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Turin L, Surini S, Wheelhouse N, Rocchi MS. Recent advances and public health implications for environmental exposure to Chlamydia abortus: from enzootic to zoonotic disease. Vet Res 2022; 53:37. [PMID: 35642008 PMCID: PMC9152823 DOI: 10.1186/s13567-022-01052-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/29/2022] [Indexed: 11/24/2022] Open
Abstract
Environmental transmission of Chlamydia abortus as a result of enzootic disease or disease outbreaks and the threats posed by this pathogen has been previously reported, however a state-of-the-science review of these reports and the identification of future research priorities in this area is still lacking. This study provides an overview of the current knowledge of host–pathogen–environment interactions, addressing public health risks and identifying critical questions and research gaps. We performed a systematic PubMed and Web of Science search for publications related to Chlamydia abortus in the past four decades, and we reviewed and combined the evidence critically discussing and commenting the results. A total of 182 studies, 5 chapters of specific books and the “OIE terrestrial manual” were included in this review. There were substantial variations between the studies in topic addressed and experimental design. Overall, the literature largely supports the crucial role played by environmental exposure on the acquisition of zoonotic disease caused by Chlamydia abortus. We also identify the paucity of information related to interspecies transmission and pathogen adaptation in relation to environmental dissemination and zoonotic risk. This analysis further highlights the need for additional research given that environmental transmission represents a serious risk not only to susceptible patients (pregnant women and immunocompromised individuals), but also for other species including wildlife.
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Affiliation(s)
- Lauretta Turin
- Department of Veterinary Medicine (DIMEVET), University of Milan, Milan, Italy.
| | - Sara Surini
- Department of Veterinary Medicine (DIMEVET), University of Milan, Milan, Italy
| | - Nick Wheelhouse
- School of Applied Sciences, Edinburgh Napier University, Sighthill Court, Edinburgh, EH11 4BN, UK
| | - Mara Silvia Rocchi
- Moredun Research Institute, Bush Loan, Pentlands Science Park, Penicuik, EH26 0PZ, Scotland, UK
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Chen J, Wang L, Jin X, Wan J, Zhang L, Je BI, Zhao K, Kong F, Huang J, Tian M. Oryza sativa ObgC1 Acts as a Key Regulator of DNA Replication and Ribosome Biogenesis in Chloroplast Nucleoids. RICE (NEW YORK, N.Y.) 2021; 14:65. [PMID: 34251486 PMCID: PMC8275814 DOI: 10.1186/s12284-021-00498-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 05/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The Spo0B-associated GTP-binding protein (Obg) GTPase, has diverse and important functions in bacteria, including morphological development, DNA replication and ribosome maturation. Homologs of the Bacillus subtilis Obg have been also found in chloroplast of Oryza sativa, but their primary roles remain unknown. RESULTS We clarify that OsObgC1 is a functional homolog of AtObgC. The mutant obgc1-d1 exhibited hypersensitivity to the DNA replication inhibitor hydroxyurea. Quantitative PCR results showed that the ratio of chloroplast DNA to nuclear DNA in the mutants was higher than that of the wild-type plants. After DAPI staining, OsObgC1 mutants showed abnormal nucleoid architectures. The specific punctate staining pattern of OsObgC1-GFP signal suggests that this protein localizes to the chloroplast nucleoids. Furthermore, loss-of-function mutation in OsObgC1 led to a severe suppression of protein biosynthesis by affecting plastid rRNA processing. It was also demonstrated through rRNA profiling that plastid rRNA processing was decreased in obgc1-d mutants, which resulted in impaired ribosome biogenesis. The sucrose density gradient profiles revealed a defective chloroplast ribosome maturation of obgc1-d1 mutants. CONCLUSION Our findings here indicate that the OsObgC1 retains the evolutionarily biological conserved roles of prokaryotic Obg, which acts as a signaling hub that regulates DNA replication and ribosome biogenesis in chloroplast nucleoids.
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Affiliation(s)
- Ji Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Li Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaowan Jin
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Wan
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lang Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Byoung Il Je
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 61005, China
| | - Ke Zhao
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fanlei Kong
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Huang
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 61005, China.
| | - Mengliang Tian
- Institute for New Rural Development, Sichuan Agricultural University, Yaan, 625000, China.
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Chatterjee A, Acharjee A, Das S, Datta PP. Deletion analyses reveal insights into the domain specific activities of an essential GTPase CgtA in Vibrio cholerae. Arch Biochem Biophys 2019; 665:143-151. [PMID: 30894284 DOI: 10.1016/j.abb.2019.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
CgtA is an essential bacterial GTPase protein involved in multiple cellular activities. In the presence of 50S ribosome, its GTPase activity increases significantly. Through sequential deletions of CgtA protein of Vibrio cholerae (CgtAvc) we found that its N terminal Obg domain is essential for ribosome binding and augmenting the ribosome mediated GTPase activity. Strategic deletions of the three glycine rich loops of Obg domain revealed that loop 1 of Obg domain is involved in anchoring the protein into the 50S, whereas, loop 2 & loop 3 are involved in conveying the effect of interaction of the Obg domain with the 50S to the GTPase domain through an interdomain linker, followed by GTP hydrolysis. On the other hand, the non-conserved C-terminal domain (CTD) is not directly involved in ribosome binding but shows negative impact on GTPase activity.
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Affiliation(s)
- Ananya Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, West Bengal, India; Viral Research and Diagnostic Laboratories, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beliaghata, P.O. Box-177, Kolkata, 700 010, West Bengal, India
| | - Arita Acharjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, West Bengal, India
| | - Sagarika Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, West Bengal, India
| | - Partha P Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, West Bengal, India.
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Shahid MA, Marenda MS, Markham PF, Noormohammadi AH. Complementation of the Mycoplasma synoviae MS-H vaccine strain with wild-type obg influencing its growth characteristics. PLoS One 2018; 13:e0194528. [PMID: 29590172 PMCID: PMC5874028 DOI: 10.1371/journal.pone.0194528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 03/05/2018] [Indexed: 11/19/2022] Open
Abstract
The temperature-sensitive (ts+) Mycoplasma synoviae vaccine strain MS-H harbors a non-synonymous mutation which results in Glycine to Arginine substitution at position 123 in the highly conserved glycine-rich motif of Obg-fold in the GTP-binding protein Obg. In-silico analysis of the wild-type and mutant Obgs of M. synoviae has indicated that this amino acid substitution affects structure of the protein, potentially leading to abrogation of Obg function in vivo. Present study was conducted to develop the first expression vector for M. synoviae and to investigate the potential effect(s) of complementation of MS-H vaccine with the wild-type obg from 86079/7NS, the parent strain of MS-H. An oriC vector, pKS-VOTL, harboring the 86079/7NS obg gene, downstream of the variable lipoprotein haemagglutinin (vlhA) gene promoter, also cloned from 86079/7NS, was used to transform MS-H. The plasmid was localised at the chromosomal oriC locus of MS-H without any detectable integration at the chromosomal obg locus. Analysis of the MS-H transformants revealed abundant obg transcripts as well as Obg protein, when compared to the MS-H transformed with a similar vector, pMAS-LoriC, lacking obg coding sequence. The MS-H transformants complemented with wild-type Obg maintained their original temperature-sensitivity phenotype (consistent with MS-H vaccine) but, when compared to the MS-H transformed with pMAS-LoriC, had significantly higher (p < 0.05) growth rate and viability at the permissive (33°C) and non-permissive temperature (39.5°C), respectively. Analysis of Obg expression in MS-H and its wild-type parent strain revealed comparatively lower levels of Obg in MS-H. These results indicate that not only the mutation in Obg, but also the level of Obg expression, can confer functional abnormalities in the bacterial host. Furthermore, with the construction of first expression vector for M. synoviae, this study has set foundation for the development of recombinant vaccine(s) based on MS-H.
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Affiliation(s)
- Muhammad A. Shahid
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Marc S. Marenda
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Philip F. Markham
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Amir H. Noormohammadi
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
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Chen J, Deng F, Deng M, Han J, Chen J, Wang L, Yan S, Tong K, Liu F, Tian M. Identification and Characterization of a Chloroplast-Targeted Obg GTPase in Dendrobium officinale. DNA Cell Biol 2016; 35:802-811. [PMID: 27710025 DOI: 10.1089/dna.2016.3413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacterial homologous chloroplast-targeted Obg GTPases (ObgCs) belong to the plant-typical Obg group, which is involved in diverse physiological processes during chloroplast development. However, the evolutionarily conserved function of ObgC in plants remains elusive and requires further investigation. In this study, we identified DoObgC from an epiphytic plant Dendrobium officinale and demonstrated the characteristics of DoObgC. Sequence analysis indicated that DoObgC is highly conserved with other plant ObgCs, which contain the chloroplast transit peptide (cTP), Obg fold, G domain, and OCT regions. The C terminus of DoObgC lacking the chloroplast-targeting cTP region, DoObgCΔ1-160, showed strong similarity to ObgE and other bacterial Obgs. Overexpression of DoObgCΔ1-160 in Escherichia coli caused slow cell growth and an increased number of elongated cells. This phenotype was consistent with the phenotype of cells overexpressing ObgE. Furthermore, the expression of recombinant DoObgCΔ1-160 enhanced the cell persistence of E. coli to streptomycin. Results of transient expression assays revealed that DoObgC was localized to chloroplasts. Moreover, we demonstrated that DoObgC could rescue the embryotic lethal phenotype of the Arabidopsis obgc-t mutant, suggesting that DoObgC is a functional homolog to Arabidopsis AtObgC in D. officinale. Gene expression profiles showed that DoObgC was expressed in leaf-specific and light-dependent patterns and that DoObgC responded to wounding treatments. Our previous and present studies reveal that ObgC has an evolutionarily conserved role in ribosome biogenesis to adapt chloroplast development to the environment.
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Affiliation(s)
- Ji Chen
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Feng Deng
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Mengsheng Deng
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Jincheng Han
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Jianbin Chen
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Li Wang
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Shen Yan
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Kai Tong
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Fan Liu
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Mengliang Tian
- 2 Institute for New Rural Development, Sichuan Agricultural University , Yaan, China
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6
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Chatterjee A, Datta PP. Intrinsic GTPase activity of a ribosomal maturation protein CgtA is associated with its inter-domain movement: insights from MD simulations and biochemical studies. J Biomol Struct Dyn 2016; 35:2578-2587. [PMID: 27677930 DOI: 10.1080/07391102.2016.1224732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ananya Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Partha P. Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, Nadia, West Bengal 741246, India
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Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation. Infect Immun 2016; 84:2703-13. [PMID: 27400720 DOI: 10.1128/iai.00377-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/05/2016] [Indexed: 12/16/2022] Open
Abstract
In evolving to an obligate intracellular niche, Chlamydia has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However, Chlamydia can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-γ), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from Chlamydia Thus, how Chlamydia, a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question. We previously observed that C. pneumoniae responds to this stress by globally increasing transcription while globally decreasing translation, an unusual response. Here, we sought to understand this and hypothesized that the Trp codon content of a given gene would determine its transcription level. We quantified transcripts from C. pneumoniae genes that were either rich or poor in Trp codons and found that Trp codon-rich transcripts were increased, whereas those that lacked Trp codons were unchanged or even decreased. There were exceptions, and these involved operons or large genes with multiple Trp codons: downstream transcripts were less abundant after Trp codon-rich sequences. These data suggest that ribosome stalling on Trp codons causes a negative polar effect on downstream sequences. Finally, reassessing previous C. pneumoniae microarray data based on codon content, we found that upregulated transcripts were enriched in Trp codons, thus supporting our hypothesis.
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Zielke RA, Wierzbicki IH, Baarda BI, Sikora AE. The Neisseria gonorrhoeae Obg protein is an essential ribosome-associated GTPase and a potential drug target. BMC Microbiol 2015; 15:129. [PMID: 26122105 PMCID: PMC4487204 DOI: 10.1186/s12866-015-0453-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background Neisseria gonorrhoeae (GC) is a Gram-negative pathogen that most commonly infects mucosal surfaces, causing sexually transmitted urethritis in men and endocervicitis in women. Serious complications associated with these infections are frequent and include pelvic inflammatory disease, ectopic pregnancy, and infertility. The incidence of gonorrhea cases remains high globally while antibiotic treatment options, the sole counter measures against gonorrhea, are declining due to the remarkable ability of GC to acquire resistance. Evaluating of potential drug targets is essential to provide opportunities for developing antimicrobials with new mechanisms of action. We propose the GC Obg protein, belonging to the Obg/CgtA GTPase subfamily, as a potential target for the development of therapeutic interventions against gonorrhea, and in this study perform its initial functional and biochemical characterization. Results We report that NGO1990 encodes Obg protein, which is an essential factor for GC viability, associates predominantly with the large 50S ribosomal subunit, and is stably expressed under conditions relevant to infection of the human host. The anti-Obg antisera cross-reacts with a panel of contemporary GC clinical isolates, demonstrating the ubiquitous nature of Obg. The cellular levels of Obg reach a maximum in the early logarithmic phase and remain constant throughout bacterial growth. The in vitro binding and hydrolysis of the fluorescent guanine nucleotide analogs mant-GTP and mant-GDP by recombinant wild type and T192AT193A mutated variants of Obg are also assessed. Conclusions Characterization of the GC Obg at the molecular and functional levels presented herein may facilitate the future targeting of this protein with small molecule inhibitors and the evaluation of identified lead compounds for bactericidal activity against GC and other drug-resistant bacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0453-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Igor H Wierzbicki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Benjamin I Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
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Kint C, Verstraeten N, Hofkens J, Fauvart M, Michiels J. Bacterial Obg proteins: GTPases at the nexus of protein and DNA synthesis. Crit Rev Microbiol 2013; 40:207-24. [PMID: 23537324 DOI: 10.3109/1040841x.2013.776510] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Obg proteins (also known as ObgE, YhbZ and CgtA) are conserved P-loop GTPases, essential for growth in bacteria. Like other GTPases, Obg proteins cycle between a GTP-bound ON and a GDP-bound OFF state, thereby controlling cellular processes. Interestingly, the in vitro biochemical properties of Obg proteins suggest that they act as sensors for the cellular GDP/GTP pools and adjust their activity according to the cellular energy status. Obg proteins have been attributed a host of cellular functions, including roles in essential cellular processes (DNA replication, ribosome maturation) and roles in different stress adaptation pathways (stringent response, sporulation, general stress response). This review summarizes the current knowledge on Obg activity and function. Furthermore, we present a model that integrates the different functions of Obg by assigning it a fundamental role in cellular physiology, at the hub of protein and DNA synthesis. In particular, we believe that Obg proteins might provide a connection between different global pathways in order to fine-tune cellular processes in response to a given energy status.
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Affiliation(s)
- Cyrielle Kint
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven , Kasteelpark Arenberg 20, 3001 Heverlee , Kasteelpark Arenberg 20, 3001 Heverlee and
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10
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Kint CI, Verstraeten N, Wens I, Liebens VR, Hofkens J, Versées W, Fauvart M, Michiels J. The Escherichia coli GTPase ObgE modulates hydroxyl radical levels in response to DNA replication fork arrest. FEBS J 2012; 279:3692-3704. [PMID: 22863262 DOI: 10.1111/j.1742-4658.2012.08731.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Obg proteins are universally conserved GTP-binding proteins that are essential for viability in bacteria. Homologs in different organisms are involved in various cellular processes, including DNA replication. The goal of this study was to analyse the structure-function relationship of Escherichia coli ObgE with regard to DNA replication in general and sensitivity to stalled replication forks in particular. Defined C-terminal chromosomal deletion mutants of obgE were constructed and tested for sensitivity to the replication inhibitor hydroxyurea. The ObgE C-terminal domain was shown to be dispensable for normal growth of E.coli. However, a region within this domain is involved in the cellular response to replication fork stress. In addition, a mutant obgE over-expression library was constructed by error-prone PCR and screened for increased hydroxyurea sensitivity. ObgE proteins with substitutions L159Q, G163V, P168V, G216A or R237C, located within distinct domains of ObgE, display dominant-negative effects leading to hydroxyurea hypersensitivity when over-expressed. These effects are abolished in strains with a single deletion of the iron transporter TonB or combined deletions the toxin/antitoxin modules RelBE/MazEF, strains both of which have been shown to be involved in a pathway that stimulates hydroxyl radical formation following hydroxyurea treatment. Moreover, the observed dominant-negative effects are lost in the presence of the hydroxyl radical scavenger thiourea. Together, these results indicate involvement of hydroxyl radical toxicity in ObgE-mediated protection against replication fork stress.
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Affiliation(s)
- Cyrielle I Kint
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Inez Wens
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Veerle R Liebens
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Johan Hofkens
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Wim Versées
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
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The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev 2012; 75:507-42, second and third pages of table of contents. [PMID: 21885683 DOI: 10.1128/mmbr.00009-11] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, "It may never again be possible to capture [GTPases] in a family portrait" (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins.
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Atkinson GC, Tenson T, Hauryliuk V. The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS One 2011; 6:e23479. [PMID: 21858139 PMCID: PMC3153485 DOI: 10.1371/journal.pone.0023479] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/18/2011] [Indexed: 12/01/2022] Open
Abstract
RelA/SpoT Homologue (RSH) proteins, named for their sequence similarity to the RelA and SpoT enzymes of Escherichia coli, comprise a superfamily of enzymes that synthesize and/or hydrolyze the alarmone ppGpp, activator of the “stringent” response and regulator of cellular metabolism. The classical “long” RSHs Rel, RelA and SpoT with the ppGpp hydrolase, synthetase, TGS and ACT domain architecture have been found across diverse bacteria and plant chloroplasts, while dedicated single domain ppGpp-synthesizing and -hydrolyzing RSHs have also been discovered in disparate bacteria and animals respectively. However, there is considerable confusion in terms of nomenclature and no comprehensive phylogenetic and sequence analyses have previously been carried out to classify RSHs on a genomic scale. We have performed high-throughput sensitive sequence searching of over 1000 genomes from across the tree of life, in combination with phylogenetic analyses to consolidate previous ad hoc identification of diverse RSHs in different organisms and provide a much-needed unifying terminology for the field. We classify RSHs into 30 subgroups comprising three groups: long RSHs, small alarmone synthetases (SASs), and small alarmone hydrolases (SAHs). Members of nineteen previously unidentified RSH subgroups can now be studied experimentally, including previously unknown RSHs in archaea, expanding the “stringent response” to this domain of life. We have analyzed possible combinations of RSH proteins and their domains in bacterial genomes and compared RSH content with available RSH knock-out data for various organisms to determine the rules of combining RSHs. Through comparative sequence analysis of long and small RSHs, we find exposed sites limited in conservation to the long RSHs that we propose are involved in transmitting regulatory signals. Such signals may be transmitted via NTD to CTD intra-molecular interactions, or inter-molecular interactions either among individual RSH molecules or among long RSHs and other binding partners such as the ribosome.
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