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Perez-Gil J, Behrendorff J, Douw A, Vickers CE. The methylerythritol phosphate pathway as an oxidative stress sense and response system. Nat Commun 2024; 15:5303. [PMID: 38906898 PMCID: PMC11192765 DOI: 10.1038/s41467-024-49483-8] [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: 12/22/2023] [Accepted: 06/05/2024] [Indexed: 06/23/2024] Open
Abstract
The methylerythritol phosphate (MEP) pathway is responsible for biosynthesis of the precursors of isoprenoid compounds in eubacteria and plastids. It is a metabolic alternative to the well-known mevalonate pathway for isoprenoid production found in archaea and eukaryotes. Recently, a role for the MEP pathway in oxidative stress detection, signalling, and response has been identified. This role is executed in part through the unusual cyclic intermediate, methylerythritol cyclodiphosphate (MEcDP). We postulate that this response is triggered through the oxygen sensitivity of the MEP pathway's terminal iron-sulfur (Fe-S) cluster enzymes. MEcDP is the substrate of IspG, the first Fe-S cluster enzyme in the pathway; it accumulates under oxidative stress conditions and acts as a signalling molecule. It may also act as an antioxidant. Furthermore, evidence is emerging for a broader and highly nuanced role of the MEP pathway in oxidative stress responses, implemented through a complex system of differential regulation and sensitivity at numerous nodes in the pathway. Here, we explore the evidence for such a role (including the contribution of the Fe-S cluster enzymes and different pathway metabolites, especially MEcDP), the evolutionary implications, and the many questions remaining about the behaviour of the MEP pathway in the presence of oxidative stress.
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Affiliation(s)
- Jordi Perez-Gil
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - James Behrendorff
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Andrew Douw
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
- BioBuilt Solutions, Corinda, QLD, 4075, Australia.
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He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. THE PLANT CELL 2024; 36:1829-1843. [PMID: 38309957 PMCID: PMC11062459 DOI: 10.1093/plcell/koae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 02/05/2024]
Abstract
In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates heterochromatin condensation by enhancing inter- and intrachromosomal interactions between and within heterochromatic regions of the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives HF formation via phase separation, which requires its C-terminal intrinsically disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci or recover HF in the h1 mutant background, whereas C-IDR with a short stretch of the globular domain (18 out of 71 amino acids) is sufficient to rescue both defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome repeat length and DNA methylation in Arabidopsis, indicating that phase separation capability is required for chromatin functions of H1. Our data suggest that bacterial H1-like proteins, which have been shown to condense DNA, are intrinsically disordered and capable of mediating phase separation. Therefore, we propose that phase separation mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing chromatin and DNA.
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Affiliation(s)
- Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yiming Yu
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Liang Wang
- Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyi Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhengyong Bai
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Guohong Li
- Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoqi Feng
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
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Sajib SA, Kandel M, Prity SA, Oukacine C, Gakière B, Merendino L. Role of plastids and mitochondria in the early development of seedlings in dark growth conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1272822. [PMID: 37841629 PMCID: PMC10570830 DOI: 10.3389/fpls.2023.1272822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Establishment of the seedlings is a crucial stage of the plant life cycle. The success of this process is essential for the growth of the mature plant. In Nature, when seeds germinate under the soil, seedlings follow a dark-specific program called skotomorphogenesis, which is characterized by small, non-green cotyledons, long hypocotyl, and an apical hook-protecting meristematic cells. These developmental structures are required for the seedlings to emerge quickly and safely through the soil and gain autotrophy before the complete depletion of seed resources. Due to the lack of photosynthesis during this period, the seed nutrient stocks are the primary energy source for seedling development. The energy is provided by the bioenergetic organelles, mitochondria, and etioplast (plastid in the dark), to the cell in the form of ATP through mitochondrial respiration and etio-respiration processes, respectively. Recent studies suggest that the limitation of the plastidial or mitochondrial gene expression induces a drastic reprogramming of the seedling morphology in the dark. Here, we discuss the dark signaling mechanisms involved during a regular skotomorphogenesis and how the dysfunction of the bioenergetic organelles is perceived by the nucleus leading to developmental changes. We also describe the probable involvement of several plastid retrograde pathways and the interconnection between plastid and mitochondria during seedling development. Understanding the integration mechanisms of organellar signals in the developmental program of seedlings can be utilized in the future for better emergence of crops through the soil.
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Affiliation(s)
- Salek Ahmed Sajib
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Margot Kandel
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Sadia Akter Prity
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Cylia Oukacine
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Bertrand Gakière
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Livia Merendino
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
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Cortina ME, Bishop RC, DeVasure BA, Coppens I, Derré I. The inclusion membrane protein IncS is critical for initiation of the Chlamydia intracellular developmental cycle. PLoS Pathog 2022; 18:e1010818. [PMID: 36084160 PMCID: PMC9491573 DOI: 10.1371/journal.ppat.1010818] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 09/21/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
All Chlamydia species are obligate intracellular bacteria that undergo a unique biphasic developmental cycle strictly in the lumen of a membrane bound compartment, the inclusion. Chlamydia specific Type III secreted effectors, known as inclusion membrane proteins (Inc), are embedded into the inclusion membrane. Progression through the developmental cycle, in particular early events of conversion from infectious (EB) to replicative (RB) bacteria, is important for intracellular replication, but poorly understood. Here, we identified the inclusion membrane protein IncS as a critical factor for Chlamydia development. We show that a C. trachomatis conditional mutant is impaired in transition from EB to RB in human cells, and C. muridarum mutant bacteria fail to develop in a mouse model of Chlamydia infection. Thus, IncS represents a promising target for therapeutic intervention of the leading cause of sexually transmitted infections of bacterial origin.
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Affiliation(s)
- María Eugenia Cortina
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - R. Clayton Bishop
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Brittany A. DeVasure
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Isabelle Derré
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- * E-mail:
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The Small Molecule H89 Inhibits Chlamydia Inclusion Growth and Production of Infectious Progeny. Infect Immun 2021; 89:e0072920. [PMID: 33820812 PMCID: PMC8373235 DOI: 10.1128/iai.00729-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Chlamydia is an obligate intracellular bacterium and the most common reportable cause of human infection in the United States. This pathogen proliferates inside a eukaryotic host cell, where it resides within a membrane-bound compartment called the chlamydial inclusion. It has an unusual developmental cycle, marked by conversion between a replicating form, the reticulate body (RB), and an infectious form, the elementary body (EB). We found that the small molecule H89 slowed inclusion growth and decreased overall RB replication by 2-fold but caused a 25-fold reduction in infectious EBs. This disproportionate effect on EB production was mainly due to a defect in RB-to-EB conversion and not to the induction of chlamydial persistence, which is an altered growth state. Although H89 is a known inhibitor of specific protein kinases and vesicular transport to and from the Golgi apparatus, it did not cause these anti-chlamydial effects by blocking protein kinase A or C or by inhibiting protein or lipid transport. Thus, H89 is a novel anti-chlamydial compound that has a unique combination of effects on an intracellular Chlamydia infection.
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Hölzer M, Barf LM, Lamkiewicz K, Vorimore F, Lataretu M, Favaroni A, Schnee C, Laroucau K, Marz M, Sachse K. Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species. Pathogens 2020; 9:E899. [PMID: 33126635 PMCID: PMC7694038 DOI: 10.3390/pathogens9110899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
To identify genome-based features characteristic of the avian and human pathogen Chlamydia(C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.
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Affiliation(s)
- Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Lisa-Marie Barf
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Fabien Vorimore
- Animal Health Laboratory, Bacterial Zoonoses Unit, University Paris-Est, Anses, 94706 Maisons-Alfort, France; (F.V.); (K.L.)
| | - Marie Lataretu
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Alison Favaroni
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany; (A.F.); (C.S.)
| | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany; (A.F.); (C.S.)
| | - Karine Laroucau
- Animal Health Laboratory, Bacterial Zoonoses Unit, University Paris-Est, Anses, 94706 Maisons-Alfort, France; (F.V.); (K.L.)
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Konrad Sachse
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
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Unal D, García-Caparrós P, Kumar V, Dietz KJ. Chloroplast-associated molecular patterns as concept for fine-tuned operational retrograde signalling. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190443. [PMID: 32362264 DOI: 10.1098/rstb.2019.0443] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chloroplasts compose about one-quarter of the mesophyll cell volume and contain about 60% of the cell protein. Photosynthetic carbon assimilation is the dominating metabolism in illuminated leaves. To optimize the resource expenditure in these costly organelles and to control and adjust chloroplast metabolism, an intensive transfer of information between nucleus-cytoplasm and chloroplasts occurs in both directions as anterograde and retrograde signalling. Recent research identified multiple retrograde pathways that use metabolite transfer and include reaction products of lipids and carotenoids with reactive oxygen species (ROS). Other pathways use metabolites of carbon, sulfur and nitrogen metabolism, low molecular weight antioxidants and hormone precursors to carry information between the cell compartments. This review focuses on redox- and ROS-related retrograde signalling pathways. In analogy to the microbe-associated molecular pattern, we propose the term 'chloroplast-associated molecular pattern' which connects chloroplast performance to extrachloroplast processes such as nuclear gene transcription, posttranscriptional processing, including translation, and RNA and protein fate. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
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Affiliation(s)
- Dilek Unal
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany.,Molecular Biology and Genetic, Faculty of Science and Letter, Bilecik Seyh Edebali University, 11230 Bilecik, Turkey
| | - Pedro García-Caparrós
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany.,Department of Agronomy, University of Almeria, Higher Engineering School, Agrifood Campus of International Excellence ceiA3, Carretera de Sacramento s/n, La Cañada de San Urbano 04120, Almeria, Spain
| | - Vijay Kumar
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
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Patiño LH, Camargo M, Muñoz M, Ríos-Chaparro DI, Patarroyo MA, Ramírez JD. Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis. Front Microbiol 2018; 9:1854. [PMID: 30186244 PMCID: PMC6113918 DOI: 10.3389/fmicb.2018.01854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct.
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Affiliation(s)
- Luz H. Patiño
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan D. Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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Impact of Active Metabolism on Chlamydia trachomatis Elementary Body Transcript Profile and Infectivity. J Bacteriol 2018; 200:JB.00065-18. [PMID: 29735758 DOI: 10.1128/jb.00065-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/01/2018] [Indexed: 11/20/2022] Open
Abstract
Bacteria of the genus Chlamydia include the significant human pathogens Chlamydia trachomatis and C. pneumoniae All chlamydiae are obligate intracellular parasites that depend on infection of a host cell and transition through a biphasic developmental cycle. Following host cell invasion by the infectious elementary body (EB), the pathogen transitions to the replicative but noninfectious reticulate body (RB). Differentiation of the RB back to the EB is essential to generate infectious progeny. While the EB form has historically been regarded as metabolically inert, maintenance of infectivity during incubation with specific nutrients has revealed active maintenance of the infectious phenotype. Using transcriptome sequencing, we show that the transcriptome of extracellular EBs incubated under metabolically stimulating conditions does not cluster with germinating EBs but rather with the transcriptome of EBs isolated directly from infected cells. In addition, the transcriptional profile of the extracellular metabolizing EBs more closely resembled that of EB production than germination. Maintenance of infectivity of extracellular EBs was achieved by metabolizing chemically diverse compounds, including glucose 6-phosphate, ATP, and amino acids, all of which can be found in extracellular environments, including mucosal secretions. We further show that the EB cell type actively maintains infectivity in the inclusion after terminal differentiation. Overall, these findings contribute to the emerging understanding that the EB cell form is actively maintained through metabolic processes after terminal differentiation to facilitate prolonged infectivity within the inclusion and under host cell free conditions, for example, following deposition at mucosal surfaces.IMPORTANCE Chlamydiae are obligate intracellular Gram-negative bacteria that are responsible for a wide range of diseases in both animal and human hosts. According to the Centers for Disease Control and Prevention, C. trachomatis is the most frequently reported sexually transmitted infection in the United States, costing the American health care system nearly $2.4 billion annually. Every year, there are over 4 million new cases of Chlamydia infections in the United States and an estimated 100 million cases worldwide. To cause disease, Chlamydia must successfully complete its complex biphasic developmental cycle, alternating between an infectious cell form (EB) specialized for initiating entry into target cells and a replicative form (RB) specialized for creating and maintaining the intracellular replication niche. The EB cell form has historically been considered metabolically quiescent, a passive entity simply waiting for contact with a host cell to initiate the next round of infection. Recent studies and data presented here demonstrate that the EB maintains its infectious phenotype by actively metabolizing a variety of nutrients. Therefore, the EB appears to have an active role in chlamydial biology, possibly within multiple environments, such as mucosal surfaces, fomites, and inside the host cell after formation.
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de Souza A, Wang JZ, Dehesh K. Retrograde Signals: Integrators of Interorganellar Communication and Orchestrators of Plant Development. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:85-108. [PMID: 27813652 DOI: 10.1146/annurev-arplant-042916-041007] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Interorganellar cooperation maintained via exquisitely controlled retrograde-signaling pathways is an evolutionary necessity for maintenance of cellular homeostasis. This signaling feature has therefore attracted much research attention aimed at improving understanding of the nature of these communication signals, how the signals are sensed, and ultimately the mechanism by which they integrate targeted processes that collectively culminate in organellar cooperativity. The answers to these questions will provide insight into how retrograde-signal-mediated regulatory mechanisms are recruited and which biological processes are targeted, and will advance our understanding of how organisms balance metabolic investments in growth against adaptation to environmental stress. This review summarizes the present understanding of the nature and the functional complexity of retrograde signals as integrators of interorganellar communication and orchestrators of plant development, and offers a perspective on the future of this critical and dynamic area of research.
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Affiliation(s)
- Amancio de Souza
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521;
| | - Jin-Zheng Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521;
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521;
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Lu W, Xin Z, Shida W, Jiyao L, Xin X. [Role of small noncoding RNA in the regulation of bacterial virulence]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2017; 34:433-438. [PMID: 28317367 DOI: 10.7518/hxkq.2016.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the long-term interaction between pathogens and host, the pathogens regulate the expression of related viru-lence genes to fit the host environment in response to the changes in the host microenvironment. Gene expression was believed to be controlled mainly at the level of transcription initiation by repressors or activators. Recent studies have revealed that small noncoding RNAs (sRNAs) are key regulators in bacterial pathogenesis. sRNA in bacteria is a noncoding RNA with length ranging from 50 to 500 nucleotides. Pathogens can sense the changes in the host environment and consequently regulate the expression of virulence genes by sRNAs. This condition promotes the ability of pathogens to survive within the host, which is beneficial to the invasion and pathogenicity of pathogens. In contrast to transcriptional factors, sRNA-mediated gene regu-lation makes rapid and sensitive responses to environmental cues. Many sRNAs involved in bacterial virulence and pathogenesis have been identified. These sRNAs are key components of coordinated regulation networks, playing important roles in regulating the expression of virulence genes at post-transcriptional level. This review aims to provide an overview on the molecular mechanisms and roles of sRNAs in the regulation of bacterial virulence.
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Affiliation(s)
- Wang Lu
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zheng Xin
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Wang Shida
- State Key Laboratory of Oral Diseases, Dept. of General Clinic, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Li Jiyao
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xu Xin
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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12
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Rolando M, Gomez-Valero L, Buchrieser C. Bacterial remodelling of the host epigenome: functional role and evolution of effectors methylating host histones. Cell Microbiol 2016; 17:1098-107. [PMID: 26031999 DOI: 10.1111/cmi.12463] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/15/2015] [Accepted: 05/25/2015] [Indexed: 12/25/2022]
Abstract
The modulation of the chromatin organization of eukaryotic cells plays an important role in regulating key cellular processes including host defence mechanisms against pathogens. Thus, to successfully survive in a host cell, a sophisticated bacterial strategy is the subversion of nuclear processes of the eukaryotic cell. Indeed, the number of bacterial proteins that target host chromatin to remodel the host epigenetic machinery is expanding. Some of the identified bacterial effectors that target the chromatin machinery are 'eukaryotic-like' proteins as they mimic eukaryotic histone writers in carrying the same enzymatic activities. The best-studied examples are the SET domain proteins that methylate histones to change the chromatin landscape. In this review, we will discuss SET domain proteins identified in the Legionella, Chlamydia and Bacillus genomes that encode enzymatic activities targeting host histones. Moreover, we discuss their possible origin as having evolved from prokaryotic ancestors or having been acquired from their eukaryotic hosts during their co-evolution. The characterization of such bacterial effectors as modifiers of the host chromatin landscape is an exciting field of research as it elucidates new bacterial strategies to not only manipulate host functions through histone modifications but it may also identify new modifications of the mammalian host cells not known before.
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Affiliation(s)
- Monica Rolando
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, Paris, France
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13
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Abstract
The lifestyle of Chlamydiae is unique: the bacteria alternate between two morphologically distinct forms, an infectious non-replicative elementary body (EB), and a replicative, non-infectious reticulate body (RB). This review focuses on recent advances in understanding the structure and function of the infectious form of the best-studied member of the phylum, the human pathogen Chlamydia trachomatis. Once considered as an inert particle of little functional capacity, the EB is now perceived as a sophisticated entity that encounters at least three different environments during each infectious cycle. We review current knowledge on its composition and morphology, and emerging metabolic activities. These features confer resistance to the extracellular environment, the ability to penetrate a host cell and ultimately enable the EB to establish a niche enabling bacterial survival and growth. The bacterial and host molecules involved in these processes are beginning to emerge.
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14
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Orillard E, Tan M. Functional analysis of three topoisomerases that regulate DNA supercoiling levels in Chlamydia. Mol Microbiol 2015; 99:484-96. [PMID: 26447825 DOI: 10.1111/mmi.13241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2015] [Indexed: 02/01/2023]
Abstract
Chlamydia is a medically important bacterium that infects eukaryotic cells. Temporal expression of chlamydial genes during the intracellular infection is proposed to be regulated by changes in DNA supercoiling levels. To understand how chlamydial supercoiling levels are regulated, we purified and analyzed three putative Chlamydia trachomatis topoisomerases. As predicted by sequence homology, CT189/190 are the two subunits of DNA gyrase, whereas CT643 is a topoisomerase I. CT660/661 have been predicted to form a second DNA gyrase, but the reconstitute holoenzyme decatenated and relaxed DNA, indicating that the proteins are subunits of topoisomerase IV. Promoter analysis showed that each topoisomerase is transcribed from its own operon by the major chlamydial RNA polymerase. Surprisingly, all three topoisomerase promoters had higher activity from a more supercoiled DNA template. This supercoiling-responsivesness is consistent with negative feedback control of topoisomerase I and topoisomerase IV expression, which is typical of other bacteria. However, activation of the chlamydial gyrase promoter by increased supercoiling is unorthodox compared with the relaxation-induced transcription of gyrase in other bacteria. We present a model in which supercoiling levels during the intracellular chlamydial developmental cycle are regulated by unusual positive feedback control of the gyrase promoter and the temporal expression of three topoisomerases.
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Affiliation(s)
- Emilie Orillard
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
| | - Ming Tan
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA.,Department of Medicine, University of California, Irvine, CA, USA
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15
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Chi W, Feng P, Ma J, Zhang L. Metabolites and chloroplast retrograde signaling. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:32-8. [PMID: 25912815 DOI: 10.1016/j.pbi.2015.04.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 05/23/2023]
Abstract
Intracellular signaling from chloroplast to nucleus followed by a subsequent response in the chloroplast is called retrograde signaling. It not only coordinates the expression of nuclear and chloroplast genes, which is essential for chloroplast biogenesis, but also maintains chloroplast function at optimal levels in response to fluxes in metabolites and changes in environmental conditions. In recent years several putative retrograde signals have been identified and signaling pathways have been proposed. Here we review retrograde signals derived from tetrapyrroles, carotenoids, nucleotides and isoprene precursors in response to abiotic stresses, including oxidative stress. We discuss the responses that these signals elicit and show that they not only modify chloroplast function but also influence other aspects of plant development and adaptation.
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Affiliation(s)
- Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Peiqiang Feng
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinfang Ma
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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16
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Oliva G, Sahr T, Buchrieser C. Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence. FEMS Microbiol Rev 2015; 39:331-349. [DOI: 10.1093/femsre/fuv022] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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17
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Grieshaber NA, Tattersall JS, Liguori J, Lipat JN, Runac J, Grieshaber SS. Identification of the base-pairing requirements for repression of hctA translation by the small RNA IhtA leads to the discovery of a new mRNA target in Chlamydia trachomatis. PLoS One 2015; 10:e0116593. [PMID: 25756658 PMCID: PMC4355289 DOI: 10.1371/journal.pone.0116593] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
The non-coding small RNA, IhtA expressed by the obligate intracellular human pathogen Chlamydia trachomatis modulates the translation of HctA, a key protein involved in replicative to infectious cell type differentiation. Using a combination of bioinformatics and mutagenesis we sought to identify the base pairing requirement for functional repression of HctA protein expression, with an eye to applying our findings towards the identification of additional targets. IhtA is predicted to fold into a three stem:loop structure. We found that loop 1 occludes the initiation codon of hctA, while loop 2 and 3 are not required for function. This 7 nucleotide region forms G/C rich interactions surrounding the AUG of hctA. Two additional genes in the chlamydial genome, CTL0322 and CTL0097, contained some elements of the hctA:IhtA recognition sequence. The mRNA of both CTL0322and CTL0097 interacted with IhtA in vitro as measured by biolayer interferometry. However, using a CheZ reporter expression system, IhtA only inhibited the translation of CTL0322. The proposed IhtA recognition site in the CTL0322 message contains significant G/C base pairing on either side of the initiation codon while CTL0097 only contains G/C base pairing 3' to the AUG initiation codon. These data suggest that as the functional interacting region is only 6-7nt in length that full translation repression is dependent on the degree of G/C base pairing. Additionally our results indicate that IhtA may regulate multiple mRNAs involved in the chlamydial infectious cycle.
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Affiliation(s)
- Nicole A. Grieshaber
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, United States of America
| | - Jeremiah S. Tattersall
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Johella Liguori
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Joseph N. Lipat
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Justin Runac
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Scott S. Grieshaber
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, United States of America
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18
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Banerjee A, Sharkey TD. Methylerythritol 4-phosphate (MEP) pathway metabolic regulation. Nat Prod Rep 2014; 31:1043-55. [DOI: 10.1039/c3np70124g] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The methylerythritol 4-phosphate pathway provides precursors for isoprenoids in bacteria, some eukaryotic parasites, and chloroplasts of plants. Metabolic regulatory mechanisms control flux through the pathway and the concentration of a central intermediate, methylerythritol cyclodiphosphate.
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Affiliation(s)
- A. Banerjee
- Department of Biochemistry and Molecular Biology
- Michigan State University
- East Lansing, 48824 USA
| | - T. D. Sharkey
- Department of Biochemistry and Molecular Biology
- Michigan State University
- East Lansing, 48824 USA
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19
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Xiao Y, Wang J, Dehesh K. Review of stress specific organelles-to-nucleus metabolic signal molecules in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 212:102-7. [PMID: 24094057 DOI: 10.1016/j.plantsci.2013.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 05/08/2023]
Abstract
Plants, as sessile organisms, have evolved an exquisitely tuned response network to survive environmental perturbations. Organelles-to-nucleus signaling, termed retrograde signaling, plays a key role in stress responses by communicating subcellular perturbations to the nucleus, thereby coordinating expression of stress specific nuclear genes essential for adaptive responses to hostile environment. Recently, several stress specific retrograde signals have been identified; most notable amongst them are reactive oxygen species, tetrapyrroles, 2-C-methyl-d-erythritol 2,4-cyclodiphosphate (MEcPP), unsaturated fatty acids, nitric oxide (NO), 3'-phosphoadenosine 5'-phosphate (PAP), and β-cyclocitral (β-CC). It is expected that this trend will continue to provide fundamental insight into the integrative network of sensory systems central to the adaptive responses of plants to the prevailing environment. This review focuses on the recent advancements in the field.
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Affiliation(s)
- Yanmei Xiao
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
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20
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Woodson JD, Chory J. Organelle signaling: how stressed chloroplasts communicate with the nucleus. Curr Biol 2013; 22:R690-2. [PMID: 22974998 PMCID: PMC4854192 DOI: 10.1016/j.cub.2012.07.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Plastids are able to relay information to the nucleus to regulate stress responses. A new genetic screen has identified an isoprenoid intermediate that accumulates in stressed plastids and acts as a novel retrograde signal.
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Affiliation(s)
- Jesse D Woodson
- Plant Biology Laboratory, The Salk Institute, La Jolla, CA 92037, USA.
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21
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Tattersall J, Rao GV, Runac J, Hackstadt T, Grieshaber SS, Grieshaber NA. Translation inhibition of the developmental cycle protein HctA by the small RNA IhtA is conserved across Chlamydia. PLoS One 2012; 7:e47439. [PMID: 23071807 PMCID: PMC3469542 DOI: 10.1371/journal.pone.0047439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 09/17/2012] [Indexed: 11/18/2022] Open
Abstract
The developmental cycle of the obligate intracellular pathogen Chlamydia trachomatis serovar L2 is controlled in part by the small non-coding RNA (sRNA), IhtA. All Chlamydia alternate in a regulated fashion between the infectious elementary body (EB) and the replicative reticulate body (RB) which asynchronously re-differentiates back to the terminal EB form at the end of the cycle. The histone like protein HctA is central to RB:EB differentiation late in the cycle as it binds to and occludes the genome, thereby repressing transcription and translation. The sRNA IhtA is a critical component of this regulatory loop as it represses translation of hctA until late in infection at which point IhtA transcription decreases, allowing HctA expression to occur and RB to EB differentiation to proceed. It has been reported that IhtA is expressed during infection by the human pathogens C. trachomatis serovars L2, D and L2b and C. pneumoniae. We show in this work that IhtA is also expressed by the animal pathogens C. caviae and C. muridarum. Expression of HctA in E. coli is lethal and co-expression of IhtA relieves this phenotype. To determine if regulation of HctA by IhtA is a conserved mechanism across pathogenic chlamydial species, we cloned hctA and ihtA from C. trachomatis serovar D, C. muridarum, C. caviae and C. pneumoniae and assayed for rescue of growth repression in E. coli co-expression studies. In each case, co-expression of ihtA with the cognate hctA resulted in relief of growth repression. In addition, expression of each chlamydial species IhtA rescued the lethal phenotype of C. trachomatis serovar L2 HctA expression. As biolayer interferometry studies indicate that IhtA interacts directly with hctA message for all species tested, we predict that conserved sequences of IhtA are necessary for function and/or binding.
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Affiliation(s)
- Jeremiah Tattersall
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Geeta Vittal Rao
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Justin Runac
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Ted Hackstadt
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Scott S. Grieshaber
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Nicole A. Grieshaber
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
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22
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The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire. Microbiol Mol Biol Rev 2012; 76:405-43. [PMID: 22688818 DOI: 10.1128/mmbr.05013-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One form of immune evasion is a developmental state called "persistence" whereby chlamydial pathogens respond to the host-mediated withdrawal of L-tryptophan (Trp). A sophisticated survival mode of reversible quiescence is implemented. A mechanism has evolved which suppresses gene products necessary for rapid pathogen proliferation but allows expression of gene products that underlie the morphological and developmental characteristics of persistence. This switch from one translational profile to an alternative translational profile of newly synthesized proteins is proposed to be accomplished by maximizing the Trp content of some proteins needed for rapid proliferation (e.g., ADP/ATP translocase, hexose-phosphate transporter, phosphoenolpyruvate [PEP] carboxykinase, the Trp transporter, the Pmp protein superfamily for cell adhesion and antigenic variation, and components of the cell division pathway) while minimizing the Trp content of other proteins supporting the state of persistence. The Trp starvation mechanism is best understood in the human-Chlamydia trachomatis relationship, but the similarity of up-Trp and down-Trp proteomic profiles in all of the pathogenic Chlamydiaceae suggests that Trp availability is an underlying cue relied upon by this family of pathogens to trigger developmental transitions. The biochemically expensive pathogen strategy of selectively increased Trp usage to guide the translational profile can be leveraged significantly with minimal overall Trp usage by (i) regional concentration of Trp residue placements, (ii) amplified Trp content of a single protein that is required for expression or maturation of multiple proteins with low Trp content, and (iii) Achilles'-heel vulnerabilities of complex pathways to high Trp content of one or a few enzymes.
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23
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Xiao Y, Savchenko T, Baidoo EEK, Chehab WE, Hayden DM, Tolstikov V, Corwin JA, Kliebenstein DJ, Keasling JD, Dehesh K. Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes. Cell 2012; 149:1525-35. [PMID: 22726439 DOI: 10.1016/j.cell.2012.04.038] [Citation(s) in RCA: 262] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 11/05/2011] [Accepted: 04/02/2012] [Indexed: 12/15/2022]
Abstract
Plastid-derived signals are known to coordinate expression of nuclear genes encoding plastid-localized proteins in a process termed retrograde signaling. To date, the identity of retrograde-signaling molecules has remained elusive. Here, we show that methylerythritol cyclodiphosphate (MEcPP), a precursor of isoprenoids produced by the plastidial methylerythritol phosphate (MEP) pathway, elicits the expression of selected stress-responsive nuclear-encoded plastidial proteins. Genetic and pharmacological manipulations of the individual MEP pathway metabolite levels demonstrate the high specificity of MEcPP as an inducer of these targeted stress-responsive genes. We further demonstrate that abiotic stresses elevate MEcPP levels, eliciting the expression of the aforementioned genes. We propose that the MEP pathway, in addition to producing isoprenoids, functions as a stress sensor and a coordinator of expression of targeted stress-responsive nuclear genes via modulation of the levels of MEcPP, a specific and critical retrograde-signaling metabolite.
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Affiliation(s)
- Yanmei Xiao
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
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24
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Multilocus sequence typing of urogenital Chlamydia trachomatis from patients with different degrees of clinical symptoms. Sex Transm Dis 2012; 38:490-4. [PMID: 21301388 DOI: 10.1097/olq.0b013e31820b8be0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND In the past, contradictory results have been obtained linking Chlamydia trachomatis serovars (ompA gene) to different clinical courses of infection. METHODS A high resolution multilocus sequence typing (MLST) system was used to genotype 6 genetic regions, including ompA, in 70 Dutch urogenital C. trachomatis strains from patients with different degrees of defined clinical symptoms (asymptomatic, symptomatic, and lower abdominal pain), to determine if MLST genotypes correlated with clinical manifestations of infection. RESULTS AND CONCLUSIONS We identified 46 MLST types, with only a small overlap to Swedish MLST types. This study found no correlation between MLST profiles and symptomatology. To understand the clinical course of infection, future studies should not only consider bacterial factors but also look on the immunogenetics of the host.
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25
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Estavillo GM, Chan KX, Phua SY, Pogson BJ. Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast. FRONTIERS IN PLANT SCIENCE 2012; 3:300. [PMID: 23316207 PMCID: PMC3539676 DOI: 10.3389/fpls.2012.00300] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 12/12/2012] [Indexed: 05/18/2023]
Abstract
Plant organelles produce retrograde signals to alter nuclear gene expression in order to coordinate their biogenesis, maintain homeostasis, or optimize their performance under adverse conditions. Many signals of different chemical nature have been described in the past decades, including chlorophyll intermediates, reactive oxygen species (ROS), and adenosine derivatives. While the effects of retrograde signaling on gene expression are well understood, the initiation and transport of the signals and their mode of action have either not been resolved, or are a matter of speculation. Moreover, retrograde signaling should be considered as part of a broader cellular network, instead of as separate pathways, required to adjust to changing physiologically relevant conditions. Here we summarize current plastid retrograde signaling models in plants, with a focus on new signaling pathways, SAL1-PAP, methylerythritol cyclodiphosphate (MEcPP), and β-cyclocitral (β-CC), and outline missing links or future areas of research that we believe need to be addressed to have a better understanding of plant intracellular signaling networks.
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Affiliation(s)
| | | | | | - Barry J. Pogson
- *Correspondence: Barry J. Pogson, ARC Centre of Excellence in Plant Energy of Biology, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia. e-mail:
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26
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Anuchin AM, Goncharenko AV, Demidenok OI, Kaprelyants AS. Histone-like proteins of bacteria (review). APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683811060020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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27
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Abdelrahman YM, Rose LA, Belland RJ. Developmental expression of non-coding RNAs in Chlamydia trachomatis during normal and persistent growth. Nucleic Acids Res 2010; 39:1843-54. [PMID: 21051342 PMCID: PMC3061062 DOI: 10.1093/nar/gkq1065] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chlamydia trachomatis is an obligate intracellular bacterium that exhibits a unique biphasic developmental cycle that can be disrupted by growth in the presence of IFN-γ and β-lactams, giving rise to an abnormal growth state termed persistence. Here we have examined the expression of a family of non-coding RNAs (ncRNAs) that are differentially expressed during the developmental cycle and the induction of persistence and reactivation. ncRNAs were initially identified using an intergenic tiling microarray and were confirmed by northern blotting. ncRNAs were mapped, characterized and compared with the previously described chlamydial ncRNAs. The 5'- and 3'-ends of the ncRNAs were determined using an RNA circularization procedure. Promoter predictions indicated that all ncRNAs were expressed from σ(66) promoters and eight ncRNAs contained non-templated 3'-poly-A or poly-AG additions. Expression of ncRNAs was studied by northern blotting during (i) the normal developmental cycle, (ii) IFN-γ-induced persistence and (iii) carbenicillin-induced persistence. Differential temporal expression during the developmental cycle was seen for all ncRNAs and distinct differences in expression were seen during IFN-γ and carbenicillin-induced persistence and reactivation. A heterologous co-expression system was used to demonstrate that one of the identified ncRNAs regulated the expression of FtsI by inducing degradation of ftsI mRNA.
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Affiliation(s)
- Yasser M Abdelrahman
- Department of Microbiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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28
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Pennini ME, Perrinet S, Dautry-Varsat A, Subtil A. Histone methylation by NUE, a novel nuclear effector of the intracellular pathogen Chlamydia trachomatis. PLoS Pathog 2010; 6:e1000995. [PMID: 20657819 PMCID: PMC2904774 DOI: 10.1371/journal.ppat.1000995] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 06/10/2010] [Indexed: 12/30/2022] Open
Abstract
Sequence analysis of the genome of the strict intracellular pathogen Chlamydia trachomatis revealed the presence of a SET domain containing protein, proteins that primarily function as histone methyltransferases. In these studies, we demonstrated secretion of this protein via a type III secretion mechanism. During infection, the protein is translocated to the host cell nucleus and associates with chromatin. We therefore named the protein nuclear effector (NUE). Expression of NUE in mammalian cells by transfection reconstituted nuclear targeting and chromatin association. In vitro methylation assays confirmed NUE is a histone methyltransferase that targets histones H2B, H3 and H4 and itself (automethylation). Mutants deficient in automethylation demonstrated diminished activity towards histones suggesting automethylation functions to enhance enzymatic activity. Thus, NUE is secreted by Chlamydia, translocates to the host cell nucleus and has enzymatic activity towards eukaryotic substrates. This work is the first description of a bacterial effector that directly targets mammalian histones.
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Affiliation(s)
- Meghan E. Pennini
- Institut Pasteur, Unité de Biologie des Interactions Cellulaires, Paris, France
- CNRS URA 2582, Paris, France
| | - Stéphanie Perrinet
- Institut Pasteur, Unité de Biologie des Interactions Cellulaires, Paris, France
- CNRS URA 2582, Paris, France
| | - Alice Dautry-Varsat
- Institut Pasteur, Unité de Biologie des Interactions Cellulaires, Paris, France
- CNRS URA 2582, Paris, France
| | - Agathe Subtil
- Institut Pasteur, Unité de Biologie des Interactions Cellulaires, Paris, France
- CNRS URA 2582, Paris, France
- * E-mail:
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29
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Anuchin AM, Goncharenko AV, Galon IV, Demidenok OI, Kudykina YK, Moisenovich MM, Mulyukin AL, Kaprelyants AS. The model of resting forms of micobacteria for testing of chemodrugs for latent forms of tuberculosis. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810030063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Anuchin AM, Goncharenko AV, Demina GR, Mulyukin AL, Ostrovsky DN, Kaprelyants AS. The role of histone-like protein, Hlp, in Mycobacterium smegmatis dormancy. FEMS Microbiol Lett 2010; 308:101-7. [PMID: 20497227 DOI: 10.1111/j.1574-6968.2010.01988.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The role of histone-like protein (Hlp) in the development of a dormant state in long-incubated stationary-phase Mycobacterium smegmatis cells was studied in two models: (1) adoption of 'nonculturable' (NC) state, which is reversible due to resuscitation with proteinaceous resuscitation-promoting factor (Rpf) and (2) the formation of morphologically distinct, ovoid resting forms. In the first model, inactivation of the hlp gene resulted in prolongation of culturability of starved cells followed by irreversible nonculturability when mycobacterial cells were unresponsive to resuscitation with Rpf. In the second model, M. smegmatis strain with the inactivated hlp gene was able to form dormant ovoid cells, but they were less resistant to heating and UV radiation than those of wild-type strain. The susceptibility of ovoid cells produced by Delta hlp mutant to these damaging factors was probably due to a less condensed state of DNA, as revealed by fluorescent microscopy and DAPI staining. Evidently, Hlp is essential for cell viability at a later stage of NC dormancy or provides a greater stability of specialized dormant forms.
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Affiliation(s)
- Aleksey M Anuchin
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.
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Kim SM, Kuzuyama T, Kobayashi A, Sando T, Chang YJ, Kim SU. 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (IDS) is encoded by multicopy genes in gymnosperms Ginkgo biloba and Pinus taeda. PLANTA 2008; 227:287-98. [PMID: 17763867 DOI: 10.1007/s00425-007-0616-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 08/19/2007] [Indexed: 05/17/2023]
Abstract
Isoprenoids are synthesized through the condensation of five-carbon intermediates, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), derived from two distinct biosynthetic routes: cytosolic mevalonate (MVA) and plastidial 2-C-methyl-D: -erythritol 4-phosphate (MEP) pathways. 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (IDS; EC 1.17.1.2), which catalyzes the last step of MEP pathway, was cloned as a multicopy gene from gymnosperms Ginkgo biloba (GbIDS1, GbIDS2, and GbIDS2-1) and Pinus taeda (PtIDS1 and PtIDS2), and characterized. Phylogenetic tree constructed with other plant IDSs demonstrated gymnosperm IDSs were distinctively different from angiosperm IDSs. The gymnosperm IDS clade contained two subclades, one composed of GbIDS1 and PtIDS1, and the other composed of GbIDS2, GbIDS2-1, and PtIDS2. G. biloba IDSs, except GbIDS2-1, successfully complemented Escherichia coli DLYT1, a lytB disruptant, confirming the in vivo competency of isozymes. During the 4 weeks study period, although transcript levels of GbIDS1s were similar both in roots and leaves of cultured G. biloba embryo, the transcripts of GbIDS2 predominantly occurred in the embryo roots, where diterpene ginkgolides are biosynthesized. Levels of PtIDS2 transcripts in the diterpenoid resin-producing wood were 4-5 times higher than those in other tissues. Higher levels of GbIDS1 transcripts were induced by light, whereas those of GbIDS2 were increased by methyl jasmonate treatment. These results strongly imply GbIDS2 and PtIDS2 have high correlation with secondary metabolism. In Arabidopsis transient expression system, N-terminal 100 amino acid residues of GbIDS1 delivered fused GFP protein into chloroplast as well as cytosol and nucleus, whereas those of GbIDS2, GbIDS2-1, and two PtIDSs delivered GFP only into chloroplast.
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Affiliation(s)
- Sang-Min Kim
- Program in Applied Life Chemistry, Department of Agricultural Biotechnology, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul, 151-921, Korea
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