1
|
Zhang L, Shi Y, Xu Q, Yu J, Li Q, Huang L, Kang X, Wang S, Qiao J. Mixed organic acids as an effective green modifier for enhancing PAH degradation by ZIF-8@ B. subtilis ZL09-26. ENVIRONMENTAL RESEARCH 2025; 280:121920. [PMID: 40409447 DOI: 10.1016/j.envres.2025.121920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2025] [Revised: 05/14/2025] [Accepted: 05/21/2025] [Indexed: 05/25/2025]
Abstract
Although a protective shell based on a metal-organic framework (MOF) can effectively improve the remediation of polycyclic aromatic hydrocarbons (PAHs) by microorganisms, the functional characteristics of the shell are often limited by the surface charge, chemical properties and intrinsic strain characteristics. This study explored the potential of mixed organic acids (MA) as an eco-friendly modifier for zeolite imidazolate framework-8 (ZIF-8), facilitating the formation of a biomimetic mineralized shell around Bacillus subtilis ZL09-26. The addition of MA into the ZIF-8 protective shell was found to stimulate growth and bolster cell viability. Notably, adding MA contribute resulted in a 1.98- fold enhancement of the PHE degradation efficiency. After five cycles of reuse, ZIF-8-MA@B. subtilis ZL09-26 still maintained almost 90 % of the initial PHE degradation ability. Proteomic analysis revealed a coordinated regulation of multiple metabolic pathways that facilitated PHE uptake and degradation, including central carbon metabolism, direct PHE biodegradation, oxidative phosphorylation, aminoacyl-tRNA biosynthesis, fatty acid biosynthesis, ABC transporters, and the biosynthesis of valine, leucine, isoleucine, and lysine. This work broadens the application potential of biomineralized microorganisms, providing novel strategies for the sustainable bioremediation of xenobiotic pollutants in the environment.
Collapse
Affiliation(s)
- Lei Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Technology Innovation Center, Lianyungang, 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Yong Shi
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Qinyu Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jingbo Yu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Qingya Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Lirong Huang
- College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Xinxin Kang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Technology Innovation Center, Lianyungang, 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Technology Innovation Center, Lianyungang, 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang, 222005, China.
| | - Jie Qiao
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, China.
| |
Collapse
|
2
|
Biochemical characterization of an E. coli cell division factor FtsE shows ATPase cycles similar to the NBDs of ABC-transporters. Biosci Rep 2021; 41:227313. [PMID: 33320186 PMCID: PMC7791547 DOI: 10.1042/bsr20203034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022] Open
Abstract
The peptidoglycan (PG) layer is an intricate and dynamic component of the bacterial cell wall, which requires a constant balance between its synthesis and hydrolysis. FtsEX complex present on the inner membrane is shown to transduce signals to induce PG hydrolysis. FtsE has sequence similarity with the nucleotide-binding domains (NBDs) of ABC transporters. The NBDs in most of the ABC transporters couple ATP hydrolysis to transport molecules inside or outside the cell. Also, this reaction cycle is driven by the dimerization of NBDs. Though extensive studies have been carried out on the Escherchia coli FtsEX complex, it remains elusive regarding how FtsEX complex helps in signal transduction or transportation of molecules. Also, very little is known about the biochemical properties and ATPase activities of FtsE. Because of its strong interaction with the membrane-bound protein FtsX, FtsE stays insoluble upon overexpression in E. coli, and thus, most studies on E. coli FtsE (FtsEEc) in the past have used refolded FtsE. Here in the present paper, for the first time, we report the soluble expression, purification, and biochemical characterization of FtsE from E. coli. The purified soluble FtsE exhibits high thermal stability, exhibits ATPase activity and has more than one ATP-binding site. We have also demonstrated a direct interaction between FtsE and the cytoplasmic loop of FtsX. Together, our findings suggest that during bacterial division, the ATPase cycle of FtsE and its interaction with the FtsX cytoplasmic loop may help to regulate the PG hydrolysis at the mid cell.
Collapse
|
3
|
Araújo CL, Blanco I, Souza L, Tiwari S, Pereira LC, Ghosh P, Azevedo V, Silva A, Folador A. In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis. PeerJ 2020; 8:e9643. [PMID: 32913672 PMCID: PMC7456259 DOI: 10.7717/peerj.9643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/10/2020] [Indexed: 12/30/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species—the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein–protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.
Collapse
Affiliation(s)
- Carlos Leonardo Araújo
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Iago Blanco
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Luciana Souza
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Sandeep Tiwari
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lino César Pereira
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Adriana Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| |
Collapse
|
4
|
Mir MA, Srinivasan R, Ajitkumar P. MtFtsX a predicted membrane domain of ABC transporter complex MtFtsEX of Mycobacterium tuberculosis interacts with the cell division protein MtFtsZ. Int J Mycobacteriol 2019; 8:281-286. [PMID: 31512605 DOI: 10.4103/ijmy.ijmy_98_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Bacterial cytokinesis is orchestrated by a complex of dozen of proteins called 'divisome' at the mid-cell site. FtsZ, the eukaryotic tubulin homolog, localizes to the mid-cell site where it polymerizes and forms a cytokinetic Z-ring. The Z-ring acts as a docking platform for other proteins to localize. In model organisms, Escherichia coli and Bacillus subtilis, FtsZ is known to interact with several proteins. The role of few of these interactions is known, while of others is yet to be studied. In Mycobacterium tuberculosis, the cell division and its regulation are poorly studied. Although, most of the divisome proteins are conserved in M. tuberculosis, surprisingly the homologues of the protein factors required for membrane association of Z-ring and its stabilization are absent. In E. coli FtsE and FtsX, the constituent ATPase and membrane domains of the ABC transporter complex, localize to the Z-ring immediately after Z-ring stabilizing proteins, ZipA and FtsA. Therefore, investigation of the interaction between MtFtsX and MtFtsZ is demanding. Methods Bacterial two-hybrid system was used to identify the interaction between MtFtsE and MtFtsZ. This interaction was further confirmed by biochemical methods of Ni2+-NTA agarose pull-down and coimmunoprecipitation. Results and Conclusion Here, we demonstrated that MtFtsX interacts with MtFtsZ in vivo and ex-vivo. Further, we showed that self-interacting MtFtsX interacts with MtFtsE. However, we did not find any interaction between MtFtsE and MtFtsZ. These results suggest that the membrane domain MtFtsX of the ABC transporter complex 'MtFtsEX' might be the membrane-tethering and stabilizing factor for Z-ring in M. tuberculosis.
Collapse
Affiliation(s)
- Mushtaq Ahmad Mir
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Asir, Saudi Arabia
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
| |
Collapse
|
5
|
Margulieux KR, Liebov BK, Tirumala VSKKS, Singh A, Bushweller JH, Nakamoto RK, Hughes MA. Bacillus anthracis Peptidoglycan Integrity Is Disrupted by the Chemokine CXCL10 through the FtsE/X Complex. Front Microbiol 2017; 8:740. [PMID: 28496437 PMCID: PMC5406473 DOI: 10.3389/fmicb.2017.00740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/10/2017] [Indexed: 01/07/2023] Open
Abstract
The antimicrobial activity of the chemokine CXCL10 against vegetative cells of Bacillus anthracis occurs via both bacterial FtsE/X-dependent and-independent pathways. Previous studies established that the FtsE/X-dependent pathway was mediated through interaction of the N-terminal region(s) of CXCL10 with a functional FtsE/X complex, while the FtsE/X-independent pathway was mediated through the C-terminal α-helix of CXCL10. Both pathways result in cell lysis and death of B. anthracis. In other bacterial species, it has been shown that FtsE/X is involved in cellular elongation though activation of complex-associated peptidoglycan hydrolases. Thus, we hypothesized that the CXCL10-mediated killing of vegetative cells of B. anthracis through the FtsE/X-dependent pathway resulted from the disruption of peptidoglycan processing. Immunofluorescence microscopy studies using fluorescent peptidoglycan probes revealed that incubation of B. anthracis Sterne (parent) strain with CXCL10 or a C-terminal truncated CXCL10 (CTTC) affected peptidoglycan processing and/or incorporation of precursors into the cell wall. B. anthracis ΔftsX or ftsE(K123A/D481N) mutant strains, which lacked a functional FtsE/X complex, exhibited little to no evidence of disruption in peptidoglycan processing by either CXCL10 or CTTC. Additional studies demonstrated that the B. anthracis parent strain exhibited a statistically significant increase in peptidoglycan release in the presence of either CXCL10 or CTTC. While B. anthracis ΔftsX strain showed increased peptidoglycan release in the presence of CXCL10, no increase was observed with CTTC, suggesting that the FtsE/X-independent pathway was responsible for the activity observed with CXCL10. These results indicate that FtsE/X-dependent killing of vegetative cells of B. anthracis results from a loss of cell wall integrity due to disruption of peptidoglycan processing and suggest that FtsE/X may be an important antimicrobial target to study in the search for alternative microbial therapeutics.
Collapse
Affiliation(s)
- Katie R Margulieux
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, University of Virginia, CharlottesvilleVA, USA
| | - Benjamin K Liebov
- Department of Chemistry, University of Virginia, CharlottesvilleVA, USA
| | - Venkata S K K S Tirumala
- Department of Molecular Physiology and Biological Physics, University of Virginia, CharlottesvilleVA, USA
| | - Arpita Singh
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, University of Virginia, CharlottesvilleVA, USA
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, CharlottesvilleVA, USA
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, CharlottesvilleVA, USA
| | - Molly A Hughes
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, University of Virginia, CharlottesvilleVA, USA
| |
Collapse
|
6
|
Abstract
Bacillus anthracis is killed by the interferon-inducible, ELR(−) CXC chemokine CXCL10. Previous studies showed that disruption of the gene encoding FtsX, a conserved membrane component of the ATP-binding cassette transporter-like complex FtsE/X, resulted in resistance to CXCL10. FtsX exhibits some sequence similarity to the mammalian CXCL10 receptor, CXCR3, suggesting that the CXCL10 N-terminal region that interacts with CXCR3 may also interact with FtsX. A C-terminal truncated CXCL10 was tested to determine if the FtsX-dependent antimicrobial activity is associated with the CXCR3-interacting N terminus. The truncated CXCL10 exhibited antimicrobial activity against the B. anthracis parent strain but not the ΔftsX mutant, which supports a key role for the CXCL10 N terminus. Mutations in FtsE, the conserved ATP-binding protein of the FtsE/X complex, resulted in resistance to both CXCL10 and truncated CXCL10, indicating that both FtsX and FtsE are important. Higher concentrations of CXCL10 overcame the resistance of the ΔftsX mutant to CXCL10, suggesting an FtsX-independent killing mechanism, likely involving its C-terminal α-helix, which resembles a cationic antimicrobial peptide. Membrane depolarization studies revealed that CXCL10 disrupted membranes of the B. anthracis parent strain and the ΔftsX mutant, but only the parent strain underwent depolarization with truncated CXCL10. These findings suggest that CXCL10 is a bifunctional molecule that kills B. anthracis by two mechanisms. FtsE/X-dependent killing is mediated through an N-terminal portion of CXCL10 and is not reliant upon the C-terminal α-helix. The FtsE/X-independent mechanism involves membrane depolarization by CXCL10, likely because of its α-helix. These findings present a new paradigm for understanding mechanisms by which CXCL10 and related chemokines kill bacteria. Chemokines are a class of molecules known for their chemoattractant properties but more recently have been shown to possess antimicrobial activity against a wide range of Gram-positive and Gram-negative bacterial pathogens. The mechanism(s) by which these chemokines kill bacteria is not well understood, but it is generally thought to be due to the conserved amphipathic C-terminal α-helix that resembles cationic antimicrobial peptides in charge and secondary structure. Our present study indicates that the interferon-inducible, ELR(−) chemokine CXCL10 kills the Gram-positive pathogen Bacillus anthracis through multiple molecular mechanisms. One mechanism is mediated by interaction of CXCL10 with the bacterial FtsE/X complex and does not require the presence of the CXCL10 C-terminal α-helix. The second mechanism is FtsE/X receptor independent and kills through membrane disruption due to the C-terminal α-helix. This study represents a new paradigm for understanding how chemokines exert an antimicrobial effect that may prove applicable to other bacterial species.
Collapse
|
7
|
Bajaj R, Bruce KE, Davidson AL, Rued BE, Stauffacher CV, Winkler ME. Biochemical characterization of essential cell division proteins FtsX and FtsE that mediate peptidoglycan hydrolysis by PcsB in Streptococcus pneumoniae. Microbiologyopen 2016; 5:738-752. [PMID: 27167971 PMCID: PMC5061712 DOI: 10.1002/mbo3.366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/14/2016] [Accepted: 03/23/2016] [Indexed: 01/02/2023] Open
Abstract
The FtsEX:PcsB complex forms a molecular machine that carries out peptidoglycan (PG) hydrolysis during normal cell division of the major respiratory pathogenic bacterium, Streptococcus pneumoniae (pneumococcus). FtsX is an integral membrane protein and FtsE is a cytoplasmic ATPase that together structurally resemble ABC transporters. Instead of transport, FtsEX transduces signals from the cell division apparatus to stimulate PG hydrolysis by PcsB, which interacts with extracellular domains of FtsX. Structural studies of PcsB and one extracellular domain of FtsX have recently appeared, but little is known about the biochemical properties of the FtsE ATPase or the intact FtsX transducer protein. We report here purifications and characterizations of tagged FtsX and FtsE proteins. Pneumococcal FtsX‐GFP‐His and FtsX‐His could be overexpressed in Escherichia coli without toxicity, and FtsE‐His remained soluble during purification. FtsX‐His dimerizes in detergent micelles and when reconstituted in phospholipid nanodiscs. FtsE‐His binds an ATP analog with an affinity comparable to that of ATPase subunits of ABC transporters, and FtsE‐His preparations have a low, detectable ATPase activity. However, attempts to detect complexes of purified FtsX‐His, FtsE‐His, and PcsB‐His or coexpressed tagged FtsX and FtsE were not successful with the constructs and conditions tested so far. In working with nanodiscs, we found that PcsB‐His has an affinity for charged phospholipids, mediated partly by interactions with its coiled‐coil domain. Together, these findings represent first steps toward reconstituting the FtsEX:PcsB complex biochemically and provide information that may be relevant to the assembly of the complex on the surface of pneumococcal cells.
Collapse
Affiliation(s)
- Ruchika Bajaj
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Kevin E Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, 47405
| | - Amy L Davidson
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Britta E Rued
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, 47405
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, 47405.
| |
Collapse
|
8
|
Mycobacterium tuberculosis Cell Division Protein, FtsE, is an ATPase in Dimeric Form. Protein J 2014; 34:35-47. [DOI: 10.1007/s10930-014-9593-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
9
|
Donovan C, Bramkamp M. Cell division in Corynebacterineae. Front Microbiol 2014; 5:132. [PMID: 24782835 PMCID: PMC3989709 DOI: 10.3389/fmicb.2014.00132] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/14/2014] [Indexed: 12/02/2022] Open
Abstract
Bacterial cells must coordinate a number of events during the cell cycle. Spatio-temporal regulation of bacterial cytokinesis is indispensable for the production of viable, genetically identical offspring. In many rod-shaped bacteria, precise midcell assembly of the division machinery relies on inhibitory systems such as Min and Noc. In rod-shaped Actinobacteria, for example Corynebacterium glutamicum and Mycobacterium tuberculosis, the divisome assembles in the proximity of the midcell region, however more spatial flexibility is observed compared to Escherichia coli and Bacillus subtilis. Actinobacteria represent a group of bacteria that spatially regulate cytokinesis in the absence of recognizable Min and Noc homologs. The key cell division steps in E. coli and B. subtilis have been subject to intensive study and are well-understood. In comparison, only a minimal set of positive and negative regulators of cytokinesis are known in Actinobacteria. Nonetheless, the timing of cytokinesis and the placement of the division septum is coordinated with growth as well as initiation of chromosome replication and segregation. We summarize here the current knowledge on cytokinesis and division site selection in the Actinobacteria suborder Corynebacterineae.
Collapse
Affiliation(s)
- Catriona Donovan
- Department of Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| |
Collapse
|
10
|
Chen LC, Yeh HY, Yeh CY, Arias CR, Soo VW. Identifying co-targets to fight drug resistance based on a random walk model. BMC SYSTEMS BIOLOGY 2012; 6:5. [PMID: 22257493 PMCID: PMC3296574 DOI: 10.1186/1752-0509-6-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 01/19/2012] [Indexed: 11/17/2022]
Abstract
BACKGROUND Drug resistance has now posed more severe and emergent threats to human health and infectious disease treatment. However, wet-lab approaches alone to counter drug resistance have so far still achieved limited success due to less knowledge about the underlying mechanisms of drug resistance. Our approach apply a heuristic search algorithm in order to extract active network under drug treatment and use a random walk model to identify potential co-targets for effective antibacterial drugs. RESULTS We use interactome network of Mycobacterium tuberculosis and gene expression data which are treated with two kinds of antibiotic, Isoniazid and Ethionamide as our test data. Our analysis shows that the active drug-treated networks are associated with the trigger of fatty acid metabolism and synthesis and nicotinamide adenine dinucleotide (NADH)-related processes and those results are consistent with the recent experimental findings. Efflux pumps processes appear to be the major mechanisms of resistance but SOS response is significantly up-regulation under Isoniazid treatment. We also successfully identify the potential co-targets with literature confirmed evidences which are related to the glycine-rich membrane, adenosine triphosphate energy and cell wall processes. CONCLUSIONS With gene expression and interactome data supported, our study points out possible pathways leading to the emergence of drug resistance under drug treatment. We develop a computational workflow for giving new insights to bacterial drug resistance which can be gained by a systematic and global analysis of the bacterial regulation network. Our study also discovers the potential co-targets with good properties in biological and graph theory aspects to overcome the problem of drug resistance.
Collapse
Affiliation(s)
- Liang-Chun Chen
- Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan
| | - Hsiang-Yuan Yeh
- Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan
| | - Cheng-Yu Yeh
- Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan
| | - Carlos Roberto Arias
- Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan
| | - Von-Wun Soo
- Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan
- Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan
| |
Collapse
|
11
|
Roy S, Vijay S, Arumugam M, Anand D, Mir M, Ajitkumar P. Mycobacterium tuberculosis expresses ftsE gene through multiple transcripts. Curr Microbiol 2011; 62:1581-9. [PMID: 21336990 DOI: 10.1007/s00284-011-9897-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 02/06/2011] [Indexed: 11/25/2022]
Abstract
Bacterial FtsE gene codes for the ATP-binding protein, FtsE, which in complex with the transmembrane protein, FtsX, participates in diverse cellular processes. Therefore, regulated expression of FtsE and FtsX might be critical to the human pathogen, Mycobacterium tuberculosis, under stress conditions. Although ftsX gene of M. tuberculosis (MtftsX) is known to be transcribed from a promoter inside the upstream gene, ftsE, the transcriptional status of ftsE gene of M. tuberculosis (MtftsE) remains unknown. Therefore, the authors initiated transcriptional analyses of MtftsE, using total RNA from M. tuberculosis cells that were grown under stress conditions, which the pathogen is exposed to, in granuloma in tuberculosis patients. Primer extension experiments showed the presence of putative transcripts, T1, T2, T3, and T4. T1 originated from the intergenic region between the upstream gene, MRA_3135, and MtftsE. T2 and T3 were found initiated from within MRA_3135. T4 was transcribed from a region upstream of MRA_3135. RT-PCR confirmed co-transcription of MRA_3135 and MtftsE. The cloned putative promoter regions for T1, T2, and T3 elicited transcriptional activity in Mycobacterium smegmatis transformants. T1, T2, and T3, but no new transcript, were present in the M. tuberculosis cells that were grown under the stress conditions, which the pathogen is exposed to in granuloma in tuberculosis patients. It showed lack of modulation of MtftsE transcripts under the stress conditions tested, indicating that ftsE may not have a stress response-specific function in M. tuberculosis.
Collapse
Affiliation(s)
- Sougata Roy
- Indian Institute of Science, Microbiology and Cell Biology, Bangalore, Karnataka
| | | | | | | | | | | |
Collapse
|
12
|
Abstract
Brucellosis is a prevalent zoonotic disease and is endemic in the Middle East, South America, and other areas of the world. In this study, complete inventories of putative functional ABC systems of five Brucella species have been compiled and compared. ABC systems of Brucella melitensis 16M, Brucella abortus 9-941, Brucella canis RM6/66, Brucella suis 1330, and Brucella ovis 63/290 were identified and aligned. High numbers of ABC systems, particularly nutrient importers, were found in all Brucella species. However, differences in the total numbers of ABC systems were identified (B. melitensis, 79; B. suis, 72; B. abortus 64; B. canis, 74; B. ovis, 59) as well as specific differences in the functional ABC systems of the Brucella species. Since B. ovis is not known to cause human brucellosis, functional ABC systems absent in the B. ovis genome may represent virulence factors in human brucellosis.
Collapse
|
13
|
Detection and characterization of an ABC transporter in Clostridium hathewayi. Arch Microbiol 2008; 190:417-26. [PMID: 18504552 DOI: 10.1007/s00203-008-0385-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 04/30/2008] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
Abstract
An ABC transporter gene from Clostridium hathewayi is characterized. It has duplicated ATPase domains in addition to a transmembrane protein. Its deduced amino acid sequence has conserved functional domains with ATPase components of the multidrug efflux pump genes of several bacteria. Cloning this transporter gene into C. perfringens and E. coli resulted in decreased sensitivities of these bacteria to fluoroquinolones. It also decreased the accumulation and increased the efflux of ethidium bromide from cells containing the cloned gene. Carbonyl cyanide-m-chlorophenylhydrazone (CCCP) inhibited both accumulation and efflux of ethidium bromide from these cells. The ATPase mRNA was overexpressed in the fluoroquinolone-resistant strain when exposed to ciprofloxacin. This is the first report of an ABC transporter in C. hathewayi.
Collapse
|
14
|
Bacterial growth and cell division: a mycobacterial perspective. Microbiol Mol Biol Rev 2008; 72:126-56, table of contents. [PMID: 18322037 DOI: 10.1128/mmbr.00028-07] [Citation(s) in RCA: 282] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Mycobacterium is best known for its two major pathogenic species, M. tuberculosis and M. leprae, the causative agents of two of the world's oldest diseases, tuberculosis and leprosy, respectively. M. tuberculosis kills approximately two million people each year and is thought to latently infect one-third of the world's population. One of the most remarkable features of the nonsporulating M. tuberculosis is its ability to remain dormant within an individual for decades before reactivating into active tuberculosis. Thus, control of cell division is a critical part of the disease. The mycobacterial cell wall has unique characteristics and is impermeable to a number of compounds, a feature in part responsible for inherent resistance to numerous drugs. The complexity of the cell wall represents a challenge to the organism, requiring specialized mechanisms to allow cell division to occur. Besides these mycobacterial specializations, all bacteria face some common challenges when they divide. First, they must maintain their normal architecture during and after cell division. In the case of mycobacteria, that means synthesizing the many layers of complex cell wall and maintaining their rod shape. Second, they need to coordinate synthesis and breakdown of cell wall components to maintain integrity throughout division. Finally, they need to regulate cell division in response to environmental stimuli. Here we discuss these challenges and the mechanisms that mycobacteria employ to meet them. Because these organisms are difficult to study, in many cases we extrapolate from information known for gram-negative bacteria or more closely related GC-rich gram-positive organisms.
Collapse
|
15
|
Letek M, Fiuza M, Ordóñez E, Villadangos AF, Ramos A, Mateos LM, Gil JA. Cell growth and cell division in the rod-shaped actinomycete Corynebacterium glutamicum. Antonie van Leeuwenhoek 2008; 94:99-109. [PMID: 18283557 DOI: 10.1007/s10482-008-9224-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 01/29/2008] [Indexed: 10/22/2022]
Abstract
Bacterial cell growth and cell division are highly complicated and diversified biological processes. In most rod-shaped bacteria, actin-like MreB homologues produce helicoidal structures along the cell that support elongation of the lateral cell wall. An exception to this rule is peptidoglycan synthesis in the rod-shaped actinomycete Corynebacterium glutamicum, which is MreB-independent. Instead, during cell elongation this bacterium synthesizes new cell-wall material at the cell poles whereas the lateral wall remains inert. Thus, the strategy employed by C. glutamicum to acquire a rod-shaped morphology is completely different from that of Escherichia coli or Bacillus subtilis. Cell division in C. glutamicum also differs profoundly by the apparent absence in its genome of homologues of spatial or temporal regulators of cell division, and its cell division apparatus seems to be simpler than those of other bacteria. Here we review recent advances in our knowledge of the C. glutamicum cell cycle in order to further understand this very different model of rod-shape acquisition.
Collapse
Affiliation(s)
- Michal Letek
- Departamento de Biología Molecular. Area de Microbiología. Facultad de Biología, Universidad de León, Leon 24071, Spain
| | | | | | | | | | | | | |
Collapse
|
16
|
Reddy M. Role of FtsEX in cell division of Escherichia coli: viability of ftsEX mutants is dependent on functional SufI or high osmotic strength. J Bacteriol 2006; 189:98-108. [PMID: 17071757 PMCID: PMC1797223 DOI: 10.1128/jb.01347-06] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, at least 12 proteins, FtsZ, ZipA, FtsA, FtsE/X, FtsK, FtsQ, FtsL, FtsB, FtsW, FtsI, FtsN, and AmiC, are known to localize to the septal ring in an interdependent and sequential pathway to coordinate the septum formation at the midcell. The FtsEX complex is the latest recruit of this pathway, and unlike other division proteins, it is shown to be essential only on low-salt media. In this study, it is shown that ftsEX null mutations are not only salt remedial but also osmoremedial, which suggests that FtsEX may not be involved in salt transport as previously thought. Increased coexpression of cell division proteins FtsQ-FtsA-FtsZ or FtsN alone restored the growth defects of ftsEX mutants. ftsEX deletion exacerbated the defects of most of the mutants affected in Z ring localization and septal assembly; however, the ftsZ84 allele was a weak suppressor of ftsEX. The viability of ftsEX mutants in high-osmolarity conditions was shown to be dependent on the presence of a periplasmic protein, SufI, a substrate of twin-arginine translocase. In addition, SufI in multiple copies could substitute for the functions of FtsEX. Taken together, these results suggest that FtsE and FtsX are absolutely required for the process of cell division in conditions of low osmotic strength for the stability of the septal ring assembly and that, during high-osmolarity conditions, the FtsEX and SufI functions are redundant for this essential process.
Collapse
Affiliation(s)
- Manjula Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| |
Collapse
|