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Tišma M, Kaljević J, Gruber S, Le TBK, Dekker C. Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies. FEMS Microbiol Rev 2024; 48:fuad067. [PMID: 38142222 PMCID: PMC10786196 DOI: 10.1093/femsre/fuad067] [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: 11/20/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023] Open
Abstract
Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome segregation during the bacterial cell cycle. Over the past decades, research has greatly advanced our knowledge of the ParABS system. However, many intricate details of the mechanism of ParB proteins were only recently uncovered using in vitro single-molecule techniques. These approaches allowed the exploration of ParB proteins in precisely controlled environments, free from the complexities of the cellular milieu. This review covers the early developments of this field but emphasizes recent advances in our knowledge of the mechanistic understanding of ParB proteins as revealed by in vitro single-molecule methods. Furthermore, we provide an outlook on future endeavors in investigating ParB, ParB-like proteins, and their interaction partners.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology; Van der Maasweg 9, Delft, the Netherlands
| | - Jovana Kaljević
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH Norwich, United Kingdom
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, UNIL-Sorge, Biophore, CH-1015 Lausanne, Switzerland
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH Norwich, United Kingdom
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology; Van der Maasweg 9, Delft, the Netherlands
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2
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Rudakova NL, Sabirova AR, Khasanov DI, Danilova IV, Sharipova MR. Regulating Pathways of Bacillus pumilus Adamalysin-like Metalloendopeptidase Expression. Int J Mol Sci 2023; 25:62. [PMID: 38203233 PMCID: PMC10779165 DOI: 10.3390/ijms25010062] [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: 11/11/2023] [Revised: 12/14/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The minor secreted proteinase of B. pumilus 3-19 MprBp classified as the unique bacillary adamalysin-like enzyme of the metzincin clan. The functional role of this metalloproteinase in the bacilli cells is not clear. Analysis of the regulatory region of the mprBp gene showed the presence of potential binding sites to the transcription regulatory factors Spo0A (sporulation) and DegU (biodegradation). The study of mprBp activity in mutant strains of B. subtilis defective in regulatory proteins of the Spo- and Deg-systems showed that the mprBp gene is partially controlled by the Deg-system of signal transduction and independent from the Spo-system.
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Affiliation(s)
| | | | | | | | - Margarita R. Sharipova
- Institute of Fundamental Medicine, Kazan Federal University, Kremlevskaya St. 18, 420008 Kazan, Russia; (N.L.R.); (D.I.K.); (I.V.D.)
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3
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Gogou C, Japaridze A, Dekker C. Mechanisms for Chromosome Segregation in Bacteria. Front Microbiol 2021; 12:685687. [PMID: 34220773 PMCID: PMC8242196 DOI: 10.3389/fmicb.2021.685687] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
The process of DNA segregation, the redistribution of newly replicated genomic material to daughter cells, is a crucial step in the life cycle of all living systems. Here, we review DNA segregation in bacteria which evolved a variety of mechanisms for partitioning newly replicated DNA. Bacterial species such as Caulobacter crescentus and Bacillus subtilis contain pushing and pulling mechanisms that exert forces and directionality to mediate the moving of newly synthesized chromosomes to the bacterial poles. Other bacteria such as Escherichia coli lack such active segregation systems, yet exhibit a spontaneous de-mixing of chromosomes due to entropic forces as DNA is being replicated under the confinement of the cell wall. Furthermore, we present a synopsis of the main players that contribute to prokaryotic genome segregation. We finish with emphasizing the importance of bottom-up approaches for the investigation of the various factors that contribute to genome segregation.
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Affiliation(s)
- Christos Gogou
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
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4
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Abstract
Proper chromosome segregation during cell division is essential in all domains of life. In the majority of bacterial species, faithful chromosome segregation is mediated by the tripartite ParABS system, consisting of an ATPase protein ParA, a CTPase and DNA-binding protein ParB, and a centromere-like parS site. The parS site is most often located near the origin of replication and is segregated first after chromosome replication. ParB nucleates on parS before binding to adjacent non-specific DNA to form a multimeric nucleoprotein complex. ParA interacts with ParB to drive the higher-order ParB–DNA complex, and hence the replicating chromosomes, to each daughter cell. Here, we review the various models for the formation of the ParABS complex and describe its role in segregating the origin-proximal region of the chromosome. Additionally, we discuss outstanding questions and challenges in understanding bacterial chromosome segregation.
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Affiliation(s)
- Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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5
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Mierzejewska J, Jagura-Burdzy G. Prokaryotic ParA-ParB-parS system links bacterial chromosome segregation with the cell cycle. Plasmid 2011; 67:1-14. [PMID: 21924286 DOI: 10.1016/j.plasmid.2011.08.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 12/17/2022]
Abstract
While the essential role of episomal par loci in plasmid DNA partitioning has long been appreciated, the function of chromosomally encoded par loci is less clear. The chromosomal parA-parB genes are conserved throughout the bacterial kingdom and encode proteins homologous to those of the plasmidic Type I active partitioning systems. The third conserved element, the centromere-like sequence called parS, occurs in several copies in the chromosome. Recent studies show that the ParA-ParB-parS system is a key player of a mitosis-like process ensuring proper intracellular localization of certain chromosomal regions such as oriC domain and their active and directed segregation. Moreover, the chromosomal par systems link chromosome segregation with initiation of DNA replication and the cell cycle.
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Affiliation(s)
- Jolanta Mierzejewska
- The Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Pawinskiego 5A, Poland
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6
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Fikrig E, Narasimhan S, Neelakanta G, Pal U, Chen M, Flavell R. Toll-like receptors 1 and 2 heterodimers alter Borrelia burgdorferi gene expression in mice and ticks. J Infect Dis 2009; 200:1331-40. [PMID: 19754309 DOI: 10.1086/605950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Borrelia burgdorferi, the agent of Lyme disease, is recognized by Toll-like receptor (TLR) 1 and 2 heterodimers. Microarray analysis of in vivo B. burgdorferi gene expression in murine skin showed that several genes were altered in TLR1/2-deficient animals compared with wild-type mice. For example, expression of bbe21 (a gene involved in B. burgdorferi lp25 plasmid maintenance) and bb0665 (a gene encoding a glycosyl transferase) were higher in TLR1/2-deficient mice than in control animals. In contrast, messenger RNA levels for bb0731 (a spoJ-like gene) and bba74 (a gene encoding a periplasmic protein) were lower in TLR1/2-deficient mice than in wild-type animals. The expression profiles of some of these genes were altered similarly in B. burgdorferi-infected ticks fed on control or TLR1/2-deficient mice. Quantitative reverse-transcription polymerase chain reaction analysis supported the microarray analysis and suggested that spirochete gene expression is altered by the milieu created by specific host TLRs, both in the murine host and in the arthropod vector.
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Affiliation(s)
- Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, 2Howard Hughes Medical Institute, and 3Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut
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7
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Griffith KL, Grossman AD. Inducible protein degradation in Bacillus subtilis using heterologous peptide tags and adaptor proteins to target substrates to the protease ClpXP. Mol Microbiol 2008; 70:1012-25. [PMID: 18811726 DOI: 10.1111/j.1365-2958.2008.06467.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The ability to manipulate protein levels is useful for dissecting regulatory pathways, elucidating gene function and constructing synthetic biological circuits. We engineered an inducible protein degradation system for use in Bacillus subtilis based on Escherichia coli and Caulobacter crescentusssrA tags and SspB adaptors that deliver proteins to ClpXP for proteolysis. In this system, modified ssrA degradation tags are fused onto the 3' end of the genes of interest. Unlike wild-type ssrA, these modified tags require the adaptor protein SspB to target tagged proteins for proteolysis. In the absence of SspB, the tagged proteins accumulate to near physiological levels. By inducing SspB expression from a regulated promoter, the tagged substrates are rapidly delivered to the B. subtilis ClpXP protease for degradation. We used this system to degrade the reporter GFP and several native B. subtilis proteins, including, the transcription factor ComA, two sporulation kinases (KinA, KinB) and the sporulation and chromosome partitioning protein Spo0J. We also used modified E. coli and C. crescentus ssrA tags to independently control the degradation of two different proteins in the same cell. These tools will be useful for studying biological processes in B. subtilis and can potentially be modified for use in other bacteria.
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Affiliation(s)
- Kevin L Griffith
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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8
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Dubarry N, Pasta F, Lane D. ParABS systems of the four replicons of Burkholderia cenocepacia: new chromosome centromeres confer partition specificity. J Bacteriol 2006; 188:1489-96. [PMID: 16452432 PMCID: PMC1367244 DOI: 10.1128/jb.188.4.1489-1496.2006] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most bacterial chromosomes carry an analogue of the parABS systems that govern plasmid partition, but their role in chromosome partition is ambiguous. parABS systems might be particularly important for orderly segregation of multipartite genomes, where their role may thus be easier to evaluate. We have characterized parABS systems in Burkholderia cenocepacia, whose genome comprises three chromosomes and one low-copy-number plasmid. A single parAB locus and a set of ParB-binding (parS) centromere sites are located near the origin of each replicon. ParA and ParB of the longest chromosome are phylogenetically similar to analogues in other multichromosome and monochromosome bacteria but are distinct from those of smaller chromosomes. The latter form subgroups that correspond to the taxa of their hosts, indicating evolution from plasmids. The parS sites on the smaller chromosomes and the plasmid are similar to the "universal" parS of the main chromosome but with a sequence specific to their replicon. In an Escherichia coli plasmid stabilization test, each parAB exhibits partition activity only with the parS of its own replicon. Hence, parABS function is based on the independent partition of individual chromosomes rather than on a single communal system or network of interacting systems. Stabilization by the smaller chromosome and plasmid systems was enhanced by mutation of parS sites and a promoter internal to their parAB operons, suggesting autoregulatory mechanisms. The small chromosome ParBs were found to silence transcription, a property relevant to autoregulation.
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Affiliation(s)
- Nelly Dubarry
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de Recherche Scientifique, 118 route de Narbonne, 31062 Toulouse, France
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9
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Abstract
We report here that HtrA plays a role in controlling growth and competence development for genetic transformation in Streptococcus mutans. Disruption of the gene for HtrA resulted in slow growth at 37 degrees C, reduced thermal tolerance at 42 degrees C, and altered sucrose-dependent biofilm formation on polystyrene surfaces. The htrA mutant also displayed a significantly reduced ability to undergo genetic transformation. A direct association between HtrA and genetic competence was demonstrated by the increased expression of the htrA gene upon exposure to competence-stimulating peptide. The induction of htrA gradually reached a maximum at around 20 min, suggesting that HtrA may be involved in a late competence response. Complementation of the htrA mutation in a single copy on the chromosome of the mutant could rescue the defective growth phenotypes but not transformability, apparently because a second gene, spo0J, immediately downstream of htrA, also affects transformation. The htrA and spo0J genes were shown to be both individually transcribed and cotranscribed and probably have a functional connection in competence development. HtrA regulation appears to be finely tuned in S. mutans, since strains containing multiple copies of htrA exhibited abnormal growth phenotypes. Collectively, the results reveal HtrA to be an integral component of the regulatory network connecting cellular growth, stress tolerance, biofilm formation, and competence development and reveal a novel role for the spo0J gene in genetic transformation.
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Affiliation(s)
- Sang-Joon Ahn
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL 32610, USA
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10
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Abstract
The ParA family protein Soj appears to negatively regulate sporulation in Bacillus subtilis by inhibiting transcription from promoters that are activated by phosphorylated Spo0A. We tested in vitro Soj inhibition of Spo0A-independent variants of a promoter that Soj inhibited (PspoIIG). Transcription from the variants was less sensitive to Soj inhibition, suggesting that inhibition of wild-type PspoIIG was linked to transcription activation by Spo0A.
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Affiliation(s)
- Brett N McLeod
- Department of Microbiology and Immunology, University of British Columbia, 6174 University Blvd., Vancouver, British Columbia V6T 1Z3, Canada.
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11
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Shafikhani SH, Núñez E, Leighton T. Hpr (ScoC) and the phosphorelay couple cell cycle and sporulation inBacillus subtilis. FEMS Microbiol Lett 2004; 231:99-110. [PMID: 14769473 DOI: 10.1016/s0378-1097(03)00936-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2003] [Revised: 12/01/2003] [Accepted: 12/07/2003] [Indexed: 11/25/2022] Open
Abstract
Bacillus subtilis sporulation is a developmental process that culminates in the formation of a highly resistant and persistent endospore. Inhibiting DNA synthesis prior to the completion of the final round of DNA replication blocks sporulation at an early stage. Conditions that prevent compartmentalization of gene expression, i.e. inhibition of asymmetric septum formation or chromosome partitioning, also block sporulation at an early stage. Multiple mechanisms including a RecA-dependent, a RecA-independent, and the soj-spo0J operon have been implicated in signal transduction, connecting DNA replication and chromosome partitioning to the onset of sporulation in B. subtilis. We suggest that a single mechanism involving Hpr (ScoC) and Sda couple cell cycle signaling to sporulation initiation. We show that transcription of phosphorelay sensory chain genes is adversely affected by post-exponential perturbation of the cell cycle. DNA replication arrest by chemical treatments, such as hydroxyphenylazouracil, hydroxyurea, nalidixic acid, and through genetic means using dnaA1ts and dnaB19ts temperature-sensitive mutants caused substantial down-regulation of spo0F and kinA expression and elevated the expression of spo0A and spo0H (sigH). Despite the elevation in spo0A expression, Spo0A approximately P-dependent sinI expression was substantially down-regulated indicating that in vivo Spo0A approximately P levels may be diminished. Similar alterations in gene expression patterns were observed in an ftsA279ts mutant background, indicating that cytokinesis and sporulation may also be coupled by a similar mechanism. Loss of function mutation in hpr (scoC) restored sporulation in a dnaA1ts mutant, blocked the DNA replication arrest induction of spo0A expression and restored expression of spo0F, kinA and sinI. Moreover, hpr expression was up-regulated in response to DNA replication arrest. The increase in hpr expression required Sda. These results suggest a role for Hpr (ScoC) in mediating the coupling of cell cycle events to the onset of sporulation.
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Affiliation(s)
- Sasha H Shafikhani
- Department of Molecular and Cellular Biology, Division of Biochemistry and Molecular Biology, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
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12
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Figge RM, Easter J, Gober JW. Productive interaction between the chromosome partitioning proteins, ParA and ParB, is required for the progression of the cell cycle in Caulobacter crescentus. Mol Microbiol 2003; 47:1225-37. [PMID: 12603730 DOI: 10.1046/j.1365-2958.2003.03367.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Caulobacter crescentus the partitioning proteins ParA and ParB operate a molecular switch that couples chromosome partitioning to cytokinesis. Homologues of these proteins have been shown to be important for the stable inheritance of F-plasmids and the prophage form of bacteriophage P1. In C. crescentus, ParB binds to sequences adjacent to the origin of replication and is required for the initiation of cell division. Additionally, ParB influences the nucleotide-bound state of ParA by acting as a nucleotide exchange factor. Here we have performed a genetic analysis of the chromosome partitioning protein ParB. We show that C. crescentus ParB, like its plasmid homologues, is composed of three domains: a carboxyl-terminal dimerization domain; a central DNA-binding, helix-turn-helix domain; and an amino-terminal domain required for the interaction with ParA. In vivo expression of amino-terminally deleted parB alleles has a dominant lethal effect resulting in the inhibition of cell division. Fluorescent in situ hybridization experiments indicate that this phenotype is not caused by a chromosome partitioning defect, but by the reversal of the amounts of ATP- versus ADP- bound ParA inside the cell. We present evidence suggesting that amino-terminally truncated and full-length, wild-type ParB form heterodimers which fail to interact with ParA, thereby reversing the intracellular ParA-ATP to ParA-ADP ratio. We hypothesize that the amino-terminus of ParB is required to regulate the nucleotide exchange of ParA which, in turn, regulates the initiation of cell division.
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Affiliation(s)
- Rainer M Figge
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
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13
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Abstract
Recent studies have made great strides toward our understanding of the mechanisms of microbial chromosome segregation and partitioning. This review first describes the mechanisms that function to segregate newly replicated chromosomes, generating daughter molecules that are viable substrates for partitioning. Then experiments that address the mechanisms of bulk chromosome movement are summarized. Recent evidence indicates that a stationary DNA replication factory may be responsible for supplying the force necessary to move newly duplicated DNA toward the cell poles. Some factors contributing to the directionality of chromosome movement probably include centromere-like-binding proteins, DNA condensation proteins, and DNA translocation proteins.
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Affiliation(s)
- Geoffrey C Draper
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 90095-1569, USA
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14
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Sebert ME, Palmer LM, Rosenberg M, Weiser JN. Microarray-based identification of htrA, a Streptococcus pneumoniae gene that is regulated by the CiaRH two-component system and contributes to nasopharyngeal colonization. Infect Immun 2002; 70:4059-67. [PMID: 12117912 PMCID: PMC128155 DOI: 10.1128/iai.70.8.4059-4067.2002] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nasopharyngeal carriage is the reservoir from which most disease with Streptococcus pneumoniae arises. Survival as a commensal in this environment is likely to require a set of adaptations distinct from those needed to cause disease, some of which may be mediated by two-component signal transduction systems (TCSTS). We examined the contributions of nine pneumococcal TCSTS to the process of nasopharyngeal colonization by using an infant rat model. Whereas deletions in all but one of these systems have been associated previously with a high degree of attenuation in a murine model of pneumonia, only the CiaRH system was necessary for efficient carriage. Transcriptional analysis by using microarray hybridization identified a locus consisting of two adjacent genes, htrA and spoJ, that was specifically and strongly downregulated in a DeltaciaRH-null mutant. A S. pneumoniae strain lacking the htrA gene encoding a putative serine protease, but not one lacking spoJ, showed decreased fitness in a competitive model of colonization, a finding consistent with this gene mediating a portion of the carriage deficit observed with the DeltaciaRH strain.
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Affiliation(s)
- M E Sebert
- Department of Pediatrics, Children's Hospital of Philadelphia, Pennsylvania 19104, USA
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15
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Godfrin-Estevenon AM, Pasta F, Lane D. The parAB gene products of Pseudomonas putida exhibit partition activity in both P. putida and Escherichia coli. Mol Microbiol 2002; 43:39-49. [PMID: 11849535 DOI: 10.1046/j.1365-2958.2002.02735.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bacteria for which there is evidence that proteins of the ParAB family act in chromosome segregation also undergo developmental transitions that involve the ParAB homologues, raising the question of whether the partition activity is equivalent to that of plasmid partition systems. We have investigated the role in partition of the parAB locus of a free-living bacterium, Pseudomonas putida, not known to pass through developmental phases. A parAB deletion mutant, compared with wild type, showed slightly higher frequencies of anucleate cells in exponentially growing cultures but much higher frequencies in deceleration phase. This increase was growth medium dependent. Oversupply of ParA and ParB proteins also raised anucleate cell levels, specifically in the deceleration phase, in wild-type and mutant strains and regardless of medium, as well as generating abnormal cell morphologies. Absence or oversupply of ParAB function had either slight or considerable effects on growth rate, depending on temperature and medium. The need for the Par proteins in chromosome partition thus appears to be subject to the cell's physiological state. Three sequences similar to cis-acting stabilization sites of Bacillus subtilis are present in the P. putida oriC-parAB region. One was inserted into an unstable mini-F and shown to stabilize it in E. coli in a ParAB-dependent manner.
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16
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Abstract
A pair of genes designated parA and parB are encoded by many low copy number plasmids and bacterial chromosomes. They work with one or more cis-acting sites termed centromere-like sequences to ensure better than random predivisional partitioning of the DNA molecule that encodes them. The centromere-like sequences nucleate binding of ParB and titrate sufficient protein to create foci, which are easily visible by immuno-fluorescence microscopy. These foci normally follow the plasmid or the chromosomal replication oriC complexes. ParA is a membrane-associated ATPase that is essential for this symmetric movement of the ParB foci. In Bacillus subtilis ParA oscillates from end to end of the cell as does MinD of E. coli, a relative of the ParA family. ParA may facilitate ParB movement along the inner surface of the cytoplasmic membrane to encounter and become tethered to the next replication zone. The ATP-bound form of ParA appears to adopt the conformation needed to drive partition. Hydrolysis to create ParA-ADP or free ParA appears to favour a form that is not located at the pole and binds to DNA rather than the partition complex. Definition of the protein domains needed for interaction with membranes and the conformational changes that occur on interaction with ATP/ADP will provide insights into the partitioning mechanism and possible targets for inhibitors of partitioning.
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Affiliation(s)
- C Bignell
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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17
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Quisel JD, Grossman AD. Control of sporulation gene expression in Bacillus subtilis by the chromosome partitioning proteins Soj (ParA) and Spo0J (ParB). J Bacteriol 2000; 182:3446-51. [PMID: 10852876 PMCID: PMC101922 DOI: 10.1128/jb.182.12.3446-3451.2000] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two chromosome partitioning proteins, Soj (ParA) and Spo0J (ParB), regulate the initiation of sporulation in Bacillus subtilis. In a spo0J null mutant, sporulation is inhibited by the action of Soj. Soj negatively regulates expression of several sporulation genes by binding to the promoter regions and inhibiting transcription. All of the genes known to be inhibited by Soj are also activated by the phosphorylated form of the transcription factor Spo0A (Spo0A approximately P). We found that, in a spo0J null mutant, Soj affected sporulation, in part, by decreasing the level of Spo0A protein. Soj negatively regulated transcription of spo0A and associated with the spo0A promoter region in vivo. Expression of spo0A from a heterologous promoter in a spo0J null mutant restored Spo0A levels and partly bypassed the sporulation and gene expression defects. Soj did not appear to significantly affect phosphorylation of Spo0A. Thus, in the absence of Spo0J, Soj inhibits sporulation and sporulation gene expression by inhibiting accumulation of the activator protein Spo0A and by acting downstream of Spo0A to inhibit gene expression directly.
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Affiliation(s)
- J D Quisel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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18
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Cervin MA, Spiegelman GB, Raether B, Ohlsen K, Perego M, Hoch JA. A negative regulator linking chromosome segregation to developmental transcription in Bacillus subtilis. Mol Microbiol 1998; 29:85-95. [PMID: 9701805 DOI: 10.1046/j.1365-2958.1998.00905.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The SpoOJA and SpoOJB proteins of Bacillus subtilis are similar to the ParA and ParB plasmid-partitioning proteins, respectively, and mutation of spoOJB prevents the expression of stage II genes of sporulation. This phenotype is a consequence of SpoOJA activity in the absence of SpoOJB, and its basis was unknown. In the studies reported here, SpoOJA was found specifically to dissociate transcription initiation complexes formed in vitro by the phosphorylated sporulation transcription factor SpoOA and RNA polymerase with the spollG promoter. This repressor-like activity is likely to be the basis for preventing the onset of differentiation in vivo. SpoOJB is known to neutralize SpoOJA activity in vivo and also to interact with a mitotic-like apparatus responsible for chromosome partitioning. These data suggest that SpoOJA and SpoOJB form a regulatory link between chromosome partition and development gene expression.
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Affiliation(s)
- M A Cervin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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19
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Gasc AM, Giammarinaro P, Richter S, Sicard M. Organization around the dnaA gene of Streptococcus pneumoniae. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 2):433-439. [PMID: 9493380 DOI: 10.1099/00221287-144-2-433] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The dnaA gene region of Streptococcus pneumoniae was cloned and sequenced. A tRNA gene, seven ORFs and three DnaA box clusters were identified. The order of the genes and intergene regions found was tRNA(Arg)-orf1-DnaA box cluster 3-htrA-spoOJ-DnaA box cluster 2-dnaA-DnaA box cluster 1-dnaN-orfX-orfY. Five ORFs are homologous to known bacterial genes. The tRNA(Arg) gene and orf1, also called orfL, have already been described in pneumococci and have been reported to be preceded by the competence regulation locus comCDE. In Escherichia coli, htrA encodes a serine protease. In Bacillus subtilis, spoOJ plays a role in sporulation and partition. dnaA encodes an initiator replication protein, very well conserved in several bacteria and dnaN encodes the beta subunit of DNA polymerase III in E. coli. The function of orfX is unknown. The N-terminal part of another reading frame, orfY, revealed high homology with a GTP-binding protein, DnaA box clusters were found upstream and downstream from dnaA. The presence of two such clusters suggests that the chromosomal origin of S. pneumoniae is located within this region. The position of dnaA, and therefore the putative origin of replication, were localized on the physical map of S. pneumoniae.
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Affiliation(s)
- Anne-Marie Gasc
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France
| | - Philippe Giammarinaro
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France
| | - Stefan Richter
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, D-14195 Berlin, Germany
| | - Michel Sicard
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France
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20
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Niki H, Hiraga S. Subcellular distribution of actively partitioning F plasmid during the cell division cycle in E. coli. Cell 1997; 90:951-7. [PMID: 9298906 DOI: 10.1016/s0092-8674(00)80359-1] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
F plasmid is partitioned with fidelity to daughter cells during cell division cycle owing to two trans-acting genes, sopA and sopB, and a cis-acting site, sopC. We visualized the subcellular distribution of mini-F-plasmid molecules by fluorescence in situ hybridization. Mini-F-plasmid molecules having the sopABC segment were localized at midcell in newborn cells. Replicated plasmid molecules migrated to cell positions 1/4 and 3/4 without coupling with cell elongation and were tethered to these positions until completion of cell division. In contrast, molecules of a mini F plasmid lacking the sopABC segment were distributed randomly in spaces not occupied by nucleoids. The sopABC system caused replicated plasmid molecules to be positioned and tethered at the cell quarter sites.
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Affiliation(s)
- H Niki
- Department of Molecular Cell Biology, Institute of Medical Embryology and Genetics, Kumamoto University School of Medicine, Kumamoto, Japan.
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21
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Glaser P, Sharpe ME, Raether B, Perego M, Ohlsen K, Errington J. Dynamic, mitotic-like behavior of a bacterial protein required for accurate chromosome partitioning. Genes Dev 1997; 11:1160-8. [PMID: 9159397 DOI: 10.1101/gad.11.9.1160] [Citation(s) in RCA: 267] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Bacillus subtilis spo0J gene is required for accurate chromosome partitioning during growth and sporulation. We have characterized the subcellular localization of Spo0J protein by immunofluorescence and, in living cells, by use of a spo0J-gfp fusion. We show that the Spo0J protein forms discrete stable foci usually located close to the cell poles. The foci replicate in concert with the initiation of new rounds of DNA replication, after which the daughter foci migrate apart inside the cell. This migration is independent of cell length extension, and presumably serves to direct the daughter chromosomes toward opposite poles of the cell, ready for division. During sporulation, the foci move to the extreme poles of the cell, where they function to position the oriC region of the chromosome ready for polar septation. These observations provide strong evidence for the existence of a dynamic, mitotic-like apparatus responsible for chromosome partitioning in bacteria.
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Affiliation(s)
- P Glaser
- Sir William Dunn School of Pathology, University of Oxford, UK
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22
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Mohl DA, Gober JW. Cell cycle-dependent polar localization of chromosome partitioning proteins in Caulobacter crescentus. Cell 1997; 88:675-84. [PMID: 9054507 DOI: 10.1016/s0092-8674(00)81910-8] [Citation(s) in RCA: 257] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In the bacterium C. crescentus, the cellular homologs of plasmid partitioning proteins, ParA and ParB, localize to both poles of the predivisional cell following the completion of DNA replication. ParB binds to DNA sequences adjacent to the origin of replication suggesting that this region of the genome is tethered to the poles of the cell at a specific time in the cell cycle. Increasing the cellular levels of ParA and ParB disrupts polar localization and results in defects in both cell division and chromosome partitioning. These results suggest that ParA and ParB are involved in partitioning newly replicated chromosomes to the poles of the predivisional cell and may function as components of a bacterial mitotic apparatus.
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Affiliation(s)
- D A Mohl
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles 90095-1569, USA
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23
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Oh MK, Kim BG, Park SH. Importance of spore mutants for fed-batch and continuous fermentation ofBacillus subtilis. Biotechnol Bioeng 1995; 47:696-702. [DOI: 10.1002/bit.260470610] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Lin Z, Howe D, Mallavia LP. Roa307, a protein encoded on Coxiella burnetii plasmid QpH1, shows homology to proteins encoded in the replication origin region of bacterial chromosomes. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:487-90. [PMID: 7565613 DOI: 10.1007/bf02191649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
TnphoA mutagenesis identified an open reading frame, roa307, immediately upstream of the partition locus qsopAB on the Coxiella burnetii plasmid QpH1. The protein sequence deduced from roa307 displayed homology to Orf290 of Pseudomonas putida, Orf283 and Orf282 (SpoOJ) of Bacillus subtilis-hypothetical products of genes in the chromosomal replication origin region. Expression of roa307 was demonstrated by PhoA activity of an Roa307-PhoA fusion.
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Affiliation(s)
- Z Lin
- Department of Microbiology, Washington State University, Pullman 99164-4233, USA
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25
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Oh MK, Park SH, Kim BG. Enhanced subtilisin production with spore mutants of Bacillus subtilis and their characterization. Ann N Y Acad Sci 1995; 750:444-51. [PMID: 7785875 DOI: 10.1111/j.1749-6632.1995.tb19994.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- M K Oh
- Institute for Molecular Biology and Genetics, Seoul National University, Korea
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26
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Ireton K, Gunther NW, Grossman AD. spo0J is required for normal chromosome segregation as well as the initiation of sporulation in Bacillus subtilis. J Bacteriol 1994; 176:5320-9. [PMID: 8071208 PMCID: PMC196717 DOI: 10.1128/jb.176.17.5320-5329.1994] [Citation(s) in RCA: 290] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The spo0J gene of Bacillus subtilis is required for the initiation of sporulation. We show that the sporulation defect caused by null mutations in spo0J is suppressed by a null mutation in the gene located directly upstream from spo0J, soj (suppressor of spo0J). These results indicate that Soj inhibits the initiation of sporulation and that Spo0J antagonizes that inhibition. Further genetic experiments indicated that Soj ultimately affects sporulation by inhibiting the activation (phosphorylation) of the developmental transcription factor encoded by spo0A. In addition, the temperature-sensitive sporulation phenotype caused by the ftsA279 (spoIIN279) mutation was partly suppressed by the soj null mutation, indicating that FtsA might also affect the activity of Soj. Soj and Spo0J are known to be similar in sequence to a family of proteins involved in plasmid partitioning, including ParA and ParB of prophage P1, SopA and SopB of F, and IncC and KorB of RK2, spo0J was found to be required for normal chromosome partitioning as well as for sporulation. spo0J null mutants produced a significant proportion of anucleate cells during vegetative growth. The dual functions of Spo0J could provide a mechanism for regulating the initiation of sporulation in response to activity of the chromosome partition machinery.
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Affiliation(s)
- K Ireton
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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27
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Abstract
The initiation of sporulation in Bacillus subtilis is regulated by a signal transduction system leading to activation (by phosphorylation) of the Spo0A transcription factor. Activated Spo0A controls the expression of genes encoding different RNA polymerase sigma factors, whose synthesis and activities are related to morphological events and intercompartmental communication between the developing forespore and the mother cell.
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Affiliation(s)
- M A Strauch
- Department of Molecular and Experimental Medicine, Scripps Research Institute La Jolla, CA 92037
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28
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Errington J. Bacillus subtilis sporulation: regulation of gene expression and control of morphogenesis. Microbiol Rev 1993; 57:1-33. [PMID: 8464402 PMCID: PMC372899 DOI: 10.1128/mr.57.1.1-33.1993] [Citation(s) in RCA: 332] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bacillus subtilis sporulation is an adaptive response to nutritional stress and involves the differential development of two cells. In the last 10 years or so, virtually all of the regulatory genes controlling sporulation, and many genes directing the structural and morphological changes that accompany sporulation, have been cloned and characterized. This review describes our current knowledge of the program of gene expression during sporulation and summarizes what is known about the functions of the genes that determine the specialized biochemical and morphological properties of sporulating cells. Most steps in the genetic program are controlled by transcription factors that have been characterized in vitro. Two sporulation-specific sigma factors, sigma E and sigma F, appear to segregate at septation, effectively determining the differential development of the mother cell and prespore. Later, each sigma is replaced by a second cell-specific sigma factor, sigma K in the mother cell and sigma G in the prespore. The synthesis of each sigma factor is tightly regulated at both the transcriptional and posttranslational levels. Usually this regulation involves an intercellular interaction that coordinates the developmental programmes of the two cells. At least two other transcription factors fine tune the timing and levels of expression of genes in the sigma E and sigma K regulons. The controlled synthesis of the sigma factors and other transcription factors leads to a spatially and temporally ordered program of gene expression. The gene products made during each successive stage of sporulation help to bring about a sequence of gross morphological changes and biochemical adaptations. The formation of the asymmetric spore septum, engulfment of the prespore by the mother cell, and formation of the spore core, cortex, and coat are described. The importance of these structures in the development of the resistance, dormancy, and germination properties of the spore is assessed.
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Affiliation(s)
- J Errington
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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29
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Hoch JA. Regulation of the onset of the stationary phase and sporulation in Bacillus subtilis. Adv Microb Physiol 1993; 35:111-33. [PMID: 8310879 DOI: 10.1016/s0065-2911(08)60098-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- J A Hoch
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037
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30
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Predich M, Nair G, Smith I. Bacillus subtilis early sporulation genes kinA, spo0F, and spo0A are transcribed by the RNA polymerase containing sigma H. J Bacteriol 1992; 174:2771-8. [PMID: 1569009 PMCID: PMC205927 DOI: 10.1128/jb.174.9.2771-2778.1992] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Bacillus subtilis genes kinA (spoIIJ), spo0F, and spo0A encode components of the sporulation signal transduction pathway. Recent work has suggested that these genes are transcribed by a minor form of RNA polymerase, E sigma H (sigma H is the product of spo0H, another early sporulation gene). We directly tested this hypothesis by performing in vitro transcription assays with reconstituted E sigma H and a set of plasmids containing the kinA, spo0F, and spo0A promoter regions. We were able to obtain distinct transcripts of the expected sizes with all three genes by using linearized or supercoiled templates. Furthermore, primer extension experiments indicate that the transcription start sites for the three genes in vitro and in vivo are the same. In addition, we measured steady-state levels of kinA, spo0F, and spo0A mRNAs during growth in sporulation medium; all of them were increased at or near the beginning of the stationary phase.
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Affiliation(s)
- M Predich
- Department of Microbiology, Public Health Research Institute, New York, New York
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31
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Ogasawara N, Yoshikawa H. Genes and their organization in the replication origin region of the bacterial chromosome. Mol Microbiol 1992; 6:629-34. [PMID: 1552862 DOI: 10.1111/j.1365-2958.1992.tb01510.x] [Citation(s) in RCA: 156] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genes and their organization are conserved in the replication origin region of the bacterial chromosome. To determine the extent of the conserved region in Gram-positive and Gram-negative bacteria, which diverged 1.2 billion years ago, we have further sequenced the region upstream from the dnaA genes in Bacillus subtilis and Pseudomonas putida. Fifteen open reading frames (ORFs) and 11 ORFs were identified in the 13.6 kb and the 9.8 kb fragments in B. subtilis and P. putida, respectively. Eight consecutive P. putida genes, except for one small ORF (homologous to gene 9K of Escherichia coli) in between, are homologous in sequence and relative locations to genes in B. subtilis. Altogether, 12 genes and their organization are conserved in B. subtilis and P. putida in the origin region. We found that the conserved region terminated on one side after the orf290 in P. putida (orf282 in B. subtilis). In the B. subtilis chromosome, five additional ORFs were found in between the conserved genes, suggesting that they are added after Gram-positive bacteria were diverged from the Gram-negative bacteria. One of the ORFs is a duplicate of the conserved gene. The third non-translatable region containing multiple repeats of DnaA-box (second in the case of P. putida) was found flanking gidA in both organisms. This result shows clearly that E. coli oriC and flanking genes gidA and gidB have been translocated by the inversion of some 40 kb fragment.
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Affiliation(s)
- N Ogasawara
- Department of Genetics, Osaka University Medical School, Suita, Japan
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