1
|
Lu P, Bai R, Gao T, Chen J, Jiang K, Zhu Y, Lu Y, Zhang S, Xu F, Zhao H. Systemic metabolic engineering of Enterobacter aerogenes for efficient 2,3-butanediol production. Appl Microbiol Biotechnol 2024; 108:146. [PMID: 38240862 PMCID: PMC10798932 DOI: 10.1007/s00253-023-12911-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 01/22/2024]
Abstract
2,3-Butanediol (2,3-BDO) is an important gateway molecule for many chemical derivatives. Currently, microbial production is gradually being recognized as a green and sustainable alternative to petrochemical synthesis, but the titer, yield, and productivity of microbial 2,3-BDO remain suboptimal. Here, we used systemic metabolic engineering strategies to debottleneck the 2,3-BDO production in Enterobacter aerogenes. Firstly, the pyruvate metabolic network was reconstructed by deleting genes for by-product synthesis to improve the flux toward 2,3-BDO synthesis, which resulted in a 90% increase of the product titer. Secondly, the 2,3-BDO productivity of the IAM1183-LPCT/D was increased by 55% due to the heterologous expression of DR1558 which boosted cell resistance to abiotic stress. Thirdly, carbon sources were optimized to further improve the yield of target products. The IAM1183-LPCT/D showed the highest titer of 2,3-BDO from sucrose, 20% higher than that from glucose, and the yield of 2,3-BDO reached 0.49 g/g. Finally, the titer of 2,3-BDO of IAM1183-LPCT/D in a 5-L fermenter reached 22.93 g/L, 85% higher than the wild-type strain, and the titer of by-products except ethanol was very low. KEY POINTS: Deletion of five key genes in E. aerogenes improved 2,3-BDO production The titer of 2,3-BDO was increased by 90% by regulating metabolic flux Response regulator DR1558 was expressed to increase 2,3-BDO productivity.
Collapse
Affiliation(s)
- Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiale Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yalun Zhu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ye Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuting Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fangxu Xu
- Liaoning Province Key Laboratory of Cordyceps Militaris With Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| |
Collapse
|
2
|
Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [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] [Received: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
Collapse
Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| |
Collapse
|
3
|
Liu X, Zhang Y, Du X, Luo X, Tan W, Guan X, Zhang L. Effect of yhfS gene on Bt LLP29 antioxidant and UV ray resistance. PEST MANAGEMENT SCIENCE 2023; 79:2087-2097. [PMID: 36715224 DOI: 10.1002/ps.7385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bacillus thuringiensis (Bt) is a widely used microbial insecticide. However, its persistence is limited because of ultraviolet (UV) rays or other environmental factors. The yhfS gene, which encodes acetyl-CoA acyltransferase, plays an important role in lipid transport and metabolism in many organisms. To explore whether it is related to the stress resistance of Bt LLP29, the yhfS gene knockout strain LLP29 Δ-yhfS and the complementary strain LLP29 R-yhfS were generated successfully by homologous recombination technology, and the related phenotypic changes were compared in this study. RESULTS Gene yhfS was found to be functional in response to UV radiation in Bt by comparing the survival rates of Bt LLP29 harboring yhfS or not under UV light. Enzyme activity assays of key enzymes showed the the Embden-Meyerhof-Parnas pathway was enhanced yet the tricarboxylic acid cycle as well as butanoate synthesis were repressed when the gene was deleted. At the same time, the amino acid content was decreased, but reduced nicotinamide adenine dinucleotide (NADH) and reactive oxygen species (ROS) content were increased. Most noteworthy, antioxidase (such as superoxide dismutase and peroxidase) activities and contents of some potent antioxidants (such as pyruvate, carotenoids and NADPH) were lower in LLP29 Δ-yhfS than in LLP29. CONCLUSION These tests revealed that the loss of the yhfS gene led to metabolic disorders and reduction of the antioxidant ability of Bt. Higher ROS level and lower anti-oxidative capacity might be responsible for the reduced UV resistance when the gene was deleted. These results not only greatly enrich understanding of the mechanism of Bt UV resistance, but also provide an important theoretical basis for Bt application. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Xihua Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, China
| | - Yile Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Du
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingyu Luo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilong Tan
- Center for Disease Control and Prevention of Eastern Command, Nanjing, Jiangsu, China
| | - Xiong Guan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingling Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
4
|
Cai J, Pan C, Zhao Y, Xu H, Tian B, Wang L, Hua Y. DRJAMM Is Involved in the Oxidative Resistance in Deinococcus radiodurans. Front Microbiol 2022; 12:756867. [PMID: 35154022 PMCID: PMC8832034 DOI: 10.3389/fmicb.2021.756867] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Proteins containing JAB1/MPN/MOV34 metalloenzyme (JAMM/MPN+) domains that have Zn2+-dependent deubiquitinase (DUB) activity are ubiquitous across among all domains of life. Recently, a homolog in Deinococcus radiodurans, DRJAMM, was reported to possess the ability to cleave DRMoaD-MoaE. However, the detailed biochemical characteristics of DRJAMM in vitro and its biological mechanism in vivo remain unclear. Here, we show that DRJAMM has an efficient in vitro catalytic activity in the presence of Mn2+, Ca2+, Mg2+, and Ni2+ in addition to the well-reported Zn2+, and strong adaptability at a wide range of temperatures. Disruption of drJAMM led to elevated sensitivity in response to H2O2in vivo compared to the wild-type R1. In particular, the expression level of MoaE, a product of DRJAMM cleavage, was also increased under H2O2 stress, indicating that DRJAMM is needed in the antioxidant process. Moreover, DRJAMM was also demonstrated to be necessary for dimethyl sulfoxide respiratory system in D. radiodurans. These data suggest that DRJAMM plays key roles in the process of oxidative resistance in D. radiodurans with multiple-choice of metal ions and temperatures.
Collapse
|
5
|
Nakashima Y, Shiiyama N, Urabe T, Yamashita H, Yasuda S, Igoshi K, Kinoshita H. Functions of small RNAs in Lactobacillus casei-Pediococcus group of lactic acid bacteria using fragment analysis. FEMS Microbiol Lett 2021; 367:5928547. [PMID: 33068404 DOI: 10.1093/femsle/fnaa154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Small RNAs (sRNA) are non-cording RNAs composed of 50∼400 nt responsible for coordinating the adaption of Escherichia coli and other bacteria to changing environmental conditions, including pH and temperature. However, the role of sRNAs in lactic acid bacteria (LAB) has not yet been clarified. In this study, we used the Lactobacillus casei-Pediococcus group to evaluate the function of sRNAs in LAB, using RNA sequencing in the exponential growth phase and stationary phase to map and analyze sRNA fragments, which were categorized as Pediococcus pentosaceus and Lactobacillus paracasei. We evaluated the role of sRNAs in nutrient synthesis for cell growth in exponential growth phase and in protein and biofilm biosynthesis for cell body durability. During exponential growth, the sRNA fragments were found to be involved in the stress response in Pediococcus pentosaceus and in environmental adaption in Lactobacillus paracasei. The results suggest that the function of sRNA can be characterized from sRNA fragments using RNA sequencing during the exponential growth and stationary phases in Lactobacillus casei-Pediococcus group.
Collapse
Affiliation(s)
- Yuki Nakashima
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Narumi Shiiyama
- Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Taihei Urabe
- Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Hideji Yamashita
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Shin Yasuda
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Keiji Igoshi
- Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Hideki Kinoshita
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| |
Collapse
|
6
|
Xu J, Wu C, Yang Z, Liu W, Chen H, Batool K, Yao J, Fan X, Wu J, Rao W, Huang T, Xu L, Guan X, Zhang L. For: Pesticide biochemistry and physiology recG is involved with the resistance of Bt to UV. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 167:104599. [PMID: 32527443 DOI: 10.1016/j.pestbp.2020.104599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/07/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
As an ATP-dependent DNA helicase, RecG can repair DNA replication forks in many organisms. However, knowledge of recG in Bacillus thuringiensis (Bt) is limited. In our previous study, recG was found damaged in Bt LLP29-M19, which was more resistant to ultraviolet light (UV) after exposing Bt LLP29 to UV for 19 generations. To further understand the function of recG in the mechanism of Bt UV resistance, recG was knocked out and recovered with homologous recombination technology in Bt LLP29. Comparing the resistance of the different mutants to UVB, Bt ∆recG-LLP29 lacking recG was found more sensitive to UVB, hydroxyurea (HU) and H2O2 than LLP29 and the complementation strain. To compare the expression level of recG in the Bt strains under different UV treatments, Quantitative Real-time PCR (RT-qPCR) of recG was performed in the tested Bt strains, which showed that the expression level of recG in Bt ∆recG-LLP29 was substantially lower than that in the original strain and complementation strain. Interestingly, when exposed to UV for 20 min, RecG expression in both Bt LLP29 and Bt recG-R was the highest. The unwinding activity of recG in Bt LLP29 and the complementation strain were also found higher than that of the recG knockout strain, Bt ∆recG-LLP29. These results demonstrate that recG is involved with the resistance of Bt to UV. These findings not only enhance the understanding of the Bt UV resistance mechanism, but also provide an important theoretical basis for the application of Bt.
Collapse
Affiliation(s)
- Jin Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chenxu Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhaohui Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wencheng Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Hong Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Khadija Batool
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Junmin Yao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiao Fan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Juan Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wenhua Rao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tianpei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lei Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiong Guan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lingling Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| |
Collapse
|
7
|
Wang W, Ma Y, He J, Qi H, Xiao F, He S. Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans. Gene 2019; 715:144008. [DOI: 10.1016/j.gene.2019.144008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023]
|
8
|
Villa JK, Amador P, Janovsky J, Bhuyan A, Saldanha R, Lamkin TJ, Contreras LM. A Genome-Wide Search for Ionizing-Radiation-Responsive Elements in Deinococcus radiodurans Reveals a Regulatory Role for the DNA Gyrase Subunit A Gene's 5' Untranslated Region in the Radiation and Desiccation Response. Appl Environ Microbiol 2017; 83:e00039-17. [PMID: 28411225 PMCID: PMC5452802 DOI: 10.1128/aem.00039-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022] Open
Abstract
Tight regulation of gene expression is important for the survival of Deinococcus radiodurans, a model bacterium of extreme stress resistance. Few studies have examined the use of regulatory RNAs as a possible contributing mechanism to ionizing radiation (IR) resistance, despite their proffered efficient and dynamic gene expression regulation under IR stress. This work presents a transcriptome-based approach for the identification of stress-responsive regulatory 5' untranslated region (5'-UTR) elements in D. radiodurans R1 that can be broadly applied to other bacteria. Using this platform and an in vivo fluorescence screen, we uncovered the presence of a radiation-responsive regulatory motif in the 5' UTR of the DNA gyrase subunit A gene. Additional screens under H2O2-induced oxidative stress revealed the specificity of the response of this element to IR stress. Further examination of the sequence revealed a regulatory motif of the radiation and desiccation response (RDR) in the 5' UTR that is necessary for the recovery of D. radiodurans from high doses of IR. Furthermore, we suggest that it is the preservation of predicted RNA structure, in addition to DNA sequence consensus of the motif, that permits this important regulatory ability.IMPORTANCEDeinococcus radiodurans is an extremely stress-resistant bacterium capable of tolerating up to 3,000 times more ionizing radiation than human cells. As an integral part of the stress response mechanism of this organism, we suspect that it maintains stringent control of gene expression. However, understanding of its regulatory pathways remains incomplete to date. Untranslated RNA elements have been demonstrated to play crucial roles in gene regulation throughout bacteria. In this work, we focus on searching for and characterizing responsive RNA elements under radiation stress and propose that multiple levels of gene regulation work simultaneously to enable this organism to efficiently recover from exposure to ionizing radiation. The model we propose serves as a generic template to investigate similar mechanisms of gene regulation under stress that have likely evolved in other bacterial species.
Collapse
Affiliation(s)
- Jordan K Villa
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Paul Amador
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Justin Janovsky
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Arijit Bhuyan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
| | | | - Thomas J Lamkin
- Air Force Research Laboratory/XPRA Wright-Patterson AFB, Ohio, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
| |
Collapse
|
9
|
Rossi CC, Bossé JT, Li Y, Witney AA, Gould KA, Langford PR, Bazzolli DMS. A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae. RNA (NEW YORK, N.Y.) 2016; 22:1373-85. [PMID: 27402897 PMCID: PMC4986893 DOI: 10.1261/rna.055129.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 05/24/2016] [Indexed: 05/26/2023]
Abstract
Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.
Collapse
Affiliation(s)
- Ciro C Rossi
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Janine T Bossé
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Yanwen Li
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Kate A Gould
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Denise M S Bazzolli
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| |
Collapse
|
10
|
Agapov AA, Kulbachinskiy AV. Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans. BIOCHEMISTRY (MOSCOW) 2016; 80:1201-16. [PMID: 26567564 DOI: 10.1134/s0006297915100016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.
Collapse
Affiliation(s)
- A A Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| | | |
Collapse
|