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The AtoC family response regulator upregulates an operon encoding putative outer membrane proteins sorted by type IX secretion system in Porphyromonas gingivalis. J Oral Biosci 2023; 65:80-87. [PMID: 36375735 DOI: 10.1016/j.job.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/02/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Porphyromonas gingivalis, a keystone periodontopathogen, has multiple two-component systems that are thought to modulate virulence. In this study, we focused on PGN_0775 response regulator (RR), an AtoC homolog, and attempted to identify the target gene that it regulates in P. gingivalis. METHODS Comparative proteomic analyses comprising two-dimensional electrophoresis and peptide mass fingerprinting were applied to total protein samples from parent (WT) and atoC gene knockout (KO) strains to screen for affected protein spots. Fluctuations in the expression of corresponding genes were further confirmed using relative quantitative real-time polymerase chain reaction (RQPCR). RESULTS Five protein spots with fluctuating expression levels were identified in pgn_0775 KO strains along with their masses and physiological features, which contained two hypothetical proteins with higher expression levels in the WT than in the KO strains. RQPCR analysis confirmed that mRNA levels were consistently decreased in KO and recovered in pgn_0775-complemented KO strains. The two hypothetical proteins appeared to be the products of an operon that comprises four genes encoding three hypothetical but putative type IX secretion system sorting domain-containing proteins and an N-terminal region of the C25 cysteine peptidase. CONCLUSIONS The AtoC RR homolog in P. gingivalis upregulates the expression of the operon encoding potentially antigenic proteins retained on the cell surface; thus, it could be a promising target for P. gingivalis-specific antivirulence therapy.
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Guillén-Chable F, Avila Castro LA, Rodríguez-Escamilla Z, Martínez-Núñez MA. Insights into coastal microbial antibiotic resistome through a meta-transcriptomic approach in Yucatan. Front Microbiol 2022; 13:972267. [PMID: 36325016 PMCID: PMC9618888 DOI: 10.3389/fmicb.2022.972267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/26/2022] [Indexed: 11/21/2022] Open
Abstract
Antibiotic resistance (AR) is one of the greatest human and clinical challenges associated with different pathogenic organisms. However, in recent years it has also become an environmental problem due to the widespread use of antibiotics in humans and livestock activities. The ability to resist antibiotics comes from antibiotic resistance genes (ARGs) and our understanding of their presence in coastal environments is still limited. Therefore, the objective of the present study was to explore the presence and possible differences in the microbial resistome of four sites from the Yucatan coast through the evaluation of the composition and abundance of ARGs using a high-throughput analysis of metatranscriptomic sequences. In total, 3,498 ARGs were uncovered, which participate in the resistance to tetracycline, macrolide, rifamycin, fluoroquinolone, phenicol, aminoglycoside, cephalosporin, and other antibiotics. The molecular mechanisms of these ARGs were mainly efflux pump, antibiotic target alteration and antibiotic target replacement. In the same way, ARGs were detected in the samples but showing dissimilar enrichment levels. With respect to the sampling sites, the ARGs were present in all the samples collected, either from preserved or contaminated areas. Importantly, sediments of the preserved area of Dzilam presented the second highest level of ARGs detected, probably as a consequence of the antibiotics dragged to the coast by submarine groundwater discharge. In general, the resistance to a single antibiotic was greater than multiresistance, both at the level of gene and organisms; and multiresistance in organisms is acquired mainly by recruiting different monoresistance genes. To our knowledge, this is the first study that describes and compares the resistome of different samples of the Yucatan coast. This study contributes to generating information about the current state of antibiotic resistance on the Yucatan coasts for a better understanding of ARGs dissemination and could facilitate the management of ARGs pollution in the environment.
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Affiliation(s)
- Francisco Guillén-Chable
- Unidad Multidisciplinaria de Docencia e Investigación (UMDI)-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Sisal, Yucatán, Mexico
| | - Luis Alejandro Avila Castro
- Escuela Nacional de Estudios Superiores-Mérida, Universidad Nacional Autónoma de México (UNAM), Ucú, Yucatán, Mexico
| | - Zuemy Rodríguez-Escamilla
- Escuela Nacional de Estudios Superiores-Mérida, Universidad Nacional Autónoma de México (UNAM), Ucú, Yucatán, Mexico
- Zuemy Rodríguez-Escamilla,
| | - Mario Alberto Martínez-Núñez
- Unidad Multidisciplinaria de Docencia e Investigación (UMDI)-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Sisal, Yucatán, Mexico
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas (IIMAS), Universidad Nacional Autónoma de México (UNAM), Mérida, Yucatán, Mexico
- *Correspondence: Mario Alberto Martínez-Núñez,
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3
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Zhu L, Gong T, Wood TL, Yamasaki R, Wood TK. σ 54 -Dependent regulator DVU2956 switches Desulfovibrio vulgaris from biofilm formation to planktonic growth and regulates hydrogen sulfide production. Environ Microbiol 2019; 21:3564-3576. [PMID: 31087603 DOI: 10.1111/1462-2920.14679] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/11/2019] [Indexed: 11/30/2022]
Abstract
Microbiologically influenced corrosion causes $100 billion in damage per year, and biofilms formed by sulfate-reducing bacteria (SRB) are the major culprit. However, little is known about the regulation of SRB biofilm formation. Using Desulfovibrio vulgaris as a model SRB organism, we compared the transcriptomes of biofilm and planktonic cells and identified that the gene for σ54 -dependent regulator DVU2956 is repressed in biofilms. Utilizing a novel promoter that is primarily transcribed in biofilms (Pdvu0304 ), we found production of DVU2956 inhibits biofilm formation by 70%. Corroborating this result, deleting dvu2956 increased biofilm formation, and this biofilm phenotype could be complemented. By producing proteins in biofilms from genes controlled by DVU2956 (dvu2960 and dvu2962), biofilm formation was inhibited almost completely. A second round of RNA-seq for the production of DVU2956 revealed DVU2956 influences electron transport via an Hmc complex (high-molecular-weight cytochrome c encoded by dvu0531-dvu0536) and the Fe-only hydrogenase (encoded by dvu1769, hydA and dvu1770, hydB) to control H2 S production. Corroborating these results, producing DVU2956 in biofilms decreased H2 S production by half, deleting dvu2956 increased H2 S production by 131 ± 5%, and producing DVU2956 in the dvu2956 strain reduced H2 S production. Therefore, DVU2956 maintains SRB in the planktonic state and reduces H2 S formation.
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Affiliation(s)
- Lei Zhu
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Ting Gong
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thammajun L Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Ryota Yamasaki
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
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4
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Genome sequence and analysis of Escherichia coli production strain LS5218. Metab Eng Commun 2017; 5:78-83. [PMID: 29188187 PMCID: PMC5699524 DOI: 10.1016/j.meteno.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/29/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023] Open
Abstract
Escherichia coli strain LS5218 is a useful host for the production of fatty acid derived products, but the genetics underlying this utility have not been fully investigated. Here, we report the genome sequence of LS5218 and a list of large mutations and single nucleotide permutations (SNPs) relative to E. coli K-12 strain MG1655. We discuss how genetic differences may affect the physiological differences between LS5218 and MG1655. We find that LS5218 is more closely related to E. coli strain NCM3722 and suspect that small genetic differences between K-12 derived strains may have a significant impact on metabolic engineering efforts.
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5
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Rand JM, Pisithkul T, Clark RL, Thiede JM, Mehrer CR, Agnew DE, Campbell CE, Markley AL, Price MN, Ray J, Wetmore KM, Suh Y, Arkin AP, Deutschbauer AM, Amador-Noguez D, Pfleger BF. A metabolic pathway for catabolizing levulinic acid in bacteria. Nat Microbiol 2017; 2:1624-1634. [PMID: 28947739 PMCID: PMC5705400 DOI: 10.1038/s41564-017-0028-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/16/2017] [Indexed: 12/21/2022]
Abstract
Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. This discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.
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Affiliation(s)
- Jacqueline M Rand
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Tippapha Pisithkul
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ryan L Clark
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joshua M Thiede
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Christopher R Mehrer
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel E Agnew
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Candace E Campbell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Andrew L Markley
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yumi Suh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Daniel Amador-Noguez
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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6
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Nilgiriwala KS, Jiménez J, Rivera PM, Del Vecchio D. Synthetic tunable amplifying buffer circuit in E. coli. ACS Synth Biol 2015; 4:577-84. [PMID: 25279430 DOI: 10.1021/sb5002533] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
While predictable design of a genetic circuit's output is a major goal of synthetic biology, it remains a significant challenge because DNA binding sites in the cell affect the concentration of available transcription factors (TF). To mitigate this problem, we propose to use a TF that results from the (reversible) phosphorylation of protein substrate as a circuit's output. We demonstrate that by comparatively increasing the amounts of substrate and phosphatase, the TF concentration becomes robust to the presence of DNA binding sites and can be kept at a desired value. The circuit's input/output gain can, in turn, be tuned by changing the relative amounts of the substrate and phosphatase, realizing an amplifying buffer circuit with tunable gain. In our experiments in E. coli, we employ phospho-NRI as the output TF, phosphorylated by the NRII kinase, and dephosphorylated by the NRII phosphatase. Amplifying buffer circuits such as ours could be used to insulate a circuit's output from the context, bringing synthetic biology one step closer to modular design.
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Affiliation(s)
- Kayzad Soli Nilgiriwala
- Department of Mechanical
Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - José Jiménez
- Department of Mechanical
Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Phillip Michael Rivera
- Department of Mechanical
Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Domitilla Del Vecchio
- Department of Mechanical
Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139-4307, United States
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7
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Peng Q, Wang G, Liu G, Zhang J, Song F. Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis. Front Microbiol 2015; 6:407. [PMID: 26029175 PMCID: PMC4428206 DOI: 10.3389/fmicb.2015.00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022] Open
Abstract
Sigma(54) (σ(54)) regulates nitrogen and carbon utilization in bacteria. Promoters that are σ(54)-dependent are highly conserved and contain short sequences located at the -24 and -12 positions upstream of the transcription initiation site. σ(54) requires regulatory proteins known as bacterial enhancer-binding proteins (bEBPs) to activate gene transcription. We show that σ(54) regulates the capacity to grow on various nitrogen sources using a Bacillus thuringiensis HD73 mutant lacking the sigL gene encoding σ(54) (ΔsigL). A 2-fold-change cutoff and a false discovery rate cutoff of P < 0.05 were used to analyze the DNA microarray data, which revealed 255 genes that were downregulated and 121 that were upregulated in the ΔsigL mutant relative to the wild-type HD73 strain. The σ(54) regulon (stationary phase) was characterized by DNA microarray, bioinformatics, and functional assay; 16 operons containing 47 genes were identified whose promoter regions contain the conserved -12/-24 element and whose transcriptional activities were abolished or reduced in the ΔsigL mutant. Eight σ(54)-dependent transcriptional bEBPs were found in the Bt HD73 genome, and they regulated nine σ(54)-dependent promoters. The metabolic pathways activated by σ(54) in this process have yet to be identified in Bacillus thuringiensis; nonetheless, the present analysis of the σ(54) regulon provides a better understanding of the physiological roles of σ factors in bacteria.
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Affiliation(s)
- Qi Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Guannan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Guiming Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
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8
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Hendrickson EL, Wang T, Beck DAC, Dickinson BC, Wright CJ, J Lamont R, Hackett M. Proteomics of Fusobacterium nucleatum within a model developing oral microbial community. Microbiologyopen 2014; 3:729-51. [PMID: 25155235 PMCID: PMC4234264 DOI: 10.1002/mbo3.204] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 07/01/2014] [Accepted: 07/08/2014] [Indexed: 11/29/2022] Open
Abstract
Fusobacterium nucleatum is a common oral organism that can provide adhesive and metabolic support to developing periodontal bacterial communities. It is within the context of these communities that disease occurs. We have previously reported whole cell proteomics analyses of Porphyromonas gingivalis and Streptococcus gordonii in early-stage communities with each other and with F. nucleatum, modeled using 18 h pellets. Here, we report the adaptation of F. nucleatum to the same experimental conditions as measured by differential protein expression. About 1210 F. nucleatum proteins were detected in single species F. nucleatum control samples, 1192 in communities with P. gingivalis, 1224 with S. gordonii, and 1135 with all three species. Quantitative comparisons among the proteomes revealed important changes in all mixed samples with distinct responses to P. gingivalis or S. gordonii alone and in combination. The results were inspected manually and an ontology analysis conducted using DAVID (Database for annotation, visualization, and integrated discovery). Extensive changes were detected in energy metabolism. All multispecies comparisons showed reductions in amino acid fermentation and a shift toward butanoate as a metabolic byproduct, although the two organism model community with S. gordonii showed increases in alanine, threonine, methionine, and cysteine pathways, and in the three species samples there were increases in lysine and methionine. The communities with P. gingivalis or all three organisms showed reduced glycolysis proteins, but F. nucleatum paired with S. gordonii displayed increased glycolysis/gluconeogenesis proteins. The S. gordonii containing two organism model also showed increases in the ethanolamine pathway while the three species sample showed decreases relative to the F. nucleatum single organism control. All of the nascent model communities displayed reduced translation, lipopolysaccharide, and cell wall biosynthesis, DNA replication and DNA repair.
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Affiliation(s)
- Erik L Hendrickson
- Department of Chemical Engineering and Center for Microbial Proteomics, University of Washington, Box 355014, Seattle, Washington, 98195
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9
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Lee FJ, Rusch DB, Stewart FJ, Mattila HR, Newton ILG. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environ Microbiol 2014; 17:796-815. [PMID: 24905222 DOI: 10.1111/1462-2920.12526] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 11/30/2022]
Abstract
The honey bee, the world's most important agricultural pollinator, relies exclusively on plant-derived foods for nutrition. Nectar and pollen collected by honey bees are processed and matured within the nest through the activities of honey bee-derived microbes and enzymes. In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome. The function of the microbial community in the honey bee, as revealed by metatranscriptome sequencing, resembles that of other animal guts and food-processing environments. We identified three major bacterial classes that are active in the gut (γ-Proteobacteria, Bacilli and Actinobacteria), all of which are predicted to participate in the breakdown of complex macromolecules (e.g. polysaccharides and polypeptides), the fermentation of component parts of these macromolecules, and the generation of various fermentation products, such as short-chain fatty acids and alcohol. The ability of the microbial community to metabolize these carbon-rich food sources was confirmed through the use of community-level physiological profiling. Collectively, these findings suggest that the gut microflora of the honey bee harbours bacterial members with unique roles, which ultimately can contribute to the processing of plant-derived food for colonies.
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Affiliation(s)
- Fredrick J Lee
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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Theodorou EC, Theodorou MC, Kyriakidis DA. Regulation of poly-(R)-(3-hydroxybutyrate-co-3-hydroxyvalerate) biosynthesis by the AtoSCDAEB regulon in phaCAB+ Escherichia coli. Appl Microbiol Biotechnol 2013; 97:5259-74. [PMID: 23546423 DOI: 10.1007/s00253-013-4843-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 11/28/2022]
Abstract
AtoSC two-component system (TCS) upregulates the high-molecular weight poly-(R)-3-hydroxybutyrate (PHB) biosynthesis in recombinant phaCAB (+) Escherichia coli strains, with the Cupriavidus necator phaCAB operon. We report here that AtoSC upregulates also the copolymer P(3HB-co-3HV) biosynthesis in phaCAB (+) E. coli. Acetoacetate-induced AtoSC maximized P(3HB-co-3HV) to 1.27 g/l with a 3HV fraction of 25.5 % wt. and biopolymer content of 75 % w/w in a time-dependent process. The atoSC locus deletion in the ∆atoSC strains resulted in 4.5-fold P(3HB-co-3HV) reduction, while the 3HV fraction of the copolymer was restricted to only 6.4 % wt. The ∆atoSC phenotype was restored by extrachromosomal introduction of AtoSC. Deletion of the atoDAEB operon triggered a significant decrease in P(3HB-co-3HV) synthesis and 3HV content in ∆atoDAEB strains. However, the acetoacetate-induced AtoSC in those strains increased P(3HB-co-3HV) to 0.8 g/l with 21 % 3HV, while AtoC or AtoS expression increased P(3HB-co-3HV) synthesis 3.6- or 2.4-fold, respectively, upon acetoacetate. Complementation of the ∆atoDAEB phenotype was achieved by the extrachromosomal introduction of the atoSCDAEB regulon. Individual inhibition of β-oxidation and mainly fatty acid biosynthesis pathways by acrylic acid or cerulenin, respectively, reduced P(3HB-co-3HV) biosynthesis. Under those conditions, introduction of atoSC or atoSCDAEB regulon was capable of upregulating biopolymer accumulation. Concurrent inhibition of both the fatty acid metabolic pathways eliminated P(3HB-co-3HV) production. P(3HB-co-3HV) upregulation in phaCAB (+) E. coli by AtoSC signaling through atoDAEB operon and its participation in the fatty acids metabolism interplay provide additional perceptions of AtoSC critical involvement in E. coli regulatory processes towards biotechnologically improved polyhydroxyalkanoates biosynthesis.
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Affiliation(s)
- Evangelos C Theodorou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece.
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11
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Theodorou MC, Kyriakidis DA. Calcium channels blockers inhibit the signal transduction through the AtoSC system in Escherichia coli. Eur J Pharm Sci 2012; 47:84-96. [PMID: 22634222 DOI: 10.1016/j.ejps.2012.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/05/2012] [Accepted: 05/09/2012] [Indexed: 01/17/2023]
Abstract
Verapamil, diltiazem and nifedipine are Ca(2+)-channel blockers used in cardiovascular diseases. We report here that the Escherichia coli AtoSC signaling is inhibited by those blockers. AtoSC two-component system plays a pivotal role in sophisticated signaling networks in E. coli regulating processes implicated in bacterial homeostasis and pathogenicity. The Ca(2+)-channel blockers abrogated the in vitro full-length AtoS kinase autophosphorylation. However, they demonstrated no effect on the AtoS cytoplasmic form autophosphorylation. AtoC protected AtoS from verapamil or diltiazem but not from nifedipine, when the two constituents formed complex. The blockers did not affect the AtoS≈P to AtoC phosphotransfer. The blockers-mediated AtoSC inhibition was verified in vivo on the atoDAEB expression, which was inhibited only in AtoSC-expressing bacteria upon acetoacetate. The AtoS and AtoC protein or their genes transcription levels were unaffected by the blockers. Blockers demonstrated differential effects in the regulation of both the cytosolic- and most potently the membrane-bound-cPHB. Extracellular Ca(2+) counteracted the verapamil-mediated effect on cPHB only in atoSC(+) cells. Extracellular Ca(2+) reversed the diltiazem-mediated cPHB decreases in cells of both genetic backgrounds, yet a Ca(2+)-concentration dependent reversion was observed only in the AtoSC-regulated cPHB. Nifedipine caused a more pronounced cPHB down-regulation that was not reversed by extracellular Ca(2+). The AtoSC signaling inhibition by Ca(2+)-channel blockers used for human treatment, and their differential effects on cPHB-formed Ca(2+)-channels, signify their implications in bacterial-host interactions through the two-component signaling and could stimulate the design of Ca(2+)-channels blockers derivatives acting as inhibitors of two-component systems.
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Affiliation(s)
- Marina C Theodorou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece.
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12
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Involvement of AtoSC two-component system in Escherichia coli flagellar regulon. Amino Acids 2011; 43:833-44. [PMID: 22083893 DOI: 10.1007/s00726-011-1140-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
Abstract
The AtoSC two-component system in Escherichia coli is a key regulator of many physiological processes. We report here the contribution of AtoSC in E. coli motility and chemotaxis. AtoSC locus deletion in ΔatoSC cells renders cells not motile or responsive against any chemoattractant or repellent independently of the AtoSC inducer's presence. AtoSC expression through plasmid complemented the ΔatoSC phenotype. Cells expressing either AtoS or AtoC demonstrated analogous motility and chemotactic phenotypes as ΔatoSC cells, independently of AtoSC inducer's presence. Mutations of AtoC phosphate-acceptor sites diminished or abrogated E. coli chemotaxis. trAtoC, the AtoC constitutive active form which lacks its receiver domain, up-regulated E. coli motility. AtoSC enhanced the transcription of the flhDC and fliAZY operons and to a lesser extent of the flgBCDEFGHIJKL operon. The AtoSC-mediated regulation of motility and chemotactic response required also the expression of the CheAY system. The AtoSC inducers enhanced the AtoSC-mediated motility and chemotaxis. Acetoacetate or spermidine further promoted the responses of only AtoSC-expressing cells, while Ca(2+) demonstrated its effects independently of AtoSC. Histamine regulated bacterial chemotaxis only in atoSC (+) cells in a concentration-dependent manner while reversed the AtoSC-mediated effects when added at high concentrations. The trAtoC-controlled motility effects were enhanced by acetoacetate or spermidine, but not by histamine. These data reveal that AtoSC system regulates the motility and chemotaxis of E. coli, participating in the transcriptional induction of the main promoters of the chemotactic regulon and modifying the motility and chemotactic phenotypes in an induction-dependent mechanism.
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13
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Filippou PS, Koini EN, Calogeropoulou T, Kalliakmani P, Panagiotidis CA, Kyriakidis DA. Regulation of the Escherichia coli AtoSC two component system by synthetic biologically active 5;7;8-trimethyl-1;4-benzoxazine analogues. Bioorg Med Chem 2011; 19:5061-70. [DOI: 10.1016/j.bmc.2011.06.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 06/01/2011] [Accepted: 06/08/2011] [Indexed: 11/29/2022]
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Krushkal J, Sontineni S, Leang C, Qu Y, Adkins RM, Lovley DR. Genome diversity of the TetR family of transcriptional regulators in a metal-reducing bacterial family Geobacteraceae and other microbial species. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:495-506. [PMID: 21699403 DOI: 10.1089/omi.2010.0117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Members of the TetR family of bacterial transcriptional regulators affect expression of genes whose products are involved in a variety of important functions, including osmotic stress, catabolic pathways, homeostasis, biosynthesis of antibiotics, expression of efflux pumps, multidrug resistance, and virulence of pathogenic bacteria. We used genome sequence information to carry out phylogenetic classification of 864 TetR family members with a special focus on TetR regulators in Geobacteraceae, an environmentally important family of delta-Proteobacteria. The genome of Geobacter sulfurreducens, a model representative of Geobacteraceae, contains nine genes from the tetR family. Several of these genes are located immediately upstream of operons encoding functionally important c-type cytochromes. Computational analyses identified the presence of conserved promoters and other regulatory binding sites upstream of several G. sulfurreducens tetR genes. This suggests the possibility of an intermediary role of TetR family proteins in Geobacteraceae in regulatory cascades involving a variety of sigma factors. In order to understand the role of the TetR regulatory family in Geobacteraceae, we have inferred phylogenetic relationships among the Geobacteraceae TetR proteins and their homologs in other microbial species.
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Affiliation(s)
- Julia Krushkal
- Department of Preventive Medicine, the University of Tennessee Health Science Center, Memphis, USA.
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Pilalis E, Chatziioannou AA, Grigoroudis AI, Panagiotidis CA, Kolisis FN, Kyriakidis DA. Escherichia coli genome-wide promoter analysis: identification of additional AtoC binding target elements. BMC Genomics 2011; 12:238. [PMID: 21569465 PMCID: PMC3118216 DOI: 10.1186/1471-2164-12-238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Accepted: 05/13/2011] [Indexed: 11/16/2022] Open
Abstract
Background Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of E. coli activates the expression of atoDAEB operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that atoSC is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the atoDAEB promoter as the single, cis-regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the E. coli genome. Results Through the implementation of a computational de novo motif detection workflow, a set of candidate motifs was generated, representing putative AtoC binding targets within the E. coli genome. In order to assess the biological relevance of the motifs and to select for experimental validation of those sequences related robustly with distinct cellular functions, we implemented a novel approach that applies Gene Ontology Term Analysis to the motif hits and selected those that were qualified through this procedure. The computational results were validated using Chromatin Immunoprecipitation assays to assess the in vivo binding of AtoC to the predicted sites. This process verified twenty-two additional AtoC binding sites, located not only within intergenic regions, but also within gene-encoding sequences. Conclusions This study, by tracing a number of putative AtoC binding sites, has indicated an AtoC-related cross-regulatory function. This highlights the significance of computational genome-wide approaches in elucidating complex patterns of bacterial cell regulation.
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Affiliation(s)
- Eleftherios Pilalis
- Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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Theodorou EC, Theodorou MC, Kyriakidis DA. AtoSC two-component system is involved in cPHB biosynthesis through fatty acid metabolism in E. coli. Biochim Biophys Acta Gen Subj 2011; 1810:561-8. [DOI: 10.1016/j.bbagen.2011.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 01/18/2011] [Accepted: 01/25/2011] [Indexed: 10/18/2022]
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Papadopoulos G, Grigoroudis AI, Kyriakidis DA. Dimerization of the AtoC response regulator and modelling of its binding to DNA. J Mol Graph Model 2010; 29:565-72. [PMID: 21115262 DOI: 10.1016/j.jmgm.2010.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 10/12/2010] [Accepted: 10/18/2010] [Indexed: 11/28/2022]
Abstract
Bacterial signal transduction systems can be viewed as an entity of multi-sensory and output domains, whereas the functions of response regulators play a pivotal role in the complex network interactions. One crucial property among response regulators functions is their oligomerization and subsequent binding to DNA. The AtoS-AtoC two component system, functionally modulated by various agents, influences fundamental cellular processes such as short-chain fatty acid catabolism and poly-(R)-3-hydroxybutyrate biosynthesis in Escherichia coli. Among the already reported characteristic properties, AtoC binds to a specific site, a palindromic repeat of 20 nucleotides within the atoDAEB promoter. Since experimental structures of AtoC or its complex with DNA are not yet available, an almost complete homology model of AtoC and of its putative entity as a dimer is constructed for this study, as well as a model of its binding to its target DNA sequence. The latter is associated with large conformational changes, as shown by molecular dynamics simulations. Subsequent biochemical study, including cross-linking via chemical agents, revealed the ability of AtoC to form oligomers in vitro.
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Affiliation(s)
- G Papadopoulos
- Department of Biochemistry & Biotechnology, University of Thessaly Ploutonos 26 & Aeolou, Larisa GR-41221, Greece
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Zhang JB, Pan ZX, Lin F, Ma XS, Liu HL. [Biochemical methods for the analysis of DNA-protein interactions]. YI CHUAN = HEREDITAS 2009; 31:325-336. [PMID: 19273448 DOI: 10.3724/sp.j.1005.2009.00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Investigation of DNA-protein interactions is fundamental to understand the mechanism underlying a variety of life processes. In this article, various types of biochemical methods in DNA-protein interaction study in vivo and in vitro at the level of DNA, protein, and the complex, respectively were briefly reviewed. Traditional assays including Nitrocellulose filter-binding assay, Footprinting, EMSA, and Southwestern blotting were summarized. In addition, chromatin immunoprecipitation techniques including nChIP, xChIP, and ChIP-on-chip, which were widely used in epigenetics, were particularly introduced.
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Affiliation(s)
- Jin-Bi Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm. Amino Acids 2009; 37:443-58. [PMID: 19198978 DOI: 10.1007/s00726-009-0241-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 01/12/2009] [Indexed: 02/07/2023]
Abstract
Adaptive signal transduction within microbial cells involves a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile two-component systems (TCS), arisen early in bacterial evolution. In Escherichia coli, cross-talk between the AtoS histidine kinase and the AtoC response regulator, forming the AtoSC TCS, through His --> Asp phosphotransfer, activates AtoC directly to induce atoDAEB operon expression, thus modulating diverse fundamental cellular processes such as short-chain fatty acid catabolism, poly-(R)-3-hydroxybutyrate biosynthesis and chemotaxis. Among the inducers hitherto identified, acetoacetate is the classical activator. The AtoSC TCS functional modulation by polyamines, histamine and Ca(2+), as well as the role of AtoC as transcriptional regulator, add new promising perspectives in the physiological significance and potential pharmacological exploitation of this TCS in cell proliferation, bacteria-host interactions, chemotaxis, and adaptation.
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Extracellular Ca2+ transients affect poly-(R)-3-hydroxybutyrate regulation by the AtoS-AtoC system in Escherichia coli. Biochem J 2009; 417:667-72. [DOI: 10.1042/bj20081169] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Escherichia coli is exposed to wide extracellular concentrations of Ca2+, whereas the cytosolic levels of the ion are subject to stringent control and are implicated in many physiological functions. The present study shows that extracellular Ca2+ controls cPHB [complexed poly-(R)-3-hydroxybutyrate] biosynthesis through the AtoS-AtoC two-component system. Maximal cPHB accumulation was observed at higher [Ca2+]e (extracellular Ca2+ concentration) in AtoS-AtoC-expressing E. coli compared with their ΔatoSC counterparts, in both cytosolic and membrane fractions. The reversal of EGTA-mediated down-regulation of cPHB biosynthesis by the addition of Ca2+ and Mg2+ was under the control of the AtoS-AtoC system. Moreover, the Ca2+-channel blocker verapamil reduced total and membrane-bound cPHB levels, the inhibitory effect being circumvented by Ca2+ addition only in atoSC+ bacteria. Histamine and compound 48/80 affected cPHB accumulation in a [Ca2+]e-dependent manner directed by the AtoS-AtoC system. In conclusion, these data provide evidence for the involvement of external Ca2+ on cPHB synthesis regulated by the AtoS-AtoC two-component system, thus linking Ca2+ with a signal transduction system, most probably through a transporter.
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High-mobility group protein A1 binds herpes simplex virus gene regulatory sequences and affects their expression. Arch Virol 2008; 153:1251-62. [PMID: 18506571 DOI: 10.1007/s00705-008-0112-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 03/31/2008] [Indexed: 10/22/2022]
Abstract
The high-mobility group protein A1 (HMGA1), which regulates mammalian gene expression by altering chromatin architecture, was found to bind at multiple sites within the promoter regions of all of the herpes simplex virus type 1 (HSV-1) immediate early genes, as well as a representative early (tk) gene and one late (gC) gene, both in vitro and in vivo. Infected cell polypeptide (ICP) 4, the major HSV-1 regulatory protein, binds these promoters both in vitro and in vivo, and HMGA1 enhances its in vitro binding. In transient expression experiments, HMGA1 modified the effects of both ICP4 and ICP0, another virus transactivator, on virus gene expression in a promoter-specific manner, but it had no effect on the transactivation of immediate-early promoters by VP16. These data indicate that host-cell architectural chromatin proteins could influence the interactions of host-cell and viral transcription factors with the virus DNA regulatory elements and affect HSV-1 gene expression.
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Functional characterization of the histidine kinase of the E. coli two-component signal transduction system AtoS-AtoC. Biochim Biophys Acta Gen Subj 2008; 1780:1023-31. [PMID: 18534200 DOI: 10.1016/j.bbagen.2008.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 05/05/2008] [Accepted: 05/05/2008] [Indexed: 11/22/2022]
Abstract
The Escherichia coli AtoS-AtoC two-component signal transduction system regulates the expression of the atoDAEB operon genes, whose products are required for short-chain fatty acid catabolism. In this study purified his-tagged wild-type and mutant AtoS proteins were used to prove that these proteins are true sensor kinases. The phosphorylated residue was identified as the histidine-398, which was located in a conserved Eta-box since AtoS carrying a mutation at this site failed to phosphorylate. This inability to phosphorylate was not due to gross structural alterations of AtoS since the H398L mutant retained its capability to bind ATP. Furthermore, the H398L mutant AtoS was competent to catalyze the trans-phosphorylation of an AtoS G-box (G565A) mutant protein which otherwise failed to autophosphorylate due to its inability to bind ATP. The formation of homodimers between the various AtoS proteins was also shown by cross-linking experiments both in vitro and in vivo.
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