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Wang Y, Lu L, Hong Y, Wu J, Zhu G, Ye F, Li Z. Divergent responses of taxonomic and predicted functional profiles of bacterioplankton to reservoir impoundment. ENVIRONMENTAL RESEARCH 2020; 182:109083. [PMID: 31901627 DOI: 10.1016/j.envres.2019.109083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%-58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.
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Affiliation(s)
- Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Lunhui Lu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Zhe Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.
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Lee HN, Ji CJ, Lee HH, Park J, Seo YS, Lee JW, Oh JI. Roles of three FurA paralogs in the regulation of genes pertaining to peroxide defense in Mycobacterium smegmatis mc 2 155. Mol Microbiol 2018; 108:661-682. [PMID: 29569300 DOI: 10.1111/mmi.13956] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2018] [Indexed: 11/28/2022]
Abstract
Mycobacterium smegmatis mc2 155 has three genes (MSMEG_6383, furA1; MSMEG_3460, furA2; MSMEG_6253, furA3) encoding FurA (ferric-uptake regulator A) paralogs. Three FurA paralogs in M. smegmatis are functionally redundant and negatively regulate expression of a subset of genes involved in peroxide detoxification such as ahpC, katG1 and katG2, as well as their own genes. The FurA paralogs sense H2 O2 via metal-catalyzed His oxidation (MCHO) in the same way as PerR. The propensity of FurA2 and FurA3 for MCHO is greater than that of FurA1. The three furA genes are transcribed into leaderless mRNAs lacking the Shine-Dalgarno (SD) sequence. FurA1 and FurA3 have the quaternary structure of homodimers like most Fur homologs, whereas FurA2 occurs as a monomer. The monomeric structure of FurA2 is determined by the C-terminal region of its dimerization domain. FurA2 monomers appear to cooperatively bind to the FurA-binding site with an inverted repeat configuration and have a broader binding specificity for the target DNA than dimeric FurA1 and FurA3. Comparative transcriptomic analysis revealed that the FurA paralogs do not regulate genes related to iron homeostasis in M. smegmatis, and that expression of SigF-regulated genes is significantly decreased in a furA triple mutant relative to the wild-type strain of M. smegmatis.
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Affiliation(s)
- Ha-Na Lee
- Department of Microbiology, Pusan National University, Busan, 46241, Korea
| | - Chang-Jun Ji
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan, 46241, Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan, 46241, Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 46241, Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, 46241, Korea
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Yang J, Li X, Huang L, Jiang H. Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau. Front Microbiol 2015; 6:1345. [PMID: 26648925 PMCID: PMC4663260 DOI: 10.3389/fmicb.2015.01345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/16/2015] [Indexed: 11/13/2022] Open
Abstract
The actinobacterial diversity was investigated in the sediments of five cold springs in Wuli region on the Qinghai-Tibet Plateau using 16S rRNA gene phylogenetic analysis. The actinobacterial communities of the studied cold springs were diverse and the obtained actinobacterial operational taxonomic units were classified into 12 actinobacterial orders (e.g., Acidimicrobiales, Corynebacteriales, Gaiellales, Geodermatophilales, Jiangellales, Kineosporiales, Micromonosporales, Micrococcales, Nakamurellales, Propionibacteriales, Pseudonocardiales, Streptomycetales) and unclassified Actinobacteria. The actinobacterial composition varied among the investigated cold springs and were significantly correlated (r = 0.748, P = 0.021) to environmental variables. The actinobacterial communities in the cold springs were more diverse than other cold habitats on the Tibetan Plateau, and their compositions showed unique geographical distribution characteristics. Statistical analyses showed that biogeographical isolation and unique environmental conditions might be major factors influencing actinobacterial distribution among the investigated cold springs.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Xiaoyan Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
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Furnholm TR, Tisa LS. The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. BMC Genomics 2014; 15:1092. [PMID: 25495525 PMCID: PMC4531530 DOI: 10.1186/1471-2164-15-1092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison. RESULTS Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia. CONCLUSIONS Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.
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Affiliation(s)
- Teal R Furnholm
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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Abstract
Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments.
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Hwang G, Dong T, Islam MS, Sheng Z, Pérez-Estrada LA, Liu Y, Gamal El-Din M. The impacts of ozonation on oil sands process-affected water biodegradability and biofilm formation characteristics in bioreactors. BIORESOURCE TECHNOLOGY 2013; 130:269-277. [PMID: 23313671 DOI: 10.1016/j.biortech.2012.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 11/29/2012] [Accepted: 12/01/2012] [Indexed: 06/01/2023]
Abstract
To examine the effects of the ozonation process (as an oxidation treatment for water and wastewater treatment applications) on microbial biofilm formation and biodegradability of organic compounds present in oil sands process-affected water (OSPW), biofilm reactors were operated continuously for 6weeks. Two types of biofilm substrate materials: polyethylene (PE) and polyvinylchloride (PVC), and two types of OSPW-fresh and ozonated OSPWs-were tested. Endogenous microorganisms, in OSPW, quickly formed biofilms in the reactors. Without ozonation, the bioreactor (using endogenous microorganisms) removed 13.8% of the total acid-extractable organics (TAO) and 18.5% of the parent naphthenic acids (NAs) from fresh OSPW. The combined ozonation and biodegradation process removed 87.2% of the OSPW TAO and over 99% of the OSPW parent NAs. Further UPLC/HRMS analysis showed that NA biodegradability decreased as the NA cyclization number increased. Microbial biofilm formation was found to depend on the biofilm substrate type.
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Affiliation(s)
- Geelsu Hwang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2W2
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Madhaiyan M, Hu CJ, Kim SJ, Weon HY, Kwon SW, Ji L. Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L. Int J Syst Evol Microbiol 2012; 63:1241-1248. [PMID: 22798659 DOI: 10.1099/ijs.0.039685-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of Jatropha curcas cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera Frankia (family Frankiaceae) and Acidothermus (family Acidothermaceae) and the other by members of the genera Geodermatophilus, Blastococcus and Modestobacter (family Geodermatophilaceae). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be N-glycolylated. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C18 : 1ω9c, anteiso-C17 : 0 and C17 : 1ω8c. The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain S9-650(T) represents a novel species in a new genus, for which the name Jatrophihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650(T) ( = DSM 45627(T) = KACC 16232(T)).
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | - Chuan Jiong Hu
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | - Soo-Jin Kim
- Korean Agricultural Culture Collection (KACC), Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
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Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010; 5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. RESULTS I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. CONCLUSION Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
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Schröder J, Jochmann N, Rodionov DA, Tauch A. The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics 2010; 11:12. [PMID: 20055984 PMCID: PMC2823685 DOI: 10.1186/1471-2164-11-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 01/07/2010] [Indexed: 12/30/2022] Open
Abstract
Background Zinc is considered as an essential element for all living organisms, but it can be toxic at large concentrations. Bacteria therefore tightly regulate zinc metabolism. The Cg2502 protein of Corynebacterium glutamicum was a candidate to control zinc metabolism in this species, since it was classified as metalloregulator of the zinc uptake regulator (Zur) subgroup of the ferric uptake regulator (Fur) family of DNA-binding transcription regulators. Results The cg2502 (zur) gene was deleted in the chromosome of C. glutamicum ATCC 13032 by an allelic exchange procedure to generate the zur-deficient mutant C. glutamicum JS2502. Whole-genome DNA microarray hybridizations and real-time RT-PCR assays comparing the gene expression in C. glutamicum JS2502 with that of the wild-type strain detected 18 genes with enhanced expression in the zur mutant. The expression data were combined with results from cross-genome comparisons of shared regulatory sites, revealing the presence of candidate Zur-binding sites in the mapped promoter regions of five transcription units encoding components of potential zinc ABC-type transporters (cg0041-cg0042/cg0043; cg2911-cg2912-cg2913), a putative secreted protein (cg0040), a putative oxidoreductase (cg0795), and a putative P-loop GTPase of the COG0523 protein family (cg0794). Enhanced transcript levels of the respective genes in C. glutamicum JS2502 were verified by real-time RT-PCR, and complementation of the mutant with a wild-type zur gene reversed the effect of differential gene expression. The zinc-dependent expression of the putative cg0042 and cg2911 operons was detected in vivo with a gfp reporter system. Moreover, the zinc-dependent binding of purified Zur protein to double-stranded 40-mer oligonucleotides containing candidate Zur-binding sites was demonstrated in vitro by DNA band shift assays. Conclusion Whole-genome expression profiling and DNA band shift assays demonstrated that Zur directly represses in a zinc-dependent manner the expression of nine genes organized in five transcription units. Accordingly, the Zur (Cg2502) protein is the key transcription regulator for genes involved in zinc homeostasis in C. glutamicum.
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Affiliation(s)
- Jasmin Schröder
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, D-33615 Bielefeld, Germany
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Forizs L, Lestrade S, Mol A, Dierick JF, Gerbaux C, Diallo B, El Jaziri M, Baucher M, Vandeputte OM. Metabolic shift in the phytopathogen Rhodococcus fascians in response to cell-free extract of infected tobacco plant tissues. Curr Microbiol 2009; 58:483-7. [PMID: 19219499 DOI: 10.1007/s00284-008-9352-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 11/28/2008] [Accepted: 12/23/2008] [Indexed: 10/21/2022]
Abstract
The phytopathogen Rhodococcus fascians induces the development of leafy gall, which is considered to be its ecological niche. To obtain a view of the metabolic changes occurring in R. fascians during this process, an in vitro system was used where bacteria are grown in the presence of a leafy gall extract, a condition mimicking that found by the bacteria in infected plants. Proteins of R. fascians grown for 24 h under these conditions were displayed by two-dimensional polyacrylamide gel electrophoresis. Fifteen polypeptides showing a differential accumulation in response to the inducing conditions were analyzed by mass spectrometry. Two polypeptides potentially linked to the Krebs cycle, a pyruvate dehydrogenase and a fumarate hydratase, were further characterized and shown to be downregulated at the transcriptional level. The identification of these two enzymes suggests that R. fascians may shift its metabolism during the interaction with plants from the Krebs cycle to the glyoxylate shunt.
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Affiliation(s)
- Laetitia Forizs
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, Gosselies, Belgium
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Santos CL, Tavares F, Thioulouse J, Normand P. A phylogenomic analysis of bacterial helix-turn-helix transcription factors. FEMS Microbiol Rev 2008; 33:411-29. [PMID: 19076237 DOI: 10.1111/j.1574-6976.2008.00154.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Perception by each individual organism of its environment's parameters is a key factor for survival. In a constantly changing environment, the ability to assess nutrient sources and potentially stressful situations constitutes the main basis for ecological adaptability. Transcription regulators are key decision-making proteins that mediate the communication between environmental conditions and DNA transcription through a multifaceted network. The parallel study of these regulators across microbial organisms adapted to contrasting biotopes constitutes an unexplored approach to understand the evolution of genome plasticity and cell function. We present here a reassessment of bacterial helix-turn-helix regulator diversity in different organisms from a multidisciplinary perspective, on the interface that links metabolism, ecology and phylogeny, further sustained by a statistically based approach. The present revision brought to light evidence of patterns among families of regulators, suggesting that multiple selective forces modulate the number and kind of regulators present in a given genome. Besides being an important step towards understanding the adaptive traits that influence the microbial responses to the varying environment on the very first and most prevalent line of reaction, the transcription of DNA, this approach is a promising tool to extract biological trends from genomic databases.
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Affiliation(s)
- Catarina L Santos
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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