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Kumar PKR, Mizuno H. Metal ion-dependent anti-termination of transcriptional regulation of ribonucleoprotein complexes. Biophys Rev 2014; 6:215-226. [PMID: 28510182 DOI: 10.1007/s12551-014-0138-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 01/30/2014] [Indexed: 12/01/2022] Open
Abstract
Anti-terminator proteins are frequently used by bacteria to sense a specific metabolite signal and direct RNA polymerase to either terminate or continue transcription of the genes downstream of an operon. One such protein is HutP, which binds to upstream cis-regulatory sequences to regulate expression of the histidine utilization (hut) operon in Bacillus subtilis. HutP must be activated by L-histidine and divalent metal ions before binding to hut mRNA; binding of activated HutP prevents termination of transcription. Thus, HutP appears to regulate the hut operon in a unique fashion in this class of regulatory proteins. To understand gene (hut operon) regulation by HutP, we performed several biochemical and structural studies. These studies reveal events in the regulatory mechanism, starting with the activation of HutP and ending with the unwinding of hut terminator RNA. In this review, we describe the unique regulatory mechanisms commonly used by many Bacillus species.
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Affiliation(s)
- Penmetcha K R Kumar
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1 Higashi, Tsukuba City, 305-8566, Ibaraki, Japan.
| | - Hiroshi Mizuno
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1 Higashi, Tsukuba City, 305-8566, Ibaraki, Japan
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2
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Thiruselvam V, Sivaraman P, Kumarevel T, Ponnuswamy MN. Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans. Biochem Biophys Res Commun 2014; 446:945-51. [PMID: 24650662 DOI: 10.1016/j.bbrc.2014.03.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
RNA binding proteins control gene expression by the attenuation/antitermination mechanism. HutP is an RNA binding antitermination protein. It regulates the expression of hut operon when it binds with RNA by modulating the secondary structure of single-stranded hut mRNA. HutP necessitates the presence of l-histidine and divalent metal ion to bind with RNA. Herein, we report the crystal structures of ternary complex (HutP-l-histidine-Mg(2+)) and EDTA (0.5 M) treated ternary complex (HutP-l-histidine-Mg(2+)), solved at 1.9 Å and 2.5 Å resolutions, respectively, from Geobacillus thermodenitrificans. The addition of 0.5 M EDTA does not affect the overall metal-ion mediated ternary complex structure and however, the metal ions at the non-specific binding sites are chelated, as evidenced from the results of structural features.
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Affiliation(s)
- Viswanathan Thiruselvam
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Padavattan Sivaraman
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kuoto, Sayo, Hyogo 679-5148, Japan
| | - Thirumananseri Kumarevel
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kuoto, Sayo, Hyogo 679-5148, Japan; Structural Biology Laboratory, RIKEN Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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Dhakshnamoorthy B, Mizuno H, Kumar PKR. Alternative binding modes of l-histidine guided by metal ions for the activation of the antiterminator protein HutP of Bacillus subtilis. J Struct Biol 2013; 183:512-518. [PMID: 23748184 DOI: 10.1016/j.jsb.2013.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 05/11/2013] [Accepted: 05/29/2013] [Indexed: 11/26/2022]
Abstract
Anti-terminator proteins control gene expression by recognizing control signals within cognate transcripts and then preventing transcription termination. HutP is such a regulatory protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences in hut mRNAs. During the anti-termination process, l-histidine and a divalent ion are required for hutP to bind to the specific sequence within the hut mRNA. Our previous crystal structure of the HutP-l-histidine-Mg(2+)-RNA ternary complex demonstrated that the l-histidine ligand and Mg(2+) bind together such that the backbone nitrogen and carboxyl oxygen of l-histidine coordinate with Mg(2+). In addition to the Mg(2+), other divalent ions are also known to efficiently support the l-histidine-dependent anti-termination of the hut operon, and the best divalent ion is Zn(2+). In this study, we determined the crystal structure of the HutP-l-histidine-Zn(2+) complex and found that the orientation of l-histidine coordinated to Zn(2+) is reversed relative to that of l-histidine coordinated to Mg(2+), i.e., the imidazole side chain nitrogen of l-histidine coordinates to Zn(2+). This alternative binding mode of the l-histidine ligand to a divalent ion provides further insight into the mechanisms responsible for the activation of RNA binding during the hut anti-termination process.
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Affiliation(s)
- Balasundaresan Dhakshnamoorthy
- RNA Processing Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central-6, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Hiroshi Mizuno
- RNA Processing Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central-6, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Penmetcha K R Kumar
- RNA Processing Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central-6, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
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4
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Kulis-Horn RK, Persicke M, Kalinowski J. Histidine biosynthesis, its regulation and biotechnological application in Corynebacterium glutamicum. Microb Biotechnol 2013; 7:5-25. [PMID: 23617600 PMCID: PMC3896937 DOI: 10.1111/1751-7915.12055] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/01/2013] [Accepted: 03/05/2013] [Indexed: 01/12/2023] Open
Abstract
l-Histidine biosynthesis is an ancient metabolic pathway present in bacteria, archaea, lower eukaryotes, and plants. For decades l-histidine biosynthesis has been studied mainly in Escherichia coli and Salmonella typhimurium, revealing fundamental regulatory processes in bacteria. Furthermore, in the last 15 years this pathway has been also investigated intensively in the industrial amino acid-producing bacterium Corynebacterium glutamicum, revealing similarities to E. coli and S. typhimurium, as well as differences. This review summarizes the current knowledge of l-histidine biosynthesis in C. glutamicum. The genes involved and corresponding enzymes are described, in particular focusing on the imidazoleglycerol-phosphate synthase (HisFH) and the histidinol-phosphate phosphatase (HisN). The transcriptional organization of his genes in C. glutamicum is also reported, including the four histidine operons and their promoters. Knowledge of transcriptional regulation during stringent response and by histidine itself is summarized and a translational regulation mechanism is discussed, as well as clues about a histidine transport system. Finally, we discuss the potential of using this knowledge to create or improve C. glutamicum strains for the industrial l-histidine production.
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Affiliation(s)
- Robert K Kulis-Horn
- Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany
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Abstract
The ability to degrade the amino acid histidine to ammonia, glutamate, and a one-carbon compound (formate or formamide) is a property that is widely distributed among bacteria. The four or five enzymatic steps of the pathway are highly conserved, and the chemistry of the reactions displays several unusual features, including the rearrangement of a portion of the histidase polypeptide chain to yield an unusual imidazole structure at the active site and the use of a tightly bound NAD molecule as an electrophile rather than a redox-active element in urocanase. Given the importance of this amino acid, it is not surprising that the degradation of histidine is tightly regulated. The study of that regulation led to three central paradigms in bacterial regulation: catabolite repression by glucose and other carbon sources, nitrogen regulation and two-component regulators in general, and autoregulation of bacterial regulators. This review focuses on three groups of organisms for which studies are most complete: the enteric bacteria, for which the regulation is best understood; the pseudomonads, for which the chemistry is best characterized; and Bacillus subtilis, for which the regulatory mechanisms are very different from those of the Gram-negative bacteria. The Hut pathway is fundamentally a catabolic pathway that allows cells to use histidine as a source of carbon, energy, and nitrogen, but other roles for the pathway are also considered briefly here.
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Williams BS, Isokpehi RD, Mbah AN, Hollman AL, Bernard CO, Simmons SS, Ayensu WK, Garner BL. Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium. Bioinform Biol Insights 2012; 6:275-86. [PMID: 23226010 PMCID: PMC3511254 DOI: 10.4137/bbi.s7977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacillus species form an heterogeneous group of Gram-positive bacteria that include members that are disease-causing, biotechnologically-relevant, and can serve as biological research tools. A common feature of Bacillus species is their ability to survive in harsh environmental conditions by formation of resistant endospores. Genes encoding the universal stress protein (USP) domain confer cellular and organismal survival during unfavorable conditions such as nutrient depletion. As of February 2012, the genome sequences and a variety of functional annotations for at least 123 Bacillus isolates including 45 Bacillus cereus isolates were available in public domain bioinformatics resources. Additionally, the genome sequencing status of 10 of the B. cereus isolates were annotated as finished with each genome encoded 3 USP genes. The conservation of gene neighborhood of the 140 aa universal stress protein in the B. cereus genomes led to the identification of a predicted plasmid-encoded transcriptional unit that includes a USP gene and a sulfate uptake gene in the soil-inhabiting Bacillus megaterium. Gene neighborhood analysis combined with visual analytics of chemical ligand binding sites data provided knowledge-building biological insights on possible cellular functions of B. megaterium universal stress proteins. These functions include sulfate and potassium uptake, acid extrusion, cellular energy-level sensing, survival in high oxygen conditions and acetate utilization. Of particular interest was a two-gene transcriptional unit that consisted of genes for a universal stress protein and a sirtuin Sir2 (deacetylase enzyme for NAD+-dependent acetate utilization). The predicted transcriptional units for stress responsive inorganic sulfate uptake and acetate utilization could explain biological mechanisms for survival of soil-inhabiting Bacillus species in sulfate and acetate limiting conditions. Considering the key role of sirtuins in mammalian physiology additional research on the USP-Sir2 transcriptional unit of B. megaterium could help explain mammalian acetate metabolism in glucose-limiting conditions such as caloric restriction. Finally, the deep-rooted position of B. megaterium in the phylogeny of Bacillus species makes the investigation of the functional coupling acetate utilization and stress response compelling.
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Affiliation(s)
- Baraka S Williams
- Center for Bioinformatics and Computational Biology, Department of Biology, Jackson State University, Jackson, MS, USA. ; Department of Biology, Division of Natural Science, Tougaloo College, 500 West County Line Road, Tougaloo, MS, USA
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Townsend MK, Carr NJ, Iyer JG, Horne SM, Gibbs PS, Prüss BM. Pleiotropic phenotypes of a Yersinia enterocolitica flhD mutant include reduced lethality in a chicken embryo model. BMC Microbiol 2008; 8:12. [PMID: 18215272 PMCID: PMC2262085 DOI: 10.1186/1471-2180-8-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 01/23/2008] [Indexed: 11/22/2022] Open
Abstract
Background The Yersinia enterocolitica flagellar master regulator FlhD/FlhC affects the expression levels of non-flagellar genes, including 21 genes that are involved in central metabolism. The sigma factor of the flagellar system, FliA, has a negative effect on the expression levels of seven plasmid-encoded virulence genes in addition to its positive effect on the expression levels of eight of the flagellar operons. This study investigates the phenotypes of flhD and fliA mutants that result from the complex gene regulation. Results Phenotypes relating to central metabolism were investigated with Phenotype MicroArrays. Compared to the wild-type strain, isogenic flhD and fliA mutants exhibited increased growth on purines and reduced growth on N-acetyl-D-glucosamine and D-mannose, when used as a sole carbon source. Both mutants grew more poorly on pyrimidines and L-histidine as sole nitrogen source. Several intermediates of the tricarboxylic acid and the urea cycle, as well as several dipeptides, provided differential growth conditions for the two mutants. Gene expression was determined for selected genes and correlated with the observed phenotypes. Phenotypes relating to virulence were determined with the chicken embryo lethality assay. The assay that was previously established for Escherichia coli strains was modified for Y. enterocolitica. The flhD mutant caused reduced chicken embryo lethality when compared to wild-type bacteria. In contrast, the fliA mutant caused wild-type lethality. This indicates that the virulence phenotype of the flhD mutant might be due to genes that are regulated by FlhD/FlhC but not FliA, such as those that encode the flagellar type III secretion system. Conclusion Phenotypes of flhD and fliA mutants are related to central metabolism and virulence and correlate with gene regulation.
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Affiliation(s)
- Megan K Townsend
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, USA.
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Kumarevel T. Structural insights of HutP-mediated regulation of transcription of the hut operon in Bacillus subtilis. Biophys Chem 2007; 128:1-12. [PMID: 17395359 DOI: 10.1016/j.bpc.2007.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 03/01/2007] [Accepted: 03/01/2007] [Indexed: 11/20/2022]
Abstract
Regulating gene expression directly at the mRNA level represents a novel approach to control cellular processes in all organisms. In this respect, an RNA-binding protein plays a key role by targeting the mRNA to regulate the expression by attenuation or an anti-termination mechanism only in the presence of their cognate ligands. Although many proteins are known to use these mechanisms to regulate the gene expression, no structural insights have been revealed to date to explain how these proteins trigger the conformation for the recognition of RNA. This review describes the activated conformation of HutP, brought by the coordination of L-histidine and Mg(2+) ions, based on our recently solved crystal structures [uncomplexed HutP, HutP-Mg(2+), HutP-L-histidine, HutP-Mg(2+)-L-histidine, HutP-Mg(2+)-L-histidine-RNA]. Once the HutP is activated, the protein binds specifically to bases within the terminator region, without undergoing further structural rearrangement. Also, a high resolution (1.48 A) crystal structure of the quaternary complex containing the three GAG motifs is presented. This analysis clearly demonstrates that the first base in the UAG motifs is not important for the function and is consistent with our previous observations.
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MESH Headings
- Allosteric Regulation
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Cations, Divalent/metabolism
- Crystallography, X-Ray
- Histidine/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Transcription, Genetic
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Affiliation(s)
- Thirumananseri Kumarevel
- Biometals Laboratory and Advanced Protein Crystallography Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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Yu Y, Liang YH, Brostromer E, Quan JM, Panjikar S, Dong YH, Su XD. A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis. J Biol Chem 2006; 281:36929-36. [PMID: 16990261 DOI: 10.1074/jbc.m607703200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Imidazolonepropionase (EC 3.5.2.7) catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-l-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-A resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small beta-sandwich domain. The TIM barrel domain is quite similar to the members of the alpha/beta barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 A away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme.
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Affiliation(s)
- Yamei Yu
- The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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Enkh-Amgalan J, Kawasaki H, Oh-oka H, Seki T. Cloning and characterization of a novel gene involved in nitrogen fixation in Heliobacterium chlorum: a possible regulatory gene. Arch Microbiol 2006; 186:327-37. [PMID: 16932909 DOI: 10.1007/s00203-006-0148-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 05/19/2006] [Accepted: 07/10/2006] [Indexed: 11/25/2022]
Abstract
In the present study, the transcriptional properties of the nitrogen fixation gene cluster of Hbt. chlorum, a strictly anaerobic, gram-positive, phototrophic bacterium, were explored. The cluster consisted of eleven genes in the same orientation in the order nifI ( 1 ) , nifI ( 2 ) , nifH, nifD, nifK, nifE, nifN, nifX, fdx, nifB, and nifV as detected previously. An open reading frame (orf1) preceding these genes was revealed by further cloning. The orf1 was co-transcribed with downstream nif genes in a single polycistronic transcript, the transcription start site (TSS) was located upstream of the orf1, and a putative promoter was identified 10 bp preceding the TSS. Unlike most diazotrophs which have a sigma(54)-dependent -24/-12 promoter, the promoter was similar to the -35/-10 E. coli promoter. The orf1 had no nif homolog in DNA databases, and the highest level of identity (27% at amino acid level) was found with hutP, a positive regulatory gene of the histidine utilization (hut) operon in B. subtilis. Analogous to the regulatory mechanism of the hut operon in B. subtilis, it is conceivable that the orf1 product interacts with the terminator-like structure located downstream of the orf1 during N-deficient condition and prevents transcription termination; thus, the transcription continues into the nif structural genes.
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Affiliation(s)
- Jigjiddorj Enkh-Amgalan
- The International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 560-0871, Japan
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Kumarevel T, Fujimoto Z, Karthe P, Oda M, Mizuno H, Kumar PKR. Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis. Structure 2005; 12:1269-80. [PMID: 15242603 DOI: 10.1016/j.str.2004.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 05/06/2004] [Accepted: 05/10/2004] [Indexed: 10/26/2022]
Abstract
HutP is an L-histidine-activated RNA binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on the hut mRNA. The crystal structure of HutP complexed with an L-histidine analog showed a novel fold; there are four antiparallel beta strands in the central region of each monomer, with two alpha helices each on the front and back. Two HutP monomers form a dimer, and three dimers are arranged in crystallographic 3-fold symmetry to form a hexamer. A histidine analog was located in between the two monomers of HutP, with the imidazole group of L-histidine hydrogen bonded to Glu81. An activation mechanism is proposed based on the identification of key residues of HutP. The HutP binding region in hut mRNA was defined: it consists of three UAG trinucleotide motifs separated by four spacer nucleotides. Residues of HutP potentially important for RNA binding were identified.
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Affiliation(s)
- Thirumananseri Kumarevel
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
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Kumarevel TS, Fujimoto Z, Mizuno H, Kumar PKR. Crystallization and preliminary X-ray diffraction studies of the metal-ion-mediated ternary complex of the HutP protein with L-histidine and its cognate RNA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1702:125-8. [PMID: 15450857 DOI: 10.1016/j.bbapap.2004.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 07/18/2004] [Accepted: 07/19/2004] [Indexed: 10/26/2022]
Abstract
HutP is an RNA-binding protein that regulates the expression of the Bacillus subtilis hut operon by binding to cis-acting regulatory sequences within hut mRNA, exclusively in the presence of L-histidine. We recently solved the crystal structure of a binary complex (HutP with an L-histidine analog) that revealed a novel RNA-binding fold, and identified the important residues that interact with the L-histidine analog. In addition, we have defined the minimal RNA binding segment that is required for HutP recognition. Interestingly, we showed that ternary complex formation depends on the availability of not only L-histidine but also divalent metal ions. Here we report the crystallization and preliminary X-ray diffraction analysis of the HutP ternary complex. The ternary complex was crystallized in the presence of Mg2+ along with L-histidine and hut mRNA, using the hanging drop vapor diffusion method. The crystal belongs to the R3 space group, with unit cell parameters a=b=75.30 A, c=133.8 A. A complete data set at 1.60 A was collected.
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Affiliation(s)
- T S Kumarevel
- Functional Nucleic Acids Group, Institute for Biological Resources and Function, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
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Kumarevel TS, Gopinath SCB, Nishikawa S, Mizuno H, Kumar PKR. Identification of important chemical groups of the hut mRNA for HutP interactions that regulate the hut operon in Bacillus subtilis. Nucleic Acids Res 2004; 32:3904-12. [PMID: 15273277 PMCID: PMC506810 DOI: 10.1093/nar/gkh725] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
HutP is an RNA binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus species by binding to cis-acting regulatory sequences on hut mRNA. We recently solved the HutP crystal structure, which revealed a novel fold where three dimers are arranged in a 3-fold axis to form the hexamer. We also identified a minimal RNA binding element sufficient for HutP binding: three UAG trinucleotide motifs, each separated by 4 nt, located just upstream of the terminator. In the present study we have identified important RNA chemical groups essential for HutP interactions, by combining an in vitro selection strategy and analyses by site-specific base substitutions. These analyses suggest that each HutP molecule recognizes one UAG motif, where the first base (U) can be substituted with other bases, while the second and third bases (A and G) are required for the interactions. Further analyses of the chemical groups of the A and G bases in the UAG motif by modified base analogs suggested the importance of the exocyclic NH2 group in these bases. Also, in this motif, only the 2'-OH group of A is important for HutP recognition. Considering the important chemical groups identified here, as well as the electrostatic potential analysis of HutP, we propose that Glu137 is one of the important residues for the HutP-RNA interactions.
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Affiliation(s)
- T S Kumarevel
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Japan
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14
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Oda M, Kobayashi N, Fujita M, Miyazaki Y, Sadaie Y, Kurusu Y, Nishikawa S. Analysis of HutP-dependent transcription antitermination in the Bacillus subtilis hut operon: identification of HutP binding sites on hut antiterminator RNA and the involvement of the N-terminus of HutP in binding of HutP to the antiterminator RNA. Mol Microbiol 2004; 51:1155-68. [PMID: 14763987 DOI: 10.1046/j.1365-2958.2003.03891.x] [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] [Indexed: 11/20/2022]
Abstract
We investigated HutP-dependent transcription antitermination of the Bacillus subtilis hut operon. In vitro transcription assays with the B. subtilissigmaA-containing RNA polymerase indicated that HutP inhibits transcription termination at the internal terminator by binding to the antiterminator on hut mRNA in the presence of histidine. Ethylnitrosourea modification interference assays and mutational analyses of the interference sites showed that interaction of HutP with a region containing three UAG trinucleotide sequences, which is located on top of the antiterminator structure, is critical for hut antitermination in vivo. Results from kinetic analysis of binding of HutP to RNA containing various portions of the antiterminator sequences indicated that secondary structure is required for binding of HutP to the region containing three UAG triplets in the antiterminator. The in vivo HutP antiterminator activity was reduced by the mutations in the N-terminal region of HutP. The HutP variants with H4A, R7A, I9A and Q26A mutations exhibited reduced binding affinities to the antiterminator RNA in vitro. A 25-mer peptide consisting of amino acid residues 2-26 of HutP bound to the antiterminator RNA. These results indicated that the N-terminus of HutP is involved in binding of HutP to the antiterminator RNA.
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Affiliation(s)
- Masanao Oda
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba City, Ibaraki, Japan.
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15
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Wahlström E, Vitikainen M, Kontinen VP, Sarvas M. The extracytoplasmic folding factor PrsA is required for protein secretion only in the presence of the cell wall in Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 2003; 149:569-577. [PMID: 12634326 DOI: 10.1099/mic.0.25511-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pulse-chase labelling was used to study the role of the cell wall microenvironment in the functioning of Bacillus subtilis PrsA, an extracellular lipoprotein and member of the parvulin family of peptidylprolyl cis/trans-isomerases. It was found that in protoplasts, and thus in the absence of a cell wall matrix, the post-translocational folding, stability and secretion of the AmyQ alpha-amylase were independent of PrsA, in contrast to the strict dependency found in rods. The results indicate that PrsA is dedicated to assisting the folding and stability of exported proteins in the particular microenvironment of the cytoplasmic membrane-cell wall interface, possibly as a chaperone preventing unproductive interactions with the wall. The data also provide evidence for a crucial role of the wall in protein secretion. The presence of the wall directly or indirectly facilitates the release of AmyQ from the cell membrane and affects the rate of the signal peptide processing.
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Affiliation(s)
- Eva Wahlström
- Vaccine Development Laboratory, National Public Health Institute, Mannerheimintie 166, FIN-00300, Helsinki, Finland
| | - Marika Vitikainen
- Vaccine Development Laboratory, National Public Health Institute, Mannerheimintie 166, FIN-00300, Helsinki, Finland
| | - Vesa P Kontinen
- Vaccine Development Laboratory, National Public Health Institute, Mannerheimintie 166, FIN-00300, Helsinki, Finland
| | - Matti Sarvas
- Vaccine Development Laboratory, National Public Health Institute, Mannerheimintie 166, FIN-00300, Helsinki, Finland
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16
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Kumarevel TS, Fujimoto Z, Padmanabhan B, Oda M, Nishikawa S, Mizuno H, Kumar PKR. Crystallization and preliminary X-ray diffraction studies of HutP protein: an RNA-binding protein that regulates the transcription of hut operon in Bacillus subtilis. J Struct Biol 2002; 138:237-40. [PMID: 12217662 DOI: 10.1016/s1047-8477(02)00024-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HutP is an RNA-binding protein and regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on hut mRNA. HutP and its mutant, which has increased affinity for the regulatory sequences, were purified and crystallized by the hanging-drop vapor diffusion method. The space group was P2(1)3 with unit cell dimensions a=b=c=95.6A for HutP and a=b=c=96.8A for the mutant. Complete data sets of 3.0-A resolution for wild-type HutP and of 2.70-A resolution for the mutant HutP were collected.
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Affiliation(s)
- T S Kumarevel
- Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
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17
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Woodall CA, Warner KL, Oremland RS, Murrell JC, McDonald IR. Identification of methyl halide-utilizing genes in the methyl bromide-utilizing bacterial strain IMB-1 suggests a high degree of conservation of methyl halide-specific genes in gram-negative bacteria. Appl Environ Microbiol 2001; 67:1959-63. [PMID: 11282657 PMCID: PMC92821 DOI: 10.1128/aem.67.4.1959-1963.2001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain IMB-1, an aerobic methylotrophic member of the alpha subgroup of the Proteobacteria, can grow with methyl bromide as a sole carbon and energy source. A single cmu gene cluster was identified in IMB-1 that contained six open reading frames: cmuC, cmuA, orf146, paaE, hutI, and partial metF. CmuA from IMB-1 has high sequence homology to the methyltransferase CmuA from Methylobacterium chloromethanicum and Hyphomicrobium chloromethanicum and contains a C-terminal corrinoid-binding motif and an N-terminal methyltransferase motif. However, cmuB, identified in M. chloromethanicum and H. chloromethanicum, was not detected in IMB-1.
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Affiliation(s)
- C A Woodall
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
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18
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Eda S, Hoshino T, Oda M. Role of the DNA sequence downstream of the Bacillus subtilis hut promoter in regulation of the hut operon. Biosci Biotechnol Biochem 2000; 64:484-91. [PMID: 10803944 DOI: 10.1271/bbb.64.484] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To identify the role of the downstream region of a hut promoter in regulation of the Bacillus subtilis hut operon, three single-base substitutions (+9G-->A, +14C-->T, and +23T-->G) were introduced into the hut operon. Analysis of expression of the hut operon containing each of these three single-base substitutions and the hut-lacZ fusions with the single-base substitutions at position +14 showed that the position at +14 and probably the position at +23 were required for amino acid repression at the hut promoter, while the position at +14 was not required for catabolite repression at the hut promoter. The position at +9 was required for a histidine-dependent increase of activity of the hut promoter. Analysis of expression of the hut-lacZ fusions and the hut operon in the codY mutant indicated that the position at +14 and probably the position at +23 were involved in CodY-mediated amino acid repression at the hut promoter and that CodY was not required for catabolite repression at the hut promoter.
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Affiliation(s)
- S Eda
- Institute of Applied Biochemistry, University of Tsukuba, Tsukuba City, Ibaraki, Japan
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19
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Oda M, Kobayashi N, Ito A, Kurusu Y, Taira K. cis-acting regulatory sequences for antitermination in the transcript of the Bacillus subtilis hut operon and histidine-dependent binding of HutP to the transcript containing the regulatory sequences. Mol Microbiol 2000; 35:1244-54. [PMID: 10712704 DOI: 10.1046/j.1365-2958.2000.01795.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The location of the cis-acting regulatory region for histidine-dependent antitermination of the Bacillus subtilis hut operon was determined. A secondary structure, whose sequences partially overlap with the downstream terminator, was found in the regulatory region of the hut transcript. Mutational analysis of the regulatory region showed that the secondary structure was required for histidine-dependent antitermination. An electrophoretic mobility-shift assay demonstrated that, in response to the presence of histidine and Mg2+, purified HutP bound hut RNA bearing putative secondary structure but not RNA lacking the potential to form putative secondary structure. Native gel electrophoresis showed that HutP existed as a hexamer. A filter-binding assay revealed that the concentration of histidine required for half-maximal binding of HutP to RNA was 3.1 mM and that the Kd for binding of HutP to RNA was approximately 0.56 microM in the presence of histidine. These results suggested that putative secondary structure in the regulatory region of hut mRNA could function as an antiterminator to inhibit the formation of the terminator structure and that HutP causes expression of the hut structural genes by binding to the putative antiterminator structure in response to the presence of histidine.
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Affiliation(s)
- M Oda
- National Institute of Bioscience and Human Technology, Agency of Industrial Science and Technology, MITI, Tsukuba City, Ibaraki 305-8566, Japan.
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20
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Cann IK, Kocherginskaya S, King MR, White BA, Mackie RI. Molecular cloning, sequencing, and expression of a novel multidomain mannanase gene from Thermoanaerobacterium polysaccharolyticum. J Bacteriol 1999; 181:1643-51. [PMID: 10049399 PMCID: PMC93557 DOI: 10.1128/jb.181.5.1643-1651.1999] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The manA gene of Thermoanaerobacterium polysaccharolyticum was cloned in Escherichia coli. The open reading frame of manA is composed of 3,291 bases and codes for a preprotein of 1,097 amino acids with an estimated molecular mass of 119,627 Da. The start codon is preceded by a strong putative ribosome binding site (TAAGGCGGTG) and a putative -35 (TTCGC) and -10 (TAAAAT) promoter sequence. The ManA of T. polysaccharolyticum is a modular protein. Sequence comparison and biochemical analyses demonstrate the presence of an N-terminal leader peptide, and three other domains in the following order: a putative mannanase-cellulase catalytic domain, cellulose binding domains 1 (CBD1) and CBD2, and a surface-layer-like protein region (SLH-1, SLH-2, and SLH-3). The CBD domains show no sequence homology to any cellulose binding domain yet reported, hence suggesting a novel CBD. The duplicated CBDs, which lack a disulfide bridge, exhibit 69% identity, and their deletion resulted in both failure to bind to cellulose and an apparent loss of carboxymethyl cellulase and mannanase activities. At the C-terminal region of the gene are three repeats of 59, 67, and 56 amino acids which are homologous to conserved sequences found in the S-layer-associated regions within the xylanases and cellulases of thermophilic members of the Bacillus-Clostridium cluster. The ManA of T. polysaccharolyticum, besides being an extremely active enzyme, is the only mannanase gene cloned which shows this domain structure.
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Affiliation(s)
- I K Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL 61801, USA
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21
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Zalieckas JM, Wray LV, Ferson AE, Fisher SH. Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons. Mol Microbiol 1998; 27:1031-8. [PMID: 9535092 DOI: 10.1046/j.1365-2958.1998.00751.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A Bacillus subtilis mutant that partially relieves carbon catabolite repression (CCR) of the hut operon was isolated by transposon mutagenesis. Characterization of this mutant revealed that the transposon had inserted into the gene, mfd, that encodes transcription-repair coupling factor. The Mfd protein is known to promote strand-specific DNA repair by displacing RNA polymerase stalled at a nucleotide lesion and directing the (A)BC excinuclease to the DNA damage site. A set of transcriptional lacZ fusions was used to demonstrate that the mfd mutation relieves CCR of hut and gnt expression at the cis-acting cre sequences located downstream of the transcriptional start site but does not affect CCR at sites located at the promoters. CCR of the amyE and bglPH genes, which contain cre sequences that overlap their promoters, is not altered by the mfd mutation. These results support a model in which the Mfd protein displaces RNA polymerase stalled at downstream cre sites that function as transcriptional roadblocks and reveal a new role for Mfd in cellular physiology.
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Affiliation(s)
- J M Zalieckas
- Department of Microbiology, Boston University School of Medicine, MA 02118, USA
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22
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Perozich J, Hempel J, Morris SM. Roles of conserved residues in the arginase family. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1382:23-37. [PMID: 9507056 DOI: 10.1016/s0167-4838(97)00131-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Arginases and related enzymes metabolize arginine or similar nitrogen-containing compounds to urea or formamide. In the present report a sequence alignment of 31 members of this family was generated. The alignment, together with the crystal structure of rat liver arginase, allowed the assignment of possible functional or structural roles to 32 conserved residues and conservative substitutions. Two of these residues were previously identified as functionally essential by analysis of inherited defects in the type I arginase gene. Nearly half of the conserved residues are either glycines or prolines located at critical bends in the protein structure. Most metal-coordinating residues, including one histidine and four aspartic acid residues, are strictly conserved. Two additional histidines involved in metal-binding and catalysis are conserved in all arginases and in almost all other family members. Two positions with invariant similarities may serve as indirect metal ligands. Evolutionary relationships within this family were also suggested. Vertebrate type I and II arginases appear to have developed independently from an early gene duplication event. A ureohydrolase sequence from Caenorhabditis elegans is more closely related to other arginases than previously appreciated, while unclassified enzymes from Methanococcus jannaschii and Methanothermus fervidus appear more similar to arginase-related enzymes. In addition, enzymes from Arabidopsis thaliana and Synechocystis, previously identified as arginases, more closely resemble arginase-related enzymes than currently known arginases.
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Affiliation(s)
- J Perozich
- Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, PA 15261, USA.
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23
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Sadaie Y, Yata K, Fujita M, Sagai H, Itaya M, Kasahara Y, Ogasawara N. Nucleotide sequence and analysis of the phoB-rrnE-groESL region of the Bacillus subtilis chromosome. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 6):1861-1866. [PMID: 9202461 DOI: 10.1099/00221287-143-6-1861] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A 36 kb sequence of the phoB-rrnE-groESL region of the Bacillus subtilis chromosome at around 55 degrees has been determined. The sequenced region contains 36 ORFs including the phoB and groESL genes, and the whole rrnE operon. The phoB gene is transcribed in the direction opposite to that of chromosome replication, while most ORFs, including groESL and the rrnE operon, are transcribed in the same direction. Two newly identified tRNA genes upstream of the rrnE operon were those for Arg-tRNA and Gly-tRNA. The sequenced region contains an operon consisting of genes for degradation and uptake of mannan. The rrnE operon and its downstream ORFs are well conserved among Mycoplasma genitalium, Haemophilus influenzae, Synechocystis sp. and Methanococcus jannaschii. delta H consensus sequences are present in the promoter regions of three ORFs, including groESL.
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Affiliation(s)
- Yoshito Sadaie
- Radioisotope Center, National Institute of Genetics, Mishima 411, Japan
| | - Katsunori Yata
- Radioisotope Center, National Institute of Genetics, Mishima 411, Japan
| | - Masaya Fujita
- Radioisotope Center, National Institute of Genetics, Mishima 411, Japan
| | - Hitoshi Sagai
- Laboratory for Pharmacology, Asahi Chemical Industry Co. Ltd, Shizuoka, Ohito 410-23, Japan
| | - Mitsuhiro Itaya
- Mitsubishi-kasei Institute of Life Sciences, Minami-Oya 11, Machida-shi, Tokyo 194, Japan
| | - Yasuhiro Kasahara
- Advanced Institute of Science and Technology, Nara, Ikoma 630-01, Japan
| | - Naotake Ogasawara
- Advanced Institute of Science and Technology, Nara, Ikoma 630-01, Japan
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24
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Parro V, Román MS, Galindo I, Purnelle B, Bolotin A, Sorokin A, Mellado RP. A 23911 bp region of the Bacillus subtilis genome comprising genes located upstream and downstream of the lev operon. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 4):1321-1326. [PMID: 9141695 DOI: 10.1099/00221287-143-4-1321] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Within the framework of the European project to sequence the whole Bacillus subtilis 168 genome, a 23911 bp long chromosomal DNA fragment located around 233 degrees on the B. subtilis genetic map was cloned and sequenced. From the generated sequencing data and the results of the homology search, the primary structure of this region was determined. In addition to the whole lev operon, the region contains putative genes for an amino acid permease, two different alcohol dehydrogenases, a chitosanase, a protein belonging to the LysR family of transcriptional regulators, a protein related to the MerR transcriptional regulator, up to four proteins related to the product of the spoF gene, and genes coding for nine more inferred proteins of unknown function.
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Affiliation(s)
- Víctor Parro
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Marta San Román
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Inmaculada Galindo
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Bénédicte Purnelle
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Place Croix-du-Sud, 2/20, 1348 Louvain-la-Neuve, Belgium
| | - Alexander Bolotin
- Laboratoire de Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France
| | - Alexei Sorokin
- Laboratoire de Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France
| | - Rafael P Mellado
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
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25
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Abstract
Bacillus subtilis mutants deficient in amino acid repression of the histidine utilization (hut) operon were isolated by transposon mutagenesis. Genetic characterization of these mutants indicated that they most likely contained transposon insertions within the codVWXY operon. The codY gene is required for nutritional regulation of the dipeptide permease (dpp) operon. An examination of hut expression in a delta codY mutant demonstrated that amino acid repression exerted at the hutOA operator, which lies immediately downstream of the hut promoter, was defective in a delta codY mutant. The codY gene product was not required for amino acid regulation of either hut induction or the expression of proline oxidase, the first enzyme in proline degradation. This indicates that more than one mechanism of amino acid repression is present in B. subtilis. An examination of dpp and hut expression in cells during exponential growth in various media revealed that the level of CodY-dependent regulation appeared to be related to the growth rate of the culture.
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Affiliation(s)
- S H Fisher
- Department of Microbiology, Boston University School of Medicine, Massachusetts 02118, USA
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26
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Yamamoto H, Uchiyama S, Fajar AN, Ogasawara N, Sekiguchi J. Determination of a 12 kb nucleotide sequence around the 76 degrees region of the Bacillus subtilis chromosome. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 6):1417-1421. [PMID: 8704981 DOI: 10.1099/13500872-142-6-1417] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The nucleotide sequence of a 12361 bp DNA segment in the 76 degrees region of the Bacillus subtilis chromosome has been determined. Ten putative ORFs were identified. The deduced amino acid sequences of the products of two of them (glv-1 and glv-2) exhibited high similarity to those of glvG (6-phospho-beta-glucosidase gene) and glvC [permease (the IIC domain) of the phosphotransferase system (PTS)], respectively, in the glv operon of Escherichia coli. The C-terminal region of Glv-2 exhibited similarity to the entire region of GlvB (the IIB domain of PTS) of E. coli, suggesting fusion of the glvC and glvB genes in B. subtilis. glv-1, yfiA and glv-2 seem to form an operon of a phosphoenolpyruvate:sugar PTS, followed by a presumed four-membered operon of an ABC transport system. Moreover, a presumed sugar symporter and its regulatory genes were located in this region.
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Affiliation(s)
- Hiroki Yamamoto
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda-shi, Nagano 386, Japan
| | - Shigeki Uchiyama
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda-shi, Nagano 386, Japan
| | - Aji N Fajar
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda-shi, Nagano 386, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-01, Japan
| | - Junichi Sekiguchi
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda-shi, Nagano 386, Japan
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27
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Beloin C, Hirschbein L, Le Hégarat F. Suppression of the Bgl+ phenotype of a delta hns strain of Escherichia coli by a Bacillus subtilis antiterminator binding site. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:761-6. [PMID: 8628237 DOI: 10.1007/bf02172988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bacillus subtilis, like Escherichia coli, possesses several sets of genes involved in the utilization of beta-glucosides. In E. coli, all these genes are cryptic, including the genes forming the bgl operon, thus leading to a Bgl- phenotype. We screened for B. subtilis chromosomal DNA fragments capable of reverting the Bgl+ phenotype associated with an E. coli hns mutant to the Bgl- wild-type phenotype. One B. subtilis chromosomal fragment having this property was selected. It contained a putative Ribonucleic AntiTerminator binding site (RAT sequence) upstream from the bgl gene. Deletion studies as well as subcloning experiments allowed us to prove that the putative B. subtilis of the E. coli bgl operon. We propose that this repression results from the titration of the BglG antiterminator protein of E. coli bgl operon by our putative B. subtilis bglP RAT sequence. Thus, we report evidence for a new cross interaction between heterologous RAT-antiterminator protein pairs.
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Affiliation(s)
- C Beloin
- Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
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28
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Saxild HH, Andersen LN, Hammer K. Dra-nupC-pdp operon of Bacillus subtilis: nucleotide sequence, induction by deoxyribonucleosides, and transcriptional regulation by the deoR-encoded DeoR repressor protein. J Bacteriol 1996; 178:424-34. [PMID: 8550462 PMCID: PMC177674 DOI: 10.1128/jb.178.2.424-434.1996] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The genes encoding deoxyriboaldolase (dra), nucleoside uptake protein (nupC), and pyrimidine nucleoside sequences were determined. Sequence analysis showed that the genes were localized immediately downstream of the hut operon. Insertional gene disruption studies indicated that the three genes constitute an operon with the gene order dra-nupC-pdp. A promoter mapping immediately upstream of the dra gene was identified, and downstream of the pdp gene the nucleotide sequence indicated the existence of a factor-independent transcription terminator structure. In wild-type cells growing in succinate minimal medium, the pyrimidine nucleoside phosphorylase and deoxyriboaldolase levels were five- to eightfold higher in the presence of thymidine and fourfold higher in the presence of deoxyadenosine. By the use of lacZ fusions, the regulation was found to be at the level of transcription. The operon expression was subject to glucose repression. Upstream of the dra gene an open reading frame of 313 amino acids was identified. Inactivation of this gene led to an approximately 10-fold increase in the levels of deoxyriboaldolase and pyrimidine nucleoside phosphorylase, and no further induction was seen upon the addition of deoxyribonucleosides. The upstream gene most likely encodes the regulator for the dra-nupC-pdp operon and was designated deoR (stands for deoxyribonucleoside regulator).
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Affiliation(s)
- H H Saxild
- Department of Microbiology, Technical University of Denmark, Lyngby, Denmark
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