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Lyu F, Yang D, Rao L, Liao X. Alanine and glutamate catabolism collaborate to ensure the success of Bacillus subtilis sporulation. Microbiol Res 2024; 286:127828. [PMID: 38991478 DOI: 10.1016/j.micres.2024.127828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024]
Abstract
Sporulation as a typical bacterial differentiation process has been studied for decades. However, two crucial aspects of sporulation, (i) the energy sources supporting the process, and (ii) the maintenance of spore dormancy throughout sporulation, are scarcely explored. Here, we reported the crucial role of RocG-mediated glutamate catabolism in regulating mother cell lysis, a critical step for sporulation completion of Bacillus subtilis, likely by providing energy metabolite ATP. Notably, rocG overexpression resulted in an excessive ATP accumulation in sporulating cells, leading to adverse effects on future spore properties, e.g. increased germination efficiency, reduced DPA content, and lowered heat resistance. Additionally, we revealed that Ald-mediated alanine metabolism was highly related to the inhibition of premature germination and the maintenance of spore dormancy during sporulation, which might be achieved by decreasing the typical germinant L-alanine concentration in sporulating environment. Our data inferred that sporulation of B. subtilis was a highly orchestrated biological process requiring a delicate balance in diverse metabolic pathways, hence ensuring both the completion of sporulation and production of high-quality spores.
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Affiliation(s)
- Fengzhi Lyu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China
| | - Dong Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China
| | - Lei Rao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China.
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China
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2
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Kasu IR, Reyes-Matte O, Bonive-Boscan A, Derman AI, Lopez-Garrido J. Catabolism of germinant amino acids is required to prevent premature spore germination in Bacillus subtilis. mBio 2024; 15:e0056224. [PMID: 38564667 PMCID: PMC11077977 DOI: 10.1128/mbio.00562-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Spores of Bacillus subtilis germinate in response to specific germinant molecules that are recognized by receptors in the spore envelope. Germinants signal to the dormant spore that the environment can support vegetative growth, so many germinants, such as alanine and valine, are also essential metabolites. As such, they are also required to build the spore. Here we show that these germinants cause premature germination if they are still present at the latter stages of spore formation and beyond, but that B. subtilis metabolism is configured to prevent this: alanine and valine are catabolized and cleared from wild-type cultures even when alternative carbon and nitrogen sources are present. Alanine and valine accumulate in the spent media of mutants that are unable to catabolize these amino acids, and premature germination is pervasive. Premature germination does not occur if the germinant receptor that responds to alanine and valine is eliminated, or if wild-type strains that are able to catabolize and clear alanine and valine are also present in coculture. Our findings demonstrate that spore-forming bacteria must fine-tune the concentration of any metabolite that can also function as a germinant to a level that is high enough to allow for spore development to proceed, but not so high as to promote premature germination. These results indicate that germinant selection and metabolism are tightly linked, and suggest that germinant receptors evolve in tandem with the catabolic priorities of the spore-forming bacterium. IMPORTANCE Many bacterial species produce dormant cells called endospores, which are not killed by antibiotics or common disinfection practices. Endospores pose critical challenges in the food industry, where endospore contaminations cause food spoilage, and in hospitals, where infections by pathogenic endospore formers threaten the life of millions every year. Endospores lose their resistance properties and can be killed easily when they germinate and exit dormancy. We have discovered that the enzymes that break down the amino acids alanine and valine are critical for the production of stable endospores. If these enzymes are absent, endospores germinate as they are formed or shortly thereafter in response to alanine, which can initiate the germination of many different species' endospores, or to valine. By blocking the activity of alanine dehydrogenase, the enzyme that breaks down alanine and is not present in mammals, it may be possible to inactivate endospores by triggering premature and unproductive germination.
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Affiliation(s)
- Iqra R. Kasu
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | | | - Alan I. Derman
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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Maeno M, Ohmori T, Nukada D, Sakuraba H, Satomura T, Ohshima T. Two different alanine dehydrogenases from Geobacillus kaustophilus: Their biochemical characteristics and differential expression in vegetative cells and spores. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140904. [PMID: 36918121 DOI: 10.1016/j.bbapap.2023.140904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
Two putative alanine dehydrogenase (AlaDH) genes (GK2752 and GK3448) were found in the genome of a thermophilic spore-forming bacterium, Geobacillus kaustophilus. The amino acid sequences deduced from the two genes showed mutually high homology (71%), and the phylogenetic tree based on the amino acid sequences of the two putative AlaDHs and the homologous proteins showed that the two putative AlaDH genes (GK2752 and GK3448) belong to different groups. Both of the recombinant gene products exhibited high NAD+-dependent AlaDH activity and were purified to homogeneity and characterized in detail. Both enzymes showed high stability against low and high pHs and high temperatures (70 °C). Kinetic analyses showed that the activities of both enzymes proceeded according to the same sequentially ordered Bi-Ter mechanism. X-ray crystallographic analysis showed the two AlaDHs to have similar homohexameric structures. Notably, GK3448-AlaDH was detected in vegetative cells of G. kaustophilus but not spores, while GK2752-AlaDH was present only in the spores. This is the first report showing the presence of two AlaDHs separately expressed in vegetative cells and spores.
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Affiliation(s)
- Miku Maeno
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Taketo Ohmori
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Daiki Nukada
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
| | - Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, Fukui 910-8507, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan.
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4
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Liu Y, Weng T, Pan X, Wen Y, Yang H, Chen J, Xia L. Construction of an alanine dehydrogenase gene deletion strain for vaccine development against Nocardia seriolae in hybrid snakehead (Channa maculata ♀ × Channa argus ♂). FISH & SHELLFISH IMMUNOLOGY 2023; 138:108827. [PMID: 37207887 DOI: 10.1016/j.fsi.2023.108827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Nocardia seriolae is the main pathogen of fish nocardiosis. In our previous study, alanine dehydrogenase was identified as a potential virulence factor of N. seriolae. On the basis of this fact, the alanine dehydrogenase gene of N. seriolae (NsAld) was knocked out to establish the strain ΔNsAld for vaccine development against fish nocardiosis in this study. The LD50 of strain ΔNsAld was 3.90 × 105 CFU/fish, higher than that of wild strain (5.28 × 104 CFU/fish) significantly (p < 0.05). When the strain ΔNsAld was used as a live vaccine to immunize hybrid snakehead (Channa maculata ♀ × Channa argus ♂) at 2.47 × 105 CFU/fish by intraperitoneal injection, the non-specific immune indexes (LZM, CAT, AKP, ACP and SOD activities), specific antibody (IgM) titers and several immune-related genes (CD4, CD8α, IL-1β, MHCIα, MHCIIα and TNFα) were up-regulated in different tissues, indicating that this vaccine could induce humoral and cell-mediated immune responses. Furthermore, the relative percentage survival (RPS) of ΔNsAld vaccine was calculated as 76.48% after wild N. seriolae challenge. All these results suggest that the strain ΔNsAld could be a potential candidate for live vaccine development to control fish nocardiosis in aquaculture.
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Affiliation(s)
- Yansheng Liu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Tingting Weng
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Xuhao Pan
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yiming Wen
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Huiyuan Yang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Jianlin Chen
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China.
| | - Liqun Xia
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China.
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5
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Noell SE, Brennan E, Washburn Q, Davis EW, Hellweger FL, Giovannoni SJ. Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility. Environ Microbiol 2023. [PMID: 36826469 DOI: 10.1111/1462-2920.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [14 C]l-alanine, we confirmed that l-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate l-alanine oxidation at patch l-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of l-alanine metabolism would produce 12% of their standing ATP stock upon encountering an l-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth Brennan
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Oregon, USA
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6
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Li Q, Zhang H, Song Y, Wang M, Hua C, Li Y, Chen S, Dixon R, Li J. Alanine synthesized by alanine dehydrogenase enables ammonium-tolerant nitrogen fixation in Paenibacillus sabinae T27. Proc Natl Acad Sci U S A 2022; 119:e2215855119. [PMID: 36459643 PMCID: PMC9894248 DOI: 10.1073/pnas.2215855119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/08/2022] [Indexed: 12/04/2022] Open
Abstract
Most diazotrophs fix nitrogen only under nitrogen-limiting conditions, for example, in the presence of relatively low concentrations of NH4+ (0 to 2 mM). However, Paenibacillus sabinae T27 exhibits an unusual pattern of nitrogen regulation of nitrogen fixation, since although nitrogenase activities are high under nitrogen-limiting conditions (0 to 3 mM NH4+) and are repressed under conditions of nitrogen sufficiency (4 to 30 mM NH4+), nitrogenase activity is reestablished when very high levels of NH4+ (30 to 300 mM) are present in the medium. To further understand this pattern of nitrogen fixation regulation, we carried out transcriptome analyses of P. sabinae T27 in response to increasing ammonium concentrations. As anticipated, the nif genes were highly expressed, either in the absence of fixed nitrogen or in the presence of a high concentration of NH4+ (100 mM), but were subject to negative feedback regulation at an intermediate concentration of NH4+ (10 mM). Among the differentially expressed genes, ald1, encoding alanine dehydrogenase (ADH1), was highly expressed in the presence of a high level of NH4+ (100 mM). Mutation and complementation experiments revealed that ald1 is required for nitrogen fixation at high ammonium concentrations. We demonstrate that alanine, synthesized by ADH1 from pyruvate and NH4+, inhibits GS activity, leading to a low intracellular glutamine concentration that prevents feedback inhibition of GS and mimics nitrogen limitation, enabling activation of nif transcription by the nitrogen-responsive regulator GlnR in the presence of high levels of extracellular ammonium.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Yi Song
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Minyang Wang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Chongchong Hua
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Yashi Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Jilun Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
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7
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Re-designing Escherichia coli for high-yield production of β-alanine by metabolic engineering. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Aktaş F. Heterologous Expression and Partial Characterization of a New Alanine Dehydrogenase from Amycolatopsis sulphurea. Protein J 2021; 40:342-347. [PMID: 33818657 DOI: 10.1007/s10930-021-09982-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2021] [Indexed: 10/21/2022]
Abstract
A novel alanine dehydrogenase (AlaDH; EC.1.4.1.1) was isolated from Amycolatopsis sulphurea and the AlaDH gene was cloned into a pET28a(+) plasmid and expressed in E. coli BL21 (DE3). The molecular mass of this enzyme was calculated as 41.09 kDa and the amino acid residues of the pure protein indicated the presence of N terminus polyhistidine tags. Its enzyme kinetic values were Km 2.03 mM, kcat 13.24 (s-1), and kcat/Km 6.53 (s-1 mM-1). AlaDH catalyzes the reversible conversion of L-alanine and pyruvate, which has an important role in the TCA energy cycle. Maximum AlaDH activity occurred at about pH 10.5 and 25 °C for the oxidative deamination of L-alanine. AlaDH retained about 10% of its relative activity at 55 °C and it remained about 90% active at 50 °C. These findings show that the AsAlaDH from A. sulphurea has the ability to produce valuable molecules for various industrial purposes and could represent a new potential biocatalyst for biotechnological applications after further characterization and improvement of its catalytic properties.
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Affiliation(s)
- Fatih Aktaş
- Faculty of Engineering, Düzce University, 81600, Düzce, Turkey.
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9
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Oliveira R, Bush MJ, Pires S, Chandra G, Casas-Pastor D, Fritz G, Mendes MV. The novel ECF56 SigG1-RsfG system modulates morphological differentiation and metal-ion homeostasis in Streptomyces tsukubaensis. Sci Rep 2020; 10:21728. [PMID: 33303917 PMCID: PMC7730460 DOI: 10.1038/s41598-020-78520-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Extracytoplasmic function (ECF) sigma factors are key transcriptional regulators that prokaryotes have evolved to respond to environmental challenges. Streptomyces tsukubaensis harbours 42 ECFs to reprogram stress-responsive gene expression. Among them, SigG1 features a minimal conserved ECF σ2-σ4 architecture and an additional C-terminal extension that encodes a SnoaL_2 domain, which is characteristic for ECF σ factors of group ECF56. Although proteins with such domain organisation are widely found among Actinobacteria, the functional role of ECFs with a fused SnoaL_2 domain remains unknown. Our results show that in addition to predicted self-regulatory intramolecular amino acid interactions between the SnoaL_2 domain and the ECF core, SigG1 activity is controlled by the cognate anti-sigma protein RsfG, encoded by a co-transcribed sigG1-neighbouring gene. Characterisation of ∆sigG1 and ∆rsfG strains combined with RNA-seq and ChIP-seq experiments, suggests the involvement of SigG1 in the morphological differentiation programme of S. tsukubaensis. SigG1 regulates the expression of alanine dehydrogenase, ald and the WhiB-like regulator, wblC required for differentiation, in addition to iron and copper trafficking systems. Overall, our work establishes a model in which the activity of a σ factor of group ECF56, regulates morphogenesis and metal-ions homeostasis during development to ensure the timely progression of multicellular differentiation.
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Affiliation(s)
- Rute Oliveira
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCBiology), ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sílvia Pires
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Delia Casas-Pastor
- Center for Synthetic Microbiology, Philipps-University Marburg, 35032, Marburg, Germany
| | - Georg Fritz
- School for Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| | - Marta V Mendes
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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10
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Sidiq KR, Chow MW, Zhao Z, Daniel RA. Alanine metabolism in Bacillus subtilis. Mol Microbiol 2020; 115:739-757. [PMID: 33155333 DOI: 10.1111/mmi.14640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022]
Abstract
Both isomeric forms of alanine play a crucial role in bacterial growth and viability; the L-isomer of this amino acid is one of the building blocks for protein synthesis, and the D-isomer is incorporated into the bacterial cell wall. Despite a long history of genetic manipulation of Bacillus subtilis using auxotrophic markers, the genes involved in alanine metabolism have not been characterized fully. In this work, we genetically characterized the major enzymes involved in B. subtilis alanine biosynthesis and identified an alanine permease, AlaP (YtnA), which we show has a major role in the assimilation of D-alanine from the environment. Our results provide explanations for the puzzling fact that growth of B. subtilis does not result in the significant accumulation of extracellular D-alanine. Interestingly, we find that in B. subtilis, unlike E. coli where multiple enzymes have a biochemical activity that can generate alanine, the primary synthetic enzyme for alanine is encoded by alaT, although a second gene, dat, can support slow growth of an L-alanine auxotroph. However, our results also show that Dat mediates the synthesis of D-alanine and its activity is influenced by the abundance of L-alanine. This work provides valuable insights into alanine metabolism that suggests that the relative abundance of D- and L-alanine might be linked with cytosolic pool of D and L-glutamate, thereby coupling protein and cell envelope synthesis with the metabolic status of the cell. The results also suggest that, although some of the purified enzymes involved in alanine biosynthesis have been shown to catalyze reversible reactions in vitro, most of them function unidirectionally in vivo.
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Affiliation(s)
- Karzan R Sidiq
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Man W Chow
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Zhao Zhao
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
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11
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Hu X, Bai Y, Fan TP, Zheng X, Cai Y. A novel type alanine dehydrogenase from Helicobacter aurati: Molecular characterization and application. Int J Biol Macromol 2020; 161:636-642. [PMID: 32534087 DOI: 10.1016/j.ijbiomac.2020.06.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 01/07/2023]
Abstract
A novel alanine dehydrogenase (ADH; EC.1.4.1.1) with high pyruvate reduced activity was isolated from Helicobacter aurati and expressed in Escherichia coli BL21 (DE3). The optimum pH of the reduction and oxidation reaction were 8.0 and 9.0, respectively, and the optimum temperature was 55 °C. With pyruvate and alanine as substrates, the specific activity of HAADH1 were 268 U·mg-1 and 26 U·mg-1, respectively. HAADH1 had a prominent substrate specificity for alanine (Km = 2.23 mM, kcat/Km = 8.1 s-1·mM-1). In the reduction reaction, HAADH1 showed the highest substrate affinity for pyruvate (Km = 0.56 mM, kcat/Km = 364 s-1·mM-1). Compared to pyruvate, oxaloacetic acid, 2-ketobutyric acid, 3-fluoropyruvate, α-ketoglutaric acids, glyoxylic acid showed a residual activity of 93.30%, 8.93%, 5.62%, 2.57%, 2.51%, respectively. Phylogenetic tree analysis showed that this is a new type of ADH which have a low sequence similarity to available ADH reported in references. 3-Fluoropyruvate was effectively reduced to 3-fluoro-L-alanine by whole-cell catalysis.
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Affiliation(s)
- Xiaoxiang Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shanxi 710069, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1T, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shanxi 710069, China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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12
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Dempwolff F, Sanchez S, Kearns DB. Tn FLX: a Third-Generation mariner-Based Transposon System for Bacillus subtilis. Appl Environ Microbiol 2020; 86:e02893-19. [PMID: 32169936 PMCID: PMC7205501 DOI: 10.1128/aem.02893-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/26/2020] [Indexed: 01/05/2023] Open
Abstract
Random transposon mutagenesis is a powerful and unbiased genetic approach to answer fundamental biological questions. Here, we introduce an improved mariner-based transposon system with enhanced stability during propagation and versatile applications in mutagenesis. We used a low-copy-number plasmid as a transposon delivery vehicle, which affords a lower frequency of unintended recombination during vector construction and propagation in Escherichia coli We generated a variety of transposons allowing for gene disruption or artificial overexpression, each in combination with one of four different antibiotic resistance markers. In addition, we provide transposons that will report gene/protein expression due to transcriptional or translational coupling. We believe that the TnFLX system will help enhance the flexibility of future transposon modification and application in Bacillus and other organisms.IMPORTANCE The stability of transposase-encoding vectors during cloning and propagation is crucial for the reliable application of transposons. Here, we increased the stability of the mariner delivery vehicle in E. coli Moreover, the TnFLX transposon system will improve the application of forward genetic methods with an increased number of antibiotic resistance markers and the ability to generate unbiased green fluorescent protein (GFP) fusions to report on protein translation and subcellular localization.
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Affiliation(s)
- Felix Dempwolff
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Sandra Sanchez
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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13
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Van Wieren A, Cook R, Majumdar S. Characterization of Alanine Dehydrogenase and Its Effect on Streptomyces coelicolorA3(2) Development in Liquid Culture. J Mol Microbiol Biotechnol 2019; 29:57-65. [PMID: 31851994 DOI: 10.1159/000504709] [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: 08/16/2019] [Accepted: 11/10/2019] [Indexed: 11/19/2022] Open
Abstract
Streptomyces, the most important group of industrial microorganisms, is harvested in liquid cultures for the production of two-thirds of all clinically relevant secondary metabolites. It is demonstrated here that the growth of Streptomyces coelicolor A3(2) is impacted by the deletion of the alanine dehydrogenase (ALD), an essential enzyme that plays a central role in the carbon and nitrogen metabolism. A long lag-phase growth followed by a slow exponential growth of S. coelicolor due to ALD gene deletion was observed in liquid yeast extract mineral salt culture. The slow lag-phase growth was replaced by the normal wild-type like growth by ALD complementation engineering. The ALD enzyme from S. coelicolor was also heterologously cloned and expressed in Escherichia coli for characterization. The optimum enzyme activity for the oxidative deamination reaction was found at 30°C, pH 9.5 with a catalytic efficiency, kcat/KM, of 2.0 ± 0.1 mM-1 s-1. The optimum enzyme activity for the reductive amination reaction was found at 30°C, pH 9.0 with a catalytic efficiency, kcat/KM, of 1.9 ± 0.1 mM-1 s-1.
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Affiliation(s)
- Arie Van Wieren
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Ryan Cook
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA.,West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Sudipta Majumdar
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA,
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14
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Abstract
Alanine dehydrogenase (AlaDH) (E.C.1.4.1.1) is a microbial enzyme that catalyzes a reversible conversion of L-alanine to pyruvate. Inter-conversion of alanine and pyruvate by AlaDH is central to metabolism in microorganisms. Its oxidative deamination reaction produces pyruvate which plays a pivotal role in the generation of energy through the tricarboxylic acid cycle for sporulation in the microorganisms. Its reductive amination reaction provides a route for the incorporation of ammonia and produces L-alanine which is required for synthesis of the peptidoglycan layer, proteins, and other amino acids. Also, AlaDH helps in redox balancing as its deamination/amination reaction is linked to the reduction/oxidation of NAD+/NADH in microorganisms. AlaDH from a few microorganisms can also reduce glyoxylate into glycine (aminoacetate) in a nonreversible reaction. Both its oxidative and reductive reactions exhibit remarkable applications in the pharmaceutical, environmental, and food industries. The literature addressing the characteristics and applications of AlaDH from a wide range of microorganisms is summarized in the current review.
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Affiliation(s)
| | - Ravi-Kumar Kadeppagari
- b Centre for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology Campus , Bengaluru , India
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15
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Dave UC, Kadeppagari RK. Purification and characterization of Alanine dehydrogenase from Streptomyces anulatus for its application as a bioreceptor in biosensor. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.02.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Chowdhury-Paul S, Pando-Robles V, Jiménez-Jacinto V, Segura D, Espín G, Núñez C. Proteomic analysis revealed proteins induced upon Azotobacter vinelandii encystment. J Proteomics 2018; 181:47-59. [PMID: 29605291 DOI: 10.1016/j.jprot.2018.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/09/2018] [Accepted: 03/27/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Sangita Chowdhury-Paul
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Victoria Pando-Robles
- Instituto Nacional de Salud Pública, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Universidad No. 655 Colonia Santa María Ahuacatitlán, Cerrada Los Pinos y Caminera, C.P. 62100 Cuernavaca, Morelos, México
| | - Verónica Jiménez-Jacinto
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnologia, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México.
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17
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He G, Xu S, Wang S, Zhang Q, Liu D, Chen Y, Ju J, Zhao B. A conserved residue of l -alanine dehydrogenase from Bacillus pseudofirmus , Lys-73, participates in the catalytic reaction through hydrogen bonding. Enzyme Microb Technol 2018; 110:61-68. [DOI: 10.1016/j.enzmictec.2017.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/25/2017] [Accepted: 10/10/2017] [Indexed: 11/30/2022]
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18
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Phogosee S, Hibino T, Kageyama H, Waditee-Sirisattha R. Bifunctional alanine dehydrogenase from the halotolerant cyanobacterium Aphanothece halophytica: characterization and molecular properties. Arch Microbiol 2018; 200:719-727. [DOI: 10.1007/s00203-018-1481-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/18/2018] [Indexed: 11/28/2022]
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19
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Mutlu A, Trauth S, Ziesack M, Nagler K, Bergeest JP, Rohr K, Becker N, Höfer T, Bischofs IB. Phenotypic memory in Bacillus subtilis links dormancy entry and exit by a spore quantity-quality tradeoff. Nat Commun 2018; 9:69. [PMID: 29302032 PMCID: PMC5754360 DOI: 10.1038/s41467-017-02477-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/04/2017] [Indexed: 12/15/2022] Open
Abstract
Some bacteria, such as Bacillus subtilis, withstand starvation by forming dormant spores that revive when nutrients become available. Although sporulation and spore revival jointly determine survival in fluctuating environments, the relationship between them has been unclear. Here we show that these two processes are linked by a phenotypic “memory” that arises from a carry-over of molecules from the vegetative cell into the spore. By imaging life histories of individual B. subtilis cells using fluorescent reporters, we demonstrate that sporulation timing controls nutrient-induced spore revival. Alanine dehydrogenase contributes to spore memory and controls alanine-induced outgrowth, thereby coupling a spore’s revival capacity to the gene expression and growth history of its progenitors. A theoretical analysis, and experiments with signaling mutants exhibiting altered sporulation timing, support the hypothesis that such an intrinsically generated memory leads to a tradeoff between spore quantity and spore quality, which could drive the emergence of complex microbial traits. Bacillus subtilis withstands starvation by forming dormant spores that revive when nutrients become available. Here, Mutlu et al. show that sporulation timing controls spore revival through a phenotypic ‘memory’ that arises from the carry-over of a metabolic enzyme from the vegetative cell into the spore.
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Affiliation(s)
- Alper Mutlu
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Stephanie Trauth
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Marika Ziesack
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Katja Nagler
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jan-Philip Bergeest
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Karl Rohr
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Nils Becker
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Thomas Höfer
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany. .,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany. .,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
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20
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Li SY, Ng IS, Chen PT, Chiang CJ, Chao YP. Biorefining of protein waste for production of sustainable fuels and chemicals. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:256. [PMID: 30250508 PMCID: PMC6146663 DOI: 10.1186/s13068-018-1234-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/22/2018] [Indexed: 05/21/2023]
Abstract
To mitigate the climate change caused by CO2 emission, the global incentive to the low-carbon alternatives as replacement of fossil fuel-derived products continuously expands the need for renewable feedstock. There will be accompanied by the generation of enormous protein waste as a result. The economical viability of the biorefinery platform can be realized once the surplus protein waste is recycled in a circular economy scenario. In this context, the present review focuses on the current development of biotechnology with the emphasis on biotransformation and metabolic engineering to refine protein-derived amino acids for production of fuels and chemicals. Its scope starts with the explosion of potential feedstock sources rich in protein waste. The availability of techniques is applied for purification and hydrolysis of various feedstock proteins to amino acids. Useful lessons are leaned from the microbial catabolism of amino acids and lay a foundation for the development of the protein-based biotechnology. At last, the future perspective of the biorefinery scheme based on protein waste is discussed associated with remarks on possible solutions to overcome the technical bottlenecks.
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Affiliation(s)
- Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung, 402 Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Po Ting Chen
- Department of Biotechnology, Southern Taiwan University of Science and Technology, Tainan, 710 Taiwan
| | - Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
- Department of Health and Nutrition Biotechnology, Asia University, Taichung, 41354 Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan
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21
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Duque E, Daddaoua A, Cordero BF, De la Torre J, Antonia Molina-Henares M, Ramos JL. Identification and elucidation of in vivo function of two alanine racemases from Pseudomonas putida KT2440. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:581-588. [PMID: 28799718 DOI: 10.1111/1758-2229.12576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
The genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D-alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D-alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D-alanine. These results indicate that PP_5269 is an alr allele and that it is the essential alanine racemase in P. putida. We observed that the PP_5269 mutant grew very slowly, while the double PP_5269/PP_3722 mutant did not grow at all. This suggests that PP_3722 may replace PP_5269 in vivo. In fact, when the ORF encoding PP_3772 was cloned into a wide host range expression vector, ORF PP_3722 successfully complemented P. putida PP_5269 mutants. We purified both proteins to homogeneity and while they exhibit similar KM values, the Vmax of PP_5269 is fourfold higher than that of PP_3722. Here, we propose that PP_5269 and PP_3722 encode functional alanine racemases and that these genes be named alr-1 and alr-2 respectively.
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Affiliation(s)
- Estrella Duque
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | - Baldo F Cordero
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | - Jesús De la Torre
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | | | - Juan-Luis Ramos
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
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22
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da Silva ES, Gómez-Vallejo V, Baz Z, Llop J, López-Gallego F. Efficient Enzymatic Preparation of (13) N-Labelled Amino Acids: Towards Multipurpose Synthetic Systems. Chemistry 2016; 22:13619-26. [PMID: 27515007 DOI: 10.1002/chem.201602471] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Indexed: 01/27/2023]
Abstract
Nitrogen-13 can be efficiently produced in biomedical cyclotrons in different chemical forms, and its stable isotopes are present in the majority of biologically active molecules. Hence, it may constitute a convenient alternative to Fluorine-18 and Carbon-11 for the preparation of positron-emitter-labelled radiotracers; however, its short half-life demands for the development of simple, fast, and efficient synthetic processes. Herein, we report the one-pot, enzymatic and non-carrier-added synthesis of the (13) N-labelled amino acids l-[(13) N]alanine, [(13) N]glycine, and l-[(13) N]serine by using l-alanine dehydrogenase from Bacillus subtilis, an enzyme that catalyses the reductive amination of α-keto acids by using nicotinamide adenine dinucleotide (NADH) as the redox cofactor and ammonia as the amine source. The integration of both l-alanine dehydrogenase and formate dehydrogenase from Candida boidinii in the same reaction vessel to facilitate the in situ regeneration of NADH during the radiochemical synthesis of the amino acids allowed a 50-fold decrease in the concentration of the cofactor without compromising reaction yields. After optimization of the experimental conditions, radiochemical yields were sufficient to carry out in vivo imaging studies in small rodents.
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Affiliation(s)
- Eunice S da Silva
- Radiochemistry and Nuclear Imaging Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain
| | - Vanessa Gómez-Vallejo
- Radiochemistry Platform, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain
| | - Zuriñe Baz
- Radiochemistry and Nuclear Imaging Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain
| | - Jordi Llop
- Radiochemistry and Nuclear Imaging Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain.
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain. .,IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Bizkaia, Spain.
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23
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Stepanek JJ, Schäkermann S, Wenzel M, Prochnow P, Bandow JE. Purine biosynthesis is the bottleneck in trimethoprim-treated Bacillus subtilis. Proteomics Clin Appl 2016; 10:1036-1048. [PMID: 27329548 DOI: 10.1002/prca.201600039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 06/01/2016] [Accepted: 06/15/2016] [Indexed: 11/11/2022]
Abstract
PURPOSE Trimethoprim is a folate biosynthesis inhibitor. Tetrahydrofolates are essential for the transfer of C1 units in several biochemical pathways including purine, thymine, methionine, and glycine biosynthesis. This study addressed the effects of folate biosynthesis inhibition on bacterial physiology. EXPERIMENTAL DESIGN Two complementary proteomic approaches were employed to analyze the response of Bacillus subtilis to trimethoprim. Acute changes in protein synthesis rates were monitored by radioactive pulse labeling of newly synthesized proteins and subsequent 2DE analysis. Changes in protein levels were detected using gel-free quantitative MS. RESULTS Proteins involved in purine and histidine biosynthesis, the σB -dependent general stress response, and sporulation were upregulated. Most prominently, the PurR-regulon required for de novo purine biosynthesis was derepressed indicating purine depletion. The general stress response was activated energy dependently and in a subpopulation of treated cultures an early onset of sporulation was observed, most likely triggered by low guanosine triphosphate levels. Supplementation of adenosine triphosphate, adenosine, and guanosine to the medium substantially decreased antibacterial activity, showing that purine depletion becomes the bottleneck in trimethoprim-treated B. subtilis. CONCLUSIONS AND CLINICAL RELEVANCE The frequently prescribed antibiotic trimethoprim causes purine depletion in B. subtilis, which can be complemented by supplementing purines to the medium.
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Affiliation(s)
| | | | - Michaela Wenzel
- Ruhr-Universität Bochum, Applied Microbiology, Bochum, Germany
| | - Pascal Prochnow
- Ruhr-Universität Bochum, Applied Microbiology, Bochum, Germany
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24
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Radkov AD, McNeill K, Uda K, Moe LA. D-Amino Acid Catabolism Is Common Among Soil-Dwelling Bacteria. Microbes Environ 2016; 31:165-8. [PMID: 27169790 PMCID: PMC4912152 DOI: 10.1264/jsme2.me15126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Soil and rhizosphere environments were examined in order to determine the identity and relative abundance of bacteria that catabolize d- and l-amino acids as the sole source of carbon and nitrogen. All substrates were readily catabolized by bacteria from both environments, with most d-amino acids giving similar CFU counts to their l-amino acid counterparts. CFU count ratios between l- and d-amino acids typically ranged between 2 and 1. Isolates were phylogenetically typed in order to determine the identity of d-amino acid catabolizers. Actinobacteria, specifically the Arthrobacter genus, were abundant along with members of the α- and β-Proteobacteria classes.
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25
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Holzer AK, Hiebler K, Mutti FG, Simon RC, Lauterbach L, Lenz O, Kroutil W. Asymmetric Biocatalytic Amination of Ketones at the Expense of NH3 and Molecular Hydrogen. Org Lett 2015; 17:2431-3. [DOI: 10.1021/acs.orglett.5b01154] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anja K. Holzer
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Katharina Hiebler
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Francesco G. Mutti
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Robert C. Simon
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Lars Lauterbach
- Department
of Chemistry, Technische Universität Berlin, Straße des
17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Department
of Chemistry, Technische Universität Berlin, Straße des
17. Juni 135, 10623 Berlin, Germany
| | - Wolfgang Kroutil
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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26
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Fernandes P, Aldeborgh H, Carlucci L, Walsh L, Wasserman J, Zhou E, Lefurgy ST, Mundorff EC. Alteration of substrate specificity of alanine dehydrogenase. Protein Eng Des Sel 2014; 28:29-35. [PMID: 25538307 DOI: 10.1093/protein/gzu053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The l-alanine dehydrogenase (AlaDH) has a natural history that suggests it would not be a promising candidate for expansion of substrate specificity by protein engineering: it is the only amino acid dehydrogenase in its fold family, it has no sequence or structural similarity to any known amino acid dehydrogenase, and it has a strong preference for l-alanine over all other substrates. By contrast, engineering of the amino acid dehydrogenase superfamily members has produced catalysts with expanded substrate specificity; yet, this enzyme family already contains members that accept a broad range of substrates. To test whether the natural history of an enzyme is a predictor of its innate evolvability, directed evolution was carried out on AlaDH. A single mutation identified through molecular modeling, F94S, introduced into the AlaDH from Mycobacterium tuberculosis (MtAlaDH) completely alters its substrate specificity pattern, enabling activity toward a range of larger amino acids. Saturation mutagenesis libraries in this mutant background additionally identified a double mutant (F94S/Y117L) showing improved activity toward hydrophobic amino acids. The catalytic efficiencies achieved in AlaDH are comparable with those that resulted from similar efforts in the amino acid dehydrogenase superfamily and demonstrate the evolvability of MtAlaDH specificity toward other amino acid substrates.
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Affiliation(s)
- Puja Fernandes
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Hannah Aldeborgh
- Chemistry Department, Vassar College, Poughkeepsie, NY 12604, USA
| | - Lauren Carlucci
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Lauren Walsh
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Jordan Wasserman
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Edward Zhou
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Scott T Lefurgy
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Emily C Mundorff
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
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27
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Fuchs CS, Simon RC, Riethorst W, Zepeck F, Kroutil W. Synthesis of (R)- or (S)-valinol using ω-transaminases in aqueous and organic media. Bioorg Med Chem 2014; 22:5558-62. [PMID: 24951100 DOI: 10.1016/j.bmc.2014.05.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
Valinol is part of numerous pharmaceuticals and has various other important applications. Optically pure valinol (ee >99%) was prepared employing different ω-transaminases from the corresponding prochiral hydroxy ketone. By the choice of the enzyme the (R)- as well as the (S)-enantiomer were accessible. Reductive amination was performed in organic solvent (MTBE) using 2-propyl amine as amine donor whereas alanine was applied in or in aqueous medium. Transformations in phosphate buffer were successfully performed even at 200 mM substrate concentration (20.4 g/L) leading to 99% (R) and 94% (S) conversion with perfect optical purity (>99% ee).
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Affiliation(s)
| | - Robert C Simon
- University of Graz, Institute of Chemistry, Organic- and Bioorganic Chemistry, NAWI Graz, 8010 Graz, Austria
| | - Waander Riethorst
- Sandoz GmbH, Development Anti-Infectives, Biochemiestraße 10, 6250 Kundl/Tirol, Austria
| | - Ferdinand Zepeck
- Sandoz GmbH, Development Anti-Infectives, Biochemiestraße 10, 6250 Kundl/Tirol, Austria
| | - Wolfgang Kroutil
- University of Graz, Institute of Chemistry, Organic- and Bioorganic Chemistry, NAWI Graz, 8010 Graz, Austria.
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28
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Fuchs CS, Hollauf M, Meissner M, Simon RC, Besset T, Reek JNH, Riethorst W, Zepeck F, Kroutil W. Dynamic Kinetic Resolution of 2-Phenylpropanal Derivatives to Yield β-Chiral Primary AminesviaBioamination. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400217] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Molecular dynamics simulations of mutated Mycobacterium tuberculosis l-alanine dehydrogenase to illuminate the role of key residues. J Mol Graph Model 2014; 50:61-70. [DOI: 10.1016/j.jmgm.2014.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/23/2014] [Accepted: 03/25/2014] [Indexed: 11/23/2022]
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30
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Miura H, Yagisawa Y, Kato Y, Hayashi K, Fujita N, Ōmura S, Takahashi Y. Transcriptional analysis of genes encoding proteins significantly increased in Kitasatospora setae KM-6054(T) under submerged culture. J GEN APPL MICROBIOL 2014; 60:276-80. [PMID: 25742980 DOI: 10.2323/jgam.60.276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hiromi Miura
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan; Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
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31
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Simon RC, Richter N, Busto E, Kroutil W. Recent Developments of Cascade Reactions Involving ω-Transaminases. ACS Catal 2013. [DOI: 10.1021/cs400930v] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert C. Simon
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Nina Richter
- ACIB GmbH, c/o Heinrichstraße
28, 8010 Graz, Austria
| | - Eduardo Busto
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
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32
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Salerno P, Persson J, Bucca G, Laing E, Ausmees N, Smith CP, Flärdh K. Identification of new developmentally regulated genes involved in Streptomyces coelicolor sporulation. BMC Microbiol 2013; 13:281. [PMID: 24308424 PMCID: PMC3878966 DOI: 10.1186/1471-2180-13-281] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background The sporulation of aerial hyphae of Streptomyces coelicolor is a complex developmental process. Only a limited number of the genes involved in this intriguing morphological differentiation programme are known, including some key regulatory genes. The aim of this study was to expand our knowledge of the gene repertoire involved in S. coelicolor sporulation. Results We report a DNA microarray-based investigation of developmentally controlled gene expression in S. coelicolor. By comparing global transcription patterns of the wild-type parent and two mutants lacking key regulators of aerial hyphal sporulation, we found a total of 114 genes that had significantly different expression in at least one of the two mutants compared to the wild-type during sporulation. A whiA mutant showed the largest effects on gene expression, while only a few genes were specifically affected by whiH mutation. Seven new sporulation loci were investigated in more detail with respect to expression patterns and mutant phenotypes. These included SCO7449-7451 that affect spore pigment biogenesis; SCO1773-1774 that encode an L-alanine dehydrogenase and a regulator-like protein and are required for maturation of spores; SCO3857 that encodes a protein highly similar to a nosiheptide resistance regulator and affects spore maturation; and four additional loci (SCO4421, SCO4157, SCO0934, SCO1195) that show developmental regulation but no overt mutant phenotype. Furthermore, we describe a new promoter-probe vector that takes advantage of the red fluorescent protein mCherry as a reporter of cell type-specific promoter activity. Conclusion Aerial hyphal sporulation in S. coelicolor is a technically challenging process for global transcriptomic investigations since it occurs only as a small fraction of the colony biomass and is not highly synchronized. Here we show that by comparing a wild-type to mutants lacking regulators that are specifically affecting processes in aerial hypha, it is possible to identify previously unknown genes with important roles in sporulation. The transcriptomic data reported here should also serve as a basis for identification of further developmentally important genes in future functional studies.
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Affiliation(s)
| | | | | | | | | | | | - Klas Flärdh
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
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Fajardo C, Saccà ML, Martinez-Gomariz M, Costa G, Nande M, Martin M. Transcriptional and proteomic stress responses of a soil bacterium Bacillus cereus to nanosized zero-valent iron (nZVI) particles. CHEMOSPHERE 2013; 93:1077-83. [PMID: 23816452 DOI: 10.1016/j.chemosphere.2013.05.082] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/27/2013] [Accepted: 05/28/2013] [Indexed: 05/20/2023]
Abstract
Nanosized zero valent iron (nZVI) is emerging as an option for treating contaminated soil and groundwater even though the potentially toxic impact exerted by nZVI on soil microorganisms remains uncertain. In this work, we focus on nanotoxicological studies performed in vitro using commercial nZVI and one common soil bacterium (Bacillus cereus). Results showed a negative impact of nZVI on B. cereus growth capability, consistent with the entrance of cells in an early sporulation stage, observed by TEM. Despite no changes at the transcriptional level are detected in genes of particular relevance in cellular activity (narG, nirS, pykA, gyrA and katB), the proteomic approach used highlights differentially expressed proteins in B. cereus under nZVI exposure. We demonstrate that proteins involved in oxidative stress-response and tricarboxilic acid cycle (TCA) modulation are overexpressed; moreover proteins involved in motility and wall biosynthesis are repressed. Our results enable to detect a molecular-level response as early warning signal, providing new insight into first line defense response of a soil bacterium after nZVI exposure.
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Affiliation(s)
- C Fajardo
- Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
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34
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Abstract
D-Amino acids have been shown to play an increasingly diverse role in bacterial physiology, yet much remains to be learned about their synthesis and catabolism. Here we used the model soil- and rhizosphere-dwelling organism Pseudomonas putida KT2440 to elaborate on the genomics and enzymology of d-amino acid metabolism. P. putida KT2440 catabolized the d-stereoisomers of lysine, phenylalanine, arginine, alanine, and hydroxyproline as the sole carbon and nitrogen sources. With the exception of phenylalanine, each of these amino acids was racemized by P. putida KT2440 enzymes. Three amino acid racemases were identified from a genomic screen, and the enzymes were further characterized in vitro. The putative biosynthetic alanine racemase Alr showed broad substrate specificity, exhibiting measurable racemase activity with 9 of the 19 chiral amino acids. Among these amino acids, activity was the highest with lysine, and the k(cat)/K(m) values with l- and d-lysine were 3 orders of magnitude greater than the k(cat)/K(m) values with l- and d-alanine. Conversely, the putative catabolic alanine racemase DadX showed narrow substrate specificity, clearly preferring only the alanine stereoisomers as the substrates. However, DadX did show 6- and 9-fold higher k(cat)/K(m) values than Alr with l- and d-alanine, respectively. The annotated proline racemase ProR of P. putida KT2440 showed negligible activity with either stereoisomer of the 19 chiral amino acids but exhibited strong epimerization activity with hydroxyproline as the substrate. Comparative genomic analysis revealed differences among pseudomonads with respect to alanine racemase genes that may point to different roles for these genes among closely related species.
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35
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Lu X, Yi Q, Zhang G, Zhu X, Zhou H, Dong H. Crystallization and preliminary X-ray analysis of an alanine dehydrogenase from Bacillus megaterium WSH-002. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:934-6. [PMID: 23908047 PMCID: PMC3729178 DOI: 10.1107/s1744309113019672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/16/2013] [Indexed: 11/10/2022]
Abstract
Alanine dehydrogenase (L-AlaDH) from Bacillus megaterium WSH-002 catalyses the NAD⁺-dependent interconversion of L-alanine and pyruvate. The enzyme was expressed in Escherichia coli BL21 (DE3) cells and purified with a His6 tag by Ni²⁺-chelating affinity chromatography for X-ray crystallographic analysis. Crystals were grown in a solution consisting of 0.1 M HEPES pH 8.0, 12%(w/v) polyethylene glycol 8000, 8%(v/v) ethylene glycol at a concentration of 15 mg ml⁻¹ purified protein. The crystal diffracted to 2.35 Å resolution and belonged to the trigonal space group R32, with unit-cell parameters a = b = 125.918, c = 144.698 Å.
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Affiliation(s)
- Xiaoyun Lu
- Tianjin University of Science and Technology, Tianjin 300222, People’s Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, People’s Republic of China
| | - Qiufen Yi
- Tianjin University of Science and Technology, Tianjin 300222, People’s Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, People’s Republic of China
| | - Guofang Zhang
- Tianjin University of Science and Technology, Tianjin 300222, People’s Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, People’s Republic of China
| | - Xianming Zhu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, People’s Republic of China
| | - Honggang Zhou
- College of Pharmacy, Nankai University, Tianjin 300071, People’s Republic of China
| | - Hui Dong
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, People’s Republic of China
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36
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Wu R, Gu M, Wilton R, Babnigg G, Kim Y, Pokkuluri PR, Szurmant H, Joachimiak A, Schiffer M. Insight into the sporulation phosphorelay: crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD. Protein Sci 2013; 22:564-76. [PMID: 23436677 DOI: 10.1002/pro.2237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/11/2022]
Abstract
The Bacillus subtilis KinD signal-transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extracytoplasmic sensing domain of KinD, which was copurified and crystallized with a pyruvate ligand. The structure of a ligand-binding site mutant was also determined; it was copurified and crystallized with an acetate ligand. The structure of the KinD extracytoplasmic segment is similar to that of several other sensing domains of signal transduction proteins and is composed of tandem Per-Arnt-Sim (PAS)-like domains. The KinD ligand-binding site is located on the membrane distal PAS-like domain and appears to be highly selective; a single mutation, R131A, abolishes pyruvate binding and the mutant binds acetate instead. Differential scanning fluorimetry, using a variety of monocarboxylic and dicarboxylic acids, identified pyruvate, propionate, and butyrate but not lactate, acetate, or malate as KinD ligands. A recent report found that malate induces biofilm formation in a KinD-dependent manner. It was suggested that malate might induce a metabolic shift and increased secretion of the KinD ligand of unknown identity. The structure and binding assays now suggests that this ligand is pyruvate and/or other small monocarboxylic acids. In summary, this study gives a first insight into the identity of a molecular ligand for one of the five phosphorelay kinases of B. subtilis.
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Affiliation(s)
- R Wu
- The Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, USA
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37
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AdeR, a PucR-type transcription factor, activates expression of L-alanine dehydrogenase and is required for sporulation of Bacillus subtilis. J Bacteriol 2012; 194:4995-5001. [PMID: 22797752 DOI: 10.1128/jb.00778-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis ald gene encodes L-alanine dehydrogenase, which catalyzes the NAD(+)-dependent deamination of L-alanine to pyruvate for the generation of energy and is required for normal sporulation. The transcription of ald is induced by alanine, but the mechanism underlying alanine induction remains unknown. Here we report that a gene (formerly yukF and now designated adeR) located upstream of ald is essential for the basal and alanine-inducible expression of ald. The disruption of the adeR gene caused a sporulation defect, whereas the complementation of an adeR mutation with an intact adeR gene restored the sporulation ability. adeR expression was not subject to autoregulation and alanine induction. Deletion and mutation analyses revealed that an inverted repeat, centered at position -74.5 relative to the transcriptional initiation site of ald, was required for ald expression and also likely served as a ρ-independent transcription terminator. Electrophoretic mobility shift assays showed that purified His-tagged AdeR was a specific DNA-binding protein and that this inverted repeat was required for AdeR binding. AdeR shows no significant amino acid sequence similarity to the known transcriptional activators of ald genes from other bacteria. AdeR appears to be a member of the PucR family of transcriptional regulators. Its orthologs of unknown function are present in some other Bacillus species. Collectively, these findings support the notion that AdeR is a transcriptional activator which mediates ald expression in response to alanine availability and is important for normal sporulation in B. subtilis.
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38
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Ling B, Sun M, Bi S, Jing Z, Liu Y. Molecular dynamics simulations of the coenzyme induced conformational changes of Mycobacterium tuberculosis L-alanine dehydrogenase. J Mol Graph Model 2012; 35:1-10. [PMID: 22459692 DOI: 10.1016/j.jmgm.2012.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/31/2011] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
Abstract
Mycobacterium tuberculosis L-alanine dehydrogenase (L-MtAlaDH) catalyzes the NADH-dependent reversible oxidative deamination of L-alanine to pyruvate and ammonia. L-MtAlaDH has been proposed to be a potential target in the treatment of tuberculosis. Based on the crystal structures of this enzyme, molecular dynamics simulations were performed to investigate the conformational changes of L-MtAlaDH induced by coenzyme NADH. The results show that the presence of NADH in the binding domain restricts the motions and conformational distributions of L-MtAlaDH. There are two loops (residues 94-99 and 238-251) playing important roles for the binding of NADH, while another loop (residues 267-293) is responsible for the binding of substrate. The opening/closing and twisting motions of two domains are closely related to the conformational changes of L-MtAlaDH induced by NADH.
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Affiliation(s)
- Baoping Ling
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China
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39
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ald of Mycobacterium tuberculosis encodes both the alanine dehydrogenase and the putative glycine dehydrogenase. J Bacteriol 2011; 194:1045-54. [PMID: 22210765 DOI: 10.1128/jb.05914-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The putative glycine dehydrogenase of Mycobacterium tuberculosis catalyzes the reductive amination of glyoxylate to glycine but not the reverse reaction. The enzyme was purified and identified as the previously characterized alanine dehydrogenase. The Ald enzyme was expressed in Escherichia coli and had both pyruvate and glyoxylate aminating activities. The gene, ald, was inactivated in M. tuberculosis, which resulted in the loss of all activities. Both enzyme activities were found associated with the cell and were not detected in the extracellular filtrate. By using an anti-Ald antibody, the protein was localized to the cell membrane, with a smaller fraction in the cytosol. None was detected in the extracellular medium. The ald knockout strain grew without alanine or glycine and was able to utilize glycine but not alanine as a nitrogen source. Transcription of ald was induced when alanine was the sole nitrogen source, and higher levels of Ald enzyme were measured. Ald is proposed to have several functions, including ammonium incorporation and alanine breakdown.
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40
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Mutti FG, Fuchs CS, Pressnitz D, Turrini NG, Sattler JH, Lerchner A, Skerra A, Kroutil W. Amination of Ketones by Employing Two New (S)-Selective ω-Transaminases and the His-Tagged ω-TA from Vibrio fluvialis. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101476] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Mutti FG, Fuchs CS, Pressnitz D, Sattler JH, Kroutil W. Stereoselectivity of Four (R)-Selective Transaminases for the Asymmetric Amination of Ketones. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100558] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Ambily Nath IV, Loka Bharathi PA. Diversity in transcripts and translational pattern of stress proteins in marine extremophiles. Extremophiles 2011; 15:129-53. [DOI: 10.1007/s00792-010-0348-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 12/09/2010] [Indexed: 11/28/2022]
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43
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Heterologous expression of the Bacillus subtilis (natto) alanine dehydrogenase in Escherichia coli and Lactococcus lactis. Microbiol Res 2010; 165:268-75. [DOI: 10.1016/j.micres.2009.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Revised: 05/18/2009] [Accepted: 05/22/2009] [Indexed: 11/18/2022]
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44
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Unell M, Abraham PE, Shah M, Zhang B, Rückert C, VerBerkmoes NC, Jansson JK. Impact of phenolic substrate and growth temperature on the Arthrobacter chlorophenolicus proteome. J Proteome Res 2009; 8:1953-64. [PMID: 19714879 DOI: 10.1021/pr800897c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol, or phenol at 5 and 28 degrees C, both for the wild-type and a mutant strain with mass spectrometry based proteomics. A label-free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol-degradation pathway was confirmed, but not that for phenol.
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Affiliation(s)
- Maria Unell
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden
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45
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Tripathi SM, Ramachandran R. Crystal structures of the Mycobacterium tuberculosis secretory antigen alanine dehydrogenase (Rv2780) in apo and ternary complex forms captures "open" and "closed" enzyme conformations. Proteins 2008; 72:1089-95. [PMID: 18491387 DOI: 10.1002/prot.22101] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sarvind Mani Tripathi
- Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow, India
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46
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Tripathi SM, Ramachandran R. Overexpression, purification, crystallization and preliminary X-ray analysis of Rv2780 from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:367-70. [PMID: 18453703 PMCID: PMC2376397 DOI: 10.1107/s1744309108007653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2008] [Accepted: 03/20/2008] [Indexed: 11/10/2022]
Abstract
Rv2780, an alanine dehydrogenase from Mycobacterium tuberculosis (MtAlaDH), catalyzes the NAD-dependent interconversion of alanine and pyruvate. Alanine dehydrogenase is released into the culture medium in substantial amounts by virulent strains of mycobacteria and is not found in the vaccine strain of tuberculosis. Crystals of recombinant MtAlaDH were grown from 2 M ammonium sulfate solution at approximately 12 mg ml(-1) protein concentration in two crystal forms which occur in the presence and absence of NAD/pyruvate, respectively. Diffraction data extending to 2.6 A were collected at room temperature from both apo and ternary complex crystals. Crystals of the apoenzyme have unit-cell parameters a = 173.89, b = 127.07, c = 135.95 A. They are rod-like in shape and belong to space group C2. They contain a hexamer in the asymmetric unit. Crystals of the ternary complex belong to space group P4(3)2(1)2 and have unit-cell parameters a = b = 88.99, c = 373.85 A. There are three subunits in the asymmetric unit of the holoenzyme crystals.
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Affiliation(s)
- Sarvind Mani Tripathi
- Molecular and Structural Biology Division, Central Drug Research Institute, PO Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, Central Drug Research Institute, PO Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
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47
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Krásný L, Tiserová H, Jonák J, Rejman D, Sanderová H. The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis. Mol Microbiol 2008; 69:42-54. [PMID: 18433449 DOI: 10.1111/j.1365-2958.2008.06256.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We identify here a pattern in the transcription start sites (+1A or +1G) of sigma(A)-dependent promoters of genes that are up-/downregulated in response to amino acid starvation (stringent response) in Bacillus subtilis. Upregulated promoters initiate mostly with ATP and downregulated promoters with GTP. These promoters appear to be sensitive to changes in initiating nucleoside triphosphate concentrations. During the stringent response in B. subtilis, when ATP and GTP levels change reciprocally, the identity of the +1 position (A or G) of these promoters is a factor important in their regulation. Mutations that change the identity of position +1 (A for G and vice versa) change the response of the promoter to amino acid starvation.
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Affiliation(s)
- Libor Krásný
- Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology ASCR, Vídenská 1083, Prague 142 20, Czech Republic.
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48
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Tabata K, Hashimoto SI. Fermentative production of L-alanyl-L-glutamine by a metabolically engineered Escherichia coli strain expressing L-amino acid alpha-ligase. Appl Environ Microbiol 2007; 73:6378-85. [PMID: 17720844 PMCID: PMC2075057 DOI: 10.1128/aem.01249-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In spite of its clinical and nutritional importance, l-alanyl-l-glutamine (Ala-Gln) has not been widely used due to the absence of an efficient manufacturing method. Here, we present a novel method for the fermentative production of Ala-Gln using an Escherichia coli strain expressing l-amino acid alpha-ligase (Lal), which catalyzes the formation of dipeptides by combining two amino acids in an ATP-dependent manner. Two metabolic manipulations were necessary for the production of Ala-Gln: reduction of dipeptide-degrading activity by combinatorial disruption of the dpp and pep genes and enhancement of the supply of substrate amino acids by deregulation of glutamine biosynthesis and overexpression of heterologous l-alanine dehydrogenase (Ald). Since expression of Lal was found to hamper cell growth, it was controlled using a stationary-phase-specific promoter. The final strain constructed was designated JKYPQ3 (pepA pepB pepD pepN dpp glnE glnB putA) containing pPE167 (lal and ald expressed under the control of the uspA promoter) or pPE177 (lal and ald expressed under the control of the rpoH promoter). Either strain produced more than 100 mM Ala-Gln extracellularly, in fed-batch cultivation on glucose-ammonium salt medium, without added alanine and glutamine. Because of the characteristics of Lal, no longer peptides (such as tripeptides) or dipeptides containing d-amino acids were formed.
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Affiliation(s)
- Kazuhiko Tabata
- Technical Research Laboratories, Kyowa Hakko Kogyo Co. Ltd., 1-1 Kyowa-cho, Hofu-shi, 747-8522 Yamaguchi, Japan
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49
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Luo Y, Vilain S, Voigt B, Albrecht D, Hecker M, Brözel VS. Proteomic analysis of Bacillus cereus growing in liquid soil organic matter. FEMS Microbiol Lett 2007; 271:40-7. [PMID: 17391366 DOI: 10.1111/j.1574-6968.2007.00692.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacillus cereus is believed to be a soil bacterium, but studied solely in laboratory culture media. The aim of this study was to assess the physiology of B. cereus growing on soil organic matter by a proteomic approach. Cells were cultured to mid-exponential phase in soil extracted solubilized organic matter (SESOM), which mimics the nutrient composition of soil, and in Luria-Bertani broth as control. Silver staining of the two-dimensional gels revealed 234 proteins spots up-regulated when cells were growing in SESOM, with 201 protein spots down-regulated. Forty-three of these differentially expressed proteins were detected by Colloidal Coomassie staining and identified by matrix assisted laser desorption ionization-time of flight MS of tryptic digests. These differentially expressed proteins covered a range of functions, primarily amino acid, lipid, carbohydrate and nucleic acid metabolism. These results suggested growth on soil-associated carbohydrates, fatty acids and/or amino acids, concomitant with shifts in cellular structure.
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Affiliation(s)
- Yun Luo
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
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50
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Lin W, Kovacikova G, Skorupski K. The quorum sensing regulator HapR downregulates the expression of the virulence gene transcription factor AphA in Vibrio cholerae by antagonizing Lrp- and VpsR-mediated activation. Mol Microbiol 2007; 64:953-67. [PMID: 17501920 DOI: 10.1111/j.1365-2958.2007.05693.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HapR is a quorum sensing-regulated transcription factor that represses the virulence cascade in Vibrio cholerae by binding to a specific site centred at -71 in the aphA promoter, ultimately preventing activation of the tcpPH promoter on the Vibrio pathogenicity island. In an effort to elucidate the mechanism by which HapR represses aphA expression, we identified two transcriptional regulators, Lrp and VpsR, both of which activate the aphA promoter. Lrp, the leucine-responsive regulatory protein, binds to a region between -136 and -123 in the promoter to initiate aphA expression. VpsR, the response regulator that controls biofilm formation, binds to a region between -123 and -73 to activate aphA expression. HapR represses aphA expression by antagonizing the functions of both of these activators. The HapR binding site at -71 lies downstream of the Lrp binding site and overlaps the VpsR binding site. HapR binding thus directly blocks access of VpsR to the promoter. A naturally occurring point mutation in the aphA promoter (G-77T), which has previously been shown to prevent HapR binding, also prevents VpsR binding. In the absence of HapR, either Lrp or VpsR is capable of achieving nearly full expression of the aphA promoter, but when present together their effects are to some degree additive. The aphA promoter is also negatively autoregulated and an AphA binding site is centred at -20. The results here provide a model for the dual activation of the aphA promoter by Lrp and VpsR as well as its dual repression by HapR and AphA.
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Affiliation(s)
- Wei Lin
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755, USA
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