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Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches

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

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 27106

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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,

In last few decades a substantial progress has been made in the understanding of mechanisms of gene expression regulation at the molecular level. This knowledge has been extended into the different areas of cell biology and beyond enabling to realize 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. Comprised of a large number of molecular and genetic components with an even larger number of their interactions, the process with such enormous complexity requires holistic study approach. Systems biology enables to represent large sets of components and their interactions as a network. This information then can be utilized to design and engineer biological systems for synthetic biology applications. However, whereas genomics, transcriptomics, proteomics, and metabolomics data allows to build and explore metabolic and some signaling networks, the knowledge of gene expression regulatory components and their functions is still far from complete. This limits the development and availability of comprehensive gene regulatory networks and overall understanding of gene expression regulation.

We invite authors to submit both original research, and review articles that focusses on molecular mechanisms controlling gene expression, as well as use and applications of systems and synthetic approaches for exploring gene regulation.

Dr. Naglis Malys
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
microRNAs
riboswitches
ribosome binding sites
gene regulatory networks
molecular mechanisms
systems and synthetic approaches

Published Papers (9 papers)

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Research

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16 pages, 5396 KiB

Open AccessArticle

Identification of a Putative CodY Regulon in the Gram-Negative Phylum Synergistetes

by Jianing Geng, Sainan Luo, Hui-Ru Shieh, Hsing-Yi Wang, Songnian Hu and Yi-Ywan M. Chen

Int. J. Mol. Sci. 2022, 23(14), 7911; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23147911 - 18 Jul 2022

Viewed by 1410

Abstract

CodY is a dominant regulator in low G + C, Gram-positive Firmicutes that governs the regulation of various metabolic pathways and cellular processes. By using various bioinformatics analyses and DNA affinity precipitation assay (DAPA), this study confirmed the presence of CodY orthologues and corresponding regulons in Gram-negative Synergistetes. A novel palindromic sequence consisting of AT-rich arms separated by a spacer region of variable length and sequence was identified in the promoters of the putative codY-containing operons in Synergistetes. The consensus sequence from genera Synergistes and Cloacibacillus (5′-AATTTTCTTAAAATTTCSCTTGATATTTACAATTTT) contained three AT-rich regions, resulting in two palindromic sequences; one of which is identical to Firmicutes CodY box (5′-AATTTTCWGAAAATT). The function of the consensus sequence was tested by using a recombinant CodY protein (His-CodY_DSM) of Cloacibacillus evryensis DSM19522 in DAPA. Mutations in the central AT-rich sequence reduced significantly the binding of His-CodY_DSM, whereas mutations in the 5′ or 3′ end AT-rich sequence slightly reduced the binding, indicating that CodY_DSM could recognize both palindromic sequences. The proposed binding sequences were found in the promoters of multiple genes involved in amino acids biosynthesis, metabolism, regulation, and stress responses in Synergistetes. Thus, a CodY-like protein from Synergistetes may function similarly to Firmicutes CodY. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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16 pages, 3003 KiB

Open AccessArticle

The Exploring Functional Role of Ammonium Transporters of Aspergillus oryzae in Nitrogen Metabolism: Challenges towards Cell Biomass Production

by Chanikul Chutrakul, Sarocha Panchanawaporn, Tayvich Vorapreeda, Sukanya Jeennor, Jutamas Anantayanon and Kobkul Laoteng

Int. J. Mol. Sci. 2022, 23(14), 7567; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23147567 - 08 Jul 2022

Viewed by 1564

Abstract

Ammonium is a source of fermentable inorganic nitrogen essential for the growth and development of filamentous fungi. It is involved in several cellular metabolic pathways underlying nitrogen transport and assimilation. Ammonium can be transferred into the cell by an ammonium transporter. This study explored the role of ammonium transporters in nitrogen metabolism and cell biomass production in Aspergillus oryzae strain BCC 7051. Specific sequences encoding ammonium transporters (Amts) in A. oryzae were identified using genomic analysis. Four of the identified ammonium transporter genes, aoamt1-aoamt4, showed similarity in deduced amino acid sequences to the proteins in the ammonium transporter/methylammonium permease (AMT/MEP) family. Transcriptional analysis showed that the expression of aoamt2 and aoamt3 was ammonium-dependent, and was highly upregulated under ammonium-limited conditions. Their functional roles are characterized by genetic perturbations. The gene disruption and overexpression of aoamt3 indicated that the protein encoded by it was a crucial ammonium transporter associated with nitrogen metabolism and was required for filamentous growth. Compared with the wild type, the aoamt3-overexpressing strain showed superior growth performance, high biomass yield, and low glucose consumption. These results shed light on further improvements in the production of potent bioproducts by A. oryzae by manipulating the ammonium uptake capacity and nitrogen metabolism. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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12 pages, 1695 KiB

Open AccessArticle

Development and Characterization of Indole-Responsive Whole-Cell Biosensor Based on the Inducible Gene Expression System from Pseudomonas putida KT2440

by Paulius Matulis, Ingrida Kutraite, Ernesta Augustiniene, Egle Valanciene, Ilona Jonuskiene and Naglis Malys

Int. J. Mol. Sci. 2022, 23(9), 4649; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23094649 - 22 Apr 2022

Cited by 2 | Viewed by 3409

Abstract

Indole is a biologically active compound naturally occurring in plants and some bacteria. It is an important specialty chemical that is used as a precursor by the pharmaceutical and chemical industries, as well as in agriculture. Recently, indole has been identified as an important signaling molecule for bacteria in the mammalian gut. The regulation of indole biosynthesis has been studied in several bacterial species. However, this has been limited by the lack of in vivo tools suitable for indole-producing species identification and monitoring. The genetically encoded biosensors have been shown to be useful for real-time quantitative metabolite analysis. This paper describes the identification and characterization of the indole-inducible system PpTrpI/P_{PP_RS00425} from Pseudomonas putida KT2440. Indole whole-cell biosensors based on Escherichia coli and Cupriavidus necator strains are developed and validated. The specificity and dynamics of biosensors in response to indole and its structurally similar derivatives are investigated. The gene expression system PpTrpI/P_{PP_RS00425} is shown to be specifically induced up to 639.6-fold by indole, exhibiting a linear response in the concentration range from approximately 0.4 to 5 mM. The results of this study form the basis for the use of whole-cell biosensors in indole metabolism-relevant bacterial species screening and characterization. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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14 pages, 5226 KiB

Open AccessArticle

Expression of the AHPND Toxins PirA^vp and PirB^vp Is Regulated by Components of the Vibrio parahaemolyticus Quorum Sensing (QS) System

by Shin-Jen Lin, Jiun-Yan Huang, Phuoc-Thien Le, Chung-Te Lee, Che-Chang Chang, Yi-Yuan Yang, Emily Chia-Yu Su, Chu-Fang Lo and Hao-Ching Wang

Int. J. Mol. Sci. 2022, 23(5), 2889; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23052889 - 07 Mar 2022

Cited by 9 | Viewed by 3399

Abstract

Acute hepatopancreatic necrosis disease (AHPND) in shrimp is caused by Vibrio strains that harbor a pVA1-like plasmid containing the pirA and pirB genes. It is also known that the production of the PirA and PirB proteins, which are the key factors that drive the observed symptoms of AHPND, can be influenced by environmental conditions and that this leads to changes in the virulence of the bacteria. However, to our knowledge, the mechanisms involved in regulating the expression of the pirA/pirB genes have not previously been investigated. In this study, we show that in the AHPND-causing Vibrio parahaemolyticus 3HP strain, the pirA^vp and pirB^vp genes are highly expressed in the early log phase of the growth curve. Subsequently, the expression of the PirA^vp and PirB^vp proteins continues throughout the log phase. When we compared mutant strains with a deletion or substitution in two of the quorum sensing (QS) master regulators, luxO and/or opaR (luxO^D47E, ΔopaR, ΔluxO, and ΔopaRΔluxO), our results suggested that expression of the pirA^vp and pirB^vp genes was related to the QS system, with luxO acting as a negative regulator of pirA^vp and pirB^vp without any mediation by opaR^vp. In the promoter region of the pirA^vp/pirB^vp operon, we also identified a putative consensus binding site for the QS transcriptional regulator AphB. Real-time PCR further showed that aphB^vp was negatively controlled by LuxO^vp, and that its expression paralleled the expression patterns of pirA^vp and pirB^vp. An electrophoretic mobility shift assay (EMSA) showed that AphB^vp could bind to this predicted region, even though another QS transcriptional regulator, AphA^vp, could not. Taken together, these findings suggest that the QS system may regulate pirA^vp/pirB^vp expression through AphB^vp. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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29 pages, 3688 KiB

Open AccessArticle

Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach

by Anna Kloska, Grzegorz M. Cech, Dariusz Nowicki, Monika Maciąg-Dorszyńska, Aleksandra E. Bogucka, Stephanie Markert, Dörte Becher, Katarzyna Potrykus, Paulina Czaplewska and Agnieszka Szalewska-Pałasz

Int. J. Mol. Sci. 2022, 23(2), 619; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23020619 - 06 Jan 2022

Cited by 2 | Viewed by 2145

Abstract

Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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15 pages, 1148 KiB

Open AccessArticle

Reprogramming mRNA Expression in Response to Defect in RNA Polymerase III Assembly in the Yeast Saccharomyces cerevisiae

by Izabela Rudzińska, Małgorzata Cieśla, Tomasz W. Turowski, Alicja Armatowska, Ewa Leśniewska and Magdalena Boguta

Int. J. Mol. Sci. 2021, 22(14), 7298; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147298 - 07 Jul 2021

Cited by 2 | Viewed by 2172

Abstract

The coordinated transcription of the genome is the fundamental mechanism in molecular biology. Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. The purpose of this study was to determine the mRNA levels in the yeast mutant rpc128-1007 and its overdose suppressors, RBS1 and PRT1. The rpc128-1007 mutant prevents assembly of the Pol III complex and functionally mimics similar mutations in human Pol III, which cause hypomyelinating leukodystrophies. We applied RNAseq followed by the hierarchical clustering of our complete RNA-seq transcriptome and functional analysis of genes from the clusters. mRNA upregulation in rpc128-1007 cells was generally stronger than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the derepression of general transcription factor Gcn4, differently modulated by suppressor genes. rpc128-1007 mutation, regardless of the presence of suppressors, also resulted in a weak increase in the expression of ribosome biogenesis genes. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. In summary, our results provide the regulatory links affected by Pol III assembly that contribute differently to cellular fitness. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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15 pages, 1818 KiB

Open AccessArticle

Novel S. cerevisiae Hybrid Synthetic Promoters Based on Foreign Core Promoter Sequences

by Xiaofan Feng and Mario Andrea Marchisio

Int. J. Mol. Sci. 2021, 22(11), 5704; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115704 - 27 May 2021

Cited by 13 | Viewed by 4400

Abstract

Promoters are fundamental components of synthetic gene circuits. They are DNA segments where transcription initiation takes place. New constitutive and regulated promoters are constantly engineered in order to meet the requirements for protein and RNA expression into different genetic networks. In this work, we constructed and optimized new synthetic constitutive promoters for the yeast Saccharomyces cerevisiae. We started from foreign (e.g., viral) core promoters as templates. They are, usually, unfunctional in yeast but can be activated by extending them with a short sequence, from the CYC1 promoter, containing various transcription start sites (TSSs). Transcription was modulated by mutating the TATA box composition and varying its distance from the TSS. We found that gene expression is maximized when the TATA box has the form TATAAAA or TATATAA and lies between 30 and 70 nucleotides upstream of the TSS. Core promoters were turned into stronger promoters via the addition of a short UAS. In particular, the 40 nt bipartite UAS from the GPD promoter can enhance protein synthesis considerably when placed 150 nt upstream of the TATA box. Overall, we extended the pool of S. cerevisiae promoters with 59 new samples, the strongest overcoming the native TEF2 promoter. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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29 pages, 6763 KiB

Open AccessArticle

The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa

by Karolina Kotecka, Adam Kawalek, Kamil Kobylecki and Aneta Agnieszka Bartosik

Int. J. Mol. Sci. 2021, 22(10), 5066; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105066 - 11 May 2021

Cited by 11 | Viewed by 3163

Abstract

Pseudomonas aeruginosa encodes a large set of transcriptional regulators (TRs) that modulate and manage cellular metabolism to survive in variable environmental conditions including that of the human body. The AraC family regulators are an abundant group of TRs in bacteria, mostly acting as gene expression activators, controlling diverse cellular functions (e.g., carbon metabolism, stress response, and virulence). The PA3027 protein from P. aeruginosa has been classified in silico as a putative AraC-type TR. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3027 revealed a spectacular increase in the mRNA levels of PA3026-PA3024 (divergent to PA3027), PA3464, and PA3342 genes encoding proteins potentially involved in glycerolipid metabolism. Concomitantly, chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that at least 22 regions are bound by PA3027 in the PAO1161 genome. These encompass promoter regions of PA3026, PA3464, and PA3342, showing the major increase in expression in response to PA3027 excess. In Vitro DNA binding assay confirmed interactions of PA3027 with these regions. Furthermore, promoter-reporter assays in a heterologous host showed the PA3027-dependent activation of the promoter of the PA3026-PA3024 operon. Two motifs representing the preferred binding sites for PA3027, one localized upstream and one overlapping with the −35 promoter sequence, were identified in PA3026p and our data indicate that both motifs are required for full activation of this promoter by PA3027. Overall, the presented data show that PA3027 acts as a transcriptional regulator in P. aeruginosa, activating genes likely engaged in glycerolipid metabolism. The GliR name, from a glycerolipid metabolism regulator, is proposed for PA3027 of P. aeruginosa. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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Review

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15 pages, 6297 KiB

Open AccessReview

The Role of RNA Secondary Structure in Regulation of Gene Expression in Bacteria

by Agnieszka Chełkowska-Pauszek, Jan Grzegorz Kosiński, Klementyna Marciniak, Marta Wysocka, Kamilla Bąkowska-Żywicka and Marek Żywicki

Int. J. Mol. Sci. 2021, 22(15), 7845; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22157845 - 22 Jul 2021

Cited by 14 | Viewed by 4350

Abstract

Due to the high exposition to changing environmental conditions, bacteria have developed many mechanisms enabling immediate adjustments of gene expression. In many cases, the required speed and plasticity of the response are provided by RNA-dependent regulatory mechanisms. This is possible due to the very high dynamics and flexibility of an RNA structure, which provide the necessary sensitivity and specificity for efficient sensing and transduction of environmental signals. In this review, we will discuss the current knowledge about known bacterial regulatory mechanisms which rely on RNA structure. To better understand the structure-driven modulation of gene expression, we describe the basic theory on RNA structure folding and dynamics. Next, we present examples of multiple mechanisms employed by RNA regulators in the control of bacterial transcription and translation. Full article

(This article belongs to the Special Issue Gene Expression Regulation in Microorganisms: Molecular Mechanisms, Systems and Synthetic Approaches)

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