pathway analysis, we found that these interacting proteins are mainly involved in translation, protein catabolic process, ribosome assembly, cytoskeleton formation, amino acid metabolism, and PPAR signaling pathway. Further yeast spotting analyses identified four interacting proteins of Tnfaip1, namely, Ubxn7, Tubb4b, Rpl10, and Ybx1. The Tnfaip1-interacting proteins, screened from zebrafish embryo cDNA in this study, increased our understanding of the network of Tnfaip1-interacting proteins during the earliest embryo development and provided a molecular foundation for the future exploration of tnfaip1’s biological functions. Full article
(This article belongs to the Special Issue Microbial Engineering: Gene Expression Regulation and Its Application)
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18 pages, 2807 KiB  
Article
Large-Scale Production of Anti-RNase A VHH Expressed in pyrG Auxotrophic Aspergillus oryzae
by Elif Karaman, Alp Ertunga Eyüpoğlu, Lena Mahmoudi Azar and Serdar Uysal
Curr. Issues Mol. Biol. 2023, 45(6), 4778-4795; https://doi.org/10.3390/cimb45060304 - 31 May 2023
Cited by 3 | Viewed by 2109
Abstract
Nanobodies, also referred to as VHH antibodies, are the smallest fragments of naturally produced camelid antibodies and are ideal affinity reagents due to their remarkable properties. They are considered an alternative to monoclonal antibodies (mAbs) with potential utility in imaging, diagnostic, and other [...] Read more.
Nanobodies, also referred to as VHH antibodies, are the smallest fragments of naturally produced camelid antibodies and are ideal affinity reagents due to their remarkable properties. They are considered an alternative to monoclonal antibodies (mAbs) with potential utility in imaging, diagnostic, and other biotechnological applications given the difficulties associated with mAb expression. Aspergillus oryzae (A. oryzae) is a potential system for the large-scale expression and production of functional VHH antibodies that can be used to meet the demand for affinity reagents. In this study, anti-RNase A VHH was expressed under the control of the glucoamylase promoter in pyrG auxotrophic A. oryzae grown in a fermenter. The feature of pyrG auxotrophy, selected for the construction of a stable and efficient platform, was established using homologous recombination. Pull-down assay, size exclusion chromatography, and surface plasmon resonance were used to confirm the binding specificity of anti-RNase A VHH to RNase A. The affinity of anti-RNase A VHH was nearly 18.3-fold higher (1.9 nM) when expressed in pyrG auxotrophic A. oryzae rather than in Escherichia coli. This demonstrates that pyrG auxotrophic A. oryzae is a practical, industrially scalable, and promising biotechnological platform for the large-scale production of functional VHH antibodies with high binding activity. Full article
(This article belongs to the Special Issue Microbial Engineering: Gene Expression Regulation and Its Application)
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8 pages, 1125 KiB  
Communication
How Does the Sample Preparation of Phytophthora infestans Mycelium Affect the Quality of Isolated RNA?
by Artemii A. Ivanov, Alexandr V. Tyapkin and Tatiana S. Golubeva
Curr. Issues Mol. Biol. 2023, 45(4), 3517-3524; https://doi.org/10.3390/cimb45040230 - 18 Apr 2023
Viewed by 1448
Abstract
RNA isolation from fungi and fungus-like organisms is not an easy task. Active endogenous RNases quickly hydrolyze RNA after the sample collection, and the thick cell wall prevents inhibitors from penetrating the cells. Therefore, the initial collection and grinding steps may be crucial [...] Read more.
RNA isolation from fungi and fungus-like organisms is not an easy task. Active endogenous RNases quickly hydrolyze RNA after the sample collection, and the thick cell wall prevents inhibitors from penetrating the cells. Therefore, the initial collection and grinding steps may be crucial for the total RNA isolation from the mycelium. When isolating RNA from Phytophthora infestans, we varied the grinding time of the Tissue Lyser and used TRIzol and beta-mercaptoethanol to inhibit the RNase. In addition, we tested the mortar and pestle grinding of mycelium in liquid nitrogen, with this method showing the most consistent results. During the sample grinding with the Tissue Lyser device, adding an RNase inhibitor proved to be a prerequisite, and the best results were achieved using TRIzol. We considered ten different combinations of grinding conditions and isolation methods. The classical combination of a mortar and pestle, followed by TRIzol, has proved to be the most efficient. Full article
(This article belongs to the Special Issue Microbial Engineering: Gene Expression Regulation and Its Application)
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17 pages, 4382 KiB  
Article
Analysis of the Properties of 44 ABC Transporter Genes from Biocontrol Agent Trichoderma asperellum ACCC30536 and Their Responses to Pathogenic Alternaria alternata Toxin Stress
by Hua-Ying Du, Yu-Zhou Zhang, Kuo Liu, Pei-Wen Gu, Shuang Cao, Xiang Gao, Zhi-Ying Wang, Zhi-Hua Liu and Ze-Yang Yu
Curr. Issues Mol. Biol. 2023, 45(2), 1570-1586; https://doi.org/10.3390/cimb45020101 - 12 Feb 2023
Cited by 5 | Viewed by 1792
Abstract
ATP-binding cassette (ABC) transporters are involved in transporting multiple substrates, such as toxins, and may be important for the survival of Trichoderma when encountering biotic toxins. In this study, genome searching revealed that there are 44 ABC transporters encoded in the genome of [...] Read more.
ATP-binding cassette (ABC) transporters are involved in transporting multiple substrates, such as toxins, and may be important for the survival of Trichoderma when encountering biotic toxins. In this study, genome searching revealed that there are 44 ABC transporters encoded in the genome of Trichoderma asperellum. These ABC transporters were divided into six types based on three-dimensional (3D) structure prediction, of which four, represented by 39 ABCs, are involved in transport and the remaining two, represented by 5 ABCs, are involved in regulating translation. The characteristics of nucleotide-binding domain (NBD) are important in the identification of ABC proteins. Even though the 3D structures of the 79 NBDs in the 44 ABCs are similar, multiple sequence alignment showed they can be divided into three classes. In total, 794 motifs were found in the promoter regions of the 44 ABC genes, of which 541 were cis-regulators related to stress responses. To characterize how their ABCs respond when T. asperellum interact with fungi or plants, T. asperellum was cultivated in either minimal media (MM) control, C-hungry, N-hungry, or poplar medium (PdPap) to simulate normal conditions, competition with pathogens, interaction with pathogens, and interaction with plants, respectively. The results show that 17 of 39 transport ABCs are highly expressed in at least one condition, whereas four of the five translation-regulating ABCs are highly expressed in at least one condition. Of these 21 highly expressed ABCs, 6 were chosen for RT-qPCR expression under the toxin stress of phytopathogen Alternaria alternata, and the results show ABC01, ABC04, ABC05, and ABC31 were highly expressed and may be involved in pathogen interaction and detoxifying toxins from A. alternata. Full article
(This article belongs to the Special Issue Microbial Engineering: Gene Expression Regulation and Its Application)
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14 pages, 3121 KiB  
Article
Genome-Wide Identification and Analysis of the Heat-Shock Protein Gene in L. edodes and Expression Pattern Analysis under Heat Shock
by Xu Zhao, Kaiyong Yin, Rencai Feng, Renyun Miao, Junbin Lin, Luping Cao, Yanqing Ni, Wensheng Li and Qin Zhang
Curr. Issues Mol. Biol. 2023, 45(1), 614-627; https://doi.org/10.3390/cimb45010041 - 9 Jan 2023
Cited by 6 | Viewed by 2347
Abstract
Lentinula edodes (L. edodes), one of the most popular edible mushrooms in China, is adversely affected by high temperature. Heat shock proteins (HSPs) play a crucial role in regulating the defense responses against the abiotic stresses in L. edodes. Some [...] Read more.
Lentinula edodes (L. edodes), one of the most popular edible mushrooms in China, is adversely affected by high temperature. Heat shock proteins (HSPs) play a crucial role in regulating the defense responses against the abiotic stresses in L. edodes. Some HSPs in L. edodes have been described previously, but a genome-wide analysis of these proteins is still lacking. Here, the HSP genes across the entire genome of the L. edodes mushroom were identified. The 34 LeHSP genes were subsequently classified into six subfamilies according to their molecular weights and the phylogenetic analysis. Sequence analysis showed that LeHSP proteins from the same subfamily have conserved domains and one to five similar motifs. Except for Chr 5 and 9, 34 LeHSPs genes were distributed on the other eight chromosomes. Three pairs of paralogs were identified because of sequence alignment and were confirmed as arising from segmental duplication. In LeHSPs’ promoters, different numbers of heat shock elements (HSEs) were predicted. The expression profiles of LeHSPs in 18N44 and 18 suggested that the thermo-tolerance of strain 18N44 might be related to high levels of LeHSPs transcript in response to heat stress. The quantitative real-time PCR (qRT-PCR) analysis of the 16 LeHSP genes in strains Le015 and Le027 verified their stress-inducible expression patterns under heat stress. Therefore, these comprehensive findings provide useful in-depth information on the evolution and function of LeHSPs and lay a theoretical foundation in breeding thermotolerant L. edodes varieties. Full article
(This article belongs to the Special Issue Microbial Engineering: Gene Expression Regulation and Its Application)
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Review

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19 pages, 1033 KiB  
Review
Disarm The Bacteria: What Temperate Phages Can Do
by Shiyue Zhou, Zhengjie Liu, Jiaoyang Song and Yibao Chen
Curr. Issues Mol. Biol. 2023, 45(2), 1149-1167; https://doi.org/10.3390/cimb45020076 - 1 Feb 2023
Cited by 10 | Viewed by 7955
Abstract
In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate [...] Read more.
In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections. Full article
(This article belongs to the Special Issue Microbial Engineering: Gene Expression Regulation and Its Application)
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