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Pradhan M, Kumar A, Kirti A, Pandey S, Rajaram H. NtcA, LexA and heptamer repeats involved in the multifaceted regulation of DNA repair genes recF, recO and recR in the cyanobacterium Nostoc PCC7120. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194907. [PMID: 36638863 DOI: 10.1016/j.bbagrm.2023.194907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 01/11/2023]
Abstract
Regulation of DNA repair genes in cyanobacteria is an unexplored field despite some of them exhibiting high radio-resistance. With RecF pathway speculated to be the major double strand break repair pathway in Nostoc sp. strain PCC7120, regulation of recF, recO and recR genes was investigated. Bioinformatic approach-based identification of promoter and regulatory elements was validated using qRT-PCR analysis, reporter gene and DNA binding assays. Different deletion constructs of the upstream regulatory regions of these genes were analysed in host Nostoc as well as heterologous system Escherichia coli. Studies revealed: (1) Positive regulation of all three genes by NtcA, (2) Negative regulation by LexA, (3) Involvement of contiguous heptamer repeats with/without its yet to be identified interacting partner in regulating (i) binding of NtcA and LexA to recO promoter and its translation, (ii) transcription or translation of recF, (4) Translational regulation of recF and recO through non-canonical and distant S.D. sequence and of recR through a rare initiation codon. Presence of NtcA either precludes binding of LexA to AnLexA-Box or negates its repressive action resulting in higher expression of these genes under nitrogen-fixing conditions in Nostoc. Thus, in Nostoc, expression of recF, recO and recR genes is intricately regulated through multiple regulatory elements/proteins. Contiguous heptamer repeats present across the Nostoc genome in the vicinity of start codon or promoter is likely to have a global regulatory role. This is the first report detailing regulation of DSB repair genes in any algae.
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Affiliation(s)
- Mitali Pradhan
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arvind Kumar
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Anurag Kirti
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Sarita Pandey
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Hema Rajaram
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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Bhattacharjee MK, Mehta BS, Akukwe B. Maillard reaction products inhibit the periodontal pathogen Aggregatibacter actinomycetemcomitans by chelating iron. Arch Oral Biol 2020; 122:104989. [PMID: 33249361 DOI: 10.1016/j.archoralbio.2020.104989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To determine the mechanism of growth inhibition of Aggregatibacter actinomycetemcomitans by Maillard reaction products (MRP). DESIGN Growth and cell viabilities in the presence or absence of MRP were measured for both the rough and smooth variants of the bacteria. Effects of addition of ferrous and ferric ions on the inhibition of the bacteria by MRP were determined. RESULTS MRPs decreased the extent of complex formation of Chrome Azurol S with iron suggesting that MRPs can chelate iron effectively. The chelation causes growth inhibition of both the rough and smooth strains. At low concentrations of the inhibitor, lag time was extended by approximately 12 h while at high concentrations, cells were killed, decreasing cell viability by up to 8 orders of magnitude. Growth of both the rough and smooth strains could be restored to original level by addition of iron. For the rough strain, both ferrous and ferric ions could relieve the inhibition by MRP while for the smooth strain only ferrous ion was effective. CONCLUSION MRPs inhibit the growth of A. actinomycetemcomitans by chelating iron and the inhibition can be relieved by addition of iron.
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Affiliation(s)
| | - Binal S Mehta
- Department of Pharmacology and Toxicology, Long Island University, Brooklyn, NY, USA
| | - Bernadine Akukwe
- Department of Chemistry and Biochemistry, Long Island University, Brooklyn, NY, USA
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Guo Y, Hu D, Guo J, Li X, Guo J, Wang X, Xiao Y, Jin H, Liu M, Li Z, Bi D, Zhou Z. The Role of the Regulator Fur in Gene Regulation and Virulence of Riemerella anatipestifer Assessed Using an Unmarked Gene Deletion System. Front Cell Infect Microbiol 2017; 7:382. [PMID: 28971067 PMCID: PMC5609570 DOI: 10.3389/fcimb.2017.00382] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/09/2017] [Indexed: 11/29/2022] Open
Abstract
Riemerella anatipestifer, an avian pathogen, has resulted in enormous economic losses to the duck industry globally. Notwithstanding, little is known regarding the physiological, pathogenic and virulence mechanisms of Riemerella anatipestifer (RA) infection. However, the role of Ferric uptake regulator (Fur) in the virulence of R. anatipestifer has not, to date, been demonstrated. Using a genetic approach, unmarked gene deletion system, we evaluated the function of fur gene in the virulence of R. anatipestifer. For this purpose, we constructed a suicide vector containing pheS as a counter selectable marker for unmarked deletion of fur gene to investigate its role in the virulence. After successful transformation of the newly constructed vector, a mutant strain was characterized for genes regulated by iron and Fur using RNA-sequencing and a comparison was made between wild type and mutant strains in both iron restricted and enriched conditions. RNA-seq analysis of the mutant strain in a restricted iron environment showed the downregulation and upregulation of genes which were involved in either important metabolic pathways, transport processes, growth or cell membrane synthesis. Electrophoretic mobility shift assay was performed to identify the putative sequences recognized by Fur. The putative Fur-box sequence was 5′-GATAATGATAATCATTATC-3′. Lastly, the median lethal dose and histopathological investigations of animal tissues also illustrated mild pathological lesions produced by the mutant strain as compared to the wild type RA strain, hence showing declined virulence. Conclusively, an unmarked gene deletion system was successfully developed for RA and the role of the fur gene in virulence was explored comprehensively.
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Affiliation(s)
- Yunqing Guo
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Di Hu
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Jie Guo
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Xiaowen Li
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Jinyue Guo
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Xiliang Wang
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Yuncai Xiao
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Hui Jin
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Mei Liu
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Zili Li
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Dingren Bi
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Zutao Zhou
- College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Lab of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural UniversityWuhan, China
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Stacy A, Abraham N, Jorth P, Whiteley M. Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection. PLoS Pathog 2016; 12:e1006084. [PMID: 27973608 PMCID: PMC5156373 DOI: 10.1371/journal.ppat.1006084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/21/2016] [Indexed: 01/07/2023] Open
Abstract
Iron is an essential nutrient for bacterial pathogenesis, but in the host, iron is tightly sequestered, limiting its availability for bacterial growth. Although this is an important arm of host immunity, most studies examine how bacteria respond to iron restriction in laboratory rather than host settings, where the microbiome can potentially alter pathogen strategies for acquiring iron. One of the most important transcriptional regulators controlling bacterial iron homeostasis is Fur. Here we used a combination of RNA-seq and chromatin immunoprecipitation (ChIP)-seq to characterize the iron-restricted and Fur regulons of the biofilm-forming opportunistic pathogen Aggregatibacter actinomycetemcomitans. We discovered that iron restriction and Fur regulate 4% and 3.5% of the genome, respectively. While most genes in these regulons were related to iron uptake and metabolism, we found that Fur also directly regulates the biofilm-dispersing enzyme Dispersin B, allowing A. actinomycetemcomitans to escape from iron-scarce environments. We then leveraged these datasets to assess the availability of iron to A. actinomycetemcomitans in its primary infection sites, abscesses and the oral cavity. We found that A. actinomycetemcomitans is not restricted for iron in a murine abscess mono-infection, but becomes restricted for iron upon co-infection with the oral commensal Streptococcus gordonii. Furthermore, in the transition from health to disease in human gum infection, A. actinomycetemcomitans also becomes restricted for iron. These results suggest that host iron availability is heterogeneous and dependent on the infecting bacterial community. One of the most well-studied phenomena in microbiology is nutritional immunity, or how the host withholds nutrients such as iron to combat infection. As part of this, researchers have characterized how many pathogens respond to iron restriction. However, these studies are often conducted in laboratory media rather than the host. As a result, they overlook how the host environment, such as its microbiome, might alter pathogen behavior regarding iron during infection. To address this gap, we used an opportunistic pathogen that causes abscess and oral cavity infections. We defined how it responds to iron restriction in vitro and then used this data to assess its iron status in vivo. Our results show that in mono-culture abscesses the pathogen is not starved for iron but in co-culture abscesses and multispecies gum disease it is starved for iron. Therefore, host environments are not uniformly restricted for iron, and the microbiome can modulate iron availability to pathogens.
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Affiliation(s)
- Apollo Stacy
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Nader Abraham
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Peter Jorth
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Marvin Whiteley
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
- * E-mail:
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Troxell B, Hassan HM. Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria. Front Cell Infect Microbiol 2013; 3:59. [PMID: 24106689 PMCID: PMC3788343 DOI: 10.3389/fcimb.2013.00059] [Citation(s) in RCA: 304] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/16/2022] Open
Abstract
In the ancient anaerobic environment, ferrous iron (Fe2+) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe3+) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe3+, bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe3+. However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe2+ as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.
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Affiliation(s)
- Bryan Troxell
- Department of Immunology and Microbiology, Indiana University School of Medicine Indianapolis, IN, USA
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Henderson B, Ward JM, Ready D. Aggregatibacter (Actinobacillus) actinomycetemcomitans: a triple A* periodontopathogen? Periodontol 2000 2010; 54:78-105. [DOI: 10.1111/j.1600-0757.2009.00331.x] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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MONARD C, MARTIN-LAURENT F, DEVERS-LAMRANI M, LIMA O, VANDENKOORNHUYSE P, BINET F. atzgene expressions during atrazine degradation in the soil drilosphere. Mol Ecol 2010; 19:749-59. [DOI: 10.1111/j.1365-294x.2009.04503.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
In gram-negative bacteria, iron acquisition proteins are commonly regulated by Fur (ferric uptake regulator), which binds iron-regulated promoters (the Fur box). We hypothesized that Coxiella burnetii requires iron and employs an iron-regulatory system and used various approaches to define a Fur regulon. Cloned C. burnetii fur complemented an Escherichia coli fur deletion mutant. A ferrous iron transporter gene (CBU1766), a putative iron binding protein-encoding gene (CBU0970), and a cation efflux pump gene (CBU1362) were identified by genome annotation and using a Fur titration assay. Bioinformatically predicted Fur box-containing promoters were tested for transcriptional control by iron. Five genes demonstrated at least a twofold induction with minimal iron. Putatively regulated genes were evaluated in a two-plasmid regulator/promoter heterologous expression system. These data suggested a very limited Fur-regulated system in C. burnetii. In an in vitro tissue culture model, a significant increase in bacterial growth was observed with infected cells treated with deferoxamine in comparison to growth under iron-replete conditions. In an iron-overloaded animal model in vivo, the level of bacterial growth detected in the iron-injected animals was significantly decreased in comparison to growth in control animals. In a low-iron-diet animal model, a significant increase in splenomegaly was observed, but no significant change in bacterial growth was identified. The small number of predicted iron acquisition systems, few Fur-regulated genes, and enhanced replication under a decreased iron level predict a requirement of a low level of iron for survival, perhaps to avoid creation of additional reactive oxygen radicals.
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Actinomycetemcomitin: a new bacteriocin produced by Aggregatibacter (Actinobacillus) actinomycetemcomitans. J Ind Microbiol Biotechnol 2007; 35:103-10. [DOI: 10.1007/s10295-007-0271-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 10/18/2007] [Indexed: 11/26/2022]
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Bender KS, Yen HCB, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, Wall JD. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2007; 73:5389-400. [PMID: 17630305 PMCID: PMC2042090 DOI: 10.1128/aem.00276-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous experiments examining the transcriptional profile of the anaerobe Desulfovibrio vulgaris demonstrated up-regulation of the Fur regulon in response to various environmental stressors. To test the involvement of Fur in the growth response and transcriptional regulation of D. vulgaris, a targeted mutagenesis procedure was used for deleting the fur gene. Growth of the resulting Deltafur mutant (JW707) was not affected by iron availability, but the mutant did exhibit increased sensitivity to nitrite and osmotic stresses compared to the wild type. Transcriptional profiling of JW707 indicated that iron-bound Fur acts as a traditional repressor for ferrous iron uptake genes (feoAB) and other genes containing a predicted Fur binding site within their promoter. Despite the apparent lack of siderophore biosynthesis genes within the D. vulgaris genome, a large 12-gene operon encoding orthologs to TonB and TolQR also appeared to be repressed by iron-bound Fur. While other genes predicted to be involved in iron homeostasis were unaffected by the presence or absence of Fur, alternative expression patterns that could be interpreted as repression or activation by iron-free Fur were observed. Both the physiological and transcriptional data implicate a global regulatory role for Fur in the sulfate-reducing bacterium D. vulgaris.
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Affiliation(s)
- Kelly S Bender
- Department of Biochemistry, 117 Schweitzer Hall, Columbia, MO 65211, USA
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Fine DH, Kaplan JB, Kachlany SC, Schreiner HC. How we got attached to Actinobacillus actinomycetemcomitans: A model for infectious diseases. Periodontol 2000 2006; 42:114-57. [PMID: 16930309 DOI: 10.1111/j.1600-0757.2006.00189.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Daniel H Fine
- Center for Oral Infectious Diseases, Department of Oral Biology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA
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