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Wang X, Luo L, Xu J, Lu Q, Xia H, Huang Y, Zhang L, Xie L, Jiwa H, Liang S, Luo X, Luo J. Echinatin inhibits tumor growth and synergizes with chemotherapeutic agents against human bladder cancer cells by activating p38 and suppressing Wnt/β-catenin pathways. Genes Dis 2024; 11:1050-1065. [PMID: 37692489 PMCID: PMC10491917 DOI: 10.1016/j.gendis.2023.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/13/2023] [Accepted: 03/29/2023] [Indexed: 09/12/2023] Open
Abstract
Bladder cancer (BC) is one of the most common malignant tumors in the urinary system. Due to the poor prognosis and high mortality rate of the disease, it is urgent to develop new drugs with high efficacy and low toxicity to treat BC. Echinatin (Ecn) is a bioactive natural flavonoid oflicorice that has attracted special attention for its promising anti-tumor potential. Herein, we explored the inhibitory effects of Echinatin on BC cells and probed the possible molecular mechanism. We found that Ecnin vitro inhibited the proliferation, migration, and invasion, arrested the cell cycle at the G2/M phase, and promoted apoptosis in BC cells. Besides, Ecn had no notable cytotoxicity towards human normal cells. We subsequently confirmed that Ecn restrained xenograft tumor growth and metastasis of BC cells in vivo. Mechanistically, Ecn activated the p38 signaling pathway but inactivated the Wnt/β-catenin signaling pathway, while over-expression of β-catenin and the p38 inhibitor both attenuated the inhibitory effects of Ecn on BC cells. Remarkably, Ecn combined with cisplatin (DDP) or gemcitabine (Gem) had synergistic inhibitory effects on BC cells. In summary, our results validate that Ecn inhibits the tumor growth of human BC cells via p38 and Wnt/β-catenin signaling pathways. More meaningfully, our results suggest a potential strategy to enhance DDP- or Gem-induced inhibitory effects on BC cells by combining with Ecn.
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Affiliation(s)
- Xiaoxuan Wang
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lijuan Luo
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jingtao Xu
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Qiuping Lu
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Haichao Xia
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yanran Huang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Lulu Zhang
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Liping Xie
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Habu Jiwa
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Shiqiong Liang
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoji Luo
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Jinyong Luo
- Key Laboratory of Diagnostic Medicine Designated By the Chinese Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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2
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Barton IS, Ren Z, Cribb CB, Pitzer JE, Baglivo I, Martin DW, Wang X, Roop RM. Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid. mBio 2023; 14:e0220123. [PMID: 37847580 PMCID: PMC10746212 DOI: 10.1128/mbio.02201-23] [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: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Histone-like nucleoid structuring (H-NS) and H-NS-like proteins coordinate host-associated behaviors in many pathogenic bacteria, often through forming silencer/counter-silencer pairs with signal-responsive transcriptional activators to tightly control gene expression. Brucella and related bacteria do not encode H-NS or homologs of known H-NS-like proteins, and it is unclear if they have other proteins that perform analogous functions during pathogenesis. In this work, we provide compelling evidence for the role of MucR as a novel H-NS-like protein in Brucella. We show that MucR possesses many of the known functions attributed to H-NS and H-NS-like proteins, including the formation of silencer/counter-silencer pairs to control virulence gene expression and global structuring of the nucleoid. These results uncover a new role for MucR as a nucleoid structuring protein and support the importance of temporal control of gene expression in Brucella and related bacteria.
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Affiliation(s)
- Ian S. Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Connor B. Cribb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Joshua E. Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Daniel W. Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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3
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Akar R, Fink MJ, Omnus DJ, Jonas K. Regulation of the general stress response sigma factor σ T by Lon-mediated proteolysis. J Bacteriol 2023; 205:e0022823. [PMID: 37930077 PMCID: PMC10662116 DOI: 10.1128/jb.00228-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Regulated protein degradation is a critical process in all cell types, which contributes to the precise regulation of protein amounts in response to internal and external cues. In bacteria, protein degradation is carried out by ATP-dependent proteases. Although past work revealed detailed insights into the operation principles of these proteases, there is limited knowledge about the substrate proteins that are degraded by distinct proteases and the regulatory role of proteolysis in cellular processes. This study reveals a direct role of the conserved protease Lon in regulating σT, a transcriptional regulator of the general stress response in α-proteobacteria. Our work is significant as it underscores the importance of regulated proteolysis in modulating the levels of key regulatory proteins under changing conditions.
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Affiliation(s)
- Roya Akar
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius, Stockholm, Sweden
| | - Matthias J. Fink
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius, Stockholm, Sweden
| | - Deike J. Omnus
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius, Stockholm, Sweden
| | - Kristina Jonas
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius, Stockholm, Sweden
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4
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Alakavuklar MA, Fiebig A, Crosson S. The Brucella Cell Envelope. Annu Rev Microbiol 2023; 77:233-253. [PMID: 37104660 PMCID: PMC10787603 DOI: 10.1146/annurev-micro-032521-013159] [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] [Indexed: 04/29/2023]
Abstract
The cell envelope is a multilayered structure that insulates the interior of bacterial cells from an often chaotic outside world. Common features define the envelope across the bacterial kingdom, but the molecular mechanisms by which cells build and regulate this critical barrier are diverse and reflect the evolutionary histories of bacterial lineages. Intracellular pathogens of the genus Brucella exhibit marked differences in cell envelope structure, regulation, and biogenesis when compared to more commonly studied gram-negative bacteria and therefore provide an excellent comparative model for study of the gram-negative envelope. We review distinct features of the Brucella envelope, highlighting a conserved regulatory system that links cell cycle progression to envelope biogenesis and cell division. We further discuss recently discovered structural features of the Brucella envelope that ensure envelope integrity and that facilitate cell survival in the face of host immune stressors.
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Affiliation(s)
- Melene A Alakavuklar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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5
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Kint N, Viollier PH. Extracellular transfer of a conserved polymerization factor for multi-flagellin filament assembly in Caulobacter. Cell Rep 2023; 42:112890. [PMID: 37515768 DOI: 10.1016/j.celrep.2023.112890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 07/31/2023] Open
Abstract
Unidirectional growth of filamentous protein assemblies including the bacterial flagellum relies on dedicated polymerization factors (PFs). The molecular determinants and structural transitions imposed by PFs on multi-subunit assembly are poorly understood. Here, we unveil FlaY from the polarized α-proteobacterium Caulobacter crescentus as a defining member of an alternative class of specialized flagellin PFs. Unlike the paradigmatic FliD capping protein, FlaY relies on a funnel-like β-propeller fold for flagellin polymerization. FlaY binds flagellin and is secreted by the flagellar secretion apparatus, yet it can also promote flagellin polymerization exogenously when donated from flagellin-deficient cells, serving as a transferable, extracellular public good. While the surge in FlaY abundance precedes bulk flagellin synthesis, FlaY-independent filament assembly is enhanced by mutation of a conserved region in multiple flagellin paralogs. We suggest that FlaYs are (multi-)flagellin PFs that evolved convergently to FliDs yet appropriated the versatile β-propeller fold implicated in human diseases for chaperone-assisted filament assembly.
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Affiliation(s)
- Nicolas Kint
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Genève, Switzerland.
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Genève, Switzerland.
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6
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Xuyang L, Cristina LM, Laura MA, Xu P. A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression. Nucleic Acids Res 2023; 51:1724-1739. [PMID: 36727447 PMCID: PMC9976892 DOI: 10.1093/nar/gkad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/30/2022] [Accepted: 01/29/2023] [Indexed: 02/03/2023] Open
Abstract
Cell cycle regulation is crucial for all living organisms and is often targeted by viruses to facilitate their own propagation, yet cell cycle progression control is largely underexplored in archaea. In this work, we reveal a cell cycle regulator (aCcr1) carrying a ribbon-helix-helix (RHH) domain and ubiquitous in the Thermoproteota of the order Sulfolobales and their viruses. Overexpression of several aCcr1 members including gp21 of rudivirus SIRV2 and its host homolog SiL_0190 of Saccharolobus islandicus LAL14/1 results in impairment of cell division, evidenced by growth retardation, cell enlargement and an increase in cellular DNA content. Additionally, both gp21 and SiL_0190 can bind to the motif AGTATTA conserved in the promoter of several genes involved in cell division, DNA replication and cellular metabolism thereby repressing or inducing their transcription. Our results suggest that aCcr1 silences cell division and drives progression to the S-phase in Sulfolobales, a function exploited by viruses to facilitate viral propagation.
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Affiliation(s)
- Li Xuyang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Lozano-Madueño Cristina
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Martínez-Alvarez Laura
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peng Xu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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7
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Synchronized Swarmers and Sticky Stalks: Caulobacter crescentus as a Model for Bacterial Cell Biology. J Bacteriol 2023; 205:e0038422. [PMID: 36715542 PMCID: PMC9945503 DOI: 10.1128/jb.00384-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.
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8
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Transcription Regulation of Cell Cycle Regulatory Genes Mediated by NtrX to Affect Sinorhizobium meliloti Cell Division. Genes (Basel) 2022; 13:genes13061066. [PMID: 35741828 PMCID: PMC9223101 DOI: 10.3390/genes13061066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/10/2022] Open
Abstract
The cell division of the alfalfa symbiont, Sinorhizobium meliloti, is dictated by a cell cycle regulatory pathway containing the key transcription factors CtrA, GcrA, and DnaA. In this study, we found that NtrX, one of the regulators of nitrogen metabolism, can directly regulate the expression of ctrA, gcrA, and dnaA from the cell cycle pathway. Three sets of S. meliloti ntrX mutants showed similar cell division defects, such as slow growth, abnormal morphology of some cells, and delayed DNA synthesis. Transcription of ctrA and gcrA was upregulated, whereas the transcription of dnaA and ftsZ1 was downregulated in the insertion mutant and the strain of Sm1021 expressing ntrXD53E. Correspondingly, the inducible transcription of ntrX activates the expression of dnaA and ftsZ1, but represses ctrA and gcrA in the depletion strain. The expression levels of CtrA and GcrA were confirmed by Western blotting. The transcription regulation of these genes requires phosphorylation of the conserved 53rd aspartate in the NtrX protein that binds directly to the promoter regions of ctrA, gcrA, dnaA, and ftsZ1 by recognizing the characteristic sequence CAAN2-5TTG. Our findings suggest that NtrX affects S. meliloti cell division by regulating the transcription of the key cell cycle regulatory genes.
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9
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Beroual W, Prévost K, Lalaouna D, Ben Zaina N, Valette O, Denis Y, Djendli M, Brasseur G, Brilli M, Robledo Garrido M, Jimenez-Zurdo JI, Massé E, Biondi EG. The noncoding RNA CcnA modulates the master cell cycle regulators CtrA and GcrA in Caulobacter crescentus. PLoS Biol 2022; 20:e3001528. [PMID: 35192605 PMCID: PMC8959179 DOI: 10.1371/journal.pbio.3001528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/28/2022] [Accepted: 01/05/2022] [Indexed: 12/01/2022] Open
Abstract
Bacteria are powerful models for understanding how cells divide and accomplish global regulatory programs. In Caulobacter crescentus, a cascade of essential master regulators supervises the correct and sequential activation of DNA replication, cell division, and development of different cell types. Among them, the response regulator CtrA plays a crucial role coordinating all those functions. Here, for the first time, we describe the role of a novel factor named CcnA (cell cycle noncoding RNA A), a cell cycle–regulated noncoding RNA (ncRNA) located at the origin of replication, presumably activated by CtrA, and responsible for the accumulation of CtrA itself. In addition, CcnA may be also involved in the inhibition of translation of the S-phase regulator, GcrA, by interacting with its 5′ untranslated region (5′ UTR). Performing in vitro experiments and mutagenesis, we propose a mechanism of action of CcnA based on liberation (ctrA) or sequestration (gcrA) of their ribosome-binding site (RBS). Finally, its role may be conserved in other alphaproteobacterial species, such as Sinorhizobium meliloti, representing indeed a potentially conserved process modulating cell cycle in Caulobacterales and Rhizobiales. During cell cycle progression in the bacterium Caulobacter crescentus, the master cell cycle regulator CtrA is controlled by CcnA, a cell cycle-regulated non-coding RNA transcribed from a gene located at the origin of replication.
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Affiliation(s)
- Wanassa Beroual
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Karine Prévost
- Département de biochimie et de génomique fonctionnelle, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - David Lalaouna
- Département de biochimie et de génomique fonctionnelle, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Nadia Ben Zaina
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Odile Valette
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Yann Denis
- Aix-Marseille Univ, CNRS, Plate-forme Transcriptome, IMM, Marseille, France
| | - Meriem Djendli
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Gaël Brasseur
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Matteo Brilli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biosciences, University of Milan, Milan, Italy
| | - Marta Robledo Garrido
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jose-Ignacio Jimenez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Eric Massé
- Département de biochimie et de génomique fonctionnelle, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Emanuele G. Biondi
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
- * E-mail:
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10
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11
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Menikpurage IP, Woo K, Mera PE. Transcriptional Activity of the Bacterial Replication Initiator DnaA. Front Microbiol 2021; 12:662317. [PMID: 34140937 PMCID: PMC8203912 DOI: 10.3389/fmicb.2021.662317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
In bacteria, DnaA is the most conserved DNA replication initiator protein. DnaA is a DNA binding protein that is part of the AAA+ ATPase family. In addition to initiating chromosome replication, DnaA can also function as a transcription factor either as an activator or repressor. The first gene identified to be regulated by DnaA at the transcriptional levels was dnaA. DnaA has been shown to regulate genes involved in a variety of cellular events including those that trigger sporulation, DNA repair, and cell cycle regulation. DnaA's dual functions (replication initiator and transcription factor) is a potential mechanism for DnaA to temporally coordinate diverse cellular events with the onset of chromosome replication. This strategy of using chromosome replication initiator proteins as regulators of gene expression has also been observed in archaea and eukaryotes. In this mini review, we focus on our current understanding of DnaA's transcriptional activity in various bacterial species.
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Affiliation(s)
- Inoka P Menikpurage
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kristin Woo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Paola E Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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12
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Tomasch J, Koppenhöfer S, Lang AS. Connection Between Chromosomal Location and Function of CtrA Phosphorelay Genes in Alphaproteobacteria. Front Microbiol 2021; 12:662907. [PMID: 33995326 PMCID: PMC8116508 DOI: 10.3389/fmicb.2021.662907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022] Open
Abstract
Most bacterial chromosomes are circular, with replication starting at one origin (ori) and proceeding on both replichores toward the terminus (ter). Several studies have shown that the location of genes relative to ori and ter can have profound effects on regulatory networks and physiological processes. The CtrA phosphorelay is a gene regulatory system conserved in most alphaproteobacteria. It was first discovered in Caulobacter crescentus where it controls replication and division into a stalked and a motile cell in coordination with other factors. The locations of the ctrA gene and targets of this response regulator on the chromosome affect their expression through replication-induced DNA hemi-methylation and specific positioning along a CtrA activity gradient in the dividing cell, respectively. Here we asked to what extent the location of CtrA regulatory network genes might be conserved in the alphaproteobacteria. We determined the locations of the CtrA phosphorelay and associated genes in closed genomes with unambiguously identifiable ori from members of five alphaproteobacterial orders. The location of the phosphorelay genes was the least conserved in the Rhodospirillales followed by the Sphingomonadales. In the Rhizobiales a trend toward certain chromosomal positions could be observed. Compared to the other orders, the CtrA phosphorelay genes were conserved closer to ori in the Caulobacterales. In contrast, the genes were highly conserved closer to ter in the Rhodobacterales. Our data suggest selection pressure results in differential positioning of CtrA phosphorelay and associated genes in alphaproteobacteria, particularly in the orders Rhodobacterales, Caulobacterales and Rhizobiales that is worth deeper investigation.
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Affiliation(s)
- Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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13
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The DUF1013 protein TrcR tracks with RNA polymerase to control the bacterial cell cycle and protect against antibiotics. Proc Natl Acad Sci U S A 2021; 118:2010357118. [PMID: 33602809 DOI: 10.1073/pnas.2010357118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How DNA-dependent RNA polymerase (RNAP) acts on bacterial cell cycle progression during transcription elongation is poorly investigated. A forward genetic selection for Caulobacter crescentus cell cycle mutants unearthed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR promotes the accumulation of the essential cell cycle transcriptional activator CtrA in late S-phase but also affects transcription at a global level to protect cells from the quinolone antibiotic nalidixic acid that induces a multidrug efflux pump and from the RNAP inhibitor rifampicin that blocks transcription elongation. We show that TrcR associates with promoters and coding sequences in vivo in a rifampicin-dependent manner and that it interacts physically and genetically with RNAP. We show that TrcR function and its RNAP-dependent chromatin recruitment are conserved in symbiotic Sinorhizobium sp. and pathogenic Brucella spp Thus, TrcR represents a hitherto unknown antibiotic target and the founding member of the DUF1013 family, an uncharacterized class of transcriptional regulators that track with RNAP during the elongation phase to promote transcription during the cell cycle.
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14
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Structural Insight of the Full-Length Ros Protein: A Prototype of the Prokaryotic Zinc-Finger Family. Sci Rep 2020; 10:9283. [PMID: 32518326 PMCID: PMC7283297 DOI: 10.1038/s41598-020-66204-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022] Open
Abstract
Ros/MucR is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription. NMR solution structure of Ros DNA-binding domain (region 56–142, i.e. Ros87) has been solved by our group and shows that the prokaryotic ZF domain shows interesting structural and functional features that differentiate it from its eukaryotic counterpart as it folds in a significantly larger zinc-binding globular domain. We have recently proposed a novel functional model for this family of proteins suggesting that they may act as H-NS-‘like’ gene silencers. Indeed, the N-terminal region of this family of proteins appears to be responsible for the formation of functional oligomers. No structural characterization of the Ros N-terminal domain (region 1–55) is available to date, mainly because of serious solubility problems of the full-length protein. Here we report the first structural characterization of the N-terminal domain of the prokaryotic ZF family examining by means of MD and NMR the structural preferences of the full-length Ros protein from Agrobacterium tumefaciens.
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15
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Delaby M, Panis G, Viollier PH. Bacterial cell cycle and growth phase switch by the essential transcriptional regulator CtrA. Nucleic Acids Res 2020; 47:10628-10644. [PMID: 31598724 PMCID: PMC6847485 DOI: 10.1093/nar/gkz846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/13/2019] [Accepted: 10/05/2019] [Indexed: 11/13/2022] Open
Abstract
Many bacteria acquire dissemination and virulence traits in G1-phase. CtrA, an essential and conserved cell cycle transcriptional regulator identified in the dimorphic alpha-proteobacterium Caulobacter crescentus, first activates promoters in late S-phase and then mysteriously switches to different target promoters in G1-phase. We uncovered a highly conserved determinant in the DNA-binding domain (DBD) of CtrA uncoupling this promoter switch. We also show that it reprograms CtrA occupancy in stationary cells inducing a (p)ppGpp alarmone signal perceived by the RNA polymerase beta subunit. A simple side chain modification in a critical residue within the core DBD imposes opposing developmental phenotypes and transcriptional activities of CtrA and a proximal residue can direct CtrA towards activation of the dispersal (G1-phase) program. Hence, we propose that this conserved determinant in the CtrA primary structure dictates promoter reprogramming during the growth transition in other alpha-proteobacteria that differentiate from replicative cells into dispersal cells.
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Affiliation(s)
- Marie Delaby
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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16
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Lasker K, von Diezmann L, Zhou X, Ahrens DG, Mann TH, Moerner WE, Shapiro L. Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus. Nat Microbiol 2020; 5:418-429. [PMID: 31959967 PMCID: PMC7549192 DOI: 10.1038/s41564-019-0647-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Selective recruitment and concentration of signalling proteins within membraneless compartments is a ubiquitous mechanism for subcellular organization1-3. The dynamic flow of molecules into and out of these compartments occurs on faster timescales than for membrane-enclosed organelles, presenting a possible mechanism to control spatial patterning within cells. Here, we combine single-molecule tracking and super-resolution microscopy, light-induced subcellular localization, reaction-diffusion modelling and a spatially resolved promoter activation assay to study signal exchange in and out of the 200 nm cytoplasmic pole-organizing protein popZ (PopZ) microdomain at the cell pole of the asymmetrically dividing bacterium Caulobacter crescentus4-8. Two phospho-signalling proteins, the transmembrane histidine kinase CckA and the cytoplasmic phosphotransferase ChpT, provide the only phosphate source for the cell fate-determining transcription factor CtrA9-18. We find that all three proteins exhibit restricted rates of entry into and escape from the microdomain as well as enhanced phospho-signalling within, leading to a submicron gradient of activated CtrA-P19 that is stable and sublinear. Entry into the microdomain is selective for cytosolic proteins and requires a binding pathway to PopZ. Our work demonstrates how nanoscale protein assemblies can modulate signal propagation with fine spatial resolution, and that in Caulobacter, this modulation serves to reinforce asymmetry and differential cell fate of the two daughter cells.
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Affiliation(s)
- Keren Lasker
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lexy von Diezmann
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Xiaofeng Zhou
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel G Ahrens
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas H Mann
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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17
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Meléndez AB, Menikpurage IP, Mera PE. Chromosome Dynamics in Bacteria: Triggering Replication at the Opposite Location and Segregation in the Opposite Direction. mBio 2019; 10:e01002-19. [PMID: 31363028 PMCID: PMC6667618 DOI: 10.1128/mbio.01002-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
Maintaining the integrity of the genome is essential to cell survival. In the bacterium Caulobacter crescentus, the single circular chromosome exhibits a specific orientation in the cell, with the replication origin (ori) residing at the pole of the cell bearing a stalk. Upon initiation of replication, the duplicated centromere-like region parS and ori move rapidly to the opposite pole where parS is captured by a microdomain hosting a unique set of proteins that contribute to the identity of progeny cells. Many questions remain as to how this organization is maintained. In this study, we constructed strains of Caulobacter in which ori and the parS centromere can be induced to move to the opposite cell pole in the absence of chromosome replication, allowing us to ask whether once these chromosomal foci were positioned at the wrong pole, replication initiation and chromosome segregation can proceed in the opposite orientation. Our data reveal that DnaA can initiate replication and ParA can orchestrate segregation from either cell pole. The cell reconstructs the organization of its ParA gradient in the opposite orientation to segregate one replicated centromere from the new pole toward the stalked pole (i.e., opposite direction), while displaying no detectable viability defects. Thus, the unique polar microdomains exhibit remarkable flexibility in serving as a platform for directional chromosome segregation along the long axis of the cell.IMPORTANCE Bacteria can accomplish surprising levels of organization in the absence of membrane organelles by constructing subcellular asymmetric protein gradients. These gradients are composed of regulators that can either trigger or inhibit cell cycle events from distinct cell poles. In Caulobacter crescentus, the onset of chromosome replication and segregation from the stalked pole are regulated by asymmetric protein gradients. We show that the activators of chromosome replication and segregation are not restricted to the stalked pole and that their organization and directionality can be flipped in orientation. Our results also indicate that the subcellular location of key chromosomal loci play important roles in the establishment of the asymmetric organization of cell cycle regulators.
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Affiliation(s)
- Ady B Meléndez
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
| | - Inoka P Menikpurage
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
| | - Paola E Mera
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
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18
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González-Flores YE, de Dios R, Reyes-Ramírez F, Santero E. The response of Sphingopyxis granuli strain TFA to the hostile anoxic condition. Sci Rep 2019; 9:6297. [PMID: 31000749 PMCID: PMC6472365 DOI: 10.1038/s41598-019-42768-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/05/2019] [Indexed: 01/02/2023] Open
Abstract
Sphingomonads comprises a group of interesting aerobic bacteria because of their ubiquity and metabolic capability of degrading many recalcitrant contaminants. The tetralin-degrader Sphingopyxis granuli strain TFA has been recently reported as able to anaerobically grow using nitrate as the alternative electron acceptor and so far is the only bacterium with this ability within the sphingomonads group. To understand how strain TFA thrives under anoxic conditions, a differential transcriptomic analysis while growing under aerobic or anoxic conditions was performed. This analysis has been validated and complemented with transcription kinetics of representative genes of different functional categories. Results show an extensive change of the expression pattern of this strain in the different conditions. Consistently, the most induced operon in anoxia codes for proteases, presumably required for extensive changes in the protein profile. Besides genes that respond to lack of oxygen in other bacteria, there are a number of genes that respond to stress or to damage of macromolecules, including genes of the SOS DNA-damage response, which suggest that anoxic conditions represent a hostile environment for this bacterium. Interestingly, growth under anoxic conditions also resulted in repression of all flagellar and type IV pilin genes, which suggested that this strain shaves its appendages off while growing in anaerobiosis.
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Affiliation(s)
- Yolanda Elisabet González-Flores
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Rubén de Dios
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Francisca Reyes-Ramírez
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain.
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
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Koppenhöfer S, Wang H, Scharfe M, Kaever V, Wagner-Döbler I, Tomasch J. Integrated Transcriptional Regulatory Network of Quorum Sensing, Replication Control, and SOS Response in Dinoroseobacter shibae. Front Microbiol 2019; 10:803. [PMID: 31031742 PMCID: PMC6473078 DOI: 10.3389/fmicb.2019.00803] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/28/2019] [Indexed: 12/13/2022] Open
Abstract
Quorum sensing (QS) coordinates population wide gene expression of bacterial species. Highly adaptive traits like gene transfer agents (GTA), morphological heterogeneity, type 4 secretion systems (T4SS), and flagella are QS controlled in Dinoroseobacter shibae, a Roseobacter model organism. Its QS regulatory network is integrated with the CtrA phosphorelay that controls cell division in alphaproteobacteria. To elucidate the network topology, we analyzed the transcriptional response of the QS-negative D. shibae strain ΔluxI1 toward externally added autoinducer (AI) over a time period of 3 h. The signaling cascade is initiated by the CtrA phosphorelay, followed by the QS genes and other target genes, including the second messenger c-di-GMP, competence, flagella and pili. Identification of transcription factor binding sites in promoters of QS induced genes revealed the integration of QS, CtrA phosphorelay and the SOS stress response mediated by LexA. The concentration of regulatory genes located close to the origin or terminus of replication suggests that gene regulation and replication are tightly coupled. Indeed, addition of AI first stimulates and then represses replication. The restart of replication comes along with increased c-di-GMP levels. We propose a model in which QS induces replication followed by differentiation into GTA producing and non-producing cells. CtrA-activity is controlled by the c-di-GMP level, allowing some of the daughter cells to replicate again. The size of the GTA producing subpopulation is tightly controlled by QS via the AI Synthase LuxI2. Finally, induction of the SOS response allows for integration of GTA DNA into the host chromosome.
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Affiliation(s)
- Sonja Koppenhöfer
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hui Wang
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Maren Scharfe
- Group Genomic Analytics, Helmholtz Centre for Infection Research, Helmholtz Association of German Research Centers, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Hanover, Germany
| | - Irene Wagner-Döbler
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Jürgen Tomasch
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
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20
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Li JX, Wei CY, Cao SG, Xia MW. Elevated nuclear auto-antigenic sperm protein promotes melanoma progression by inducing cell proliferation. Onco Targets Ther 2019; 12:2105-2113. [PMID: 30962692 PMCID: PMC6433116 DOI: 10.2147/ott.s197813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Nuclear auto-antigenic sperm protein (NASP) has been implicated in tumorigenesis. However, its role in melanoma is still unclear. Materials and methods In the present study, we detected the mRNA and protein level of NASP in melanoma cell lines and tissues. Then the role of NASP was investigated by transfecting with NASP siRNAs. Finally, the prognosis of NASP was analyzed in 100 melanoma patients through Cox regression and Kaplan-Meier analyses. Results We showed that NASP was significantly overexpressed in melanoma tissues, and unregulated NASP promoted melanoma cell proliferation via promoting cell cycle G1/S phase transition. Additionally, the expression of NASP was closely related to proliferating cell nuclear antigen, a widely accepted biomarker for cell proliferation. Clinically, we found that a high level of NASP predicated poor overall survival and high cumulative recurrence rates. Multivariate analysis revealed that NASP was a risk biomarker for predicting the prognosis of melanoma patients. Conclusion Elevated NASP plays an important role in melanoma cell proliferation and tumor progression, and it can be used as an independent prognostic biomarker for melanoma patients.
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Affiliation(s)
- Jia-Xia Li
- Department of Neurology, Hefei Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230000, People's Republic of China,
| | - Chuan-Yuan Wei
- Department of Plastic Surgery, Fudan University, Shanghai 200032, People's Republic of China
| | - Shu-Gang Cao
- Department of Neurology, Hefei Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230000, People's Republic of China,
| | - Ming-Wu Xia
- Department of Neurology, Hefei Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230000, People's Republic of China,
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21
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Heindl JE, Crosby D, Brar S, Pinto JF, Singletary T, Merenich D, Eagan JL, Buechlein AM, Bruger EL, Waters CM, Fuqua C. Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens. MICROBIOLOGY (READING, ENGLAND) 2019; 165:146-162. [PMID: 30620265 PMCID: PMC7003649 DOI: 10.1099/mic.0.000758] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/28/2018] [Indexed: 12/13/2022]
Abstract
A core regulatory pathway that directs developmental transitions and cellular asymmetries in Agrobacterium tumefaciens involves two overlapping, integrated phosphorelays. One of these phosphorelays putatively includes four histidine sensor kinase homologues, DivJ, PleC, PdhS1 and PdhS2, and two response regulators, DivK and PleD. In several different alphaproteobacteria, this pathway influences a conserved downstream phosphorelay that ultimately controls the phosphorylation state of the CtrA master response regulator. The PdhS2 sensor kinase reciprocally regulates biofilm formation and swimming motility. In the current study, the mechanisms by which the A. tumefaciens sensor kinase PdhS2 directs this regulation are delineated. PdhS2 lacking a key residue implicated in phosphatase activity is markedly deficient in proper control of attachment and motility phenotypes, whereas a kinase-deficient PdhS2 mutant is only modestly affected. A genetic interaction between DivK and PdhS2 is revealed, unmasking one of several connections between PdhS2-dependent phenotypes and transcriptional control by CtrA. Epistasis experiments suggest that PdhS2 may function independently of the CckA sensor kinase, the cognate sensor kinase for CtrA, which is inhibited by DivK. Global expression analysis of the pdhS2 mutant reveals a restricted regulon, most likely functioning through CtrA to separately control motility and regulate the levels of the intracellular signal cyclic diguanylate monophosphate (cdGMP), thereby affecting the production of adhesive polysaccharides and attachment. We hypothesize that in A. tumefaciens the CtrA regulatory circuit has expanded to include additional inputs through the addition of PdhS-type sensor kinases, likely fine-tuning the response of this organism to the soil microenvironment.
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Affiliation(s)
- Jason E. Heindl
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel Crosby
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA
- Present address: Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sukhdev Brar
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA
| | - John F. Pinto
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA
| | - Tiyan Singletary
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel Merenich
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA
| | - Justin L. Eagan
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Aaron M. Buechlein
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Eric L. Bruger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Present address: Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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22
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Herrou J, Willett JW, Fiebig A, Varesio LM, Czyż DM, Cheng JX, Ultee E, Briegel A, Bigelow L, Babnigg G, Kim Y, Crosson S. Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus. Mol Microbiol 2019; 111:637-661. [PMID: 30536925 DOI: 10.1111/mmi.14178] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
Abstract
Molecular components of the Brucella abortus cell envelope play a major role in its ability to infect, colonize and survive inside mammalian host cells. In this study, we have defined a role for a conserved gene of unknown function in B. abortus envelope stress resistance and infection. Expression of this gene, which we name eipA, is directly activated by the essential cell cycle regulator, CtrA. eipA encodes a soluble periplasmic protein that adopts an unusual eight-stranded β-barrel fold. Deletion of eipA attenuates replication and survival in macrophage and mouse infection models, and results in sensitivity to treatments that compromise the cell envelope integrity. Transposon disruption of genes required for LPS O-polysaccharide biosynthesis is synthetically lethal with eipA deletion. This genetic connection between O-polysaccharide and eipA is corroborated by our discovery that eipA is essential in Brucella ovis, a naturally rough species that harbors mutations in several genes required for O-polysaccharide production. Conditional depletion of eipA expression in B. ovis results in a cell chaining phenotype, providing evidence that eipA directly or indirectly influences cell division in Brucella. We conclude that EipA is a molecular determinant of Brucella virulence that functions to maintain cell envelope integrity and influences cell division.
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Affiliation(s)
- Julien Herrou
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jonathan W Willett
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Aretha Fiebig
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Lydia M Varesio
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Daniel M Czyż
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Jason X Cheng
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Eveline Ultee
- Department of Biology, Universiteit Leiden, Leiden, Netherlands
| | - Ariane Briegel
- Department of Biology, Universiteit Leiden, Leiden, Netherlands
| | - Lance Bigelow
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Gyorgy Babnigg
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Youngchang Kim
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
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23
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Identifying the region responsible for Brucella abortus MucR higher-order oligomer formation and examining its role in gene regulation. Sci Rep 2018; 8:17238. [PMID: 30467359 PMCID: PMC6250670 DOI: 10.1038/s41598-018-35432-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022] Open
Abstract
MucR is a member of the Ros/MucR family of prokaryotic zinc-finger proteins found in the α-proteobacteria which regulate the expression of genes required for the successful pathogenic and symbiotic interactions of these bacteria with the eukaryotic hosts. The structure and function of their distinctive zinc-finger domain has been well-studied, but only recently the quaternary structure of the full length proteins was investigated demonstrating their ability to form higher-order oligomers. The aim of this study was to identify the region of MucR involved in higher-order oligomer formation by analysing deletion and point mutants of this protein by Light Scattering, and to determine the role that MucR oligomerization plays in the regulatory function of this protein. Here we demonstrate that a conserved hydrophobic region at the N-terminus of MucR is responsible for higher-order oligomer formation and that MucR oligomerization is essential for its regulatory function in Brucella. All these features of MucR are shared by the histone-like nucleoid structuring protein, (H-NS), leading us to propose that the prokaryotic zinc-finger proteins in the MucR/Ros family control gene expression employing a mechanism similar to that used by the H-NS proteins, rather than working as classical transcriptional regulators.
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24
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Felletti M, Omnus DJ, Jonas K. Regulation of the replication initiator DnaA in Caulobacter crescentus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:697-705. [PMID: 29382570 DOI: 10.1016/j.bbagrm.2018.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/10/2018] [Indexed: 11/18/2022]
Abstract
The decision to initiate DNA replication is a critical step in the cell cycle of all organisms. In nearly all bacteria, replication initiation requires the activity of the conserved replication initiation protein DnaA. Due to its central role in cell cycle progression, DnaA activity must be precisely regulated. This review summarizes the current state of DnaA regulation in the asymmetrically dividing α-proteobacterium Caulobacter crescentus, an important model for bacterial cell cycle studies. Mechanisms will be discussed that regulate DnaA activity and abundance under optimal conditions and in coordination with the asymmetric Caulobacter cell cycle. Furthermore, we highlight recent findings of how regulated DnaA synthesis and degradation collaborate to adjust DnaA abundance under stress conditions. The mechanisms described provide important examples of how DNA replication is regulated in an α-proteobacterium and thus represent an important starting point for the study of DNA replication in many other bacteria. This article is part of a Special Issue entitled: Dynamic gene expression, edited by Prof. Patrick Viollier.
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Affiliation(s)
- Michele Felletti
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Deike J Omnus
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Kristina Jonas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden.
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25
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Bayramova F, Jacquier N, Greub G. Insight in the biology of Chlamydia-related bacteria. Microbes Infect 2017; 20:432-440. [PMID: 29269129 DOI: 10.1016/j.micinf.2017.11.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/14/2017] [Accepted: 11/21/2017] [Indexed: 01/21/2023]
Abstract
The Chlamydiales order is composed of obligate intracellular bacteria and includes the Chlamydiaceae family and several family-level lineages called Chlamydia-related bacteria. In this review we will highlight the conserved and distinct biological features between these two groups. We will show how a better characterization of Chlamydia-related bacteria may increase our understanding on the Chlamydiales order evolution, and may help identifying new therapeutic targets to treat chlamydial infections.
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Affiliation(s)
- Firuza Bayramova
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Nicolas Jacquier
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Gilbert Greub
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland.
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26
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Co(II) Coordination in Prokaryotic Zinc Finger Domains as Revealed by UV-Vis Spectroscopy. Bioinorg Chem Appl 2017; 2017:1527247. [PMID: 29386985 PMCID: PMC5745721 DOI: 10.1155/2017/1527247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/03/2017] [Accepted: 10/16/2017] [Indexed: 11/23/2022] Open
Abstract
Co(II) electronic configuration allows its use as a spectroscopic probe in UV-Vis experiments to characterize the metal coordination sphere that is an essential component of the functional structure of zinc-binding proteins and to evaluate the metal ion affinities of these proteins. Here, exploiting the capability of the prokaryotic zinc finger to use different combinations of residues to properly coordinate the structural metal ion, we provide the UV-Vis characterization of Co(II) addition to Ros87 and its mutant Ros87_C27D which bears an unusual CysAspHis2 coordination sphere. Zinc finger sites containing only one cysteine have been infrequently characterized. We show for the CysAspHis2 coordination an intense d-d transition band, blue-shifted with respect to the Cys2His2 sphere. These data complemented by NMR and CD data demonstrate that the tetrahedral geometry of the metal site is retained also in the case of a single-cysteine coordination sphere.
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27
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Bergé M, Viollier PH. End-in-Sight: Cell Polarization by the Polygamic Organizer PopZ. Trends Microbiol 2017; 26:363-375. [PMID: 29198650 DOI: 10.1016/j.tim.2017.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/02/2017] [Accepted: 11/09/2017] [Indexed: 12/18/2022]
Abstract
Understanding how asymmetries in cellular constituents are achieved and how such positional information directs the construction of structures in a nonrandom fashion is a fundamental problem in cell biology. The recent identification of determinants that self-assemble into macromolecular complexes at the bacterial cell pole provides new insight into the underlying organizational principles in bacterial cells. Specifically, polarity studies in host-associated or free-living α-proteobacteria, a lineage of Gram-negative (diderm) bacteria, reveals that functional and cytological mono- and bipolarity is often conferred by the multivalent polar organizer PopZ, originally identified as a component of a polar chromosome anchor in the cell cycle model system Caulobacter crescentus. PopZ-dependent polarization appears to be widespread and also functional in obligate intracellular pathogens. Here, we discuss how PopZ polarization and the establishment of polar complexes occurs, and we detail the physiological roles of these complexes.
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Affiliation(s)
- Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, CH-1211 Geneva, Switzerland.
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, CH-1211 Geneva, Switzerland.
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More than a Tad: spatiotemporal control of Caulobacter pili. Curr Opin Microbiol 2017; 42:79-86. [PMID: 29161615 DOI: 10.1016/j.mib.2017.10.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 01/09/2023]
Abstract
The Type IV pilus (T4P) is a powerful and sophisticated bacterial nanomachine involved in numerous cellular processes, including adhesion, DNA uptake and motility. Aside from the well-described subtype T4aP of the Gram-negative genera, including Myxococcus, Pseudomonas and Neisseria, the Tad (tight adherence) pilus secretion system re-shuffles homologous parts from other secretion systems along with uncharacterized components into a new type of protein translocation apparatus. A representative of the Tad apparatus, the Caulobacter crescentus pilus assembly (Cpa) machine is built exclusively at the newborn cell pole once per cell cycle. Recent comprehensive genetic analyses unearthed a myriad of spatiotemporal determinants acting on the Tad/Cpa system, many of which are conserved in other α-proteobacteria, including obligate intracellular pathogens and symbionts.
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Caccamo PD, Brun YV. The Molecular Basis of Noncanonical Bacterial Morphology. Trends Microbiol 2017; 26:191-208. [PMID: 29056293 DOI: 10.1016/j.tim.2017.09.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/08/2017] [Accepted: 09/28/2017] [Indexed: 01/04/2023]
Abstract
Bacteria come in a wide variety of shapes and sizes. The true picture of bacterial morphological diversity is likely skewed due to an experimental focus on pathogens and industrially relevant organisms. Indeed, most of the work elucidating the genes and molecular processes involved in maintaining bacterial morphology has been limited to rod- or coccal-shaped model systems. The mechanisms of shape evolution, the molecular processes underlying diverse shapes and growth modes, and how individual cells can dynamically modulate their shape are just beginning to be revealed. Here we discuss recent work aimed at advancing our knowledge of shape diversity and uncovering the molecular basis for shape generation in noncanonical and morphologically complex bacteria.
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Affiliation(s)
- Paul D Caccamo
- Department of Biology, Indiana University, 1001 E. 3rd St, Bloomington, IN 47405, USA
| | - Yves V Brun
- Department of Biology, Indiana University, 1001 E. 3rd St, Bloomington, IN 47405, USA.
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Woodcock CB, Yakubov AB, Reich NO. Caulobacter crescentus Cell Cycle-Regulated DNA Methyltransferase Uses a Novel Mechanism for Substrate Recognition. Biochemistry 2017; 56:3913-3922. [PMID: 28661661 DOI: 10.1021/acs.biochem.7b00378] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Caulobacter crescentus relies on DNA methylation by the cell cycle-regulated methyltransferase (CcrM) in addition to key transcription factors to control the cell cycle and direct cellular differentiation. CcrM is shown here to efficiently methylate its cognate recognition site 5'-GANTC-3' in single-stranded and hemimethylated double-stranded DNA. We report the Km, kcat, kmethylation, and Kd for single-stranded and hemimethylated substrates, revealing discrimination of 107-fold for noncognate sequences. The enzyme also shows a similar discrimination against single-stranded RNA. Two independent assays clearly show that CcrM is highly processive with single-stranded and hemimethylated DNA. Collectively, the data provide evidence that CcrM and other DNA-modifying enzymes may use a new mechanism to recognize DNA in a key epigenetic process.
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Affiliation(s)
- Clayton B Woodcock
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Aziz B Yakubov
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
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31
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Mignolet J, Holden S, Bergé M, Panis G, Eroglu E, Théraulaz L, Manley S, Viollier PH. Functional dichotomy and distinct nanoscale assemblies of a cell cycle-controlled bipolar zinc-finger regulator. eLife 2016; 5. [PMID: 28008851 PMCID: PMC5182063 DOI: 10.7554/elife.18647] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/01/2016] [Indexed: 11/13/2022] Open
Abstract
Protein polarization underlies differentiation in metazoans and in bacteria. How symmetric polarization can instate functional asymmetry remains elusive. Here, we show by super-resolution photo-activated localization microscopy and edgetic mutations that the bitopic zinc-finger protein ZitP implements specialized developmental functions – pilus biogenesis and multifactorial swarming motility – while shaping distinct nanoscale (bi)polar architectures in the asymmetric model bacterium Caulobacter crescentus. Polar assemblage and accumulation of ZitP and its effector protein CpaM are orchestrated in time and space by conserved components of the cell cycle circuitry that coordinate polar morphogenesis with cell cycle progression, and also act on the master cell cycle regulator CtrA. Thus, this novel class of potentially widespread multifunctional polarity regulators is deeply embedded in the cell cycle circuitry. DOI:http://dx.doi.org/10.7554/eLife.18647.001 Living cells become asymmetric for many different reasons and how they do so has been a long-standing question in biology. In some cells, the asymmetry arises because a given protein accumulates at one side of the cell. In particular, this process happens before some cells divide to produce two non-identical daughter cells that then go on to develop in very different ways – which is vital for the development of almost all multicellular organisms. The single-celled bacterium Caulobacter crescentus also undergoes this type of asymmetric division. The polarized Caulobacter cell produces two very different offsprings – a stationary cell and a nomadic cell that swims using a propeller-like structure, called a flagellum, and has projections called pili on its surface. Before it divides asymmetrically, the Caulobacter cell must accumulate specific proteins at its extremities, or poles. Two such proteins are ZitP and CpaM, which appear to have multiple roles and are thought to interact with other factors that regulate cell division. However, little is known about how ZitP and CpaM become organized at the poles at the right time and how they interact with these regulators of cell division. Mignolet et al. explored how ZitP becomes polarized in Caulobacter crescentus using a combination of approaches including biochemical and genetic analyses and very high-resolution microscopy. This revealed that ZitP accumulated via different pathways at the two poles and that it formed distinct structures at each pole. These structures were associated with different roles for ZitP. While ZitP recruited proteins, including CpaM, required for assembly of pili to one of the poles, it acted differently at the opposite pole. By mutating regions of ZitP, Mignolet et al. went on to show that different regions of the protein carry out these roles. Further experiments demonstrated that regulators of the cell division cycle influenced how ZitP and CpaM accumulated and behaved in cells, ensuring that the proteins carry out their roles at the correct time during division. These findings provide more evidence that proteins can have different roles at distinct sites within a cell, in this case at opposite poles of a cell. Future studies will be needed to determine whether this is seen in cells other than Caulobacter including more complex, non-bacterial cells. DOI:http://dx.doi.org/10.7554/eLife.18647.002
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Affiliation(s)
- Johann Mignolet
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Seamus Holden
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
| | - Matthieu Bergé
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ezgi Eroglu
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurence Théraulaz
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria. PLoS Genet 2016; 12:e1006499. [PMID: 27997543 PMCID: PMC5172544 DOI: 10.1371/journal.pgen.1006499] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/22/2016] [Indexed: 11/19/2022] Open
Abstract
Heritable DNA methylation imprints are ubiquitous and underlie genetic variability from bacteria to humans. In microbial genomes, DNA methylation has been implicated in gene transcription, DNA replication and repair, nucleoid segregation, transposition and virulence of pathogenic strains. Despite the importance of local (hypo)methylation at specific loci, how and when these patterns are established during the cell cycle remains poorly characterized. Taking advantage of the small genomes and the synchronizability of α-proteobacteria, we discovered that conserved determinants of the cell cycle transcriptional circuitry establish specific hypomethylation patterns in the cell cycle model system Caulobacter crescentus. We used genome-wide methyl-N6-adenine (m6A-) analyses by restriction-enzyme-cleavage sequencing (REC-Seq) and single-molecule real-time (SMRT) sequencing to show that MucR, a transcriptional regulator that represses virulence and cell cycle genes in S-phase but no longer in G1-phase, occludes 5'-GANTC-3' sequence motifs that are methylated by the DNA adenine methyltransferase CcrM. Constitutive expression of CcrM or heterologous methylases in at least two different α-proteobacteria homogenizes m6A patterns even when MucR is present and affects promoter activity. Environmental stress (phosphate limitation) can override and reconfigure local hypomethylation patterns imposed by the cell cycle circuitry that dictate when and where local hypomethylation is instated.
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In-phase oscillation of global regulons is orchestrated by a pole-specific organizer. Proc Natl Acad Sci U S A 2016; 113:12550-12555. [PMID: 27791133 PMCID: PMC5098664 DOI: 10.1073/pnas.1610723113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cell fate determination in the asymmetric bacterium Caulobacter crescentus (Caulobacter) is triggered by the localization of the developmental regulator SpmX to the old (stalked) cell pole during the G1→S transition. Although SpmX is required to localize and activate the cell fate-determining kinase DivJ at the stalked pole in Caulobacter, in cousins such as Asticcacaulis, SpmX directs organelle (stalk) positioning and possibly other functions. We define the conserved σ54-dependent transcriptional activator TacA as a global regulator in Caulobacter whose activation by phosphorylation is indirectly down-regulated by SpmX. Using a combination of forward genetics and cytological screening, we uncover a previously uncharacterized and polarized component (SpmY) of the TacA phosphorylation control system, and we show that SpmY function and localization are conserved. Thus, SpmX organizes a site-specific, ancestral, and multifunctional regulatory hub integrating the in-phase oscillation of two global transcriptional regulators, CtrA (the master cell cycle transcriptional regulator A) and TacA, that perform important cell cycle functions.
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An intracellular compass spatially coordinates cell cycle modules in Caulobacter crescentus. Curr Opin Microbiol 2016; 33:131-139. [PMID: 27517351 DOI: 10.1016/j.mib.2016.06.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/24/2016] [Indexed: 12/27/2022]
Abstract
Cellular functions in Bacteria, such as chromosome segregation and cytokinesis, result from cascades of molecular events operating largely as self-contained modules. Regulated timing of these cellular modules stems from global genetic circuits that allow precise temporal activation with respect to cell cycle progression and cell differentiation. Critically, many of these functions occur at defined locations within the cell, and therefore regulators of each module must communicate to remain coordinated in space. In this perspective, we highlight recent discoveries in Caulobacter crescentus asymmetric cell division to illuminate diverse mechanisms by which a cellular compass, composed of scaffolding and signaling proteins, directs cell cycle modules to their exact cellular addresses.
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Adhikari S, Curtis PD. DNA methyltransferases and epigenetic regulation in bacteria. FEMS Microbiol Rev 2016; 40:575-91. [PMID: 27476077 DOI: 10.1093/femsre/fuw023] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Epigenetics is a change in gene expression that is heritable without a change in DNA sequence itself. This phenomenon is well studied in eukaryotes, particularly in humans for its role in cellular differentiation, X chromosome inactivation and diseases like cancer. However, comparatively little is known about epigenetic regulation in bacteria. Bacterial epigenetics is mainly present in the form of DNA methylation where DNA methyltransferases add methyl groups to nucleotides. This review focuses on two methyltransferases well characterized for their roles in gene regulation: Dam and CcrM. Dam methyltransferase in Escherichia coli is important for expression of certain genes such as the pap operon, as well as other cellular processes like DNA replication initiation and DNA repair. In Caulobacter crescentus and other Alphaproteobacteria, the methyltransferase CcrM is cell cycle regulated and is involved in the cell-cycle-dependent regulation of several genes. The diversity of regulatory targets as well as regulatory mechanisms suggests that gene regulation by methylation could be a widespread and potent method of regulation in bacteria.
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Affiliation(s)
- Satish Adhikari
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Patrick D Curtis
- Department of Biology, University of Mississippi, University, MS 38677, USA
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Abstract
DNA does not make phenotypes on its own. In this volume entitled "Genes and Phenotypic Evolution," the present review draws the attention on the process of phenotype construction-including development of multicellular organisms-and the multiple interactions and feedbacks between DNA, organism, and environment at various levels and timescales in the evolutionary process. First, during the construction of an individual's phenotype, DNA is recruited as a template for building blocks within the cellular context and may in addition be involved in dynamical feedback loops that depend on the environmental and organismal context. Second, in the production of phenotypic variation among individuals, stochastic, environmental, genetic, and parental sources of variation act jointly. While in controlled laboratory settings, various genetic and environmental factors can be tested one at a time or in various combinations, they cannot be separated in natural populations because the environment is not controlled and the genotype can rarely be replicated. Third, along generations, genotype and environment each have specific properties concerning the origin of their variation, the hereditary transmission of this variation, and the evolutionary feedbacks. Natural selection acts as a feedback from phenotype and environment to genotype. This review integrates recent results and concrete examples that illustrate these three points. Although some themes are shared with recent calls and claims to a new conceptual framework in evolutionary biology, the viewpoint presented here only means to add flesh to the standard evolutionary synthesis.
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Affiliation(s)
- M-A Félix
- Institut de Biologie Ecole Normale Supérieure, CNRS, Paris, France.
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37
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D'Abrosca G, Russo L, Palmieri M, Baglivo I, Netti F, de Paola I, Zaccaro L, Farina B, Iacovino R, Pedone PV, Isernia C, Fattorusso R, Malgieri G. The (unusual) aspartic acid in the metal coordination sphere of the prokaryotic zinc finger domain. J Inorg Biochem 2016; 161:91-8. [PMID: 27238756 DOI: 10.1016/j.jinorgbio.2016.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 11/29/2022]
Abstract
The possibility of choices of protein ligands and coordination geometries leads to diverse Zn(II) binding sites in zinc-proteins, allowing a range of important biological roles. The prokaryotic Cys2His2 zinc finger domain (originally found in the Ros protein from Agrobacterium tumefaciens) tetrahedrally coordinates zinc through two cysteine and two histidine residues and it does not adopt a correct fold in the absence of the metal ion. Ros is the first structurally characterized member of a family of bacterial proteins that presents several amino acid changes in the positions occupied in Ros by the zinc coordinating residues. In particular, the second position is very often occupied by an aspartic acid although the coordination of structural zinc by an aspartate in eukaryotic zinc fingers is very unusual. Here, by appropriately mutating the protein Ros, we characterize the aspartate role within the coordination sphere of this family of proteins demonstrating how the presence of this residue only slightly perturbs the functional structure of the prokaryotic zinc finger domain while it greatly influences its thermodynamic properties.
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Affiliation(s)
- Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Fortuna Netti
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ivan de Paola
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Laura Zaccaro
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Rosa Iacovino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy.
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Frage B, Döhlemann J, Robledo M, Lucena D, Sobetzko P, Graumann PL, Becker A. Spatiotemporal choreography of chromosome and megaplasmids in theSinorhizobium meliloticell cycle. Mol Microbiol 2016; 100:808-23. [DOI: 10.1111/mmi.13351] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Frage
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Marta Robledo
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Daniella Lucena
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032; Marburg Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Peter L. Graumann
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032; Marburg Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
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de Barsy M, Frandi A, Panis G, Théraulaz L, Pillonel T, Greub G, Viollier PH. Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum. ISME JOURNAL 2016; 10:2129-44. [PMID: 26953603 PMCID: PMC4989314 DOI: 10.1038/ismej.2016.23] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 01/17/2023]
Abstract
Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.
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Affiliation(s)
- Marie de Barsy
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Antonio Frandi
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurence Théraulaz
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Cell cycle control in Alphaproteobacteria. Curr Opin Microbiol 2016; 30:107-113. [PMID: 26871482 DOI: 10.1016/j.mib.2016.01.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 11/22/2022]
Abstract
Alphaproteobacteria include many medically and environmentally important organisms. Despite the diversity of their niches and lifestyles, from free-living to host-associated, they usually rely on very similar mechanisms to control their cell cycles. Studies on Caulobacter crescentus still lay the foundation for understanding the molecular details of pathways regulating DNA replication and cell division and coordinating these two processes with other events of the cell cycle. This review highlights recent discoveries on the regulation and the mode of action of conserved global regulators and small molecules like c-di-GMP and (p)ppGpp, which play key roles in cell cycle control. It also describes several newly identified mechanisms that modulate cell cycle progression in response to stresses or environmental conditions.
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Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle. J Bacteriol 2016; 198:1149-59. [PMID: 26833409 DOI: 10.1128/jb.00896-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/24/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The dimorphic alphaproteobacterium Prosthecomicrobium hirschii has both short-stalked and long-stalked morphotypes. Notably, these morphologies do not arise from transitions in a cell cycle. Instead, the maternal cell morphology is typically reproduced in daughter cells, which results in microcolonies of a single cell type. In this work, we further characterized the short-stalked cells and found that these cells have a Caulobacter-like life cycle in which cell division leads to the generation of two morphologically distinct daughter cells. Using a microfluidic device and total internal reflection fluorescence (TIRF) microscopy, we observed that motile short-stalked cells attach to a surface by means of a polar adhesin. Cells attached at their poles elongate and ultimately release motile daughter cells. Robust biofilm growth occurs in the microfluidic device, enabling the collection of synchronous motile cells and downstream analysis of cell growth and attachment. Analysis of a draft P. hirschii genome sequence indicates the presence of CtrA-dependent cell cycle regulation. This characterization of P. hirschii will enable future studies on the mechanisms underlying complex morphologies and polymorphic cell cycles. IMPORTANCE Bacterial cell shape plays a critical role in regulating important behaviors, such as attachment to surfaces, motility, predation, and cellular differentiation; however, most studies on these behaviors focus on bacteria with relatively simple morphologies, such as rods and spheres. Notably, complex morphologies abound throughout the bacteria, with striking examples, such as P. hirschii, found within the stalked Alphaproteobacteria. P. hirschii is an outstanding candidate for studies of complex morphology generation and polymorphic cell cycles. Here, the cell cycle and genome of P. hirschii are characterized. This work sets the stage for future studies of the impact of complex cell shapes on bacterial behaviors.
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Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris. J Bacteriol 2015; 198:867-76. [PMID: 26712940 DOI: 10.1128/jb.00771-15] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Rhodopseudomonas palustris is an alphaproteobacterium that has served as a model organism for studies of photophosphorylation, regulation of nitrogen fixation, production of hydrogen as a biofuel, and anaerobic degradation of aromatic compounds. This bacterium is able to transition between anaerobic photoautotrophic growth, anaerobic photoheterotrophic growth, and aerobic heterotrophic growth. As a starting point to explore the genetic basis for the metabolic versatility of R. palustris, we used transposon mutagenesis and Tn-seq to identify 552 genes as essential for viability in cells growing aerobically on semirich medium. Of these, 323 have essential gene homologs in the alphaproteobacterium Caulobacter crescentus, and 187 have essential gene homologs in Escherichia coli. There were 24 R. palustris genes that were essential for viability under aerobic growth conditions that have low sequence identity but are likely to be functionally homologous to essential E. coli genes. As expected, certain functional categories of essential genes were highly conserved among the three organisms, including translation, ribosome structure and biogenesis, secretion, and lipid metabolism. R. palustris cells divide by budding in which a sessile cell gives rise to a motile swarmer cell. Conserved cell cycle genes required for this developmental process were essential in both C. crescentus and R. palustris. Our results suggest that despite vast differences in lifestyles, members of the alphaproteobacteria have a common set of essential genes that is specific to this group and distinct from that of gammaproteobacteria like E. coli. IMPORTANCE Essential genes in bacteria and other organisms are those absolutely required for viability. Rhodopseudomonas palustris has served as a model organism for studies of anaerobic aromatic compound degradation, hydrogen gas production, nitrogen fixation, and photosynthesis. We used the technique of Tn-seq to determine the essential genes of R. palustris grown under heterotrophic aerobic conditions. The transposon library generated in this study will be useful for future studies to identify R. palustris genes essential for viability under specialized growth conditions and also for survival under conditions of stress.
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Ardissone S, Viollier PH. Interplay between flagellation and cell cycle control in Caulobacter. Curr Opin Microbiol 2015; 28:83-92. [PMID: 26476805 DOI: 10.1016/j.mib.2015.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 12/21/2022]
Abstract
The assembly of the flagellum, a sophisticated nanomachine powering bacterial locomotion in liquids and across surfaces, is highly regulated. In the synchronizable α-Proteobacterium Caulobacter crescentus, the flagellum is built at a pre-selected cell pole and flagellar transcript abundance oscillates during the cell cycle. Conserved regulators not only dictate when the transcripts encoding flagellar structural proteins peak, but also those encoding polarization factors. Additionally, post-transcriptional cell cycle cues facilitate flagellar (dis-)assembly at the new cell pole. Because of this regulatory complexity and the power of bacterial genetics, motility is a suitable and simple proxy for dissecting how bacteria implement cell cycle progression and polarity, while also providing clues on how bacteria might decide when and where to display other surface structures.
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Affiliation(s)
- Silvia Ardissone
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Geneva 4, Switzerland.
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Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
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Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
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